BioGenomics2017 - Global Biodiversity Genomics Conference
February 21-23, 2017
Smithsonian National Museum of Natural History | Washington, D.C.

Program - Single Session

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Population Genomics

Room: Salon 2, Marriott Hotel

14:00 - 15:30

Moderator: Tomas Marques, IBE (UPF-CSIC)

11.1  14:10  Genomic diversity and historical demography of the sperm whale (Physeter macrocephalus); from bottleneck to global distribution in 4000 generations. Morin PA*, Southwest Fisheries Science Center; Alexander A, University of Kansas; Baker CS, Oregon State University; Hancock-Hanser BL, Southwest Fisheries Science Center; Mate B, Oregon State University; Mesnick SL, Southwest Fisheries Science Center; Rosel P, Southeast Fisheries Science Center; Whitehead H, Dalhousie University

Population and phylogeographic structure are common in large, highly mobile cetaceans despite the lack of obvious barriers to dispersal and their ability to travel great distances. Several of the largest globally distributed baleen whales are divided into multiple subspecies, usually associated with major ocean basins. In contrast, several of the larger, globally distributed social odontocetes (sperm, killer, and short-finned pilot whales) exhibit low mitochondrial DNA (mtDNA) diversity and limited evidence of phylogeographic differentiation. Sperm whales, for example, are distributed in all of the world's oceans with pre-whaling abundance likely more than one million and current abundance >360,000 individuals. Despite their wide geographic range and abundance, mtDNA control region (CR) diversity is low, with >70% globally distributed samples possessing one of 3 common haplotypes. Here, we investigate global sperm whale phylogeography and past demography using complete mitochondrial genomes from 175 samples throughout the sperm whale's range, as well as a PSMC analysis of the complete sperm whale genome. In particular, we focus on whether a recent population expansion could be responsible for the low observed mtDNA CR diversity. In contrast to mtDNA CR data, complete mitogenome haplotypes are separated into clades representing the Atlantic and Pacific Oceans, with only one shared haplotype. Demographic analyses of both the mitogenomes and the single complete sperm whale genome indicate a global expansion beginning approximately 125,000 years ago, correlating with the Eemian warm period following the last long glacial cycle (Saale glaciation, >80kyr). Patterns of mitogenome diversity suggest that sperm whales were limited to the Pacific during the cold period and have subsequently colonized the Atlantic several times, or that lineages from the Pacific supplanted existing lineages in the Atlantic.

11.2  14:30  On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics . Bernatchez *, Louis

Species across the globe are experiencing drastic changes in environmental conditions as a result of human activities. Understanding and predicting how organisms respond to human-driven environmental change is therefore a major concern. In this talk, I will discuss several mechanisms that may enhance the maintenance of genetic variation and evolutionary potential, which have been overlooked and should be considered in future theoretical development and predictive models: the prevalence of soft sweeps, polygenic basis of adaptation, balancing selection and transient polymorphisms, parallel evolution, as well as epigenetic variation. Research on fish population genomics has provided ample evidence for local adaptation at the genome level. However, pervasive adaptive evolution seems to almost never involve the fixation of beneficial alleles. Instead, adaptation apparently proceeds most commonly by soft sweeps entailing shifts in frequencies of alleles being shared between differentially adapted populations. One obvious factor contributing to the maintenance of standing genetic variation in the face of new environmental selective pressures is that adaptive phenotypic traits are most often highly polygenic, and consequently the response to selection should derive mostly from allelic co-variances among causative loci rather than pronounced allele frequency changes. Balancing selection of various forms may also play an important role in maintaining adaptive genetic variation and contribute to maintaining the evolutionary potential of species to cope with environmental change. A large body of literature on fish also shows that repeated evolution of adaptive phenotypes is a ubiquitous evolutionary phenomenon that seems to occur most often via different genetic solutions, further adding to the potential of species to cope with a changing environment. Moreover, a new paradox seems to be emerging from recent fish studies whereby populations of highly reduced effective population sizes and impoverished genetic diversity can apparently retain their adaptive potential. Although more empirical support is needed, several recent studies suggest that epigenetic variation could account for this apparent paradox. Therefore, epigenetic variation should be fully integrated with considerations pertaining to role of soft sweeps, polygenic and balancing selection, as well as repeated adaptation involving different genetic basis towards improving models predicting the evolutionary potential of species to cope with a changing world.

