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Title
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Batrachochytrium Dendrobatidis (BD) Prevalence: An Analysis of the Atelopus Species Population Decline in Panama and Costa Rica
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Creator
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Lloyd, Diana Esperanza
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Date
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2020
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extracted text
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BATRACHOCHYTRIUM DENDROBATIDIS (BD) PREVALENCE: AN ANALYSIS OF
THE ATELOPUS SPECIES POPULATION DECLINE IN PANAMA AND COSTA
RICA
by
Diana Esperanza
A Thesis
Submitted in partial fulfillment
of the requirements for the degree
Master of Environmental Studies
The Evergreen State College
September 2020
2020 by Diana Esperanza. All rights reserved.
This Thesis for the Master of Environmental Studies Degree
by
Diana Esperanza
has been approved for
The Evergreen State College
by
________________________
John Withey, Ph. D.
Member of the Faculty
September 2020
ABSTRACT
Batrachochytrium Dendrobatidis (Bd) Prevalence: An Analysis of the Atelopus Species
Population Decline in Panama and Costa Rica
Diana Esperanza
The amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd) has caused
amphibian declines and extinctions around the world. Bd has spread in Costa Rica
throughout Panama and has caused some populations of the endemic Atelopus genus to
decline and some species to become extinct. In this thesis, I addressed the life history,
and ecological traits of Atelopus species of Costa Rica and Panama using data from La
Marca et al. (2005) and the International Union for Conservation of Nature’s Red List of
Threatened Species (IUCN) to determine the connection to their population decline and
extinction. Then, I addressed the connection of the Atelopus species genetics with
population decline and extinction using DNA sequencing from 5 Atelopus species of
Costa Rica and Panama. Lastly, I addressed the connection between Bd prevalence and
bioclimatic variables in Atelopus species of Panama and Costa Rica. The results revealed
that (1) a pattern of extinction in Atelopus species that occurred at the highest elevation in
isolated geographic areas. (2) the Atelopus species vulnerability to population decline and
extinction may have been caused by their geographic isolation resulting in weaker
immune system. (3) Bioclimatic variables could have contributed to Bd prevalence that
caused extinction or population decline in the Atelopus species of Costa Rica and Panama
due to patterns of low temperature and high precipitation. The results suggest that
environmental factors and the Atelopus response to disease may have contributed to their
population decline and extinction.
Table of Contents
CHAPTER 1
Introduction ...................................................................................................... 1
1.1
General Pattern of Amphibian Extinction ...................................................................... 1
1.2
Positionality Statement ................................................................................................... 2
CHAPTER 2
Literature Review.............................................................................................. 4
2.1
Introduction .................................................................................................................... 4
2.2
The Importance of Amphibian Species .......................................................................... 6
2.3
Life History and Transmission of Bd ............................................................................. 7
2.4
Pathology of Bd .............................................................................................................. 8
2.5
Origin of Batrachochytrium dendrobatidis (Bd) and the Cause of its Spread ............. 11
2.6
How did Bd Spread Around the World? ...................................................................... 12
2.7
Major Trends in Amphibian Extinctions ...................................................................... 13
2.8
The Harlequin Frogs (Genus Atelopus) of Panama and Costa Rica ............................. 13
2.9
Detailed history of Bd and Amphibian Extinction in Panama...................................... 16
2.10
Bd Spread Across the East of the Panama Canal ......................................................... 18
2.11
Is there a Relationship between Bd and Climate Change? ........................................... 20
2.12
Panamanian Frogs Face Conservation Challenges ....................................................... 23
2.13
Are Amphibians in Panama Surviving Bd? .................................................................. 26
2.14
The Effect of Ecological Variables in Amphibians’ Skin Defenses Against Bd.......... 27
2.15
Reintroduction of the Atelopus limosus into the Wild .................................................. 29
2.16
Conclusion .................................................................................................................... 30
CHAPTER 3
Methods ........................................................................................................... 33
3.1
Forensic History of the Atelopus Species in Costa Rica and Panama .......................... 33
3.2
Atelopus Species Phylogenetic Tree ............................................................................. 33
3.3
Correlation Between Bd Prevalence in Atelopus Species and Climatic Variables in
Panama and Costa Rica ............................................................................................................. 34
CHAPTER 4
Results ............................................................................................................. 36
4.1
Forensic History of the Atelopus species in Costa Rica and Panama ........................... 36
4.1.1
Chiriquí Harlequin Frog (Atelopus chiriquiensis) ............................................... 36
4.1.2
Variable Harlequin Frog (Atelopus varius).......................................................... 38
4.1.3
Limosa Harlequin Frog (Atelopus limosus) ......................................................... 42
4.1.4
Panamanian Golden Frog (Atelopus zeteki) ......................................................... 44
4.1.5
Pirre Harlequin Frog (Atelopus glyphus) ............................................................. 47
4.1.6
The Darien Stubfoot Toad (Atelopus certus) ....................................................... 49
4.1.7
The Chirripó Stubfoot Toad (Atelopus chirripoensis) ......................................... 51
4.1.8
Pass Stubfoot Toad (Atelopus senex) ................................................................... 53
iv
4.2
Atelopus Species Phylogenetic Tree ............................................................................. 55
4.3
Connection Between Bd Prevalence and Bioclimatic Variables in Atelopus Species of
Panama and Costa Rica ............................................................................................................. 57
4.3.1
Chiriquí Harlequin Frog (Atelopus chiriquiensis) ............................................... 58
4.3.2
Variable Harlequin Frog (Atelopus varius).......................................................... 61
4.3.3
Darien Stubfoot Toad (Atelopus certus) .............................................................. 64
4.3.4
Pass Stubfoot Toad (Atelopus senex) ................................................................... 66
CHAPTER 5
Discussion ....................................................................................................... 70
5.1
Discussion..................................................................................................................... 70
5.2
Limitations of the Study ............................................................................................... 72
5.4
Next Steps and Future Studies ...................................................................................... 74
5.5
Conclusion .................................................................................................................... 74
Bibliography……… ...................................................................................................................... 77
v
List of Figures
Figure 1. Redness of the skin indicates the presence of Bd. .............................................. 8
Figure 2. Zoosporangium releases zoospores .................................................................... 8
Figure 3. Bd lifecycle starts when spores burrow into the frog’s skin. Source: Rosenblum
et al. (2010). ........................................................................................................................ 9
Figure 4. Map of Bd detection from Mexico through Central America. Source: Cheng et
al. (2011). .......................................................................................................................... 10
Figure 5. Distribution map for Atelopus species in Costa Rica and Panama. Species
missing on this map: A. senex and A. chirripoensis. Source: Lewis et al. (2018)........... 15
Figure 6. Map of Costa Rica and west Panama with sites of amphibian declines. The
lines mean date and location of the declines. Source: Lips et al. (2006). ......................... 17
Figure 7. Timeline of Bd Detection Throughout Costa Rica and Panama ....................... 20
Figure 8. Survival patterns of frogs treated with J lividum before Bd exposure and frogs
exposed to Bd without treatment. 118 days after exposure the treated frogs were infected
by Bd. J lividum bacteria was not present at the death of the treated frogs. Source: Becker
et al., (2011). ..................................................................................................................... 25
Figure 9. Map of Panama and the four sites studied. Source: Varela et al. (2018). ......... 28
Figure 10. Bacterial community composition in D. auratus across the sites near the
Panama Canal. Varela et al. (2018) used linear discriminant analysis (LDA) scores to find
the most significance in bacterial composition. Source: Varela et al. (2018)................... 29
Figure 11. The mean elevation of Costa Rica and Panama ranges from 600 m to 3450 m.
........................................................................................................................................... 55
Figure 12. Atelopus Species Phylogenetic Tree and IUCN Red List Assessment ........... 56
Figure 13. ggplot of BIO1 (left) with temp. range from 7C to 20 C per year and BIO12
(right) with precipitation. range from 2000 mm to 5000mm per year in Costa Rica and
Panama. ............................................................................................................................. 57
Figure 14. Map of the Atelopus chiriquiensis Distribution in Costa Rica and Panama ... 58
Figure 15. Atelopus chiriquiensis Response to Bioclimatic variables range of values
based on the estimates of the probability of occurrences. ................................................ 60
Figure 16. Predicting Recent Climatic Habitat Suitability on the Atelopus chiriquiensis
range .................................................................................................................................. 61
Figure 17. Map of the Atelopus varius Distribution in Costa Rica throughout Panama .. 61
Figure 18. Atelopus varius Response to Bioclimatic variables range of values based on
the estimates of the probability of occurrences. ................................................................ 63
Figure 19. Predicting Recent Climatic Habitat Suitability of the Atelopus varius range . 63
Figure 20. Map of the Atelopus limosus Distribution in Panama.... Error! Bookmark not
defined.
Figure 21. Atelopus limosus Response to Bioclimatic variables range of values based on
the estimates of the probability of occurrences. .................Error! Bookmark not defined.
Figure 22. Predicting Recent Climatic Habitat Suitability of the Atelopus limosus range
............................................................................................Error! Bookmark not defined.
Figure 23. Map of the Atelopus zeteki Distribution in Panama ...... Error! Bookmark not
defined.
Figure 24. Predicting Recent Climatic Habitat Suitability of the Atelopus zeteki range
............................................................................................Error! Bookmark not defined.
vi
Figure 25. Map of the Atelopus glyphus Distribution in Panama ... Error! Bookmark not
defined.
Figure 26. Predicting Recent Climatic Habitat Suitability of the Atelopus glyphus range
............................................................................................Error! Bookmark not defined.
Figure 27. Map of the Atelopus certus Distribution in Panama ...... Error! Bookmark not
defined.
Figure 28. Atelopus certus Response to Bioclimatic variables range of values based on
the estimates of the probability of occurrences..................Error! Bookmark not defined.
Figure 29. Predicting Recent Bioclimatic Habitat Suitability of the Atelopus certus range.
........................................................................................................................................... 66
Figure 30. Map of the Atelopus chirripoensis Distribution in Costa Rica................. Error!
Bookmark not defined.
Figure 31. Map of the Atelopus senex Distribution in Costa Rica .................................. 66
Figure 32. Atelopus senex Response to Bioclimatic variables range of values based on the
estimates of the probability of occurrences. ..................................................................... 68
Figure 33. Predicting Recent Bioclimatic Habitat Suitability of the Atelopus senex range.
........................................................................................................................................... 68
vii
List of Tables
Table 1. IUCN 2019 assessment of the amphibian species by groups. From the 6,892 of
amphibians assessed 6,098 species are frogs and toads, and 40% (2,409 species) are
extinct or threatened. ......................................................................................................... 13
Table 2. Amphibian decline in El Copé, Central Panama. Loss of diversity was measured
by four indicators: named species, candidate species, lineages (named + candidate
species), and PD (sum of branch lengths obtained by MPL analysis of phylogenetic tree).
Source: Crawford et al. (2010).......................................................................................... 18
Table 3. Atelopus zeteki infection intensity (number of zoospores on skin swabs) and
zoospore output (number of zoospores released per minute) at death. Source: DiRenzo et
al. (2014). .......................................................................................................................... 26
Table 4. Summary data on Atelopus species. Prot. areas: Bd presence in protected areas.
Yr. of last record: year of most recent record; Yr. Bd presence of Bd: year(s)
documented; Hab. destr: occurrence of significant habitat destruction/ Status: Stable,
Decline* ............................................................................................................................ 54
Table 5. Summary of Location, Coordinates Minimum, Mean, and Maximum Elevation
of Atelopus Species Occurrences...................................................................................... 55
Table 6. . List of 19 bioclimatic variables used in bioclimatic model development. Names
and descriptions are in reference to the WorldClim, Hijmans, 2017. .............................. 58
Table 7. Summary of the Atelopus species' Probability of Occurrence in BIO1 and
BIO12, and the Probability of Occurrence with Habitat Suitability ................................. 69
viii
Acknowledgments
I would like to thank my thesis reader, John Withey, Ph.D., for his
encouragement, guidance, and support through my thesis process facilitating with
analysis using R and RStudio, and successfully executing my research I was hoping to
achieve. I would like to thank my former thesis reader, Kevin Francis, Ph.D., for his
words of wisdom, and for supporting me through my initial thesis process.
I would not have made it this far without the understanding and support of my
children, Alyssa, Adam, and Aaron for supporting me while going to night classes. I
thank you and love you.
ix
CHAPTER 1 Introduction
1.1
General Pattern of Amphibian Extinction
Many factors can affect amphibian population declines. Amphibian species
around the world are facing threats such as habitat loss, introduced invasive species,
pollution and disease (Baillie et al., 2004). However, one major cause of amphibian
declines is a skin infection called Chytridiomycosis. Chytridiomycosis is caused by the
amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd from this point on;
Crawford et al., 2010). Bd has been spreading throughout Central American countries
since at least the 1980’s and has caused the loss of amphibian diversity.
Batrachochytrium dendrobatidis is a chytrid fungus that infects the skin of
vertebrate species (Longcore et al., 1999). Bd grows in humid environments (Kirshtein et
al., 2007) and low temperatures (Longcore et al., 1999), suggesting that amphibians
living in high elevation habitats are most at risk of Bd infections (LaMarca et al., 2005).
The first detection of Bd in Central America was in the late 1980’s and caused the
extinction of the Costa Rican Golden toad (Bufo periglenes) (Baillie et al., 2004). Since
1993, Bd has been detected in the highlands of the Panamanian tropical rainforest,
including Eastern Panama and across the Panama Canal (Rodriguez-Brenes et al., 2016).
Bd is rapidly approaching Panamanian sites with minimal human occupation.
New research indicates that some amphibian species endemic to Panama may be
resisting Bd through skin defenses. In 2014, nine amphibian species appeared to be
recovering from Bd at the same location of the breakout a decade ago in 2004, including
the harlequin frog (Atelopus varius), and the rocket frog (Colostethus panamansis)
1
(Voyles et al., 2018). These authors suggested that the abundance of amphibian skin
microbiome may impact their vulnerability to Bd, and that evolution in this microbiome
may have created a resistance to Bd (Voyles et al., 2018).
1.2
Positionality Statement
My thesis is intended to bring awareness of the loss of Atelopus species in the Costa
Rican and the Panamanian tropical rainforest and how important it is to conserve these
Central American native amphibian species that are threatened with extinction due to the
chytrid fungus, Batrachochytrium dendrobatidis, (Bd). The Panamanian golden
frog (Atelopus zeteki) one of the species severely affected by Bd, is the national symbol
of luck in the Panamanian culture. As a Panamanian, I have always appreciated the flora
and fauna biodiversity of my country. In addition, Bd has also been found in amphibians
native to Washington State (Hayes et al., 2009). My thesis will benefit professionals and
concerned citizens interested in aquatic habitat conservation. We must understand the
role of ecological and bioclimatic factors that contribute to amphibian decline, and my
positionality will maintain neutral to the interpretation of the results. This means that
there is a real issue that is affecting amphibian species in the tropics and around the
world, and we need to find ways to help protect and conserve these and other species
affected by Bd.
