Ecological niche divergence or ecological niche partitioning in a widespread Neotropical bird lineage.

Ecological niche divergence is generally considered to be a facet of evolution that may accompany geographic isolation and diversification in allopatry, contributing to species' evolutionary distinctiveness through time. The null expectation for any two diverging species in geographic isolation is that of niche conservatism, wherein populations do not rapidly shift to or adapt to novel environments. Here, I test ecological niche divergence for a widespread, pan-American lineage, the avian genus of martins (Progne). The genus Progne includes migrant and resident species, as well as geographically restricted taxa and widespread, intercontinentally distributed taxa, thus providing an ideal group in which to study the nature of niche divergence within a broad geographic mosaic. I obtained distributional information for the genus from publicly available databases and created ecological niche models for each species to create pairwise comparisons of environmental space. I combined these data with the most up-to-date phylogeny of Progne currently available to examine the patterns of niche evolution within the genus. I found limited evidence for niche divergence across the breeding distributions of Progne, and much stronger support for niche conservatism with patterns of niche partitioning. The ancestral Progne had a relatively broad ecological niche, like extant basal Progne lineages, and several geographically localized descendant species occupy only portions of this larger ancestral niche. I recovered strong evidence of breeding niche divergence for four of 36 taxon pairs but only one of these divergent pairs involved two widespread species (Southern Martin P. elegans vs. Gray-breasted Martin P. chalybea). Potential niche expansion from the ancestral species was observed in the most wide-ranging present-day species, namely the North American Purple Martin P. subis and P. chalybea. I analyzed populations of P. subis separately, as a microcosm of Progne evolution, and again found only limited evidence of niche divergence. This study adds to the mounting evidence for niche conservatism as a dominant feature of diversifying lineages, and sheds light on the ways in which apparently divergent niches may arise through allopatry while not involving any true niche shifts through evolutionary time. Even taxa that appear unique in terms of habitat or behavior may not be diversifying with respect to their ecological niches, but merely partitioning ancestral niches among descendant taxa.

The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird.

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.

Population structure in Mixornis tit-babblers across Sunda Shelf matches interfluvia of paleo-rivers.

Rivers constitute an important biogeographic divide in vast areas of tropical rainforest, such as the Amazon and Congo Basins. Southeast Asia's rainforests are currently fragmented across islands divided by sea, which has long obscured their extensive history of terrestrial connectivity as part of a vast (but now submerged) subcontinent - Sundaland - during most of the Quaternary. The role of paleo-rivers in determining population structure in Sundaic rainforests at a time when these forests were connected remains little understood. We examined the coloration of museum skins and used the genomic DNA of museum samples and freshly-collected blood tissue of a pair of Sundaic songbird species, the pin-striped and bold-striped tit-babblers (Mixornis gularis and M. bornensis, respectively), to assess the genetic affinity of populations on small Sundaic islands that have largely been ignored by modern research. Our genomic and morphological results place the populations from the Anambas and Natuna Islands firmly within M. gularis from the Malay Peninsula in western Sundaland, even though some of these islands are geographically much closer to Borneo, where M. bornensis resides. Our results reveal genetic structure consistent with the course of Sundaic paleo-rivers and the location of the interfluvia they formed, and add to a small but growing body of evidence that rivers would have been of equal biogeographic importance in Sundaland's former connected forest landscape as they are in Amazonia and the Congo Basin today.

Selective selfishness in alarm calling behaviour by some members of wintering mixed-species groups of crested tits and willow tits.

Animals adjust their use of alarm calls depending on social environments. We tested whether dominant (adult) and subordinate (juvenile non-kin) male crested tits (Lophophanes cristatus) warn each other and heterospecific willow tits (Poecile montanus) across the wintering season. Birds rarely alarm called when feeding alone. Both adult and juvenile crested tits warned each other in early winter, and adults did so in the middle of wintering season. However, juvenile males rarely warned conspecific adult males in the middle of the winter. Both adult and juvenile males stopped giving alarm calls when feeding together at the end of wintering season. The results suggest that the mid-winter reduction of juvenile alarms could increase the likelihood of successful predator attacks on adults, increasing the chances for juveniles to replace adults and acquire their territories. By contrast, both adult and juvenile males produced alarm calls throughout the season when foraging together with willow tits. Whether juvenile male crested tits could be selectively altering alarm call propensity to endanger adult males, thereby selfishly enhancing their own succession to territory ownership, is discussed. The results add to the understanding of the origin of mixed-species groups and explain the dynamics of social communication. This article is part of the theme issue 'Mixed-species groups and aggregations: shaping ecological and behavioural patterns and processes'.

