Pliocene and Pleistocene diversification and multiple refugia in a Eurasian shrew (Crocidura suaveolens group)

We sequenced 998 base pairs (bp) of mitochondrial DNA cytochrome b and 799 bp of nuclear gene BRCA1 in the Lesser white-toothed shrew (Crocidura suaveolens group) over its geographic range from Portugal to Japan. The aims of the study were to identify the main clades within the group and respective refugia resulting from Pleistocene glaciations. Analyses revealed the Asian lesser white-toothed shrew (C. shantungensis) as the basal clade, followed by a major branch of C. suaveolens, subdivided sensu stricto into six clades, which split-up in the Upper Pliocene and Lower Pleistocene (1.9-0.9 Myr). The largest clade, occurring over a huge range from east Europe to Mongolia, shows evidence of population expansion after a bottleneck. West European clades originated from Iberian and Italo-Balkanic refugia. In the Near East, three clades evolved in an apparent hotspot of refugia (west Turkey, south-west and south-east of the Caucasus). Most clades include specimens of different morphotypes and the validity of many taxa in the C. suaveolens group has to be re-evaluated.     

Following the rivers: historical reconstruction of California voles Microtus californicus (Rodentia: Cricetidae) in the deserts of eastern California

The California vole, Microtus californicus, restricted to habitat patches where water is available nearly year‐round, is a remnant of the mesic history of the southern Great Basin and Mojave deserts of eastern California. The history of voles in this region is a model for species‐edge population dynamics through periods of climatic change. We sampled voles from the eastern deserts of California and examined variation in the mitochondrial cytb gene, three nuclear intron regions, and across 12 nuclear microsatellite markers. Samples are allocated to two mitochondrial clades: one associated with southern California and the other with central and northern California. The limited mtDNA structure largely recovers the geographical distribution, replicated by both nuclear introns and microsatellites. The most remote population, Microtus californicus scirpensis at Tecopa near Death Valley, was the most distinct. This population shares microsatellite alleles with both mtDNA clades, and both its northern clade nuclear introns and southern clade mtDNA sequences support a hybrid origin for this endangered population. The overall patterns support two major invasions into the desert through an ancient system of riparian corridors along streams and lake margins during the latter part of the Pleistocene followed by local in situ divergence subsequent to late Pleistocene and Holocene drying events. Changes in current water resource use could easily remove California voles from parts of the desert landscape.     

Phylogeography of the Eurasian green woodpecker (Picus viridis)

Aim In this paper we investigate the evolutionary history of the Eurasian green woodpecker (Picus viridis) using molecular markers. We specifically focus on the respective roles of Pleistocene climatic oscillations and geographical barriers in shaping the current population genetics within this species. In addition, we discuss the validity of current species and subspecies limits. Location Western Palaearctic: Europe to western Russia, and Africa north of the Sahara. Methods We sequenced two mitochondrial genes and five nuclear introns for 17 Eurasian green woodpeckers. Multilocus phylogenetic analyses were conducted using maximum likelihood and Bayesian algorithms. In addition, we sequenced a fragment of the cytochrome b gene (cyt b, 427 bp) and of the Z‐linked BRM intron 15 for 113 and 85 individuals, respectively. The latter data set was analysed using population genetic methods. Results Our phylogenetic results support the monophyly of Picus viridis and suggest that this taxon comprises three allopatric/parapatric lineages distributed in North Africa, the Iberian Peninsula and Europe, respectively. The North African lineage split from the Iberian/European clade during the early Pleistocene (1.6–2.2 Ma). The divergence event between the Iberian and the European lineages occurred during the mid‐Pleistocene (0.7–1.2 Ma). Our results also support a post‐glacial range expansion of these two lineages from distinct refugia located in the Iberian Peninsula and possibly in eastern Europe or Anatolia, which led to the establishment of a secondary contact zone in southern France. Main conclusions Our results emphasize the crucial role of both Pleistocene climatic oscillations and geographical barriers (Strait of Gibraltar, Pyrenees chain) in shaping the current genetic structure of the Eurasian green woodpecker. Our molecular data, in combination with diagnosable plumage characters, suggest that the North African green woodpecker (Levaillant’s woodpecker) merits species rank as Picus vaillantii (Malherbe, 1847). The two European lineages could be distinguished by molecular and phenotypic characters over most of their respective geographical ranges, but they locally exchange genes in southern France. Consequently, we prefer to treat them as subspecies (P. viridis viridis, P. viridis sharpei) pending further studies.     

