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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Vertebrate Genomics

Room: Salon 4, Marriott Hotel

09:00 - 10:30

Moderator: Stephen O'Brien, Nova Southeastern University

18.1  09:10  Conservation genomics of the highly endangered Iberian lynx: what we learned from whole genomes. Godoy J.A.*, Estacion Biologica de Donana, CSIC; Abascal F., Structural Computational Biology Group, CNIO, Madrid, Spain; Cruz F., Estacion Biologica de Donana, CSIC; Martinez-Cruz B., Estacion Biologica de Donana, CSIC; Rubio-Camarillo M., Structural Computational Biology Group, CNIO, Madrid, Spain; Derdak S., CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona, Spain; Alioto T., CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona, Spain; Valencia A., Structural Computational Biology Group, CNIO, Madrid, Spain

The Iberian lynx (Lynx pardinus) is the most endangered felid and a good example of species at the brink of extinction. Intensive monitoring and management -which includes captive breeding, translocations and reintroductions- provide a good opportunity for the study of genetic erosion with novel genomic tools. Here we use the first annotated draft of the Iberian lynx genome along with re-sequencing data for 11 Iberian and one Eurasian lynx to explore Iberian lynx demography and genome-wide patterns of variation. We inferred a series of three severe population bottlenecks that predate the well-known demographic decline occurring during the 20th century, the last one dated around 300 years ago. Such series of bottlenecks have drastically shaped the patterns of genomic variation in various ways, including reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion, increased rates of fixation of transposable elements, and multiple signatures of genetic erosion. The Iberian lynx shows the lowest genome-wide heterozygosity reported to date, and high ratios of non-synonymous to synonymous diversity (πN/πS) and substitution rates (dN/dS) indicate the accumulation of potentially deleterious variants. These effects are not homogenously distributed across the genome, revealing the differential action of genetic drift, mutation, recombination and selection. For example, loss of genetic diversity has been more intense in the X chromosomes (X) than in autosomes (A), resulting in X/A diversity ratios well below the neutral expectation of 0.75. Additionally, regions of the genome with maximal or minimal difference in heterozygosity between Eurasian and Iberian lynx are enriched for genes related to olfactory perception, while regions of smallest difference tend to concentrate near telomeres. Although the genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential, the knowledge and the resources developed in this study will hopefully benefit the on-going conservation and management of this emblematic species, by improving current genetic management aimed at maximizing overall diversity and minimizing inbreeding, and most notably by facilitating the identification and eventual management of deleterious traits currently segregating in the captive population.

18.2  09:30  Diet adaptation and Leopard Genome: carnivore, omnivore, and herbivore genomes. Kim Soonok, National Institute of Biological Resources; Yeo Joo-Hong, National Institute of Biological Resources; Cho Yun Sung, UNIST; Bhak Jong*, UNIST; Kim Hak-Min, UNIST

Diet is the most critical computational selection forces in all life forms on Earth. Here we present voromics, genomics of diet adaptation, analyses using 18 high quality mammalian genomes. In doing so, we also introduce a high quality leopard genome assembly constructed by short mate-pair sequences. We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our voromic analyses also provide useful resources for diet-related genetic and health research. We also present the concept of variome reference where a reference contains population variome information in the standard reference genome for the future species genomics projects such as Genome 10k.

18.3  09:50  The ruminant genome project. Heller R*, University of Copenhagen; Lei C, Kunming Institute of Zoology; Zhang G, University of Copenhagen; Jiang Y, Kunming Institute of Zoology; Hvilsom C, Copenhagen Zoo; Epps CW, Oregon State University; Zhang C, Northwest Polytechnical University; Siegismund HR, University of Copenhagen; Wang W, Kunming Institute of Zoology

The ruminants form one of the most economically and ecologically important animal groups on Earth. Within this group are two of the most successful and diverse mammal families, the deer (Cervidae) and the bovids (Bovidae). Collectively these make up by far the majority of the medium-to-large sized mammal species in existence. The bovids in particular exhibit a vast range of ecological and evolutionary specializations, ranging in size from the minuscule Royal antelope (2 kg) to the huge gaur (1200 kg). Bovids have adapted to almost every major type of habitat on Earth, from the high arctic to deserts, rainforests and swamps. This explosive radiation has occurred within a relatively short time span, about 25 million years. Furthermore, the bovids include five of the most important livestock species: the cow, water buffalo, yak, sheep and goat. Despite the remarkable diversity and evolutionary success of the ruminants relatively little is known about the evolutionary genomics of the group. There are still only a few published ruminant genomes, focusing mainly on the domesticated species. In an international consortium including Danish and Chinese research groups we are in the process of sequencing high coverage and high quality de novo genomes from ~40 ruminant species, with an emphasis on bovids. With this data we plan to bring our knowledge about the evolutionary genomics in this important animal group to a whole new level. Specific questions that we will ask include how important evolutionary innovations such as the rumen have evolved, and how niche separation and adaptive evolution have allowed the ruminants to become so speciose and diverse. We will look at a number of specific ecological and physiological adaptations and try to find the genomic background for them. Finally we will use the de novo genomes as references for a series of population genomic resequencing projects on selected species or species complexes.

18.4  10:10  Conservation genomics of the highly endangered red siskin. Lim HC*, Smithsonian Institution; Coyle B, Smithsonian Institution; Frandsen P, Smithsonian Institution; Dikow R, Smithsonian Institution; Johnson W, Smithsonian Institution; Braun M, Smithsonian Institution

The Red Siskin (Spinus cucullatus) is a highly endangered South American bird threatened by wildlife trafficking and loss of habitat due to development and agriculture. It is a common bird in the global pet trade that is frequently hybridized with the domestic canary (Serinus canaria domestica) to introduce red plumage coloration into the latter species. Preventing introgression of canary DNA into wild Red Siskin populations is a high priority concern for ongoing conservation efforts. We are investigating critical questions about Red Siskin genetics and creating genome scale molecular tools to develop a well-informed conservation breeding and reintroduction program that aims to restore siskin populations across the native range. We sequenced and assembled a de novo reference genome and performed low-coverage resequencing of nine additional individuals to facilitate the following goals: 1) better understand genetic diversity, population structure and evolutionary history of the Red Siskin; 2) design markers to interrogate historical samples and individuals used for captive breeding. Using both short (Illumina, PE150) and long reads (PacBio, ~10 kb), we applied a hybrid approach to assemble the reference genome using MaSuRCA. This resulted in a genome with high contiguity (contig N50 = 554 kb) and high BUSCO score (94.5% complete). Genome annotation was conducted using MAKER. Population genetic analysis reveals two distinct populations from Guyana and Venezuela. We also carried out site-frequency spectrum analysis of the two populations to reveal population divergence history. A sliding-window approach was used to reveal genetic diversity, linkage disequilibrium and signatures of selection across the genomes. These resources will also be used for in situ and ex situ breeding management and population monitoring and to verify genetic purity of any birds selected as founders for conservation breeding. Additionally, this work provides important opportunities for comparative genomics that may yield valuable insights for conservation of other endangered and highly bottlenecked species.

10:30 - 11:00 Break

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