Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: Analysis of nuclear RAG1 gene

Shedko, S. V.; Miroshnichenko, I. L.; Nemkova, G. A.

doi:10.1134/s1022795412050201

Cited by 36 publications

(31 citation statements)

References 20 publications

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“…Despite the broad confi dence interval of absolute time estimates of the stages of charr divergence, the data presented are comparable with the time estimates obtained using other genetic data, based on sequence analysis of certain nuclear and mitochondrial genes [32,55] and on the general ized data for the five mitochondrial genes [32]. It should be noted that the calculations in the works cited were made with several calibration points, along with more exact statistical methods allowing nonstrict con stancy of the molecular evolution rates in different lineages.…”

Section: Phylogenesis Of Charrs Of the Genus Salvelinussupporting

confidence: 80%

Phylogeny of charrs of the genus Salvelinus based on mitochondrial DNA data

2015

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Charrs of the genus Salvelinus (including Salvethymus) represent a monophyletic group of salmo nid fishes that diverged from the common ancestor without subdivision into subgenera. The phylogenesis of the genus is characterized by four cycles of mitochondrial genome divergence. The first one, belonging to the Late Miocene-the border between Miocene and Pliocene (6 to 4 million years ago)-was associated with the consecutive divergence of the S. fontinalis, S. namaycush, S. levanidovi, and S. leucomaenis basal branches. Two divergence events, including separation of the ancestral lineage of Western Pacific group of S. m. krascheninnikovi and the following segregation of the common ancestor into two mitochondrial phyla, happened within the period of 3 to 2 million years ago. The next cycle is attributed to the time interval of about 1 million years ago and includes the divergence of both phyla. In one phylum, a relatively quick isolation of Arctic and Eastern Pacific phylogroups, along with the divergence of the latter phylogroup into S. confluentus and S. m. lordi lineages, took place. At the same time, the second phylum diverged into the S. m. malma and S. alpinus phylogenetic groups. At the final stage (Middle to Late Pleistocene), differentiation of the taxa within the phylogenetic groups took place.

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Section: Phylogenesis Of Charrs Of the Genus Salvelinussupporting

confidence: 80%

Phylogeny of charrs of the genus Salvelinus based on mitochondrial DNA data

2015

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“…Two of these, the mammalian order Desmostylia entering during the Early Oligocene (Beatty, ; Ray, Domning, & McKenna, ) and the bear‐like amphicynodontid genus Kolponomos entering in the Late Oligocene (Tedford, Barnes, & Ray, ) are extinct. The other groups are still extant: sea lions and fur seals (Pinnipedimorpha), known first in the Late Oligocene (Poust & Boessenecker, ); the sea‐otter Enhydra , entering during the Pliocene (Willemsen, ); and Pacific salmon of the genus Oncorhynchus , whose freshwater ancestors first became partly marine in the Early Miocene (Crespi & Fulton, ; Crête‐Lafrenière, Weir, & Bernatchez, ; Shedko, Miroshnichenko, & Nemkova, ). It is likely that the Desmostylia and the sea otter entered from the Asian side, whereas pinnipeds, Kolponomos and Salmonidae almost certainly entered the North Pacific from North America.…”

