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.

Biogeographic factors contributing to the diversification of Euphoniinae (Aves, Passeriformes, Fringillidae): a phylogenetic and ancestral areas analysis.

Factors such as the Andean uplift, Isthmus of Panama, and climate changes have influenced bird diversity in the Neotropical region. Studying bird species that are widespread in Neotropical highlands and lowlands can help us understand the impact of these factors on taxa diversification. Our main objectives were to determine the biogeographic factors that contributed to the diversification of Euphoniinae and re-evaluate their phylogenetic relationships. The nextRAD and mitochondrial data were utilized to construct phylogenies. The ancestral distribution range was then estimated using a time-calibrated phylogeny, current species ranges, and neotropical regionalization. The phylogenies revealed two main Euphoniinae clades, Chlorophonia and Euphonia, similar to previous findings. Furthermore, each genus has distinctive subclades corresponding to morphology and geography. The biogeographic results suggest that the Andean uplift and the establishment of the western Amazon drove the vicariance of Chlorophonia and Euphonia during the Miocene. The Chlorophonia lineage originated in the Andes mountains and spread to Central America and the Mesoamerican highlands after the formation of the Isthmus of Panama. Meanwhile, the ancestral area of Euphonia was the Amazonas, from which it spread to trans-Andean areas during the Pliocene and Pleistocene due to the separation of the west lowlands from Amazonas due to the Northern Andean uplift. Chlorophonia and Euphonia species migrated to the Atlantic Forest during the Pleistocene through corridors from the East Andean Humid Forest and Amazonas. These two genera had Caribbean invasions with distinct geographic origins and ages. Finally, we suggested taxonomic changes in the genus Euphonia based on the study's phylogenetic, morphological, and biogeographic findings.

Phylogenetic relationships and systematics of a subclade of Mesoamerican emerald hummingbirds (Aves: Trochilidae: Trochilini).

Phylogenetic relationships among major hummingbird clades are relatively well resolved, yet due to the lack of morphological synapomorphies and relative phenotypic homogeneity, the systematics of several hummingbird groups remain unresolved. Here, we present the results of a multilocus study of a clade of emerald hummingbirds composed of Cynanthus, Chlorostilbon, Riccordia and Phaeoptila (sensu Stiles et al. 2017). We include taxa not analyzed in previous studies (C. lawrencei, C. auriceps and C. forficatus, from Tres Marías Islands, Western Mexico, and Cozumel Island, respectively), and this allows us to develop a new hypothesis for the phylogenetic relationships within this group. We found that this clade originated in Mesoamerica about 12 million years ago, and comprises four geographically congruent clades: (a) the most basal clade, Phaeoptila sordida, of the Balsas River basin, Mexico; (b) Riccordia bicolor, R. maugaeus, R. ricordii and R. swainsonii of the West Indies; (c) Chlorostilbon assimilis, C. aureoventris, C. melanorhynchus, C. mellisugus, C. poortmani and C. pucherani, all of South America, except C. assimilis of Central America; and (d) a Mesoamerican clade with two Cynanthus subclades: a widespread Mexican clade that includes species formerly belonging to the genus Chlorostilbon: Cynanthus auriceps, C. canivetii, C. doubledayi and C. forficatus; and a clade restricted to the west coast of Mexico and the Tres Marías Islands and composed of C. latirostris and C. lawrencei. Our results help clarify the systematics of this group of emeralds, reconstruct its true evolutionary history, and advance understanding of phenotypic evolution in hummingbirds.

Genetic and morphometric divergence in the Garnet-Throated Hummingbird Lamprolaima rhami (Aves: Trochilidae).

