Integrative species delimitation in practice: Revealing cryptic lineages within the short-nosed skink Plestiodon brevirostris (Squamata: Scincidae).

Integrative taxonomy has been generally considered as a goal in systematics for more than a decade. Here, we employed environmental, molecular, and morphological data to evaluate the species boundaries within the short-nosed skink Plestiodon brevirostris from south-central Mexico, one member of the morphologically conservative P. brevirostris group. Our molecular dataset includes one mitochondrial and two nuclear loci. The mitochondrial fragment includes the full length of the gene coding for the NADH dehydrogenase subunit 1 protein, a segment of the gene coding for 16S ribosomal RNA, and flanking tRNAs. The nuclear dataset includes fragments of the genes coding for the megakaryoblastic leukemia 1 and RNA fingerprint 35 proteins. We employed phylogenetic reconstruction, analyses of population structure and morphological variation, and species delimitation methods (including the integration of the three kinds of data in a unified probabilistic framework) to evaluate species limits. Our results suggest that P. brevirostris represents four distinct species. The information provided by each kind of data allowed us to discern between alternative explanations for the observed patterns of geographic structure. Two of the newly recognized lineages are poorly differentiated morphologically but apparently differ in environmental preferences and are allopatric. Additionally, one lineage is microendemic and parapatric with respect to another one. Moreover, our phylogenetic analyses suggest that other taxa within the P. brevirostris group may represent species complexes. We discuss our results in the context of integrative species delimitation.

Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae).

The New World avian family Polioptilidae (gnatcatchers and gnatwrens) is distributed from Argentina to Canada and includes 15 species and more than 60 subspecies. No study to date has evaluated phylogenetic relationships within this family and the historical pattern of diversification within the group remains unknown. Moreover, species limits, particularly in widespread taxa that show geographic variation, remain unclear. In this study, we delimited species and estimated phylogenetic relationships using multilocus data for the entire family. We then used the inferred diversity along with alternative taxonomic classification schemes to evaluate how lumping and splitting of both taxa and geographical areas influenced biogeographic inference. Species-tree analyses grouped Polioptilidae into four main clades: Microbates, Ramphocaenus, a Polioptila guianensis complex, and the remaining members of Polioptila. Ramphocaenus melanurus was sister to the clade containing M. cinereiventris and M. collaris, which formed a clade sister to all species within Polioptila. Polioptila was composed of two clades, the first of which included the P. guianensis complex; the other contained all remaining species in the genus. Using multispecies coalescent modeling, we inferred a more than 3-fold increase in species diversity, of which 87% represent currently recognized species or subspecies. Much of this diversity corresponded to subspecies that occur in the Neotropics. We identified three polyphyletic species, and delimited 4-6 previously undescribed candidate taxa. Probabilistic modeling of geographic ranges on the species tree indicated that the family likely had an ancestral origin in South America, with all three genera independently colonizing North America. Support for this hypothesis, however, was sensitive to the taxonomic classification scheme used and the number of geographical areas allowed. Our study proposes the first phylogenetic hypothesis for Polioptilidae and provides genealogical support for the reclassification of species limits. Species limits and the resolution of geographical areas that taxa inhabit influence the inferred spatial diversification history.

A multilocus phylogeny of a major New World avian radiation: the Vireonidae.

The family Vireonidae represents one of the most widespread and well-known New World avian radiations, but a robust species-level phylogeny of the group is lacking. Here, we infer a phylogeny of Vireonidae using multilocus data obtained from 221 individuals from 46 of 52 vireonid species (representing all four genera) and five "core Corvoidea" outgroups. Our results show Vireonidae to be monophyletic, consistent with a single colonization of the New World by an Asian ancestor. Cyclarhis and Vireolanius are monophyletic genera that diverged early from the rest of Vireonidae. Hylophilus is polyphyletic, represented by three distinct clades concordant with differences in morphology, habitat, and voice. The poorly known South American species Hylophilus sclateri is embedded within the genus Vireo. Vireo, in turn, consists of several well-supported intrageneric clades. Overall, tropical vireonid species show much higher levels of intraspecific genetic structure than temperate species and several currently recognized species are probably comprised of multiple cryptic species.

