Genetic similarity among Eurasian subspecies of boreal owls Aegolius funereus

Boreal owls Aegolius funereus (referred to as Tengmalm's owls in Europe) breed in boreal forests throughout the Holarctic region and in high-elevation subalpine forests further south. They are currently classified as seven subspecies; six found throughout Eurasia, and one in North America. The geographic distribution of boreal owls in North America and Eurasia is similar, as are their patterns of dispersal and irruption. Because a recent genetic study of boreal owls in North America found very little genetic differentiation among widely disparate locations, we expected that boreal owls in Eurasia similarly would have very little genetic differentiation. Using seven microsatellite markers, we analyzed genetic samples from 275 boreal owls in North America, 36 in Norway, and five in eastern Russia. We found no detectable genetic differentiation between Norwegian and Russian owls, but notable differentiation between North American and Eurasian owls. Low intra-continental genetic differentiation likely results from high rates of long-distance dispersal among subpopulations of boreal owls. In light of these results, we recommend further genetic sampling of boreal owls throughout Eurasia in order to determine whether six separate subspecies here are warranted.     

Refugial origins of reindeer (Rangifer tarandus L.) inferred from mitochondrial DNA sequences

The glacial-interglacial cycles of the upper Pleistocene have had a major impact on the recent evolutionary history of Arctic species. To assess the effects of these large-scale climatic fluctuations to a large, migratory Arctic mammal, we assessed the phylogeography of reindeer (Rangifer tarandus) as inferred from mitochondrial DNA (mtDNA) sequence variation in the control region. Phylogenetic relationships among haplotypes seem to reflect historical patterns of fragmentation and colonization rather than clear-cut relationships among extant populations and subspecies. Three major haplogroups were detected, presumably representing three separate populations during the last glacial. The most influential one has contributed to the gene pool of all extant subspecies and seems to represent a large and continuous glacial population extending from Beringia and far into Eurasia. A smaller, more localized refugium was most likely isolated in connection with ice expansion in western Eurasia. A third glacial refugium was presumably located south of the ice sheet in North America, possibly comprising several separate refugial populations. Significant demographic population expansion was detected for the two haplogroups representing the western Eurasian and Beringian glacial populations. The former apparently expanded when the ice cap retreated by the end of the last glacial. The large continuous one, in contrast, seems to have expanded by the end of the last interglacial, indicating that the warm interglacial climate accompanied by marine transgression and forest expansion significantly confined population size on the continental mainland. Our data demonstrate that the current subspecies designation does not reflect the mtDNA phylogeography of the species, which in turn may indicate that morphological differences among subspecies have evolved as adaptive responses to postglacial environmental change.     

Are subspecies useful in evolutionary and conservation biology?

The taxonomic rank of subspecies remains highly contentious, largely because traditional subspecies boundaries have sometimes been contradicted by molecular phylogenetic data. The most complete meta-analysis to date, for instance, found that only 3% of traditional avian subspecies represented distinct phylogenetic lineages. However, the global generality of this phenomenon remains unclear due to this previous study's narrow geographic focus on continental Nearctic and Palearctic subspecies. Here, we present a new global analysis of avian subspecies and show that 36% of avian subspecies are, in fact, phylogenetically distinct. Among biogeographic realms we find significant differences in the proportion of subspecies that are phylogenetically distinct, with Nearctic/Palearctic subspecies showing significantly reduced levels of differentiation. Additionally, there are differences between island and continental subspecies, with continental subspecies significantly less likely to be genetically distinct. These results indicate that the overall level of congruence between taxonomic subspecies and molecular phylogenetic data is greater than previously thought. We suggest that the widespread impression that avian subspecies are not real arises from a predominance of studies focusing on continental subspecies in North America and Eurasia, regions which show unusually low levels of genetic differentiation. The broader picture is that avian subspecies often provide an effective short-cut for estimating patterns of intraspecific genetic diversity, thereby providing a useful tool for the study of evolutionary divergence and conservation.     