Layered evolution of gene expression in "superfast" muscles for courtship.

Identifying the molecular process of complex trait evolution is a core goal of biology. However, pinpointing the specific context and timing of trait-associated changes within the molecular evolutionary history of an organism remains an elusive goal. We study this topic by exploring the molecular basis of elaborate courtship evolution, which represents an extraordinary example of trait innovation. Within the behaviorally diverse radiation of Central and South American manakin birds, species from two separate lineages beat their wings together using specialized "superfast" muscles to generate a "snap" that helps attract mates. Here, we develop an empirical approach to analyze phylogenetic lineage-specific shifts in gene expression in the key snap-performing muscle and then integrate these findings with comparative transcriptomic sequence analysis. We find that rapid wing displays are associated with changes to a wide range of molecular processes that underlie extreme muscle performance, including changes to calcium trafficking, myocyte homeostasis and metabolism, and hormone action. We furthermore show that these changes occur gradually in a layered manner across the species history, wherein which ancestral genetic changes to many of these molecular systems are built upon by later species-specific shifts that likely finalized the process of display performance adaptation. Our study demonstrates the potential for combining phylogenetic modeling of tissue-specific gene expression shifts with phylogenetic analysis of lineage-specific sequence changes to reveal holistic evolutionary histories of complex traits.

A supergene underlies linked variation in color and morphology in a Holarctic songbird.

The genetic architecture of a phenotype can have considerable effects on the evolution of a trait or species. Characterizing genetic architecture provides insight into the complexity of a given phenotype and, potentially, the role of the phenotype in evolutionary processes like speciation. We use genome sequences to investigate the genetic basis of phenotypic variation in redpoll finches (Acanthis spp.). We demonstrate that variation in redpoll phenotype is broadly controlled by a ~55-Mb chromosomal inversion. Within this inversion, we find multiple candidate genes related to melanogenesis, carotenoid coloration, and bill shape, suggesting the inversion acts as a supergene controlling multiple linked traits. A latitudinal gradient in ecotype distribution suggests supergene driven variation in color and bill morphology are likely under environmental selection, maintaining supergene haplotypes as a balanced polymorphism. Our results provide a mechanism for the maintenance of ecotype variation in redpolls despite a genome largely homogenized by gene flow.

Cytogenetic Evidence Clarifies the Phylogeny of the Family Rhynchocyclidae (Aves: Passeriformes).

The phylogenetic position and taxonomic status of Rhynchocyclidae (Aves: Passeriformes) have been the subject of debate since their first description. In most models, Rhynchocyclidae represents a subfamily-level taxon placed within the Tyrant Flycatchers (Tyrannidae). Considering that this classification does not include cytotaxonomic characters, we tested the hypothesis that the chromosome organization of Rhynchocyclidae members differs from that of Tyrannidae. Hence, we selected two species, Tolmomyias sulphurescens, and Pitangus sulphuratus, representing Rhynchocyclidae and Tyrannidae, respectively. Results revealed a diploid number (2n) of 60 in T. sulphurescens and 2n = 80 in P. sulphuratus, indicating significant chromosomal differences. Chromosome mapping of Gallus gallus (GGA) and Taeniopygia guttata bacterial artificial chromosome (BAC) corresponding to chromosomes GGA1-28 (except 16) revealed that the genome evolution of T. sulphurescens involved extensive chromosome fusions of macrochromosomes and microchromosomes. On the other hand, P. sulphuratus retained the ancestral pattern of organization of macrochromosomes (except the centric fission involving GGA1) and microchromosomes. In conclusion, comparing our results with previous studies in Tyrant Flycatchers and allies indicates that P. sulphuratus has similar karyotypes to other Tyrannidae members. However, T. sulphurescens does not resemble the Tyrannidae family, reinforcing family status to the clade named Rhynchocyclidae.

