Most standard sized academic posters should be able to be accommodated; a guideline of maximum 1.2 m x 1.2 m (4 ft x 4 ft) is typical for academic conferences.

 #1  Mitogenomic analysis of a late Pleistocene jaguar from North America

Megha Srigyan (UC Santa Cruz)

The jaguar (Panthera onca) is among the few large carnivores that survived the end-Pleistocene megafaunal extinction event in the Americas. However, Pleistocene jaguar from North America are up to ~20% larger than extant jaguars, leading some to hypothesize that these specimens represent now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). To examine the taxonomic and phylogenetic affinities of the North American Pleistocene jaguar, we sampled a terminal Pleistocene specimen from Kingston Saltpeter Cave, Georgia, USA, for ancient DNA analysis. We used a hybridization capture approach to generate a full mitochondrial genome at 28X coverage and compared it to mitochondrial genomes from other extinct and living large felids and modern jaguars. Phylogenetic analyses indicate that this individual represents a modern jaguar instead of a distinct Pleistocene species or subspecies despite its larger size. Further, Bayesian analyses of modern jaguar mitochondrial lineages suggest that modern jaguars arise between 0.5mya – 1.5mya, with the Pleistocene individual falling into one of two sub-clades of modern jaguars. While older specimens are required to test the presence of a separate lineage in early Pleistocene, our results suggest that late Pleistocene North American jaguars, such as the one recovered in this study, likely represent lineages arising due to reinvasion of jaguars from South America. The data generated in this study represents the first full mitochondrial genome of a Pleistocene jaguar and could be helpful in clarifying proposed hypotheses about jaguar population history in the Pleistocene.

#2  One Fish, Two Fish, Sea Fish, Bee Fish: Assessing State-Level Biodiversity Policy

Cooper Kimball-Rhines (University of Massachusetts, Boston)

Preservation of biodiversity is the goal at the heart of conservation. For decades, policymakers in the United States have relied on both federal and state-level Endangered Species Acts to identify, protect, and recover species one at a time. Policymakers have more recently turned to policies targeting many species at once to curtail the ongoing extinction crisis in the face of funding limitations and changing climates. However, very few of these conservation policies have ever been assessed for their real impacts on biodiversity. We performed a systematic review of papers analyzing changes in biodiversity after implementation of a range of policy mechanisms at the state level. We found that across the country, fewer than two dozen state conservation policies have ever had published academic assessments of their biodiversity impacts. We present a brief overview of the policy mechanisms that have been assessed, the states where they have been implemented, and their impacts on biodiversity. The lack of comprehensive policy assessment in this field presents a great opportunity for future collaborations between academics, state conservation officials, and policymakers. To this end, we also summarize the metrics used for policy assessment to encourage standardization. 

#3  Functional Genomic Diversity is More Strongly Correlated with Long Than Short-Term Estimates of Neutral Genetic Diversity in Populations of an Endangered Rattlesnake

H. Lisle Gibbs (Department of EEOB, Ohio State University)

Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation, yet this widely used approach has recently been questioned in the genomics era. Here we leverage a chromosome level genome assembly of an endangered rattlesnake (Sistrurus catenatus) combined with whole genome resequencing data (N=110 individuals) to evaluate the relationship between levels of genome-wide neutral and functional diversity over long and short timescales. As predicted, we found positive correlations between genome-wide estimates of neutral genetic diversity (π) and inferred levels of adaptive variation and an estimate of inbreeding mutation load, and a negative relationship between neutral diversity and an estimate of drift mutation load. However, these correlations were half as strong for short-term (< 10 generations) estimates of neutral diversity based on contemporary effective population sizes. Broadly, our results confirm that estimates of diversity based on neutral genetic variation provide an accurate measure of genetic erosion in populations of a threatened vertebrate. Our findings provide nuance to the neutral-functional diversity controversy by suggesting that while these correlations are present anthropogenetic impacts may have weakened these associations in the recent past and into the future.

#4  Genomic Consequences of Population Isolation in Timber Rattlesnakes

Marissa Roseman (The Ohio State University)

Habitat loss and fragmentation has reduced the vast historic range of timber rattlesnakes (Crotalus horridus) in the eastern United States. In Ohio, they persist in a few small, isolated patches of habitat, where elevated inbreeding, reduced genetic diversity, and accumulation of harmful mutations could pose a threat to species persistence. We leveraged our recent assembly of a timber rattlesnake reference genome to investigate genetic erosion in Ohio’s timber rattlesnakes in comparison to larger and less-isolated populations from Pennsylvania and Indiana. We assessed genetic diversity, identified runs of homozygosity (ROH) as indicators of inbreeding, and quantified mutation load, parsing putatively deleterious mutations into masked and realized load. We found that low genetic diversity and high realized mutation load was associated with small habitat patch size. The Ohio population with the greatest proportion of the genome in ROH had intermediate levels of genetic diversity and carried a high masked mutation load.

#5  Conservation genomics of the endangered Devils Hole pupfish (Cyprinodon diabolis)

David Tian  (UC Berkeley )

Small populations with limited geographic distributions are predicted to be threatened by inbreeding and lack of genetic diversity, both of which may negatively impact fitness and exacerbate population decline. Following the receding of pluvial lakes during the late Pleistocene, desert pupfishes in the Death Valley region became isolated in springs and creeks, with limited population sizes and levels of genetic connectivity. One of the most extreme examples is the Devils Hole pupfish (Cyprinodon diabolis), an iconic and critically endangered species with the smallest known habitat range of any vertebrate. This imperiled species has experienced severe declines in population size over the last thirty years and suffered major, repeated bottlenecks in 2007 and 2013, when the population sunk to 38 and 35 individuals, respectively.  Here, we present two chromosome scale de novo reference genomes of C. diabolis and C. nevadensis mionectes and 150 resequenced genomes of Death Valley and Ash Meadows desert pupfishes. We assess population structure, genetic diversity, and infer past demographic history across desert pupfishes. Moving forward, we are working on measuring inbreeding and mutation load, comparing wild and captive populations of C. diabolis, and identifying the genetic basis of a putative lethal heart defect in some developing C. diabolis embryos.

#6  Homozygosity and Deleterious Variation in Setophaga warblers

Anna Maria Calderon (The Pennsylvania State University)

Runs of homozygosity (ROH) are homozygous chromosomal segments that arise from population bottlenecks, isolation, and inbreeding. In addition to providing insights into levels of inbreeding and genetic diseases, quantifying the distribution of ROH can also illuminate population history. We used ~19X whole genome sequencing to calculate the distribution of runs of homozygosity and characterize patterns of deleterious variation within ROH segments in three species of warblers in the Setophaga genus (Setophaga citrina, Setophaga ruticilla, and Setophaga kirtlandii) one of which was endangered. Although Setophaga kirtlandii populations are now above the recovery goal, ROH analysis shows that they are highly inbred. We used SIFT4G to build a protein database and predict the deleteriousness of variants in order to investigate how demographic processes such as bottlenecks and inbreeding influence the prevalence of harmful variants even after population size recoveries.

