Subspecies Groups Research Articles

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.

Nuclear mtDNA pseudogenes as a source of new variants of mitochondrial genes: A case study of Siberian rubythroat Luscinia calliope (muscicapidae, aves).

First evidence for the presence of copies of mitochondrial cytochrome b gene of the subspecies group Luscinia calliope anadyrensis-L. c. camtschatkensis in the nuclear genome of nominative L. c. calliope was obtained, which indirectly indicates the nuclear origin of the subspecies-specific mitochondrial haplotypes in Siberian rubythroat. This fact clarifies the appearance of mitochondrial haplotypes of eastern subspecies by exchange between the homologous regions of the nuclear and mitochondrial genomes followed by fixation by the founder effect. This is the first study to propose a mechanism of DNA fragment exchange between the nucleus and mitochondria (intergenomic recombination) and to show the role of nuclear copies of mtDNA as a source of new taxon-specific mitochondrial haplotypes, which implies their involvement in the microevolutionary processes and morphogenesis.

Genome-wide SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range

The koala (Phascolarctos cinereus) is an iconic Australian species that is currently undergoing a number of threatening processes, including disease and habitat loss. A thorough understanding of population genetic structuring and genomic variability of this species is essential to effectively manage populations across the species range. Using a reduced representation genome sequencing method known as double digest restriction-associated sequencing, this study has provided the first genome-wide SNP marker panel in the koala. In this study, 33,019 loci were identified in the koala and a filtered panel of 3060 high-utility SNP markers, including 95 sex-linked markers, were used to provide key insights into population variability and genomic variation in 171 koalas from eight populations across their geographic range. Broad-scale genetic differentiation between geographically separated populations (including sub-species) was assessed and revealed significant differentiation between all populations (FST range = 0.01–0.28), with the largest divergence observed between the three geographically distant subgroups (QLD, NSW and VIC) along the east coast of Australia (average FST range = 0.17–0.23). Sub-group divergence appears to be a reflection of an isolation by distance effect and sampling strategy rather than true evidence of sub-speciation. This is further supported by low proportions of AMOVA variation between sub-species groups (11.19 %). Fine-scale analysis using genome-wide SNP loci and the NETVIEW pipeline revealed cryptic genetic sub-structuring within localised geographic regions, which corresponded to the hierarchical mating system of the species. High levels of genome-wide SNP heterozygosity were observed amongst all populations (He = 0.25–0.35), and when evaluating across the species to other vertebrate taxa were amongst the highest values observed. This illustrates that the species as a whole still retains high levels of diversity which is comparable to other outbred vertebrate taxa for genome-wide SNPs. Insights into the potential for adaptive variation in the koala were also gained using outlier analysis of genome-wide SNPs. A total of 10 putative outlier SNPs were identified indicating the high likelihood of local adaptations within populations and regions. This is the first use of genome-wide markers to assess population differentiation at a broad-scale in the koala and the first time that sex-linked SNPs have been identified in this species. The application of this novel genomic resource to populations across the species range will provide in-depth information allowing informed conservation priorities and management plans for in situ koalas across Australia and ex situ around the world.

Tracing the eastward dispersal of the house mouse, Mus musculus.

Here we describe recent advances in our understanding of the natural history of the house mouse, Mus musculus, with a focus on the genetic characteristics of the home territories and how this relates to prehistoric eastward movements from the predicted source areas. Recent studies of mitochondrial and nuclear gene sequences provide insight into the ancient divergence of the three subspecies groups, M. m. castaneus (CAS), M. m. domesticus (DOM), and M. m. musculus (MUS), with inferred natural habits (homelands) in central (Iran, Afghanistan, Pakistan, and India), western (western Iran), and northern (central Asia) areas, respectively. Our mitochondrial DNA and nuclear gene analyses indicate that only one local lineage of CAS extended its range via historical rapid expansion at two different times to Southeast Asia and East Asia, including Japan and southern Sakhalin. This is suggestive of a rapid range expansion of CAS out of its homeland, perhaps associated with the spread of agricultural practices in Asia. The subspecies group MUS now occurs in a large portion of northern Eurasia from eastern Europe in the West to the Japanese Islands in the East, including Uzbekistan, Kazakhstan, southern Siberia, northern China, and Korea, showing divergent patterns in terms of Mus musculus genetics, particularly in relation to nuclear gene sequences, allozymes (e.g., hemoglobin), morphological characteristics, and cytogenetic C-banding patterns. In this review article, we explain the complex spatial patterns of MUS. We postulate that two historical dispersal events took place, from two different source areas, and tentatively assign the taxon names “musculus” and “wagneri” to the two populations, which are associated with distinct genetic modules.

Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation.

Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.

Differentiation between <I>Yersinia pestis</I> Strains of Altaic-Hissar Group of Non-Main Subspecies by Means of PCR

On the basis of comparison between the genome-wide sequences of Altaic and Hissar strains of non-main subspecies and strains from Talas high-mountain plague focus, identified have been two novel DNA-targets, the usage of which provides for easy rapid subdivision of these closely-related strains of non-main subspecies that fall into separate phylogenetic brunches of plague agent evolution, applying PCR assay. One of the targets is allocated to intergenic region between YPO3333 and YPO3332 genes. In strains of altaica ssp. it contains 122 bps deletion. The other target is YPO2412 gene region which contains 72 bps deletion in Talas strains. Special primers for DNA-targets have been designed. Established have also been test specifications. Efficacy of the method for differentiation between the strains of Altaic-Hissar group of non-main subspecies is validated on 97 Y. pestis strains of various ssp.

Ancient onset of geographical divergence, interpopulation genetic exchange, and natural selection on theMc1rcoat-colour gene in the house mouse (Mus musculus)

We examined genetic variation in house mice from India and Pakistan, a predominant part of the predicted homeland of this species and also the territory of the subspecies Mus musculus castaneus (CAS), using a nuclear marker for seven tandemly arranged genes (Fanca–Spire2–Tcf25–Mc1r–Def8–Afg3l1–Dbndd1) and compared them with those previously determined for mice from other parts of Eurasia. Construction of a network with the concatenate sequences yielded three distinct clusters representing the three major subspecies groups: CAS, Mus musculus domesticus (DOM) and Mus musculus musculus (MUS). STRUCTURE analysis provided evidence for further subdivision of CAS into two main haplogroups within the Indian subcontinent. Single-gene networks revealed not only gene-specific architecture for subgrouping in CAS, but also allelic exchange among subspecies. These results suggest the earlier onset of allopatric divergence in the predicted homeland (the Middle East and Indian subcontinent) and subsequent intermittent admixing via gene flow across the CAS haplogroups and among the three subspecies groups. A comparison of the levels of nucleotide diversity among the gene regions revealed a less divergent state in the chromosome region containing Mc1r and its adjacent genes, indicative of a selective sweep, suggesting the involvement of natural selection in the Mc1r allelic variation.

Plumage pigment differences underlying the yellow-red differentiation in the Northern Flicker (Colaptes auratus).

Elucidating the processes that create species differences is a central goal of evolutionary biology. The Northern Flicker (Colaptes auratus) exists as two well-differentiated subspecies groups in North America, the Yellow-shafted (auratus group) and Red-shafted Flickers (cafer group), which differ strikingly in the color of the underside and rachises of flight feathers, and of malar and nuchal patches. We investigated the physiological basis of these conspicuous phenotypic differences by identifying and quantifying the pigments involved. The yellow feathers of auratus contained carotenoids commonly found in nature (lutein, β-cryptoxanthin, zeaxanthin and β-carotene). The orange to red shafts/vanes of cafer and hybrids contained these carotenoids as well as mono- and diketo-carotenoids (notably adonirubin, α-doradexanthin, canthaxanthin, astaxanthin), representing oxygenated products at carbon C4(4') of the carotenoids present in auratus. Oxygenation of feather carotenoids at C4(4') correlated closely with shaft/vane redness. Carotenoid hydroxylation at C3(3') and the proportion of carotenoids with ε end-rings also varied with color and belie differences in the activity of several carotenoid-modifying enzymes between the two subspecies groups. Curiously, occasional yellow feathers in red-shafted individuals had the carotenoids of auratus, hence the differences are not constitutive in cafer, underscoring regulatory differences. The red malar stripe of cafer, the black malar stripe and red nuchal patch of auratus all contained similar types and amounts of carotenoids, mostly 3-hydroxy-4-keto-carotenoids. The biochemical differences between two strongly differentiated forms we uncovered shed light on how plumage coloration can change over evolutionary time and point to further avenues of research.

