Recent genetic, phenetic and ecological divergence across the Mesoamerican highlands: a study case with Diglossa baritula (Aves: Thraupidae)

The topographical, geological, climatic and biodiversity complexity of Mesoamerica has made it a primary research focus. The Mesoamerican highlands is a region with particularly high species richness and within-species variation. The Cinnamon-bellied Flowerpiercer, Diglossa baritula (Wagler, 1832), is a species endemic to the Mesoamerican highlands, with three allopatric subspecies currently recognized. To characterize divergence within this species, we integrated genomics, morphology, coloration and ecological niche modeling approaches, obtained from sampling individuals across the entire geographic distribution of the species. Our results revealed a clear genomic divergence between the populations to the east versus the west of the Isthmus of Tehuantepec. In contrast to the genomic results, morphology and coloration analyses showed intermediate levels of differentiation, indicating that population groups within D. baritula have probably been under similar selective pressures. Our morphology results indicated that the only sexually dimorphic morphological variable is the wing chord, with males having a longer wing chord than females. Finally, ecological data indicated that there are differences in ecological niche within D. baritula. Our data suggest that D. baritula could contain two or more incipient species at the intermediate phase of the speciation continuum. These results highlight the importance of the geographical barrier of the Isthmus of Tehuantepec and Pleistocene climatic events in driving isolation and population divergence in D. baritula. The present investigation illustrates the speciation potential of the D. baritula complex and the capacity of Mesoamerican highlands to create cryptic biodiversity and endemism.

Estimation of species divergence times in presence of cross-species gene flow

Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies coalescent (MSC) model, we demonstrate that by accounting for incomplete lineage sorting and introgression using large phylogenomic data sets this problem can be avoided. The multispecies-coalescent-with-introgression (MSci) model is capable of accurately estimating both divergence times and ancestral effective population sizes, even when only a single diploid individual per species is sampled. We characterize some general expectations for biases in divergence time estimation under three different scenarios: 1) introgression between sister species, 2) introgression between non-sister species, and 3) introgression from an unsampled (i.e., ghost) outgroup lineage. We also conducted simulations under the isolation-with-migration (IM) model and found that the MSci model assuming episodic gene flow was able to accurately estimate species divergence times despite high levels of continuous gene flow. We estimated divergence times under the MSC and MSci models from two published empirical datasets with previous evidence of introgression, one of 372 target-enrichment loci from baobabs (Adansonia), and another of 1000 transcriptome loci from 14 species of the tomato relative, Jaltomata. The empirical analyses not only confirm our findings from simulations, demonstrating that the MSci model can reliably estimate divergence times but also show that divergence time estimation under the MSC can be robust to the presence of small amounts of introgression in empirical datasets with extensive taxon sampling. [divergence time; gene flow; hybridization; introgression; MSci model; multispecies coalescent].

Phylogeography and taxonomy of Coleonyx elegans Gray 1845 (Squamata: Eublepharidae) in Mesoamerica: The Isthmus of Tehuantepec as an environmental barrier

Population divergence leading to speciation is often explained by physical barriers causing allopatric distributions of historically connected populations. Environmental barriers have increasingly been shown to cause population divergence through local adaptation to distinct ecological characteristics. In this study, we evaluate population structuring and phylogeographic history within the Yucatán banded gecko Coleonyx elegans Gray 1845 to assess the role of both physical and environmental barriers in shaping the spatio-genetic distribution of a Mesoamerican tropical forest taxon. We generated RADseq and multi-locus Sanger datasets that included sampling across the entire species' range. Results find support for two distinct evolutionary lineages that diverged during the late Pliocene and show recent population expansions. Furthermore, these genetic lineages largely align with subspecies boundaries defined by morphology. Several mountain ranges identified as phylogeographic barriers in other taxa act as physical barriers to gene flow between the two clades. Despite the absence of a physical barrier between lineages across the lowland Isthmus of Tehuantepec, no introgression was observed. Here, a steep environmental cline associated with seasonality of precipitation corresponds exactly with the distributional limits of the lineages, whose closest samples are only 30 km apart. The combination of molecular and environmental evidence, and in conjunction with previous morphological evidence, allows us to reassess the current taxonomy in an integrative framework. Based on our findings, we elevate the previously recognized subspecies from the Pacific versant, the Colima banded gecko C. nemoralis Klauber 1945, to full species status and comment on conservation implications.