In chapter 2, my literature review, I discuss the importance of amphibians species, the
biology and ecology of Batrachochytrium dendrobatidis (Bd), theories of the origin of
Bd, the harlequin frogs (Atelopus species) of Panama and Costa Rica, Bd prevalence
throughout Panama, the relationship between Bd and climate change, the conservation
2
challenges Panamanian amphibians face, amphibian survival, the effect of ecological
variables in amphibian microbiome against Bd, and the reintroduction of the Atelopus
limosus to the wild.
In chapter 3, I discuss the methods used to create forensic history of 8 Atelopus
species in Panama and Costa Rica using literature dated from 1972 to 2019 to provide a
timeline of Bd detection, Atelopus decline, extinction and recovery, and Atelopus life
history. In my second methods, I discussed how DNA sequence data was collected to
produce a phylogenetic tree and analyze the connection of the Atelopus species genetics
with extinction or decline. In my last method, I discussed how I used R (R Core Team
2020) to produce a species distribution model using unbiased data to analyze climatically
suitable habitats based on historical bioclimatic variables from 1970 to 2000.
In chapter 4, I discuss the results of the forensic history of 8 Atelopus species in Costa
Rica and Panama, the Atelopus species phylogenetic tree and the connection with their
extinction and decline and discuss the correlation between Bd prevalence and bioclimatic
variables.
In chapter 5, the discussion, I review and verify the findings, and discuss the
importance of bioclimatic variables and ecological traits, and genetic similarities that are
connected with Bd prevalence and amphibian extinction. I also present the limitations of
the thesis, next steps and future studies, and a conclusion of the thesis.
3
CHAPTER 2 Literature Review
2.1
Introduction
Amphibians are the most vulnerable animals in the world. According to the
Amphibian Survival Alliance (2017), of the over 6,000 amphibian species in the world,
42% are threatened to become extinct (Amphibian Red List Authority, 2017). Since the
1980s, a total of 122 amphibian species are critically endangered, and of these species,
113 are extinct in the wild, most of them from Central and South America (Baillie et al.,
2004). Additionally, 34 extinct amphibian species have been reported, of which 20 of
these species, endemic from Sri Lanka, vanished more than one hundred years ago
(2004). Moreover, extinctions may have accelerated in recent years. In the 1980’s, 11 of
the 34 species disappeared suddenly, including the Australian Gastric-brooding frogs,
(Rheobatrachus spp.), the Costa Rican Monteverde Golden frog (Incilius periglenes), the
Wyoming toad (Bufo baxteri), the Panamanian golden frog (Atelopus zeteki), and the
Puerto Rican Golden Coqui frog (Eleutherodactylus jasper) (Berger et al., 1998). Most
amphibian decline happened in tropical areas with elevation above 500 meters in Central
America and above 1,000 meters in South America, where the majority of these
endangered amphibians are endemic to their home range (Collins, Crump, & Lovejoy,
2009). Bd has affected amphibian species in mountainous areas.
Bd is threatening the Darwin’s Frogs (Rhinodermatidae) from Chile and
Argentina the New Zealand frogs (Leiopelmatidae), and another frog family (Bufonidae)
including the Harlequin frog (Atelopus varius) from Panama and Costa Rica, is at risk to
become extinct (2004) (Baillie et al., 2004). The chytrid fungus is causing a major impact
on many amphibians on a global scale.
4
The decline of amphibians has been so overwhelming that about 40% of
amphibians in Costa Rica were extinct by the late 1980s (Baillie et al., 2004). One major
factor of the extinction of these species may have been the fungal disease,
Chytridiomycosis caused by an amphibian fungal pathogen, Batrachochytrium
dendrobatidis (Bd) (2004).
Two amphibian species, endemic to Panama and Costa Rica are likely extinct in
the wild due to Bd: The Harlequin frog (Atelopus limosus) and the Panamanian Golden
frog, (Lips et al., 2008), the national symbol of good luck in Panamanian culture. Other
Atelopus species endemic to Panama and Costa Rica are experiencing severe population
declines and are threatened with extinction.
The Atelopus species may be the most impacted in Central America. Rohr et al.
(2008) suggest that sixty-seven species were extinct since the 1980s. The harlequin frog
(Atelopus varius) have disappeared from its natural habitat in Costa Rica and Western
Panama due to Bd, and possibly related to interactions with climate change. The spread
of this fungal disease approached the East of Panama. (Crawford et al., 2010; Lips et al.,
2008). Although a study revealed that Bd has spread far East of Panama in the region of
Tortí (Rebollar et al., 2014), there has not been a study of Bd detection in Atelopus
species in East Panama.
Many anthropogenic factors have contributed to the loss of amphibian
biodiversity around the world (Young et al., 2001). One factor of amphibian extinction is
introduced species, which can prey on or compete with native species (Young et al.,
2001). Another factor is overexploitation; for example, international trading (Rosenblum
et al., 2010). Factors like contamination with chemicals such as pesticides and fertilizers
5
can kill amphibians (Collins et al., 2009). However, different patterns of temperature can
also affect amphibian biodiversity (Young et al., 2001), and diseases like
Chytridiomycosis caused by Bd leads to amphibian decline (Lips et al., 2008). One main
reason of the amphibian extinction around the world may be the connection between Bd
and climate change.
If Bd is one major factor of amphibian population decline and extinction, what
makes it so prevalent? How can Bd impact the aquatic habitat in the tropical rainforest?
What is the relationship between the amphibian chytrid fungal disease and climate
change?
In this literature review, first I discuss amphibians from an ecological perspective
and how we have benefited from them. Then I cover the biology, ecology, and pathology
of Batrachochytrium dendrobatidis (Bd), the various origins of Bd, the history of Bd and
amphibian extinction, the connection of Bd with climate change, how some amphibians
may be recovering from Bd. I also discuss efforts to reintroduce Atelopus limosus to the
wild.
2.2
The Importance of Amphibian Species
Why should we care about the loss of amphibians? Amphibians contribute to
science and education as well as our self-benefit. We should care about amphibians as
much as we should care about any other animal or plant species (Dodd Jr., 2009). We use
amphibians as pets and food, and as test subjects for medical research, and schools
(2009). Amphibians can contribute to finding cure for many human health problems. The
loss of amphibian species biodiversity can create a disadvantage in scientific research for
6
human health (Halliday, 2008). This means amphibians have been playing an important
part in saving human lives and in our preparation to higher education.
Amphibians are an important part of nature as both prey and predator. They
contribute to maintaining an ecological balance and are vital for the survival other living
organisms in forest and wetland ecosystems in the Neotropics (Valencia-Aguilar, CortésGómez, & Ruiz-Agudelo, 2013). This means that amphibians are important part of the
food chain as food source to other animals.
Habitat alteration can impact amphibian biodiversity. Amphibians can negatively
respond to ecological changes, for example, change in the environment and pollution, as
they need water to survive (Halliday, 2008). Halliday indicated that amphibian’s skin
does not absorb water, so they depend on aquatic habitats (2008). As contributors to
scientific research and human health, amphibians need to be protected around the world.
2.3
Life History and Transmission of Bd
Chytridiomycosis is a rare disease. Bd infects amphibian species (Longcore et al.,
1999). One study found that Bd reproduces asexually, and it consists of two fundamental
structures: “a round, permanent zoosporangium, about 10 to 40 micrometers (μm) in
diameter, and a zoospore with moving flagellums about 2 μm in diameter, which
mobilize quickly to find a substrate to settle” (Rosenblum et al., 2008). In this case, the
substrate is the frog’s skin. The reproductive body, zoosporangium, develops zoospores
and then discharges them from its tubes into the surrounding environment (Longcore et
al., 1999). Collins et al., (2009) indicated that zoospores are Bd’s only reproductive stage
7
and zoospores need water to discharge (2009). The zoospores attach to the host’s skin
and reproduce zoosporangia (Figs. 1 and 2, Longcore et al., 1999; Collins et al., 2009).
Figure 2. Zoosporangium releases zoospores
from its tubes. Source: Longcore et al. (1999).
2.4
Figure 1. Redness of the skin indicates the presence of Bd.
Bottom: Loss of beak and Bd infection on legs, face and
upper body. Source: Longcore et al. (1999).
Pathology of Bd
What makes Bd so deadly to amphibians? One study revealed that Bd swims in
the water, then enters the amphibian skin and zoospores colonize the skin cells,
thickening the outer layer of the frog’s skin (Rosenblum et al., 2010). Because
amphibians use their skin as a respiratory function, the infected frogs suffocate and die
(Rosenblum et al., 2010). Once the frog is dead, Bd comes out of the skin of the dead
frog and goes back into the water to find a new host (Fig. 3, Rosenblum et al., 2010).
Kirshtein et al. (2007) indicate that Bd thrives in water. Walker et al., (2007) analyzed
water and sediment samples from ponds in Spain and found that Bd can live 12 weeks in
moist riverbanks and rocks without an amphibian host. These findings may explain the
reason Bd is very persistent in aquatic environment.
8
Figure 3. Bd lifecycle starts when spores burrow into the frog’s skin. Source: Rosenblum et al. (2010).
The infection process of Bd takes place in water bodies, often in mountainous
areas. A research study found that there are three ecological characteristics of Bd, (Baillie
et al., 2004). Bd thrives in cooler temperature, but cannot survive warmer temperatures,
which means that amphibians living in higher elevation will be affected by Bd than the
lowland amphibians. Bd only thrives in freshwater habitats, which explains the decrease
of amphibians living near streams (Baillie et al., 2004). Bd is more common in forests
with humid climate and is likely to infect amphibians breeding upstream.
Bd may be the cause of the loss of amphibian biodiversity in Central America.
How does Bd affect amphibians? Bd affects the frog’s skin layers and the nervous system
(Longcore et al., 1999). For example, a sick frog may have faded skin, rough, peeled skin
layer, especially on their feet (Frog Chytrid Fungus, 2017). Affected frogs’ legs are
spread away from its body, instead of tucked in, and in worst cases, the frog’s back legs
lose movement and drag behind it (Frog Chytrid Fungus, 2017). Tadpoles can also
9
become infected. Bd infects the beak when the tadpole is in a metamorphosis stage.
(Longcore et al., 1999). As the tadpole develops, Bd will spread in the legs, and as it
grows into a frog, the Bd will spread in any part of the skin (Longcore et al., 1999).
Longcore et al. (1999) have found that frogs and tadpoles can get infected with Bd by
direct contact between them and through exposure to infected water.
Bd is presumed to be the main factor of amphibian fluctuation in the neotropics.
Neotropics are regions from Central and South America, southern Mexico and the
Caribbean. Although the amphibian declines have been reported since 1970 (Fig. 4,
Cheng et al. 2011) and has been affecting the endemic species from the border of Mexico
to the tip of South America, Bd was first identified in 1998 as the cause of amphibian
decline in North and Central America, Europe, and Australia (Crawford et al., 2010;
Kilpatrick et al., 2010). The loss of endemic amphibian species may have a significant
ecological impact on the aquatic habitat.
Figure 4. Map of Bd detection from Mexico through Central America. Source: Cheng et al. (2011).
10
2.5
Origin of Batrachochytrium dendrobatidis (Bd) and the Cause of its Spread
Two studies have been conducted to find the first incident of the deadly infectious
disease. The two main theories are that the origin of Bd is either African (Weldon et al.,
2004 used samples of Xenopus spp., which are native to Africa), or Asian (O’Hanlon et
al., 2018 used amphibian genomes to find when Bd began to spread for the first time).
Although both theories may have compelling evidence, there are still many challenges in
finding the actual timing of the origin of Bd.
Weldon et al., (2004) state that Bd could have originated in Africa. They studied
697 specimens of 3 Xenopus species collected between 1879 and 1999 (Weldon et al.
2004). The study showed that Chytridiomycosis was present in African clawed frogs
(Xenopus laevis) specimens dated in 1938, (Weldon et al., 2004). The researchers
indicated that Bd was found in these African endemic species more than 20 years before
reports of the first case of Bd beyond this continent (2004). This theory is suggesting that
Bd may have originated in Africa and spread around the world.
The other theory (O’Hanlon et al., 2018) argues that Bd could have originated
from another part of the world. O’Hanlon et al. conducted a study using genetic lineage
to identify the source of Bd on infected amphibian populations from Africa, North
America, South America, East Asia and Japan (2018). O’Hanlon et al. collected 177
samples of genomes to arrange in sequence and incorporated analysis of sample genomes
from Ferrer et al., (2011), Rosenblum et al. (2010), and Weldon et al., (2004). A total of
234 samples, of which were isolated for study (2018). The analysis found lineages from
Africa, Europe, Brazil, and one global lineage (O’Hanlon et al., 2018). Lineages found in
the European samples which the researchers thought came from Switzerland have now
11
been classified in the Asian lineage because of another ancient Asian lineage that was
found in the North American bullfrogs with a genetic relation to an endemic amphibian
species in Brazil (O’Hanlon et al., 2018). These results indicated that multiple Bd
lineages were found in endemic amphibian species in Asia and then globally spread in
East Asia, during the early 20th century when the global amphibian trade increased.
O’Hanlon et al. (2018) used phylogenetic analysis to trace the source of Bd in Asia.
These two theories bring persuasive argument about the origin of Bd. It may be
safe to say that DNA sequencing of Bd from around the world may be an accurate
analysis. However, there are still many challenges in finding the actual timing of the
origin of Bd.
2.6
How did Bd Spread Around the World?
The international trade of one frog species may have caused the spread of the
chytrid fungus. Bd spread started with the exportation of African clawed frogs (Xenopus
laevis) used for human pregnancy testing in the 1940s and 1950s (Weldon et al. 2004).
The pregnancy test functioned when the urine of pregnant women was injected into the
African clawed frog triggering its ovulation due to the high levels of estrogen in the urine
(Weldon et al., 2004). Rosenblum et al. (2010), suggested that international trading of
the American bullfrog (Rana catesbeiana) may have caused the spread of Bd in other
countries, as Bd was first found in this amphibian species in South Carolina in 1978. The
international trade of the African clawed frog may have introduced Bd around the world
including the United States.