#7  American black bear habituation correlates with decreased gut microbiome diversity and increased antibiotic resistance

Summer Vance (UC Berkeley)

Globally increasing urbanization has resulted in increased wildlife habituation and human-wildlife conflict. However, we know little about the physiological ramifications of habituation. To address this topic, we investigate American black bear gut microbiomes across a spectrum of lifestyles including wild, habituated, and captive using 16S and shotgun sequencing. Wildlife microbiomes are relevant not only to the host animal health, but also to zoonotic disease and the environmental spread of antibiotic resistance and other virulence factors. Additionally, microbiomes are in turn affected by anthropogenic factors including captivity, climate change, habitat destruction, and antibiotic use. Despite this, wildlife gut microbiomes are largely uncharacterized, both in community structure and function. We show that habituated bears have lower microbiome diversity and higher levels of antibiotic resistance genes. Additionally, the three bear cohorts show unique toxin signatures. Our results demonstrate previously undescribed physiological and epidemiological consequences of wildlife habituation.

#8  Contrasting hybrid zones and post-glacial range expansion in a Nearctic orchid

Brett Morgan (Smithsonian Environmental Research Center)

Hybridization between divergent lineages has the potential to introduce new genetic variants that are preadapted to novel environments. However, barriers such as disruptive selection pressure can prevent hybridization, and the efficacy of these barriers may be context-dependent. We used RAD loci to explore these ideas in two contrasting hybrid populations of Cypripedium, an orchid distributed across temperate North America. One hybrid population in Washington co-occurs with both parental genotypes, while another hybrid population in Alaska lacks individuals with parental genotypes. We propose hypotheses to explain the observed patterns in the context of post-glacial range expansions. We then compare the distribution of SNPs that are fixed in the parent populations, and use demographic models to estimate the timing of hybridization events. Potential implications of this work include a better understanding of barriers to natural hybridization, how those barriers can break down, and how genetic admixture can facilitate expansion into new niches.

#9  Evidence of bottleneck and genetic differentiation in locally extinct populations of a key ungulate from a fragmented landscape of inland Atlantic Forest in Brazil

Anna Carolina Mazará  (Universidade Federal do ABC (UFABC))

Habitat loss and fragmentation can result in population bottlenecks, genetic differentiation between populations, and intrapopulation loss of genetic diversity, which contributes to local extinctions.  White-lipped peccary (WLP, Tayassu pecari) is critically endangered in the Atlantic Forest due to hunting pressure, habitat loss, and fragmentation. We evaluated the genetic status of a population of WLP that was locally extinct in a highly fragmented landscape of the Atlantic Forest, in Brazil, due to anthropogenic activities. We genotyped 11 microsatellites for 49 blood samples collected from three remnant forest fragments (Morro do Diabo State Park – MDSP, Fazenda Ponte Branca – FPB, and Fazenda Santa Mônica – FSM) just before the local extinction. As expected for fragmented populations, we found evidence of bottleneck for the three populations. The populations were structured in two genetic clusters (MDSP+FPB and FSM) with admixed individuals, with significant genetic differentiation (FST = 0.13) between MDSP and FSM. The genetic diversity indices were similar in the three fragments and comparable to that of well-preserved populations.  However, the evidence of genetic differentiation over a small spatial scale (distances of 10.5 to 36.0 km between fragments) observed here is unusual for the species in well-preserved areas. Associated with the evidence of bottlenecks, it could indicate the role of anthropized landscapes in reducing population size and promoting genetic differentiation in WLP populations. It is important to delineate conservation actions for populations in similar conditions, aiming to reduce the chances of local extinction in other regions.

#10  How does harmful genetic variation affect the individual – Characterizing deleterious mutations in a small population of captive tigers

Vinay Sagar (National Centre for Biological Sciences, Bangalore, India)

Captive breeding of tigers in zoos serves to protect their numbers. However, most of the tigers in a zoo originate from a few founding members with high levels of inbreeding in their pedigree. Inbreeding or mating between relatives causes loss of genetic variation and increased genome-wide homozygosity, which can translate to the accumulation and expression of recessive deleterious mutations. This may cause drastic health effects in inbred individuals and reduce their reproductive fitness, a phenomenon called inbreeding depression. Captive tigers of Nandan Kanan Zoo, Bhubaneswar (NKB), show a strong association of inbreeding coefficients of individuals with mortality due to disease conditions. We have identified several putative deleterious mutations using whole genome sequences of five NKB tigers. Of those, 997 Loss of function (LOF) mutations are present in a homozygous state in at least one individual and could be driving the early age mortality. We are bioinformatically characterizing these mutations by looking at protein sequences, their known functions, disease association, and loss of function effects in other species. Through this analysis, we hope to identify some large-effect harmful mutations that could be causing inbreeding depression in NKB tigers and could be followed for functional validation. Our work holds promise in understanding and tackling the problem of inbreeding and inbreeding depression in isolated populations of wild tigers such as Ranthambore Tiger Reserve and Similipal Tiger Reserve.

#11  Speciation by compensatory evolution in small populations

Bruno Nevado (cE3c, Faculty of Sciences, University of Lisbon)

While the effect of small population sizes on rapid speciation has long been proposed, previous studies have focused on the effect of drift on sorting of ancestral variation and evolution of pre-zygotic incompatibilities. In this work we are testing the hypothesis that small population sizes drive reproductive isolation via fixation of novel genetic variants that cause post-zygotic isolation. Specifically, we predict that genetic drift in small populations causes fixation of deleterious mutations, which in turn drive fixation of compensatory mutations – with these pairs of deleterious and compensatory mutations causing rapid onset of reproductive isolation. I will summarise ongoing work in my research group to test this “compensatory speciation hypothesis” using experimental evolution in C. elegans, analyses of genomic data from large evolutionary radiations in New World Lupinus, and controlled interspecific crosses to estimate degree of reproductive isolation between species belonging to different lineages.

#12  Extinction is forever: long-term consequences could exceed short-term benefits of ex situ conservation of eastern black rhinoceros

Anubhab Khan (University of Glasgow)

Many wild animal species need active management to reduce risks of extinction. Several populations need geneflow from captive born individuals to supplement the existing genepool but captive animals face fitness landscapes that are different from wild conditions and also maybe admixed. Using the critically endangered eastern black rhinoceros as an example we compared the benefits of natural dispersal (in situ conservation) and active translocation from captive populations (ex situ conservation). Based on whole genome resequencing, we find that increasing natural dispersal or translocating individuals from captivity to the both reduce inbreeding and increase heterozygosity and genetic diversity compared to closed (nondispersing) native populations. However, it came at a potential cost: the load of deleterious loss-of-function mutations was higher compared to both other groups. However, the  deleterious alleles in native individuals showed higher levels of homozygosity, whereas they are sheltered by heterozygosity in translocated individuals. Since this could increase risks of inbreeding depression if captive founders are subsequently allowed to inbreed after translocation, our study highlights the importance of natural dispersal and reiterates the importance of maintaining habitat corridors between populations.

