The Role of Infectious Disease in Amphibian Population Decline and Extinction
James P. Collins School of Life Sciences Arizona State University
University of Tennessee Department of Forestry, Wildlife and Fisheries Center for Wildlife Health Knoxville, Tennessee 22 April 2010
OUTLINE Introduction: A grand challenge problem
A model system: What is the evidence for ranaviruses as a cause of amphibian decline and extinction?
A model system: What is the evidence for the amphibian chytrid fungus as a cause of amphibian decline and extinction?
Conclusions
Introduction: Two grand challenges for 21st century environmental biology
1. Global loss of biodiversity 2. Emerging infectious diseases
Do emerging infectious diseases have a role in the decline and extinction of species?
1 A theoretical problem When is emerging infectious disease a force in extinction?
Conventional theory suggests that a pathogen is unable to drive a host population to extinc tion (Kermack & McKendrick 1927, Anderson & May 1979)
Assumptions: density dependent transmission homogeneous mixing no alternate hosts no environmental reservoirs
Proportion of DENSITY susceptible hosts that DEPENDENT become infected TRANSMISSION
Density (# infected / volume)
StiblSusceptible TiiTransmission IfInfect tded
Proportion of DENSITY susceptible hosts that INDEPENDENT become infected TRANSMISSION
Prevalence (# infected / total # of hosts)
Empirical claims Proposed declines due to EIDs
Chestnut blight Dutch elm disease Sudden oak death White nose syndrome in bats Coral bleaching disease
2 Empirical claims Proposed major extinctions due to EIDs
• Hawaiian birds (Reynolds et al. 2003)
• Amphibians (Stuart et al. 2004) • Pleistocene large mammals (MacPhee & Marx 1997) Proposed single species extinctions due to EIDs
• Polynesian snail (Daszak and Cunningham 1999) • Sharp-snouted day frog (Schloegel et al. 2006) • Endemic Christmas Island rat (Wyatt et al. 2008)
Causes of amphibian declines • Commercial use • Introduced species • Land use change • CtContami nan ts • Climate change • Infectious disease
Amphibian diseases: Macroparasites • Johnson et al. flatworm parasites and deformities
• Trematode-agriculture runoff hypothesis (Kiesecker et al. 2002; Johnson et al. 2007; Rohr et al. 2008)
Alaria: a trematode parasite of amphibians
Pacific tree frog
Scan by Sessions & Ballengee
3 Amphibian diseases: Microparasites Bacteria Protozoa – Saprolegnia ferax
Chytrid – a fungal pathogen of frogs and salamanders - Batrachochytrium dendrobatidis (Bd)
Ranavirus – a genus of viruses infecting cold blooded vertebrates
A model system: Ranavirus Do the transmission dynamics of Ambystoma tigrinum virus (ATV) place ATV-infected amphibian populations at risk for pathogen-induced extinction?
Amphibian diseases: Viruses Viral groups that infect amphibians: 1. Adenoviruses 2. Caliciviruses 3. Flaviviruses 4. Parvoviruses 5. RiRetroviruses 6. Togaviruses 7. Herpesviruses Pathogenic 8. Iridoviruses Herpesviruses - cause rare renal tumors in frogs; not implicated in decline or extinction Iridoviruses - common and involved in epidemics
4 Amphibian diseases: Iridoviruses Genera of Iridoviridae: 1. Iridovirus infects invertebrates, mainly insects 2. Chloriridovirus infects mosquitoes 3. Lymphocystivirus infects fish 4. Ranavirus infects salamanders, frogs, fish, and reptiles
Amphibian diseases: Iridoviruses Eight Ranavirus strains are reported from amphibians and may infect multiple species or only one: • Bohle iridovirus infects amphibians, fish, and reptiles. • Frog virus 3 is reported from almost a dozen frog species and one salamander species. • Ambystoma tigrinum virus is reported only from salamanders.
Frog Ranavirus relationships 100 FV3 100 SSTIV Turtle 100 TFV Frog ATV Salamander 100 99 EHNV Fish GIV 94 100 SGIV LCDV-1
100 LCDV-C Fish ISKNV
100 OSGIV 100 RBIV CIV Insect 100 MIV
0.1 (Jancovich et al. 2003. Virology)
5 Ranavirus host range and origin
?
Ranavirus genomic DNA analysis
Suggests that the most recent common ancestor of Ranavirus was a fish virus followed by a jump from fish to salamanders or frogs
Human involvement in Ranavirus host shifts? Movement of hosts/disease by humans?
Movement of tiger salamanders as bait
(Source: Picco and Collins. 2008. Conservation Biology)
6 Amphibian commerce as a source of pathogen pollution Wild populations Wild populations, lakes
virus?
(Source: Picco and Collins. 2008. Conservation Biology)
ATV and population dynamics
Host: Ambystoma tigrinum nebulosum Pathogen: Ambystoma tigrinum virus (ATV)
Study area
Kaibab Plateau
7 Salamander life history
(Brunner et al. 2004)
8 Virus transmission
ATV is transmitted by direct physical contact (bumping, biting, and cannibalism) as well as by necrophagy and indirectly via water and fomites.
