Dataset Information

A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae).

ABSTRACT: The increased availability of large phylogenomic datasets is often accompanied by difficulties in disentangling and harnessing the data. These difficulties may be enhanced for species resulting from reticulate evolution and/or rapid radiations producing large-scale discordance. As a result, there is a need for methods to investigate discordance, and in turn, use this conflict to inform and aid in downstream analyses. Therefore, we drew upon multiple analytical tools to investigate the evolution of Micranthes (Saxifragaceae), a clade of primarily arctic-alpine herbs impacted by reticulate and rapid radiations. To elucidate the evolution of Micranthes we sought near-complete taxon sampling with multiple accessions per species and assembled extensive nuclear (518 putatively single copy loci) and plastid (95 loci) datasets. In addition to a robust phylogeny for Micranthes, this research shows that genetic discordance presents a valuable opportunity to develop hypotheses about its underlying causes, such as hybridization, polyploidization, and range shifts. Specifically, we present a multi-step approach that incorporates multiple checks points for paralogy, including reciprocally blasting targeted genes against transcriptomes, running paralogy checks during the assembly step, and grouping genes into gene families to look for duplications. We demonstrate that a thorough assessment of discordance can be a source of evidence for evolutionary processes that were not adequately captured by a bifurcating tree model, and helped to clarify processes that have structured the evolution of Micranthes.

SUBMITTER: Stubbs RL

PROVIDER: S-EPMC7020907 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade <i>Micranthes</i> (Saxifragaceae).

Stubbs Rebecca L RL Folk Ryan A RA Xiang Chun-Lei CL Chen Shichao S Soltis Douglas E DE Cellinese Nico N

Frontiers in plant science 20200207

The increased availability of large phylogenomic datasets is often accompanied by difficulties in disentangling and harnessing the data. These difficulties may be enhanced for species resulting from reticulate evolution and/or rapid radiations producing large-scale discordance. As a result, there is a need for methods to investigate discordance, and in turn, use this conflict to inform and aid in downstream analyses. Therefore, we drew upon multiple analytical tools to investigate the evolution ...[more]

PMID: 32117341

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Project description:Background and aimsThe Arctic tundra, with its extreme temperatures and short growing season, is evolutionarily young and harbours one of the most species-poor floras on Earth. Arctic species often show little phenotypic and genetic divergence across circumpolar ranges. However, strong intraspecific post-zygotic reproductive isolation (RI) in terms of hybrid sterility has frequently evolved within selfing Arctic species of the genus Draba. Here we assess whether incipient biological species are common in the Arctic flora.MethodsWe conducted an extensive crossing experiment including six species representing four phylogenetically distant families collected across the circumpolar Arctic. We crossed conspecific parental populations representing different spatial scales, raised 740 F1 hybrids to maturity and measured fertility under laboratory conditions. We examined genetic divergence between populations for two of these species (Cardamine bellidifolia and Ranunculus pygmaeus).Key resultsIn five of the six species, we find extensive reduction in pollen fertility and seed set in F1 hybrids; 219 (46 %) of the 477 F1 hybrids generated between parents separated by ≥427 km had <20 % pollen fertility. Isolation with migration (IM) and *BEAST analyses of sequences of eight nuclear genes in C. bellidifolia suggests that reproductively isolated populations of this species diverged during, or even after, the last glaciation. Likewise, Arctic populations of R. pygmaeus were genetically very similar despite exhibiting strongly reduced fertility in crosses, suggesting that RI evolved recently also in this species.ConclusionWe show that post-zygotic RI has developed multiple times within taxonomically recognized Arctic species belonging to several distantly related lineages, and that RI may have developed over just a few millennia. Rapid and widespread evolution of incipient biological species in the Arctic flora might be associated with frequent bottlenecks due to glacial cycles, and/or selfing mating systems, which are common in the harsh Arctic environment where pollinators are scarce.

Dataset Information

A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae).

Publications

A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade <i>Micranthes</i> (Saxifragaceae).

Similar Datasets

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