#13  Prey in Peril: Impact of Habitat Alterations on two Large Herbivores in Central Indian Landscape

Abhinav Tyagi (National Centre for Biological Sciences, Bangalore, India)

In current times, habitat fragmentation and loss are the major threats to biodiversity worldwide. Reduction of habitat to smaller patches and increased distance between patches, lead to small isolated populations that pose an increased risk of loss of genetic diversity, inbreeding and genetic load. Maintaining gene-flow among these fragmented habitat patches is critical for long-term species persistence. Several natural and anthropogenic landscape features impede animal movement. Identifying these features is crucial for effective conservation planning. Genetic approaches aid in quantifying connectivity but most studies have focussed on a single species, usually, a large carnivore. Despite playing important role in ecosystem functioning and habitat maintenance, herbivores have been largely neglected. Here, we address genetic connectivity of two large herbivores, Gaur (Bos gaurus) and Sambar (Rusa unicolor) in central India. We collected fecal samples to generate genome-wide SNP data using ddRAD sequencing for 124 Gaur and 99 Sambar individuals. We demonstrate that gaur population in central India is fragmented and exhibit high genetic differentiation, especially in small populations like Umred Karhandala WLS. Although Sambar shows low genetic structure, small population in Bor Tiger Reserve exhibits slight differentiation. Our results suggest that although forest degradation and roads restrict animal movement, the extent of the impact varies with species’ ecology. Our findings reveal that different species exhibit varied responses to various landscape features. We identify small and isolated populations which need conservation intervention. We opine a shift from large and charismatic species focussed conservation to a multi-species holistic landscape conservation approach.


Sophie Preckler-Quisquater (University of California Davis)

The San Joaquin kit fox (SJKF; Vulpes macrotis mutica) is a federally endangered species. Today, fewer than 5,000 individuals are thought to occur across their range, and the contemporary metapopulation is distributed across three core regions and several smaller satellite populations. While anthropogenic habitat loss is believed to be the fundamental cause of the historical decline of the SJKF, localized disease outbreaks today proximately threaten remaining populations both demographically and genetically. For example, in the last decade, sarcoptic mange has caused significant declines in a formerly abundant urban SJKF population in Bakersfield. As part of a broader range-wide genomic study, we present data comparing the genetic diversity of SJKF in Bakersfield before and after the mange outbreak. We used reduced-representation genomic sequencing to compare population structure, landscape connectivity, and local genetic diversity of historical SJKF individuals sampled prior to the mange outbreak (n = 57) as well as of individuals sampled from the contemporary population (n = 95), focusing on both urban (n = 54) and exurban (n = 98) regions.

#15  Genomics underlie disease severity in Yellowstone National Park wolves

Alexandra DeCandia (Georgetown University)

Theory predicts that genetic variation buffers against disease risk in wildlife. Termed the “monoculture effect”, the universality of this prediction remains unknown. To bridge this gap, we explored the relationship between genomic variation and sarcoptic mange severity in the closely monitored population of gray wolves reintroduced to Yellowstone National Park. We generated a genomic dataset of 76,859 genomic variants in 408 wolves, and subsequently characterized the relationship between genetic variation and disease. Among mange-infected individuals, we found an inverse relationship between genome-wide variation and infection severity, and additionally identified 410 variants associated with severe mange with annotations related to inflammation and immunity. At the population-level, we observed reduced genome-wide variation since the initial reintroduction event, and reported evidence of natural selection acting against severe disease-associated loci. Results obtained from this study yield system-specific insights while also highlighting the utility of genomic techniques for addressing wildlife disease ecology and management.

#16  Temperature-induced canalization of gene expression in a genetically homogenized population

Anthony Snead (New York University)

Genetic drift more effectively culls genetic variation in small populations. Considering natural selection requires heritable phenotypic variation (i.e., phenotypic variation underlain by genetic variation) to drive local adaptation, the limited genetic variation often found in small populations can reduce the potential of evolutionary rescue. Phenotypic plasticity or the ability of organisms to alter their phenotype in response to environmental change be either adaptive or maladaptive by shifting the distribution of trait values closer to or farther away from the new trait optimum. Kryptolebias marmoratus, henceforth ‘rivulus’, is a plastic androdioecious eurythermal killifish that primarily self-fertilizes, and, after many generations of selfing, rivulus forms nearly-isogenic lineages. Rivulus also has documented plastic responses to temperature throughout egg development with observed changes in growth rate and sexual phenotype that depend on exposure to cold temperatures during the thermolabile period (Developmental Stage 31). Using a single isogenic lineage, we expose eggs to either cold (20°C) or warm (25°C) water before or during the thermolabile period and quantify gene expression. While cold temperatures early in development did impact gene expression, the vast majority of differential gene expression was driven by exposure to cold temperatures during the thermolabile period with no change in gene expression between the warm treatments. Early in development, there was low variation in gene expression within treatments indicating high resistance to stochastic changes in gene expression. However, after the thermolabile period, there was greater variation in gene expression in the warm treatment and reduced variation in the cold treatment suggesting cold temperatures during the thermolabile period canalize genetic expression. If reduced variation in gene expression result in less phenotypic variation, the temperature of the embryonic environment could drive a concerted plastic response within a lineage and reduce the phenotypic variation observed in the population. Rivulus often naturally exist in genetically depauperate populations, sometimes with only a single genotype occurring. Hence, temperature during the thermolabile period of development could drive population-level phenotypic responses that may be maladaptive.

#17  The High Stakes of Low Diversity – Predicting population-specific genomic consequences of dispersal barriers and inbreeding in California Mountain Lions

Nicolas Alexandre (Postdoc, UC Santa Cruz)

The California Conservation Genomics Project (CCGP) is a state-funded initiative to produce comprehensive genomic datasets, assess regional biodiversity, and facilitate the management of widespread, foundational, or endangered species. One focal species of the CCGP is puma (Puma concolor), due to their ecological role as an apex predator and broad geographic distribution, which spans habitats from lowland deserts to high montane forests. Pumas have large home ranges and a proclivity for long distance dispersal, which makes them susceptible to habitat fragmentation.  Recent studies show, for example, that roads and housing developments stemming from coastal urban centers act as barriers to dispersal between puma populations, resulting in losses of genetic diversity and localized inbreeding. To explore the role of recent and historic habitat fragmentation on puma diversity and potential endangerment, we generated whole-genome data from 500 pumas living across California. We estimate the distribution of puma genetic diversity across the state, including inbreeding, genetic load, and recent and historic population connectivity. We correlate observed changes in puma diversity and connectivity with historical records of human land-use change to evaluate the impact of establishment of roads, cities, farms, and other human infrastructure on California’s pumas. Finally, we use these data to explore the potential of dispersal corridors for genetic rescue. Our data showcase the potential of comprehensive genomic data sets like those generated as part of the CCGP to inform future conservation decision-making.