12
2.7
Major Trends in Amphibian Extinctions
To understand the gravity of the problem, the International Union for
Conservation of Nature (IUCN) categorized all known amphibian species by their
conservation status through a global species assessment (Baillie et al., 2004). They found
that amphibian diversity is declining around the world. The IUCN assessed a total of
6,892 amphibian species, of which 6,098 species are frogs and toads. 40% (2,409 species)
are extinct or threatened (Table 1, IUCN, 2020). 80% of Atelopus species are critically
endangered and 70% have declining populations (IUCN, 2020). About 30 out of the 113
Atelopus species are extinct in the wild (La Marca et al., 2005). Bd has caused the
population decline and loss of the Harlequin frog (Atelopus varius) across Central
America (La Marca et al., 2005; Lips et al., 2008). The loss of 3 Atelopus species in
Costa Rica and Panama could have a negative effect in their ecosystems.
Table 1. IUCN 2019 assessment of the amphibian species by groups. From the 6,892 of amphibians assessed 6,098
species are frogs and toads, and 40% (2,409 species) are extinct or threatened.
ORDER
Anura
Frogs & Toads
Caudata
Salamanders &
Newts
Gymnophiona
Caecilians
Subtotal
2.8
EX
EW
CR
PEW
3
CR
EN
VU
NT
DD
LC
2
CR/
PE
124
32
TOTAL
502
851
565
330
1192
2624
6098
% Threatened/
extinct
40%
3
0
7
0
107
133
104
55
42
167
611
67%
0
0
0
0
1
9
4
2
102
65
183
9%
35
2
131
3
610
993
673
387
1336
2856
6892
41%
The Harlequin Frogs (Genus Atelopus) of Panama and Costa Rica
Located in Central America, Costa Rica, and Panama tropical rainforests are the
richest and the most biodiverse regions in the world (Stephen Fry, 2015). Historically,
13
these two regions had the most amphibian abundance than Borneo and the Philippines
(Norman J. Scott, Jr., 1976). However, these regions suffered a decline in their amphibian
populations. For example, Harlequin frogs, genus Atelopus, once abundant, are
distributed from Costa Rica down to Bolivia and in the Southeast or the Guianas
(González-Maya, Gómez-Hoyos, Cruz-Lizano, & Schipper, 2018), have significantly
declined since the late 1980s. There are 113 Atelopus species dispersed from Costa Rica
to South America, 42 species have decreased 50% of their population from 1984 to 1996,
and only 10 are stable (LaMarca et al. 2005). Costa Rica and Panama harbor 362
amphibian species (Dirzo and Bonilla, 2013), but there are only 8 documented Atelopus
species distributed through Panama to Costa Rica (Fig. 5) (Savage, 1972). Panama has
six described species of Atelopus: A. certus, A. chiriquiensis, A. glyphus, A. limosus, A.
varius, A. zeteki, and at least one undescribed species: Atelopus aff. limosus (Flechas et
al., 2017). The only Panamanian Atelopus species that occupy one region close to the
Costa Rica-Panama border are the A. chiriquiensis and the A. varius (Savage, 1972). The
Atelopus senex is a described species from Costa Rica and the Atelopus chirripoensis is
possibly extinct in Costa Rica (Savage and Bolaños, 2009).
This Atelopus genus is dangerously approaching extinction and is perhaps the
most threatened in the world (Lewis et al., 2019). The tropical rainforests of Central may
be losing their biodiversity and can expose a change in their ecosystems. Costa Rica
suffered the decline of the Monteverde golden toad (Pounds & Crump, 1994) and the
decline of the Atelopus chiriquiensis due to Chytridiomycosis (Lips, 1998). The loss of
the Atelopus species can negatively impact the tropical rainforest ecosystems in these
regions.
14
Figure 5. Distribution map for Atelopus species in Costa Rica and Panama. Species missing on this map: A. senex and
A. chirripoensis. Source: Lewis et al. (2018).
Abiotic factors, such as temperature, precipitation, and climate, can be influenced
by the altitude of a region. Cold tolerance is frequently intense at high altitudes, and
species of the same genus living in the same habitat demonstrate significant differences
(Vo and Griddi-Papp, 2017). Most Atelopus species are endemic to remote tropical areas
in high elevation. All species living in elevations above 1000 m have declined, and 75%
have disappeared (LaMarca et al., 2005). High elevation, and precipitation and cool
weather make an ideal condition for Bd to spread. There were no data collected before
the Bd epidemic started in Central Panama (Crawford et al., 2010). The endemic
amphibians may not be able to survive if Bd is prevalent in their home range. The
remaining 25% of the Atelopus population may become extinct if Panamanian and Costa
Rican authorities do not have a mitigation plan to conserve these species.
15
The disappearance of endemic amphibian species in Costa Rica and Panama is
staggering. The golden toad (Incilius periglenes) and the harlequin frog (Atelopus varius)
were abundant in Monte Verde, Costa Rica from 1972 through the late 1980s (Pounds &
Crump, 1994). However, after 1988 both species started to decline in population and by
1992, both species have vanished (1994). The Panamanian Golden frog population was
abundant in El Valle de Antón in Central Panama about 15 years ago, but by 2004 the
frogs vanished (Kolbert, 2014). The amphibian population is being affected by an
infectious skin disease caused by Bd (Rodríguez-Brenes et al., 2016), and has spread
across the Eastern side of the Panama Canal.
2.9
Detailed history of Bd and Amphibian Extinction in Panama
In 1998, scientists found that the amphibian population in the mountains of
Panama is decreasing. Dr. Crawford, Dr. Lips, and Dr. Bermingham, (2010) from the
Smithsonian Tropical Research Institute (STRI), surveyed the loss of amphibian species
diversity in the tropical rainforest of Central Panama, located in El Copé, in the province
of Coclé, after the detection of Bd in Costa Rica in the 1980s (2010). In 1998, Crawford
et al. (2010) conducted a study of Bd spread at Omar Torrijos National Park, with an
elevation of 800 m, another location near El Copé. Crawford et al. (2010) indicated that
there is no data collected before the Bd epidemic started at El Copé in 2004. All these
locations are on the west side of the Panama Canal (Fig. 6).
16
Figure 6. Map of Costa Rica and west Panama with sites of amphibian declines. The lines mean date and location of
the declines. Source: Lips et al. (2006).
The scientists identified the amphibian species most affected by Bd. Crawford et
al. (2010) first detected Bd in 2004 in El Copé, then collected data on the number of
amphibians and conducted a 7-year comparison of their data of diversity loss caused by
Bd. Using a DNA barcode method to identify the diversification and lineage of
amphibian species, Crawford et al. (2010) found 63 Panamanian amphibian species of
which are categorized by taxonomic families including Aromobatidae, Bufonidae;
Caecilidae (a caecilian) and Plethodontidae (salamanders) among others, before the
amphibian decline caused by Bd. An additional survey was conducted between 2006 and
2008 and found that out of the 63 known amphibian species, 25 were extinct (2010). A
genetic analysis was conducted out of the remaining 11 known amphibian species in the
Panamanian tropical rainforest and found that 5 species lineages are extinct with a total
loss of 30 amphibian species caused by Bd (Table 2, Crawford et al., 2010). The
amphibian chytrid fungus could be slowly spreading across the eastern highlands of the
Panamanian tropical rainforest, and the decline of amphibian species is alarming.
17
Table 2. Amphibian decline in El Copé, Central Panama. Loss of diversity was measured by four indicators: named
species, candidate species, lineages (named + candidate species), and PD (sum of branch lengths obtained by MPL
analysis of phylogenetic tree). Source: Crawford et al. (2010).
Species removed (by decline category)
Extirpated and DD-extirpated
Extirpated, DD-extirpated and critical
Extirpated, DD-extirpated, critical and declined
2.10
Named
Species
lost (n = 63)
25 (40%)
34 (54%)
42 (67%)
Candidate
species
lost (n = 11)
5 (45%)
5 (45%)
6 (55%)
Lineages
lost (n = 74)
30 (41%)
39 (53%)
48 (65%)
PD
lost
(%)
33
41
61
Bd Spread Across the East of the Panama Canal
Bd is presumed to be spreading in lowlands in Panama. Not only can Bd spread in
streams of mountainous areas, but also the lower elevations of the Panamanian tropical
rainforest. Rodríguez-Brenes et al. (2016), focused their study on the spread of Bd in the
Túngara frogs (Engystomops pustulosus) that inhabit the lowlands of Panama (2016).
Ibañes et al., (1999) describe the Túngara frog as a small frog with a squat body
and short limbs with a grayish-brown dorsal surface. Males are about 33 mm long, and
females are about 36 mm long (1999). Ibañes et al. indicated that Túngaras are also
found in streams up to 1,500 m in elevation and can live in different types of habitats
(1999). However, Túngaras are most likely to thrive in warmer environments. Vo and
Gridi-Papp (2017), argue that Túngara frogs live in tropical freshwater habitats with
warm temperatures and do not respond well to cold temperatures (2017).
Bd was spreading more slowly on Túngara frogs than any other amphibians in the
lowlands of Panama. Vo and Gridi-Papp measured the rate of Bd spread in the Túngaras
since the first case of Bd positive in Túngaras and concluded that the Bd is spreading at a
slower rate in Túngaras in the lowlands at 34 miles/year, comparing to rate spread in
18
other amphibians in the same location at 19 to 108 miles/year (2017). Vo and Gridi-Papp
found that the rate of Bd spread from three locations along the Panama Canal watershed,
Summit, Chagres and Gamboa, were the slowest calculating it at 5 miles/year (2017). In
addition, amphibian species most vulnerable to Bd infection are populations that occur in
higher elevation (Woodhams et al., 2008). This means that the low rate of Bd spread
may be affected by the lowland habitats with warmer temperature. This is important
because amphibians in the lowlands may be able to survive Bd.
Bd spread slowly approached the Eastern side of Panama (Fig. 7). RodríguezBrenes et al., (2016) analyzed the Túngara frogs from 2009 to 2014 during June and
November in 7 sites (2016). The sites were Chiriquí in the far west, El Valle in Central
Panama, Gamboa and Summit, located near the Panama Canal, Metetí and Yaviza in the
East, and El Real and Rancho Frío located in the in the Darien National Park, in the far
East of Panama (Rodríguez-Brenes et al., 2016). Rodríguez-Brenes et al. concluded that
the Western and Central sites were Bd positive as predicted (2016). Although the
Gamboa area was Bd negative in 2010, one year later in 2011, Bd was detected in
Túngaras, and by 2014, all sites were tested positive for Bd (Rodríguez-Brenes et al.,
2016). Bd has extended throughout the highlands and the lowlands of Panama suggesting
that more studies are needed to identify the cause of such change.
19
Figure 7. Timeline of Bd Detection Throughout Costa Rica and Panama
Mamoní Valley
Sites of Bd detection throughout Panama.
Sites of Túngara frog samples.
Mamoní Valley was added to show the location of the released Limosa Harlequin frogs by STRI.
Source: Rodríguez-Brenes et al. (2016).
2.11
Is there a Relationship between Bd and Climate Change?
Early studies suggested climate change played a big role in extinction. Two
studies were conducted to find the connection between Bd and climate change. Pounds et
al., (1994) theorized that the Golden toads (Incilius periglenes) and Harlequin frogs
(Atelopus varius) might have disappeared from the Costa Rican rainforest due to climate
change (1994). Pounds et al. suggested that 20 anuran species were extinct in 4 years and
other species declined but were not extinct (1994). To analyze their theory, Pounds et al.
indicated that by 1992 the Atelopus varius became extinct in the Costa Rican Monte
Verde tropical rainforest (1994). The authors analyzed patterns of precipitation, stream
flow, weather, and seasonal El Niño patterns from July 1986 to June 1987 to examine
changes in amphibian abundance may be related to climate change (1994). Pounds et al.
indicated that the 1986-1987 cycle was the driest (1994). Wind flow has moved upward
20
to the Caribbean slope, reducing moisture in the rainforest affecting amphibians (1994).
The authors indicated that the decrease in rainfall between May 1986 and August 1987
and a decrease of stream flow between during July 1986-June 1987 cycle, as well as an
increase of minimum and maximum temperatures (1994). The researchers found that
some natural patterns coincide with their theory. Amphibian population decreased during
El Niño season when precipitation was the lowest in Monte Verde, Costa Rica from 1986
to 1987 (Pounds et al., 1994). Pounds et al. concluded that the decline of amphibian
biodiversity has a connection with climate change (1994). The authors indicated that
climate change will impact higher elevations forests, (Pounds et al., 1994). This theory
suggests that some amphibian species like the golden toad and the Harlequin frog may
have been affected significantly by the dry conditions caused by El Niño season in 1987
and may have cause these amphibians to become extinct in Monte Verde. This is
important because we may not know for certain the cause of their extinction.
Later, authors called this climate change theory into question. Blaustein et al.
(2011) suggested that the temperature pattern hypothesis of Pounds et al. (1994) that
cloud cover in higher elevations of the tropical rainforest can influence Bd spread may be
questionable (2011). Blaustein et al. argues that Pounds et al. only analyzed the changes
in temperature in higher and lower elevations respectively during the rainy season, when
amphibians mate, and not during the dry season (2011). This means that Pounds et al.
hypothesis may be insufficient to prove that Bd is influenced by climate change. This is
important because all types of climatic factors must be considered to determine the cause
of Bd in the tropical rainforest of Central America.
21
Another author, Lips (2008), called this climate change theory into question.
Ecological conditions may have contributed to the spread of Bd. Lips et al., (2008),
argued that environmental causes may influence the spread of Bd, not climate change
(2008). Lips et al. (2008) researched the connection of Bd outbreak and climate change
related to spatiotemporal patterns. The authors studied the data of the Atelopus species in
conjunction with data of other amphibian species from Central America and South
America to determine if Bd is invasive (Lips et al. 2008). They hypothesized that if Bd is
a widespread infection, patterns that represent space and time would suggest that Bd
spreads throughout endemic habitats. The authors also suggested that if Bd is indeed
invasive, then Australia, Central, and South America should have the same space and
time patterns (Lips et al. 2008). The authors used data from the last Atelopus alive found
in the wild including classifications of habitat loss, introduced species, the cause of
decline among others (Lips et al., 2008). The researchers compared another data from
2004 publication from the Research and Analysis Network for Neotropical Amphibians
(RANA) containing the last dates known of amphibian species observed in the wild and
used it as a substitution for the date of species extinct in the wild, although it does not
contain the actual date of amphibian extinctions (Lips et al., 2008). The authors suggested
that to better analyze the space-time patterns of Bd exposure at a location, they needed to
use the proxy for the actual date of amphibian extinction (Lips et al. 2008).