Three Babesia species in Ixodes ricinus ticks from migratory birds in Sweden.

BACKGROUND: Migratory birds can cross geographical and environmental barriers and are thereby able to facilitate transmission of tick-borne pathogens both as carriers of infected ticks and as reservoirs of pathogenic microorganisms. Ixodes ricinus is one of the most abundant tick species in the Northern Hemisphere and a main vector of several Babesia species, some which pose a potential threat to human and animal health. At present only two cases of overt babesiosis in humans have so far been reported in Sweden. To better understand the potential role of birds as disseminators of zoonotic Babesia protozoan parasites, we investigated the presence of Babesia species in ticks removed from migratory birds. METHODS: Ticks were collected from birds captured at Ottenby Bird Observatory, south-eastern Sweden, from March to November 2009. Ticks were molecularly identified to species, and morphologically to developmental stage, and the presence of Babesia protozoan parasites was determined by real-time PCR. RESULTS: In total, 4601 migratory birds of 65 species were examined for tick infestation. Ticks removed from these birds have previously been investigated for the presence of Borrelia bacteria and the tick-borne encephalitis virus. In the present study, a total of 1102 ticks were available for molecular analysis of Babesia protozoan parasites. We found that 2.4% of the ticks examined, all I. ricinus, were positive for mammal-associated Babesia species. Out of all Babesia-positive samples, Babesia venatorum was the most prevalent (58%) species, followed by Babesia microti (38%) and Babesia capreoli (4.0%). B. venatorum and B. capreoli were detected in I. ricinus larvae, whereas B. microti was only present in I. ricinus nymphs. This supports the view that the two first-mentioned species are vertically (transovarially) transmitted in the tick population, in contrast to B. microti. The largest number of Babesia-infected ticks was removed from the common redstart (Phoenicurus phoenicurus) and European robin (Erithacus rubecula). CONCLUSIONS: This study reveals that Babesia protozoan parasites are present in ticks infesting migratory birds in south-eastern Sweden, which could potentially lead to the dissemination of these tick-borne microorganisms into new areas, thus posing a threat to humans and other mammals.

Mitogenome of emAlaudala/em emcheleensis/em (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes.

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. There was slightly higher A+T content than that of G+C in the mitogenome, with an obvious C skew. The ATG codon initiated all protein-coding genes, while six terminating codons were used. The secondary structure of rrnS contained three domains and 47 helices, whereas rrnL included six domains and 60 helices. All tRNAs could be folded into a classic clover-leaf secondary structure except for trnS (AGY). The CR1 could be divided into three domains, including several conserved boxes (C-string, F, E, D, C and B-box, Bird similarity box, CSB1). Comparative analyses within Sylvioidea mitogenomes showed that most mitochondrial features were consistent with that of the A. cheleensis mitogenome. The basal position of the Alaudidae within the Sylvioidea in our phylogenetic analyses is consistent with other recent studies.

Why neotypification of emLophorina/em emsuperba/em (Pennant, 1781) (Aves: Paradisaeidae) is justified-and necessary.

We review Irestedt et al.'s (2017) neotypification of the senior species name superba Pennant, 1781 in the bird-of-paradise genus Lophorina in response to Elliott et al. (2020) who challenged the resultant shift in name from the small isolate in New Guinea's Vogelkop to the widespread species in the island's central cordillera. In nine male plumage traits which differentiate the two species, six of which had been identified as novel by Irestedt et al., we show that the only two figures of the perished male holotype of superba match the central cordillera species more closely than the Vogelkop. We find as well that not only was the trading of bird-of-paradise skins from the central cordillera to coastal ports in the Vogelkop feasible before European contact, but application of superba to the central cordillera species also promotes nomenclatural stability: the name has been used overwhelmingly at species rank for that widespread form throughout post-19th century media. Re-assessment of Irestedt et al.'s point-by-point justification of neotypification under Article 75.3 of the ICZN (1999) Code establishes, furthermore, that their case meets the requirements of every condition specified in the article; the neotypification is thus valid. Elliott et al.'s alternative to fix superba to the Vogelkop isolate by type locality restriction is not Code-compliant, nor is their evidence for interpreting J.R. Forster as the author of the name. In conclusion, we lay out the correct nomenclature for the taxa of Lophorina under the Code.

