Phylogeographic patterns in widespread corvid birds

Demographic patterns of two related desert shrubs with overlapping distributions in response to past climate changes

Numerous studies have revealed that past geological events and climatic fluctuations had profoundly affected the genetic structure and demographic patterns of species. However, related species with overlapping ranges may have responded to such environmental changes in different ways. In this study, we compared the genetic structure and population dynamics of two typical desert shrubs with overlapping distributions in northern China, Nitraria tangutorum and Nitraria sphaerocarpa, based on chloroplast DNA (cpDNA) variations and species distribution models. We sequenced two cpDNA fragments (trnH-trnA and atpH-atpI) in 633 individuals sampled from 52 natural populations. Twenty-four chlorotypes, including eight rare chlorotypes, were identified, and a single dominant haplotype (H4) widely occurred in the entire geographical ranges of the two species. There were also a few distinctive chlorotypes fixed in different geographical regions. Population structure analyses suggested that the two species had significantly different levels of total genetic diversity and interpopulation differentiation, which was highly likely correlated with the special habitat preferences of the two species. A clear phylogeographic structure was identified to exist among populations of N. sphaerocarpa, but not exist for N. tangutorum. The neutral tests, together with the distribution of pairwise differences revealed that N. tangutorum experienced a sudden demographic expansion, and its expansion approximately occurred between 21 and 7 Kya before present, while a rapid range expansion was not identified for N. sphaerocarpa. The ecological niche modeling (ENM) analysis indicated that the potential ranges of two species apparently fluctuated during the past and present periods, with obvious contraction in the Last Glacial Maximum (LGM) and recolonization in the present, respectively, comparing to the Last Interglacial (LIG). These findings suggest that the two species extensively occurred in the Northwest of China before the Quaternary, and the current populations of them originated from a few separated glacial refugia following their habitat fragmentation in the Quarternary. Our results provide new insights on the impact of past geological and climatic fluctuations on the population dynamics of desert plants in northwestern China, and further enforce the hypothesis that there were several independent glacial refugia for these species during the Quaternary glaciations.

Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Zones of secondary contact provide a good opportunity to investigate the origin and dynamics of reproductive isolation between related populations. We analyzed genetic and phenotypic patterns and gene flow between two subspecies of the Eurasian magpie Pica pica s.l. which recently came into contact after presumably long periods of isolation. We describe the distribution of subspecies in a young contact zone at Argun’ river basin in southern Siberia where populations occur in parapatry and an older hybrid population in eastern Mongolia. Based on genome-wide SNP data, we analyzed patterns and strength of gene flow between the subspecies. Our results indicate occasional hybridization with backcrossing and asymmetric introgression along a wide range in Transbaikalia and locally in eastern Mongolia. Males of P. p. jankowskii apparently exhibit higher dispersal ability towards the west compared to P. p. leucoptera (towards the east). The former occasionally migrates to eastern Mongolia and Transbaikalia where introgression of nuclear, but not mitochondrial DNA was evident. Bioacoustic investigations showed differences between the subspecies in speed and structure of vocalization. We discovered intermediate calls of hybrid magpies and bilingual birds alternating calls that are typical for the two taxa. Furthermore, we found dramatically decreased reproductive success in hybridogeneous populations. By complementing our results with established phylogeographic patterns of P. pica s.l. based on a mitochondrial marker sequence, and considering indications of sterility of hybrids in the contact zone, we propose to elevate the two corresponding subspecies to species level: P. pica for the western form and P. serica for the eastern form.