Cloud forests are one of the most endangered ecosystems in the Americas, as well as one of the richest in biological diversity in the world. The species inhabiting these forests are susceptible to environmental changes and characterized by high levels of geographic structure. The Garnet-Throated Hummingbird, Lamprolaima rhami, mainly inhabits cloud forests, but can also be found in other habitats. This species has a highly restricted distribution in Mesoamerica, and five disjunct regions have been delimited within the current geographic distribution of the species from Mexico to Honduras. According to variation in size and color, three subspecies have been described: L. r. rhami restricted to the Mexican highlands and Guatemala, L. r. occidentalis distributed in Guerrero (Mexico), and L. r. saturatior, distributed in the highlands from Honduras and El Salvador. We analyzed the levels of geographic structure in L. rhami and its taxonomic implications. We used mitochondrial and nuclear DNA to analyze genetic variation, demographic history, divergence times, reconstructed a multilocus phylogeny, and performed a species delimitation analyses. We also evaluated morphological variation in 208 specimens. We found high levels of genetic differentiation in three groups, and significant variation in morphological traits corresponding with the disjunct geographic populations. L. rhami presents population stability with the highest genetic variation explained by differences between populations. Divergence time estimates suggest that L. rhami split from its sister group around 10.55 million years ago, and the diversification of the complex was dated ca. 0.207 Mya. The hypotheses tested in the species delimitation analyses validated three independent lineages corresponding to three disjunct populations. This study provides evidence of genetic and/or morphometric differentiation between populations in the L. rhami complex where four separate evolutionary lineages are supported: (1) populations from the Sierra Madre Oriental and the highlands of Oaxaca (rhami), (2) populations from the highlands of Guerrero (occidentalis), (3) populations from the highlands of Chiapas and Guatemala (this is a non-previously proposed potential taxon: tacanensis), and (4) populations from the highlands of Honduras and El Salvador (saturatior). The main promoters of the geographic structure found in the L. rhami complex are likely the Isthmus of Tehuantepec as a geographic barrier, isolation by distance resulting from habitat fragmentation, and climatic conditions during the Pleistocene.

Deep divergence of Red-crowned Ant Tanager (Habia rubica: Cardinalidae), a multilocus phylogenetic analysis with emphasis in Mesoamerica.

Many neotropical species have a complex history of diversification as a result of the influence of geographical, ecological, climatic, and geological factors that determine the distribution of populations within a lineage. Phylogeography identifies such populations, determines their geographic distributions, and quantifies the degree of genetic divergence. In this work we explored the genetic structure of Habia rubica populations, a polytypic taxon with 17 subspecies described, in order to obtain hypotheses about their evolutionary history and processes of diversification. We undertook multilocus analyses using sequences of five molecular markers (ND2, ACOI-I9, MUSK, FGB-I5 and ODC), and sampling from across the species' distribution range, an area encompassing from Central Mexico throughout much of South America. With these data, we obtained a robust phylogenetic hypothesis, a species delimitation analysis, and estimates of divergence times for these lineages. The phylogenetic hypothesis of concatenated molecular markers shows that H. rubica can be divided in three main clades: the first includes Mexican Pacific coast populations, the second is formed by population from east of Mexico to Panama and the third comprises the South American populations. Within these clades we recognize seven principal phylogroups whose limits have a clear correspondence with important geographical discontinuities including the Isthmus of Tehuantepec in southern Mexico, the Talamanca Cordillera, and the Isthmus of Panama in North America. In South America, we observed a marked separation of two phylogroups that include the populations that inhabit mesic forests in western and central South America (Amazon Forest) and those inhabiting the seasonal forest from the eastern and northern regions of the South America (Atlantic Forest). These areas are separated by an intervening dry vegetation "diagonal" (Chaco, Cerrado and Caatinga). The geographic and genetic structure of these phylogroups describes a history of diversification more active and complex in the northern distribution of this species, producing at least seven well-supported lineages that could be considered species.

Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards.

Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z-linked sex chromosome loci. Between the two taxa, Z-linked loci (ΦST  = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST  = 0.017) but comparable to mtDNA (ΦST  = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z-linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (ΦST ) and absolute (dXY ) estimates of divergence. In contrast, the ratio of Z-linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (ΦST  = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.

The role of historical and contemporary processes on phylogeographic structure and genetic diversity in the Northern Cardinal, Cardinalis cardinalis.