A comprehensive multilocus assessment of sparrow (Aves: Passerellidae) relationships.

The New World sparrows (Emberizidae) are among the best known of songbird groups and have long-been recognized as one of the prominent components of the New World nine-primaried oscine assemblage. Despite receiving much attention from taxonomists over the years, and only recently using molecular methods, was a "core" sparrow clade established allowing the reconstruction of a phylogenetic hypothesis that includes the full sampling of sparrow species diversity. In this paper, we use mitochondrial DNA gene sequences from all 129 putative species of sparrow and four additional (nuclear) loci for a subset of these taxa to resolve both generic and species level relationships. Hypotheses derived from our mitochondrial (2184 base pairs) and nuclear (5705 base pairs) DNA data sets were generally in agreement with respect to clade constituency but differed somewhat with respect to among-clade relationships. Sparrow diversity is defined predominantly by eight well-supported clades that indicate a lack of monophyly for at least three currently recognized genera. Ammodramus is polyphyletic and requires the naming of two additional genera. Spizella is also polyphyletic with Tree Sparrow (Spizella arborea) as a taxonomic "outlier". Pselliophorus is embedded within a larger Atlapetes assemblage and should be merged with that group. This new hypothesis of sparrow relationships will form the basis for future comparative analyses of variation within songbirds.

Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape.

The widespread montane Mexican horned lizard Phrynosoma orbiculare (Squamata: Phrynosomatidae) represents an ideal species to investigate the relative impacts of Neogene vicariance and Quaternary climate change on lineage diversification across the Mexican highlands. We used mitochondrial DNA to examine the maternal history of P. orbiculare and estimate the timing and tempo of lineage diversification. Based on our results, we inferred 11 geographically structured, well supported mitochondrial lineages within this species, suggesting P. orbiculare represents a species complex. Six divergences between lineages likely occurred during the Late Miocene and Pliocene, and four splits probably happened during the Pleistocene. Diversification rate appeared relatively constant through time. Spatial and temporal divergences between lineages of P. orbiculare and co-distributed taxa suggest that a distinct period of uplifting of the Transvolcanic Belt around 7.5-3 million years ago broadly impacted diversification in taxa associated with this mountain range. To the north, several river drainages acting as filter barriers differentially subdivided co-distributed highland taxa through time. Diversification patterns observed in P. orbiculare provide additional insight into the mechanisms that impacted differentiation of highland taxa across the complex Mexican highlands.

A phylogeny of the Lampropeltis mexicana complex (Serpentes: Colubridae) based on mitochondrial DNA sequences suggests evidence for species-level polyphyly within Lampropeltis.

The systematic relationships of snakes in the Lampropeltis mexicana complex (L. mexicana, L. alterna, and L. ruthveni) are poorly known despite several taxonomic studies over the last 80 years. Mitochondrial DNA sequences were used to infer the phylogeny of the L. mexicana complex. At least one representative sample from the nine currently recognized species of Lampropeltis was sequenced. Our results suggest that a deep basal split resulted in the divergence of two groups of Lampropeltis, with one group occupying the upland areas of western United States and most of western and central Mexico, and the other northeastern Mexico and the lowland areas of the southern United States. Results also revealed that the L. mexicana complex and Lampropeltis triangulum are polyphyletic, with taxa from both groups nested together in deeply divergent northern and southern clades. These results are incongruent with previous hypotheses of phylogenetic relationships based on morphology, and suggest that morphological characters shared among the various tri-colored Lampropeltis (e.g., hemipenal structure and tri-colored pattern) may be difficult to interpret phylogenetically.