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Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two nonendemic outgroups, we report a revised phylogeny of this species flock and analyse evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into Baikal and demonstrate that several morphological features of Baikal amphipods, such as body armour and reduction in appendages and sensory organs, evolved in several lineages in parallel. Radiation of Baikal amphipods has been characterized by short phylogenetic branches and frequent episodes of positive selection which tended to be more frequent in the early phase of the second invasion of amphipods into Baikal when the most intensive diversification occurred. 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Other functional categories represented among genes likely to be under positive selection include Ca\u2010binding muscle\u2010related proteins, possibly indicating adaptation to Ca\u2010deficient low mineralization Baikal waters.<\/jats:p>","DOI":"10.1111\/mec.13927","type":"journal-article","created":{"date-parts":[[2016,11,17]],"date-time":"2016-11-17T14:52:49Z","timestamp":1479394369000},"page":"536-553","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":68,"title":["Transcriptome\u2010based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection"],"prefix":"10.1111","volume":"26","author":[{"given":"Sergey A.","family":"Naumenko","sequence":"first","affiliation":[{"name":"Belozersky Institute of Physico\u2010Chemical Biology Lomonosov Moscow State University Moscow Russia"},{"name":"Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia"},{"name":"Genetics and Genome Biology Program The Hospital For Sick Children Toronto ON Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria D.","family":"Logacheva","sequence":"additional","affiliation":[{"name":"Belozersky Institute of Physico\u2010Chemical Biology Lomonosov Moscow State University Moscow Russia"},{"name":"Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia"},{"name":"Pirogov Russian National Research Medical University Moscow Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nina V.","family":"Popova","sequence":"additional","affiliation":[{"name":"Belozersky Institute of Physico\u2010Chemical Biology Lomonosov Moscow State University Moscow Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna V.","family":"Klepikova","sequence":"additional","affiliation":[{"name":"Belozersky Institute of Physico\u2010Chemical Biology Lomonosov Moscow State University Moscow Russia"},{"name":"Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksey A.","family":"Penin","sequence":"additional","affiliation":[{"name":"Belozersky Institute of Physico\u2010Chemical Biology Lomonosov Moscow State University Moscow Russia"},{"name":"Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georgii A.","family":"Bazykin","sequence":"additional","affiliation":[{"name":"Belozersky Institute of Physico\u2010Chemical Biology Lomonosov Moscow State University Moscow Russia"},{"name":"Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia"},{"name":"Pirogov Russian National Research Medical University Moscow Russia"},{"name":"Skolkovo Institute of Science and Technology Skolkovo Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna E.","family":"Etingova","sequence":"additional","affiliation":[{"name":"Baikal Museum Irkutsk Research Center Russian Academy of Sciences Listvyanka, Irkutsk region Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8957-1931","authenticated-orcid":false,"given":"Nikolai S.","family":"Mugue","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Genetics Russian Institute for Fisheries and Oceanography (VNIRO) Moscow Russia"},{"name":"Laboratory of Experimental Embryology Koltsov Institute of Developmental Biology Moscow Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexey S.","family":"Kondrashov","sequence":"additional","affiliation":[{"name":"Belozersky Institute of Physico\u2010Chemical Biology Lomonosov Moscow State University Moscow Russia"},{"name":"Department of Ecology and Evolution University of Michigan Ann Arbor MI USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lev Y.","family":"Yampolsky","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences East Tennessee State University Johnson City TN USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2017,1,2]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10750-008-9555-1"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2332665100"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_2_6_5_1","unstructured":"AronestyE(2011)ea\u2010utils: command\u2010line tools for processing biological sequencing data. 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