BACKGROUND: Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, Cardinalis cardinalis. RESULTS: Phylogenetic analysis revealed deep mtDNA structure with six lineages across the species' range. Ecological niche models supported the same geographic breaks revealed by the mtDNA. A paleoecological niche model for the Last Glacial Maximum indicated that cardinals underwent a dramatic range reduction in eastern North America, whereas their ranges were more stable in México. In eastern North America cardinals expanded out of glacial refugia, but we found no signature of decreased genetic diversity in areas colonized after the Last Glacial Maximum. Present-day demographic data suggested that population growth across the expansion cline is positively correlated with latitude. We propose that there was no loss of genetic diversity in areas colonized after the Last Glacial Maximum because recent high-levels of gene flow across the region have homogenized genetic diversity in eastern North America. CONCLUSION: We show that both deep historical events as well as demographic processes that occurred following these events are critical in shaping genetic pattern and diversity in C. cardinalis. The general implication of our results is that patterns of genetic diversity are best understood when information on species history, ecology, and demography are considered simultaneously.

Phylogeography and population genetics of the Amethyst-throated Hummingbird (Lampornis amethystinus).

We analyzed mitochondrial DNA sequence variation across 69 Amethyst-throated Hummingbirds (Lampornis amethystinus), comparing with samples of related taxa. Although this group shows discrete phenotypic variation in throat color among populations in Oaxaca and Guerrero (Mexico), the only phylogeographic structure observed was between phenotypically similar populations north and south of the Isthmus of Tehuantepec. As such, it appears that throat color variation is of recent origin and likely based only on minor genetic differences.

Diversification of the arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) in the Mesoamerican highlands.

The arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) are among the most poorly known Neotropical rodents. We investigated species-level phylogenetic relationships among the seven described Habromys species using 1331 aligned bases from the mitochondrial ND3 and ND4 regions. Sequences were obtained from 30 specimens of the seven known species of Habromys and we performed maximum parsimony, maximum likelihood, and Bayesian probabilities analyses. The monophyly of the genus Habromys within the Neotomines was verified. The northernmost H. simulatus is sister to the remaining species of the group; within the latter, the southernmost clade (Oaxaca to Central America) is sister to the Transmexican Volcanic Belt clade. Four major clades are clearly distinguished: H. simulatus from the Sierra Madre Oriental and the closely associated Sierra Mazateca; H. delicatulus and H. schmidlyi from the Transmexican Volcanic Belt; H. lepturus, H. chinanteco, and H. ixtlani from the northern Oaxacan highlands; and H. lophurus from Nuclear Central America. Within species, the analyses suggest that H. simulatus and H. lophurus are each composed by two different taxa.

Local origin and diversification among Lampornis hummingbirds: a Mesoamerican taxon.

The huge biodiversity found in Mesoamerica is often explained by its geographic situation as a natural bridge between two large biogeographic regions. Often overlooked, however, are the high levels of speciation and diversification in the area. Here we assess the phylogenetic relationships within a Mesoamerican group of hummingbirds (Lampornis). We sequenced both mtDNA (1,143 bp of cyt b and 727 bp of ND5) and nuclear genes (505 bp of AK-5 intron and 567 bp of c-mos) for each of the seven recognised species and outgroups. We find two or three clades of similar age within this genus: L. clemenciae and L. amethystinus (singly or as each other's sister taxa) and a Central American clade. This Central-American clade presents a clear bipartition between northern (L. viridipallens and L. sybillae) and southern Mesoamerica, which is shared with many other Mesoamerican organisms. Our analyses suggest that L. hemileucus does not belong in the genus Lampornis. While we refrain to apply a time-scale to our data because of the lack of an appropriate calibration, our results indicate that the genus Lampornis predates the uprising of the Panama land-bridge, and that diversification among the isthmian species (L. castaneoventris and L. calolaema) is a very recent event. Our results strongly suggest a local Mesoamerican origin for this genus.