Limited information of the first amphibian decline by Bd challenged the authors’
research. Lips et al. (2008) indicated that their research would not determine the exact
timing of Bd spread. The authors used spatial patterns to determine the amphibian decline
by Bd. Lips et al. (2008) analyzed how error sampling from the last year amphibians
22
observed in the wild (LYO) would affect the connection of amphibian decline with
temperature in the from 1970 to 1998. They found in their analyses that Bd is most likely
an introduced pathogen (2008). The authors indicated that local ecological changes can
affect the population growth and spread of Bd and host vulnerability, consequently
influencing amphibian abundance (Lips et al., 2008). Because of strong evidence that Bd
thrives in cooler temperatures, the hypothesis of Pounds et al., (1994) is not well
supported, (Baillie et al., 2004; Lips et al. 2008). Their theory (Lips et al., 2008) suggests
that climate change may not be related to Bd spread in Central America. These findings
bring another question: how these ecological changes affect amphibians and how are they
connected to Bd spread?
The theories from Pounds et al. (1994) and Lips et al. (2008) made compelling
arguments about whether or not climate change played a role in amphibian extinctions.
Whether we believe these theories, amphibians are becoming extinct in the Costa Rican
and the Panamanian tropical rainforest. We must consider that ecological changes may
also be impacted by climate change.
2.12
Panamanian Frogs Face Conservation Challenges
Endemic Atelopus species in the Panamanian tropical rainforest, especially the
Panamanian Golden frog and the Harlequin frog, have been experiencing a population
decline since the arrival of Bd. Efforts to increase Atelopus populations are underway.
Species survival program in zoos across the United States have had successful results in
mitigating the spread of Bd, on the Panamanian golden frogs (Atelopus zeteki) (Becker et
al., 2011). Captive breeding can be the only method to ensure the survival of other
23
Atelopus species in Panama, like the Harlequin frog (Atelopus certus), the Clown frog
(Atelopus varius), the Limosa harlequin frog (Atelopus limosus), and the Pirri harlequin
frog (Atelopus glyphus) (Becker et al., 2011).
Becker et al. (2011) conducted a study to eradicate Bd using an antifungal
microorganism. They experimented with 54 Panamanian golden frogs from the Houston
Zoo with the purpose of mitigating Bd. The researchers used skin bacteria called
Janthinobacterium lividum that was known to help mitigate the Chytridiomycosis in
amphibians in the United States, on 1 group of Golden frogs to compare it with a control
group infected with Bd (Becker et al. 2011). The study lasted about 120 days due to the
overwhelming spread of Bd in both the control group and the treated group (Fig. 8), and
the Janthinobacterium lividum bacteria was not present after the death of the treated frogs
(Becker et al. 2011). The numbers of dead frogs in both groups were the same after 50
days, and one factor that negatively affected the frogs could have been the captive
environment the frogs were living before the experiment. (Becker et al., 2011). There
were successful studies in the United States, perhaps due to the difference of climate the
treatments were conducted. Many Panamanian frog species will stay in captivity to
conserve their species until scientists find a way to mitigate this disease.
24
Figure 8. Survival patterns of frogs treated with J lividum before Bd exposure and frogs exposed to Bd without
treatment. 118 days after exposure the treated frogs were infected by Bd. J lividum bacteria was not present at the
death of the treated frogs. Source: Becker et al., (2011).
Another study has been conducted to determine if one Atelopus species was ready
to return to its environment. In efforts to reintroduce the captive Panamanian Golden
frog to the wild, DiRenzo et al. (2014) tested the intensity of Bd in 5 A. zeteki that were
never exposed to Bd and 3 Atelopus zeteki injected with to Bd strain JEL427-P39 23
weeks before the experiment. DiRenzo et al. (2014) analyzed the quantity of zoospores in
the frogs’ bodies at the time of death (Table 3). When the experiment started, the authors
treated each frog with 30,000 Bd zoospores for 10 hours (2014). 7 days after the
inoculation, all frogs were monitored each day for any symptoms and tested for Bd
intensity. The days of survival for the naïve group was between 18 – 31 days with
variable Bd zoospore intensity. The days of survival from the previously exposed group
were between 18 and 33 days with variable Bd zoospore intensity. The last frog from the
previously exposed to Bd group survived for 33 days with no Bd zoospores by the time of
death (2014). The experiment from DiRenzo et al. indicated that the Bd intensity in the
A. zeteki at time of death was very high in comparison to other studies (2014). The
25
authors suggested that the A. zeteki is extremely vulnerable to Bd infection concluding
that these amphibians are not capable to being reintroduced to the wild.
Table 3. Atelopus zeteki infection intensity (number of zoospores on skin swabs) and zoospore output (number of
zoospores released per minute) at death. Source: DiRenzo et al. (2014).
Prior exposure
Naïve
Naïve
Naïve
Naïve
Naïve
Previous
Previous
Previous
2.13
Total days survived
post-inoculation
21
28
18
31
25
18
33
31
Bd infection intensity at
death
520,436
1,697,306
4,454,759
8,781,016
9,584,158
2,291,631
2,960,916
4,385,154
Zoospore output at
death
3.5
0.0
4.9
0.2
170.6
7.1
0.0
0.0
Are Amphibians in Panama Surviving Bd?
After the Bd outbreak in 2004, scientists believe that some amphibians are
recovering from Bd in the Panamanian tropical rainforest. In 2017, an Atelopus species
was observed at the same Bd prevalent site in El Copé, in Central Panama, after the Bd
wave of 2004 (Voyles et al., 2018). Voyles et al. (2018) conducted an analysis on the
frog behavior and resistance to observe changes in Bd spread in the Harlequin frog
(Atelopus varius) and the Australian green tree frog (Litoria caerulea) species. The
researchers used Bd zoospore samples collected in 2004 (historic) and Bd zoospore
samples collected in 2013 (current) from sites in Panama (Voyles et al., 2018) to compare
the Bd intensity in the frogs. Voyles et al. (2018) indicated that there was no difference in
the intensity of Bd between the two frog species.
The authors also tested both historic and current Bd samples to observe any
difference in Bd zoospore growth rate (Voyles et al., 2018). Voyles et al. (2018)
suggested that there was no difference of Bd intensity in both Atelopus varius and Litoria
caerulea. The authors looked close at the phylogenetic construction from the historic and
26
current Bd samples and found no difference or any change in the Bd infection.
Finally, the researchers tested skin secretions samples from 6 different frog
species taken before and during the outbreak, and from captive and wild Atelopus varius
species from 3 different Panamanian sites to determine the resistance against Bd (Voyles
et al., 2018). They found differences of skin secretions efficiency among the amphibian
from the two time periods. The wild Atelopus varius skin defenses were more capable to
resist Bd than the captive Atelopus varius species, concluding that some amphibians have
developed stronger skin defenses. Panamanian amphibian species are showing signs of
recovery from Bd in 3 sites near El Copé, resulting from their skin secretions response to
resist Bd throughout the years (Voyles et al., 2018). There may be an opportunity for
study to determine if the skin secretion from the Atelopus varius can be successfully used
in other Atelopus species to help resist Bd.
2.14
The Effect of Ecological Variables in Amphibians’ Skin Defenses Against Bd
Ecological factors (precipitation, soil pH level) play a role in how the frogs’ skin
bacteria affect survival against Bd. Varela et al. (2018) studied the variation of the
amphibian skin microbiota of three frog species: 58 green and black poison frogs
(Dendrobates auratus), 6 rainforest rocket frogs (Silverstoneia flotator), and 6 Talamanca
rocket frogs (Allobates talamancae). They compared 4 sites across the Panama Canal that
have different soil pH and precipitation levels: Cerro Ancón, an urban forest with an
elevation of 564 ft; Ft. Sherman (171 ft above sea level) located on the Panama Canal
watershed in the Atlantic Ocean, Pipeline Road in Gamboa (167 ft. high) located along
the Panama Canal watershed, and Barro Colorado Island (394 ft. high) that sits in the
27
middle of the Panama Canal. These sites are considered old growth forests (Fig. 9, Varela
et al. 2018).
Figure 9. Map of Panama and the four sites studied. Source: Varela et al. (2018).
No frog in this study tested positive for Bd, but Bd is prevalent near the Panama
Canal (Varela et al. 2018). The effect of the soil pH on the abundance of the skin
bacteria was examined before and after the rainy season. As a result, the variation of skin
bacteria in all 3 species are different by soil pH and rainfall. The skin
betaproteobacterium Janthinobacterium lividum, that produces compounds that prevents
Bd growth (Brucker et al., 2008), increased in 2 amphibian species at the beginning of
wet season. However, their skin bacteria diversity decreased during dry season and low
soil pH levels, and precipitation had no effect on the skin bacterial diversity (Varela et al.,
2018). They compared bacterial richness (alpha) and the changes in diversity (beta) in
each frog species. In the D. auratus, bacterial diversity had a negative correlation with
the soil pH level (Varela et al., 2018). Fort Sherman had the highest bacterial diversity
and the lowest soil pH level, Cerro Ancón and Pipeline Road in Gamboa were in the
middle, and Barro Colorado had the lowest bacterial diversity and the highest soil pH
level (Varela et al., 2018). The authors found that in Pipeline Road, the D. auratus had
28
the lowest skin bacterial diversity than the A. talamancae and the S. flotator suggesting
that the A. talamancae is more vulnerable to Bd than the other two species (Fig. 10).
Amphibian skin bacteria diversity and abundance play an important role in inhibiting Bd
growth. Although there is a significant variation of bacteria among these studied
amphibians, changes in the environment can affect amphibian microbiome structure.
Figure 10. Bacterial community composition in D. auratus across the sites near the Panama Canal. Varela et al.
(2018) used linear discriminant analysis (LDA) scores to find the most significance in bacterial composition. Source:
Varela et al. (2018).
2.15
Reintroduction of the Atelopus limosus into the Wild
The East of Panama has yet to be hit with Bd spread and could be an ideal
environment for experimenting with the survival of one Atelopus species in the wild.
With the help of the Amphibian Rescue and Conservation Project in Panama, 90 Limosa
harlequin frogs (Atelopus limosus) were released into the wild, in the Mamoní Valley
(Eastern Panama), for the first time in May 2017 (First Release Trial, 2017). The purpose
of this trial was to learn how these amphibians can survive in a natural environment after
29
being in captivity (First Release Trial, 2017). Therefore, the success of the survival of
the Harlequin frog in the wild may indicate an ideal habitat condition and a possible
reintroduction of the Panamanian Golden frog.
The Limosa harlequin frogs (Atelopus limosus) chosen for reintroduction have
never lived in the wild, so there is a probability that some frogs could die early in their
cycle. Due to the uncertainty about the frogs’ survival, the frogs were tagged with
individual numbers and marked 30 frogs’ toes with a rubber that glows with UV light for
better identification (First Release Trial, 2017).
STRI started to slowly release the frogs by allowing them to stay in cages for 1
month in the wild, so that they could adapt to their new environment (First Release Trial,
2017). STRI scientists attached mini transmitters to monitor 8 of the 30 frogs and
introduced another group of 8 frogs to the wild with no adaptation period as a control
group (First Release Trial, 2017).
This project is still in progress. Dr. Roberto Ibañez from STRI indicated that the
data on the reintroduction trial is being analyzed for publication (D. E. Lloyd personal
communication, January 10, 2019).
2.16
Conclusion
The decline of the amphibian population caused by Bd is devastating. The sudden
disappearance of the Gastric Brooding frog (Rheobatrachus silus) and the Southern Day
Frog (Taudactylus diurnus) (Baillie et al., 2004) indicated that Bd has been prevalent in
endemic amphibian species. According to Baillie et al., most of the amphibian declines
have taken place in Central and South America (2004).
30
The endemic amphibians, including the Panamanian Golden frog, are rescued and
kept in captivity. This species should not be reintroduced to the wild until we see positive
results in the reintroduction of the Harlequin frogs. Efforts to conserve these beautiful
species by STRI researchers and reintroducing some other amphibian species into the
wild is very significant. However, this is only the beginning, and the survival of these
amphibians is uncertain. Scientists are working together to find an anti-fungus to stop the
mass eradication of the amphibian species around the world (Becker et al., 2011). The
conservation of the amphibian species is vital to humans and other animal species, as
they are essential in scientific research (Halliday, 2008).
While Bd affects amphibians, we do not know how Bd interacts with climate.
The Bd fungus is mostly found in cool aquatic freshwater habitat, and its proliferation is
most likely during the rainy season when the amphibians are in their mating stage
(Rodríguez-Brenes et al., 2016). Bd has been shown to be a significant factor in the
amphibian decline. However, the hypotheses of Pounds et al. (1994) and Lips et al.
(2008) have yet to resolve with certainty how Bd caused amphibian decline relates to
climate change.
Bd is still prevalent in the Costa Rican and Panamanian rainforest. Scientists
have studied the degree of resistance to Bd of some amphibians in Panama (Varela et al.
2018). The Atelopus varius in comparison to the other species that have resisted the
pathogen, may be the most vulnerable species (Woodhams, Voyles, Lips, Carey, &
Rollins-Smith, 2006). Ecological changes in habitats may prevent immunity in
amphibians (Rollins-Smith et al., 2002). This means that habitat may be affected by a
series of bioclimatic factors that could change how amphibians respond to diseases.
31
There are limitations to these studies in the Costa Rican and Panamanian tropical
rainforests. While research hopes to find a bacterium to fight Bd, scientists and officials
around the world will need to implement a mitigation strategy to prevent infectious
pathogens that can negatively affect wildlife and public health.
We understand that amphibians are being threatened by a chytrid fungus,
Batrachochytrium dendrobatidis (Bd). We still don’t understand if the cause for their
extinction is related to the interaction of Bd with climate change. And what we still don’t
understand is my research question: If Bd is one major factor of amphibian population
decline and extinction, what makes it so prevalent? How can Bd impact the aquatic
habitat in the tropical rainforest? What is the relationship between the amphibian chytrid
fungal disease and climate change? This is why I will attempt to first perform forensic
ecology of each Atelopus species in Costa Rica and Panama, examine the phylogenetic
relationship of Atelopus with species diversity loss due to Bd, and analyze climatic
variables from the late 1980s to 2018 to determine if Bd prevalence in Costa Rica and
Panama is connected to climate change.
32
CHAPTER 3 Methods
3.1
Forensic History of the Atelopus Species in Costa Rica and Panama
For my first method, I described my attempt to collect all available sources to
create a detailed history of each Atelopus species in Costa Rica and Panama. My aim was
to provide a detailed narrative of the timeline of appearance of Bd, timeline of decline
and in some cases recovery, and important existing knowledge of location, life history,
habitat, and climate variables in order to see whether there are discernable patterns across
these species that might help us understand the cause or causes of extinction. I collected
observations from La Marca et al. (2005), the IUCN Red List of Threatened Species
(2019), data and many other sources with information on taxonomic identification,
geographic distribution, elevation range, current and past estimates of abundance, current
population status, last documented records, habitat and ecology, threats and conservation
actions. Lips (2008) provided a 30,000-foot view of the epidemic wave. I wanted to
provide a closer view (5,000 foot) for Panama and Costa Rica. Perhaps by looking at the
extinction episode at a smaller geographical scale and over a longer time period, I could
assess potential causes for decline and recovery. I determined the actual coordinates of
each Atelopus species in Panama and Costa Rica and calculated the mean elevation of
each Atelopus species occurrence.