Speciation and population divergence in a mutualistic seed dispersing bird

Bird-mediated seed dispersal is crucial for the regeneration and viability of ecosystems, often resulting in complex mutualistic species networks. Yet, how this mutualism drives the evolution of seed dispersing birds is still poorly understood. In the present study we combine whole genome re-sequencing analyses and morphometric data to assess the evolutionary processes that shaped the diversification of the Eurasian nutcracker (Nucifraga), a seed disperser known for its mutualism with pines (Pinus). Our results show that the divergence and phylogeographic patterns of nutcrackers resemble those of other non-mutualistic passerine birds and suggest that their early diversification was shaped by similar biogeographic and climatic processes. The limited variation in foraging traits indicates that local adaptation to pines likely played a minor role. Our study shows that close mutualistic relationships between bird and plant species might not necessarily act as a primary driver of evolution and diversification in resource-specialized birds.

Genomic and phylogeographic analyses indicate that resource-specialization did not play a major role in the diversification and speciation of seed dispersing nutcrackers

Investigations on Sarcocystis species in the leg muscles of the bird family Corvidae in Lithuania

Although three species of Sarcocystis, S. cornixi, S. corvusi and S. kutkienae, have been described in corvids, molecular studies of sarcocysts isolated from these birds are incomplete. Leg muscles of 83 corvids, 35 hooded crows (Corvus cornix), 21 western jackdaws (Coloeus monedula), 11 rooks (Corvus frugilegus), 9 common ravens (Corvus corax), 4 common magpies (Pica pica) and 3 Eurasian jays (Garrulus glandarius), from Lithuania were examined for the presence of Sarcocystis spp. in the present study. In methylene blue-stained squashed samples, sarcocysts were detected in 26 birds (31.0%). Under a light microscope, two morphological types of sarcocysts were distinguished (type A and type B). Sarcocysts of type A had a smooth and thin (about 1 μm) cyst wall, while cysts of type B were characterised by a thicker (1.4-2.5 μm) cyst wall. Based on ITS1 sequence comparison, sarcocysts of type A were identified as S. halieti and Sarcocystis sp. ex Corvus corax, whereas cysts of type B belonged to S. kutkienae and S. cornixi. Furthermore, it was demonstrated that a single bird could host two different Sarcocystis spp. Sarcocystis halieti was detected in corvids for the first time in the common raven and the hooded crow. Also, this study presents the first evidence of S. kutkienae in the hooded crow and the common magpie, and S. cornixi in the western jackdaw. Sarcocystis sp. ex Corvus corax was genetically characterised using almost complete 18S rDNA, partial 28S rDNA and complete ITS1 sequences. Sarcocystis sp. ex Corvus corax clustered together with S. columbae, S. corvusi and S. halieti in phylogenetic trees reconstructed using 28S rDNA and ITS1 sequences.

Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review

A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10336-021-01893-x.

A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows

Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour.

Complete mitochondrial genomes of five subspecies of the Eurasian magpie Pica pica, obtained with Oxford Nanopore MinION, and their interpretation regarding intraspecific taxonomy

The complete mitochondrial (mt) genomes of five subspecies of the Eurasian (Common) magpie Pica pica were determined for the first time. Lengths of the circular genomes comprise 13 protein-coding genes, two rRNA genes (for 12S rRNA and 16S rRNA), 22 tRNA genes, and the non-coding control region (CR). Gene content and lengths of the genomes (16,936-16,945 bp) are similar to typical vertebrate mt genomes. The subspecies studied differs by several single substitutions and indels, especially in the CR. The phylogenetic tree based on complete mt genomes shows a deep divergence of the two groups of subspecies which supports the proposed division into two distinct species: P. pica and P. serica.

Dispersal Predicts Hybrid Zone Widths across Animal Diversity: Implications for Species Borders under Incomplete Reproductive Isolation

Hybrid zones occur as range boundaries for many animal taxa. One model for how hybrid zones form and stabilize is the tension zone model, a version of which predicts that hybrid zone widths are determined by a balance between random dispersal into hybrid zones and selection against hybrids. Here, we examine whether random dispersal and proxies for selection against hybrids (genetic distances between hybridizing pairs) can explain variation in hybrid zone widths across 131 hybridizing pairs of animals. We show that these factors alone can explain ∼40% of the variation in zone width among animal hybrid zones, with dispersal explaining far more of the variation than genetic distances. Patterns within clades were idiosyncratic. Genetic distances predicted hybrid zone widths particularly well for reptiles, while this relationship was opposite tension zone predictions in birds. Last, the data suggest that dispersal and molecular divergence set lower bounds on hybrid zone widths in animals, indicating that there are geographic restrictions on hybrid zone formation. Overall, our analyses reinforce the fundamental importance of dispersal in hybrid zone formation and more generally in the ecology of range boundaries.