The complex history of a gene proposed to participate in a sexual isolation mechanism in house mice

Previous behavioral experiments showed that mouse salivary androgen-binding protein (ABP) was involved in interindividual recognition and might play a role in sexual isolation between house mouse (Mus musculus) subspecies. The pattern of evolution of Abpa, the gene for the alpha subunit of ABP, was found to be consistent with this hypothesis. Abpa apparently diverged rapidly between species and subspecies with a large excess of nonsynonymous substitutions, a lack of exon polymorphism within each of the three subspecies, and a lack of intron polymorphism in the one subspecies studied (M. musculus domesticus). Here we characterized the intron and exon sequence variations of this gene in house mouse populations from central Eurasia, a region yet unsampled and thought to be close to the cradle of the radiation of the subspecies. We also determined the intron and exon sequences in seven other species of the genus Mus. We confirmed the general pattern of rapid evolution by essentially nonsynonymous substitutions, both inter- and intraspecifically, supporting the idea that Darwinian selection has driven the evolution of this gene. We also observed a uniform intron sequence in five samples of M. musculus musculus, suggesting that a selective sweep might have occurred for that allele. In contrast to previous results, however, we found extensive intron and exon polymorphism in some house mouse populations from central Eurasia. We also found evidence for secondary admixture of the subspecies-specific alleles in regions of transition between the subspecies in central Eurasia. Furthermore, an abnormal intron phylogeny suggested that interspecific exchanges had occurred between the house mouse subspecies and three other Palearctic species. These observations appear to be at variance with the simple hypothesis that Abpa is involved in reproductive isolation. Although we do not rule out a role in recognition, the situation appears to be more complex than previously thought. Thus the selective mechanism behind the evolution of Abpa remains to be resolved, and we suggest that it may have changed during the recent colonization history of the house mouse.     

Detection of recombinant haplotypes in wild mice (Mus musculus) provides new insights into the origin of Japanese mice

Japanese house mice (Mus musculus molossinus) are thought to be a hybrid lineage derived from two prehistoric immigrants, the subspecies M. m. musculus of northern Eurasia and M. m. castaneus of South Asia. Mice of the western European subspecies M. m. domesticus have been detected in Japanese ports and airports only. We examined haplotype structuring of a 200 kb stretch on chromosome 8 for 59 mice from throughout Eurasia, determining short segments (≈ 370–600 bp) of eight nuclear genes (Fanca, Spire2, Tcf25, Mc1r, Tubb3, Def8, Afg3l1 and Dbndd1) which are intermittently arranged in this order. Where possible we identified the subspecies origin for individual gene alleles and then designated haplotypes for concatenated alleles. We recovered 11 haplotypes among 19 Japanese mice examined, identified either as ‘intact’ haplotypes derived from the subspecies musculus (57.9%), domesticus (7.9%), and castaneus (2.6%), or as ‘recombinant’ haplotypes (31.6%). We also detected recombinant haplotypes unique to Sakhalin. The complex nature of the recombinant haplotypes suggests ancient introduction of all three subspecies components into the peripheral part of Eurasia or complicated genomic admixture before the movement from source areas. ‘Intact’domesticus and castaneus haplotypes in other Japanese wild mice imply ongoing stowaway introductions. The method has general utility for assessing the history of genetic admixture and for disclosing ongoing genetic contamination.     

Evolutionary history, population genetics, and gene flow in the common rosefinch (Carpodacus erythrinus)

We analyzed sequences of two mitochondrial DNA gene regions (control region and ND2) from 186 specimens obtained from 17 Eurasian localities covering most of the distribution of the common rosefinch to assess phylogeographic structure. Populations possessed a high level of nucleotide diversity relative to many other Palearctic species, suggesting that rosefinch populations are relatively old and possess high effective sizes. Mismatch distributions suggested that many localities experienced past population expansions, which are older than those expected for post-Pleistocene climate warming and reforestation of Eurasia. Our Phi(st) analysis revealed that 12.4% of total genetic variation was distributed among localities owing in part to the existence of three incompletely isolated groups: southwestern (subspecies C. e. kubanensis), northeastern (subspecies C. e. grebnitskii), and northwestern (subspecies C. e. erythrinus and C. e. ferghanensis). The three groups are not reciprocally monophyletic which suggests that they were formed relatively recently. Gene flow among groups is restricted. Coalescence analysis indicated dispersal asymmetry.     

