Phylogeography of Hyalomma (Euhyalomma) lusitanicum (Acarina,Parasitiformes, Ixodidae) in Andalusia based on mitochondrial cytochrome oxidase I gene

The genetic population structure relationships of Hyalomma (Euhyalomma) lusitanicum in Andalusia (the south of the Iberian Peninsula) were examined using mtDNA sequence data from 887 bp of cytochrome oxidase subunit I (COI) gene. The sequence for the COI region was determined for 84 individuals collected in several localities of Andalusia, and 10 for other localities (i.e., five from Toledo, central Iberian Peninsula, four from Sicily (Italy) and one from Canary Island). Seventeen haplotypes were detected, including 27 polymorphic sites. The number of amino acid substitutions per site from mean diversity calculations for the entire population was 0.017. AMOVA analysis revealed a low gene flow that characterises the genetic population structure of this species in South Iberian Peninsula, with a haplotype diversity (h) value of 0.815. No geographically induced differentiation was observed, and separate evolutionary units were not detected. Our results indicate low genetic diversity across the geographical range of H. lusitanicum tick in Andalusia. Our data do not show any genetic discontinuity between the tick populations studied, including specimens from Canary Island and Sicily (Italy).

     

Calibrating the molecular clock beyond cytochrome b: assessing the evolutionary rate of COI in birds

Estimating the age of species or their component lineages based on sequence data is crucial for many studies in avian evolutionary biology. Although calibrations of the molecular clock in birds have been performed almost exclusively using cytochrome b (cyt b), they are commonly extrapolated to other mitochondrial genes. The existence of a large, standardized cytochrome c oxidase subunit I (COI) library generated as a result of the DNA barcoding initiative provides the opportunity to obtain a calibration for this mitochondrial gene in birds. In this study we compare the evolutionary rate of COI relative to cyt b across ten different avian orders. We obtained divergence estimates for both genes from nearly 300 phylogenetically independent pairs of species through the analysis of almost 5000 public sequences. For each pair of species we calculated the difference in divergence between COI and cyt b. Our results indicate that COI evolves on average 14% slower than cyt b, but also reveal considerable variation both among and within avian orders, precluding the use of this value as a standard adjustment for the COI molecular clock for birds. Our findings suggest that this variation is partially explained by a clear negative relationship between the difference in divergence in these genes and the age of species. Distances for cyt b are higher than those for COI for closely related species, but the values become similar as the divergence between the species increases. This appears to be the result of a stronger pattern of negative time‐dependency in the rate of cyt b than in that of COI, a difference that could be related to lower functional constraints on a small number of sites in cyt b that allow it to initially accumulate mutations more rapidly than COI.     

A new cytochrome b phylogroup of the common vole (Microtus arvalis) endemic to the Balkans and its implications for the evolutionary history of the species

The phylogeographic architecture of the common vole, Microtus arvalis, has been well‐studied using mitochondrial DNA and used to test hypotheses relating to glacial refugia. The distribution of the five described cytochrome b (cyt b) lineages in Europe west of Russia has been interpreted as a consequence of postglacial expansion from both southern and central European refugia. A recently proposed competing model suggests that the ‘cradle’ of the M. arvalis lineages is in western central Europe from where they dispersed in different directions after the Last Glacial Maximum. In the present study, we report a new cyt b lineage of the common vole from the Balkans that is not closely related to any other lineage and whose presence might help resolve these issues of glacial refugia. The Balkan phylogroup occurs along the southern distributional border of M. arvalis in central and eastern Bosnia and Herzegovina, Montenegro, and eastern Serbia. Further north and west in Slovenia, Bosnia and Herzegovina, and Serbia, common voles belong to the previously‐described Eastern lineage, whereas both lineages are sympatric in one site in Bosnia and Herzegovina. The Balkan phylogroup most reasonably occupied a glacial refugium already known for various Balkan endemic species, in contrast to the recently proposed model. South‐east Europe is an absolutely crucial area for understanding the postglacial colonization history of small mammals in Europe and the present study adds to the very few previous detailed phylogeographic studies of this region. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 788–796.     