Dispersal and speciation in purple swamphens (Rallidae:Porphyrio)

Dispersal, when accompanied by reduced gene flow and natural selection, influences speciation rates among groups of organisms. We used molecular phylogenetics, divergence time estimates, and population genetics to reconstruct the mode, pattern, and tempo of diversification within the wide-ranging purple swamphens (genus Porphyrio), with emphasis on the “supertramp” P. porphyrio. Our results suggest that the Porphyrio clade arose during the Middle Miocene in Africa, with a single colonization in the Americas and several other colonizations in Southeast Asia and the Indo-Pacific around 10 mya. We found that the widespread P. porphyrio is not monophyletic. Indeed, several subspecies and subspecies groups may represent species-level lineages. The P. p. melanotus lineage probably reached Australasia during the Pleistocene (600 kya), although some islands were colonized only in the past few hundred years. New Zealand, and some other islands, had previously been colonized (∼2.5 mya) by flying Porphyrio that evolved into flightless endemic species. Early and recent lineages are now sympatric. Widespread occupation of oceanic islands implies high dispersal and colonization rates, but gene flow probably occurs episodically and follows varying routes at different times. This pattern of colonization enables populations to differentiate and, ultimately, speciate.

A survey ofDrosophilaspecies on Santa Catalina Island with an emphasis on the repleta species group (Diptera: Drosophilidae)

Abstract Santa Catalina Island is a small island off the coast of southern California and for its modest size harbors several species of flies from the Drosophila genus. We performed an island-wide survey of Drosophila species to ascertain which species were endemic to the island and where they were most abundant. In doing so, we have assembled useful sampling information for researchers who wish to conduct field studies on Santa Catalina Island. We recorded the abundances of flies from the repleta subspecies group as well as non-repleta species. Additionally, we performed seasonal collections over one year at two locations on the island (Little Harbor Campgrounds and Wrigley Marine Science Center) to assess the best season for collections. From this seasonal survey, we observed that species abundance and composition at these two sites greatly vary in the time that we sampled. One of the seasonal sites that was sampled in two consecutive summer seasons showed that species composition had shifted between y...

British Ornithologists' Union Records Committee: 43rd Report (October 2014)

British Ornithologists' Union Records Committee: 43rd Report (October 2014)

Recent advances in ancient DNA research and their implications for archaeobotany

The scope and ambition of biomolecular archaeology is undergoing rapid change due to the development of new ‘next generation’ sequencing (NGS) methods for analysis of ancient DNA in archaeological specimens. These methods have not yet been applied extensively to archaeobotanical material but their utility has been demonstrated with desiccated, waterlogged and charred remains. The future use of NGS is likely to open up new areas of investigation that have been difficult or impossible with the traditional approach to aDNA sequencing. Species identification should become more routine with archaeobotanical explants, not just with charred grain but with most if not all species likely to be encountered in an archaeobotanical setting. Distinctions between different subspecies groups such as cereal landraces will also be possible in the near future. Phenotypic characterization, in which aDNA sequencing is used to infer the biological characteristics of an archaeological specimen, will become possible, improving our understanding of traits such as flowering behaviour of cereals, and when combined with studies of preserved RNA and protein will enable complex phenotypes such as environmental tolerance and nutritional quality to be assessed. The sequencing of entire ancient plant genomes is also likely to have significant impact. As with past studies of ancient plant DNA, realization of the new potential provided by NGS will require productive collaboration between archaeologists and geneticists within the archaeobotanical research community.

