2017
DOI: 10.1016/j.ympev.2017.06.012
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Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study

Abstract: Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic DNA markers, which have been widely used, notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies. However, with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation, phylogenies of closely related species have been resolved at a much higher detail in the last coupl… Show more

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Cited by 23 publications
(53 citation statements)
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“…Hence, the maintenance of ghost mitochondrial lineages can create mirages of cryptic species (Hinojosa et al, ), but at the same time mitochondrial capture and replacement may conceal genuine evolutionary divergences (Dufresnes, Mazepa, et al, ). Because these two phenomena might be more common than previously assumed (Dufresnes, Mazepa, et al, ), we recommend that taxonomic revisions involving taxa from refugial areas should be based on genomic evidence to make decisions on species‐level divergence (Suchan et al, ).…”
Section: Discussionmentioning
confidence: 99%
“…Hence, the maintenance of ghost mitochondrial lineages can create mirages of cryptic species (Hinojosa et al, ), but at the same time mitochondrial capture and replacement may conceal genuine evolutionary divergences (Dufresnes, Mazepa, et al, ). Because these two phenomena might be more common than previously assumed (Dufresnes, Mazepa, et al, ), we recommend that taxonomic revisions involving taxa from refugial areas should be based on genomic evidence to make decisions on species‐level divergence (Suchan et al, ).…”
Section: Discussionmentioning
confidence: 99%
“…Species with high levels of introgression are supposed to show close overall relatedness and intermixing of species in recently introgressed genes (Eaton et al., ). Historical or ongoing introgression often revealed by discordant patterns between mitochondrial and nuclear phylogenies (Linnen & Farrell, ; Papakostas et al., ; Suchan et al., ). Unlike the mitochondrial phylogeny, the nDNA phylogeny showed a clear distinction between the target species and did not support the idea of introgression at the genomic level in either Alopecosa or Pardosa .…”
Section: Discussionmentioning
confidence: 99%
“…Tests on real data were performed on ddRAD reads previously obtained for the phylogenetic study of seed parasitic pollinators from the genus Chiastocheta (Diptera: Anthomyiidae). The dataset corresponds to reads from 259 individuals sampled from 51 European populations generated by Lausanne University, Switzerland [19] (data soon available on zenodo.org). Quality scores of reads 2 (average base quality over reads and across samples of 33.98 sd 1.78) were lower than those of reads 1 (average base quality over reads and across samples of 35.15 sd 1.70), which led us to focus the analyses on reads 1.…”
Section: Application To Real Data From Chiastocheta Speciesmentioning
confidence: 99%
“…This latter treatment of predictions is considered as the default process of DiscoSnp-RAD outputs. Then, classical filters were applied to follow as much as possible the filters used in the Suchan et al [19]: a minimum genotype coverage of 6, a minimal minor allele frequency of 0.02 and a minimum of 20 samples with a non missing genotype for each variant. These filters remove less informative variants or alleles specific to a small subset of samples.…”
Section: Application To Real Data From Chiastocheta Speciesmentioning
confidence: 99%