Integrating phylogenetic, phylogeographic, and morphometric analyses to reveal cryptic lineages within the genus Asaccus (Reptilia: Squamata: Phyllodactylidae) in Iran.

The Middle Eastern endemic genus Asaccus comprises Southwest Asian leaf-toed geckos. To date, this genus includes 19 species of leaf-toed geckos (seven in Arabia and 12 in the Zagros Mountains). Despite a recent study on the taxonomy and phylogeny of Asaccus species in Iran, controversies still remain surrounding the phylogeny and phylogeography of the genus.

Brain Gene Regulatory Networks Coordinate Nest Construction in Birds.

Nest building is a vital behavior exhibited during breeding in birds, and is possibly induced by environmental and social cues. Although such behavioral plasticity has been hypothesized to be controlled by adult neuronal plasticity, empirical evidence, especially at the neurogenomic level, remains limited. Here, we aim to uncover the gene regulatory networks that govern avian nest construction and examine whether they are associated with circuit rewiring.

A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait.

The presence of feathers is a vital characteristic among birds, yet most modern birds had no feather on their feet. The discoveries of feathers on the hind limbs of basal birds and dinosaurs have sparked an interest in the evolutionary origin and genetic mechanism of feathered feet. However, the majority of studies investigating the genes associated with this trait focused on domestic populations.

A global database of bird nest traits.

The reproductive success of birds is closely tied to the characteristics of their nests. It is crucial to understand the distribution of nest traits across phylogenetic and geographic dimensions to gain insight into bird evolution and adaptation. Despite the extensive historical documentation on breeding behavior, a structured dataset describing bird nest characteristics has been lacking.

Weak gene-gene interaction facilitates the evolution of gene expression plasticity.

Background: Individual organisms may exhibit phenotypic plasticity when they acclimate to different conditions. Such plastic responses may facilitate or constrain the adaptation of their descendant populations to new environments, complicating their evolutionary trajectories beyond the genetic blueprint. Intriguingly, phenotypic plasticity itself can evolve in terms of its direction and magnitude during adaptation.

Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird.

Organisms often acquire physiological and morphological modifications to conquer ecological challenges when colonizing new environments which lead to their adaptive evolution. However, deciphering the genomic mechanism of ecological adaptation is difficult because ecological environments are often too complex for straightforward interpretation. Thus, we examined the adaptation of a widespread songbird-the rufous-capped babbler (Cyanoderma ruficeps)-to a relatively simple system: distinct environments across elevational gradients on the mountainous island of Taiwan.

The role of a synanthropic bird in the nest niche expansion of a secondary cavity nester to man-made structures.

Species with similar ecological characters often compete with each other; however, a species may also facilitate the survival or reproduction of another ecologically similar species, although such interaction is rarely documented in birds. Here, we reported a facilitative species interaction between Asian house martins () and russet sparrows (), both passerines using closed nests, in a montane farming area of Taiwan. We found that Asian house martins constructed dome-shaped nests in human houses that provided additional nest sites for russet sparrows, secondary cavity nesters with greatly declining populations in Taiwan.

Functional connections between bird eggshell stiffness and nest characteristics through risk of egg collision in nests.

Eggs and nests are two critical traits for the ecological success of birds. Their functional interactions, however, remain unclear. Here, we examined the functional connections between egg stiffness and nest attachment, site and structure for 1350 avian species.

Domestication obscures genomic estimates of population history.

Domesticated species are valuable models to examine phenotypic evolution, and knowledge on domestication history is critical for understanding the trajectories of evolutionary changes. Sequentially Markov Coalescent models are often used to infer domestication history. However, domestication practices may obscure the signal left by population history, affecting demographic inference.

Effects of artificial light at night on the nest-site selection, reproductive success and behavior of a synanthropic bird.

Understanding how artificial light at night (ALAN) impacts wildlife is increasingly important because more and more species are colonizing urban areas. As most of the bird studies on ALAN use controlled light set inside or around nest-boxes, the ecological effect of ALAN resulting from in situ streetlight on birds remains contentious. The barn swallow (Hirundo rustica) often builds open nests on buildings, which are directly exposed to varying intensity of ALAN, and thus provides a good system to examine the effect of in situ ALAN on birds.

Population genomic, climatic and anthropogenic evidence suggest the role of human forces in endangerment of green peafowl ().

Both anthropogenic impacts and historical climate change could contribute to population decline and species extinction, but their relative importance is still unclear. Emerging approaches based on genomic, climatic and anthropogenic data provide a promising analytical framework to address this question. This study applied such an integrative approach to examine potential drivers for the endangerment of the green peafowl ().

Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests.

Background: Knowledge is growing on how gut microbiota are established, but the effects of maternal symbiotic microbes throughout early microbial successions in birds remain elusive. In this study, we examined the contributions and transmission modes of maternal microbes into the neonatal microbiota of a passerine, the zebra finch (Taeniopygia guttata), based on fostering experiments.

Results: Using 16S rRNA amplicon sequencing, we found that zebra finch chicks raised by their biological or foster parents (the society finch Lonchura striata domestica) had gut microbial communities converging with those of the parents that reared them.

Barn Swallow Nest Predation by a Recent Urban Invader, the Taiwan Whistling Thrush - Implications for the Evolution of Urban Avian Communities.

