Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing

Lecaudey, Laurène Alicia; Schliewen, Ulrich K.; Osinov, A. G.; Taylor, Eric B.; Bernatchez, Louis; Weiss, Steven

doi:10.1016/j.ympev.2018.02.022

Cited by 78 publications

(100 citation statements)

References 104 publications

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“…Complex genomes that have experienced past hybridisation may contribute to rapid adaptive radiation, as established in cichlids from African Great lakes (Irisarri et al., ; Meier et al., ). Ancient introgressions have also been detected in Arctic charr ( Salvelinus ; Lecaudey et al., ), which are classic examples of sympatric divergence in high latitudes (Alekseyev et al., ; Hindar & Jonsson, ; Knudsen, Klemetsen, Amundsen, & Hermansen, ; Taylor, ). Application of advanced molecular technologies to investigations of hexaploids can contribute deeper insights into the evolutionary history of Labeobarbus (Stobie, Oosthuizen, Cunningham, & Bloomer, ).…”

Section: Discussionmentioning

confidence: 99%

Adaptive radiation of barbs of the genusLabeobarbus(Cyprinidae) in an East African river

et al. 2019

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Large African barbs of the genus Labeobarbus constitute a hexaploid lineage (2n = 150). This group is widely distributed in African freshwaters, and exhibits profound phenotypic variation that could be a prerequisite for adaptive radiation. Using morphological, molecular, and stable isotope analyses, we investigated whether an adaptive radiation has occurred in a riverine assemblage of the Labeobarbus gananensis complex. This complex is composed of six phenotypically distinct sympatric forms inhabiting the Genale River (Ethiopian highlands, East Africa) in the Juba and Wabe–Shebelle drainages (Indian Ocean basin). Of the six forms, five were divergent in their mouth morphology, corresponding to generalised, lipped, scraping (two forms), and large‐mouthed phenotypes. One form had no mouth specialisation, but differed from the others in body shape (short and deep body; short form). Stable isotope analysis revealed differences in 15N among these forms, representing different foraging strategies (omnivorous, scraping, and piscivorous). Phylogenetic analysis of two mitochondrial DNA markers confirmed the monophyly of L. gananensis, suggesting an intra‐riverine radiation. However, the Genale assemblage appears to have originated through a combination of allopatric and sympatric events. Some of the specialised forms within the Juba and Wabe–Shebelle drainage originated independently from the local generalised forms in three different river regions. Each of these cases could be considered as a small species flock composed of two or three sympatric forms. Our study shows that adaptive radiation in rivers can be enhanced by a combination of sympatric speciation and temporal geographic isolation, leading to local sympatric speciation followed by migration.

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Section: Discussionmentioning

confidence: 99%

Adaptive radiation of barbs of the genusLabeobarbus(Cyprinidae) in an East African river

et al. 2019

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“…Arctic charr sampling. Fish were sampled from nine Scottish lakes (Atlantic lineage) and nine Transbaikalian lakes (Siberian lineage) (Lecaudey et al 2018), between 1995 and 2015 using standard gill nets (Fig.1a). The sampled lake populations (we refer to all individuals within a lake as a population) contained different numbers and combinations of ecotypes (we refer to trophic specialists as ecotypes).…”

Section: Methodsmentioning

confidence: 99%

“…These ecotypes can be found in several Arctic charr lineages (Jonsson & Jonsson 2001;Alekseyev et al 2002), but are most frequent in the Atlantic and Siberian lineages, which most likely diverged before the last glacial maximum during the Pleistocene (Lecaudey et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Convergence in form and function overcomes non-parallel evolutionary histories in a Holarctic fish

Jacobs

Carruthers

Yurchenko

et al. 2018

Preprint

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AbstractUnderstanding the extent to which evolution is predictable under multifarious selection is a longstanding question in evolutionary biology. However, the interplay of stochastic and contingent factors influencing the extent of parallelism in nature is not well understood. To test the predictability of evolution, we studied a ‘natural experiment’ on different organismal levels across lakes and evolutionary lineages of a freshwater salmonid fish, Arctic charr (Salvelinus alpinus). We identified significant phenotypic parallelism between Arctic charr ecotype pairs within a continuum of parallel evolution and highly parallel adaptive morphological traits. Variability in phenotypic predictability was explained by complex demographic histories, differing genomic backgrounds and genomic responses to selection, variable genetic associations with ecotype, and environmental variation. Remarkably, gene expression was highly similar across ecotype replicates, and explained the observed parallelism continuum. Our findings suggest that parallel evolution by non-parallel evolutionary routes is possible when the regulatory molecular phenotype compensates for divergent histories.

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“…Indeed, much of our understanding of gene flow and population genetic patterns in fluvial systems comes from studies of fish and aquatic insects (e.g. Faulks, Gilligan, & Beheregaray, ; Finn & Adler, ; Finn, Blouin, & Lytle, ; Fluker, Kuhajda, & Harris, ; Fluker, Kuhajda, Lang, & Harris, ; Kang, Ma, & He, ; Lecaudey, Schliewn, Osinov, Taylor, Bernatchez, Schliewn, & Osinov, ; Robinson, Simmons, Williams, & Moyer, ; Stobie, Oosthuizen, Cunningham, & Bloomer, ). Moreover, hypotheses that predict diversity patterns across riverine landscapes have been mostly developed with data on freshwater insects and fish (reviewed by Davis et al, ; Hughes et al, ).…”

Section: Introductionmentioning

confidence: 99%

Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla

et al. 2019

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Within riverine systems, headwater populations are hypothesized to harbour higher amounts of genetic distinctiveness than populations in the main stem of a river and display increased genetic diversity in large, downstream habitats. However, these hypotheses were mostly developed with insects and fish, and they have not been tested on many invertebrate lineages. Pleuroceridae gastropods are of particular ecological importance to rivers of eastern North America, sometimes comprising over 90% of macroinvertebrate biomass. Yet, virtually nothing is known of pleurocerid landscape genetics, including whether genetic diversity follows predictions made by hypotheses developed on more mobile species. Moreover, the commonly repeated hypothesis that intraspecific morphological variation in gastropods results from ecophenotypic plasticity has not been well tested on pleurocerids. Using 2bRAD‐seq to discover single nucleotide polymorphisms, we show that the threatened, Cahaba River endemic pleurocerid, Leptoxis ampla, has limited gene flow among populations and that migration is downstream‐biased, conflicting with previous hypotheses. Both tributary and main stem populations harbour unique genomic profiles, and genetic diversity was highest in downstream populations. Furthermore, L. ampla shell morphology was more correlated with genetic differences among individuals and populations than habitat characteristics. We anticipate similar genetic and demographic patterns to be seen in other pleurocerids, and hypotheses about gene flow and population demographics that were based on more mobile taxa often, but not always, apply to freshwater gastropods. From a conservation standpoint, genetic structure of L. ampla populations suggests distinctive genetic diversity is lost with localized extirpation, a phenomenon common across the range of Pleuroceridae.

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Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing

Cited by 78 publications

References 104 publications

Adaptive radiation of barbs of the genusLabeobarbus(Cyprinidae) in an East African river

Adaptive radiation of barbs of the genusLabeobarbus(Cyprinidae) in an East African river

Convergence in form and function overcomes non-parallel evolutionary histories in a Holarctic fish

Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla

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