Shallow phylogeographic structuring of Vimba vimba across Europe suggests two distinct refugia during the last glaciation

Genetic variation and geographical structuring of vimba Vimba vimba were analysed across 26 sites (80 individuals) by means of mtDNA sequences (cyt b gene, mitochondrial control region) to localize hypothesized glacial refugia and to reconstruct postglacial recoloniation routes. Although genetic diversity among sequenced individuals was low, a combined analysis of the two sequenced fragments revealed a western (central and northern Europe: Danube, Elbe and lakes of Sweden) and an eastern clade (eastern Europe: Dnieper–South Bug, Don, Neman). Furthermore, a number of divergent ancestral haplotypes distributed around the Black and Caspian Seas became apparent. Mismatch analyses supported a sudden expansion model for the populations of the western clade between 50 and 10 000 bp . Overall, the study provides strong evidence for a northward and westward expansion of V. vimba from two refugial regions located in the Danubian drainage and the northern Pontic regions respectively.     

Multiple refugia and barriers explain the phylogeography of the Valais shrew,Sorex antinorii (Mammalia: Soricomorpha)

The aim of the present study was to investigate the genetic structure of the Valais shrew (Sorex antinorii) by a combined phylogeographical and landscape genetic approach, and thereby to infer the locations of glacial refugia and establish the influence of geographical barriers. We sequenced part of the mitochondrial cytochrome b (cyt b) gene of 179 individuals of S. antinorii sampled across the entire species' range. Six specimens attributed to S. arunchi were included in the analysis. The phylogeographical pattern was assessed by Bayesian molecular phylogenetic reconstruction, population genetic analyses, and a species distribution modelling (SDM)‐based hindcasting approach. We also used landscape genetics (including isolation‐by‐resistance) to infer the determinants of current intra‐specific genetic structure. The phylogeographical analysis revealed shallow divergence among haplotypes and no clear substructure within S. antinorii. The starlike structure of the median‐joining network is consistent with population expansion from a single refugium, probably located in the Apennines. Long branches observed on the same network also suggest that another refugium may have existed in the north‐eastern part of Italy. This result is consistent with SDM, which also suggests several habitable areas for S. antinorii in the Italian peninsula during the LGM. Therefore S. antinorii appears to have occupied disconnected glacial refugia in the Italian peninsula, supporting previous data for other species showing multiple refugia within southern refugial areas. By coupling genetic analyses and SDM, we were able to infer how past climatic suitability contributed to genetic divergence of populations. The genetic differentiation shown in the present study does not support the specific status of S. arunchi. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 864–880.     

Phylogeography of the smooth snake Coronella austriaca (Serpentes: Colubridae): evidence for a reduced gene pool and a genetic discontinuity in Central Europe

The present study considers the genetic structure and phylogeography of the smooth snake (Coronella austriaca) in Central Europe, as analyzed on the basis of 14 microsatellite markers and a 284‐bp fragment of cytochrome b. We found deep divergence between western and south‐eastern Poland, suggesting at least two different colonization routes for Central Europe, originating in at least two different refugia. The west/south‐east divide was reflected in the haplotype distribution and topology of phylogenetic trees as defined by mitochondrial DNA, and in population structuring seen in the admixture analysis of microsatellite data. The well supported western European clade suggests that another refugium might have existed. We also note the isolation‐by‐distance and moderate‐to‐pronounced structuring in the examined geographical demes. Our data fit the assumption of the recently suggested sex‐biased dispersal, in that we found a strong divide in the maternal line, as well as evidence for a small but existent gene flow based on biparentally inherited microsatellite markers. All studied populations were very similar in respect of allelic richness, observed and expected heterozygosities, and inbreeding coefficients. However, some genetic characteristics were different from those expected compared to a similar fine‐scale study of C. austriaca from Great Britain. In the present study, we observed heterozygosity deficit, high inbreeding, and low Garza–Williamson indices, suggesting a reduction in population size. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 195–210.     