Urban areas become a new habitat for an increasing number of species as they gradually adapt to the expanding, human-associated environment. The barn swallow () has constructed nests on human buildings that provide good protection against bad weather and predators over centuries. In contrast, the Taiwan whistling thrush () is one of new urban-invading species.

Sympatric competitors have driven the evolution of temporal activity patterns in Cnemaspis geckos in Southeast Asia.

It is often assumed that animals' temporal activity patterns are highly conserved throughout evolution. While most geckos are nocturnal, the species in the Cnemaspis genus are mostly diurnal (only a few are nocturnal). This raises a question about the evolution of a diel niche in the Cnemaspis genus.

Secondary contact after allopatric divergence explains avian speciation and high species diversity in the Himalayan-Hengduan Mountains.

The geographical context of speciation is important for understanding speciation and community assembly. However, the predominant mode of speciation in the Himalayan-Hengduan Mountains (HHMs), a global biodiversity hotspot, remains unknown. Here, we examined the role of geography in speciation using four pairs of sister or closely related avian species that currently co-occur in the HHMs.

To Trim or Not to Trim: Effects of Read Trimming on the De Novo Genome Assembly of a Widespread East Asian Passerine, the Rufous-Capped Babbler ( Blyth).

Trimming low quality bases from sequencing reads is considered as routine procedure for genome assembly; however, we know little about its pros and cons. Here, we used empirical data to examine how read trimming affects assembled genome quality and computational time for a widespread East Asian passerine, the rufous-capped babbler ( Blyth). We found that scaffolds assembled from raw reads were always longer than those from trimmed ones, whereas computational times for the former were sometimes much longer than the latter.

Generating brain matrices for zebra finch brain sectioning using three-dimensional printing technology.

Background: The demand to sample brain regions in non-model species is increasing as more studies are integrating neurological data into behavioural, ecological or evolutionary analysis. However, the sampling operation is difficult for researchers without neuroscience background. It is also a challenge to collect neuroanatomical regions from animals in the field.

Standing genetic variation as the predominant source for adaptation of a songbird.

What kind of genetic variation contributes the most to adaptation is a fundamental question in evolutionary biology. By resequencing genomes of 80 individuals, we inferred the origin of genomic variants associated with a complex adaptive syndrome involving multiple quantitative traits, namely, adaptation between high and low altitudes, in the vinous-throated parrotbill () in Taiwan. By comparing these variants with those in the Asian mainland population, we revealed standing variation in 24 noncoding genomic regions to be the predominant genetic source of adaptation.

Historical demography of four gecko species specializing in boulder cave habitat: Implications in the evolutionary dead end hypothesis and conservation.

Specialization in narrow ecological niches may not only help species to survive in competitive or unique environments but also contribute to their extermination over evolutionary time. Although the "evolutionary dead end" hypothesis has long been debated, empirical evidence from species with detailed information on niche specialization and evolutionary history remains rare. Here we use a group of four closely related Cnemaspis gecko species that depend highly on granite boulder caves in the Mekong Delta to investigate the potential impact of ecological specialization on their evolution and population dynamics.

The niches of nuthatches affect their lineage evolution differently across latitude.

Ecological niche evolution can promote or hinder the differentiation of taxa and determine their distribution. Niche-mediated evolution may differ among climatic regimes, and thus, species that occur across a wide latitudinal range offer a chance to test these heterogeneous evolutionary processes. In this study, we examine (a) how many lineages have evolved across the continent-wide range of the Eurasian nuthatch (Sitta europaea), (b) whether the lineages' niches are significantly divergent or conserved and (c) how their niche evolution explains their geographic distribution.

Asynchronous evolution of interdependent nest characters across the avian phylogeny.

Nest building is a widespread behavior among birds that reflects their adaptation to the environment and evolutionary history. However, it remains unclear how nests evolve and how their evolution relates to the bird phylogeny. Here, by examining the evolution of three nest characters-structure, site, and attachment-across all bird families, we reveal that nest characters did not change synchronically across the avian phylogeny but had disparate evolutionary trajectories.

Genomic Analysis of Demographic History and Ecological Niche Modeling in the Endangered Sumatran Rhinoceros Dicerorhinus sumatrensis.

The vertebrate extinction rate over the past century is approximately 22-100 times greater than background extinction rates [1], and large mammals are particularly at risk [2, 3]. Quaternary megafaunal extinctions have been attributed to climate change [4], overexploitation [5], or a combination of the two [6]. Rhinoceroses (Family: Rhinocerotidae) have a rich fossil history replete with iconic examples of climate-induced extinctions [7], but current pressures threaten to eliminate this group entirely.

Ice age unfrozen: severe effect of the last interglacial, not glacial, climate change on East Asian avifauna.

Background: The glacial-interglacial cycles in the Pleistocene caused repeated range expansion and contraction of species in several regions in the world. However, it remains uncertain whether such climate oscillations had similar impact on East Asian biota, despite its widely recognized importance in global biodiversity. Here we use both molecular and ecological niche profiles on 11 East Asian avian species with various elevational ranges to reveal their response to the late Pleistocene climate changes.

Corrigendum: Developing informative microsatellite markers for non-model species using reference mapping against a model species' genome.

This corrects the article DOI: 10.1038/srep23087.