Symposium: Biogeography & Diversification of Amphibians & Reptiles - Pacific Northwest & CA Floristic Province IIIRoom: Ballroom 111B2022-07-30 13:30 - 16:00 |
| Moderator: Jon Richmond |
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1. 13:30 Genetics versus genomics and what each tells us about western US reptile and amphibian phylogeography. H. Bradley Shaffer*, UCLA; Erin Toffelmier, UCLA brad.shaffer@ucla.edu
Over the last few decades, we’ve advanced from allozymes and mitochondrial DNA to techniques that capture some, or all, of the genome of our study organisms. In many cases, the questions remain largely the same: what are the major lineages within species, how differentiated are they from one another, how are populations and species interrelated? However, as our community makes the next major technological jump to whole-genome resequencing, a suite of new questions and potential insights are emerging. In addition to the greater resolution that millions of markers brings to any research agenda, we can now identify candidate genes associated with local adaptation, speciation, disease resistance, and future climate adaptation. I’ll review recent studies from our lab on western pond turtles, western spadefoot, foothill yellow-legged frog, southern alligator lizard, and California tiger salamander using reduced representation (RAD and target capture) approaches. These data sets have revealed a tremendous amount about both major lineage diversification and population genetics that inform evolutionary and conservation biology. I’ll then discuss the California Conservation Genomics Project (CCGP) a multi-species analysis based entirely on whole-genome resequencing, and why we feel that it is the way forward for many studies and systems. Whole genome resequencing provides a complete assessment of genomic variation, including outlier loci under strong selection and those underlying phenotypes of interest. The data are (relatively) straightforward to produce, and when paired with high-quality reference genomes, offer a permanent record of the genome that should become our standard moving forward. |
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2. 14:00 The Melting Pot, interpreting the origin of the admixed herpetofauna of coastal southern California. Robert Fisher*, USGS; Lee Grismer, La Sierra University; Samuel Fisher, La Sierra University; Jesse Grismer, La Sierra University; Brian Hinds, Herpetological Education and Research Project; Jeff Nordland, Self; Jonathan Richmond, USGS rfisher@usgs.gov
Between 1958 and 1965 Jay Savage in a series of masterful papers discusses and interprets the development of the southern California and Baja California herpetofauna. Since this work, many modern tools have been applied to help understand the evolution and formation of this fauna. Here we conduct a review of the newer understanding of this landscape and show that his interpretations have held the span of the 60 years since his work was published. Savage’s 1960 “Riding the Wave” hypothesis, as well as the Transverse Ranges Break, are discussed but the focus on the discordance between species with their northern terminal end in the region versus their southern terminal end in the regions is the target of this talk. One very important break missing from the literature is the Borderland Break, were several lineages have their northern coastal limits and one species has its southern limit. The diversification in several endemic herpetofaunal groups such as the Xantusiidae, Crotaphytidae, Anniellidae, and the genera Batrachoseps and Masticophis, is greatly increased in this area speaking to the importance of this biodiversity hot-spot for conservation and the non-replication of species in reserves on the landscape. This has led to unique combinations of species sharing microhabitats such as Batrachoseps major, Phyllodactylus nocticolus, Petrosaurus mearnsi, and Sceloporus orcutti sharing rock outcrops, or Anaxyrus californicus, Arizona elegans, and Callisaurus draconoides sharing sandy washes. As threats continue in southern California we may begin to see disarticulation of these novel communities and a simplification of the resulting herpetofauna. |
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3. 14:15 Landscape patterns of adaptive and neutral variation match between predator (Thamnophis couchii) and prey (Taricha sierrae) in the Sierra Nevada. Joshua Hallas, University of Nevada, Reno; Thomas Parchman, University of Nevada, Reno; Chris Feldman*, University of Nevada, Reno ophis@unr.edu
The Geographic Mosaic Theory of Coevolution (GMTC) predicts that coevolutionary arms races will vary over time and space because of the diverse ecological settings and population histories of interacting species across the landscape. Thus, understanding coevolution requires investigating broad sets of populations sampled across the range of the interaction, as well as underlying population structure. Here, we examine geographic patterns of prey traits and predator traits, as well as neutral patterns of genetic structure, in the the Sierra garter snake (Thamnophis couchii) and sympatric Sierra newt (Taricha sierrae). This system parallels, in space and phenotypes, a classic example of coevolution between predatory common garter snakes (Th. sirtalis) and their toxic newt prey exhibiting hotspots of newt tetrodotoxin (TTX) levels and matching snake TTX-resistance. We show strong regional patterns of trait covariation across the shared ranges of snake and newt prey. Traits differ significantly among localities, with lower newt TTX levels and snake TTX-resistance at the northern latitudes, and higher TTX levels and snake resistance at southern latitudes. Despite overall trait-matching across populations, individual variation in prey and predator traits was substantial, and may permit reciprocal selection in most populations. Newts and snakes also show similar patterns of population structure, each composed of northern and southern genomic clusters that meet in the mid-Sierra. Such concordance suggests parallel responses to common biogeographic barriers or historical events. Lastly, our results suggest that the geographic scale of these coevolutionary dynamics could be narrow, which could facilitate independent local adaptation across fine spatial scales. |