Phylogeny of the Eurasian Wren Nannus troglodytes (Aves: Passeriformes: Troglodytidae) reveals deep and complex diversification patterns of Ibero-Maghrebian and Cyrenaican populations

The Mediterranean Basin represents a Global Biodiversity Hotspot where many organisms show high inter- and intraspecific differentiation. Extant phylogeographic patterns of terrestrial circum-Mediterranean faunas were mainly shaped through Pleistocene range shifts and range fragmentations due to retreat into different glacial refugia. Thus, several extant Mediterranean bird species have diversified by surviving glaciations in different hospitable refugia and subsequently expanded their distribution ranges during the Holocene. Such a scenario was also suggested for the Eurasian Wren (Nannus troglodytes) despite the lack of genetic data for most Mediterranean subspecies. Our phylogenetic multi-locus analysis comprised 18 out of 28 currently accepted subspecies of N. troglodytes, including all but one subspecies which are present in the Mediterranean Basin. The resulting phylogenetic reconstruction dated the onset of the entire Holarctic radiation of three Nannus species to the early Pleistocene. In the Eurasian Wren, two North African subspecies represented separate basal lineages from the Maghreb (N. t. kabylorum) and from the Libyan Cyrenaica (N. t. juniperi), being only distantly related to other Mediterranean populations. Although N. troglodytes appeared to be paraphyletic with respect to the Nearctic Winter Wren (N. hiemalis), respective nodes did not receive strong statistical support. In contrast, paraphyly of the Ibero-Maghrebian taxon N. t. kabylorum was strongly supported. Southern Iberian populations of N. t. kabylorum did not clade with Maghrebian populations of the same subspecies but formed a sister clade to a highly diverse European clade (including nominate N. t. troglodytes and eight further taxa). In accordance with a pattern also found in other birds, Eurasian populations were split into a western clade (Europe, Caucasus) and an eastern clade (Central Asia, Sino-Himalayas, East Asia). This complex phylogeographic pattern revealed cryptic diversification in N. troglodytes, especially in the Iberio-Maghrebian region.

Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species

The ratio of nonsynonymous over synonymous sequence divergence, dN/dS, is a widely used estimate of the nonsynonymous over synonymous fixation rate ratio ω, which measures the extent to which natural selection modulates protein sequence evolution. Its computation is based on a phylogenetic approach and computes sequence divergence of protein-coding DNA between species, traditionally using a single representative DNA sequence per species. This approach ignores the presence of polymorphisms and relies on the indirect assumption that new mutations fix instantaneously, an assumption which is generally violated and reasonable only for distantly related species. The violation of the underlying assumption leads to a time-dependence of sequence divergence, and biased estimates of ω in particular for closely related species, where the contribution of ancestral and lineage-specific polymorphisms to sequence divergence is substantial. We here use a time-dependent Poisson random field model to derive an analytical expression of dN/dS as a function of divergence time and sample size. We then extend our framework to the estimation of the proportion of adaptive protein evolution α. This mathematical treatment enables us to show that the joint usage of polymorphism and divergence data can assist the inference of selection for closely related species. Moreover, our analytical results provide the basis for a protocol for the estimation of ω and α for closely related species. We illustrate the performance of this protocol by studying a population data set of four corvid species, which involves the estimation of ω and α at different time-scales and for several choices of sample sizes.

