Eastern Clade Research Articles

Concordance in phylogeography and ecological niche modelling identify dispersal corridors for reptiles in arid Australia

AbstractAimUsing the rock‐specialist agamid Ctenophorus caudicinctus as a model, we test hypothesized biogeographical dispersal corridors for lizards in the Australian arid zone (across the western sand deserts), and assess how these dispersal routes have shaped phylogeographical structuring.LocationArid and semi‐arid Australia.MethodsWe sequenced a c. 1400 bp fragment of mtDNA (ND2) for 134 individuals of C. caudicinctus as well as a subset of each of the mtDNA clades for five nuclear loci (BDNF, BACH1, GAPD, NTF3, and PRLR). We used phylogenetic methods to assess biogeographical patterns within C. caudicinctus, including relaxed molecular clock analyses to estimate divergence times. Ecological niche modelling (Maxent) was employed to estimate the current distribution of suitable climatic envelopes for each lineage.ResultsPhylogenetic analyses identified two deeply divergent mtDNA clades within C. caudicinctus – an eastern and western clade – separated by the Western Australian sand deserts. However, divergences pre‐date the Pleistocene sand deserts. Phylogenetic analyses of the nuclear DNA data sets generally support major mtDNA clades, suggesting past connections between the western C. c. caudicinctus populations in far eastern Pilbara (EP) and the lineages to the east of the sand deserts. Ecological niche modelling supports the continued suitability of climatic conditions between the Central Ranges and the far EP for C. c. graafi.Main conclusionsEstimates of lineage ages provide evidence of divergence between eastern and western clades during the Miocene with subsequent secondary contact during the Pliocene. Our results suggest that this secondary contact occurred via dispersal between the Central Ranges and the far EP, rather than the more southerly Giles Corridor. These events precede the origins of the western sand deserts and divergence patterns instead appear associated with Miocene and Pliocene climate change.

Designation and description of a neotype of Sclerophrys maculata(Hallowell, 1854), and reinstatement of S. pusilla (Mertens, 1937) (Amphibia: Anura: Bufonidae).

Molecular analysis indicates that African material previously referred to Amietophrynus maculatus (Hallowell, 1854; now Sclerophrys maculata), is divisible into two distinct clades: a Western Clade from Cameroon westwards and an Eastern Clade from Central African Republic eastwards, and Uganda southwards to South Africa, extending to Angola-Namibia. Preliminary morphological and bioacoustic data support this division. The two clades are recognised here as two separate species. The Western species retains the name S. maculata, with Hallowell's designated type locality of Liberia. The Eastern Clade retains the name published by Mertens (1937), S. pusilla. It is noted that a type specimen of S. maculata cannot be traced and is presumed lost; the so-called syntypes in the Philadelphia Academy of Natural Sciences are not the material described by Hallowell. None of these have been designated as a neotype, consequently a specimen from Liberia in the collection of the Natural History Museum, London, is designated here as the neotype of S. maculata.

Inferring the roles of vicariance, climate and topography in population differentiation inSalamandra algira(Caudata, Salamandridae)

Integrating information from species occurrence data, environmental variables and molecular markers can provide valuable insights about the processes of population persistence and differentiation. In this study, we present the most comprehensive overview of the evolutionary history of the North African salamander Salamandra algira (Caudata, Salamandridae) to date, including analyses of climatic and topographical variables, and sequences of two mitochondrial and two nuclear DNA fragments, with a special focus on Algerian populations, under-represented in previous studies. Coalescent-based phylogenetic analyses of mtDNA data recover four well-supported population groups corresponding to described subspecies, with a western clade including populations in north-western Morocco (with two subclades corresponding to the subspecies tingitana and splendens), and an eastern clade including populations from north-eastern Morocco (subspecies spelaea) and Algeria (subspecies algira). Inferred split times between major clades date back to the Miocene, with additional splits within each major clade in the Plio-Pleistocene. Present climatic (aridity) and topographical factors account for geographical discontinuities across population groups and help identify potential areas of secondary contact between clades corresponding to the subspecies tingitana and splendens in the Rif mountains in Morocco. Niche analysis indicates the absence of phylogenetic signal in the use of environmental space in this species.