3.2
Atelopus Species Phylogenetic Tree
For the second part of my research, I collected the 16S ribosomal RNA gene
sequence data from all Atelopus species from Central and South America from the
National Center for Biotechnology (NCBI) to determine the connection between genetics
33
and Bd . There was no16S ribosomal RNA gene sequence data from Atelopus senex. I
input each Atelopus species sequence data as text and uploaded it to the Seaview
Sequence Alignment and Phylogenetic Tree Building software. The DNA sequences of
the Atelopus species were aligned and a phylogenetic tree was constructed. The IUCN
(2019) status of each Atelopus species was supplemented as a legend labeled in different
colors to illustrate the Atelopus threatened status, which are extinct (red), extinct in the
wild (orange), critically endangered (golden), endangered (yellow), vulnerable (light
blue), near threatened (purple), least concerned (green), data deficient (dark blue), and
not evaluated (gray).
3.3
Correlation Between Bd Prevalence in Atelopus Species and Climatic
Variables in Panama and Costa Rica
For my third method, I used the distribution species collection data from the
IUCN that included duplicates, which makes the data spatially biased. Here, I analyzed
how the Worldclim 19 climatic historical bioclimatic variables from 1970 to 2000 in
Costa Rica and Panama related to a species abundance, based on unbiased datasets for 8
Atelopus species using RStudio.
I identified the coordinates of the location data of each Atelopus species
accurately to allow RStudio to recognize the Atelopus species data. To analyze unbiased
data, I removed points with no location data, points that were not in the right
geographical location, for example, I only needed coordinates for Panama and Costa
Rica. I also removed duplicates (observations from the same location), and created data
frames for points with different coordinate systems, and converted them to WGS 1984.
34
I focused on the 2 most common bioclimatic variables in Panama and Costa Rica.
For BIO1 (Mean Annual Temperature) to produce the bioclimatic response model using
dismo. I analyzed the probability of the Atelopus species occurrence in their home range
based on the temperature per year. For BIO12 (Mean Annual Precipitation), I analyzed
the probability of the Atelopus species occurrence in their home range based on
precipitation per year. The bioclimatic temperature variables in BIO1 are shown in (°C x
10). The Atelopus species habitat suitability model included values from 0 for unsuitable
habitats to 1 for suitable habitats.
35
CHAPTER 4 Results
4.1
Forensic History of the Atelopus species in Costa Rica and Panama
In this chapter, I am presenting the history of Chytridiomycosis, the skin infection
caused by Bd that has affected the Atelopus species (A. chiriquiensis, A. varius, A.
limosus, A. zeteki, A. glyphus, A. certus, A. chirripoensis, and A. senex) in the
Panamanian and Costa Rican region. This narrative describes the assessment of the
native Panamanian and Costa Rican Atelopus species distribution and population decline
caused by the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd) (La
Marca et al., 2005; Lips et al. 2008). I present a summary of the individual Atelopus
species and the Panama – Costa Rica region at the end of Section 1 in Tables 4 & 5, and
Figure 11.
4.1.1 Chiriquí Harlequin Frog (Atelopus chiriquiensis)
The Atelopus chiriquiensis has been listed as critically
endangered by the International Union for Conservation of
Nature’s Red List of Threatened Species (IUCN, 2019),
because of a severe loss in its population, possibly to be
more than 80% over 21 years. The probable cause of the loss of most of the population is
due to Chytridiomycosis. This species was last seen in the 1990s (IUCN, 2004). The
status of A. chiriquiensis is considered to be extinct in the wild with no captive
population (Lewis et al., 2019).
The A. chiriquiensis, a diurnal forest frog, is closely related to A. varius, the
harlequin frog from Monteverde (Lips, 1998), is found in streamside in the lowland
36
forests between the Cordillera de Talamanca-Chiriquí of Costa Rica (1,800-2,500 m in
elevation) and Western Panama (1,400-2,100 m in elevation) (Savage 2002). This species
has not been seen in Costa Rica since 1996 (LaMarca et al., 2005), and it is believed to be
extinct in Costa Rica and Panama (Lips et al., 2010).
This A. chiriquiensis population at one time was widespread in Costa Rica and
Panama (Lips et al., 2010). Surveys were conducted in search of this species, but it has
not been seen in their habitats since 1996 (LaMarca et al., 2005). For example, Karen
Lips surveyed Las Tablas, Costa Rica in 1990, and 1991 when the species were most
abundant (Lips, 1998). However, in 1992 and 1993, the species began to decline, and by
1994 and 1996, Lips did not find any A. chiriquiensis (1998). In their last assessment in
August 2007, the IUCN described no new detection of the A. chiriquiensis (Lips et al.,
2010), and according to Lewis et al. (2019), there is no A. chiriquiensis in captivity
(2019).
The Atelopus chiriquiensis faced threats over the years and have been observed
and documented (Lips et al., 2003). A possible cause of the extinction of this species in
Costa Rica is due to Batrachochytrium dendrobatidis (Bd) (Lips, 1998), which was
confirmed in this species in 1993 and 1994 (Lips et al., 2003). Introduction of predatory
trout, and general habitat loss both outside, and within protected areas, are also threats to
remaining populations. Climate change is considered to be a possible threat.
El Parque Nacional Chirripó (Chirripó National Park) and Parque Internacional La
Amistad (La Amistad International Park) are protected areas that cover the A.
chiriquiensis home range. If surviving species are found, there would be a conservation
plan to protect this species against Bd (Lips at al., 2010).
37
4.1.2 Variable Harlequin Frog (Atelopus varius)
The IUCN, 2020 listed the Atelopus varius as Critically
Endangered in the wild. More than 80% of its population over
21 years between 1987 and 2007 has suffered a severe decline
(Lewis et al., 2019). The population decline of this species is
due to Chytridiomycosis (Baillie et al., 2004). The population decline has been
significant in their suitable habitats at above 1000 m of elevation (LaMarca et al. 2005).
A small population of A. varius has been rediscovered in Costa Rica and Panama areas
with Bd prevalence (Lewis et al., 2019). A large population of A. varius was found in the
Bd prevalent lowland forests, in Donoso, in the Panamanian province of Chiriquí (Lewis
et al., 2019). The status of this species in captivity is secure (Lewis et al., 2019). There
are 160 A. varius in captivity in American zoos and 24 A. varius in Panama that
comprises 8 highland frogs, and in 2016, 16 lowland frogs that were collected from
Donoso (Lewis et al., 2019).
The A. varius are terrestrial, diurnal forest frogs. They are found in both Atlantic
and Pacific highland areas of the cordilleras of Costa Rica throughout El Copé in Central
Panama (Richards and Knowles 2007), up to 2,000 m in elevation (Savage, 1972). It is
also found in remote lowland areas at 16m in elevation (Pounds et al., 2010). There is a
probability that a population of A. varius occupies an unexplored montane forest in Costa
Rica (Ryan, Berlin, Gagliardo, & Lacovelli, 2005). The Panamanian and Costa Rican
Atelopus various have genetic differences. As a result, there are a wide variety of this
species dispersed in small populations (Lewis et al., 2019).
38
The Harlequin frogs were widespread in Costa Rica (Pounds et al., 2010) and
have decreased over the years. However, the severe loss was recorded in Monteverde in
1988, and the species was considered extinct in Costa Rica by 1996 (Lips et al., 1998).
According to the IUCN 2012, 80% of the Atelopus species are critically endangered,
resulting in a significant number that may be extinct (González-Maya et al., 2018). There
are surviving populations of Harlequin frogs occupying the Central Panama region after
the Chytrid fungus wave (Richards and Knowles, 2007). The Harlequin frogs might have
developed a resistance to Chytridiomycosis. Their survival in the wild can help other
amphibians resist the disease if they share similar phylogenetic lineage.
In 2003 a small population was rediscovered in Costa Rica. A group of scientists
led by Ron Gagliano, from the Atlanta Botanical Garden found 3 Harlequin frogs on the
Pacific coastal range near Quepos (Ryan et al., 2005). Gagliano conducted a second
survey in 2005 but did not find additional populations (2005). However, another type of
A. varius population was discovered in the Talamanca Mountains in 2008 and Quepos in
2015 (González-Maya et al., 2013). Although there is not enough literature with
evidence to support claims about the A. varius population in the Provinces of Veraguas,
Coclé in Central Panama and Colon in the Central side of Panama near the Caribbean Sea
(González-Maya et al., 2013), some populations including the A. varius, have declined
(Lips, 1999). In Chiriquí Province, Western Panama, a significant number of A. varius
died between 1996 and 1997 (Lips, 1999). The site was surveyed again in 1998, but the
species did not prevail (Ibañez, 1999). However, in Coclé, Central Panama, another A.
varius population has persisted Bd at the same location where the massive decline
39
occurred (Voyles et al., 2018). In Costa Rica, a population of A. varius has been
rediscovered and perhaps resisting Bd (Ryan et al., 2005).
The A. varius is a terrestrial species of humid lowland and montane forest;
specimens recorded at lowland rainforest localities were all found along high-gradient,
rocky streams, in hilly areas (Savage 2002). It is associated with small fast-flowing
streams and is often found along the banks and sitting out on rocks in streams; at night
they sleep in crevices or low vegetation. They were previously present and densely
populated during the dry season, from December to May in humid habitats (Savage
2002). Eggs are laid in water and are probably attached to rocks, and its larva disperse
through streams (Richards-Zawacki, 2009).
In the late 1980s, pet trade, habitat loss, invasive species such as trout
(Onchorhynchus and Salmo) and American bullfrog (Rana catesbeiana) (LaMarca et al.,
2005), and climate change caused the A. varius population decline (González-Maya et al.,
2013). However, chytridiomycosis is the major cause of amphibian loss which has led to
catastrophic population declines in many other montane species of Atelopus (Lips, Reeve,
& Witters, 2003). Museum specimens of this species have been found to have chytrid
fungi. The Atelopus varius began to vanish in Monteverde then its extinction in the
Tilarán Mountains in Costa Rica in 1992 (González-Maya et al., 2013). One specimen
collected in 2003 from the only known site at which the species survives in Costa Rica
tested positive for chytrid infection, and the disease was also confirmed in individuals in
1986, 1990, 1992 and 1997 (LaMarca et al., 2005). Other threats include the parasitic fly
larvae that pray on this Atelopus species (González-Maya et al., 2013), habitat loss due to
the destruction of natural forests, and predation by introduced rainbow trout. Besides Bd,
40
another major threat is the unlawful collection for the pet trade if the location of this
species population is exposed (González-Maya et al., 2013). The only known site in
Costa Rica is under serious threat of a landslide that could potentially destroy the entire
stream section where they are presently found. It was collected by the thousands in the
1970s and shipped to Germany as part of the international pet trade. In Panama,
anthropogenic activity such as the creation of dams, invasive predatory fish, water
pollution by agricultural runoff are potential cause of the Atelopus varius population
decline (Richards-Zawacki, 2009).
The A. varius is present in three undisclosed protected areas in Panama. This
species was previously found in a number of Costa Rican protected areas in Northeast of
San Vito, within the Las Tablas Protected Zone, La Amistad Biosphere Reserve
(González-Maya et al., 2013). This location is a conservation area that covers restored
forests with steep slope streams (2013). Ex-situ conservation actions are now needed to
ensure the future survival of this species, and a captive-breeding program has been
started. In Panama, the species survival program imported the A. varius to zoos in the
United States in 2001 to ensure the population of this species (Lewis et al., 2019). Then
in 2009, Zoo New England, Cheyenne Mountain Zoo, Houston Zoo, Smithsonian
National Zoo, The Smithsonian Tropical Research Institute (STRI), and Defenders of
Wildlife collaborated to create the Panama Amphibian Rescue and Conservation (PARC)
Project, located in Gamboa, Panama, to ensure the population of 12 amphibian species,
including the A. varius (2019).
41
4.1.3 Limosa Harlequin Frog (Atelopus limosus)
The IUCN, 2019 listed the Atelopus limosus as Critically
Endangered and its population is decreasing (IUCN, 2019). Its
population may have started to decline in 2009, as this species was
tested positive for Bd (Lewis et al., 2019). There is continuing
decline in the extent and quality of its forest habitat in Panama. A. limosus population
will probably have approximately 80% loss for 21 years (2019).
The A. limosus is endemic to Colón, in the eastern Atlantic side of central
Panama, but this species has a very extensive distributional range. The A. limosus is
present in low-altitude at a 10-730m in elevation (Lewis et al., 2019), in the Atlantic
slope of several areas throughout the Panama Canal (Ibañez et al., 1995), which are Coco
Solo, Brazo del Medic, the Chagres River, Madden Lake, and Gatún Lake in the province
of Colón and near Boquerón in the province of Panama (1995), and in higher elevation
sites including Cerro Bruja, Cerro Brewster, Valle de Mamoní, Cocobolo Nature Reserve
and Nusagandi within the Comarca Kuna Yala, which is an indigenous territory in the
Atlantic side of Panama (IUCN, 2019).
The A. limosus population was abundant in Santa Rita, in Colón Province in 2000
only one individual was seen in December 2002 until 2009 when Bd was discovered in
Chagres National Park (Lewis et al., 2019). Since 2009, this species has suffered a rapid
population loss in higher elevation areas including Cerro Bruja, Cerro Brewster, Sierra
Llorona, and the population in the lower elevation suffered a slight decline (2019). Since
2018, the Atelopus limosus is still present in small populations in the Cocobolo Nature
Reserve located within the Mamoní Valley Preserve in the East side of the Panama Canal
42
(Lewis et al., 2019), although some Limosa harlequin frogs have been found positive
with Bd (IUCN, 2019). The status of the A. limosus in captivity is secure with 26 frogs
that have been bred in captivity, but tadpoles from only 20 adult pairs have succeeded to
adulthood and created the current captive A. limosus community (Lewis et al., 2019).
The A. limosus is a terrestrial species of tropical lowland forest (Ibañez et al., 1995)
This species is active during the day, and is present in rocky river streams in cloud forest
(1995). The A. limosus Breeding and larval development takes place in forest streams
(Ibañez et al., 1995). The skin color of this species resembles the surface of rocks and the
streams, which serves as a disguise to protect themselves from predation (1995). The A.
limosus in the lowland differ from the A. limosus in the highland (Wilson, 2014). The
lowland type is brown with yellow nostrils and fingertips, while the highland type has
green and yellow with a black wide V-shaped pattern on the back of its body (2014). The
average generation interval for this species is 7 years (IUCN, 2019).
