National Centre for Biological Sciences, India
Future evolution and conservation of small and isolated populations of tigers
Humans have impacted most of the planet. The resulting increase in human population density, landuse landcover change, and direct hunting has resulted in fragmentation, sequestering species into small, and often isolated populations. Since small and isolated populations have high chances of extinction, it is important for us to identify them, and understand their evolutionary trajectories. We have been studying a population of tigers globally and in India from a genetic perspective for the last two decades. Our research reveals that tigers in India have high total genetic variation compared to other parts of the species range, but some populations within India are isolated. I will show two examples of isolated populations that highlight possible trajectories: that of genetic drift and inbreeding. But studying ongoing evolution is not enough. What would it take to sustain these populations in the future? Sustained movement requires the ability to address livestock depredation, and I will present some results on genetic approaches to do so. Finally, I will discuss future work aimed at understanding phenotypic trajectories of inbreeding depression, and evidence-based approaches to genetic rescue.
University of Basel, Switzerland
Long-term small populations and the drift syndrome
Populations of long-term small size or those that have undergone a phase of pronounced demographic bottlenecks typically bear the signature of reduced genetic variation due to consistent exposure to genetic drift. But, enhanced genetic drift may also constrain the efficacy of purifying and directional selection, resulting in the accumulation of mutational load and reduced adaptation. Together, they may systematically erode individual and population mean performance. In research on wild Arabidopsis lyrata, we could show that both mutational load and reduced adaptation can be considerable, but that the former has much stronger performance implications. Results evoke that if a substantial decline in genetic variation in a population is found, all negative consequences of genetic drift are present, though more data is needed to get good predictor values. Once those are established, the genetic screening of species and population for vulnerability can be promoted as good practice in conservation management.
Theoretical approaches for studying small populations
Session overview: A central component of understanding how evolution operates in small populations is developing theoretical and methodological approaches. Theory can inform us what we might expect to happen in small populations under an evolutionary model, and methods can help us infer important parameters to test hypotheses based on theory. In this session, we will hear from researchers working at the cutting edge of developing and applying new theoretical and methodological approaches for inferring the demographic and selective forces operating in small populations.
Jagiellonian University, Poland
Navigating the temporal continuum of effective population size
Effective population size, Ne, is a key evolutionary parameter that determines the levels of genetic variation and efficacy of selection. Estimation and interpretation of Ne are essential in diverse areas of evolutionary and conservation biology, ranging from assessing the evolutionary potential or extinction risk to empowering research on the genomic basis of adaptation. The diverse applications of the Ne concept resulted in largely independent methodological developments using different Ne definitions and estimating either contemporary or long-term Ne. Recently, several new approaches appeared that allow the estimation of temporal Ne trends and at various parts of the temporal Ne continuum. In my talk, I will discuss confusing aspects of Ne and provide an overview of its temporal (and spatial) characteristics to navigate the audience through the temporal continuum of Ne.
Pennsylvania State University, USA
Scanning for selection in unphased data
Haplotype-based scans to identify recent and ongoing positive selection have become commonplace in evolutionary genomics studies of numerous species across the tree of life. However, the most widely adopted approaches require phased haplotypes to compute the key statistics. Here I highlight a simple approach for adapting haplotype-based statistics to unphased data—the multi-locus genotype (MLG). Using MLGs, I re-formulate popular statistics such as nSL and XP-nSL for use on unphased data and evaluate their performance across a range of important parameters in a generic demographic history. I also demonstrate that these implementations often outperform a naïve application of the original statistics to unphased data, and that they perform with minimal to no reduction in power compared to the original statistics when phase is perfectly known. Finally, I discuss a novel method for detecting sweeps that moves beyond summary-statistic-based methods. I show how to construct a composite likelihood ratio statistic that uses MLGs to identify extreme distortions in the MLG frequency spectrum consistent with a recent sweep.