Phylogenetic relationships of Simpsonichthys subgenera (Cyprinodontiformes, Rivulidae), including a proposal for a new genus

The systematic knowledge of Simpsonichthys has changed substantially in recent years, with five subgenera having been elevated to the genus category. In view of these taxonomic changes, the aim of the present study was to identify the phylogenetic relationships among this group in order to test a hypothesis of the division of Simpsonichthys. The ATPase 8 and 6 gene sequences of 53 specimens of Simpsonichthys, Xenurolebias, Ophthalmolebias, Spectrolebias and Hypsolebias genera were assessed. The final topology divided the Simpsonichthys subgenera into five clades: clade I (Hypsolebias antenori group and Ophtalmolebias), clade II (Simpsonichtys and Spectrolebias), clade III (Hypsolebias flammeus and H. magnificus groups), clade IV (H. notatus group) and clade V, which included the Xenurolebias genus as a sister group to all the other Simpsonichthys subgenera. Simpsonichthys, Spectrolebias and Hypsolebias could therefor not be described as monophyletic groups, as has been proposed in some hypotheses. The H. antenori, H. notatus and H. magnificus groups, however, were monophyletic. The molecular results also suggested that H. ocellatus belongs to the Hypsolebias flammeus group. The phylogenetic position of H. fasciatus suggested a new group within Hypsolebias, or possibly even a new genus. The characteristics of the Hypsolebias antenori group and their phylogenetic position suggested that only the species of this group should be included in the Hypsolebias genus. The basal position of the Hypsolebias notatus group and its morphological character may represent a new genus. Although the monophyletism of Simpsonichtys could not be recovered, the branches supported the division of the western and eastern clades, possibly due to allopatric speciation. These facts suggest the division of the genus into at least two major clades. In addition, the study of morphological and molecular data is suggested to obtain a better understanding of such complex organisms, and a major taxonomic review is required.

Genetic differentiation and polyploid formation within the Cryptogramma crispa complex (Polypodiales: Pteridaceae)

The tetraploid fern Cryptogramma crispa (L.) R.Br. Ex Hook. İs distributed across alpine and high latitude regions of Europe and western Asia and is sympatric with the recently described octoploid C. Bithynica S.Jess., L.Lehm. And Bujnoch in north-central Turkey. Our analysis of a 6-region plastid DNA sequence dataset comprising 39 accessions of Cryptogramma R.Br., including 14 accessions of C. Crispa and one accession of C. Bithynica, revealed a deep genetic division between the accessions of C. Crispa from western, northern, and central Europe and the accessions of C. Crispa and C. Bithynica from Turkey and the Caucasus Mountains. This legacy likely results from Pleistocene climate fluctuations and appears to represent incipient speciation between the eastern and western clades. These plastid DNA sequence data also demonstrate that the western clade of C. Crispa, specifically the western Asian clade, is the maternal progenitor of C. Bithynica. Our analysis of DNA sequence data from the biparentally inherited nuclear locus gapCp supports an autopolyploid origin of C. Bithynica, with C. Crispa as the sole progenitor.

Alpine-Himalayan orogeny drove correlated morphological, molecular, and ecological diversification in the Persian dwarf snake (Squamata: Serpentes:Eirenis persicus)

The Persian dwarf snake Eirenis (Pseudocyclophis) persicus (Anderson, 1872) has a wide distribution range in south-western Asia. This species group was comprehensively studied here using traditional biometry, geometric morphometrics, ecological niche modelling, and genetics. Our analyses revealed that E. persicus is split into two clades. A western clade, bearing at least two different species: E. persicus, distributed in south-western Iran, and an undescribed species from south-eastern Turkey and western Iran. The eastern clade consists of at least three species: Eirenis nigrofasciatus, distributed across north-eastern Iraq, and western and southern Iran; Eirenis walteri, distributed across eastern Iran, southern Turkmenistan, and western and southern Pakistan, and Eirenis angusticeps, distributed in north-eastern Pakistan. Ecological niche modelling revealed that the distribution of the species in the western clade are mainly affected by winter precipitation, and those in the eastern clade are mainly affected by the minimum temperature of the coldest month. A molecular clock analysis revealed that the divergence and diversification of the E. persicus species group mainly correspond to Eocene to Pliocene orogeny events subsequent to the Arabia–Eurasia collision. This study confirms that specimens with the unique morphology of having 13 dorsal scale rows on the anterior dorsum, occurring in the Suleiman Mountains in central Pakistan, can be referred to Eirenis mcmahoni (Wall, 1911). However, at this moment we have insufficient data to evaluate the taxonomy of this species.

Exceptional maternal lineage diversity in brown bears (Ursus arctos) from Turkey

The genetic diversity and phylogeography of maternal lineages in Ursus arctos Linnaeus, 1758 (the brown bear) have been studied extensively over the last two decades; however, sampling has largely been limited to the northern Holarctic, and was possibly biased towards lineages that recolonized the vast expanses of the north as the Last Glacial Maximum (LGM) ended. Here we report the genetic diversity and phylogeography of U. arctos from Turkey based on 35 non-invasive samples, including five from captive individuals. Bayesian phylogenetic analyses based on a 269-bp fragment of the mitochondrial DNA control region revealed 14 novel haplotypes belonging to three major lineages. The most widespread lineage was found to be the Eastern clade 3a, whereas geographically more restricted Western and Middle Eastern lineages were reported for the first time in Turkey. A specimen from the Taurus mountain range carried a haplotype closely related to the presumably extinct bears in Lebanon. Moreover, we identify a unique new lineage that appears to have split early within the Middle Eastern clade. Despite limited sampling, our study reveals a high level of mitochondrial diversity in Turkish U. arctos, shows that the ranges of both European and Middle Eastern clades extend into Turkey, and identifies a new divergent lineage of possibly wider historical occurrence. Obtaining these results with 35 samples also demonstrates the value of proper sampling from regions that have not been significantly affected by the LGM.

