Aim We test whether populations of the Mesoamerican azure‐crowned hummingbird, Amazilia cyanocephala (Trochilidae), located east and west of the Isthmus of Tehuantepec are genetically, morphologically and environmentally differentiated and examine the relative role of drift and selection in driving diversification. Location Mexico. Methods We sequenced the mitochondrial ATPase‐6 and ATPase‐8 genes and the control region of 130 individuals collected throughout the range of the species in Mexico. Population genetic methods and coalescent tests were used to reconstruct the phylogeography of the species. Morphological and niche variation between genetic groups of A. cyanocephala were assessed. Results The data revealed two genetic groups separated by the Isthmus of Tehuantepec in the late Pleistocene (49,300–75,800 years ago), with the split occurring in the presence of gene flow. Deviations from demographic equilibrium were detected for the two genetic groups, indicating more recent population expansions. Amazilia cyanocephala individuals from populations on either side of the Isthmus of Tehuantepec differed in morphology and were distributed in unique environmental space. A coalescent‐based test indicated that selection is driving the observed morphological differentiation. Main conclusions Our findings implicate the Isthmus of Tehuantepec as a permeable barrier driving recent diversification of A. cyanocephala in the presence of gene flow. The two A. cyanocephala mitochondrial DNA (mtDNA) groups corresponding with morphological and environmental niche differences, in concert with the results of a coalescent‐based test, suggest that selection has been strong enough to counteract the effects of gene flow.

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Aim We used mitochondrial DNA sequences to reconstruct the phylogenetic relationships of Mesoamerican Amazilia hummingbirds (Trochilidae). The phylogeny was used to identify vicariance scenarios, reconstruct ancestral biogeographical areas, and investigate the role of geological events in generating genetic divergence through vicariance events.Location Mesoamerica.Methods Molecular sequence data were gathered from three mitochondrial genes (ND2, ND5 and 12S) for samples taken within the Mesoamerican region and analysed using maximum parsimony, maximum-likelihood and Bayesian approaches. Statistical dispersal-vicariance analysis (S-DIVA) was used to reconstruct biogeographical areas and changes in distribution during the evolutionary history of Amazilia. The phylogeny was calibrated using fossil dates, mean substitution rates and coalescent-based divergence time inference.Results Amazilia can be split into two divergent lineages, with high levels of sequence divergence within some Mesoamerican species. Ancestral area reconstructions favour an ancestral distribution west of the Isthmus of Tehuantepec, with subsequent dispersals east of the isthmus and to South America. Divergence time estimations suggest that major diversification events occurred in the Miocene and Pliocene, corresponding temporally and geographically to the formation of the mountain systems and establishment of the major biomes in Mesoamerica. Main conclusionsThe diversification of Amazilia corresponds to vegetation shifts in combination with regional orogenesis. Intriguingly, the timing of the major diversification events and dispersal into South America pre-dates the completion of the Panamanian isthmus c. 4 Ma before present.

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Phylogeographical work on cloud forest-adapted species provides inconsistent evidence on cloud forest dynamics during glacial cycles. A study of Rhipsalis baccifera (Cactaceae), a bird-dispersed epiphytic mistletoe cactus, was conducted to investigate genetic variation at sequence data from nuclear [internal transcribed spacer (ITS), 677 bp] and chloroplast (rpl32-trnL, 1092bp) DNA for 154 individuals across the species range in Mesoamerica to determine if such patterns are consistent with the expansion/contraction model of cloud forest during glacial cycles. We conducted population and spatial genetic analyses as well as gene flow and divergence time estimates between 24 populations comprising the distribution of R. baccifera in Mexico and Guatemala to gain insight of the evolutionary history of these populations, and a complementary species distribution modeling approach to frame information derived from the genetic analyses into an explicit paleoecological context. The results revealed a phylogeographical break at the Isthmus of Tehuantepec, and high levels of genetic diversity among populations and cloud forest areas. Despite the genetic differentiation of some R. baccifera populations, the widespread ITS ribotypes suggest effective nuclear gene flow via pollen and population differentiation shown by the rpl32-trnL suggests more restricted seed flow. Predictions of species distribution models under past last glacial maximum (LGM) climatic conditions and a significant signal of demographic expansion suggest that R. baccifera populations experienced a range expansion tracking the conditions of the cloud forest distribution and shifted to the lowlands with population connectivity during the LGM.