Diego Ortega del Vecchyo
National University of Mexico (UNAM), Mexico
Leveraging the Ancestral Recombination Graph to infer the impact of natural selection acting on putatively deleterious mutations
The ancestral recombination graph (ARG) contains the full history of coalescent and recombination events. I will present a new method that leverages the ARG to infer the impact of natural selection acting on new putatively deleterious mutations. I will show how we can use this method to infer the distribution of deleterious mutations using genomic data from individuals of small populations. I will show how this method can be used to guide conservation efforts.
Inferring complex demography from genomic variation data
Session overview: Small populations are ultimately defined by their demography, and inferring demography using genetic variation datasets has long been a central aim in population genetics. One key takeaway from studies in natural populations is that demographic trajectories are often complex and most species are far from equilibrium. In this session, we will hear from researchers working to understand complex demography in empirical systems ranging from humans to the Wrangel Island woolly mammoth population.
California State University, San Marcos, USA
The genomic impact of whaling and isolation in fin whale populations
The 20th century industrial whaling pushed several species to the brink of extinction. In the North Pacific more than 75,000 fin whales (Balaenoptera physalus) were caught. However, a small population in the Gulf of California was never targeted by whaling. We analyzed whole genome sequences from the Eastern North Pacific and Gulf of California populations to investigate their demographic history and the genomic effects of natural and human-induced population declines. We found that the Pacific population has maintained its genetic variation, while in the Gulf population there has been a decrease in heterozygosity and an increase in runs of homozygosity. These populations diverged 16 kya, then the Eastern North Pacific population expanded and during the whaling period suffered a dramatic 99% reduction in effective size. In contrast, the Gulf population remained small and isolated, receiving less than one migrant per generation. Simulations indicate that this limited gene flow has been crucial for maintaining the population’s viability. Our results suggest that genomic data from contemporary samples can help estimate the magnitude and timing of recent anthropogenic bottlenecks, expose the severity of whaling and emphasize the importance of gene flow for long-term population survival.
Stockholm University, Sweden
Temporal dynamics of woolly mammoth genome erosion prior to extinction
The woolly mammoth (Mammuthus primigenius) population on Wrangel Island is an excellent model system to investigate long-term genetic consequences of a population bottleneck. Mammoths became isolated on the island in the early Holocene due to rising sea levels, and persisted for over 200 generations. To study the evolutionary processes leading up to the extinction of the woolly mammoth on the island, we analysed 21 Siberian woolly mammoth genomes. Our results show that the Wrangel Island mammoths recovered quickly from an initially severe bottleneck, and subsequently remained demographically stable during the ensuing 6 millenia. Further, we find that highly deleterious mutations were gradually purged from the population, whereas there was an accumulation of mildly deleterious mutations. The gradual purging of highly deleterious mutations suggests an ongoing inbreeding depression for hundreds of generations. This time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked present-day populations.
Trent University, Canada
Meaningful genomic metrics and the role of demographic history
Genomic data has galvanized the conservation community with its potential to better characterize the genetic health of small populations and inform management decisions. Summary statistics derived from the genome, however, a fraught with nuance and impacted by the demographic history of focal population. Using white-tailed deer mainland and Island populations I show how Tajima’s D, mutational load, and FROH metrics collectively shed light on historical and contemporary processes reflective of population health. I also show the apparent impact of human intervention on deer genomic diversity and use the island-mainland sampling design to identify patterns of inbreeding and recessive deleterious mutations.
Duke University, USA
Inferring diverse demographic trajectories of hunter-gatherer populations during the rise of farming in Eastern Africa
The adoption of farming beginning 12ky represented a profound cultural shift that enabled the explosive growth of human populations and their expansion into regions that were formerly occupied by hunter-gatherers. The fate of these hunter-gatherer groups has been a question of interest for researchers in genetics, archeology, and paleoanthropology for decades, with the relative importance of acculturation versus demographic replacement being a major focus of debate. I investigate this topic by studying the population genetics of Southwest Ethiopia, where the transition to farming began relatively late and is currently ongoing. This part of the world is home to the Chabu people, one of the only remaining hunter-gatherer groups in the world, as well as several agriculturalist and pastoralist groups. I show that the effective population size of the Chabu has been in decline for the past 1,400 years ago, concomitant with the spread of farming into the region. Interestingly, however, I find that population decline was not a universal trend among Southwest Ethiopia. My results underscore the fact that hunter-gatherer responses to encroaching agriculture and pastoralism were highly heterogeneous, and included acculturation, gene flow, and economic specialization in addition to population decline.