Thermal adaptation and clinal mitochondrial DNA variation of European anchovy

Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy.     

Dispersal differences predict population genetic structure in Mormon crickets

Research investigating the geographical context of speciation has primarily focused on abiotic factors such as the role of Pleistocene glacial cycles, or geotectonic events. Few study systems allow a direct comparison of how biological differences, such as dispersal behaviour, affect population genetic structure of organisms that were subdivided during the Pleistocene. Mormon crickets exist in solitary and gregarious 'phases', which broadly correspond with an east-west mtDNA division across the Rocky Mountains. Gregarious individuals form bands that can move up to 2 km daily. This study assessed whether population genetic structure results mainly from deep Pleistocene vicariance or if we can also detect more recent genetic patterns due to phase and dispersal differences superimposed on the older, deeper divisions. We found that separation in refugia was a more important influence on genetic divergence than phase, with the Rockies acting as a barrier that separated Mormon cricket populations into eastern and western refugia during Pleistocene glacial cycles. However, patterns of isolation by distance differ between eastern and western clades for both mitochondrial and nuclear DNA, with greater divergence within the eastern, solitary clade. An mtDNA haplotype mismatch distribution is compatible with historical population expansion in the western clade but not in the eastern clade. A persistent (and possibly sex-biased) difference in dispersal ability has most likely influenced the greater population genetic structure seen in the eastern clade, emphasizing the importance of the interaction of Quaternary climate fluctuations and geography with biotic factors in producing the patterns of genetic subdivision observed today.     

Conservation genetics of the European brown bear - a study using excremental PCR of nuclear and mitochondrial sequences

In the Brenta area of northern Italy, a brown bear Ursus arctos population is rapidly going extinct. Restocking of the population is planned. In order to study the genetics of this highly vulnerable population with a minimum of stress to the animals we have developed a PCR-based method that allows the study of mitochondrial and nuclear gene sequences from droppings collected in the field. This method is generally applicable to animals in the wild. Using excremental as well as hair samples, we show that the Brenta population is monomorphic for one mitochondrial lineage and that female as well as male bears exist in the area. In addition, 70 samples from other parts of Europe were studied. As others have previously reported, the mitochondrial gene pool of European bears is divided into two major clades, one with a western and the other with an eastern distribution. Whereas populations generally belong to either one or the other mitochondrial clade, the Romanian population contains both clades. The bears in the Brenta belong to the western clade. The implications for the management of brown bears in the Brenta and elsewhere in Europe are discussed.     

Trans-Arctic dispersals and the evolution of a circumpolar marine fish species complex, the capelin (Mallotus villosus)