Comparative Analysis of Annotation Pipelines Using the First Japanese White-Eye (Zosterops japonicus) Genome.

Introduced into Hawaii in the early 1900s, the Japanese white-eye or warbling white-eye (Zosterops japonicus) is now the most abundant land bird in the archipelago. Here, we present the first Z. japonicus genome, sequenced from an individual in its invasive range. This genome provides an important resource for future studies in invasion genomics. We annotated the genome using two workflows-standalone AUGUSTUS and BRAKER2. We found that AUGUSTUS was more conservative with gene predictions when compared with BRAKER2. The final number of annotated gene models was similar between the two workflows, but standalone AUGUSTUS had over 70% of gene predictions with Blast2GO annotations versus under 30% using BRAKER2. Additionally, we tested whether using RNA-seq data from 47 samples had a significant impact on annotation quality when compared with data from a single sample, as generating RNA-seq data for genome annotation can be expensive and requires well preserved tissue. We found that more data did not significantly change the number of annotated genes using AUGUSTUS but using BRAKER2 the number increased substantially. The results presented here will aid researchers in annotating draft genomes of nonmodel species as well as those studying invasion success.

Asymmetric introgression reveals the genetic architecture of a plumage trait.

Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.

Seasonal metabolic adjustments in an avian evolutionary relict restricted to mountain habitat.

For endotherms, maintaining body temperature during cold winters is energetically costly.Greater increase in winter maximum thermogenic capacity (Msum) has typically been correlated with improved cold tolerance. However, seasonal studies have shown equivocal direction change in basal metabolic rate (BMR) in winter, perhaps explained by latitude or phylogeny. We examined seasonal metabolic responses in the Cape rockjumper (Chaetops frenatus; "rockjumper"), a range-restricted mountain bird. We hypothesized that, given their mountain habitat preference, rockjumpers would be physiologically specialized for cooler air temperatures compared to other subtropical passerines. We measured body condition (using the ratio of Mb/tarsus), BMR, and Msum, in wild-living rockjumpers during winter and summer (n = 12 adults in winter -- 4 females, 8 males; n = 12 adults in summer -- 6 females, 6 males). We found birds had lesser BMR and thermal conductance, and greater Msum and body condition, in winter compared to summer. These changes may help rockjumpers conserve energy in winter while still allowing birds to produce more metabolic heat during the coldest air temperatures. When compared with existing data on avian seasonal metabolic adjustments, rockjumper BMR fit general patterns observed in passerines, but their Msum was low compared with other members of the oscine Passeriformes. These patterns may be explained by the narrow temperature range of their habitat not requiring cold-adjustment, or perhaps by their basal placement within passerine phylogeny. Further work on the physiological phenotypic plasticity in habitat specialists across different latitudinal zones and taxa is needed to better understand the relationship between metabolism, habitat, and phylogeny.

Ecological niche differentiation in Chiroxiphia and Antilophia manakins (Aves: Pipridae).

Species distribution models are useful for identifying the ecological characteristics that may limit a species' geographic range and for inferring patterns of speciation. Here, we test a hypothesis of niche conservatism across evolutionary time in a group of manakins (Aves: Pipridae), with a focus on Chiroxiphia boliviana, and examine the degree of ecological differentiation with other Chiroxiphia and Antilophia manakins. We tested whether allopatric sister species were more or less similar in environmental space than expected given their phylogenetic distances, which would suggest, respectively, ecological niche conservatism over time or ecologically mediated selection (i.e. niche divergence). We modeled the distribution of nine manakin taxa (C. boliviana, C. caudata, C. lanceolata, C. linearis, C. p. pareola, C. p. regina, C. p. napensis, Antilophia galeata and A. bokermanni) using Maxent. We first performed models for each taxon and compared them. To test our hypothesis we followed three approaches: (1) we tested whether C. boliviana could predict the distribution of the other manakin taxa and vice versa; (2) we compared the ecological niches by using metrics of niche overlap, niche equivalency and niche similarity; and (3) lastly, we tested whether niche differentiation corresponded to phylogenetic distances calculated from two recent phylogenies. All models had high training and test AUC values. Mean AUC ratios were high (>0.8) for most taxa, indicating performance better than random. Results suggested niche conservatism, and high niche overlap and equivalency between C. boliviana and C. caudata, but we found very low values between C. boliviana and the rest of the taxa. We found a negative, but not significant, relationship between niche overlap and phylogenetic distance, suggesting an increase in ecological differentiation and niche divergence over evolutionary time. Overall, we give some insights into the evolution of C. boliviana, proposing that ecological selection may have influenced its speciation.

Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla).

The stipple-throated antwrens of the genus Epinecrophylla (Aves: Thamnophilidae) are represented by eight species primarily found in the lowlands of the Amazon Basin and the Guiana Shield. The genus has a long and convoluted taxonomic history, with many attempts made to address the taxonomy and systematics of the group. Here we employ massively parallel sequencing of thousands of ultraconserved elements (UCEs) to provide both the most comprehensive subspecies-level phylogeny of Epinecrophylla antwrens and the first population-level genetic analyses for most species in the genus. Most of our results are robust to a diversity of phylogenetic and population genetic methods, but we show that even with thousands of loci we are unable to fully resolve the relationships between some western Amazonian species in the haematonota group. We uncovered phylogenetic relationships between taxa and patterns of population structure that are discordant with both morphology and current taxonomy. For example, we found deep genetic breaks between taxa in the ornata group that are currently regarded as species, and in the haematonota and leucophthalma groups we found paraphyly at the species and subspecies levels, respectively. As has been found in many Amazonian taxa, our phylogenetic results show that the major river systems of the Amazon Basin appear to have an effect on the genetic structure and range limits within Epinecrophylla. Our population genetics analyses showed extensive admixture between some taxa despite their deep genetic divergence. We present a revised taxonomy for the group and suggest areas for further study.

Multiple species delimitation approaches applied to the avian lark genus Alaudala.

Species delimitation has advanced from a purely phenotypic exercise to a branch of science that integrates multiple sources of data to identify independently evolving lineages that can be treated as species. We here test species limits in the avian Lesser Short-toed Lark Alaudala rufesens-Sand Lark A. raytal complex, which has an intricate taxonomic history, ranging from a single to three recognised species, with different inclusiveness in different treatments. Our integrative taxonomic approach is based on a combination of DNA sequences, plumage, biometrics, songs, song-flights, geographical distributions, habitat, and bioclimatic data, and using various methods including a species delimitation program (STACEY) based on the multispecies coalescent model. We propose that four species should be recognised: Lesser Short-toed Lark A. rufescens (sensu stricto), Heine's Short-toed Lark A. heinei, Asian Short-toed Lark A. cheleensis and Sand Lark A. raytal. There is also some evidence suggesting lineage separation within A. cheleensis and A. raytal, but additional data are required to evaluate this. The species delimitation based on STACEY agrees well with the non-genetic data. Although computer-based species delimitation programs can be useful in identifying independently evolving lineages, we stress that whenever possible, species hypotheses proposed by these programs should be tested by independent, non-genetic data. Our results highlight the difficulty and subjectivity of delimiting lineages and species, especially at early stages in the speciation process.

Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness.

Target capture sequencing effectively generates molecular marker arrays useful for molecular systematics. These extensive data sets are advantageous where previous studies using a few loci have failed to resolve relationships confidently. Moreover, target capture is well-suited to fragmented source DNA, allowing data collection from species that lack fresh tissues. Herein we use target capture to generate data for a phylogeny of the avian family Pipridae (manakins), a group that has been the subject of many behavioral and ecological studies. Most manakin species feature lek mating systems, where males exhibit complex behavioral displays including mechanical and vocal sounds, coordinated movements of multiple males, and high speed movements. We analyzed thousands of ultraconserved element (UCE) loci along with a smaller number of coding exons and their flanking regions from all but one species of Pipridae. We examined three different methods of phylogenetic estimation (concatenation and two multispecies coalescent methods). Phylogenetic inferences using UCE data yielded strongly supported estimates of phylogeny regardless of analytical method. Exon probes had limited capability to capture sequence data and resulted in phylogeny estimates with reduced support and modest topological differences relative to the UCE trees, although these conflicts had limited support. Two genera were paraphyletic among all analyses and data sets, with Antilophia nested within Chiroxiphia and Tyranneutes nested within Neopelma. The Chiroxiphia-Antilophia clade was an exception to the generally high support we observed; the topology of this clade differed among analyses, even those based on UCE data. To further explore relationships within this group, we employed two filtering strategies to remove low-information loci. Those analyses resulted in distinct topologies, suggesting that the relationships we identified within Chiroxiphia-Antilophia should be interpreted with caution. Despite the existence of a few continuing uncertainties, our analyses resulted in a robust phylogenetic hypothesis of the family Pipridae that provides a comparative framework for future ecomorphological and behavioral studies.