Recent allopatric divergence and niche evolution in a widespread Palearctic bird,the common rosefinch (Carpodacus erythrinus)

A previously published phylogeographic analysis of mtDNA sequences from the widespread Palearctic common rosefinch (Carpodacus erythrinus) suggested the existence of three recently diverged groups, corresponding to the Caucasus, central-western Eurasia, and northeastern Eurasia. We re-evaluated the mtDNA data using coalescence methods and added sequence data from a sex-linked gene. The mtDNA gene tree and SAMOVA supported the distinctiveness of the Caucasian group but not the other two groups. However, UPGMA clustering of mtDNA Φ_ST-values among populations recovered the three groups. The sex-linked gene tree recovered no phylogeographic signal, which was attributed to recent divergence and insufficient time for sorting of alleles. Overall, coalescence methods indicated a lack of gene flow among the three groups, and population expansion in the central-western and northeastern Eurasia groups. These three groups corresponded to named subspecies, further supporting their validity. A species distribution model revealed potential refugia at the Last Glacial Maximum. These three groups, which we hypothesized are in the early stages of speciation, provided an opportunity for testing tenets of ecological speciation. We showed that the early stages of speciation were not accompanied by ecological niche divergence, consistent with other avian studies.     

Karyological and dental identification of Microtus limnophilus in a large focus of alveolar echinococcosis (Gansu, China).

A study of voles (Arvicolidae, Rodentia) from Gansu (China) designed to identify a potential host of Echinococcus multilocularis, responsible for human alveolar echinococcosis, leads to a general analysis of Microtus limnophilus population karyotypes, M1 of M. oeconomus populations from all of Eurasia and of M. limnophilus of Mongolia. The Microtus of Gansu belonging to the nominal subspecies M. limnophilus limnophilus (2n = 38; NF = 58) differs markedly in size and shape of M1 from the M. limnophilus of Mongolia, which must therefore be considered as a new subspecies M. limnophilus of malygini nov. ssp. (2n = 38; NF = 60) and the M. oeconomus of Mongolia should be ranked as M. oeconomus kharanurensis nov. ssp. (2n = 30; NF = 60).     

Out of the Qinghai-Tibet Plateau: evidence for the origin and dispersal of Eurasian temperate plants from a phylogeographic study of Hippophaë rhamnoides (Elaeagnaceae)

Numerous temperate plants now distributed across Eurasia are hypothesized to have originated and migrated from the Qinghai-Tibet Plateau (QTP) and adjacent regions. However, this hypothesis has never been tested through a phylogeographic analysis of a widely distributed species. Here, we use Hippopha? rhamnoides as a model to test this hypothesis. We collected 635 individuals from 63 populations of the nine subspecies of H. rhamnoides. We sequenced two maternally inherited chloroplast (cp) DNA fragments and also the bi-paternally inherited nuclear ribosomal ITS. We recovered five major clades in phylogenetic trees constructed from cpDNA and internal transcribed spacer (ITS) sequence variation. Most sampled individuals of six subspecies that are distributed in northern China, central Asia and Asia Minor/Europe, respectively, comprised monophyletic clades (or subclades) nested within those found in the QTP. Two subspecies in the QTP were paraphyletic, while the placement of another subspecies from the Mongolian Plateau differed between the ITS and cpDNA phylogenetic trees. Our phylogeographic analyses supported an 'out-of-QTP' hypothesis for H. rhamnoides followed by allopatric divergence, hybridization and introgression. These findings highlight the complexity of intraspecific evolutions and the importance of the QTP as a center of origin for many temperate plants.     

Breeding biology of two wagtail subspecies on Ulleung Island,Korea: Amur Wagtails,Motacilla alba leucopsis and Black-backed Wagtails,M. a. lugens

There is much controversy over the species and subspecies status of the white wagtail complex, which is further compounded by interbreeding between two subspecies, the Amur Wagtail (Motacilla alba leucopsis) and the Black-backed Wagtail (M. a. lugens). This study presents preliminary information on the breeding biology of both subspecies on Ulleung Island, Korea, over two breeding seasons (2012–2013). Mixed pairs of the two subspecies were common on this island, with almost 50% of all pairs being heterotypic or intermediate pairs; however, assortative mating was still present. Females of both subspecies were more likely to be paired with Amur wagtail males, whereas intermediate females were more likely to be paired with Black-backed Wagtail males. Clutch size, egg size and mass, and reproductive parameters (such as hatching success and nest success) did not significantly differ from each other. However, the mean values were low in intermediate pairs. Our results indicate no reproductive barrier between the two subspecies, but that some post-isolating mechanisms are still in progress.     