Novel approaches for measuring fitness in small populations
Session overview: A distinctive feature of small populations is that elevated genetic drift can overwhelm the effects of positive and negative natural selection. However, quantifying the effects of selection and identifying the mutations controlling fitness in natural populations has long posed a major challenge in the field. In this session, we will hear from researchers working to infer the selective effects of mutations and understand their impact on fitness in small populations.
University of Rochester, USA
Maintenance of genetic variation for fitness in a pedigreed wild population
A fundamental question in evolutionary biology concerns the persistence of high levels of genetic variation despite strong stabilizing and directional selection. Here, we perform a fine-scale dissection of selection components using a 25-year genomic, phenotypic, and pedigree dataset in the Federally Threatened Florida Scrub-Jay (Aphelocoma coerulescens). A population of Florida Scrub-Jays at Archbold Biological Station has been studied since 1969, resulting in lifetime fitness measures for thousands of individuals on a 14-generation pedigree. We genotyped every individual in our study population over the past two decades at 15,416 genome-wide SNPs. To test for selection at specific life-stages, we modified existing selection component analysis frameworks to take full advantage of exhaustive population sampling. We identified several loci under gametic, viability, or fecundity selection and found evidence of sexual conflict and antagonistic pleiotropy genome-wide. Our results provide important insights on the role of selection in maintaining genetic variation in a natural population.
University of Ferrara, Italy
Fifty bears isolated in Central Italy: is the analysis of their genomes useful for saving them?
We used several approaches to reconstruct the demographic and selective history of a small brown bear population isolated in Central Italy since several thousand years. Genomic analyses suggest uneven distribution of variation across the genome, with some accumulation of realized load. Cell cultures are used to test the effects of mutations predicted to be deleterious. Simulations do not support the immediate need of genetic rescue, and some evidence of reduced aggressiveness genetically controlled indicates that the coexistence with humans is favored in this iconic and endangered group.
Smithsonian-Mason School of Conservation, USA
Conservation genomics of black-footed ferrets: diversity and functional aspects
Despite narrowly escaping extinction in the 1980s, the black-footed ferret (Mustela nigripes) remains at risk due to disease susceptibility and health challenges, including male fertility. We sequenced the genomes of 54 ferrets from wild, captive, and reintroduced populations, finding extremely low genetic diversity, high inbreeding, and an increased deleterious mutation load. Despite these, vital fitness-related genes retain variation. Notably, loss-of-function mutations were found in genes linked to sperm function. Our findings provide crucial insights into the genetic consequences of the founder bottleneck, informing strategies to restore lost genetic diversity and reduce extinction risk.
Session overview: A key application of research on molecular evolution in small populations is informing conservation management strategies for threatened or endangered species. The consequences of small population size, including greater genetic drift and inbreeding, can often contribute to fitness declines and further exacerbate extinction risk. In this session, we will hear from researchers using genomic approaches to inform conservation strategies for species ranging from kākāpō to the dama gazelle.