#18  Genomic analyses of the extinct American Cheetah, Miracinonyx trumani, reveal the persistence of a small effective population size and show signatures of arctic adaptation

Molly Cassatt-Johnstone (UC Santa Cruz)

The extinct American cheetah, Miracinonyx trumani, was an iconic member of North America’s ice age megafauna community. However, little is known about its geographical range, ecological preferences, or evolutionary relationship to its extant sister species, the mountain lion, Puma concolor. M. trumani and P. concolor were thought to have coexisted as competitors due to strong niche partitioning, as M. trumani was a highly-specialized predator of the pronghorn antelope. We recovered and sequenced DNA from three Pleistocene-age felid bones recovered from permafrost deposits in Yukon, Canada. We generate high-coverage mitochondrial genomes from all three fossils, confirming that these bone remains belong to M. trumani. Additionally, we recover 39X coverage of the nuclear genome from one of these high-latitude fossils, resolving their positioning as sister taxa to P. concolor and inferring these two lineages diverged roughly 2.9 mya. Analysis of this high-coverage paleogenome indicates that the American cheetah had low genome-wide diversity and maintained a small, long-term effective population size consistent with top predators. Scans for selection reveal a suite of potential cold-adapted genes for this Beringian individual. Our results significantly expand the known range and the inferred life history of M. trumani, providing a new perspective on the ecology in Pleistocene Beringia.

#19  Genetic Assessment of Isle Royale Wolves (Canis lupus)

Sam Hervey (Michigan Technological University)

Isolated populations of wildlife will accumulate deleterious alleles, negatively impacting their fitness. This was well documented over the last two decades for the gray wolves (Canis lupus) of Isle Royale. In 2017, only two wolves remained, and were unlikely to produce viable offspring due to a high level of inbreeding. To restore ecosystem dynamics to Isle Royale, 19 wolves were translocated from the Great Lakes Region, starting in 2018. It is essential to monitor inbreeding for this population to determine if future management actions are warranted. To monitor inbreeding on Isle Royale we reconstructed a pedigree to estimate inbreeding coefficients using a variety of sample sources including blood, tissue, scat, and fur. Of the wolves genotyped so far, two breeding pairs have been identified, one of which consists of two full siblings. Inbreeding has increased steadily since the initial translocation, which justifies continued monitoring of this population.

#20  Whole genome sequences reveal substantial recent inbreeding in the Sierra Nevada red fox

Cate Quinn (California Department of Fish and Wildlife)

The threat of inbreeding depression is greatest after sudden declines, as selection has insufficient time to purge recessive deleterious alleles before fixation. In data-deficient species, however, the demographic trajectory that led to low levels of contemporary genetic diversity may be too poorly resolved to predict fitness consequences. Here we sequenced 31 whole genomes of red foxes to evaluate the likelihood of inbreeding depression in montane populations of the contiguous western U.S. We found high levels of inbreeding (FROH = 0.21–0.57) in the federally and California-state listed Sierra Nevada red fox (Vulpes vulpes necator), most of which could be attributed to consanguineous mating within the last 15 generations. Demographic reconstruction and analysis of deleterious variation suggest fragmentation of the montane lineage into separate subspecies occurred too recently to influence total genetic load, but that drift and inbreeding in isolated populations have increased its expression. Findings support the use of conservation translocations to reverse genetic erosion of the Sierra Nevada subspecies, with multiple populations indicated as appropriate source candidates. 

#21  Deleterious mutations and genetic load in inbred Scandinavian wolves

Linnéa Smeds (Uppsala University)

The Scandinavian wolf population was founded 40 years ago by three individuals, a recovery occurring after the original population had become extinct by persecution. The small number of founders in combination with geographic isolation from other wolf populations have led to extreme inbreeding. Still, the population has grown to over 500 individuals and wolf management is subject to an extensive political debate in both Sweden and Norway.

We have used functional annotation and evolutionary conservation scores on 209 whole genome wolf sequences from Scandinavia and neighbouring populations in Finland and Russia to study deleterious variation and how inbreeding and the founding bottleneck have affected the genetic load. Our observations provide genome-wide insight into the character of genetic load and genetic rescue at the molecular level, and in relation to population history. Our results emphasize the importance of securing gene flow in the management of endangered populations.

#22  Genomic signatures of divergence and admixture in pilot whales (Globicephala spp.)

Amy Van Cise (University of Washington)

Preliminary mitogenomic and nuclear evidence indicate processes of sympatric and allopatric divergence within the short-finned pilot whale species. I examined the evolutionary demography of three diverging lineages within the short-finned pilot whales using a representative genome from each lineage, and compare these three lineages with the genomes of long-finned pilot whales and killer whales. Using PSMC analysis of the three pilot whale genomes and pairwise pseudo-hybrids, I found evidence supporting a deeper divergence among lineages than previously reported. While I found no statistical support for admixture among the three short-finned pilot whale lineages, I do find significant support for introgression from long-finned pilot whales into two of the three short-finned pilot whale lineages. The preliminary research presented here represents the basis of a larger proposed study examining 80 genomes across all evolutionary lineages within both species of pilot whale in comparison to the asocial harbor porpoise, in order to characterize evolutionary processes in each of these three species and begin to compare both neutral and adaptive evolutionary processes in social vs. asocial marine species.

#23  Characterisation of deleterious genetic variants in non-model organisms: from present to extinct species

Julia Höglund (Stockholm University & Wageningen University and Research)

Animals have always been exposed to extinctions. When a population becomes smaller, it becomes prone to inbreeding, genetic variation will be lost, and deleterious variation will increase in frequency. This leads to a worse ability to adapt to changing environments, due to lowered fitness, and could lead to extinction. Hence, there is a crucial need to characterise and quantify damaging variation and its contribution to decline. Such characterisation can be based on predicted deleteriousness. These types of scores are often species specific. Thus, models need to expand accurate prediction of deleterious genetic variation beyond model species. Here, we used domesticated pig genomes to develop such a tool to score deleterious variants from sequence data. The scoring model will then be trained within domesticated pig, validated with in wild boar and lastly tested in endangered pig species. It has the long-term goal of estimating how much genetic variation contributes to extinction.

