Karchner Sibel I.

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Karchner
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Sibel I.
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Subject: Comparative genomics ×

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The landscape of extreme genomic variation in the highly adaptable Atlantic killifish

2017-03-01 , Reid, Noah M. , Jackson, Craig E. , Gilbert, Don , Minx, Patrick , Montague, Michael J. , Hampton, Thomas H. , Helfrich, Lily W. , King, Benjamin L. , Nacci, Diane E. , Aluru, Neelakanteswar , Karchner, Sibel I. , Colbourne, John K. , Hahn, Mark E. , Shaw, Joseph R. , Oleksiak, Marjorie F. , Crawford, Douglas L. , Warren, Wesley C. , Whitehead, Andrew

Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments.

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The African coelacanth genome provides insights into tetrapod evolution

2013-04-17 , Amemiya, Chris T. , Alfoldi, Jessica , Lee, Alison P. , Fan, Shaohua , Philippe, Herve , MacCallum, Iain , Braasch, Ingo , Manousaki, Tereza , Schneider, Igor , Rohner, Nicolas , Organ, Chris , Chalopin, Domitille , Smith, Jeramiah J. , Robinson, Mark , Dorrington, Rosemary A. , Gerdol, Marco , Aken, Bronwen , Assunta Biscotti, Maria , Barucca, Marco , Baurain, Denis , Berlin, Aaron M. , Blatch, Gregory L. , Buonocore, Francesco , Burmester, Thorsten , Campbell, Michael S. , Canapa, Adriana , Cannon, John P. , Christoffels, Alan , De Moro, Gianluca , Edkins, Adrienne L. , Fan, Lin , Fausto, Anna Maria , Feiner, Nathalie , Forconi, Mariko , Gamieldien, Junaid , Gnerre, Sante , Gnirke, Andreas , Goldstone, Jared V. , Haerty, Wilfried , Hahn, Mark E. , Hesse, Uljana , Hoffmann, Steve , Johnson, Jeremy , Karchner, Sibel I. , Kuraku, Shigehiro , Lara, Marcia , Levin, Joshua Z. , Litman, Gary W. , Mauceli, Evan , Miyake, Tsutomu , Mueller, M. Gail , Nelson, David R. , Nitsche, Anne , Olmo, Ettore , Ota, Tatsuya , Pallavicini, Alberto , Panji, Sumir , Picone, Barbara , Ponting, Chris P. , Prohaska, Sonja J. , Przybylski, Dariusz , Ratan Saha, Nil , Ravi, Vydianathan , Ribeiro, Filipe J. , Sauka-Spengler, Tatjana , Scapigliati, Giuseppe , Searle, Stephen M. J. , Sharpe, Ted , Simakov, Oleg , Stadler, Peter F. , Stegeman, John J. , Sumiyama, Kenta , Tabbaa, Diana , Tafer, Hakim , Turner-Maier, Jason , van Heusden, Peter , White, Simon , Williams, Louise , Yandell, Mark , Brinkmann, Henner , Volff, Jean-Nicolas , Tabin, Clifford J. , Shubin, Neil , Schartl, Manfred , Jaffe, David B. , Postlethwait, John H. , Venkatesh, Byrappa , Di Palma, Federica , Lander, Eric S. , Meyer, Axel , Lindblad-Toh, Kerstin

The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.

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