The complete mitochondrial genome of Daurian jackdaw (Corvus dauuricus)

In this study, the complete mitochondrial genome of Daurian jackdaw (Corvus dauuricus, Pallas, 1776) was sequenced and deposited to GeneBank for the first time using muscle tissue. This mitochondrial genome is a circular molecule of 16921 bp in length and sequence analysis showed it contains 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes and D_loop. The phylogenetic analysis basis of 12 protein-coding genes except for ND6 gene of 13 species shows that most of the genus of Corvus were grouped into two clades, and C. dauuricus was basal to all other Corvus.

Population genomics of two congeneric Palaearctic shorebirds reveals differential impacts of Quaternary climate oscillations across habitats types

Intracontinental biotic divisions across the vast Palaearctic region are not well-characterized. Past research has revealed patterns ranging from a lack of population structure to deep divergences along varied lines of separation. Here we compared biogeographic patterns of two Palaearctic shorebirds with different habitat preferences, Whimbrel (Numenius phaeopus) and Eurasian curlew (N. arquata). Using genome-wide markers from populations across the Palaearctic, we applied a multitude of population genomic and phylogenomic approaches to elucidate population structure. Most importantly, we tested for isolation by distance and visualized barriers and corridors to gene flow. We found shallow Palaearctic population structure in subpolar bog and tundra-breeding whimbrels, consistent with other species breeding at a similarly high latitude, indicating connectivity across the tundra belt, both presently and during southward shifts in periods of global cooling. In contrast, the temperate grassland-breeding Eurasian curlew emerged in three distinct clades corresponding to glacial refugia. Barriers to gene flow coincided with areas of topographic relief in the central Palaearctic for whimbrels and further east for Eurasian curlews. Our findings highlight the interplay of historic and ecological factors in influencing present-day population structure of Palaearctic biota.

New insights into population structure of the European golden eagle (Aquila chrysaetos) revealed by microsatellite analysis

Connectivity between golden eagle (Aquila chrysaetos) populations is poorly understood. Field studies exploring natal dispersal suggest that this raptor is a philopatric species, but with the ability to roam far. However, little is known about the population structure of the species in Europe. Our study is based on 14 microsatellite loci and is complemented by new and previously published mitochondrial control region DNA data. The present dataset includes 121 eagles from Scotland, Norway, Finland, Estonia, the Mediterranean and Alpine regions. Our sampling focused on the Alpine and Mediterranean populations because both mitochondrial DNA (mtDNA) lineages found in golden eagles, the Holarctic and the Mediterranean, are known to co-occur there. Cluster analyses of nuclear DNA support a shallow split into northern and southern populations in Europe, similar to the distribution of the two mtDNA lineages, with the Holarctic lineage occurring in the north and the Mediterranean lineage predominating in the south. Additionally, Scotland shows significant differentiation and low relative migration levels that indicate isolation from the mainland populations. Alpine and Mediterranean golden eagles do not show nuclear structure corresponding to divergent mtDNA lineages. This indicates that the presence of northern Holarctic mitochondrial haplotypes in the Alps and the Mediterranean is attributable to past admixture rather than recent long-distance dispersal.

Deep Phylogeographic Breaks in Magpie Pica pica Across the Holarctic: Concordance with Bioacoustics and Phenotypes

We examined sequences of the mitochondrial control region in magpies (Pica pica) from the entire distribution range and found deep genetic splits into four major lineages: (1) group West (Europe-Siberia), (2) group East (southern Far East), (3) P. p. mauritanica (North Africa), and (4) P. p. hudsonia (North America). These lineages show a geographic pattern corresponding to known subspecies or subspecies groups. Genetic variation within the widely-distributed group West is low and neutrality tests supported a recent expansion scenario. The haplotypes from Kamchatka, representing a separated sublineage with clear affinity to the European-Siberian group, are almost identical, implying a recent bottleneck. Group East contained two subclades without clear geographic pattern, presumably due to admixing of populations that had diverged in Pleistocene refuges. The homogeneity of the Kyushu population supports historical reports of introduction of the species from Korea. In contrast, the high variation in the recently established Hokkaido population may reflect an ongoing invasion from several populations of the Far Eastern mainland. Bioacoustic data based on chatter call differentiate groups of subspecies and reflect phylogeographic patterns, i.e., mitochondrial lineages. Furthermore, we report the fast spreading of P. p. jankowskii towards the west along the upper Amur River, and a slower shifting of P. p. leucoptera in the opposite direction thus yielding a new contact zone. Overall, our data support a scenario of divergence in geographic isolation, but the ongoing expansion of distribution ranges may lead to major changes in phylogeographic patterns.