#24  Signals of positive selection in the fin whale’s (Balaenoptera physalus) genome

Omar Ramirez-Flores (Universidad Autónoma de Baja California Sur (UABCS) México)

Fin whales (Balaenoptera physalus) were one of the main target species during whaling and presented a heavy decline in their populations globally. Recently, its populations have increased, but questions remain regarding the status of their adaptive variation. In the eastern Pacific, we can find three populations of fin whales, one in the US (Eastern North Pacific – ENP), the second in the Gulf of California (Mexico – GC), and the third one in the coasts of Chile (Eastern South Pacific – ESP). Recent genomic studies have indicated the GC population is a resident, small population, that has adapted to the specific oceanographic and climate conditions of the Gulf of California. Given these three populations have experienced different anthropogenic and environmental stressors, the aim of my project is to decipher the distinct adaptations of fin whales from the Eastern Pacific by implementing comparative and population genomic techniques.

#25  The Trojan rhino: mutational load and purifying selection in Black rhino conservation

Franziska Elsner-Gearing (The University of Manchester)

Due to the poaching crisis, the black rhino has undergone a rapid and precipitous bottleneck necessitating intensive management of many small populations. Past efforts to maintain viable breeding populations involved crossing two deeply divergent evolutionary units: the Eastern and the Southern black rhino. Here we demonstrate that the introduction of a Southern male to a population of Eastern black rhino resulted in elevated mutational load in admixed compared to unadmixed animals, in spite of ongoing purging. In comparison, in the European zoo population we describe lower mutational load, but also show that weakly deleterious mutations are accumulating over generations.

While poaching represents an immediate threat to the species, altered evolutionary dynamics as a result of small populations and artificial fitness landscapes may pose a long-term challenge. Furthermore, this could be a widespread issue across taxa with implications for endangered species management and genetic rescue strategies.

#26  Recent population collapse shapes deleterious variation across subpopulations of the endangered Florida scrub-jay.

Mitchell Lokey (Cornell University)

Conservation genetic theory predicts that small and declining populations have a greater risk of extinction due to: 1) elevated deleterious allele frequencies and 2) increased homozygosity of deleterious variants. One of the most exciting opportunities to investigate these predictions is in the endangered Florida scrub-jay (FSJ; Aphelocoma coerulescens) which has declined to <10% their former size. Here we explore the evolution of deleterious variation across demographically diverse subpopulations of FSJ using whole-genome sequencing of 244 birds. To identify putatively-deleterious variants (PDVs) we apply gene prediction and conservation-based approaches. We quantify the impacts of small and declining population size on the efficacy of purifying selection by contrasting the site frequency spectra of PDVs and neutral variation across subpopulations as well as the burden of PDVs across individuals. We then use forward-genetic simulations to verify the effects of demographic processes are consistent with observed variation and to predict subpopulation’s future PDV burden.

#27  Evaluating gene flow among structured populations of California towhee (Melozone crissalis) with a focus on the small isolated population in Inyo, California

Jong Yoon Jeon (Purdue University)

The California Towhee (Melozone crissalis) is a large non-migratory sparrow, with a current range from Oregon USA to Baja California, Mexico. The Inyo towhee is located in the Argus Mountains of California and is a former subspecies (M. c. eremorphila) of the California Towhee (the Inyo towhee is now considered to be an isolated population of the broadly distributed M. c. crissalis as of 2022). This isolated population was listed as federally listed as “Threatened” in 1984, largely due to habitat degradation. In 2013, the US Fish and Wildlife Service proposed to delist this subspecies from the Federal list of endangered and threatened wildlife based on successful conservation efforts to increase the size of the population, including management of riparian habitats and restriction of development. In this study, using whole genome data from towhee sampled across a majority of its range, we employed landscape genetics approaches to characterize population genetic structure and gene flow patterns of California towhee. The genomic results identified a well-connected gene flow pattern among well-distinguished populations, and also relatively high levels of heterozygosity and modest levels of inbreeding, which collectively support the delisting decision.

#28  Can population genomics inform on-the-ground conservation efforts?

Erangi Heenkenda (Purdue University)

Assisted translocations of individuals from a healthy source population can help rejuvenate declining wildlife populations, but successful translocations must consider genetic factors such as genetic diversity in the source population and relatedness of translocated individuals. This study assesses the population genomics of Northern Bobwhite (Colinus virginianus) from different source sites in South Texas as a part of an assisted translocation program to help reestablish populations in a Wildlife Management Area. We employed whole-genome resequencing of 76 individuals from three donor populations (Los Lazos Ranch (LL)=49; Carrizo Springs (CS)=12; Santa Rita Ranch (SR)=15) to assess overall variability, genetic structure among sites, and pairwise individual relatedness. Genome-wide variability was unremarkable (heterozygosities ranged from 0.00516 – 0.00601, similar to other avian species). Individual genome-wide heterozygosity was nearly identical among source populations (LL=0.00584, CS =0.00586, SR=0.00567). Genome-wide differentiation among populations was low (measured by Fst; CS vs LL=0.021; CS vs SR=0.078; LL vs SR=0.064), suggesting historical gene flow among the three donor sites. Pairwise relatedness analyses revealed a high level of relatedness among translocated birds (Nrelated=54% from SR; Nrelated=41% from CS; and Nrelated=29% from LL). We will conduct forward-time simulations of whole-genome sequence data to quantify the temporal accumulation of inbreeding in the recipient population. We show that including close relatives in assisted translocations can increase inbreeding in the destination population, which can negatively impact mean fitness. Our population genomics analyses of donor populations plus forward-time computer simulations provide a general framework for the future analysis of translocation dynamics in wildlife species of conservation concern.

#29  Purging on high impact mutations on Wallacea’s endemic island ungulates and its implication for conservation

Sabhrina Aninta (Queen Mary University of London)

Historically small populations are expected to be more vulnerable to anthropogenic disturbances, as they likely possess elevated levels of genetic load due to drift. Few studies have nonetheless been able to assess this prediction empirically in large and small populations of the same species. Here, we analyzed 120 genomes of anoa (Bubalus spp.) and babirusa (Babyrousa spp.) which are found in islands of vastly different sizes within the Wallacea archipelago. Using a new composite likelihood method to quantify differences in site frequency spectrum (SFS) for different impact mutations, we show that despite possessing higher load in total, the small island populations purge highly deleterious alleles faster than larger populations. This indicates that even the smallest population has the potential to survive and small islands should not be overlooked in regional conservation plans.