Larval salamanders become infectious soon after exposure to ATV and their propensity to infect others increases with time.
(Source: Brunner, Schock, Collins. 2007. Transmission dynamics of the amphibian ranavirus, Ambystoma tigrinum virus. Diseases of Aquatic Organisms)
Testing density dependent transmission. The experiment varied number of susceptible hosts and number of infected hosts within a 55 L aquarium. (Amy Greer)
Susceptible Infected Volume (L) Density Prevalence Replicates hosts hosts (I/V) (I/N) 115510.57 885580.54 40 40 55 40 0.5 4 1 8 5580.897 8085580.094 115510.53 40 40 55 40 0.5 3
Experimental design: 1059 larvae
Infected Sham infected Susceptible
hosts (I) hosts (Ic) hosts (S) 5 days
Volume = 55L aquarium Housed Exposure time = 24 hours Housed individually for 28 individually for 28 days Laboratory days diagnostic testing
9 Experimental design: 1059 larvae
Results
• 504 susceptible salamanders exposed in treatment replicates • 468 developed signs of infection and died • 36 uninfected after 28 days (no sub-lethal infections)
Proportion of susceptible larvae infected at each density. Vertical bars equal 1 SE.
1
0.8
infected 0.6 ceptible hosts e
0.4
0.2 that becam
Proportion of sus 0 0 10 20 30 40 Density of infected hosts (# I / 55L)
10 Estimating the transmission constant (β) for a range of transmission functions
Type of Function β Additional Neg. AICc ΔAIC Akaike transmission (units) parameters log- value weight (units) likely- hood
Power βSIq 1.38 q = 0.255 20.20 44.9 0.00 0.588 (H-q (dimension- day-1) less)
Negative k ln 7.72 k = 0.578 20.66 45.9 0.92 0.371 binomial (1+βI/k)S (H-1 (day-1) day-1)
Constant risk, asymptotic, density dependent, and frequency dependent functions were evaluated but none was significant.
What explains the high transmission rate?
• Transmission 1 via water? 0.9 –Asymptomatic 0.8 animals shed high 0.7
numbers of viral 0.6 le hosts infected particles per daday b 0.5
• Non-random 0.4
contact? 0.3
–Behavioral changes 0.2 at low densities Proportion of suscepti 0.1 cause clumping of 0 hosts (Brunkow and 0 5 10 15 20 25 30 35 40 45 Collins 1998) Density of infected hosts (# I / 55L)
What about transmission in the field?
11 Field surveys
• Mark-recapture • Tissue samples for ATV screening • Environmental data
Results
100 p<0.001
80 p=0.05
Percentage of 60 p>0.05 ATV positive 40 ponds 20 0 <25% 25% - >75% 75% Percent emergent vegetation
How does habitat affect transmission?
Hypothesis: Habitat fragmentation buffers disease transmission by decreasing larval contact rates
Prediction: e Contact rat Contact
Amount of vegetation
12 Experimental design
Sparse Dense vegetation vegetation
• Mark-recapture by site of origin • Tissue sample
Larval distribution in a pond varies with amount of emergent vegetation
14%
4% 13% 5%
6% 12%
7%
11% 8%
9% 10% Sparse Dense
Results
• Fragmentation • “Halo effect” A lower incidence of ATV in heavily vegetated ponds is caused by lower effective density rather than buffered transmission
13 Host – pathogen theory
A pathogen is unable to drive a host population to extinction (Kermack & McKendrick 1927, Anderson & May 1979) Assumptions Density dependent transmission Yes Yes Homogeneous mixing No Yes No alternative hosts N/A Yes No environmental reservoirs No Yes
Empirical tests of the theory Do the transmission dynamics of Ambystoma tigrinum virus (ATV) place ATV-infected amphibian populations at risk for pathogen- induced extinction?
Best evidence suggests the answer is “No:” Amy Greer et al. (2008) Jesse Brunner et al. (2007)
14 Model system: Amphibian chytrid
Do the transmission dynamics of Batrachochytrium debdrobatidis (Bd) place Bd- infected amphibian populations at risk for pathogen-induced extinction?
The amphibian chytrid
• By the mid-1990s it was suspected that the chytrid fungus Batrachochytrium dendrobatidis might be an emerging infectious amphibian disease (EID).
• EIDs are diseases that are newly recognized, newly appeared in a population, or rapidly increasing in incidence, virulence, or geographic range.
Amphibian chytrid life cycle
(Source: Rosenblum et al. 2010. PLoS Pathogens)
15 Chytrid - amphibian system •Chytrid is associated with anuran declines and extinctions in Australia, Europe, Africa, Central, South, and North America, but also coexists with non- declining species.
•It infects most amphibian species tested with effects varying from no clinical disease to 100% mortality.
•Microenvironment affects (K. Lips) susceptibility to chytrid.
p = 1 (habitat can support chytrid)
p = 0 (habitat cannot support chytrid)
The model was also extended using Eastern Hemisphere data.