Paraphyly of the Blue Tit (Parus caeruleus) suggested from cytochrome b sequences

The phylogenetic relationships of the Blue Tit-Azure Tit assemblage (genus Parus; Aves: Passeriformes) were studied using mitochondrial DNA sequences of 24 specimens representing seven subspecies from Eurasia and North Africa. Previous work based on comparative morphological and acoustic data suggested a division of the Blue Tit (Parus caeruleus) into two species. Our analyses clearly indicate that the Blue Tit represents a paraphyletic assemblage, including a European/Middle Asian clade that is the sister group to the Azure Tit (Parus cyanus) and a North African clade. The North African clade (teneriffae subspecies group) is a sister group to the European Blue Tit/Azure Tit clade. We suggest a division of the Blue Tit into two separate species, Eurasian Blue Tit (Parus caeruleus s. str.) and African Blue Tit (Parus teneriffae). However, our data give no support for assigning species rank to Parus cyanus flavipectus, a subspecies of the Azure Tit, as suggested by several authors on morphological grounds.     

Satellite telemetry reveals long‐distance migration in the Asian great bustard Otis tarda dybowskii

The range of the great bustard stretches 10 000 km across Eurasia, one of the largest ranges of any threatened species. While movement patterns of the western subspecies of great bustard are relatively well‐understood, this is the first research to monitor the movements of the more endangered Asian subspecies of great bustard through telemetry and to link a breeding population of Asian great bustards to their wintering grounds. Using Argos/GPS platform transmitter terminals, we identified the annual movement patterns of three female great bustards captured at their breeding sites in northern Mongolia. The 4000 km round‐trip migration we have recorded terminated at wintering grounds in Shaanxi, China. This route is twice as long as has previously been reported for great bustards, which are among the heaviest flying birds. The journey was accomplished in approximately two months each way, at ground velocities of 48–98 km h^?1, and incorporated multiple and variable stopover sites. On their wintering grounds these birds moved itinerantly across relatively large home ranges. Our findings confirm that migratory behavior in this species varies longitudinally. This variation may be attributable to longitudinal gradients in seasonality and severity of winter across Eurasia. The distance and duration of the migratory route taken by great bustards breeding in Mongolia, the crossing of an international border, the incorporation of many stopovers, and the use of a large wintering territory present challenges to the conservation of the Asian subspecies of great bustard in this rapidly changing part of the world.     

Lumpy jaw in wild sheep and its evolutionary implications

The distribution and prevalence of mandibular osteomyelitis, lumpy jaw, and other dental anomalies in wild sheep were investigated and their biological and evolutionary implications were assessed. Our survey was based on 3,363 mandibles of wild sheep and 1,028 from domesticated varieties. Lumpy jaw is widespread in wild sheep of North America, but it is rare or absent in wild sheep from Eurasia. Among the subspecies of Ovis spp. in North American, the thinhorn sheep (Ovis dalli) were the most seriously impacted, with a prevalence in Dall's sheep (O. dalli dalli) of 23.3% and 29.3% in Stone's sheep (O. dalli stonei). Among the bighorns (O. canadensis), the Rocky Mountain subspecies (O. canadensis canadensis) had a higher rate (12.1%) than other subspecies. Lumpy jaw was not documented in the desert sheep of Baja California (O. canadensis cremnobates, O. canadensis weemsii). Based on data from affected thinhorn sheep, it appears there is an inverse relationship between age of a subspecies in a long term evolutionary context and susceptibility to lumpy jaw. In Eurasian wild sheep lumpy jaw is rare or absent with prevalences ranging from 0 to 7.1% among suspecies, and in domesticated breeds the prevalence averaged 5.0%. The impact of lumpy jaw on different age classes or longevity is equivocal, although females are more susceptible than males. Lumpy jaw appears to effect horn development in males.     

Melanin-based color variation in the Bearded Vulture suggests a thermoregulatory function.