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4. 14:30 Historical isolation and connectivity influence coevolutionary patterns of toxin resistance in the aquatic garter snake (Thamnophis atratus). Joshua Hallas*, University of Nevada Reno; Thomas Parchman, University of Nevada Reno; Anthony Gilbert, University of Virginia; Edmund Brodie III, University of Virginia; Michael Pfrender, University of Notre Dame; Edmund Brodie Jr, Utah State University; Chris Feldman, University of Nevada Reno joshua.hallas@gmail.com
Coevolutionary interactions, where taxa evolve in response to reciprocal natural selection, are thought to be important drivers of molecular and phenotypic diversification. The form and outcome of such interactions, however, often varies among populations and across landscapes due to environmental heterogeneity, changes in community composition, biogeographic history, and population connectivity. Here, we examined the distribution of tetrodotoxin (TTX) resistant phenotypes in Thamnophis atratus and allelic variation in the associated SCN4A gene across the landscape. These data were then compared to spatial genetic structure characterized from 12,473 genome-wide single nucleotide polymorphisms. Our goal was to examine the impact from the antagonistic coevolutionary interactions between Th. atratus and Taricha sp. and biogeographic history on the distribution of TTX resistance and spatial genetic structure. As expected, the distribution of TTX resistance to be largely associated with SCN4A allelic variation. We also found that spatial genetic structure and phylogenetic relationships were strongly differentiated and paralleled the regionality of TTX resistant phenotypes. Alleles that confer weak resistance were mainly distributed north of the Sacramento-San Joaquin River Delta, while high resistance alleles were south representing a strong barrier to dispersal. The patterns observed in Th. atratus differ from the sympatric Th. sirtalis. |
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5. 14:45 Genomic Approaches to Detecting Signals of Local Adaptation with Application using Western Herpetofauna. Tereza Jezkova*, Miami University; Keaka Farleigh, Miami University jezkovt@miamioh.edu
Traditionally, evidence of local adaptation has been inferred using reciprocal transplant studies that assess outcomes of native and non-native individuals subjected to common treatments. Alternatively, however, recent advancements in sequencing and bioinformatics have allowed researchers to search for signals of adaptive selection directly from the genome. This approach involves the identification of loci that exhibit a signal of selection, determining the association between these loci and environmental or phenotypic data, and linking these loci to candidate genes and relevant biological functions. As such, this approach can provide a landscape-level understanding of how environmental heterogeneity influences populations across the species range and lead to the discovery of new genes and biological processes involved in local adaptation. We caution however, that these candidate loci and genes should be considered to be only purportedly adaptive until further supported through experimental methods. Herein, we present an overview of available methods to detect genetic signals of local adaptation. These methods can be divided into two main groups: methods that search for loci exhibiting high differentiation versus the genome-wide average (i.e., outlier analyses) and methods that search for loci associated with environmental conditions (i.e., genotype-environment association analyses). We show examples of these different methods used on empirical data for several reptile species of the western United States. |
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6. 15:00 Applying genetics to inform the three R's (resiliency, redundancy, and representation) for conservation of California’s rich diversity of herpetofauna. Amy Vandergast*, USGS Western Ecological Research Center; Dustin Wood, USGS Western Ecological Research Center; Paul Maier, FamilyTreeDNA, Gene By Gene avandergast@usgs.gov
The state of California includes 70% of the California Floristic Province, a recognized global hotspot of diversity and endemism. Amphibians and reptiles exhibit fine scale endemism and high species and lineage richness, with cryptic diversity revealed with molecular tools. In addition to harboring this rich evolutionary heritage, unfortunately California is also a hotspot of endangerment, with 36 federally and state listed amphibians and reptiles. Below the species level, genetic analysis of populations can provide quantitative guidance for management and inform the three R’s of species conservation. Species with higher resiliency, redundancy, and representation can be better protected from stochastic and catastrophic impacts and may be better able to adapt to changing conditions. Representation can be measured by the breath of environmental and genetic diversity within and among populations, redundancy assessed through the number of genetically-identified populations and their degree of connectivity, and resiliency characterized through the genetic effective population size and adaptive capacity. Monitoring these genetic metrics over time can track responses to changing conditions and management action. We highlight recent findings of some of our studies of rare California species, including the San Francisco gartersnake, Yosemite toad and Coachella Valley fringe-toed lizard, conducted to inform Department of the Interior and other management partners in ongoing conservation efforts for these species. Finally, genome-wide genetic data collection coupled with field studies of fitness may provide crucial and quantitative links between adaptive capacity and population persistence. |