Although deforestation of habitat for agricultural use and general infrastructure
development, water pollution, stream sedimentation (IUCN, 2019), and gold mining
(Ibañes et al., 1995), are considered major threats to this species a significant quantity of
A. limosus population have declined from their home range due to the chytrid fungus, Bd,
which appears to be more prevalent at high elevations sites (Lewis et al., 2019).
However, in a 2018 survey, the A. limosus in the wild have been persisting Bd at several
sites within the Mamoní Valley (2019). The population of A. limosus in the lowlands
have not been significantly affected by Bd. This population can prevent Bd infections due
the warmer temperature at lower elevations sites (Flechas et al., 2012). The skin
43
microbiome on the A. limosus may be a significant influence in preventing
chytridiomycosis (2012).
A significant population of A. limosus has been documented from Parque
Chagres National Park and Comarca Kuna Yala, but habitats within the Mamoní Valley
Preserve are high priority for the Panama’s National Amphibian Conservation Action
Plan (ANAM) and PARC established to support habitat protection and research
(Gratwicke et al. 2016).
A reintroduction of A. limosus has been initiated. In 2017, PARC started a release
trial of 90 A. limosus at Mamoní Valley Preserve (Lewis et al., 2019). Scientists used a
direct release to the wild and a soft release approach with a small frog group, which
means that captive frogs would remain ex-situ for 30 days before their release to the wild
(2019). Tracking radio transmitters were attached to some frogs, however most of them
scattered out of the monitoring range after their release and contributed to a small
recapture percentage (2019). Efforts to reintroduce captive frogs in Mamoní Valley
Preserve continues to understand the outcome of this species in Bd prevalent sites as a
tool to mitigate chytridiomycosis.
4.1.4 Panamanian Golden Frog (Atelopus zeteki)
The Atelopus zeteki is culturally significant to the people
of Panama (Markle, 2012), with a history dating back to the
Mayan civilization (2012). The IUCN listed the Atelopus zeteki
as Critically Endangered, Possibly Extinct in the Wild (IUCN,
2019). Karen Lips reported a significant population of Panamanian golden frog in 1992
44
(Markle, 2012). In 1996, Lips reported that this species has suffered a severe decline
(2012). The Atelopus zeteki have been rescued and relocated to captive breeding centers
(Zippel, 2002), to protect them from Bd (Lips, 2006). The last Atelopus zeteki in the wild
was seen in 2009 (Lewis et al., 2019). It is estimated that more than 80% of the A. zeteki
population has vanished over the last 10 years, probably due to chytridiomycosis (IUCN,
2019).
The Atelopus zeteki, an endemic species to Panama, was present in the rainforests
and cloud forests east of the main Tabasará ridge in Coclé in low elevations at 335 m, in
middle elevation around El Valle de Antón in Coclé at 760 m (Savage, 1972), to high
elevation at 1,315 m (Stuart et al. 2008), in Cerro Campana (Richards and Knowles
2007). The A. zeteki is limited to these areas and has not distributed from its home range.
The Atelopus zeteki was abundant at a number of sites in north of El Copé within
the Omar Torrijos National Park in the Coclé Province (Lips, 2006), but this species is
now extinct in the wild (IUCN, 2019). Lips surveyed these areas for 4 years from 2000
and July 2004 (2006). By September and October 2004, Populations have been declining
due to chytridiomycosis, and the well-known El Copé population collapsed, and vanished
(2006). Consequently, A fraction of the last A. zeteki population on Cerro Campana and
in the El Valle de Antón have disappeared due to Bd (McCaffery et al. 2015). The last
wild Atelopus zeteki was seen in 2009 (Lewis et al., 2019). The status of the Atelopus
zeteki in captivity is secure (2019), PARC has collected 4 wild adults highland Atelopus
zeteki in Panama. The Golden Frog Species Survival Program in the United States
helped breed 32 captive Atelopus zeteki, which include 12 lowland frogs and 20 highland
45
frogs (Lewis et al., 2019). The 2 groups of captive frogs reproduced more than 1300 adult
frogs in captivity (2019).
The A. zeteki is a terrestrial species of tropical montane wet forest, and montane
dry forest (Poole, 2006), with breeding and larval development taking place in forest
streams (Savage 1972). The tropical montane wet forest is larger and more dispersed in
and along the streams (up to 3m above the ground). The habitat typically includes
waterfalls and large boulders covered with moss that they utilize as visible territories.
These frogs sleep on big leaves at night (Poole, 2006). The Atelopus zeteki from the
tropical dry forest are smaller than the highland golden frogs and more visible on the
forest floor (2006). The Atelopus zeteki uses its skin secretions to protect themselves
from predators (Savage 2002).
The major threat is chytridiomycosis, which has led to catastrophic population
declines in many other species of the Atelopus species (Pounds et al., 2006; McCaffery et
al., 2015, Becker et al., 2015). In the 1960’s the Atelopus zeteki was collected severely
for pharmaceutical purposes in Europe and the United States (La Marca et al., 2005), and
pet trade (Lewis et al., 2019). The first declines caused by Bd were documented in 2004
in el Cope, near El Valle de Anton, Central Panama (Poole, 2006). Another threat to the
Atelopus zeteki is habitat loss due to deforestation, as well as water pollution (La Marca
et al., 2005). Sedimentation significantly affected river streams near El Valle de Antón,
due to road constructions (Lewis et al., 2019).
Although the Atelopus zeteki is protected in areas of Altos de Campana National
Park in and Omar Torrijos Herrera National Park by national legislation decree No. 23 of
January 30, 1967 (Zippel et al., 2006), it is possibly extinct in the wild (IUCN, 2019).
46
PARC has started a captive-breeding program with zoos in the United States, to
create stable populations in captivity (Poole, 2006). However, the reintroduction of this
species in the wild is not possible until existing threats can be addressed. Another
program from PARC is El Valle Amphibian Conservation Center, (EVACC), which is an
in-situ program with 2 locations at El Valle de Antón in the Western Panama and at
Gamboa (ARCC), near the Panama Canal, which has an amphibian exhibition and a
research center dedicated to the efforts to mitigate Bd (Lewis et al., 2019).
4.1.5
Pirre Harlequin Frog (Atelopus glyphus)
The IUCN, 2019 listed the Atelopus limosus as
Critically Endangered and its population is decreasing
(IUCN, 2019). The population of this species was
considered stable in 2002 (La Marca et al., 2005). In 2015,
a single Atelopus glyphus frog was first found positive for Bd (Lewis et al., 2019).
Studies show that after Bd is detected in a species, the entire population experience a
severe decline (Lips et al., 2008). In 2018, another Atelopus glyphus individual was
detected positive for Bd (Lewis et al., 2019) The population of the Atelopus glyphus will
probably to decline 87% over the next 21 years, suggested from declines in other
Atelopus species in the same region, due to Bd (Gratwicke et al., 2016).
The Atelopus glyphus species is present in Darién, eastern Panama, in the
mountainous site of Serranía de Pirre (Savage, 1972) at a mean elevation of 1192 m.
Previous assessment by the IUCN stated that the Atelopus glyphus was also found in the
Chocó of Colombia, but these records have not been confirmed (IUCN, 2019).
47
Consequently, the home range of this species has been restricted to the Panamanian site
within the Darien National Park and the updated extent of occurrence is 381 km2, (2019)
The A. glyphus population is decreasing. This species was considered to be
common within its home range (Savage, 1972). It was still abundant in September 2002
in the Serranía de Pirre, above Cana, in Darién, eastern Panama (Ibañez, 2015). The
status of the Atelopus glyphus in captivity is almost secure (Lewis et al., 2019). 18 of the
20 founders Atelopus glyphus produced surviving captive descendants, resulting in being
below population goals required by the Amphibian Ark, which has 350 adult amphibians
in captivity (2019). The goal of the Amphibian Ark was to reach up to 500 adult frogs
including captive-bred offspring (2019). In 2015, scientists reported dead Atelopus
glyphus frogs were positive for Bd, in the first field observations (Lewis et al., 2019).
The last surveys to Cana in January 2018 recorded only a single individual with three
days of searching (2019). There is no recent information about the Atelopus glyphus
population in the Darien area as the roads are inaccessible due to a political situation by
the guerrilla movement the Revolutionary Armed Forces of Colombia (FARC) in the
eastern Panamanian border (Ibañez, 2018).
The Atelopus glyphus is a terrestrial species of tropical mountainous rainforest at
884 -1,500 m in elevation (Savage, 1972). Amphibians living in riparian, montane
habitats stay within their own home range (Stuart et al., 2008). The Atelopus glyphus
species breed in forest streams (Ibañez, 2004) There is no information on whether or not
this species can survive in degraded habitats (2004). The Atelopus glyphus can live up to
7 years in captivity (Gratwicke et al., 2016)
48
The most significant threat to the Atelopus glyphus is chytridiomycosis, due to the
chytrid fungus Bd that caused a devastating population declines in Atelopus species
(Pounds et al., 2006; McCaffery et al., 2015, Becker et al., 2015). About 80% of Atelopus
species have suffered a decline in their population (La Marca et al., 2005). Other threat
to this species is habitat loss due to agricultural development (including the planting of
illegal crops by the FARC guerilla), logging, and human settlement, and pollution
resulting from the spraying of illegal crops (Ibañez, 2018).
The Atelopus glyphus has been recorded from two protected areas: Darién
National Park (a World Heritage Site) in Eastern Panama and Parque Nacional Natural
los Katíos in Colombia. Considering the severe risk of Bd infection on Atelopus species,
an ex-situ population has been established by PARC (Gratwicke et al., 2016), however
the conservation site in Cana has been difficult to access due to the FARC guerrilla
(Ibañez, 2018).
4.1.6
The Darien Stubfoot Toad (Atelopus certus)
The Atelopus certus is listed by the IUCN as
Critically Endangered (IUCN, 2019). It is inferred that this
species will probably undergo a population decline due to
Bd, estimated by La Marca et al. (2005), to be more than
80% over the next 21 years, recognized from declines in other high altitude Atelopus
species in the same region (IUCN, 2019).
49
The Atelopus certus is endemic to the eastern slope of Cerro Sapo in Darién
Province of Panama at 50 -1,150 m of elevation (Savage, 1972), located south west
outside of Darien National Park (Lewis et al., 2019).
The Atelopus certus species is present within its small range. There were less
frogs documented than anticipated in the last survey in 2016, in Darién (Lewis et al,
2019). No single Atelopus certus was found positive for Bd during the survey (2019). It
is not clear if the decline of this species is related to Bd, or the source was the drought
caused by El Niño in 2016 (2019). The status of the Atelopus certus in captivity is secure.
From the 28 captive Atelopus certus, 22 produced adult descendants and the captive
population is about 350 adult frogs (2019).
The Atelopus certus is a terrestrial species of tropical montane and submontane
forest (Savage, 1972). Breeding and larval development takes place in forest streams.
The Atelopus certus species breed in forest streams (Ibañez, 2004) The eggs are large
and unpigmented (Duellman & Lynch, 1969). Tadpoles have a large suction disc on the
belly, used to cling to rocks and pebbles in streams (1969). This and can live up to 7
years in captivity (Gratwicke et al., 2016).
There are no records of population decline for the Atelopus certus species due to
Bd. However, the Atelopus species is significantly vulnerable to Bd, with the highest
mortality rates (Stuart et al., 2008; Gratwicke et al. 2016). The Atelopus certus is
expected to decline about 80% of its population in the next 3 generations (La Marca et
al., 2005). Although this species is present in lower elevation habitats, population loss
has been recorded in low elevations in the Atelopus limosus species (Lewis et al., 2019).
50
Other threats to the Atelopus certus outside of its protected range, Darien National
Park, may be deforestation of habitat for agricultural use water pollution logging, and
human settlement. Due to the political situation by the FARC guerrilla in the eastern
Panamanian border there is no accessibility outside Darien National Park (Ibañez, 2018).
There is a conservation action in place for the Atelopus certus. The majority of its
range is within the Parque Nacional Darién, with 91-100% of the population believed to
be protected. In 2010, PARC set an expedition to the Darien area and brought back a
founding population of Atelopus certus to begin an ex-situ conservation program at the
Gamboa Amphibian Research and Conservation Center where the breeding process was
successful (Gratwicke et al. 2016). The Atelopus certus is considered a priority species
by the Panama's National Amphibian Conservation Action Plan (ANAM 2011).
4.1.7
The Chirripó Stubfoot Toad (Atelopus chirripoensis)
The Atelopus chirripoensis is listed by the IUCN as Critically Endangered,
Possibly Extinct (IUCN, 2013). In 1980 one single individual was discovered (Savage &
Bolaños, 2008). No single Atelopus chirripoensis has been found after many surveys
following the discovery of this species, and it is believed that this species is extinct
(2008). However, the IUCN indicates that if the species is still existing, there would be
less than 50 and 160 adult frogs (IUCN, 2013).
Only one individual of Atelopus chirripoensis species has been seen 4 km north of
the summit of Cerro Chirripó, Chirripó National Park in Costa Rica (Savage & Bolaños
2008). Cerro Chirripó elevational range is 3,400-3,500 m. Surveys in this area suggest
that this species would be endemic to Cerro Chirripó (IUCN 2013).
51
In March of 1980, a Costa Rican biologist, Luis Gómez, collected a single frog
was from a breeding accumulation of Atelopus chirripoensis north of Cerro Chirripó
Grande in Costa Rica. Although many surveys have been conducted at the original site
between 1980 and 1985, the Atelopus chirripoensis species has not been seen since
(Savage and Bolaños 2008).
The Atelopus chirripoensis was present in high altitude grassland and shrubland
qualified as Tropical Subalpine Pluvial Paramo region (Savage & Bolaños 2008). Dr.
Gómez stated that there were many frogs of Atelopus chirripoensis species when he
collected a single individual in 1980 (2008). The frog was found among a number of
small shallow ponds that evaporate each season (2008). Although there is no information
on its reproductive biology, it is presumed to breed by larval development in temporary
ponds as observed by Dr Gómez (2008).
The Atelopus chirripoensis species has no records of population decline due to Bd
(IUCN, 2019). The habitat of the species is not threatened because it is located in a
remote, well-protected Chirripó National Park (Savage & Bolaños 2008). Cerro Chirripó
is within the Talamanca mountain range, where Bd has been recorded (González-Maya,
et al., 2013). Therefore, it is possible that the Atelopus chirripoensis species has
disappeared seen since its discovery in 1980 due to Bd (IUCN, 2013).