Morphological variation and sexual dimorphism of the common leopard (Panthera pardus) in the Middle East and their implications for species taxonomy and conservation

Designation of subspecies in wild cats (Carnivora: Felidae) often results from arbitrary description of morphological characters and it can be confounded by geographic variation and sexual dimorphism. To test the contribution of these factors to subspecies grouping, I studied 22 cranial shape variables in 55 skulls of the common leopard (Panthera pardus) from the Middle East and estimated their differences between the three subspecies groups in this region, namely the Persian leopard (P.p. ciscaucasica Satunin, 1914), Anatolian leopard (P.p. tulliana Valenciennes, 1856) and Arabian leopard (P.p. nimr Hemprich et Ehrenberg, 1833), among sexes. Male and female skulls increased in size with latitude (Bergmann's rule) and female skull size also significantly increased with longitude. Results suggest that taxonomic grouping was determined only by female skulls which showed high variation between the groups, unlike male skulls which varied more within the groups. Inter-group variation of female skulls, presence of only four cranial variables which are significantly different between the groups in all skulls, and the lack of historical barriers for subspeciation may suggest the existence of one leopard subspecies in the Middle East. Independent genetic and ecological studies are required to settle this taxonomic issue. This study urges for securing connectivity between the two remnant, taxonomically identical populations in the region, namely in (i) Iran and neighbouring countries and (ii) four Arab countries and Israel, with more research and conservation efforts in these populations and in the Fertile Crescent lying between them.

Species taxonomy of birds: Which null hypothesis?

The polytypic species concept unites populations that theoretically could and would interbreed were the opportunity to arise. This concept places the burden of proof of reproductive incapability and species status on those claiming species or higher rank. Advances in our understanding of the nature of reproductive isolation, the genetics of speciation, the limited role of gene flow, the power of directional selection, and the dynamics of hybridization support a different null hypothesis for taxonomic decisions, one that places the burden of proof on ‘lumping' rather than on ‘splitting' taxa at the species level. Switching the burden of proof provides an improved conceptual basis for the recognition of many allopatric island taxa and subspecies groups that merit species status. Taxonomic revisions based on these advances predictably confirm that distinct sister populations once lumped as polytypic species are independent evolutionary lineages that exhibit essential reproductive isolation. Release from the concerns about hybridization also positions proposed species for timely taxonomic decisions. The stage is set to proactively redefine polytypic species to separate component species for the 21st century. The improved species classification will better reflect phylogeny and evolutionary status, characterize biodiversity more accurately, guide improved sampling patterns of bird populations for systematic studies, and enable informed conservation decisions.

British Ornithologists' Union Records Committee: 42nd Report (October 2013)

British Ornithologists' Union Records Committee: 42nd Report (October 2013)

Differentiation of subspecies and sexes of Beringian Dunlins using morphometric measures