#30  Evolutionary diversification and repeated gene capture by telomeric retrotransposons across the Drosophila genus

Jae Hak Son (Rutgers University)

Telomere-specialized retrotransposons in Drosophila have traditionally been known for their mutualistic relationship with their host. However, a recent study found that the D. melanogaster TART-A telomere-specialized transposon has captured a portion of the piRNA pathway gene, nxf2, which allows it to target nxf2 for suppression. To reveal whether the antagonistic evolution between the telomeric transposons and the host occurs across the Drosophila genus, we have examined the evolutionary diversification of telomere-specialized retrotransposons across the Drosophila genus using publicly available long-read genome assemblies from 106 Drosophila species genomes. We identify 6 major telomeric retrotransposon clades from the gag gene and the pol gene. We find that the capture of an aubergine (aub) gene fragment appears to have occurred independently at least four times within the vittiger subgroup of Zaprionus. These gene capture events exhibit a complex pattern of gain, loss, and horizontal transfer among Zaprionus species. The repeated gain and loss of aub gene capture by telomeric TEs of Zaprionus is consistent with antagonistic evolution between these TEs and their host.

#31  Evolutionary shortcuts via multi-nucleotide substitutions and their impact on natural selection analyses

Alexander Lucaci (Temple University)

Inference and interpretation of evolutionary processes, in particular of the types and targets of natural selection affecting coding sequences, are critically influenced by the assumptions built into statistical models and tests. If certain aspects of the substitution process (even when they are not of direct interest) are presumed absent or are modeled with too crude of a simplification, estimates of key model parameters can become biased, often systematically, and lead to poor statistical performance.  Because multi-nucleotide substitutions have a significant impact on natural selection detection even at the level of an entire gene, we recommend that selection analyses of this type consider their inclusion as a matter of routine. To facilitate this procedure, we developed, implemented, and benchmarked a simple and well-performing model testing selection detection framework able to screen an alignment for positive selection with two biologically important confounding processes: site-to-site synonymous rate variation, and multi-nucleotide instantaneous substitutions.

#32  Transcription factor binding sites are frequently under accelerated evolution in primates

Xinru Zhang (Penn State University)

Recent comparative genomic studies have identified many human accelerated elements (HARs) with elevated substitution rates in the human lineage. However, it remains unknown to what extent transcription factor binding sites (TFBSs) are under accelerated evolution in humans and other primates. Here, we introduce two pooling-based phylogenetic methods with dramatically enhanced sensitivity to examine accelerated evolution in TFBSs. Using these new methods, we show that more than 6,000 TFBSs annotated in the human genome have experienced accelerated evolution in Hominini, apes, and Old World monkeys. Although these TFBSs individually show relatively weak signals of accelerated evolution, they collectively are more abundant than HARs. Also, we show that accelerated evolution in Pol III binding sites may be driven by lineage-specific positive selection, whereas accelerated evolution in other TFBSs might be driven by nonadaptive evolutionary forces. Finally, the accelerated TFBSs are enriched around neurodevelopmental and pluripotency genes, suggesting that accelerated evolution in TFBSs may drive the divergence of neurodevelopmental processes between primates.

#33  Multiple long-read de novo assemblies of House Finches enable pangenome analysis of structural variants

Bohao Fang (Harvard University)

Structural variants in the genome play a crucial role in adaptive evolution in animals, often directly underlying fitness-relevant traits. However, the identification of structural variants has been challenging with most traditional methods. The pangenome approach rejects a single reference genome and instead captures the full spectrum of allelic variants spanning single nucleotide polymorphisms to large structural variants across populations. Here we present a pangenomic study of House Finches (Haemorhous mexicanus), a model system for studying host-pathogen coevolution and sexual selection and with a unique and well-documented demographic history. We construct a pangenome representing the entire genomic content of house finches using 34 haplotype genomes assembled with PacBio HiFi reads. We found substantially higher levels of transposable elements and repeats (20%) than reported previously for most birds. We identified ~130,000 structural variants, including 116 inversions, most of which (60%) are repetitive elements. We found that the structure of immune gene families like the MHC is much more complex than previously reported in the species, and that MHC diversity increases with increasing time of population exposure to the Mycoplasma pathogen. We observed purging of highly deleterious structural variants through bottleneck in East population. The pangenomic study enables us to assess structural variation and genome complexity among house finch populations with different demographic processes.

#34  Small population sizes and associated genetic load in critically endangered Italian endemics

Maëva Gabrielli (University of Ferrara, Italy)

Small populations give a unique opportunity to investigate the relative roles of drift and selection in evolution. In particular, small populations can show an accumulation of deleterious mutations (the genetic load) due to the strong effects of drift. We here checked this hypothesis using two Italian endemics with small population sizes and threatened to extinction : the Aeolian wall lizard, endemic to the Aeolian archipelago, North of Sicily and the Marsican bear, endemic to the Apennine mountains in the centre of Italy. We analysed the genomic variation pattern and the genetic load in these two species and compared them with those observed in their sister population or species. Analyses of whole-genome sequences show a uniquely low level of polymorphism associated with a high genetic load. However, we show that genetic load is similar for small populations with different population sizes and levels of genetic variation, suggesting a maximum level of tolerable genetic load in these isolated populations.

#35  New machine learning method identifies subtle fine-scale genetic stratification in diverse populations

Xinghu Qin (Beijing Institute of Genomics, Chinese Academy of Sciences & National Center for BIoinformations)

Fine-scale genetic structure impacts genetic risk predictions and furthers the understanding of the demography of diverse population which may lead to health disparities in population health monitoring system. Epidemiology and population genetic research tries to disentangle subtle genetic differences within a population through various dimension reduction approaches (i.e., PCA, DAPC, t-SNE, and UMAP). However, one undesirable aspect of these approaches is that they either produce coarse and ambiguous cluster divisions or they fail to preserve the correct genetic distance between populations. We proposed a new machine learning algorithm (ALFDA) for better capturing fine-scale genetic structure and recapitulating geogenetic distance. ALFDA correctly estimated the genetic affinity between individuals and keep the multimodal structure within populations. Through extensive simulations and empirical data analyses, we showed that ALFDA outperformed the other approaches in identifying fine-scale genetic structure and in preserving geogenetic distance. Notably, genetic features produced from ALFDA had highest correlation with population FST under an isolation-by-distance model. We identified a rich pattern of subtle fine-scale genetic differentiation within diverse populations than those identified by existing approaches, indicating that genetic ancestry is more nuanced than previously reported. Our method was able to uncover fine-scale genetic structure within populations, which could help understand the genetic origin and diversity of individuals in understudied diverse populations thus facilitates the design of genome scan and precise health.

#36  Spatial variation in deleterious load in American black bears

Emily Puckett (University of Memphis)

Genomic diversity across the range of American black bears is due to a combination of historic lineage splitting, range expansion, admixture, and anthropogenic impacts.   Within the eastern lineage, there is high nucleotide diversity across contiguous habitat in the north, and lower diversity in southern populations many of which are isolated due to habitat fragmentation.  A managed translocation of bears from the Great Lakes to Louisiana provides an opportunity to empirically test ideas about the expression of genetic load in small populations.  We sequenced the genomes of nine black bears and estimated private and shared genetic load using SNPeff and SIFT.  We observed high genetic load in the northern Great Lakes population, and low genetic load within Louisiana.  However, runs of homozygosity were longer in the south, indicating potential for greater expression of deleterious variants and impacts on fitness.