11.3  14:50  Evolutionary insights derived from the jaguar genome project: from comparative analyses across the genus Panthera to intra-specific assessments of demography and local adaptation. Eizirik E*, PUCRS, Brazil; Figueiró HV, PUCRS, Brazil; Murphy WJ, Texas A&M University, USA; Li G, Texas A&M University, USA; Trindade FJ, PUCRS, Brazil; Santos SHD, PUCRS, Brazil; Trinca CS, PUCRS, Brazil; Rodrigues MR, PUCRS, Brazil

The jaguar (Panthera onca) is an iconic predator whose historical geographic range encompassed a large portion of the Americas, from the southern USA to the Argentinean Patagonia. It is the top predator across all the biomes in which it occurs, and as such, it plays a critical role in the dynamics of these ecosystems. Human disturbances such as habitat loss and direct persecution have dramatically impacted jaguar populations in the last century, leading to its extinction from over 50% of the original range and rampant fragmentation of most remaining populations. Initial genetic studies have provided interesting insights into the evolutionary history of this felid, as well as demonstrated that habitat fragmentation has already produced measurable loss of diversity in local populations. However, much remains to be learned about this elusive predator, from its adaptive divergence from other Panthera species to the evolutionary dynamics of neutral loci and adaptive traits in present-day populations. In this context, a complete genome sequence enables a variety of studies focusing on the target species, as well as in-depth comparisons with related taxa. In collaboration with colleagues from multiple Brazilian institutions and six additional countries (USA, Russia, Ireland, Portugal, Spain and Argentina), we have sequenced, assembled and annotated the genome of a male jaguar sampled in the Brazilian Pantanal region, and used it to perform multiple evolutionary analyses. We also generated whole genome sequence data from a leopard (P. pardus), and thus assembled a data set comprising all five living Panthera species (including three previously published genomes). We used this genome-wide alignment to perform multiple phylogenetic and divergence dating analyses, which revealed very high levels of genealogical discordance caused by both incomplete lineage sorting and post-speciation admixture. We screened these genomes for signatures of positive selection, and identified several genes bearing significant evidence of adaptive evolution in the Panthera, including loci implicated in development, metabolism and sensory perception. To investigate patterns of genome-wide intra-specific variation, we designed a custom set of exome capture probes for Panthera species, targeting ~19,000 genes (~36 Mb). We tested these probes in all five Panthera species, and then applied them to 109 jaguars sampled in multiple Brazilian biomes. After filtering the data for quality and coverage, we obtained a curated set of 67,000 SNPs, which are currently being employed to assess patterns of population structure and adaptive divergence among different habitat types. These analyses should improve our understanding of jaguar evolution across the multiple environments in which it occurs, and help incorporate an adaptive component into conservation planning initiatives on behalf of this species.

11.4  15:10  Nuclear SNPs reveal link between social and genetic structure in Hawaiian short-finned pilot whales. Van Cise AM*, Scripps Institution of Oceanography/UCSD, NOAA Southwest Fisheries Science Center; Martien KK, NOAA Southwest Fisheries Science Center; Baird RW, Cascadia Research Collective; Mahafffy SD, Cascadia Research Collective; Oleson E, NOAA Pacific Islands Fisheries Science Center; Morin PA, NOAA Southwest Fisheries Science Center, Scripps Institution of Oceanography/UCSD

Social structure has been suggested to increase genomic diversity and population structure within many marine and terrestrial species. This process may be especially important to genomic diversity in the marine environment, where there are few boundaries to dispersal. Short-finned pilot whales, due to their formation of stable social units, may exhibit socially-driven genetic population structure. We might see genetic structure driven by the retention of individuals within family units, or genetic structure driven by an effect of social structure on mate selection. Short-finned pilot whales in the Hawaiian Islands have a well-documented hierarchical social structure of resident island communities, which comprise clusters of individuals that often associate, and in turn comprise one or more social units that spend the majority of their time in association. We use 123 mitochondrial sequences (mtDNA), and 52 nuclear SNPs (nuDNA) from 112 short-finned pilot whales, to determine whether social bonds affect population structure and divergence within the Hawaiian Islands. While mitochondrial diversity is low throughout the Hawaiian Islands, the data indicate the presence of two populations, in the Main Hawaiian Islands and the northwestern Hawaiian Islands/Pelagic region (mtDNA FST p-value < 0.0001). Within the Main Hawaiian Islands, nuclear DNA indicates genetically-segregated island communities (FST p-value = 0.02) and social clusters (mean FST p-value = 0.01). Relatedness estimates from social units off Hawaii Island indicate that individuals within social units are more related than expected by chance (p < 0.0001); clusters were similarly significantly related (p < 0.0001). These results indicate that relatedness is a driver of social structure at several hierarchical levels; in turn, social structure affects genetic structure among clusters. Socially-driven population structure, as seen in Hawaiian pilot whales, can increase genomic, ecological and cultural diversity, as well as ecological resilience, but could also indicate a greater degree of vulnerability to anthropogenic threats.

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