Consilience across multiple, independent genomic data sets reveals species in a complex with limited phenotypic variation

Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genus Ehrharta, whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree of Ehrharta and to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualises multiple valu..., Please see the README document (\"README_.txt\"), the supplementary methods (SUPPLEMENTARY METHODS & FIGURES.docx) and the accompanying article:  Wootton, L.M., Forest, F., Verboom, G.A., 2022. Consilience across multiple, independent genomic data sets reveals species in a complex with limited phenotypic variation.,