Five subspecies of Dunlins (Calidris alpina) that breed in Beringia are potentially sympatric during the non-breeding season. Studying their ecology during this period requires techniques to distinguish individuals by subspecies. Our objectives were to determine (1) if five morphometric measures (body mass, culmen, head, tarsus, and wing chord) differed between sexes and among subspecies (C. a. actites, arcticola, kistchinski, pacifica, and sakhalina), and (2) if these differences were sufficient to allow for correct classification of individuals using equations derived from discriminant function analyses. We conducted analyses using morphometric data from 10 Dunlin populations breeding in northern Russia and Alaska, USA. Univariate tests revealed significant differences between sexes in most morphometric traits of all subspecies, and discriminant function equations predicted the sex of individuals with an accuracy of 83–100% for each subspecies. We provide equations to determine sex and subspecies of individuals in mixed subspecies groups, including the (1) Western Alaska group of arcticola and pacifica (known to stage together in western Alaska) and (2) East Asia group of arcticola, actites, kistchinski, and sakhalina (known to winter together in East Asia). Equations that predict the sex of individuals in mixed groups had classification accuracies between 75% and 87%, yielding reliable classification equations. We also provide equations that predict the subspecies of individuals with an accuracy of 22–96% for different mixed subspecies groups. When the sex of individuals can be predetermined, the accuracy of these equations is increased substantially. Investigators are cautioned to consider limitations due to age and feather wear when using these equations during the non-breeding season. These equations will allow determination of sexual and subspecies segregation in non-breeding areas, allowing implementation of taxonomic-specific conservation actions. Diferenciación entre subespecies y sexos de Calidris alpina usando medidas morfométricas Cinco subespecies de Calidris alpina que se reproducen en Beringia son potencialmente simpátricas durante la temporada no reproductiva. El estudio de la ecología durante este periodo requiere la clasificación de los individuos por subespecies. Nuestros objetivos en este estudio son determinar (1) si cinco medidas morfométricas (masa corporal, culmen, cabeza, tarso y cuerda alar) son diferentes entre los sexos y las subespecies (C. a. actites, arcticola, kistchinski, pacifica, y sakhalina) y (2) si estas diferencias son suficientes para permitir la correcta clasificación de los individuos usando ecuaciones derivadas de un análisis de función discriminante. Realizamos los análisis usando datos de morfología provenientes de 10 poblaciones de Calidris alpina que se reproducen en el norte de Rusia y en Alaska. Pruebas univariadas revelaron diferencias significativas entre los sexos en casi todos los caracteres morfométricos y todas las subespecies. Además, las ecuaciones de las funciones discriminantes predijeron el sexo de los individuos con una precisión del 83–100% para cada subespecie. Proveemos las ecuaciones para determinar el sexo y las subespecies de individuos que conforman grupos mixtos de subespecies, incluyendo los grupos de (1) Alaska Occidental compuesto por arcticola y pacifica (conocidos por agruparse en el oeste de Alaska) y (2) Asia Oriental compuesto por arcticola, actites, kistchinski y sakhalina (conocidos por pasar el invierno juntos en el este de Asia). Las ecuaciones que predicen el sexo de los individuos en grupos mixtos tuvieron una precisión en la clasificación de 75–87% resultando en ecuaciones de clasificación confiables. También proveemos ecuaciones que predicen la subespecie de los individuos con una precisión de 22–96% para diferentes grupos mixtos de subespecies. Cuando el sexo de los individuos puede ser previamente determinado, la precisión de estas ecuaciones incrementa sustancialmente. Sugerimos que los investigadores tomen las precauciones necesarias considerando las limitaciones de las ecuaciones debido a la edad y el desgaste del plumaje cuando se usen en individuos durante la temporada no reproductiva. Estas ecuaciones permitirán la determinación sexual y la segregación de las subespecies en áreas no reproductivas permitiendo la implementación de acciones de conservación que sean especificas para cada taxón.

Molecular Phylogeny and Biogeography of Petaurista Inferred from the Cytochrome b Gene, with Implications for the Taxonomic Status of P. caniceps, P. marica and P. sybilla

The polymorphic genus Petaurista includes a group of diverse species and subspecies that are adapted for gliding and arboreal life. This morphological diversity has resulted in taxonomic discrepancies, and molecular phylogenetic studies have been limited by taxon sampling. To clarify this controversial taxonomy, we used the cytochrome b gene to reconstruct the phylogeny to obtain a more accurate picture of the evolutionary relationships, species differentiation and divergence pattern of Petaurista. The results revealed a significant inconsistency between taxonomic designations, phylogeny and genetic distances. When 6 recognized species were included, species delimitation revealed 15 putative species, a finding that warrants a comprehensive morphological diagnosis and a re-assessment of the species status. The validity of P. caniceps and P. marica was discussed. An estimation of the molecular divergence time demonstrated that the diversification and speciation of Petaurista began during the later Miocene and may have been affected by the uplifting of the Qinghai-Tibet plateau and subsequent climate change.