#37 Detecting Nuclear Copies of Mitochondrial DNA Fragments (Numts) in the Gray Whale Genome

Rafaela Besse & Megan Johnson (Purdue University )

Nuclear copies of mitochondrial DNA fragments, or numts, are generated when portions of the mitochondrial DNA (mtDNA) molecule are integrated into the nuclear genome. Nuclear copies of numts can be mistaken for mtDNA and thus act as a potential source of contamination in mtDNA sequence analyses. The nuclear and mtDNA genomes of gray whales have been successfully characterized in previous studies, but published matrilineal phylogenies of observed mtDNA haplotypes raise the question of whether numts have inadvertently confounded evolutionary analyses. This work aims to catalog numts in the gray whale nuclear genome as part of an effort to critically evaluate the reliability of the mtDNA phylogeny and the subsequent phylogeographic inferences about gene flow between gray whale assemblages in the North Pacific.

#38  A comprehensive genomic approach for the critically endangered Apennine brown bear: predicted load, functional essays, simulations, and much more

Roberto Biello (University of Florence)

A small population of ~50 brown bears lives in complete isolation in the Italian Apennine Mountains. To elucidate the impact of extensive loss of genetic variation in a small and isolated population, we generated a chromosome-level genome assembly and compared the genetic variation among 20 new genomes from Apennine and Central Europe populations. We identified several deleterious mutations affecting genes in the Apennine population. Three predicted deleterious mutations in the mitochondrial ND5 gene were functionally characterized using cell cultures confirming their negative impact on mitochondrial functionality. Despite the generalized loss of genetic diversity, Apennine bears retained high genetic variation and private structural variants associated with immune and olfactory systems indicating that biological processes involved in the environmental interactions might play a key role in population viability. Overall, our study helps to shed light on the puzzle of Apennine bear persistence and provides key insights into the application of genomic tools in conservation efforts of small and isolated populations.

#39  Threading the Needle: Assessing the Genomic Health of the Critically Endangered Silver Boa

L. Caden Comsa (Rutgers University)

As the world’s “6th Mass Extinction” continues due to anthropogenic change, more and more species are driven to endangerment and become susceptible to the risks associated with small population sizes. One such species recently discovered in 2015, the Conception Bank Silver Boa (Chilabothrus argentum), is classified as Critically Endangered on the IUCN Red List, with an estimated census population of 128 individuals (95% confidence interval of 78-246). Unfortunately, recent (2020) legislative changes in the Bahamas have made it highly untenable to continue most externally-funded ecological research, including fulfilling critical recommendations made by the IUCN in 2019 for conservation actions to protect the Silver Boa. To prevent a full shutdown of conservation efforts, we will perform whole genome sequencing of all currently existing samples taken from Silver Boas to assess the species’ population size and genomic health. Using Illumina short read sequencing, we have successfully obtained reads for 12 individuals out of only 20 existing specimen samples, each at an estimated 30X coverage. To obtain a closely-related reference for haplotype calling, we are assembling a high-quality reference genome from the Turks and Caicos Boa (Chilabothrus chrysogaster), the closest living relative of the Silver Boa. Using these genomes, we will begin by analyzing the Silver Boa population’s level of heterozygosity and degrees of relatedness between individuals. We then aim to determine the demographic history of the population, and whether the population experienced recent decline or has been at a small size for a longer time. With this information, we hope to evaluate whether the Silver Boa population is suffering from or at risk of inbreeding depression, or has had the fortune of undergoing purging of deleterious alleles and is genetically stable at a small population size. Besides contributing to our eventual goal of sequencing every living Silver Boa, our work will allow us to gain insights into the population’s genomic health and evolutionary history and thus better inform outstanding plans that include conservation management and a breeding program.

#40  Mutational meltdown revisited 

Ulises Hernandez (University of Arizona)

Small populations are less able to purge slightly deleterious mutations. Deleterious mutations in turn lower absolute fitness and thus lower the population size. Previous models of this positive feedback loop, known as mutational meltdown, address the time taken for extinction after the tipping point toward extinction has already been crossed. Here we ask what conditions might or might not drive a population across the tipping point to extinction in the first place. Under realistically high vertebrate genome-wide deleterious mutation rates U>1, new mutations appear faster than selection can purge them, pushing even initially large populations toward meltdown. However, global negative epistasis increases the rate at which selection purges mutations, sometimes making the rate of further deleterious fixations negligible. Here we used an absolute fitness model to derive an equation for mutation-selection-drift metastable balance and found that very weakly negative epistasis can be sufficient to enable population metastability. 

#41  A panel of ancestry informative markers to determine the ancestral proportions of Puerto Ricans

Wilfredo Gonzalez (UC San Diego)

This research set out to design a panel of ancestry informative markers (AIMs) specific to the Puerto Rican population, using 108 Yorubas and 107 Iberians as reference populations whose genomes were sequenced by the 1000 Genomes Project (1000G), and 46 Native Americans of the Human Genomic Diversity Project. We determined the ancestral ratios for the 104 Puerto Ricans in the 1000G based on the 24.9 million polymorphisms that have a 95% genotype rate in the 1000G using ADMIXTURE 1.3. Different panels of AIMs were designed using Fst, two LSBL modalities and combinations of Fst with LSBL as selection criteria. The results clearly demonstrate that the selected Fst-based AIMs produce the most realistic results, and that good discrimination power is needed for only two of the three ancestries.

#42  A decision-tree framework for conservation genomics: lessons from the Eastern Massasauga Rattlesnake

Hana Thompson (Queen’s University, Canada BioGenome Project)

On December 19 2022, the Kunming-Montreal Biodiversity Framework Agreement was adopted which outlines the measures necessary for addressing the  dangerous loss of biodiversity and restoring natural ecosystems. The Framework includes 4 goals and 23 targets for achievement by 2030. There are 8 Action Targets in the Framework that specifically address species conservation. Of these, 7 address the direct threats to biodiversity: land- and sea-use change (Targets 1–3), overexploitation (Target 5), invasive species (Target 6), pollution (Target 7) and climate change (Target 8). Achieving these Action Targets will benefit many species, but a substantial number of threatened species will continue to decline without additional recovery actions. In recognition of this, Target 4 (Intensive Management), was created, which specifically aims to ensure active management actions to enable the recovery and conservation of species, including ex situ actions. There are a variety of ex situ management options and roles which can contribute to conservation efforts at different stages in a species’ declining status, from addressing the causes of primary threats and offsetting the impact of threats, to restoring wild populations and/or buying time. Often, these options require that a small population be established under human care. These populations can benefit from the integration of genomic resources. We developed a workshop-based process based on the IUCN Conservation Planning Specialist Group’s Principles and Steps and the IUCN Threat Classification Scheme. During the workshop, focused on the Eastern Massasauga Rattlesnake, managers, and other partners where species conservation efforts involve ex situ populations were guided through a decision-making process on how genomics could benefit the conservation of this critically endangered species. We piloted the process in collaboration with the Canadian Eastern Massasauga Rattlesnake Recovery Implementation Group (CEMRRIG) in February 2023. We present our framework and a summary of the outcome of the pilot workshop.