Trans-Arctic dispersals and population and range expansions during the Pleistocene enhanced opportunities for evolutionary diversification and contributed to the process of speciation within the capelin, a northern marine-fish complex exhibiting a circumpolar distribution. Capelin is composed of four highly divergent and geographically discrete mitochondrial DNA (mtDNA) clades (609 bp; cytochrome b). Two clades occur in the North Atlantic, one associated with Canadian Atlantic waters, including Hudson Bay, and the second distributed from West Greenland to the Barents Sea. Two additional clades occur in the Arctic and northeast Pacific Oceans, representing the most recent divergence within the capelin phylogenetic tree. Judged from mtDNA diversity, capelin populations comprising all clades experienced at least one demographic and spatial reduction-expansion episode during recent Pleistocene glaciations that imprinted their molecular architecture. The large contemporary populations in the northeast Pacific and Arctic Oceans exhibited significant genetic structure whereas no such structure was detected in the equally extensive North Atlantic clades. All clades are characterized by one or two prevalent mtDNA haplotypes distributed over the entire range of the clade. Assuming a Pacific ancestor for capelin, we infer that capelin dispersed on two separate occasions to the North Atlantic. A more recent event resulted in the isolation of eastern Pacific and Arctic clades, with the Arctic clade positioned for a potential third Atlantic invasion, as revealed by the presence of this clade in the Labrador Sea. The Labrador Sea is a potential contact zone for three of the four capelin clades.     

Complete taxon sampling of the avian genus Pica (magpies) reveals ancient relictual populations and synchronous Late‐Pleistocene demographic expansion across the Northern Hemisphere

Previous studies have suggested that bird populations in east Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitochondrial genes and two nuclear introns for all taxa of Pica to investigate 1) which Earth history factors have shaped the lineage divergence, and 2) whether different geographical populations were differently affected by the Pleistocene climatic changes. Our mitochondrial tree recovered three widespread lineages, 1) in east Asia, 2) across north Eurasia, and 3) in North America, respectively, with three isolated lineages in northwest Africa, Arabia and the Qinghai‐Tibet Plateau, respectively. Divergences among lineages took place 1.4–3.1 million yr ago. The northwest African population was sister to the others, which formed two main clades. In one of these, Arabia was sister to Qinghai‐Tibet, and these formed the sister clade to the east Asia clade. The other main clade comprised the North American and north Eurasian clades. There was no or very slight structure within these six geographical clades, including a lack of differentiation between the two North American species black‐billed magpie P. hudsonia and yellow‐billed magpie P. nutalli. Demographic expansion was recorded in the three most widespread lineages after 0.06 Ma. Asymmetric gene flow was recorded in the north Eurasian clade from southwestern Europe eastward, whereas the east Asian clade was rooted in south central China. Our results indicate that the fragmentation of the six clades of Pica was related to climatic cooling and aridification during periods of the Pliocene–Pleistocene. Populations on both sides of the Eurasian continent were similarly influenced by the Pleistocene climate changes and expanded concomitantly with the expansion of steppes. Based on results we also propose a revised taxonomy recognising seven species of Pica.     

Evolutionary patterns of the mitochondrial genome in the Moorish gecko, Tarentola mauritanica

A previous study on the evolutionary patterns of Tarentola mauritanica demonstrated that low levels of mitochondrial diversity observed in the European populations relative to nuclear markers were consistent with a selective sweep hypothesis. In order to unravel the mitochondrial evolutionary history in this European population and two other lineages of T. mauritanica (Iberian and North African clades), variation within 22 nearly complete mitogenomes was analyzed. Surprisingly, each clade seems to have a distinct evolutionary history; with both the European and Iberian clades presenting a decrease of polymorphism, which in the former is consistent with departure from neutrality of the mtDNA (positive or background selection), but in the latter seems to be the result of a bottleneck after a population expansion. The pattern exhibited by the North African clade seems to be a consequence of adaptation to certain mtDNA variants by positive selection.     

The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe

The glacial refugia hypothesis indicates that during the height of the Pleistocene glaciations the temperate species that are today widespread in western Europe must have survived in small and climatically favourable areas located in the southern peninsulas of Iberia, Italy and Balkans. One such species is the tawny owl, a relatively sedentary, nonmigratory bird presently distributed throughout Europe. It is a tree-nesting species closely associated with deciduous and mixed coniferous woodlands. In this study I used control region mtDNA sequences from 187 individuals distributed among 14 populations to determine whether current genetic patterns in tawny owl populations were consistent with postglacial expansion from peninsular refugia. European, North African and Asian tawny owls were found to represent three distinct lineages, where North Africa is the sister clade to all European owls. Within Europe, I found three well-supported clades that correspond to each of the three allopatric refugia. Expansion patterns indicate that owls from the Balkan refugium repopulated most of northern Europe, while expansion out of Iberia and Italy had only regional effects leading to admixture in France. Estimates of population divergence times between refugia populations are roughly similar, but one order of magnitude smaller between Greece and northern Europe. Based on a wide range of mutation rates and generation times, divergence between refugia appears to date to the Pleistocene.     

