The Mexican Sheartail (Doricha eliza), an endangered hummingbird, is endemic to Mexico where two populations have a disjunct distribution. One population is distributed along the northern tip of the Yucatan Peninsula whereas the other is mostly restricted to central Veracruz. Despite their disjunct distribution, previous work has failed to detect morphological or behavioral differences between these populations. Here we use variation in morphology, mtDNA and nuDNA sequences to determine the degree of morphological and molecular divergence between populations, their divergence time, and historical demography. We use species distribution modeling and niche divergence tests to infer the relative roles of vicariance and dispersal in driving divergence in the genus. Our Bayesian and maximum likelihood phylogenetic analyses revealed that Doricha eliza populations form a monophyletic clade and support their sister relationship with D. enicura. We found marked genetic differentiation, with reciprocal monophyly of haplotypes and highly restricted gene flow, supporting a history of isolation over the last 120,000 years. Genetic divergence between populations is consistent with the lack of overlap in environmental space and slight morphological differences between males. Our findings indicate that the divergence of the Veracruz and Yucatan populations is best explained by a combination of a short period of isolation exacerbated by subsequent divergence in climate conditions, and that rather than vicariance, the two isolated ranges of D. eliza are the product of recent colonization and divergence in isolation.

Geographical and temporal patterns of diversification in bee hummingbirds (Mellisugini) were assessed with respect to the evolution of migration, critical for colonization of North America. We generated a dated multilocus phylogeny of the Mellisugini based on a dense sampling using Bayesian inference, maximum-likelihood and maximum parsimony methods, and reconstructed the ancestral states of distributional areas in a Bayesian framework and migratory behavior using maximum parsimony, maximum-likelihood and re-rooting methods. All phylogenetic analyses confirmed monophyly of the Mellisugini and the inclusion of Atthis, Calothorax, Doricha, Eulidia, Mellisuga, Microstilbon, Myrmia, Tilmatura, and Thaumastura. Mellisugini consists of two clades: (1) South American species (including Tilmatura dupontii), and (2) species distributed in North and Central America and the Caribbean islands. The second clade consists of four subclades: Mexican (Calothorax, Doricha) and Caribbean (Archilochus, Calliphlox, Mellisuga) sheartails, Calypte, and Selasphorus (incl. Atthis). Coalescent-based dating places the origin of the Mellisugini in the mid-to-late Miocene, with crown ages of most subclades in the early Pliocene, and subsequent species splits in the Pleistocene. Bee hummingbirds reached western North America by the end of the Miocene and the ancestral mellisuginid (bee hummingbirds) was reconstructed as sedentary, with four independent gains of migratory behavior during the evolution of the Mellisugini. Early colonization of North America and subsequent evolution of migration best explained biogeographic and diversification patterns within the Mellisugini. The repeated evolution of long-distance migration by different lineages was critical for the colonization of North America, contributing to the radiation of bee hummingbirds. Comparative phylogeography is needed to test whether the repeated evolution of migration resulted from northward expansion of southern sedentary populations.

The state of Oaxaca is positioned in a rather unique biogeographical position with the highest diversity of vascular plants in Mexico. The isolation of xeric valleys surrounded by complex mountain ranges in Oaxaca supplies an excellent opportunity to investigate the influence of the Pleistocene events on xeric species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used sequences of two chloroplast markers to examine the phylogeographic patterns of the endemic mistletoe species Psittacanthus auriculatus (Loranthaceae) across its known range in Oaxaca and conducted ecological niche modeling (ENM) to explore changes of its distribution range through present, future, and palaeo periods. Our results revealed two groups corresponding to the distribution of individuals/populations from the northern locations (western valleys), and those from southern localities at central valleys of Oaxaca. A significant genetic signal of differentiation, demographic stability, and contraction of suitable habitat during the Last Glacial Maximum predicted by ENMs strongly supported a scenario of habitat fragmentation during the Late Pleistocene. We conclude that the genetic differentiation of P. auriculatus is consistent with a model of range contraction during glacial cycles and expansion during interglacials with no major range changes under future scenarios of climate change. The findings verified the profound effects of Pleistocene climatic fluctuations on this endemic mistletoe species, and the low genetic diversity within populations highlights, paradoxically, the urgency of preserving vulnerable populations of endemic yet parasitic mistletoes.

Large-scale phylogeographical patterns and the underlying factors driving species divergence in Mesoamerica are poorly understood, but it is widely documented that tectonic events and Pleistocene climate changes play an important role in determining species diversification. As glaciations in Mesoamerica developed only around high mountains, one hypothesis is that the known effects of the Last Glacial Maximum on the geographical distribution and genetic diversity of bird populations, producing the contraction/ expansion latitudinal pattern observed in temperate bird species, should be largely undetected in resident bird populations inhabiting environmentally more stable habitats. To gain insight into the effects of Quaternary habitat and climate stability on the genetic diversity, we use ecological niche modelling and generalised linear modelling to determine the role of changes in habitat stability on the genetic diversity in eight widespread or range restricted hummingbird species. We found lesser changes in suitable habitat from past to present in most of the species than those predicted by palaeodistribution models at northern temperate regions. Contemporary seasonal precipitation, Quaternary habitat and climate stability had superior explanatory power, but the magnitude and directionality of their effects on genetic diversity varied between range-restricted and widely distributed species. We observed that the species studied have not responded equally to changes in climate stability in this complex region, suggesting that habitat differences and/or the altitudinal range of the hummingbird species influenced genetic diversity, and that the species-specific responses are not only linked to habitat stability in the region but also to contemporary seasonality associated with the availability of floral resources.

We evaluate phylogeographical patterns of Psittacanthus mayanus (Loranthaceae), a widely distributed mistletoe species on the Yucatán Peninsula and Chiapas, using nuclear and plastid markers. An analysis of phylogeographic population structure and demography and Bayesian inference methods were conducted on P. mayanus from 16 localities across the range of the species. To assess the historical processes and changes through the Pleistocene climatic cycles that may have affected the distribution and demographic history of the species, the current potential distribution of the species was modelled using ecological niche modelling (ENM) and projected onto the mid Holocene (MH), Last Glacial Maximum (LGM) and Last Inter Glacial (LIG). Psittacanthus mayanus exhibited higher haplotype and nucleotide diversity in the southern part of its distribution than in the northern part. Two divergent lineages were revealed in the phylogenetic and phylogeographical analyses of ribotypes and haplotypes. Populations from the northern portion of the Yucatán Peninsula probably experienced a recent population growth, whereas populations from the southern portion of the Peninsula and Chiapas are marked by historical demographic stability and isolation. Approximate Bayesian computation (ABC) analyses strongly supported a scenario of post-glacial population growth. ENM results indicate that the distribution of P. mayanus expanded and was connected into the southern portion of the Yucatán Peninsula during LGM conditions and colonized the northern portion of the Peninsula and fragmented during MH conditions. According to the ABC and ENM results, the genetic differentiation of P. mayanus may be linked to the effects of the glacial/interglacial cycles and environmental factors, in which populations of P. mayanus expanded during the LGM into the Petén province currently covered with semideciduous tropical rain forest followed by northward expansion, southwards contractions and post-glacial colonization of the northernmost portion of the Yucatán province, a region currently covered with seasonally dry tropical deciduous forest. Our results highlight the influence of Pleistocene events in shaping the geographical distribution of genetic variation in Neotropical lowland forest. The phylogeographic and environmental patterns in P. mayanus provide an opportunity to investigate further the evolution of Mexican lowland forest biodiversity.