#43  Estimating Waiting Distances Between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent

Patrick McKenzie (Columbia University)

Genomes are composed of a mosaic of segments inherited from different ancestors, each separated by past recombination events. Consequently, genealogical relationships among multiple genomes vary spatially across different genomic regions. Expectations for the amount of genealogical variation among unlinked (uncorrelated) genomic regions is well described for either a single population (coalescent) or multiple structured populations (multispecies coalescent). However, the expected similarity among genealogies at linked regions of a genome is less well characterized. Recently, an analytical solution was derived for the expected distribution of waiting distances between changes in genealogical trees spatially across a genome for a single population with constant effective population size under the SMC’ model. I describe a generalization of this result, in terms of the expected distribution of waiting distances between changes in genealogical trees and topologies, for multiple structured populations with branch-specific effective population sizes (i.e., under the multispecies coalescent). Our solutions establish an expectation for local genealogical autocorrelation in multispecies datasets and provide a new likelihood framework that links demographic models with local ancestry turnover across genomes.

#44  The complex population structure of Canada’s Belugas

Claudio Müller (University of Manitoba)

The Beluga whale is an important species of Canada’s marine fauna and it can be found all along the  Eastern coast. However, studying these animals can be challenging as this species is made up of  different smaller stocks and populations which are not always easy to define because of their  complex migration behavior. Yet, properly identifying distinct populations and understanding their  demographic history has become essential for conservation purposes, as many of the observed  stocks have been reduced in their numbers and are at high risk of disappearing. For our project we sampled over 140 Beluga individuals from different sites along the Canadian East  coast and identified underlying population structure. We investigated the degree to which they have  diverged from each other and what potential for gene flow exists between them. We then  reconstructed how the effective population size of these animals has changed, long-term as well as in  the more recent past. We also estimated today’s effective population size and compared them to  their census size to better understand their current state. Our results indicate at least five distinct genetic populations. All of these populations appear to be  the result of a split of one large population towards the end of the last glacial period into more  isolated, smaller ones. The most endangered population, inhabiting the St. Lawrence estuary, shows  a high degree of inbreeding, however its most recent effective population size estimates shows much  larger numbers than any census results, indicating either a larger population than recently assumed,  or a lag in the ability of our estimation methods to pick up on recent decline in effective population  size.

#45  Genomic Insights into the Endangered Mouflon Populations of Anatolia and Cyprus

Eren Yüncü (Middle East Technical University)

Once widespread in their home lands, Anatolian mouflon (Ovis gmelini anatolica) and Cypriot mouflon (Ovis gmelini ophion) were both driven to near extinction during the 20th century and are currently listed as endangered subspecies by IUCN. Despite ongoing conservation efforts, populations continue to decline and their ranges are restricted to a few sites, with estimated population sizes of <2,500. Here, we study whole genome sequences of five Anatolian and ten Cypriot mouflons to investigate historical population dynamics and their consequences. We estimate the divergence time between the two subspecies as 5-10kya. The Cypriot mouflon shows an extended period of decline in effective population sizes, starting from the end of Pleistocene. Both subspecies harbor considerably high numbers of runs of homozygosity (ROH) blocks, which suggests recent severe inbreeding. Patterns of low pairwise genetic diversity, high degrees of relatedness and elevated non-synonymous to synonymous variant ratios are more dramatic in the Cypriot mouflons compared to Anatolian mouflons. These genomic patterns can be explained by early Holocene human-mediated introduction of the mouflon to Cyprus and long term isolation. Furthermore, we find a 1-2Mb peak in local heterozygosity estimates where copies of a locus with homology to a candidate paratuberculosis resistance gene (ABCC4) are located. We use data from other sheep genomes and paleogenomes to study the history of this locus. Overall, our work demonstrates how these endemic mouflon populations have been affected from demographic decline, which will help guide conservation management practices.

#46  Genomic consequences of isolation and inbreeding in an island dingo population

Ana Victoria Leon Apodaca (Pennsylvania State University)

Dingoes are wild canids from an ancient canid lineage that originated in Australia around 8000 years BP. A small protected population exists on an offshore island, K’gari. While dingoes on K’gari are protected, dingoes in the mainland are only protected in certain regions, and lethal control is commonly used. Here, we analyze 18 whole genome sequences of dingoes sampled from mainland Australia and K’gari. Our results suggest that bottlenecks and isolation have maintained low levels of genetic diversity in K’gari dingoes. Long (>1 Mb) runs of homozygosity (ROH) are elevated in both dingo populations, although K’gari dingoes showed significantly higher levels of very long ROH (>5 Mb). While both mainland and K’gari dingoes carry similar amounts of homozygous LoF variants, K’gari dingoes carry a higher burden of deleterious homozygous variants. However, purging of LoF variants in K’gari dingoes appears stronger than purging of predicted deleterious nonsynonymous variants.

#47  Mitogenomic analysis of a late Pleistocene jaguar from North America

Megha Srigyan (UC Santa Cruz)

The jaguar (Panthera onca) is among the few large carnivores that survived the end-Pleistocene megafaunal extinction event in the Americas. However, Pleistocene jaguar from North America are up to ~20% larger than extant jaguars, leading some to hypothesize that these specimens represent now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). To examine the taxonomic and phylogenetic affinities of the North American Pleistocene jaguar, we sampled a terminal Pleistocene specimen from Kingston Saltpeter Cave, Georgia, USA, for ancient DNA analysis. We used a hybridization capture approach to generate a full mitochondrial genome at 28X coverage and compared it to mitochondrial genomes from other extinct and living large felids and modern jaguars. Phylogenetic analyses indicate that this individual represents a modern jaguar instead of a distinct Pleistocene species or subspecies despite its larger size. Further, Bayesian analyses of modern jaguar mitochondrial lineages suggest that modern jaguars arise between 0.5mya – 1.5mya, with the Pleistocene individual falling into one of two sub-clades of modern jaguars. While older specimens are required to test the presence of a separate lineage in early Pleistocene, our results suggest that late Pleistocene North American jaguars, such as the one recovered in this study, likely represent lineages arising due to reinvasion of jaguars from South America. The data generated in this study represents the first full mitochondrial genome of a Pleistocene jaguar and could be helpful in clarifying proposed hypotheses about jaguar population history in the Pleistocene.