Phylogeographic inferences from the mtDNA variation of the three-toed skink, Chalcides chalcides (Reptilia: Scincidae)

Genetic diversity was analyzed in Chalcides chalcides populations from peninsular Italy, Sardinia, Sicily and Tunisia by sequencing 400 bp at the 5' end of the mitochondrial gene encoding cytochrome b (cyt b) and by restriction fragment length polymorphism (RFLP) analysis of two mitochondrial DNA segments (ND-1/2 and ND-3/4). The results of the phylogenetic analysis highlighted the presence of three main clades corresponding with three of the four main geographical areas (Tunisia, Sicily and the Italian peninsula), while Sardinia proved to be closely related to Tunisian haplotypes suggesting a colonization of this island from North Africa by human agency in historical times. On the contrary, the splitting times estimated on the basis of cyt b sequence data seem to indicate a more ancient colonization of Sicily and the Italian Peninsula, as a consequence of tectonic and climatic events that affected the Mediterranean Basin during the Pleistocene. Finally, the analysis of the genetic variability of C. chalcides populations showed a remarkable genetic homogeneity in Italian populations when compared to the Tunisian ones. This condition could be explained by a rapid post-glacial expansion from refugial populations that implied serial bottlenecking with progressive loss of haplotypes, resulting in a low genetic diversity in the populations inhabiting the more recently colonized areas.     

Phylogeny of Glaucosomatidae inferred from molecular evidence

Most species of glaucosomatids (Teleostei: Glaucosomatidae) are endemic to Australia, except Glaucosoma buergeri that is widely distributed from Australia to Japan. This study elucidated phylogenetic relationships among glaucosomatids based on the morphological characters of the saccular‐otolith sagitta, in addition to molecular evidence of mitochondrial 16S rDNA, cytochrome oxidase I (COI) and cytochrome b (cyt b) sequences, and nuclear rhodopsin sequences. The topologies of individuals' phylogenetic trees, based on 16S rDNA, COI and cyt b sequences, were statistically indistinguishable from one another, and were only slightly different from a tree based on rhodopsin sequences. These molecular tree topologies, however, differed from species relationships in morphology‐based phylogenetic hypothesis proposed in previous studies. Specimens of G. buergeri from Australia and Taiwan showed differences in the sagitta and molecular differentiation at the four genes, suggesting a possible speciation event. Both molecular and morphological evidences indicate that Glaucosoma magnificum is the plesiomorphic sister species of other glaucosomatid species. Glaucosoma hebraicum is the sister species of a clade composed of G. buergeri and Glaucosoma scapulare. Molecular and morphological evidences also support the species status of G. hebraicum.     

Phylogeography of the brown hare (Lepus europaeus) in Europe: a legacy of south‐eastern Mediterranean refugia?

Aim We analysed the population genetics of the brown hare (Lepus europaeus) in order to test the hypothesis that this species migrated into central Europe from a number of late glacial refugia, including some in Asia Minor. Location Thirty‐three localities in Greece, Bulgaria, Italy, Croatia, Serbia, Poland, Switzerland, Austria, France, Germany, the Netherlands, Spain, the United Kingdom, Turkey and Israel. Methods In total, 926 brown hares were analysed for mitochondrial DNA (mtDNA) variation by restriction fragment length polymorphism (RFLP) performed on polymerase chain reaction‐amplified products spanning cytochrome b (cyt b)/control region (CR), cytochrome oxidase I (COI) and 12S–16S rRNA. In addition, sequence analysis of the mtDNA CR‐I region was performed on 69 individuals, and the data were compared with 137 mtDNA CR‐I sequences retrieved from GenBank. Results The 112 haplotypes detected were partitioned into five phylogeographically well‐defined major haplogroups, namely the ‘south‐eastern European type haplogroup’ (SEEh), ‘Anatolian/Middle Eastern type haplogroup’ (AMh), ‘European type haplogroup, subgroup A’ (EUh‐A), ‘European type haplogroup, subgroup B’ (EUh‐B) and ‘Intermediate haplogroup’ (INTERh). Sequence data retrieved from GenBank were consistent with the haplogroups determined in this study. In Bulgaria and north‐eastern Greece numerous haplotypes of all five haplogroups were present, forming a large overlap zone. Main conclusions The mtDNA results allow us to infer post‐glacial colonization of large parts of Europe from a late glacial/early Holocene source population in the central or south‐central Balkans. The presence of Anatolian/Middle Eastern haplotypes in the large overlap zone in Bulgaria and north‐eastern Greece reveals gene flow from Anatolia to Europe across the late Pleistocene Bosporus land‐bridge. Although various restocking operations could be partly responsible for the presence of unexpected haplotypes in certain areas, we nevertheless trace a strong phylogeographic signal throughout all regions under study. Throughout Europe, mtDNA results indicate that brown hares are not separated into discernable phyletic groups.     

