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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6
Evolutionary Genomics

Room: Salon 3, Marriott Hotel

09:00 - 10:30

Moderator: Tom Gilbert, Natural History Museum of Denmark



6.1  09:10  Genomic analyses of diverse Hymenoptera shows retention of core meiotic genes across reproductive modes. Tvedte ES*, University of Iowa; Forbes AA, University of Iowa; Logsdon JM, University of Iowa

The parasitic wasp genus Diachasma (Hymenoptera: Braconidae: Opiinae) is a promising model for investigating the formation and evolutionary trajectories of new species. Native to North America, Diachasma attack Rhagoletis (Diptera: Tephritidae) flies; wasps lay eggs in fly larvae feeding inside fruit. Of particular interest, biodiversity in Diachasma has arisen as a consequence of the loss of sexual reproduction. The asexual wasp D. muliebre is geographically isolated from its sexual relatives D. alloeum and D. ferrugineum, and evidence suggests this species originated as a single loss-of-sex event 10,000YA-1MYA. New genome assemblies for Diachasma species permit the investigation of the breeding system of sexual vs. asexual wasps as an influence on lineage evolutionary trajectory. D. alloeum and D. ferrugineum possess a haplodiploid sexual system typical of hymenopteran insects. Asexual reproduction has been suggested in D. muliebre, where all documented individuals are female. Loss of sex in D. muliebre may have profound effects on the generation and maintenance of genetic variation and subsequent effects on adaptive potential. We evaluated whether asexual D. muliebre may have retained the mechanistic capacity for meiosis, a process essential for sexual reproduction. To gain insight into asexual wasp reproductive mechanisms, we surveyed meiosis genes in several diverse hymenopterans with newly available genome data to produce a meiosis gene "toolkit" of a typical hymenopteran insect. Additionally, we constructed de novo genome assemblies for Diachasma species, which were queried using meiosis toolkit genes, including eight that function specifically in meiosis. Seven of eight genes with meiosis-specific roles were found across a majority of surveyed species. Manual annotation of coding regions indicated an identical set of meiosis genes across Diachasma species. Moreover, we found no evidence of gene degradation via relaxed selection in D. muliebre, indicating these asexual wasps may have lost sex but maintain the capacity to engage in meiosis. Our results provide a framework for the study of transitions in reproductive strategies in Hymenoptera and other non-model organisms. Phylogenetic methods comparing meiosis-specific coding regions in Diachasma support topologies where sexuals and asexuals have no significant differences in evolutionary rates. Future work includes the examination of larger gene datasets, including neutrally-evolving regions such as introns, to assess whether there is a genome-wide change in evolutionary rate that accompanies sex loss in Diachasma.


6.2  09:30  Clade-specific mechanisms of genome and function evolution revealed by the Mus caroli and pahari genomes. Thybert D*, Earlham Institute, European Bioinformatic Institute; Roller M, European Bioinformatic Institute; Navarro F, Yale University; Janousek V, Prague University; Fiddes I, University of California Santa Cruz; Keane T, European Bioinformatic Institute, Sanger Institute; Odom D, Cancer Institute, University of Cambridge; Flicek P, European Bioinformatic Institute; Caroli-Pahari genome consortium ., .

Understanding the genomic mechanisms leading to lineage specific evolution is crucial if we want to understand how biodiversity is created. In mammals, the lack of sister clades with multiple high-quality genome assemblies has hindered quantitative comparisons of genome evolution required to understand the mechanisms driving lineage specific evolution. Here, we present chromosome level assemblies of Mus caroli and Mus pahari genomes, which, when combined with the Mus musculus and Rattus norvegicus genomes, are similar in phylogenetic structure and divergence times to the hominid (human-chimp-gorilla-orangutan). By comparing the evolutionary dynamics between the murids and hominids, we were able to unravel mechanisms involved in lineage specific genome evolution. Our analysis revealed that a punctuate event of chromosome reshuffling shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 to 6 MY. Our unique system of high quality genome assemblies enables high resolution studies of lineage specific repeat evolution and their functional consequences at the species level. For instance, we found that a species specific single nucleotide mutation transformed a SINE retrotransposon into a CTCF carrier, which expanded CTCF binding specifically in Mus caroli.


6.3  09:50  Interspecific differential expression of vision genes reveals patterns of adaptation in cave-adapted crayfish. Stern DB*, The George Washington University; Crandall KA, The George Washington University

A key to understanding the processes of speciation and adaptation is to be able to compare gene expression patterns in related species with morphological, physiological and/or behavioral differences. Interspecific differential expression analysis can uncover lineage specific and convergent gene expression patterns that both drive and are driven by these processes. In order to compare expression levels across multiple species, where there is no single reference transcriptome, one needs to be confident that gene-level comparisons are appropriate from an evolutionary perspective (i.e. by comparing homologous and orthologous sequences). Freshwater crayfish have evolved to live in caves multiple times, replicating the process of adaptation to an extreme environment with parallel losses of vision and pigmentation. Here we analyze RNA-seq data from five different species of freshwater crayfish, including two distantly related cave-adapted species, in order to identify candidate genes for vision loss and cave adaptation. Through identification of differentially expressed vision genes and other gene families and orthologs, we find key similarities implicated in the parallel loss of vision in cave species.


6.4  10:10  DEEPC: The deep, dark, genomic secrets of Ctenophores. DeBiasse M*, University of Florida Whitney Lab; Francis W, Ludwig Maximilians University Munich; Thuesen E, The Evergreen State College; Haddock S, Monterey Bay Aquarium Research Institute; Ryan J, University of Florida Whitney Lab

Over evolutionary timescales, many marine taxa have made transitions to and from the deep sea. Shallow and deep-sea habitats vary drastically in several parameters including light, temperature, oxygen concentration, pressure, and pH. Ctenophores, also called comb jellies due to their large ciliary paddles arranged in 'comb rows,' are monophyletic but deep and shallow species are spread across the ctenophore phylogeny, suggesting transitions from deep to shallow and from shallow to deep have occurred multiple times. To understand the evolutionary pressures that drive adaptation to extreme environments, we collected 35 ctenophore species with representatives from each major ctenophore lineage ranging from surface waters to 4000 meters deep. Our process involves sequencing and assembling transcriptomes, defining orthologs, estimating phylogenies, detecting positive selection, and identifying convergence in protein sequences. Using these data we are determining: (1) the phylogenetic relationships among these species, (2) the evolutionary lineages where depth transitions have occurred, and (3) the evolutionary genetic changes that have allowed species to adapt to shallow and deep sea habitats. This work uncovers a great mystery of how animals can adapt to extreme environments, and will provide a baseline of deep-sea ctenophore biodiversity, which will be important for understanding ecological change in the face of anthropogenic stressors.




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