Reevaluation of the status of the Central American brocket deer Mazama temama (Artiodactyla: Cervidae) subspecies based on morphological and environmental evidence

The Central American brocket deer (Mazama temama) is widespread across the Mesoamerican forests, yet it remains largely unknown. Three subspecies are recognized currently within M. temama using pelage coloration as the primary diagnostic character. However, it remains unclear if there is any pattern of morphological variation throughout its distribution. We compared two models of morphological subdivision, namely the traditional subspecies and another based on biogeographic provinces via 2D geometric morphometrics and ecological niche modeling. The second model presented a better fit to the observed variation in cranial shape and size. We found divergence in skull size between individuals from Mexico and Guatemala (northern group) relative to specimens from Honduras, Nicaragua, Costa Rica, and Panama (southern group), the latter being 8% larger than the northern group. Centroid size showed a significant correlation with geographic distance suggesting an isolation-by-distance pattern. Low geographical overlap between the two clusters suggests niche conservatism. Late Pleistocene dispersal from South to Central America and differences in available resources with subsequent isolation due to climatic barriers therefore may have promoted differentiation in size albeit without extensive changes in shape. In this context, the Motagua-Polochic-Jolotán fault system probably plays a key role in promoting morphological differentiation by climatic isolation. Finally, we suggest that M. t. temama (Kerr, 1792) and M. t. reperticia  Goldman, 1913 should remain as valid names for the two morphological and ecologically differentiated groups detected here.

Incipient speciation, high genetic diversity, and ecological divergence in the alligator bark juniper suggest complex demographic changes during the Pleistocene

The most recent glacial cycles of the Pleistocene affected the distribution, population sizes, and levels of genetic structure of temperate-forest species in the main Mexican mountain systems. Our objective was to investigate the effects these cycles had on the genetic structure and distribution of a dominant species of the "mexical" vegetation across North and Central America. We studied the genetic diversity of Juniperus deppeana, a conifer distributed from the Southwestern United States to the highlands of Central America. We combined information of one plastid marker and two nuclear markers to infer phylogeographic structure, genetic diversity and demographic changes. We also characterized the climatic niche for each variety to infer the plausible area of suitability during past climatic conditions and to evaluate climatic niche discontinuities along with the species distribution. We found a marked phylogeographic structure separating the populations North and South of the Isthmus of Tehuantepec, with populations to the South of this barrier forming a distinct genetic cluster corresponding to Juniperus deppeana var. gamboana. We also found signals of population expansion in the Northern genetic cluster. Ecological niche modeling results confirmed climatic niche differences and discontinuities among J. deppeana varieties and heterogeneous responses to climatic oscillations. Overall, J. deppeana's genetic diversity has been marked by distribution shifts, population growth and secondary contact the North, and in situ permanence in the South since the last interglacial to the present. High genetic variation suggests a wide and climatically diverse distribution during climatic oscillations. We detected the existence of two main genetic clusters, supporting previous proposals that Juniperus deppeana and Juniperus gamboana may be considered two separate species.

Glacial Expansion or Interglacial Expansion? Contrasting Demographic Models of Four Cold-Adapted Fir Species in North America and East Asia

Understanding and forecasting species’ response to climate change is a critical need for future conservation and management. Two expansion hypotheses, the glacial expansion versus the interglacial expansion, have been proposed to interpret how cold-adapted organisms in the northern hemisphere respond to Quaternary climatic fluctuations. To test these two hypotheses, we originally used two pairs of high-low elevation firs from North America (Abies lasiocarpa and Abies balsamea) and East Asia (Abies chensiensis and Abies nephrolepis). Abies lasiocarpa and Abies chensiensis are widely distributed in high-elevation regions of western North America and central China. Abies balsamea and Abies nephrolepis occur in central North America and northeast China, with much lower elevations. These fir species are typical cold-adapted species and sensitive to climate fluctuations. Here, we integrated the mtDNA and cpDNA polymorphisms involving 44 populations and 585 individuals. Based on phylogeographic analyses, recent historical range expansions were indicated in two high-elevation firs (Abies lasiocarpa and Abies chensiensis) during the last glaciation (43.8–28.4 or 21.9–14.2 kya, 53.1–34.5 or 26.6–17.2 kya). Such glacial expansions in high-elevation firs were further confirmed by the evidence of species distribution modelling, geographic-driven genetic patterns, palynological records, and current distribution patterns. Unlike the north American firs, the SDM models indicated unremarkable expansion or contraction in East Asia firs for its much more stable conditions during different historical periods. Taken together, our findings highly supported that high-elevation firs experienced glacial expansion during the Quaternary climate change in East Asia and North America, as interglacial expansion within low-elevation firs. Under this situation, the critically endangered fir species distributed in high elevation would have no enough higher elevational space to migrate. Facing the increasing global warming, thus we proposed ex-situ conservation of defining conservation units as the most meaningful strategy.