Comparative phylogeographic and demographic analyses reveal a congruent pattern of sister relationships between bird populations of the northern and south-central Atlantic Forest.

The Pernambuco Center of Endemism (PCE) is the northernmost strip of the Atlantic Forest (AF). Biogeographic affinities among avifaunas in the PCE, the southern-central Atlantic Forest (SCAF), and Amazonia (AM) have not been studied comprehensively, and current patterns of genetic diversity in the PCE remain unclear. The interplay between species' ecological attributes and historical processes, such as Pleistocene climate fluctuations or the appearance of rivers, may have affected population genetic structures in the PCE. Moreover, the role of past connections between the PCE and AM and the elevational distribution of species in assembling the PCE avifauna remain untested. Here, we investigated the biogeographic history of seven taxa endemic to the PCE within a comparative phylogeographic framework based on a mean of 3,618 independent single nucleotide polymorphisms (SNPs) extracted from flanking regions of ultraconserved elements (UCEs) and one mitochondrial gene. We found that PCE populations were more closely related to SCAF populations than they were to those in AM, regardless of their elevational range, with divergence times placed during the Mid-Pleistocene. These splits were consistent with a pattern of allopatric divergence with gene flow until the upper Pleistocene and no signal of rapid changes in population sizes. Our results support the existence of a Pleistocene refugium driving current genetic diversity in the PCE, thereby rejecting the role of the São Francisco River as a primary barrier for population divergence. Additionally, we found that connections with Amazonia also played a significant role in assembling the PCE avifauna through subsequent migration events.

Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family.

Mitochondrial genome provides useful information about species concerning its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,672 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with two rRNAs and 22 tRNAs were detected. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Duplicated control regions were found in the newly sequenced mitogenome. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over thirteen protein-coding genes in yellow-billed babbler mitogenome. Ka/Ks analysis indicated the highest synonymous substitution rate in the nad6 gene. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogeny results placed T. affinis in a separate group, a sister group of Garrulax. Overall, our results provide a useful information for future studies on the evolutionary and adaptive mechanisms of birds belong to the Leiothrichidae family.

Strict allopatric speciation of sky island Pyrrhula erythaca species complex.

Increasing evidence of post-divergence gene flow between taxa is shifting our understanding on the mode of speciation. A fundamental question arises concerning the circumstances under which strict allopatric speciation still holds true. Sky island populations might undergo reduced gene flow by niche conservatism to highland habitats and follow divergence in an allopatric manner. In this study, we tested this hypothesis in the sky island Grey-headed Bullfinch (Pyrrhula erythaca) species complex via statistical analyses of both genetic and ecological data. Results of coalescent-based analysis of multiple nuclear loci suggested that P. e. owstoni likely colonized Taiwan island during the severe mid-Pleistocene glacial climate followed by strictly allopatric divergence from P. e. erythaca distributed in Himalayas-Hengduan mountains and central North China. Results of ecological niche modeling suggested that their speciation may be attributed to the niche conservatism of these birds and the lack of a suitable ecological corridor during subsequent milder glacial episodes. In addition, we delimited the traditionally defined P. erythaca into two full species, P. erythaca in the Asian mainland and P. owstoni on the island of Taiwan, based on both genetic and behavioural evidences. These results suggest that ecology can have a dynamic role in allowing highland populations to expand their ranges and isolated by habitat barriers to diversify in a strictly allopatric manner.