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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17
Diversity Genomics

Room: Salon 3, Marriott Hotel

09:00 - 10:30

Moderator: Marie-Anne Van Sluys, USP - IB - Botanica



17.1  09:10  Incomplete lineage sorting and its evolutionary impacts on marsupial evolution. Feng SH*, Beijing Genomics Institute; Li C, Francis Crick Institute; Liu SP, Beijing Genomics Institute; Sears K, University of Illinois; Zhang GJ, Beijing Genomics Institute

Incomplete lineage sorting (ILS) and hybridization are the two major effects leading to incongruence between the species-level phylogenetic tree and individual gene trees. How to distinguish the phylogenetic signal contributed by ILS from the introgression caused by hybridization remains a challenge in systematic biology. The phylogeny of marsupial mammals, especially the origin of American marsupial monito del monte (Dromiciops gliroides), is still under debate because of potential impacts of ILS or ancient hybridization. To resolve the phylogenetic relationship between monito del monte and other marsupials and evaluate the contribution of ILS and hybridization to the marsupial evolution, we sequenced and assembled the whole genome of D. gliroides. Phylogenomic analyses with whole genome data of four representative marsupial species strongly support that monitor del monte split with all Australasian marsupials around 57 million years ago (MYA) when the rapid radiation occurred in the ancient marsupials. However, different from the whole genome phylogeny, we observed a large amount of local phylogenies (based on individual genes or genomic regions) grouping monito del monte together with one of Australian marsupials, indicating strong effect of ILS or hybridization in marsupial evolution. Our molecular analysis suggests that the divergence time of monito del monte and Australasian marsupials is much later than the coalescence time for the genomic regions with incongruent phylogenies compared to species-level phylogeny, indicating ILS rather than hybridization was the main evolutionary scenario. Our results further suggest that ILS is present in ~15% of the genome and scattered throughout the genome. The genes influenced by ILS exhibit a different evolutionary rate relative to other regions, and some of these genes likely play important roles in species-specific traits. Overall, the monito del monte genome offers new insights into understanding the evolutionary role of ILS in marsupial speciation.


17.2  09:30  The genome of Tethya wilhelma: an emerging early-branching metazoan model. Francis WR, Ludwig-Maximilians Universität München; Vargas S*, Ludwig-Maximilians Universität München; Eitel M, Ludwig-Maximilians Universität München; Erpenbeck D, Ludwig-Maximilians Universität München; Adamski M, Australian National University; Haddock S, Monterey Bay Aquarium Research Institute; Krebs S, Ludwig-Maximilians Universität München; Blum H, Ludwig-Maximilians Universität München; Wörheide G, Ludwig-Maximilians Universität München

An in vivo marine model system for arguably the most ancestral animal lineage, the sponges, has yet to be established but is thoroughly needed to address questions about the origin and early evolution of all animals. Using combination of pair-end sequencing and synthetic long-reads, our laboratory has sequenced to almost 150X coverage the 125Mb genome of the marine sponge Tethya wilhelma, a small, comparatively well-studied sponge that can be experimentally manipulated under laboratory conditions. In addition to the sponge genome, the genomes of two symbionts were completely sequenced. Here we report on the results of our (meta)genome sequencing effort to further establish T. wilhelma as a marine early-animal model organism, amenable for experimental manipulation. The T. wilhelma holobiont is capable of complex nutrient cycling but lacks important metabolic pathways involved in, for instance, oxygen sensing and circadian rhythms. Finally, a comparative genomic approach revealed several lineage specific expansions in different gene families.


17.3  09:50  Do Microbial to Animal Lateral Gene Transfers Promote BioDiversity? Werren JH*, University of Rochester

Lateral gene transfers (LGTs) of DNA from microbes to animals is a common feature of animal genomes. A key question is "How important are such transfers in the biological diversity of organisms?" There is growing evidence that such transfers can lead to acquisition of novel gene functions in animals relevant to biodiversity. In some circumstance, LGTs can play an important role in the ability of organisms to adapt to novel environments, and therefore contribute to niche expansion. Presented here is a review of lateral gene transfers, including basic methods of detection, the typical "life history" of an LGT, examples of LGTs contributing to adaptation, and their potential role as an significant contributor to biological diversity by promoting the ability of organisms to adapt to novel environments.


17.4  10:10  Empty Niches after Extinctions Increase Population Sizes of Modern Corals. Prada C*, Smithsonian Tropical Research Institute; Hanna B, The Pennsylvania State University; Budd AF, University of Iowa; Woodley CM, NOAA; Levitan D, Florida State University; Johnson K, Natural History Museum; Pandolfi J, University of Queensland; Knowlton N, Smithsonian Institution; DeGiorgio M, The Pennsylvania State University; Medina M, The Pennsylvania State University

Large environmental fluctuations often cause mass extinctions, extirpating species and transforming communities. While the effects on community structure are evident in the fossil record, demographic consequences for populations of individual species are harder to evaluate because fossils reveal relative but not absolute abundances. However, genomic analyses of living species that have survived a mass extinction event offer the potential for understanding the demographic effects of such environmental fluctuations on extant species. Here we show how environmental variation since the Pliocene has shaped demographic changes in extant corals of the genus Orbicella, major extant reef builders in the Caribbean that today are endangered. We use genomic approaches to estimate previously unknown current and past population sizes over the last 3 million years (Ma). Populations of all three Orbicella declined around 2-1 million years ago, coincident with the extinction of at least 50% of Caribbean coral species. The estimated changes in population size are consistent across the three species despite their ecological differences. Subsequently, two shallow-water specialists expanded their population sizes at least two fold, over a time that overlaps with the disappearance of their sister competitor species O. nancyi (the organ-pipe Orbicella). Our study suggests that populations of Orbicella species are capable of rebounding from reductions in population size under suitable conditions and that the effective population size of modern corals provides rich standing genetic variation for corals to adapt to climate change. For conservation genetics our study suggests the need to evaluate genetic variation under appropriate demographic models.




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