Phylogeography and Pleistocene refugia of the Little Owl Athene noctua inferred from mtDNA sequence data

Pleistocene glaciations greatly affected the distribution of genetic diversity in animal populations. The Little Owl is widely distributed in temperate regions and could have survived the last glaciations in southern refugia. To describe the phylogeographical structure of European populations, we sequenced the mitochondrial cytochrome c oxidase I (COI) and control region (CR1) in 326 individuals sampled from 22 locations. Phylogenetic analyses of COI identified two deeply divergent clades: a western haplogroup distributed in western and northwestern Europe, and an eastern haplogroup distributed in southeastern Europe. Faster evolving CR1 sequences supported the divergence between these two main clades, and identified three subgroups within the eastern clade: Balkan, southern Italian and Sardinian. Divergence times estimated from COI with fossil calibrations indicate that the western and eastern haplogroups split 2.01–1.71 Mya. Slightly different times for splits were found using the standard 2% rate and 7.3% mtDNA neutral substitution rate. CR1 sequences dated the origin of endemic Sardinian haplotypes at 1.04–0.26 Mya and the split between southern Italian and Balkan haplogroups at 0.72–0.21 Mya, coincident with the onset of two Pleistocene glaciations. Admixture of mtDNA haplotypes was detected in northern Italy and in central Europe. These findings support a model of southern Mediterranean and Balkan refugia, with postglacial expansion and secondary contacts for Little Owl populations. Central and northern Europe was predominantly recolonized by Little Owls from Iberia, whereas expansion out of the Balkans was more limited. Northward expansion of the Italian haplogroup was probably prevented by the Alps, and the Sardinian haplotypes remained confined to the island. Results showed a clear genetic pattern differentiating putative subspecies. Genetic distances between haplogroups were comparable with those recorded between different avian species.     

Phylogenetic,Demographic and Dating Analyses of Bufo gargarizans Populations from the Zhoushan Archipelago and Mainland China

Relatively little is known about the relationship between Bufo gargarizans populations from Zhoushan Archipelago and nearby continental regions on the Pacific coast of eastern China.In this paper,155 new specimens of B.gargarizans from Zhoushan Archipelago and adjacent continents and 71 published specimens of B.gargarizans from mainland China were studied.Phylogeographical and dating analyses of B.gargarizans were performed using mitochondrial DNA sequencing with a length of 1436 bp.A mt DNA tree that indicated seven major clades was obtained.The earliest split in the mt DNA tree corresponding to the divergence of populations from the western highland region occurred approximately 4.0 million years ago(mya).A subsequent clade occurred about 3.4 mya,with cladogenesis continuing toward the end of the Pleistocene.The continental clades were distributed in the western,central and northeastern regions of China.Zhoushan Archipelago clades consisted of two largely geographically overlapping subclades with the mt DNA divergence time of 0.73 mya.These results indicated there was extensive dispersal after vicariance.The B.gargarizans populations on Zhoushan Archipelago most probably originated from populations in nearby eastern continental regions of China.It was concluded that geological uplifting during the Pliocene and several sea-level changes in Pleistocene might have influenced the divergence and population demographical history of this species.     

