Data from: Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers
Noguerales, Víctor, Institute for Game and Wildlife Research
Cordero, Pedro Javier, Institute for Game and Wildlife Research
Ortego, Joaquín, Estación Biológica de Doñana
Published Jan 31, 2018 on Dryad.
Cite this dataset
Noguerales, Víctor; Cordero, Pedro Javier; Ortego, Joaquín (2018). Data from: Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers [Dataset]. Dryad. https://doi.org/10.5061/dryad.3b04j
Although resolving phylogenetic relationships and establishing species limits is a primary goal of systematics, these tasks remain challenging at both conceptual and analytical levels. Here, we integrated genomic and phenotypic data and employed a comprehensive suite of coalescent-based analyses to develop and evaluate competing phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers (Chorthippus binotatus group) composed of two species and eight putative subspecies. To resolve the evolutionary relationships within this complex, we first evaluated alternative phylogenetic hypotheses arising from multiple schemes of genomic data processing and contrasted genetic-based inferences with different sources of phenotypic information. Second, we examined the importance of number of loci, demographic priors, number and kind of phenotypic characters, and sex-based trait variation for developing alternative species delimitation hypotheses. The best-supported topology was largely compatible with phenotypic data and showed the presence of two clades corresponding to the nominative species groups, one including three well-resolved lineages and the other comprising a four-lineage polytomy and a well-differentiated sister taxon. Integrative species delimitation analyses indicated that the number of employed loci had little impact on the obtained inferences but revealed the higher power provided by an increasing number of phenotypic characters and the usefulness of assessing their phylogenetic information-content and differences between sexes in among-taxa trait variation. Overall, our study highlights the importance of integrating multiple sources of information to test competing phylogenetic hypotheses and elucidate the evolutionary history of species complexes representing early-stages of divergence where conflicting inferences are more prone to appear.
Landmarks coordinates of pronota and forewing
This ZIP file includes the raw coordinates of the landmarks employed to characterize the shape variation of the forewing and pronota. Trait shape was characterized separately for each sex. The landmarks are stored in TPS format.
01_Landmarks_raw coordinates_Pronota and forewings.zip
SVDquartets and SNAPP input files
This ZIP file includes the different inputs files for SVDquartets and SNAPP to species tree estimation. For SVDquartets analyses, six SNP matrices were employed which were obtained by setting in PyRAD different values of clustering thresholds (Wclust = 0.85 and 0.90) and minimum taxon coverage in a given locus (minCov = 4, 10 and 20). SNAPP analyses were performed employing a SNP matrix generated using Wclust = 0.90 and minCov = 10.
02_SVDquartets-SNAPP input files.zip
BPP and iBPP input files
This ZIP file includes the genetic and morphological matrices that were used to perform the BPP and iBPP analyses.