Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird

Climatic niche shifts and ecological sky-island dynamics in Mesoamerican montane birds

An ongoing challenge in evolutionary and ecological research focuses on testing biogeographic hypotheses for the understanding of both species' distributional patterns and of the factors influencing range limits. In this study, we described the climatic niches of Neotropical humid montane forest birds through the analysis of factors driving their evolution at inter- and intraspecific levels; and tested for differences among allopatric lineages within Aulacorhynchus, Chlorospingus, Cardellina, and Eupherusa. We employed ecological niche models (ENMs) along with an ordination approach with kernel smoothing to perform niche overlap analyses and test hypotheses of niche equivalence/similarity among lineages. In addition, we described the potential distributions of each lineage during the Late Pleistocene climate fluctuations, identifying historical range expansions, connectivity, and stability. Overall, we observed differences in environmental variables influencing climatic requirements and distributional patterns for our selected species. We detected the highest values of niche overlap mainly between Eupherusa and some Chlorospingus lineages. At both interspecific and intraspecific levels, sister lineages showed non-identical environmental niches. Our results offer weak support to a moist forest model, in which populations followed the expansion and contraction cycles of montane forests, leading to a lack of niche conservatism among lineages (they tend to occupy not identical climatic environments) throughout Mesoamerica. Therefore, historical climatic conditions may act as ecological barriers determining the distributional ranges of these species.

Whole-genome selection signature differences between Chaohu and Ji'an red ducks

Assessing the genetic structure of local varieties and understanding their genetic data are crucial for effective management and preservation. However, the genetic differences among local breeds require further explanation. To enhance our understanding of their population structure and genetic diversity, we conducted a genome-wide comparative study of Chaohu and Ji'an Red ducks using genome sequence and restriction site-associated DNA sequencing technology. Our analysis revealed a distinct genetic distinction between the two breeds, leading to divided groups. The phylogenetic tree for Chaohu duck displayed two branches, potentially indicating minimal impact from artificial selection. Additionally, our ROH (runs of homozygosity) analysis revealed that Chaohu ducks had a lower average inbreeding coefficient than Ji'an Red ducks. We identified several genomic regions with high genetic similarity in these indigenous duck breeds. By conducting a selective sweep analysis, we identified 574 candidate genes associated with muscle growth (BMP2, ITGA8, MYLK, and PTCH1), fat deposits (ELOVL1 and HACD2), and pigmentation (ASIP and LOC101797494). These results offer valuable insights for the further enhancement and conservation of Chinese indigenous duck breeds.

Sampling affects population genetic inference: A case study of the Allen's (Selasphorus sasin) and rufous hummingbird (Selasphorus rufus)

Gene flow can affect evolutionary inference when species are undersampled. Here, we evaluate the effects of gene flow and geographic sampling on demographic inference of 2 hummingbirds that hybridize, Allen's hummingbird (Selasphorus sasin) and rufous hummingbird (Selasphorus rufus). Using whole-genome data and extensive geographic sampling, we find widespread connectivity, with introgression far beyond the Allen's × rufous hybrid zone, although the Z chromosome resists introgression beyond the hybrid zone. We test alternative hypotheses of speciation history of Allen's, rufous, and Calliope (S. calliope) hummingbird and find that rufous hummingbird is the sister taxon to Allen's hummingbird, and Calliope hummingbird is the outgroup. A model treating the 2 subspecies of Allen's hummingbird as a single panmictic population fit observed genetic data better than models treating the subspecies as distinct populations, in contrast to morphological and behavioral differences and analyses of spatial population structure. With additional sampling, our study builds upon recent studies that came to conflicting conclusions regarding the evolutionary histories of these 2 species. Our results stress the importance of thorough geographic sampling when assessing demographic history in the presence of gene flow.

The Hummingbird Collection of the Natural History and Science Museum of the University of Porto (MHNC-UP), Portugal

BACKGROUND

The Hummingbird (Family Trochilidae) Collection of the Natural History and Science Museum of the University of Porto (MHNC-UP) is one of the oldest collections of this family harboured in European museums. Almost 2,000 specimens, that encompass most of the taxonomic diversity of this family, were collected in the late 19th Century. The collection is relevant due its antiquity and because all specimens were bought from the same provider, mainly as mounted specimens, for a Portuguese private collection of Neotropical fauna. In the early 20th Century, it was donated to the Museum that is now the MHNC-UP.

NEW INFORMATION

The information about the majority of these specimens is now available for consultation on the GBIF platform after curation of all specimens and digital cleaning of the associated metadata. In the process, hundreds of non-catalogued specimens were found and taxonomic and spatial information was updated for many of the specimens.

Recent diversification in the high Andes: unveiling the evolutionary history of the Ecuadorian hillstar,Oreotrochilus chimborazo(Apodiformes: Trochilidae)

Studying the genetic signatures of evolutionary diversification in young lineages is among the most promising approaches for unveiling the processes behind speciation. Here, we focus on Oreotrochilus chimborazo, a high Andean species of hummingbird that might have experienced rapid diversification in the recent past. To understand the evolution of this species, we generated a dataset of ten microsatellite markers and complementary data on morphometrics, plumage variation and ecological niches. We applied a series of population and coalescent-based analyses to understand the population structure and differentiation within the species, in addition to the signatures of current and historical gene flow, the location of potential contact zones and the relationships among lineages. We found that O. chimborazo comprises three genetic groups: one corresponding to subspecies O. c. chimborazo, from Chimborazo volcano and surroundings, and two corresponding to the northern and southern ranges of subspecies O. c. jamesonii, found from the extreme south of Colombia to southern Ecuador. We inferred modest levels of both contemporary and historical gene flow and proposed the location of a contact zone between lineages. Also, our coalescent-based analyses supported a rapid split among these three lineages during the mid-to-late Holocene. We discuss our results in the light of past and present potential distributions of the species, in addition to evolutionary trends seen in other Andean hummingbirds.

