title: Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection.
abstract: Endemic species flocks inhabiting ancient lakes, oceanic islands and other long-lived isolated habitats are often interpreted as adaptive radiations. 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. Notably, signatures of positive selection are frequent in genes encoding mitochondrial membrane proteins with electron transfer chain and ATP synthesis functionality. In particular, subunits of both the membrane and substrate-level ATP synthases show evidence of positive selection in the plankton species Macrohectopus branickii, possibly indicating adaptation to active plankton lifestyle and to survival under conditions of low temperature and high hydrostatic pressures known to affect membranes functioning. Other functional categories represented among genes likely to be under positive selection include Ca-binding muscle-related proteins, possibly indicating adaptation to Ca-deficient low mineralization Baikal waters.
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.|Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia.|Genetics and Genome Biology Program, The Hospital For Sick Children, Toronto, ON, Canada.
authors.forename: Sergey A
authors.initials: SA
authors.lastname: Naumenko
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.|Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia.|Pirogov Russian National Research Medical University, Moscow, Russia.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Logacheva
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Nina V
authors.initials: NV
authors.lastname: Popova
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.|Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Klepikova
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.|Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia.
authors.forename: Aleksey A
authors.initials: AA
authors.lastname: Penin
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.|Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia.|Pirogov Russian National Research Medical University, Moscow, Russia.|Skolkovo Institute of Science and Technology, Skolkovo, Russia.
authors.forename: Georgii A
authors.initials: GA
authors.lastname: Bazykin
authors.affiliation: Baikal Museum, Irkutsk Research Center, Russian Academy of Sciences, Listvyanka, Irkutsk region, Russia.
authors.forename: Anna E
authors.initials: AE
authors.lastname: Etingova
authors.affiliation: Laboratory of Molecular Genetics, Russian Institute for Fisheries and Oceanography (VNIRO), Moscow, Russia.|Laboratory of Experimental Embryology, Koltsov Institute of Developmental Biology, Moscow, Russia.
authors.forename: Nikolai S
authors.identifier: http://orcid.org/0000-0001-8957-1931
authors.initials: NS
authors.lastname: Mugue
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.|Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Alexey S
authors.initials: AS
authors.lastname: Kondrashov
authors.affiliation: Department of Biological Sciences, East Tennessee State University, Johnson City, TN, USA.
authors.forename: Lev Y
authors.initials: LY
authors.lastname: Yampolsky
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D033304:Amphipoda / Q000145:classification*; D000818:Animals; D049810:Genetic Speciation; D060106:Lakes; D010802:Phylogeny; D012641:Selection, Genetic; D012800:Siberia; D059467:Transcriptome
keywords: adaptive radiation; ancient lakes; directional selection; ecological opportunity