The Atelopus chirripoensis was known to inhabit a protected within Chirripó
National Park, which is a well-protected area, and adjacent highland areas are Las Tablas
Protected Zone, La Amistad Biosphere Reserve (González-Maya et al., 2013). Surveys
are needed to detect the existence of and threats to this Atelopus species (IUCN, 2013).
52
4.1.8
Pass Stubfoot Toad (Atelopus senex)
The Atelopus senex is listed by the IUCN as
Critically Endangered (Possibly extinct) because of a
severe decrease in its population, estimated to be more
than 80% over the last 21 years (La Marca et al., 2005),
It is presumed from the evident loss of most of the Atelopus senex population, probably
due to Bd (Bolaños, 2008).
The Atelopus senex species was present in high altitude regions of the rainforest
in the Central Valley and Talamanca Mountain Range in Costa Rica from 1,100-2,200 m
in elevation, in the headwater basin of Rio Grande de Orosi river, in only 3 isolated sites,
1 in the Barva volcano region with a lower elevation rainforest, and 2 on the extreme
northern slopes of the Cordillera de Talamanca in Cedral Mountain and Reventazon basin
which are premontane rainforests (Savage, 1972).
The Atelopus senex population was abundant on the slopes of Barba volcano but
is now believed extinct there (Savage 2002). Although there were many surveys
conducted, the last time the Atelopus senex species was seen was in 1986. This species
experienced a population loss in 1987-1988, and did not recovered (Savage, 2002).
Future surveys are needed to confirm the extinction of this species although further
searches are needed to finally confirm the extinction of this species (Bolaños, 2008).
The Atelopus senex inhabits and reproduces in stream margins in premontane
rainforest and lower montane rainforest. It is a diurnal, stream-breeding species, and used
to be found in great concentrations during the reproductive period from July to August
(Savage 2002).
53
The Atelopus senex experienced a severe population decline between 1987 and
1988, from which it has not recovered (Savage, 2002). The major threat to the Atelopus
senex may be chytridiomycosis, leading to a catastrophic population decline, as has
affected many other high-altitude species of Atelopus (La Marca et al., 2005). The
Atelopus senex may be extinct in the Volcán Barva region (Savage, 2002). Other threats
to this species may involve climate change, collecting for the pet trade, and pollution
(Bolaños et al., 2008).
The range of this species is protected by both Tapantí National Park and Braulio
Carrillo National Park (Savage, 2002). However, this species is now believed extinct in
the Braulio Carrillo National Park (Bolaños et al., 2008). There is no Atelopus senex in
captivity, therefore further survey work is required to determine whether or not this
species still persists in the wild (2008). Considering that Bd may have devastated the
Atelopus senex species surviving individuals might need to be established as a captive
population.
Table 4. Summary data on Atelopus species. Prot. areas: Bd presence in protected areas. Yr. of last record: year of
most recent record; Yr. Bd presence of Bd: year(s) documented; Hab. destr: occurrence of significant habitat
destruction/ Status: Stable, Decline*
Atelopus
species
A.
chirripoensis
A. senex
A.
chiriquiensis
A. varius
A. zeteki
A. limosus
A. certus
A. glyphus
54
Country
Elevational
range (m)
3400-3500
Prot.
areas
Y
Yr. of last
record
1980
Yr. of Bd
Presence
-
Hab.
destr.
N
IUCN
Status
Unknown
Costa Rica
Costa Rica
Panama
Costa Rica
Panama
1100-2200
1400-2100
Y
Y
1986
1996
N
Y
Decline*
Decline*
16-2000
Y
2003
Y
Decline
Panama
Panama
Panama
Panama
335-1315
10-730
50-1150
884-1500
Y
Y
Y
Y
2004
2009
2016
2018
1993
1994
1986
1990
1992
1997
2004
2009
2015
Y
Y
N
N
Decline
Decline
Decline
Decline
Costa Rica
Table 5. Summary of Location, Coordinates Minimum, Mean, and Maximum Elevation of Atelopus Species
Occurrences.
Species
Location
Longitude Latitude
Min.
Mean
Max. Elev. (m)
Elev. (m) Elev. (m)
A. chirripoensis
Chirripó NP, CR
-83.48
9.53
3400
3450
3500
A. senex
Volcán Barva, CR
-84
10
1960
2000
2040
Reventazón Basin, CR
-83.46
10.23
1280
1300
1320
Cedral Mt, CR
-84.14
9.84
2150
2285
2420
A. chiriquiensis
La Amistad, Intl. Park CR
-83.04
9.13
1400
1750
2100
A. varius
El Copé, El Valle, PAN
-80.62
8.67
758
1,036
1314
Fortuna Forest, PAN
-82.16
8.71
700
1457
2213
Monteverde, CR
-84.8
10.3
600
1200
1800
Santa Fe, NP, PAN
-81.13
8.52
430
1197
1964
A. zeteki
El Copé, El Valle, PAN
-80.13
8.62
335
825
1315
A. limosus
Chagres NP, PAN
-79.47
9.45
10
370
730
A. certus
Darién NP, PAN
-78.35
7.94
50
600
1150
A. glyphus
Darién NP, PAN
-77.72
7.8
884
1192
1500
Figure 11. The mean elevation of Costa Rica and Panama ranges from 600 m to 3450 m.
4.2
Atelopus Species Phylogenetic Tree
The Atelopus species phylogenetic tree shows the genetic variation of Atelopus species
(for which genetic data were available, see Methods) from Central and South America
(Fig. 12). The phylogenetic tree showed the top 5 Atelopus species indicates that 5 Costa
55
Rican and Panamanian. The Atelopus chiriquiensis and Atelopus varius occurred in
Costa Rica and Panama. The Atelopus limosus is endemic to Colón on eastern Atlantic
side of Central Panama, and the Atelopus zeteki and A. glyphus are also both endemic to
Panama. I hypothesized that these Atelopus species geographic isolation may have caused
the loss of their genetic variation and has endangered their immune responses to diseases.
The phylogenetic tree (Fig. 12) shows the IUCN red list assessment with the
conservation status of each the Atelopus species of Central and South America.
Figure 12. Atelopus Species Phylogenetic Tree and IUCN Red List Assessment
Atelopus Phylogenetic
Tree
2019 IUCN Red List Conservation
Status of Atelopus Species
56
4.3
Connection Between Bd Prevalence and Bioclimatic Variables in Atelopus
Species of Panama and Costa Rica
In this result, I assessed the Bd connection with the loss of Atelopus species in
Panama and Costa Rica based on bioclimatic variables (Table 6). Here, I presented the
species distribution map, bioclimatic response plots, and the species distribution model
using unbiased occurrence data of Chiriquí Harlequin Frog (Atelopus chiriquiensis),
Variable Harlequin Frog (Atelopus varius), Limosa Harlequin Frog (Atelopus limosus),
Panamanian Golden Frog (Atelopus zeteki), Pirre Harlequin Frog (Atelopus glyphus),
Darien Stubfoot Toad (Atelopus certus), Chirripó Stubfoot Toad (Atelopus chirripoensis),
and Pass Stubfoot Toad (Atelopus senex). These species were analyzed for climatic
suitability based on 19 historical bioclimatic variables from 1970 to 2000, to visualize
what the climate was like where the Atelopus species were known to be present during
the Bd wave from 1980 to 2000. How did Bd affect the Atelopus species in connection to
temperature, precipitation and elevation? The bioclimatic variables that most applied in
Panama and Costa Rica are Bio1, temperature, and Bio12, precipitation (Fig.13).
Figure 13. BIO1 (left) with temp. range from 7C to 20C per year (note, values in legend are C*10) and BIO12
(right) with precipitation. range from 2000 mm to 5000mm per year in Costa Rica and Panama.
57
Table 6. List of 19 bioclimatic variables used in bioclimatic model development. Names and descriptions are
in reference to the WorldClim, Hijmans, 2017.
Variable
Bio1
Bio2
Bio3
Bio4
Bio5
Bio6
Bio7
Bio8
Bio9
Bio10
Bio11
Bio12
Bio13
Bio14
Bio15
Bio16
Bio17
Bio18
Bio19
Description
Annual Mean Temperature
Mean Diurnal Range (Mean of monthly (max temp - min temp))
Isothermality (BIO2/BIO7) (×100)
Temperature Seasonality (standard deviation ×100)
Max Temperature of Warmest Month
Min Temperature of Coldest Month
Temperature Annual Range (BIO5-BIO6)
Mean Temperature of Wettest Quarter
Mean Temperature of Driest Quarter
Mean Temperature of Warmest Quarter
Mean Temperature of Coldest Quarter
Annual Precipitation
Precipitation of Wettest Month
Precipitation of Driest Month
Precipitation Seasonality (Coefficient of Variation)
Precipitation of Wettest Quarter
Precipitation of Driest Quarter
Precipitation of Warmest Quarter
Precipitation of Coldest Quarter
Temporal Scale
Annual
Variation
Variation
Variation
Month
Month
Annual
Quarter
Quarter
Quarter
Quarter
Annual
Month
Month
Variation
Quarter
Quarter
Quarter
Quarter
4.3.1 Chiriquí Harlequin Frog (Atelopus chiriquiensis)
This is the preliminary map (Fig. 14) of the Chiriquí Harlequin Frog (Atelopus
chiriquiensis) distribution with biased observation points to see how this species is
distributed in the lowland forests between Eastern Costa Rica (mean elevation 2,150 m)
and Western Panama (mean elevation 1,750 m).
Figure 14. Map of the Atelopus chiriquiensis Distribution in Costa Rica and Panama
58
The response plot (Fig. 15) showed how the probability of the Atelopus
chiriquiensis occurrences (y-axes), from 0 to 1, differ with each bioclimatic predictors (xaxes). I focused on the 2 most common bioclimatic variables for Panama and Costa Rica,
which are BIO1 (Mean Annual Temperature) and BIO12 (Mean Annual Precipitation).
The response plot shows thresholds, and linear and nonlinear shapes.
BIO1 showed that below the threshold of about 13C (55 F) of temperature per
year, the probability of the Atelopus chiriquiensis occurrence was 0. The probability
increases nonlinearly at about 14 C (57 F) per year, and the probability of this species
occurrence at its peak at about 16 C (61 F) per year, was 0.8, then the probability of the
Atelopus chiriquiensis occurrence plateaued at 18 C (64 F). Therefore, the probability
of this species to occur in this range was between 14 C (57 F) and 18 C (64 F) per
year. In BIO12, the probability of the Atelopus chiriquiensis occurrence below the
threshold of about 1760 mm of precipitation per year was 0. The probability of this
species occurrence increased nonlinearly at about 2500 mm of precipitation per year with
a predicted value of 0.4 and reached its peak at 2680 mm of precipitation per year with a
probability of occurrence of 1, then the probability of occurrence decreased nonlinearly at
about 2900 mm per year with a probability of occurrence of 0.4. Therefore, the
probability of the Atelopus chiriquiensis to occur in its range was between 1760 mm and
3120 mm of precipitation per year.
59
Figure 15. Atelopus chiriquiensis Response to Bioclimatic variables range of values based on the estimates of the
probability of occurrences.
What the habitat suitability plot (Fig. 16) predicted about the Atelopus
chiriquiensis distribution of suitable habitats at the border of Costa Rica and Panama was
that 30% of this species observed had suitable habitats, but 70% of Atelopus chiriquiensis
observed in places where the probability of occurrence was predicted to be low, below
the actual observations in 3 areas with suitable habitats where the probability of
occurrence was 0.4. However, there were also 7 areas with habitats where the probability
of occurrence predicted to be below 0.2, which were not suitable for the Atelopus
chiriquiensis to survive.
60
Figure 16. Predicting Recent Climatic Habitat Suitability on the Atelopus chiriquiensis range
4.3.2 Variable Harlequin Frog (Atelopus varius)
This is the preliminary map of the Variable Harlequin Frog (Atelopus
chiriquiensis) (Fig. 17), distribution with observation points to see how this species is
distributed in high montane areas of Costa Rica throughout El Copé in Central Panama
with a mean elevation of 1223 m.
Figure 17. Map of the Atelopus varius Distribution in Costa Rica throughout Panama
61
The second plot (Fig. 18) showed how the probability of the Atelopus varius
occurrences (y-axes), from 0 to 1, differ with each bioclimatic predictors (x-axes). I
focused on the 2 most common bioclimatic variables for Panama and Costa Rica, BIO1
(Mean Annual Temperature), and BIO12 (Mean Annual Precipitation). The bioclimatic
temperature variables in BIO1 are shown in °C x 10.
BIO1 shows that below the threshold of about 6C (43 F) of temperature per
year, the probability of the Atelopus varius occurrence was 0. The probability increased
nonlinearly at about 17 C (61 F) per year, and the probability of this species occurrence
at its peak at about 20.3 C (68 F) per year, is 0.8, then the probability of the Atelopus
varius occurrence plateaued at 24 C (75 F) to 25 C (77 F), and decreased at 26 C (79
F) Therefore, the probability of this species to occur in its range was between 17 C (61
F) and 25 C (77 F) per year.
BIO12 showed the probability of the Atelopus varius occurrence below the
threshold of about 1895 mm of precipitation per year is 0. The probability of this species
occurrence increases nonlinearly at about 1916 mm of precipitation per year with 0.2 and
reached its peak at 2785 mm to 3085 mm of precipitation per year with a probability of
occurrence at 0.8, then the probability of the Atelopus varius to occur decreased
nonlinearly at about 3426 mm per year. Therefore, the probability of the Atelopus varius
to occur in its range is between 1916 mm and 3426 mm of precipitation per year.
62
Figure 18. Atelopus varius Response to Bioclimatic variables range of values based on the estimates of the probability
of occurrences.
The habitat suitability plot (Fig. 19) predicted mostly areas of low suitability for
Atelopus varius. From the 62 species observations, there were also 95% had areas with
habitats where the probability of occurrence predicted to be below 0.2, which were not
suitable for the Atelopus varius to survive.
Figure 19. Predicting Recent Climatic Habitat Suitability of the Atelopus varius range
63
4.3.3 Darien Stubfoot Toad (Atelopus certus)
This is the preliminary map (Fig. 20) of the Darien Stubfoot Toad (Atelopus
certus) distribution with biased observation points to see how this species was distributed
in Darien National Park, East Panama at a mean elevation of 600 m.
Figure 20. Map of the Atelopus certus Distribution in Panama.