Biogeography and evolution of the Holarctic zooplankton genus Leptodora (Crustacea: Branchiopoda: Haplopoda)

Aim To reconstruct the phylogeographic history of the Holarctic carnivorous genus Leptodora (Crustacea: Cladocera: Haplopoda). Location We studied the DNA of between one and five specimens each from 28 populations distributed across the Holarctic, but with emphasis on Eurasia. Methods We sequenced a mitochondrial (cytochrome c oxidase subunit I) and a nuclear (elongation factor‐1α) gene, and combined this molecular information with geological and palaeoclimatological data. Haplotype networks and phylogenetic trees were constructed using a Bayesian and maximum likelihood approach. A molecular clock was applied. Results Leptodora consists of three clades (Leptodora kindtii in Europe, Leptodora richardi in China and Japan, and Leptodora sp. in North America), with insular subclades in Japan and in the eastern Mediterranean. The North American clade was not studied in detail. Leptodora richardi is the more thermophilic of the three. It extends from the Tropic of Cancer in the south to the Heilong Basin in the north. The western European L. kindtii is more cold‐water adapted than the eastern Mediterranean subclade. ‘West European’ and ‘Chinese’ clades are broadly separated by a hybrid zone in Siberia and European Russia as far west as the Volga. These hybrids have the mitochondrial DNA of L. kindtii, the nuclear DNA of L. richardi and the low‐temperature preference of L. kindtii, and may have formed as recently as the Holocene hypsithermal. A pure L. kindtii population in the Upper Irtysh catchment, east of the Dzungarian Gates, has been sequestered in endorheic Lake Wulungu, Xinjiang, since the mid‐Pleistocene. Main conclusions Application of a molecular clock places the most recent common ancestor of the North American, East Asian and European populations in the mid‐Miocene. The North American taxon is still living in isolation, while the Eurasian taxa, separated by the Alpine folding, made contact again in the Pleistocene, when the cold‐stenothermic L. kindtii repeatedly moved eastwards across Siberia and back. The population in Xinjiang is a relict of an early wave coming from western Europe: it crossed the Dzungarian Gates during a humid mid‐Pleistocene event, probably corresponding to the Apsheron transgression in the Caspian Basin. Later aridity isolated it there, and it started accumulating private haplotypes. The Holocene Euro‐Siberian hybrid zone may eventually engulf all European populations.     

Shaped by uneven Pleistocene climate: mitochondrial phylogeographic pattern and population history of white wagtail Motacilla alba (Aves: Passeriformes)

We studied the phylogeography and population history of the white wagtail Motacilla alba, which has a vast breeding range, covering areas with different Pleistocene climatic histories. The mitochondrial NADH dehydrogenase subunit II gene (ND2) and Control Region (CR) were analyzed for 273 individuals from 45 localities. Our data comprised all nine subspecies of white wagtail. Four primary clades were inferred (M, N, SW and SE), with indications of M. grandis being nested within M. alba. The oldest split was between two haplotypes from the endemic Moroccan M. a. subpersonata (clade M) and the others, at 0.63–0.96 Mya; other divergences were at 0.31–0.38 Mya. The entire differentiation falls within the part of the Pleistocene characterized by Milankovitch cycles of large amplitudes and durations. Clade N was distributed across the northern Palearctic; clade SW in southwestern Asia plus the British Isles and was predicted by Ecological niche models (ENMs) to occur also in central and south Europe; and clade SE was distributed in central and east Asia. The deep divergence within M. a. subpersonata may reflect retention of ancestral haplotypes. Regional differences in historical climates have had different impacts on different populations: clade N expanded after the last glacial maximum (LGM), whereas milder Pleistocene climate of east Asia allowed clade SE a longer expansion time (since MIS 5); clade SW expanded over a similarly long time as clade SE, which is untypical for European species. ENMs supported these conclusions in that the northern part of the Eurasian continent was unsuitable during the LGM, whereas southern parts remained suitable. The recent divergences and poor structure in the mitochondrial tree contrasts strongly with the pronounced, well defined phenotypical differentiation, indicating extremely fast plumage divergence.     