Phylogeography of the widespread white-eared hummingbird (Hylocharis leucotis): pre-glacial expansion and genetic differentiation of populations separated by the Isthmus of Tehuantepec

The Pleistocene glacial cycles had a strong influence on the demography and genetic structure of many species, particularly on northern-latitude taxa. Here we studied the phylogeography of the white-eared hummingbird (Hylocharis leucotis), a widely distributed species of the highlands of Mexico and Central America. Analysis of mitochondrial DNA (mtDNA) sequences was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. Analyses of 108 samples from 11 geographic locations revealed population structure and genetic differentiation among populations separated by the Isthmus of Tehuantepec (IT) and the Motagua-Polochic-Jocotán (MPJ) fault barriers. ENM predicted a widespread distribution of suitable habitat for H. leucotis since the Last Inter Glacial (LIG), but this habitat noticeably contracted and fragmented at the IT. Models for historical dispersal corridors based on population genetics data and ENM revealed the existence of corridors among populations west of the IT; however, the connectivity of populations across the IT has changed little since the LIG. The shallow geographic structure on either side of the isthmus and a star-like haplotype network, combined with the long-term persistence of populations across time based on genetic data and potential dispersal routes, support a scenario of divergence with migration and subsequent isolation and differentiation in Chiapas and south of the MPJ fault. Our findings corroborate the profound effects of Pleistocene climatic fluctuations on the evolutionary history of montane taxa but challenge the generality of expanded suitable habitat (pine-oak forests) during glacial cycles.

The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico

Background

Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS.

Results

We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS.

Conclusions

Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.

Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetesalbinucha (Aves, Passerellidae)

The White-naped Brushfinch (Atlapetesalbinucha) comprises up to eight allopatric subspecies mainly identified by the color of the underparts (gray vs. yellow belly). Yellow and gray bellied forms were long considered two different species (A.albinucha and A.gutturalis), but they are presently considered as one polytypic species. Previous studies in the genus Atlapetes have shown that the phylogeny, based on molecular data, is not congruent with characters such as coloration, ecology, or distributional patterns. The phylogeography of A.albinucha was analyzed using two mitochondrial DNA regions from samples including 24 different localities throughout montane areas from eastern Mexico to Colombia. Phylogeographic analyses using Bayesian inference, maximum likelihood and haplotype network revealed incomplete geographic structure. The genetic diversity pattern is congruent with a recent process of expansion, which is also supported by Ecological Niche Models (ENM) constructed for the species and projected into three past scenarios. Overall, the results revealed an incomplete genetic divergence among populations of A.albinucha in spite of the species’ ample range, which contrasts with previous results of phylogeographic patterns in other Neotropical montane forest bird species, suggesting idiosyncratic evolutionary histories for different taxa throughout the region.

Quantitative characterization of iridescent colours in biological studies: a novel method using optical theory

Iridescent colours are colours that change with viewing or illumination geometry. While they are widespread in many living organisms, most evolutionary studies on iridescence do not take into account their full complexity. Few studies try to precisely characterize what makes iridescent colours special: their angular dependency. Yet, it is likely that this angular dependency has biological functions and is therefore submitted to evolutionary pressures. For this reason, evolutionary biologists need a repeatable method to measure iridescent colours as well as variables to precisely quantify the angular dependency. In this study, we use a theoretical approach to propose five variables that allow one to fully describe iridescent colours at every angle combination. Based on the results, we propose a new measurement protocol and statistical method to reliably characterize iridescence while minimizing the required number of time-consuming measurements. We use hummingbird iridescent feathers and butterfly iridescent wings as test cases to demonstrate the strengths of this new method. We show that our method is precise enough to be potentially used at intraspecific level while being also time-efficient enough to encompass large taxonomic scales.

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.

Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird

The present day distribution and spatial genetic diversity of Mesoamerican biota reflects a long history of responses to habitat change. The hummingbird Lampornis amethystinus is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling across the species range using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites jointly analysed with phenotypic and climatic data, we (1) test whether the fragmented distribution is correlated with main evolutionary lineages, (2) assess body size and plumage color differentiation of populations in geographic isolation, and (3) evaluate a set of divergence scenarios and demographic patterns of the hummingbird populations. Analysis of genetic variation revealed four main groups: blue‐throated populations (Sierra Madre del Sur); two groups of amethyst‐throated populations (Trans‐Mexican Volcanic Belt and Sierra Madre Oriental); and populations east of the Isthmus of Tehuantepec (IT) with males showing an amethyst throat. The most basal split is estimated to have originated in the Pleistocene, 2.39–0.57 million years ago (MYA), and corresponded to groups of populations separated by the IT. However, the estimated recent divergence time between blue‐ and amethyst‐throated populations does not correspond to the 2‐MY needed to be in isolation for substantial plumage divergence, likely because structurally iridescent colors are more malleable than others. Results of species distribution modeling and Approximate Bayesian Computation analysis fit a model of lineage divergence west of the Isthmus after the Last Glacial Maximum (LGM), and that the species’ suitable habitat was disjunct during past and current conditions. These results challenge the generality of the contraction/expansion glacial model to cloud forest‐interior species and urges management of cloud forest, a highly vulnerable ecosystem to climate change and currently facing destruction, to prevent further loss of genetic diversity or extinction.