Section: Terrestrial and Freshwater Sourcesmentioning

confidence: 99%

The coastal North Pacific: Origins and history of a dominant marine biota

Vermeij

Banker

Capece

et al. 2018

Journal of Biogeography

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Aims Some biogeographical regions act primarily as donors of colonists to other regions, while others act predominantly as recipient areas. How some biotas become dominant while others do not is a largely historical question that has received surprisingly little attention from biogeographers. Here, we seek to answer this question for the cold‐water North Pacific biota, which did not exist forty million years ago but which is now the principal donor biota outside the tropics. Location We focus on the cool‐temperate coastal North Pacific Ocean over the last 36.5 million years. Taxon We consider all multicellular taxa for which adequate fossil, phylogenetic and biogeographical data exist. Methods After placing North Pacific geographical events in the broader context of ocean gateways opening and closing elsewhere in the world, we discuss the history and factors affecting the planktonic and benthic productivity in the North Pacific based on a review and critical evaluation of the literature. A synthesis of primary sources was used to evaluate the origins and fates of North Pacific lineages, with special emphasis on movements to, within and from the North Pacific during the Cenozoic era. Results During the Late Eocene to earliest Miocene, the cooling North Pacific received colonists from adjacent warm‐water regions and the cold Southern Hemisphere, where temperate conditions had existed since at least the Cretaceous. From the Miocene onward, the North Pacific biota began to spread to the Southern Hemisphere and through Bering Strait to the Arctic and North Atlantic Oceans. Within the North Pacific, lineages during the early cooling phases spread predominantly from west to east, but in the Early Middle Miocene this pattern reversed, with later expansions going in both directions. An increase in productivity, powered by the evolution of highly productive seaweeds and by consumers with high metabolic rates, accompanied the transformation of the North Pacific from a recipient to donor biota. Main conclusions The North Pacific replaced the Southern Hemisphere temperate biota as the principal donor biota during the Miocene through a combination of increasing productivity, low magnitudes of extinction and intense competition and predation in an ocean basin with a long coastline.

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“…Based on molecular genetic data, knowledge of the phylogeny of the subfamily Salmoninae has been substantially widened (see reviews: Phillips & Oakley, ; Oakley & Phillips, ; Crespi & Fulton, ), and molecular dating of the main stages of the evolutionary history of salmonids (Salmonidae, Salmoniformes) including the time of whole genome duplication has been achieved (Osinov & Lebedev, ). Molecular dating estimates obtained by different authors (Osinov & Lebedev, ; Santini et al ., ; Crete‐Lafreniere et al ., ; Shedko et al ., , ; Campbell et al ., ; Macqueen & Johnston, ) show a certain correspondence when taking into account their errors and confidence intervals (see Table S1). Priors on times, which include fossil age information, have a strong effect on molecular clock estimates (Inoue, Donaghue & Yang, ), and this effect is one of the main causes of differences in the dating obtained by various authors for salmonids.…”

Section: Discussionmentioning

confidence: 99%

Speciation and genetic divergence of three species of charr from ancient Lake El'gygytgyn (Chukotka) and their phylogenetic relationships with other representatives of the genusSalvelinus

Osinov

Senchukova

Mugue

et al. 2015

Biol. J. Linn. Soc.

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The diversity of phenotypically different and often reproductively isolated lacustrine forms of charrs of the genus Salvelinus represents a substantial problem for taxonomists and evolutionary biologists. Based on the analysis of variability of ten microsatellite loci and two fragments of mitochondrial DNA (control region and cyt‐b gene), the evolutionary history of three charr species from Lake El'gygytgyn was reconstructed, and phylogenetic relationships between the main representatives of the genus were revealed. Three species from Lake El'gygytgyn were strongly reproductively isolated. Long‐finned charr described previously as Salvethymus svetovidovi, an ancient endemic form in the lake, originated 3.5 Mya (95% Bayesian credible intervals: 1.7, 6.1). Placement of this species in the phylogenetic tree of Salvelinus was not determined strictly, but it should be located in the basal part of the clade Salvelinus alpinus – S. malma species complex. The origin of small‐mouth charr S. elgyticus and Boganida charr S. boganidae in Lake El'gygytgyn was related to allopatric speciation. Their ancestors were represented by two glacial lineages of Taranets charr S. alpinus taranetzi from Asia. In Lake El'gygytgyn, these lineages entered into secondary contact postglacially. A revision of the main phylogenetic groups within the Salvelinus alpinus – S. malma complex is conducted. The Boganida charrs from Lakes El'gygytgyn and Lama (Taimyr) belong to different phylogenetic groups of Arctic charr and should not be regarded as a single species S. boganidae. Using the charrs from Lakes El'gygytgyn and Lama as a case study, we show that a model of sympatric speciation, which seemed more probable based on previous empirical evidence, was rejected by other data.

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Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: Analysis of nuclear RAG1 gene

Cited by 36 publications

References 20 publications

Phylogeny of charrs of the genus Salvelinus based on mitochondrial DNA data

Phylogeny of charrs of the genus Salvelinus based on mitochondrial DNA data

The coastal North Pacific: Origins and history of a dominant marine biota

Speciation and genetic divergence of three species of charr from ancient Lake El'gygytgyn (Chukotka) and their phylogenetic relationships with other representatives of the genusSalvelinus

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