Evidence of a complex phylogeographic structure in the common dormouse,Muscardinus avellanarius (Rodentia: Gliridae)

This is the first mitochondrial phylogeography of the common dormouse, Muscardinus avellanarius (Linnaeus, 1758), a hibernating rodent strictly protected in Europe (Habitat Directive, annex IV; Bern Convention, annex III). The 84 individuals of M. avellanarius, sampled throughout the distributional range of the species, have been sequenced at the mitochondrial DNA gene (cytochrome b, 704 base pairs). The results revealed two highly divergent lineages, with an ancient separation around 7.7 Mya and a genetic divergence of 7.7%. Lineage 1 occurs in Western Europe (France, Belgium, and Switzerland) and Italy, and lineage 2 occurs in Central–Northern Europe (Poland, Germany, Latvia, and Lithuania), on the Balkan Peninsula, and in Turkey. Furthermore, these two lineages are subdivided into five sublineages genetically isolated with a strong geographical association. Therefore, lineage 1 branches into two further sublineages (Western European and Italian), whereas lineage 2 contained three sublineages (Central–Northern European, Turkish, and Balkan). We observed low genetic diversity within the sublineages, in contrast to the significant level of genetic differentiation between them. The understanding of genetic population structure is essential for identifying units to be conserved. Therefore, these results may have important implications for M. avellanarius conservation. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 648–664.     

Phylogenetic structure among pocket gopher populations,genus Thomomys (Rodentia: Geomyidae), on the Baja California Peninsula

We determined the phylogenetic relationships, population history, and hierarchical structure of genetic variation in pocket gophers distributed on the Baja California Peninsula (BCP), based on extensive geographic sampling. Using a fragment of the mitochondrial gene cytochrome b (cyt b), we found three latitudinal structured geographic clades (northern, central, and southern). The northern clade occurs in the border area of the USA and the north of BCP, the central clade occurs from the peninsular highlands through the Central Desert of Baja California, and the southern clade is distributed south of the San Ignacio Lagoon. AMOVA showed that genetic variation is higher among clades (64%) than within populations (18.1%). The deepest divergence among clades is very shallow (～300 000 years), which suggests that climatic changes during the Pleistocene or some inhospitable habitats have affected the structure of this group, rather than influences from older marine transgressions. Phylogenetic groups disclosed by our results do not coincide with the current infraspecific classification; therefore, we propose a change of epithet for BCP gophers (Thomomys nigricans) and a new subspecific taxonomic arrangement with four subspecies: Thomomys nigricans anitae, Thomomys nigricans martirensis, Thomomys nigricans nigricans, and Thomomys nigricans russeolus. © 2013 The Linnean Society of London     

Barcoding,molecular taxonomy,and exploration of the diversity of shrews (Soricomorpha: Soricidae) on Mount Nimba (Guinea)

We tested the efficiency of cytochrome oxidase I (COI)‐barcoding as a taxonomic tool to discriminate and identify sympatric shrew species on Mount Nimba (Guinea). We identified 148 specimens at the species level using morphological characters and comparison with type specimens, including several taxa from Mount Nimba. We identified ten morphospecies and tested aspects of genetic diversity and monophyly using genetic data from three mitochondrial (16S, cytochrome b, and COI) and one nuclear marker (the breast cancer gene, BRCA). Nine morphospecies were validated under the phylogenetic and genetic species concepts, including the recently diverged species Crocidura buettikoferi, Crocidura theresae, and Crocidura grandiceps. Under the same concepts, our analyses revealed the presence of two cryptic species amongst animals identified as Crocidura muricauda. We then tested the efficiency of barcoding thanks to commonly used phenetic methods, with the 148 specimens representing 11 potentially valid species based on morphological and molecular data. We show that COI‐barcoding is a powerful tool for shrew identification and can be used for taxonomic surveys. The comparison of genetic divergence values shows the presence of a barcoding gap (i.e. difference between the highest intraspecific and the lowest interspecific genetic divergence values). Given that only a few COI sequences are available for Afrotropical shrews, our work is an important step forward toward their enrichment. We also tested the efficiency of the three other sequenced markers and found that cytochrome b is as efficient as COI for barcoding shrews. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 672–687.     