Phylogeography and hybridization of corvid birds in the Palearctic Region

Natural hybridization increases a lot phenotypic and genetic diversity and shapes intra-species patterns, which is a subject of phylogeography. We studied mitochondrial and complete genome variation in the bird family Corvidae, genera Corvus, Pica, Cyanopica, Perisoreus and Nucifraga. In the classic case of natural hybridization between carrion and hooded crows in Siberia, we found no decreased fitness of hybrids, but instead positive assortative mating which should restrict hybrid zone width. Several genetic markers were unable to discriminate between pure carrion and hooded crows. Mitochondrial DNA sequences revealed no difference between carrion and hooded crows, but instead two diverged haplogroups within the eastern part of the distribution range of the carrion crow. NGS resulted in a clear pattern of diversification of pure forms and hybrids (by using SNPs), and showed genomic regions of increased variability, the so-called “speciation islands”. Comparing European and Siberian crow hybrid zones, differences in genome regions bearing genes of melanogenesis supposedly under divergent selection were found. Comparative phylogeographic analysis of 10 widely distributed Palearctic species revealed two kinds of patterns: one with a division into two haplogroups, western and eastern, and another one without such a division. These two phylogeographic patterns might be explained by different habitat preferences: mainly open fields for the first group and forests for the second one. One glacial refuge was assigned to the latter group, while west-east group species might have survived in several refuges. One of such species, the Eurasian magpie (Pica pica) has a gap in its range in Transbaikalia, which is currently shrinking before our eyes. The two subspecies divided by this gap differ in phenotype, mtDNA and vocalization. In their young contact zone, some hybridization occurs with small introgression limited by certain post-zygotic isolation.

Genetic and Molecular Basis of Feather Diversity in Birds

Feather diversity is striking in many aspects. Although the development of feather has been studied for decades, genetic and genomic studies of feather diversity have begun only recently. Many questions remain to be answered by multidisciplinary approaches. In this review, we discuss three levels of feather diversity: Feather morphotypes, intraspecific variations, and interspecific variations. We summarize recent studies of feather evolution in terms of genetics, genomics, and developmental biology and provide perspectives for future research. Specifically, this review includes the following topics: 1) Diversity of feather morphotype; 2) feather diversity among different breeds of domesticated birds, including variations in pigmentation pattern, in feather length or regional identity, in feather orientation, in feather distribution, and in feather structure; and 3) diversity of feathers among avian species, including plumage color and morph differences between species and the regulatory differences in downy feather development between altricial and precocial birds. Finally, we discussed future research directions.

Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family

Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella was present in the Sino‐Himalayan Mountains or these mountains and Central Asia–Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid‐Pliocene to early Pleistocene. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo‐/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacial periods, followed by fragmentation during interglacials—contrary to the usual view that glacial periods resulted mainly in fragmentations.

How do rivers, geographic distance, and dispersal behavior influence genetic structure in two sympatric New World monkeys?

