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 visualizes multiple values of K. Given that the two genomic data sets are independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both of which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in the E. setacea and E. rehmannii complexes, with the E. ramosa complex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach. [Species delimitation; genotyping-by-sequencing; population structure; integrative taxonomy; cryptic species; Ehrharta (Poaceae).].

Species Selection Regime and Phylogenetic Tree Shape.

Species selection, the effect of heritable traits in generating between-lineage diversification rate differences, provides a valuable conceptual framework for understanding the relationship between traits, diversification, and phylogenetic tree shape. An important challenge, however, is that the nature of real diversification landscapes-curves or surfaces which describe the propensity of species-level lineages to diversify as a function of one or more traits-remains poorly understood. Here, we present a novel, time-stratified extension of the QuaSSE model in which speciation/extinction rate is specified as a static or temporally shifting Gaussian or skewed-Gaussian function of the diversification trait. We then use simulations to show that the generally imbalanced nature of real phylogenetic trees, as well as their generally greater than expected frequency of deep branching events, are typical outcomes when diversification is treated as a dynamic, trait-dependent process. Focusing on four basic models (Gaussian-speciation with and without background extinction; skewed-speciation; Gaussian-extinction), we also show that particular features of the species selection regime produce distinct tree shape signatures and that, consequently, a combination of tree shape metrics has the potential to reveal the species selection regime under which a particular lineage diversified. We evaluate this idea empirically by comparing the phylogenetic trees of plant lineages diversifying within climatically and geologically stable environments of the Greater Cape Floristic Region, with those of lineages diversifying in environments that have experienced major change through the Late Miocene-Pliocene. Consistent with our expectations, the trees of lineages diversifying in a dynamic context are less balanced, show a greater concentration of branching events close to the present, and display stronger diversification rate-trait correlations. We suggest that species selection plays an important role in shaping phylogenetic trees but recognize the need for an explicit probabilistic framework within which to assess the likelihoods of alternative diversification scenarios as explanations of a particular tree shape. [Cape flora; diversification landscape; environmental change; gamma statistic; species selection; time-stratified QuaSSE model; trait-dependent diversification; tree imbalance.].