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7. 15:15 Conservation of Endemic Old-Growth Forest-Associated Amphibians in the US Northwest. Deanna Olson*, USDA Forest Service, Pacific Northwest Research Station deanna.olson@usda.gov
The conservation of endemic forest-associated amphibians in the US Northwest was greatly influenced by Dr. David Wake’s leadership in basic foundational science and applied science contributions. With the application of emerging genetic analyses over the last 2-3 decades, the understanding of northwest amphibian biodiversity has been reframed. For example, with studies from the Wake laboratory at UC Berkeley in addition to others’ contributions, seven northwest amphibian species are now recognized as 20 species. As smaller ranges of newly identified species resulted, conservation concerns from anthropogenic stressors such as timber management elevated. In particular, several salamanders have been included in state and federal management programs to advance our knowledge of those species and protect those in peril. Landscape genetic studies have augmented species descriptions to address gene flow patterns and discrete populations. Dr. Wake was at the forefront of amphibian decline issues globally since 1990. A signature development to bridge the science-management-public interface for amphibian diversity awareness and conservation was establishment of the global web portal AmphibiaWeb in 2000, founded by Dr. Wake at UC Berkeley. This portal continues to expand its breadth, with the recent addition of the amphibian disease portal, addressing the threat of the amphibian disease-causing pathogens Batrachochytrium dendrobatidis and B. salamandrivorans. Although not all amphibians are susceptible to the skin disease chytridiomycosis caused by these species, these amphibian chytrid fungi are considered the cause of the most severe multi-species disease threat known to have occurred on Earth. With US northwest origins, Dr. Wake's impact was global. |
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8. 15:30 Projected threats of climate change to stream amphibians of the Pacific Northwest. Gwen Bury*, US Forest Service gwen.bury@gmail.com
Stream amphibians in the Pacific Northwest will be negatively affected by climate change, for a wide variety of reasons. Forecasts of human-driven climate change show, on average, increased temperature, changed hydrologic patterns, and storm differences across the region. These primary changes will lead to secondary impacts such as habitat changes, increased fire, and lower summer water levels. Many of these changes have already begun. For stream obligate amphibians, climate change will cause a wide variety of threats that will interact with other human-caused environmental changes such as habitat loss, invasive species, and resource extraction. Amphibian species which will be most negatively impacted include those with narrow environmental requirements, isolated or small populations, and those subject to multiple threats. These high-risk categories include many of the species of amphibians native to the Pacific Northwest. Understanding the biogeographic history, habitat requirements, and interacting threats is required to conserve stream amphibians in a changing climate. |
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9. 15:45 Predicting Future Hotspots of Squamate Diversity in the Pacific Northwest as the Climate Changes. David S Pilliod*, U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center; Michelle I Jeffries, U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center; Robert S Arkle, U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center; Deanna H Olson, U.S.D.A. Forest Service, Pacific Northwest Research Station dpilliod@usgs.gov
Reptiles are strongly associated with environmental conditions, especially temperature, which allows for modeling and mapping species distributions at broad spatial scales and predicting changes in distributions under future climate scenarios. We used species occurrence points from all known snakes and lizards in western North America to model each species fundamental or potential climate niche under future climate scenarios. Under each scenario we predicted species richness across the West and quantified changes in richness through time. Preliminary results suggest that, of the 130 species modeled, 68% gain climate niche space regardless of future time horizon and emission scenario. Conversely, only 8.5% of species are projected to lose climate niche space. Recent projections of climate niche richness was highest around the border between the United States and Mexico and shifted northward in future horizons. Our analysis predicts most snake and lizard potential niches to expand and shift northward and many species could expand upward in elevation, where possible. Our species level assessments may provide an early warning for agencies that may have to alter their management strategies as new species begin to colonize across state or international borders while other species may go extinct despite their best efforts to retain them. |