Dispersal, one of the major factors affecting the gene flow between populations, shapes the spatial distribution of genetic diversity within species. Alouatta macconnelli and Saguinus midas are two Neotropical monkey species that sympatrically inhabit the Guiana shield in northern Amazonia and are likely to differ in their dispersal behavior and vagility. We took advantage of their sympatry to investigate, over a fine geographical scale (∼50 km long), the relationship between spatial genetic structure, on the one hand, and geographical features and the species' dispersal behavior on the other. A total of 84 A. macconnelli individuals from 25 social units and 76 S. midas individuals from 19 social units were genotyped for nine microsatellite markers. Both species displayed high genetic diversity and allelic richness. However, patterns of genetic structure differed between the two species. In A. macconnelli, no genetic substructuring was observed, while in S. midas we detected significant structuring, but this structuring was not correlated with geographical features, such as the location of individuals relative to the river and/or the distance between them. Instead, the geographical distribution of genetic variation observed for each species is predominantly explained by each species' dispersal pattern. We identified bisexual dispersal for both species, but with significant differences, either in the distance or in the rate of dispersal, between species and sexes. Genetic relatedness within social units was higher in S. midas than in A. macconnelli: gene flow between social units seems limited in S. midas, especially for females, while high dispersal characterizes A. macconnelli, where females seem to disperse at lower rate but at a longer distance than males.

Adaptive bill morphology for enhanced tool manipulation in New Caledonian crows

Early increased sophistication of human tools is thought to be underpinned by adaptive morphology for efficient tool manipulation. Such adaptive specialisation is unknown in nonhuman primates but may have evolved in the New Caledonian crow, which has sophisticated tool manufacture. The straightness of its bill, for example, may be adaptive for enhanced visually-directed use of tools. Here, we examine in detail the shape and internal structure of the New Caledonian crow’s bill using Principal Components Analysis and Computed Tomography within a comparative framework. We found that the bill has a combination of interrelated shape and structural features unique within Corvus, and possibly birds generally. The upper mandible is relatively deep and short with a straight cutting edge, and the lower mandible is strengthened and upturned. These novel combined attributes would be functional for (i) counteracting the unique loading patterns acting on the bill when manipulating tools, (ii) a strong precision grip to hold tools securely, and (iii) enhanced visually-guided tool use. Our findings indicate that the New Caledonian crow’s innovative bill has been adapted for tool manipulation to at least some degree. Early increased sophistication of tools may require the co-evolution of morphology that provides improved manipulatory skills.

Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes

The Eurasian or spotted nutcracker (Nucifraga caryocatactes) is a widespread resident corvid found throughout the Palearctic from Central Europe to Japan. Characterized by periodic bouts of irruptive dispersal in search of Pinus seed crops, this species has potential for high levels of gene flow across its range. Previous analysis of 11 individuals did not find significant range-wide population genetic structure. We investigated population structure using 924 base pairs of mitochondrial DNA control region sequence data from 62 individuals from 12 populations distributed throughout the nutcracker’s range. We complemented this analysis by incorporating additional genetic data from previously published sequences. High levels of genetic diversity and limited population genetic structure were detected suggesting that potential barriers to dispersal do not restrict gene flow in nutcrackers.

Molecular markers reveal limited population genetic structure in a North American corvid, Clark's nutcracker (Nucifraga columbiana)

The genetic impact of barriers and Pleistocene glaciations on high latitude resident species has not been widely investigated. The Clark’s nutcracker is an endemic North American corvid closely associated with Pinus-dominated forests. The nutcracker’s encompasses known barriers to dispersal for other species, and glaciated and unglaciated areas. Clark’s nutcrackers also irruptively disperse long distances in search of pine seed crops, creating the potential for gene flow among populations. Using the highly variable mitochondrial DNA control region, seven microsatellite loci, and species distribution modeling, we examined the effects of glaciations and dispersal barriers on population genetic patterns and population structure of nutcrackers. We sequenced 900 bp of mitochondrial control region for 169 individuals from 15 populations and analysed seven polymorphic microsatellite loci for 13 populations across the Clark’s nutcracker range. We used species distribution modeling and a range of phylogeographic analyses to examine evolutionary history. Clark’s nutcracker populations are not highly differentiated throughout their range, suggesting high levels of gene flow among populations, though we did find some evidence of isolation by distance and peripheral isolation. Our analyses suggested expansion from a single refugium after the last glacial maximum, but patterns of genetic diversity and paleodistribution modeling of suitable habitat were inconclusive as to the location of this refugium. Potential barriers to dispersal (e.g. mountain ranges) do not appear to restrict gene flow in Clark’s nutcracker, and postglacial expansion likely occurred quickly from a single refugium located south of the ice sheets.