We document a case of intraspecific variation in plumage colouration in Bearded Vultures that may have arisen as a functional response to climate conditions. Two subspecies, Gypaetus barbatus barbatus (Eurasia and North Africa populations) and Gypaetus barbatus meridionalis (Eastern and Southern Africa), have been described on the basis of plumage colour differences. The plumage of G. b. barbatus tends to be darker in comparison with that of G. b. meridionalis. The plumage of the two subspecies differ in the feathering of the tarsi (more abundant in G. b. barbatus) and presence/absence of dark ear tufts (only present in G. b. barbatus, and this being the most useful character to distinguish adult specimens of both subspecies). When exposing skins under the sun or to electric bulbs in a cold room, temperature increases were significantly higher in the black ear tufts than in the frontal region of the head, suggesting that the melanized ear patch of G. b. barbatus serves, at least, to heat up the air entering the ear channel and perhaps also the underlying skin. In addition, G. b. barbatus, which inhabits mountainous regions with harsh and long winters, would benefit more from feathered tarsi to prevent heat loss through the legs.     

Melanin-based color variation in the Bearded Vulture suggests a thermoregulatory function

We document a case of intraspecific variation in plumage colouration in Bearded Vultures that may have arisen as a functional response to climate conditions. Two subspecies, Gypaetus barbatus barbatus (Eurasia and North Africa populations) and Gypaetus barbatus meridionalis (Eastern and Southern Africa), have been described on the basis of plumage colour differences. The plumage of G. b. barbatus tends to be darker in comparison with that of G. b. meridionalis. The plumage of the two subspecies differ in the feathering of the tarsi (more abundant in G. b. barbatus) and presence/absence of dark ear tufts (only present in G. b. barbatus, and this being the most useful character to distinguish adult specimens of both subspecies). When exposing skins under the sun or to electric bulbs in a cold room, temperature increases were significantly higher in the black ear tufts than in the frontal region of the head, suggesting that the melanized ear patch of G. b. barbatus serves, at least, to heat up the air entering the ear channel and perhaps also the underlying skin. In addition, G. b. barbatus, which inhabits mountainous regions with harsh and long winters, would benefit more from feathered tarsi to prevent heat loss through the legs.     

<Emphasis Type="Italic">Eleocharis mamillata</Emphasis> — Distribution and infraspecific differentiation

Eleocharis mamillata is a widespread species in the temperate zone of Eurasia and North America. Populations in mountainous areas of Europe and Asia (the Pyrenees, Alps, Carpathians, Balkans, Ural, Caucasus, Altai) can be separated as subspeciesaustriaca differing mainly by the stylopodium shape from the nominate subspecies. Clear morphological criteria to create a separate infraspecific taxon in East Asia could not be found.     

The house mouse progression in Eurasia: a palaeontological and archaeozoological approach

A palaeontological and archaeozoological survey has allowed us to establish the different steps in the colonization of western Eurasia and northern Africa by the house mouse Mus musculus . After successive immigration waves of the genus Mus into this zone from the late Pliocene to the upper Pleistocene, the house mouse appeared and remained confined to the easternmost Mediterranean Basin at the uppermost Pleistocene. The first progression of this species into the Mediterranean Basin occurred in the Middle East from the Epipaleolithic to the Neolithic. Subsequently, this species was found in the western Mediterranean Basin during the Bronze Age and in north-west Europe during the Iron Age. In comparison to this latter zone, north central Europe was colonized relatively early, from the Neolithic to the Bronze Age which may, in fact, not only correspond to a much earlier invasion of Europe by M. musculus musculus but also suggest that the distribution of this subspecies extended much further west than it does nowadays, at a time when M. musculus domesticus was restricted to the Mediterranean zone. This archaeological survey is in agreement with genetic data which provide indications as to the speed, steps and pathways of progression of house mouse populations in western Eurasia.     