Variation in candidate genes CLOCK and ADCYAP1 does not consistently predict differences in migratory behavior in the songbird genus Junco

Recent studies exploring the molecular genetic basis for migratory variation in animals have identified polymorphisms in two genes ( CLOCK and ADCYAP1) that are linked to circadian rhythms and correlate with migratory propensity and phenology among individuals and populations. Results from these initial studies are mixed, however, and additional data are needed to assess the generality and diversity of the molecular mechanisms that regulate the biology of migration. We sequenced CLOCK and ADCYAP1 in 15 populations across the two species of the avian genus Junco, a North American lineage in which multiple recently diverged subspecies and populations range from sedentary to long-distance migrants. We found no consistent associations between allele length and migratory status across the genus for either CLOCK or ADCYAP1. However, within two subspecies groups, populations that migrate longer distances have longer CLOCK alleles on average. Additionally, there was a positive relationship between ADCYAP1 allele length and migratory restlessness (zugunruhe) among individuals within one of two captive populations studied—a result similar to those reported previously within captive blackcaps ( Sylvia atricapilla). We conclude that, while both ADCYAP1 and CLOCK may correlate with migratory propensity within or among certain populations or species, previously identified relationships between migratory behavior and sequence variants cannot be easily generalized across taxa.

Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata; Asteraceae)

Hybridization has played an important role in the evolution and ecological adaptation of diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata subsp. wyomingensis or as autotetraploids of diploid subspecies tridentata and vaseyana. Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies. • We used amplicon sequencing to assess phylogenetic relationships among three recognized subspecies: tridentata, vaseyana, and wyomingensis. DNA sequence data from putative genes were pyrosequenced and assembled from 329 samples. Nucleotide diversity and putative haplotypes were estimated from the high-read coverage. Phylogenies were constructed from Bayesian coalescence and neighbor-net network analyses. • Analyses support distinct diploid subspecies of tridentata and vaseyana in spite of known hybridization in ecotones. Nucleotide diversity estimates of populations compared to the total diversity indicate the relationships are predominately driven by a small proportion of the amplicons. Tetraploids, including subspecies wyomingensis, are polyphyletic occurring within and between diploid subspecies groups. • Artemisia tridentata is a species comprising phylogenetically distinct diploid progenitors and a tetraploid complex with varying degrees of phylogenetic and morphological affinities to the diploid subspecies. These analyses suggest tetraploids are formed locally or regionally from diploid tridentata and vaseyana populations via autotetraploidy, followed by introgression between tetraploid groups. Understanding the phylogenetic vs. ecological relationships of A. tridentata subspecies will have bearing on how to restore these desert ecosystems.

Where is the line? Phylogeography and secondary contact of western Palearctic coal tits (Periparus ater: Aves, Passeriformes, Paridae)

In this study, a phylogeographic scenario of the coal tit (Periparus ater) was reconstructed based on a fragment of the mitochondrial control region, and within- and between-population genetic diversity was analysed with a focus on the western Palearctic breeding range. We inferred a first pan-European delimitation of a postulated secondary contact zone among coal tits from the north-eastern Palearctic ater subspecies group and those from the south-western Palearctic abietum group. Generally, between-population differentiation was greatest in the Mediterranean range, which was explained by a greater separation in multiple Pleistocene refuge areas compared to the lower differentiation across the north-eastern Palearctic range. Genetic diversity indices were lowest on Mediterranean island populations as compared to continental populations. Pairwise ΦST values were highest among island populations and the Eurasian continent on the one hand and among the continental north-eastern ater and south-western abietum group on the other. Local co-occurrence of ater and abietum haplotypes was found all across Germany and in one Greek population. Molecular dating suggested that these two major subspecies groups separated from each other and from two further North African and Middle Eastern coal tit lineages during the early to mid-Pliocene. Successively, the Mediterranean region remained a centre of mainly insular diversification until late Pleistocene times including a long period of steady population growth. At the same time, at least four distinct genetic lineages emerged in eastern Eurasia, the nominate ater subspecies group being one of them. Finally, during the Holocene extant wide-range secondary contact in Europe was established via rapid westward range expansion from an East Asian refuge and via northeastward expansion from Mediterranean refuges.