Species status and phylogeography of two closely related Coptolabrus species (Coleoptera: Carabidae) in South Korea inferred from mitochondrial and nuclear gene sequences

We investigated the species status and intraspecific phylogeography in South Korea of two ground beetle species, Coptolabrus jankowskii and Coptolabrus smaragdinus (Coleoptera: Carabidae), using statistical parsimony networks and nested clade analyses based on sequences from the mitochondrial cytochrome oxidase subunit I (COI) and nuclear phosphoenolpyruvate carboxykinase (PepCK) and wingless (Wg) genes. Although traditional parsimony tree construction generally failed to resolve interspecific relationships and construct biologically meaningful genealogies, analysis using statistical parsimony networks yielded statistically significant inter- and intraspecific genealogical structures. We found that although these two species represent a notable case of trans-species polymorphisms in both mitochondrial and nuclear gene sequences, their status as separate species was evidenced by the nonrandom association between species and nested clades at various nesting levels. The exceptional occurrence of shared identical or very similar COI sequences was considered to be the result of introgressive hybridization. In addition, range expansion and fragmentation events across the Korean Peninsula and adjacent islands were inferred from nested clade phylogeographical analyses. The COI gene revealed the geographical divergence of major eastern and western clades and historical biogeographical events within each major clade, whereas the nuclear PepCK gene, which did not reveal corresponding east-west clades, indicated past fragmentation and range expansion across wide areas that may have been the result of older biogeographical events. Thus, phylogeographical inferences drawn from analyses of mitochondrial and nuclear genes can reveal different and potentially complementary information about phylogeographical processes.     

Phylogeography of the leaf beetle Chrysolina virgata in wetlands of Japan inferred from the distribution of mitochondrial haplotypes

The genetic differentiation among populations of the leaf beetle Chrysolina virgata living in wetlands of Japan was studied based on the sequence data of the mitochondrial cytochrome oxidase subunit I gene region (750 bp). Two distinct lineages of mitochondrial haplotypes were found: one (clade A) consisted of 26 haplotypes distributed over the distribution range of C. virgata between north‐east Honshu and Kyushu, whereas the other (clade B) was monotypic and confined to a small region in north‐east Honshu where it coexisted with clade A. Nested clade analysis for these haplotypes suggested that range expansion and following differentiation due to isolation by distance might have resulted in the present distribution pattern of the haplotypes in clade A. We discuss the evolutionary process leading to the occurrence of two distinct haplotype clades in Japan in terms of repeated colonization from the continent and range expansion and contraction during climatic changes.     

Postglacial expansion of the southern red-backed vole (Clethrionomys gapperi) in North America

Dynamic climatic oscillations of the Pleistocene dramatically changed the distributions of high latitude species. Molecular investigations of a variety of organisms show that processes of postglacial colonization of boreal regions were more complex than initially thought. Phylogeographical and coalescent analyses were conducted on partial sequences of the cytochrome b gene (600 bp) from 64 individuals of Clethrionomys gapperi from North Carolina, Pennsylvania, Minnesota, Idaho, Washington, British Columbia, Northwest Territories, and Alaska to test hypotheses relating to Pleistocene refugia and postglacial colonization routes. Three divergent clades (east, west, central) were identified with highest net divergence (dA = 5.2%) between the eastern and western clades. Populations from the recently deglaciated higher latitudes of Canada and Alaska are closely related to lower latitude populations of the central clade (dA = 1.2%) suggesting recent expansion from this midwestern region. No representatives from the east or west clade were found at latitudes higher than 50 degrees N, indicating that postglacial colonization occurred through a midcontinental route. The high latitude population from the Northwest Territories exhibited demographic patterns and genetic diversity consistent with a stable noncolonizing population. This population is found near the Mackenzie range, where the two continental ice sheets were believed to have coalesced. Molecular variation observed in this population may be the result of leading edge population diversifying in the continental corridor or may reflect the signal of a high latitude refugial population.     