Mitochondrial DNA and plumage evolution in the white wagtail Motacilla alba

We analyzed sequences of two mitochondrial DNA (mtDNA) gene regions (control region and ND2) totaling 1477 base‐pairs from 232 specimens of the white wagtail Motacilla alba obtained from 27 localities throughout Eurasia. Although overall haplotype diversity was relatively low (0.79) and the most common haplotype was shared by 45% of individuals, belonging to six subspecies, a high level of population differentiation was detected. The mtDNA tree revealed three clades: (1) most individuals from Krasnodar (belonging to M. a. alba subspecies), (2) all individuals from Almaty and some from Primor'e (belonging to M. a. personata, M. a. lugens and M. a. leucopsis subspecies), and (3) the remaining individuals (representing all subspecies and all localities except Almaty). We suggest that these three clades represent historically isolated populations that relatively recently came into secondary contact in Krasnodar and Primor'e. None of the six subspecies were reciprocally monophyletic in the mtDNA tree. The Krasnodar population appeared to receive immigrants from other localities, but distinctive haplotypes from this locality did not appear elsewhere, suggesting asymmetric gene flow. Signatures of recent gene flow between northern populations were detected, and there was no evidence of isolation by distance within the northern group of populations. Mismatch distributions for most localities were consistent with population expansions. We also analyzed 12 male plumage characters from 93 study skins sampled from 24 populations. Phylogenetic trees resulting from separate genetic and morphological analyses were incongruent. Plumage evolution seems to be under strong sexual or natural selection, which favors particular phenotypes in various areas irrespective of the mitochondrial background. Dispersal events at different evolutionary times could have obscured the effects of earlier isolation events. The mtDNA data does not support species status for M. a. lugens and M. a. personata, which shared haplotypes with other subspecies of M. alba. We recommend that M. lugens and M. personata are placed as junior synonyms of M. alba.     

A wide geographical survey of mitochondrial DNA variation in the great spotted woodpecker complex,Dendrocopos major (Aves: Picidae)

One of the fundamental goals of phylogeographical studies should be to achieve a comprehensive geographical sampling of any investigated group. In this study, we conducted the most comprehensive geographical investigation to date for the great spotted woodpecker complex (Dendrocopos major), including populations from North Africa and Eurasia [including specimens from China, Japan and southern Caucasia (Anatolia, Azerbaijan and Iran)], in order to evaluate its genetic structure and population history. At the same time, we tested species limits within the D. major complex, which currently includes 14 recognized subspecies based on morphology and coloration. We based our study on haplotypes for the mitochondrial gene NADH dehydrogenase subunit 2 (ND2). Most haplotypes were obtained from museum toe pads, although we also used some previously published data. We also tested gene flow through MDIV, and estimated divergence dates among lineages using BEAST. The analysis of 352 base pairs of the ND2 gene from 155 individuals sampled from 33 populations showed significant phylogeographical structure across the breeding range. Our results found four distinct and reciprocally monophyletic clades: China, Japan, Iran–Azerbaijan and Eurasia–North Africa, with no phylogeographical structure within them. Coalescent‐based gene flow analysis showed restricted gene flow between China and Japan and between Japan and Eurasia. On the basis of the gene flow and phylogenetic analysis results, we propose the recognition of at least four different species within the complex. We also propose that, within the Eurasia–North Africa clade, a rapid population expansion through ‘leading edge expansion’ from refugia in Iberia, Kursk and North Africa, as well as irruptive and loop migration, can explain the lack of phylogeographical structure. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Tumbleweed (Salsola, section Kali) species and speciation in California

Tumbleweeds (Salsola species, section Kali) are road side and rangeland pest plants throughout the 48 contiguous states in the US. Three described tumbleweed species and two undescribed Salsola taxa occur in California. The known species are Russian thistle, Salsola tragus, introduced from Eurasia in the 1800s, Russian barbwire thistle, S. paulsenii, which grows in the desert regions of California, and is also native to Eurasia, and the recently identified S. kali subspecies austroafricana, possibly native to South Africa. Our goals were to investigate karyology, genome size, and molecular genetic affinities of the described species and the other taxa within their ranges in California using recently developed microsatellite loci, dominant nuclear DNA markers (RAPD and ISSR), and DNA sequence data. Chromosome counts and genome size assessments made with flow cytometry were compared. These analyses indicated that one undescribed taxon is a new allopolyploid hybrid between S. tragus and S. kali subspecies austroafricana, and the other undescribed taxon appears to be a complex hybrid involving all three described species. The invasion potentials for the hybrid taxa are unknown. Tumbleweeds are the focus of biological controls efforts but the identification of suitable agents for the hybrid taxa may be problematic because of the large amount of genetic variability encompassed within this evolving Salsola complex.