Discongruence of Mhc and cytochrome b phylogeographical patterns in Myodes glareolus (Rodentia: Cricetidae)

In the present study, a phylogeographical approach was developed to analyse the influence of selection and history on a major histocompatibility complex (Mhc) class II gene polymorphism in European bank vole (Myodes glareolus) populations. We focused on exon 2 of the Dqa gene because it is highly variable in a large array of species and appears to evolve under pathogen‐mediated selection in several rodent species. Using single‐strand conformation polymorphism analysis and sequencing techniques, 17 Dqa‐exon2 alleles, belonging to at least two different copies of Dqa gene, were detected over the distribution range of M. glareolus. Evidence of selection was found using molecular and population analyses. At the molecular level, we detected 13 codons evolving under positive selection pressures, most of them corresponding to regions coding for putative antigen binding sites of the protein. At the European level, we compared patterns of population structure for the Dqa‐exon2 and cytochrome b (cyt b) gene. We did not detect any spatial genetic structure among M. glareolus populations for the Dqa‐exon2. These results strongly differed from those obtained using the cyt b gene, which indicated a recent phylogeographical history closely linked to the last glacial events. Seven mitochondrial lineages have yet been described, which correspond to major glacial refugia. Altogether, our results revealed clear evidence of balancing selection acting on Dqa‐exon2 and maintaining polymorphism over large geographical areas despite M. glareolus history. It is thus likely that Mhc phylogeographical variability could have been shaped by local adaptation to pathogens. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 881–899.     

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.     

Phylogeography of two cryptic species of African desert jerboas (Dipodidae: Jaculus)

The lesser Egyptian jerboa Jaculus jaculus is a desert dwelling rodent that inhabits a broad Arabian–Saharan arid zone. Recently, two distant sympatric lineages were described in North‐West Africa, based on morphometric and molecular data, which may correspond to two cryptic species. In the current study, phylogenetic relationships and phylogeographical structure among those lineages and geographical populations from North Africa and the Middle East were investigated. The phylogeographical patterns and genetic diversity of the cytochrome b gene (1110 bp) were addressed on 111 jerboas from 41 localities. We found that the variation in Africa is partitioned into two divergent mitochondrial clades (10.5% divergence relating to 1.65–4.92 Mya) that corresponds to the two cryptic species: J. jaculus and J. deserti. Diversifications within those cryptic species/clades were dated to 0.23–1.13 Mya, suggesting that the Middle Pleistocene climatic change and its environmental consequences affected the evolutionary history of African jerboas. The third distant clade detected, found in the Middle East region, most likely represents a distinct evolutionary unit, independent of the two African lineages. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Multiple origins of invasive and ‘native’ water frogs (Pelophylax spp.) in Switzerland

The marsh frog (Pelophylax ridibundus) has been introduced in many areas in Central and Western Europe as a result of commercial trade with Eastern Europe, and is rapidly replacing the native pool frog (P. lessonae). A large number of Pelophylax species are distributed in Eastern Europe and the strong phenotypic similarity between these species is rendering their identification hazardous. Consequently, alien populations of Pelophylax might not strictly be composed of P. ridibundus as previously suspected. In the present study, we analysed the cytochrome‐b and NADH dehydrogenase subunit 3 genes of introduced and native Pelophylax species from Switzerland (299 individuals) in order to properly identify the source populations of the invaders and the genetic status of the native species. Our study highlighted the occurrence of several genetic lineages of invasive frogs in western Switzerland. Unexpectedly, we also showed that several populations of the native pool frog (P. lessonae) cluster with the Italian pool frog P. bergeri from central Italy (considered by some authors as a subspecies of P. lessonae). Hence, these populations are probably also the result of introductions, meaning that the number of native P. lessonae populations is fewer than expected in Switzerland. These findings have important implications concerning the conservation of the endemic pool frog populations, as the presence of multiple alien species could strongly affect their long‐term subsistence. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 442–449.     

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.     