Smithsonian-Mason School of Conservation, USA
Using genomics to inform the management of ex-situ insurance populations of threatened species
Insurance populations continue to play an increasingly important role in preventing extinction by preserving populations under human care and maintaining what remains of the existing genetic diversity of a species. Yet such populations often face a number of demographic and genetic challenges due to their small founder sizes and limited gene pools. In my talk, I will present the results of an ongoing international collaborative research program into the conservation genomics of the dama gazelle (Nanger dama), the world’s largest and rarest gazelle species. More than 2,300 dama gazelles representing two subspecies (addra and mhorr) are managed in zoos and private collections around the world, with the largest number of animals found on private ranches in North America, mostly in Texas. Using whole genome sequence data from an initially small number of individuals, we evaluated heterozygosity, inbreeding, and mutational load burden in these two subspecies in light of their different founder histories in captivity. We also examined the cytogenomic differences between the two subspecies, as it has been suggested that breeding these subspecies together could potentially maximize genetic diversity and hence, adaptive potential, of the species as a whole. I will discuss how genomic data help to inform the conservation management, genetic rescue, and wild restoration of this critically endangered antelope, and more generally, how we may need to reconsider the way we manage insurance populations below the species level.
University of Canterbury, New Zealand
Improving foundational genomic resources for informed conservation strategies in a critically
There is growing interest in the role of structural variants (SVs) as drivers of local adaptation, adaptive potential, and speciation. From a conservation genomics perspective, the characterisation of SVs in threatened species provides an exciting opportunity to complement existing approaches that use single nucleotide polymorphisms (SNPs) to detect adaptive and maladaptive loci and inform conservation management decisions. However, singular reference assemblies do not adequately capture the full breadth of genomic variation within a species or population. This impedes our ability to characterize large and/or complex variants, like SVs, and ultimately impacts research outcomes. Genome graphs offer an opportunity to characterize variation missing from a single linear reference and are better able to resolve complex variation. Nevertheless, the assembly of multiple high-quality and contiguous genomes is no small task for many species of conservation concern. Here, we leverage a chromosomally assembled reference genome, long-read sequencing and chromosomic approaches to enhance foundational genomic resources for the critically endangered kākāpō (Strigops habroptilus). We explore the challenges associated with establishing a representative genome graph and present an exciting chromosomic approach to enhance genomic resources in a species of conservation concern.
Fuwen Wei [Remote talk]
Jiangxi Agriculture University & Chinese Academy of Sciences, China
Population Genomics of Flagship Species in China
Dramatic global changes to the environment have wrought unprecedented reductions in biodiversity, with more than 26% species assessed by IUCN as threatened with extinction. China, as one of the world’s megadiverse countries, plays a critical role in global biodiversity conservation. Flagship species, such as giant and red pandas, ungulates, big cats, snub-nosed monkeys, gibbons, dolphins in China, are threaten by habitat fragmentation and small populations, which need additional protection. During past decades, genomics has developed very fast, and is widely applied to non-model species especially wild animals to provide new insights to properly conserve them. In my talk, I will talk about achievements of the population genomics of several flagship mammals such as giant pandas, red pandas and takins conducted in my lab, and try to address how these new findings would be benefit to the conservation and management of these flagship species.
Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brazil
Evolutionary and conservation genomics of small jaguar populations
Jaguars (Panthera onca) have been extirpated from over 50% of their historical range, and currently exist in many populations of variable sizes. Some of them are still rather large and inter-connected, especially in the core Amazon forest, while others are isolated and extremely small, such as those persisting in remnants of the Atlantic Forest in eastern South America. Molecular studies conducted in the past 20 years have revealed evidence of strong genetic drift affecting some of these small, isolated populations, leading to loss of diversity and accelerated inter-fragment differentiation. I will describe recent and ongoing studies employing whole-genome sequences to investigate local levels of diversity and Run of Homozygosity (ROH) burden, as well as inter-population differentiation, in multiple Brazilian biomes, including isolated fragments of the Atlantic Forest. I will also discuss how these whole-genome data are being used to inform management strategies for both in-situ and ex-situ populations. Finally, I will describe ongoing efforts to use these genome sequences to develop SNP-based assays that allow quick, standardized, large-scale genotyping of jaguars (including non-invasive samples and forensic material), thus facilitating genetic monitoring of small populations and assessing the effectiveness of management programs.