(Source: Santiago Ron. 2005)
Distribution of threatened amphibians in Central America, Northern South America, and the Caribbean
(Source: Global Amphibian Assessment 2004)
16 Hypothesis: Amphibian population sizes and species richness decrease as Batrachochytrium spreads
Rate of spread 1987-88 ~28 km/yr 1993-94
2002-03
1996-97
(Source: Lips et al. 2006. Infectious disease and global biodiversity loss: pathogens and enigmatic amphibian extinctions. PNAS)
Prediction: Abrupt change in amphibian density and species richness when chytrid arrives
Amphibian density or species richness
Time
Test: estimate change in slope and date of change by fitting a segmented linear model to the data
Amphibian density changes along streams
chytrid emerges
Amphibian densities and segmented linear models for riparian and terrestrial transects (1998 – 2005) at El Cope, Panama. There was a significant change in slope for riparian (θ2 = -1.36×10-2, t = -24.44, df = 486, P < 0.0001) but not for terrestrial transects (θ2 = -1.74×10-3, t = -0.71, df = 212, P = 0.4802).
17 Amphibian species changes along streams
chytrid emerges
Amphibian species richness and segmented linear models for riparian and terrestrial transects (1998 – 2005) at El Cope, Panama. There was a highly significant change in slope for riparian transects (θ2 = -6.45×10-3, t = -6.97, df = 486, P < 0.0001) but not for terrestrial transects (θ2 = -3.77×10-3, t = -1.78, df = 212, P = 0.0757).
Central American pattern of declines • 50% of ~75 species gone in 4-6 months
• Remaining species are at 10% of abundance
• Batrachochytrium likely spread by frog-frog and frog-environment contact
• Pattern not consistent with land use change, exotic species, commercial use, climate change, or contaminants
Conclusion: Batrachochytrium is likely cause of enigmatic declines in this region
1. Extinctions in Costa Rica and Panama affected low- occupancy and endemic species resulting in homogenization of the remnant amphibian fauna.
2. Extirpations resulted in phylogenetic homogenization at the family level and ecological homogenization of reproductive mode and habitat association.
3. Amphibian declines in this region are an extinction filter, reducing regional amphibian biodiversity to highly similar relict assemblages.
18 What happens after Batrachochytrium emerges?
Batrachochytrium in frog populations after decline (Queensland, Australia; 1994-98)
•Gastric Brooding Frog –Declined to extinction in 1985-86
•Eungella Day Frog –Abundant, then sudden decline in 1985-86 –Now persists in a few small populations
Eungella Batrachochytrium Plateau was the suspected cause of the declines and is now endemic
[Source: Retallick et al. 2004. PLoS Biology]
“Our results show (i) genotypic differentiation among isolates, (ii) proteomic differentiation among isolates, (iii) no significant differences in susceptibility to caspofungin, (iv) differentiation in growth and phenotypic/morphological characters, and (v) differential virulence in B. bufo….
“Mass spectrometry has identified a set of candidate genes associated with inter-isolate variation. Our data show that, despite its rapid global emergence, Bd isolates are not identical and differ in several important characters that are linked to virulence.”
19 “Our results show that cutaneous microbes are a part of amphibians’ innate immune system, the microbial community structure on frog skins is a determinant of disease outcome and altering microbial interactions on frog skins can prevent a lethal disease outcome. A bioaugmentation strategy may be an effective management tool to control chytridiomycosis in amphibian survival assurance colonies and in nature.”
A theoretical problem When is emerging infectious disease a force in extinction?
Conventional theory suggests that a pathogen is unable to drive a host population to extinc tion (Kermack & McKendrick 1927, Anderson & May 1979)
Assumptions: density dependent transmission homogeneous mixing no alternate hosts no environmental reservoirs
A theoretical problem Assumptions: density dependent transmission homogeneous mixing no alternate hosts no environmental reservoirs
The amphibian chytrid fungus meets three conditions that could result in a pathogen causing extinction: (1) density-independent transmission (2) non-homogeneous mixing (3) alternate biotic (amphibian) hosts
20 Conclusion: Biodiversity loss and emerging infectious disease Two pathogens associated with enigmatic amphibian declines Chytrid – a fungal pathogen of frogs and salamanders - Batrachochytrium dendrobatidis (Bd)
Ranavirus – a genus of viruses infecting cold blooded vertebrates
Proportion of DENSITY DEPENDENT susceptible TRANSMISSION hosts that become infected
Density (# infected / volume) PERSISTENCE
DENSITY INDEPENDENT TRANSMISSION Proportion of susceptible hosts that become infected
Prevalence (# infected / DECLINE / EXTINCTION Images: A. Hyatt and L. Berger total # of hosts)
Causes of amphibian declines
• Commercial use • Introduced species • Land use change • Contaminants • Climate change • Infectious disease
A modern extinction event…
21 Sustainability
Back-up slides A great disappearing act… and its grand challenge questions…
Back up slides
Ranavirus host range and origin
1 3
2 EHNV
Grouper-like viruses
LCDV-like viruses
22 Ranavirus host range and origin
3 1
2 EHNV
Grouper-like viruses
LCDV-like viruses
23