Population genetic structure and phylogeography of the oak gall wasp Andricus chodjaii (Hymenoptera: Cynipidae) in Turkey as inferred from mitochondrial and nuclear DNA sequences

Sequence data of mitochondrial cytochrome b gene and nuclear ITS2 region were used to assess genetic diversity, intraspecific phylogeography and population genetic structure of the oak gall wasp Andricus chodjaii from Turkey. We examined 293 individuals from 21 localities which generated 57 cyt b haplotypes and 8 ITS2 alleles. The average genetic diversity was 0.575 for cyt b and 0.202 ITS2, and the average nucleotide diversity 0.015 for cyt b gene and 0.001 for the ITS2 region. Phylogenetic analyses of cyt b haplotypes produced mostly similar topologies with geographically significant groupings. The ITS2 data provided less resolution without robust and apparent geographic structure. Population demographic analysis indicated that some eastern populations expanded, however, some others underwent either expansion or decline resulting in genetically structured populations. Molecular clock applied to the mtDNA data indicated that ingroup haplotypes diversified from the outgroup haplotypes around Early Pliocene. Further diversification events throughout Pleistocene resulted in major clade formations. It appears that geographic formations and glacial and interglacial cycles of Pleistocene were crucial for shaping the phylogeographic structure of A. chodjaii in Turkey.     

Phylogeography and introgressive hybridization of the ground beetle Carabus yamato in Japan based on mitochondrial gene sequences

To study the phylogeography of the ground beetle Carabus yamato in Japan, we compared 1,020-bp sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene from 373 specimens from 37 localities with those of three parapatric species (C. albrechti, C. kimurai, and C. japonicus) that might share mitochondrial lineages with C. yamato through introgressive hybridization. We found 81 haplotypes from C. yamato. Of these, 17 haplotypes were considered to be of an introgressed lineage from C. albrechti, based on the phylogeny and geographic distribution. In addition, one haplotype of C. kimurai was likely an introgressant from C. yamato. Putative introgression events among the four species were restricted to these two directional cases. We analyzed the phylogeography of C. yamato using nested clade phylogeographical analysis and population genetic parameters. The mitochondrial lineages of C. yamato were estimated to have diverged no more than approximately 1.12 million years ago, implying that the estimated historical events occurred after the Early Pleistocene. Carabus yamato was inferred to have experienced a contraction of its distribution range, followed by recent range expansion. Populations in the western and eastern regions, segregated by Ise Bay and the Nobi and Okazaki Plains, diverged in the mitochondrial clades. The northern and most western populations possessed one clade only (except an introgressed lineage), whereas eastern and some southwestern populations possessed several diverged clades, which were considered to be ancestral; these populations may have been associated with refugia during glacial periods.     

Genetic differentiation of the pine processionary moth at the southern edge of its range: contrasting patterns between mitochondrial and nuclear markers

The pine processionary moth (Thaumetopoea pityocampa) is an important pest of coniferous forests at the southern edge of its range in Maghreb. Based on mitochondrial markers, a strong genetic differentiation was previously found in this species between western (pityocampa clade) and eastern Maghreb populations (ENA clade), with the contact zone between the clades located in Algeria. We focused on the moth range in Algeria, using both mitochondrial (a 648 bp fragment of the tRNA‐cox2) and nuclear (11 microsatellite loci) markers. A further analysis using a shorter mtDNA fragment and the same microsatellite loci was carried out on a transect in the contact zone between the mitochondrial clades. Mitochondrial diversity showed a strong geographical structure and a well‐defined contact zone between the two clades. In particular, in the pityocampa clade, two inner subclades were found whereas ENA did not show any further structure. Microsatellite analysis outlined a different pattern of differentiation, with two main groups not overlapping with the mitochondrial clades. The inconsistency between mitochondrial and nuclear markers is probably explained by sex‐biased dispersal and recent afforestation efforts that have bridged isolated populations.