The response plot (Fig. 21) showed how the probability of the Atelopus certus
occurrences (y-axes), from 0 to 1, differ with each bioclimatic predictors (x-axes). BIO1
showed that below the threshold of about 18C (64 F) of temperature per year, the
probability of the Atelopus certus occurrence is 0. The probability increased linearly at
about 18.5 C (65 F) per year, and the probability of this species occurrence at its peak
at about 19 C (66 F) per year, is 0.6, then the probability of the Atelopus certus
occurrence continued to increase up to 24 C (74 F) with a predicted value of 0.6, and
the probability of this species occurrence decreased at about 26 C (79 F) Therefore, the
probability of the Atelopus certus to occur in this range at a predicted value of 0.6 is
between 18.5 C (65 F) and 26 C (79 F) per year. BIO12 showed the probability of
the Atelopus certus occurrence below the threshold of about 2000 mm of precipitation per
64
year with a predicted value of 0. The probability of this species occurrence increases
nonlinearly at about 2100 mm of precipitation per year with a predicted value 0.3 and
reached its peak at 2200 mm of precipitation per year with a probability of occurrence at
0.7, then decreases nonlinearly at about 2600 mm per year with a probability of
occurrence of 0.2. Therefore, the probability of the Atelopus certus to occur in its range
was between 2100 mm and 2600 mm of precipitation per year.
Figure 21. Figure 28. Atelopus certus Response to Bioclimatic variables range of values based on the estimates of the
probability of occurrences.
What the habitat suitability plot (Fig. 22) predicted about the Atelopus certus
distribution of suitable habitats in East Panama was that 10% of this species observed had
suitable habitats predicted to be below 0.3, which were not suitable, and 90% of Atelopus
certus observed in places where the probability of occurrence was predicted to be below
0.2, which were not suitable for the Atelopus certus to survive.
65
Figure 22. Predicting Recent Bioclimatic Habitat Suitability of the Atelopus certus range.
4.3.4 Pass Stubfoot Toad (Atelopus senex)
This is the preliminary map (Fig. 23) of the Pass Stubfoot Toad (Atelopus senex)
distribution with biased observation points to see how this species was distributed in the
Central Valley and Talamanca Mountain Range in Costa Rica from at a mean elevation
of 1,650 meters.
Figure 23. Map of the Atelopus senex Distribution in Costa Rica
66
The response plot (Fig. 24) showed how the probability of the Atelopus senex
occurrences (y-axes), from 0 to 1, differ with each bioclimatic predictors (x-axes). BIO1
showed that below the threshold of about 14C (57 F) of temperature per year, the
probability of the Atelopus senex occurrence is 0. The probability of this species
occurrence increased linearly and peaked at about 15 C (59 F) per year, with a
predicted value of 0.8. The probability of the Atelopus senex occurrence plateaued from
15 C (59 F) to 22 C (72 F) with a predicted value of 0.8, and the probability of this
species occurrence decreased at about 26 C (79 F) Therefore, the probability of this
species to occur in this range at a predicted value of 0.6 is between 15 C (59 F) and 26
C (79 F) per year. BIO12 showed the probability of the Atelopus senex occurrence
below the threshold of about 2600 mm of precipitation per year with a predicted value of
0. The probability of this species occurrence increases nonlinearly at about 2680 mm of
precipitation per year with a predicted value 0.4 and reached its peak at about 2700 mm
of precipitation per year with a probability of occurrence at 0.8. The probability of this
species occurrence decreases nonlinearly at about 3700 mm per year with a probability of
occurrence of 0.4. Therefore, the probability of the Atelopus senex to occur in its range
was between 2680 mm and 3700 mm of precipitation per year.
67
Figure 24. Atelopus senex Response to Bioclimatic variables range of values based on the estimates of the probability
of occurrences.
What the habitat suitability plot (Fig. 25) predicted about the Atelopus senex
distribution of suitable habitats in Costa Rica was that 0% of this species observed had
suitable habitats, and all of Atelopus senex observed in places where the probability of
occurrence was predicted to be below 0, which were not suitable for the Atelopus certus
to survive.
Figure 25. Predicting Recent Bioclimatic Habitat Suitability of the Atelopus senex range.
68
Finally, presented in Table 7, is a summary of the probability of occurrences of
the Atelopus species in Panama and Costa Rica and how these amphibians responded to
bioclimatic variables, temperature and precipitation, elevation, and habitat suitability in
connection with species population declines and extinctions.
Table 7. Summary of the Atelopus species' Probability of Occurrence in BIO1 and BIO12, and the Probability of
Occurrence with Habitat Suitability
Atelopus
species
Country
Mean
Elev.
m
BIO1
C
BIO1
Prob of
occur
BIO12
mm
BIO12
Mean
Precip
BIO12
Prob of
occur
15-26
BIO1
Mean
Temp
C
21
A. senex
Costa Rica
2000
A.
Costa Rica
1750
chiriquiensis
Panama
A. varius
Costa Rica
Hab
Suitab
0.0
0.4
Hab
Suitab
below
0.3
-
0.6
2680-
3190
14-18
16
0.8
1760-
2440
1
70%
-
2671
0.8
100%
-
2350
0.6
100%
-
100%
3700
3120
1223
17-25
21
0.8
1916-
600
18-26
22
0.6
2100-
Panama
A. certus
Panama
3426
2600
69
CHAPTER 5 Discussion
5.1
Discussion
There are studies that have explored Batrachochytrium dendrobatidis (Bd) as the
major factor that influenced the amphibian population decline in Central and South
America. I found that there was a connection linked to the Atelopus species population
decline influenced by Bd with their ecological characteristics consistent with past
research (Lips, 2008; Crawford et al., 2010; La Marca et al., 2005). These included the
Atelopus species life history, habitat type, home range and threats.
I noticed the Atelopus species that occurred at the maximum elevation first
experienced extinction. The Costa Rican Atelopus species, Atelopus chirripoensis,
Atelopus senex, Atelopus chiriquiensis and Atelopus varius occurred at mean elevation in
descending order from 3450 m to 1750 m. However, the Panamanian Atelopus species
did not match elevational pattern of extinction or population decline. The Atelopus
glyphus of East Panama occurred at mean elevation of 1192 m and is still extant. The
Atelopus zeteki of Central Panama occurred at a mean elevation of 825 m and this species
is extinct in the wild. The persistent Atelopus limosus species occur in lower elevation
sites at mean elevation of 370 m. This could indicate that the Bd spread and prevalence
may have occurred in a geographical pattern consistent with prior studies from Lips et al.,
(2008). Although elevation has an influence in Bd spread, it is important to examine the
different types of habitats and bioclimatic conditions the Atelopus species sustained in
Panama and Costa Rica.
I noticed that the most common bioclimatic variables, temperature and
precipitation, emphasized a significant relationship with Bd infection in the Atelopus
70
species in Costa Rica and Panama. All Atelopus species, (except Atelopus chirripoensis,
Atelopus zeteki, and Atelopus glyphus), occurred in sites where the mean temperature was
between 16 ºC and 26 ºC, and the mean annual precipitation was between 1750 mm and
3190 mm. The habitats of all Atelopus species was not suitable for survival with a value
under 0.3. These bioclimatic variables made the habitat of all Atelopus species suitable
for Bd spread. These results are important because these factors could demonstrate the
reason Bd is prevalent in the Atelopus species, which thrives in streams at high elevation
montane forests but cannot survive temperatures at 28 ºC (82 ºF) in lowland forests
(Gratwicke, 2019).
The new part of my research was the phylogenetic tree that highlighted the
relationship between Atelopus species genetics and their extinction or population decline.
The phylogenetic tree split into 3 lineages, one of which developed into the
Atelopus glyphus, then the second lineage developed into the Atelopus limosus, and the
other which gave rise to Atelopus varius and Atelopus chiriquiensis. The Atelopus varius
and Atelopus chiriquiensis share a more recent genetic similarities with each other than
either shares with Atelopus glyphus, Atelopus zeteki, or Atelopus limosus. The Atelopus
varius and the Atelopus chiriquiensis are therefore more closely related to each other
than either is to Atelopus glyphus, Atelopus zeteki or Atelopus limosus. I noticed that the
phylogenetic tree organized the species by genetic similarities, and also by geographical
location of occurrence. For example, the Atelopus chiriquiensis and Atelopus varius both
occurred in Costa Rica. The Atelopus limosus and Atelopus zeteki both occurred in
Central Panama, and the Atelopus glyphus occurred in the Darien, East Panama. The
Atelopus varius, Atelopus limosus, Atelopus glyphus are considered critically
71
endangered by the IUCN (2019). The Atelopus chiriquiensis is considered extinct and
the Atelopus zeteki is considered extinct in the wild. This finding means that these
species are in serious threat of extinction. This finding also highlights that the Atelopus
species are endemic, historically isolated and have less resistance to diseases and are
significantly susceptible to Bd infection, consistent with Lips et al., (2008) hypothesis.
I learned that the decline in amphibian population has led to the extinction of
endemic species resulting from Bd infections in connection with climate change. This
means that bioclimatic factors, like temperature and precipitation has affected the
outcome of Bd spread in the Atelopus species. Understanding the Atelopus species
genetic diversity and immune defenses in connection to climate and environmental
factors is important to find solutions to Bd spread in Central America and across the
globe.
5.2
Limitations of the Study
The data to create forensic life history of the Atelopus chirripoensis from Costa
Rica, Atelopus glyphus, and Atelopus certus from Panama using literature and
information from the IUCN (2019) was deficient. There was only 1 single Atelopus
chirripoensis observed in 1980 and no sample of this species was obtained. Atelopus
glyphus, and Atelopus certus occurred in remote sites in Darién in Eastern Panama, where
Colombian guerillas occupied. Therefore, the conservation status of these Atelopus will
need further research.
I conducted a species distribution analysis using data of 8 Atelopus species using
R and utilized only occurrence data with coordinates of location focused in Costa Rica
72
and Panama, and bioclimatic variables. To obtain unbiased data for the habitat suitability
model, occurrences at the same coordinates were removed. Because of the reduction of
occurrences, the Atelopus zeteki, the Atelopus limosus and the Atelopus glyphus did not
produce results. The Atelopus chirripoensis occurrence had only 1 observation and did
not produce a result.
The data used to analyze the Atelopus genetic relationship with extinction using a
phylogenetic tree did not include the DNA sequence data of the 8 Atelopus species for
my research. There was no collection of the 16S ribosomal RNA sequence for the
Atelopus chirripoensis, Atelopus senex, and Atelopus certus to produce a DNA sequence
alignment. As a result, only 5 Atelopus species of Panama and Costa Rica were
identified.
The methods used for this research included limitations. The analysis for species
distribution model, I used R to produce a species distribution model to analyze
climatically suitable habitats based only on historical bioclimatic variables from 1970 to
2000.
The main foundation of this thesis was based on existing data of amphibian
decline and extinctions from La Marca et al. (2005), existing RNA sequence data of the
Atelopus species from The National Center for Biotechnology Information (NCBI), and
species distribution data from the International Union for Conservation of Nature’s Red
List of Threatened Species (IUCN). All peer-reviewed literature was collected from the
Evergreen State College Online library.
73
5.4
Next Steps and Future Studies
Determining the influence historical bioclimatic variables had in connection with
Bd prevalence in the Atelopus species was an important part of my thesis. The Atelopus
species life history explained important ecological traits and genetic associations that
could have impacted their population declines and extinctions.
To obtain accurate data of the Atelopus species conservation status, a new
assessment, including the Atelopus species with low occurrence observations, needs to be
implemented. In addition, there are many studies about Panamanian Atelopus species,
but little is known about the extinctions of the Costa Rican Atelopus species.
I propose future studies that can address future suitable bioclimate conditions for
the Atelopus species in the next 30 years to determine appropriate Bd mitigation plan and
amphibian conservation and management for future reintroduction of these species.
5.5
Conclusion
Amphibians around the world have been experiencing habitat loss, ecological
changes, anthropogenic impact, and disease that affect their population. However, the
primary cause of amphibian population declines, and extinction is Chytridiomycosis, an
amphibian skin infection caused by a fungus, Batrachochytrium dendrobatidis (Bd).
Amphibians are most at risk to becoming extinct. There have been many events
that have led to amphibian decline, however climatic factors could have influenced Bd
spread and infections. However, changes in their environment could impact their ability
to survive.
A significant tendency for amphibians suggests a consistent decline in diversity.
Costa Rica and Panama are well known for their rich biodiversity in Central America and
74
host the most endangered vertebrate species, the Harlequin frogs of the Atelopus genus.
Most Atelopus species occur in the upland rainforests where Bd prevalence is higher.
Three Costa Rican Atelopus species have been considered extinct, and one Panamanian
Atelopus species is extinct in the wild caused by Bd.
There have been many efforts to preserve the Atelopus species. Most of the
Atelopus species in Costa Rica are now extinct without live specimens in captivity due to
the unknown nature of their disappearance. Studies using an Atelopus species’ skin
bacteria to help reduce Bd infections have not been successful. However, one Atelopus
species in Panama has shown persistence to Bd, indicating that there is an opportunity for
further analyses to prevent Bd infections in other Atelopus species. Moreover, efforts to
reintroduce the Atelopus limosus species into the wild in East Panama in 2017 did not
identify any change in their survival rate. A captive conservation program for the
Atelopus species by the Smithsonian Tropical Research Institute have been established to
breed and ensure a sustainable population for reintroduction into the wild.
My thesis focused to determine the cause of Bd prevalence in the rainforests of
Panama and Costa Rica, the effect Bd prevalence in the Atelopus species and the
relationship of Bd with climate change. Understanding how Bd connects with climate in
the rainforest of Central and South America can help prevent future amphibian
extinctions. The effect of Bd on the Atelopus species could have been due to their
genetic lineage and bioclimatic factors such as temperature and precipitation and highaltitude environment.
The Atelopus life history and phylogenetic tree data showed a connection to
extinction and decline caused by Bd. The Atelopus species in Panama and Costa Rica
75
shared common characteristics, which are the occurrences in aquatic habitats, and high
elevational home ranges with topographic constraints that have influenced their
population declines and extinctions.
The phylogenetic tree indicated that the Atelopus species are vulnerable because
of their low genetic variation, as a consequence, the Atelopus species with close genetic
relationship experienced extinction related to their endemic environment. This data
supports the amphibian lineage and diversity loss hypothesis by Crawford, Lips and
Bermingham (2010).
Although the Atelopus species had a drastic population decline and extinction, one
species is persisting Bd infection in previously prevalent sites (Voyles et al., 2018). The
recovery of this Atelopus species provides a useful tool for future scientific research to
understand the effect of Bd and amphibian response to bioclimatic variables as a result of
climate change, in the hope of finding a solution to the chytrid epidemic around the
world. Consequently, a captive breeding program is in effect to ensure the survival of the
Atelopus species with the purpose of reintroducing these amphibian species back to the
wild.
76
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