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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Functional Genomics

Room: Salon 2, Marriott Hotel

11:00 - 12:50

Moderator: Bridgett VonHoldt, Princeton University

19.1  11:10  Coupling transcriptomics with hormone manipulations to discover the molecular mechanisms underlying aphid phenotypic plasticity. Brisson JA*, University of Rochester; Vellichirammal NN, University of Nebraska

Phenotypic plasticity is a key life history strategy used by organisms living in heterogeneous environments to produce a variety of morphological forms. A multitude of studies have investigated the costs and limits of plasticity, as well as the conditions under which it evolves. Much less well understood are the molecular genetic mechanisms that enable an organism to sense its environment and respond in a plastic manner. The pea aphid wing polyphenism is a compelling laboratory model to study these mechanisms. In this polyphenism, environmental stressors like high density cause asexual, viviparous adult female aphids to change the development of their embryos from wingless to winged morphs. Here we describe how analysis of genome-level transcriptome differences between aphids producing winged or wingless offspring implicated the importance of the hormone ecdysone. As predicted by that study, we found that injection of ecdysone or its analog caused a decreased production of winged offspring, while knockdown of the ecdysone receptor using RNAi or treatment with an ecdysone receptor antagonist resulted in an increased production of winged offspring. Our results show that an environmentally regulated maternal hormone can mediate phenotype production in the next generation and thus provide significant insight into the molecular mechanisms underlying the production of alternative, adaptive morphologies.

19.2  11:30  Genomics of Adaptation. Antunes A*, University of Porto

The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently thousand of species are having their genomes completely sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic and adaptive traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles. The findings pinpoint unique molecular products of critical relevance in species evolution, diversification and conservation, but also highlight genomic novelties of importance for environmental and biomedical research.

19.3  11:50  Origin and evolution of developmental enhancers in the mammalian neocortex . Emera D*, Yale University School of Medicine; Yin J, Yale University School of Medicine; Reilly SK, Yale University School of Medicine; Gockley J, Yale University School of Medicine; Noonan JP, Yale University School of Medicine

Morphological innovations such as the neocortex may involve the evolution of novel regulatory sequences. However, de novo birth of developmental regulatory elements has not been extensively studied in mammals. Here, we infer the phylogenetic origins of H3K27ac-defined enhancers active during mammalian corticogenesis and find that ~20% arose in the mammalian stem lineage, coincident with the emergence of the neocortex. Pathway enrichment and gene co-expression analyses indicate that mammal-specific enhancers are overrepresented near genes involved in cell migration and axon guidance, notably ephrin and semaphorin signaling. In contrast to previous studies, we find that most neocortical enhancers did not originate by en bloc exaptation of transposons. Instead, our results evoke a model of the enhancer life cycle in which enhancers emerge as short, weakly constrained 'proto-enhancers'. Proto-enhancers that survive likely undergo substantial modification, including accretion of derived sequences. Our results provide insight into the biological processes underlying neocortical origins and the mechanisms of regulatory innovation in mammals.

19.4  12:10  Establishing baselines for phytoplankton in the world oceans. Hoadley K.D*, MBARI; Worden A.Z, MBARI

Nearly half of global primary production occurs in the marine biosphere. The microbial eukaryotic algae that perform photosynthesis in marine environments come from diverse Supergroups and deep- branching lineages are still being discovered. Here we discuss high-throughput amplicon sequencing efforts to establish baseline information on the diversity and composition of phytoplankton communities in the world oceans. These diversity analyses are combined with experimentally derived analysis of key model systems, including the ecologically important and globally distributed model green algal species (Micromonas sp). Using continuous culture environmental incubation chambers, we seek to better understand their capacities to adapt or acclimate to future ocean conditions by merging the observed physiological responses with the underlying transcriptional and proteomic changes. Hence, comparative genomics and model systems studies are being combined with field research to gain a more predictive understanding of physiological responses to natural and anthropogenic perturbations. Collectively, we and others in the microbial oceanography community, aim to establish a baseline against which future changes in microbial community structure and function can be assessed.

19.5  12:30  Lizards and snakes as a model to study sex determination and sex chromosome evolution. Gamble T*, Marquette University

Sex chromosomes play a significant role in many biological processes including speciation, genetic conflict, sexual dimorphism, and perhaps most importantly, the developmental process of sex determination. However, sex chromosomes remain one of the most poorly studied regions of the genome and most of our knowledge concerning sex chromosome structure and evolution has been derived from studying just a handful of model species. Expanding studies of sex chromosome evolution to include additional clades, particularly clades with repeated transitions among sex chromosome systems, will facilitate the study of sex determination and sex chromosome evolution. Indeed, studying sex chromosomes in a wider array of taxa will help to distinguish the general principles of sex chromosome evolution from patterns unique to specific lineages. Squamates, the lizards and snakes, are well suited for this task as they possess numerous transitions among sex chromosome systems at a variety of evolutionary time scales. However, most squamate species lack readily diagnosable sex chromosomes, which has hindered their use as a model clade. I will discuss recent advances that use high throughput sequencing data to identify sex chromosome systems (XY or ZW) in species with cryptic, homomorphic sex chromosomes. I will also discuss of how whole genome sequencing has accelerated the pace of sex chromosome discovery using snake and gecko examples. Finally, I will argue that greater knowledge about squamate genomes will enhance their utility as a model clade as well as improve our understanding of the origins and evolution of sex chromosomes and sex-determining systems.

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