Differentiation in neutral genes and a candidate gene in the pied flycatcher: using biological archives to track global climate change

Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.

Phylogeny and genetic history of the Siberian salamander (Salamandrella keyserlingii, Dybowski, 1870) inferred from complete mitochondrial genomes

We assessed phylogeny of the Siberian salamander (Salamandrella keyserlingii, Dybowski, 1870), the most northern ectothermic, terrestrial vertebrate in Eurasia, by sequence analysis of complete mitochondrial genomes in 26 specimens from different localities (China, Khabarovsk region, Sakhalin, Yakutia, Magadan region, Chukotka, Kamchatka, Ural, European part of Russia). In addition, a complete mitochondrial genome of the Schrenck salamander, Salamandrella schrenckii, was determined for the first time. Bayesian phylogenetic analysis of the entire mtDNA genomes of S. keyserlingii demonstrates that two haplotype clades, AB and C, radiated about 1.4 million years ago (Mya). Bayesian skyline plots of population size change through time show an expansion around 250 thousand years ago (kya) and then a decline around the Last Glacial Maximum (25 kya) with subsequent restoration of population size. Climatic changes during the Quaternary period have dramatically affected the population genetic structure of the Siberian salamanders. In addition, complete mtDNA sequence analysis allowed us to recognize that the vast area of Northern Eurasia was colonized only by the Siberian salamander clade C1b during the last 150 kya. Meanwhile, we were unable to find evidence of molecular adaptation in this clade by analyzing the whole mitochondrial genomes of the Siberian salamanders.

An Update of Wallace’s Zoogeographic Regions of the World

Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.

Brains, tools, innovation and biogeography in crows and ravens

BACKGROUND

Crows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and well-known examples exist of several crow species having evolved innovative strategies and even use of tools in their search for food. The 40 Corvus species have also been successful dispersers and are distributed on most continents and in remote archipelagos.

RESULTS

This study presents the first molecular phylogeny including all species and a number of subspecies within the genus Corvus. We date the phylogeny and determine ancestral areas to investigate historical biogeographical patterns of the crows. Additionally, we use data on brain size and a large database on innovative behaviour and tool use to test whether brain size (i) explains innovative behaviour and success in applying tools when foraging and (ii) has some correlative role in the success of colonization of islands. Our results demonstrate that crows originated in the Palaearctic in the Miocene from where they dispersed to North America and the Caribbean, Africa and Australasia. We find that relative brain size alone does not explain tool use, innovative feeding strategies and dispersal success within crows.

CONCLUSIONS

Our study supports monophyly of the genus Corvus and further demonstrates the direction and timing of colonization from the area of origin in the Palaearctic to other continents and archipelagos. The Caribbean was probably colonized from North America, although some North American ancestor may have gone extinct, and the Pacific was colonized multiple times from Asia and Australia. We did not find a correlation between relative brain size, tool use, innovative feeding strategies and dispersal success. Hence, we propose that all crows and ravens have relatively large brains compared to other birds and thus the potential to be innovative if conditions and circumstances are right.