In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study was to monitor the changes in genetic diversity and track non-synonymous substitutions (dN) that could be implicated in the fitness of SARS-CoV-2 and its spread in different regions between December 2019 and November 2020. We analyzed 2213 complete genomes from six geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified seven frequent mutations that resulted in dN substitutions. Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein, emerged recently and have spread in Oceania and Europe. There were associations of P323L, D614G, R203K and G204R substitutions with disease severity. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

Mexico is a center of diversification for the genus Quercus, with an important number of taxa occurring along the Trans-Mexican Volcanic Belt (TMVB). However, the impact of the interaction between historical and current climatic variation and geological heterogeneity in the TMVB on the genetic and phenotypic diversification within oak species has been scarcely investigated. We used chloroplast DNA microsatellites and a geometric morphometrics analysis of leaf shape to understand differentiation between populations of Quercus deserticola, which inhabits dry highlands along the TMVB.Ecological niche modeling (ENM) for present-day conditions and projections into past scenarios were performed to evaluate the influence of environmental variables on the evolutionary history of the species. Results showed high genetic diversity (h S =0.774) and high genetic structure (R ST =0.75) and the morphological subdivision of populations into two clusters, corresponding to the west/south and east/north sectors of the Q. deserticola geographic distribution. ENM indicated that the potential distribution of the species has remained similar from the late Pleistocene to the present. Seemingly, the phylogeographic structure of the species has been shaped by low seed-mediated gene flow and mostly local migration patterns. In turn, leaf shape is responding to climate differences either through phenotypic plasticity or local adaptation. is a volcanic mountain chain with nearly 8000 volcanic structures, extending about 1200 km west to east through central Mexico, from the Pacific coast to the Gulf of Mexico coast. Furthermore, the TMVB has a large environmental heterogeneity and has experienced important climatic changes from the Pliocene and Pleistocene to the present (Gómez-Tuena et al. 2007; Ferrari et al. 2012). Based on age, orogeny and tectonic features, the TMVB has been divided into four sectors (western, central, eastern and easternmost), each with its own characteristics (Gómez-Tuena et al. 2005; Ferrari et al. 2012). The TMVB has also been considered as a complex biogeographic unit (i. e. it shows a high degree of species endemism and diversity), with two sectors, west and east (Gámez et al. 2012;Torres-Miranda et al. 2013). Four main episodes of volcanic activity of the TMVB have occurred during different periods from the early Miocene to the present, affecting this region asynchronously, first the western and later the eastern sectors (Gómez-Tuena et al. 2005; Gámez et al. 2012; Ferrari et al. 2012).Several studies have found that the physiographic context of the TMVB has been important in the genetic structuring and phenotypic divergence of different species and how climatic and geologic events have modified their distributions in various time periods (Jaramillo-Correa et al. 2008; Gámez et al. 2012;Ruiz-Sánchez and Specht 2013;Torres-Miranda et al. 2013; Mastretta-Yanes et al. 2015; Rodríguez-Gómez and Ornelas . The TMVB has been shown to be a geographic barrier that limits the dispersion of plants and animals tha...

Aim We tested whether populations of violet-crowned and green-fronted hummingbirds, Amazilia violiceps and Amazilia viridifrons, are genetically and environmentally differentiated, and examined the role of past geological and climatic changes in driving their diversification.Location Trans-Mexican Volcanic Belt.Methods Mitochondrial and nuclear DNA of individuals collected throughout the species' ranges were sequenced and then analysed using maximum-likelihood and Bayesian approaches. Species tree analysis, Bayesian species delimitation, divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of the Amazilia species, and the isolation-with-migration coalescent model was assessed to determine whether genetic divergence between Amazilia species occurred in the presence of gene flow.Results Genetic divergence between A. violiceps and A. viridifrons was shallow, with incomplete lineage sorting and introgression. Species delimitation supported three independent lineages: A. violiceps populations located north of the Trans-Mexican Volcanic Belt; a mixture of A. violiceps south of the volcanic belt and A. viridifrons populations; and A. villadai populations east of the Isthmus of Tehuantepec. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns support the model of species diversification by isolation with migration and habitat shifting in response to Pleistocene climatic fluctuations. Main conclusionsThe process of speciation in the Amazilia species complex may be explained by the combined effects of isolation resulting from the Trans-Mexican Volcanic Belt and the lowlands at the Isthmus of Tehuantepec and habitat shifting in response to Quaternary climatic changes.