Effects of current and historic habitat fragmentation on the genetic structure of the sand goby Pomatoschistus minutus (Osteichthys,Gobiidae)

Habitat fragmentation is a major force that will influence the evolution of a species and its distribution range. Pomatoschistus minutus, the sand goby, has a North Atlantic–Mediterranean distribution and shows various level of habitat fragmentation along its geographic repartition. The use of mitochondrial sequences of the cytochrome b (cyt b) gene and two co‐dominant sets of nuclear markers (introns and microsatellites) allowed us to describe the relationships between P. minutus populations belonging to several different geographical regions of Europe and to assess the structure of populations inhabiting the Golfe du Lion, along the French Mediterranean coast. The present study confirms that the taxon located in the Adriatic Sea (Venice) should be considered as a distinct species, separated approximately 1.75 Mya. The comparison of P. minutus between the Atlantic and western Mediterranean coasts using polymorphic co‐dominant markers revealed that they belong to two demographically independent units, and thus could be considered as well as distinct species, more recently separated (0.3 Mya). The Pleistocene glaciations seem therefore to have played an important role in the diversification of this complex. Finally, at a regional scale in the Golfe du Lion, P. minutus appears to form a single huge homogeneous population. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 175–198.     

Phylogeography of the large Myotis bats (Chiroptera: Vespertilionidae) in Europe,Asia Minor,and Transcaucasia

The large Myotis complex in continental Europe, Asia Minor, and Transcaucasia comprises two sibling bat species, the greater mouse‐eared bat, Myotis myotis, and the lesser mouse‐eared bat, Myotis blythii, also referred to as Myotis oxygnathus. Here, we investigate the phylogeography of these bats using two mitochondrial markers: the second hypervariable domain of the control region (HVII) and a fragment of the cytochrome b gene (cyt b). The HVII haplotypes formed six distinct haplogroups associated with different geographical regions. Most of the European HVII haplotypes were exclusive to M. myotis, whereas the majority of HVII haplotypes found in Asia Minor were exclusive to M. blythii/M. oxygnathus. The phylogenetic reconstruction based on the concatenated cyt b and HVII fragments recovered two major lineages. The first lineage comprised samples from Europe (western lineage), and the second lineage included samples from Asia Minor, Transcaucasia, Crimea, Western Ukraine, Thrace, the Balkans, and Eastern Europe (eastern lineage). The mitochondrial lineage of M. blythii, reported from Kyrgyzstan, was not present in Asia Minor and Transcaucasia. Therefore, we consider the possibility that the M. blythii/M. oxygnathus found in Europe, Asia Minor, and Transcaucasia are not recent descendants of the Central Asian M. blythii. Instead, we suggest that M. blythii/M. oxygnathus and M. myotis diverged through allopatric speciation in Asia Minor and Europe, and that they are represented by the eastern and western mitochondrial lineages. We also examine an alternative hypothesis: that the large Myotis complex consists of more than two species that diverged independently in Asia Minor and Europe through ecological speciation. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Haemosporidian infections in skylarks (<Emphasis Type="Italic">Alauda arvensis</Emphasis>): a comparative PCR-based and microscopy study on the parasite diversity and prevalence in southern Italy and the Netherlands

Changes in agricultural management have been identified as the most probable cause for the decline of Skylark (Alauda arvensis) populations in Europe. However, parasitic infections have not been considered as a possible factor influencing this process. Four hundred and thirty-four Skylarks from the Southern Italy and the Netherlands were screened for haemosporidian parasites (Haemosporida) using the microscopy and polymerase chain reaction (PCR)-based methods. The overall prevalence of infection was 19.5%; it was 41.8% in Italian birds and 8.3% in Dutch birds. The prevalence of Plasmodium spp. was 34.1% and 6.5% in Skylarks from Italy and Netherlands, respectively. Approximately 15% of all recorded haemosporidian infections were simultaneous infections both in Italian and Dutch populations. Six different mitochondrial cytochrome b (cyt b) lineages of Plasmodium spp. and three lineages of Haemoproteus tartakovskyi were found. The lineage SGS1 of Plasmodium relictum was the most prevalent at both study sites; it was recorded in 24.7% of birds in Italy and 5.5% in the Netherlands. The lineages SYAT05 of Plasmodium vaughani and GRW11 of P. relictum were also identified with a prevalence of <2% at both study sites. Two Plasmodium spp. lineages (SW2 and DELURB4) and three H. tartakovskyi lineages have been found only in Skylarks from Italy. Mitochondrial cyt b lineages SYAT05 are suggested for molecular identification of P. vaughani, a cosmopolitan malaria parasite of birds. This study reports the greatest overall prevalence of malaria infection in Skylarks during the last 100 years and shows that both Plasmodium and Haemoproteus spp. haemosporidian infections are expanding in Skylarks so it might contribute to a decrease of these bird populations in Europe.