Multilocus coalescence analyses support a mtDNA-based phylogeographic history for a widespread Palearctic passerine bird, Sitta europaea

Our understanding of species phylogeography in much of the Palearctic is incomplete. In addition, many existing studies based solely on mitochondrial DNA (mtDNA) can provide a biased view of phylogeographic history because of the effects of lineage sorting, natural selection, or hybridization. We analyzed 13 introns to assess a mtDNA study of the Eurasian nuthatch (Sitta europaea) that suggested a seemingly contemporaneous origin of distinct taxa in the Caucasus, Europe, and Asia. Neutrality tests showed no evidence of selection on either the mtDNA or nuclear sequences. Most nuclear gene trees, except for Z-linked ones, did not recover the three lineages, which we attribute to recent splitting. Analyses of the 13 introns combined revealed the same three groups as did the mtDNA and suggested that nuthatches experienced a trichotomous (or two indistinguishable) split(s) 1-2 million years ago (Mya) and have remained isolated with trifling if not zero gene flow since then, and the Asian group increased in population size. This result demonstrates the usefulness of mtDNA in discovering phylogeographic patterns. The use of multiple nuclear loci facilitated detection of an introgressed individual and improved estimates of process parameters such as divergence time and population expansion. We recommend that phylogeographic studies should be based on both mtDNA and nuclear genes.

General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq

BACKGROUND

Species with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose. Microarray-based studies in several independent male heterogametic XX/XY systems suggest that dosage compensation mechanisms are in place to mitigate the detrimental effects of gene dose differences. However, recent genomic research on female heterogametic ZZ/ZW systems has generated surprising results. In two bird species and one lepidopteran no evidence for a global dosage compensating mechanism has been found. The recent advent of massively parallel RNA sequencing now opens up the possibility to gauge the generality of this observation with a broader phylogenetic sampling. It further allows assessing the validity of microarray-based inference on dosage compensation with a novel technology.

RESULTS

We here exemplify this approach using massively parallel sequencing on barcoded individuals of a bird species, the European crow (Corvus corone), where previously no genetic resources were available. Testing for Z-linkage with quantitative PCR (qPCR,) we first establish that orthology with distantly related species (chicken, zebra finch) can be used as a good predictor for chromosomal affiliation of a gene. We then use a digital measure of gene expression (RNA-seq) on brain transcriptome and confirm a global lack of dosage compensation on the Z chromosome. RNA-seq estimates of male-to-female (m:f) expression difference on the Z compare well to previous microarray-based estimates in birds and lepidopterans. The data further lends support that an up-regulation of female Z-linked genes conveys partial compensation and suggest a relationship between sex-bias and absolute expression level of a gene. Correlation of sex-biased gene expression on the Z chromosome across all three bird species further suggests that the degree of compensation has been partly conserved across 100 million years of avian evolution.

CONCLUSIONS

This work demonstrates that the study of dosage compensation has become amenable to species where previously no genetic resources were available. Massively parallele transcriptome sequencing allows re-assessing the degree of dosage compensation with a novel tool in well-studies species and, in addition, gain valuable insights into the generality of mechanisms across independent taxonomic group for both the XX/XY and ZZ/ZW system.

Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow

Recent advances in sequencing technology promise to provide new strategies for studying population differentiation and speciation phenomena in their earliest phases. We focus here on the black carrion crow (Corvus [corone] corone), which forms a zone of hybridization and overlap with the grey coated hooded crow (Corvus [corone] cornix). However, although these semispecies are taxonomically distinct, previous analyses based on several types of genetic markers did not reveal significant molecular differentiation between them. We here corroborate this result with sequence data obtained from a set of 25 nuclear intronic loci. Thus, the system represents a case of a very early phase of species divergence that requires new molecular approaches for its description. We have therefore generated RNAseq expression profiles using barcoded massively parallel pyrosequencing of brain mRNA from six individuals of the carrion crow and five individuals from a hybrid zone with the hooded crow. We obtained 856 675 reads from two runs, with average read length of 270 nt and coverage of 8.44. Reads were assembled de novo into 19 552 contigs, 70% of which could be assigned to annotated genes in chicken and zebra finch. This resulted in a total of 7637 orthologous genes and a core set of 1301 genes that could be compared across all individuals. We find a clear clustering of expression profiles for the pure carrion crow animals and disperse profiles for the animals from the hybrid zone. These results suggest that gene expression differences may indeed be a sensitive indicator of initial species divergence.