Phylogeography of the Chinese endemic freshwater crab Sinopotamon acutum (Brachyura, Potamidae)

Phylogeographical inferences based on multiple molecular markers from different modes of inheritance (i.e. mtDNA and nucDNA) can help to explore drivers of current species divergence over different timescales and allow a deeper understanding of evolutionary processes. River systems and mountains, owing to their drainage networks and complex topography, are often a high priority when inferring external causes of phylogeographical patterns. Here, we selected the Chinese endemic freshwater crab Sinopotamon acutum inhabiting drainage networks across the Qinling–Daba Mountains, a watershed that divides northern from southern fauna in China, as a model species (1) to investigate whether river networks and mountain systems act as barriers in shaping the phylogeography of freshwater crabs and (2) to test the impact of historic environments and ecological habitats on crab distribution. Phylogenetic tree and network analyses based on mtDNA revealed divergence between eastern and western populations, but microsatellite DNA did not recover this. Frequent and male‐biased gene flow is evident. The adjacent tributaries, such as Weihe River 1 and Hanjiang River 1, although isolated by Qinling Mts, have low genetic variation in mtDNA. In addition, microsatellite DNA showed low variation between all rivers. Frequent gene flow, genetic variation and mitochondrial genetic structure in S. acutum indicated that the Qinling–Daba Mountains have had no effect on divergence in this species; instead, hydrological networks across these mountains serve as a continuous migration corridor for these crabs. Glacial refugia are probably responsible for the initial isolation of the eastern and western clades, and local adaptations after dispersal have further driven divergence. Cytonuclear discordance in phylogeographical patterns may be attributable to ongoing male‐biased gene flow.

Molecular phylogeny reveals the polyphyly of the snail genus Cepaea (Gastropoda: Helicidae)

Snails in the genus Cepaea are important model organisms in ecogenetic studies because of their colour and banding polymorphism. The monophyly of this group has been almost unanimously assumed based on superficial similarities in shell form and colouration. However, molecular phylogenetic analyses based on mitochondrial and nuclear sequences of 20 genera of Helicidae unequivocally demonstrated that Cepaea as currently understood is a polyphyletic assemblage. Only C. nemoralis and C. hortensis are retained in Cepaea, whereas C. vindobonensis is referred to Caucasotachea and C. sylvatica to Macularia based on our molecular phylogeny. Cepaea and Macularia belong to the western clade of the Helicinae, whereas Caucasotachea is nested in the eastern clade which probably diverged in the late Eocene. Because of the large phylogenetic distances between Cepaea, Macularia and Caucasotachea, it has to be shown whether the genetic mechanism underlying the simpler banding polymorphism in C. vindobonensis and M. sylvatica is a simpler version of the supergene that determines the polymorphism in Cepaea in the strict sense. This case illustrates the importance of sound phylogenetic analyses as a basis for any predictions in comparative biology.

History matters more when explaining genetic diversity within the context of the core-periphery hypothesis.

The core-periphery hypothesis (CPH) predicts that populations located at the periphery of a species' range should have lower levels of genetic variation than those at the centre of the range. However, most of the research on the CPH focuses on geographic distance and not on ecological distance, or uses categorical definitions of core and periphery to explain the distribution of genetic diversity. We use current climate data and historical climate data from the last glacial maxima to develop quantitative estimates of contemporary and historical ecological suitability using ecological niche models. We analysed genetic diversity using 12 polymorphic microsatellites to estimate changes in heterozygosity, allelic richness and population differentiation in 31 populations of the wood frog (Lithobatessylvaticus) spanning the species' entire eastern clade (33(o) to 45(o) latitude) from Alabama, USA, to Nova Scotia, Canada. Our data support predictions based on the CPH. Populations showed significant differences in genetic diversity across the range, with lower levels of genetic variation at the geographic range edge and in areas with lower levels of historical and contemporary ecological suitability. However, history and geography (not current ecological suitability) best explain the patterns. This study highlights the importance of examining more than just geography when assessing the CPH, and the importance of historical ecological suitability in the maintenance of genetic diversity and population differentiation.

Palaeo-islands as refugia and sources of genetic diversity within volcanic archipelagos: the case of the widespread endemic Canarina canariensis (Campanulaceae).

Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within-island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographical population structure, with a first divergence around 0.8Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable 'palaeo-islands' of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographical clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra-island levels of genetic diversity larger than those between-islands. We argue that volcanic eruptions and landslides after the merging of the palaeo-islands 3.5Ma played key roles in generating genetic boundaries within Tenerife, with the palaeo-islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago.

The first molecular characterization of the genus Hirudo on the territory of Serbia: estimation of endangerment

Several recent morphological studies of the genus Hirudo indicated that only Hirudo verbana is present in Serbia, while Hirudo medicinalis is completely absent. In order to test this hypothesis, specimens of medicinal leech from Serbia are analyzed for the first time by the method of DNA identification. The results show that individuals belonging to the species H. medicinalis are absent on the territory of Serbia, where only specimens of the sister (congener) species H. verbana can be found instead. All of the analyzed specimens can be related to five haplotypes. Two of the haplotypes are previously known from Ukraine, while three are newly discovered. It follows that genetic differentiation into eastern and western clades of the species H. verbana is unrealistic. Much more detailed sampling throughout the entire area is needed in order to establish the precise distribution of haplotypes. Factors posing a threat to both individual populations and the species as a whole are also considered as a basis for undertaking conservation measures for preservation of the species H. verbana. Such measures are necessary in view of the fact that for the past 8 years, H. verbana has been exported from Serbia to Western European countries instead of H. medicinalis (which does not live on the territory of Serbia). On the basis of the obtained results, the degree of threat to the species H. verbana is defined and preliminary protective measures are proposed for the conservation of this endangered species of aquatic invertebrate.

Molecular insights into geographic and morphological variation within the Eumicrotremus asperrimus species complex (Cottoidei: Cyclopteridae)

A molecular phylogeny of lumpsukers, Eumicrotremus asperrimus and related species (family Cyclopteridae), is presented on the basis of sequence variations in the cytochrome b and cytochrome c oxidase subunit 1 genes (1,659 base pairs) of mitochondrial DNA using specimens collected from across the North Pacific, including the Sea of Japan, Sea of Okhotsk, Bering Sea, and Gulf of Alaska. Specimens identified as Eumicrotremus phrynoides, Cyclopteropsis bergi, Cyclopteropsis lindbergi, and Lethotremus muticus on the basis of the presence or absence of spiny tubercles and height of the first dorsal fin did not exhibit reciprocal monophyly, but were randomly clustered with E. asperrimus. This collection of forms is therefore referred to as the “E. asperrimus species complex.” DNA sequence data presented here divided the E. asperrimus species complex into two distinct clades, corresponding to the eastern North Pacific (the Bering Sea, Aleutian Islands, and Gulf of Alaska) and the western North Pacific (the Seas of Japan and Okhotsk) regions. Slight morphometric differences between eastern and western clades were also evident, indicating that they represent at least two different species. The genetic level of divergence between the two clades suggests that the speciation event occurred during the early Pleistocene to late Pliocene. Although the presence and morphology of tubercles have been used extensively for species discrimination in Cyclopteridae, our results suggest that this character complex is confounded by intraspecific variation. Examined samples showed some sexual dimorphism in the relative development of the tubercles, although the pattern was different between the eastern and western North Pacific clades. These results underscore the need for a thorough re-examination of the taxonomy of Pacific cyclopterids, using molecular data to supplement potentially misleading tubercle morphology.

Phylogenetic relationships of Semaphore geckos (Squamata: Sphaerodactylidae: Pristurus) with an assessment of the taxonomy of Pristurus rupestris.

A molecular phylogeny of the sphaerodactylid geckos of the genus Pristurus is inferred based on an alignment of 1845 base pairs (bp) of concatenated mitochondrial (12S) and nuclear (acm4, cmos, rag1 and rag2) genes for 80 individuals, representing 18 of the 23-26 species, and the three subspecies of P. rupestris. The results indicate that P. rupestris is polyphyletic and includes two highly divergent clades: the eastern clade, found in coastal Iran and throughout the Hajar Mountain range in northern Oman and eastern UAE; and the western clade, distributed from central coastal Oman, through Yemen, Saudi Arabia and north to southern Jordan. Inferred haplotype networks for the four nuclear genes show that the eastern and western clades of "P. rupestris" are highly differentiated and do not share any alleles. Moreover, although the two clades are differentiated by a morphological multivariate analysis, no one character or set of characters was found to be diagnostic. Based on the molecular analysis of specimens from the type locality of P. rupestris rupestris, the name P. rupestris is applied to the eastern clade. The name that should apply to the western clade cannot be clarified until morphological and genetic data for "P. rupestris" is available from the vicinity of Bosaso, Somalia, and therefore we refer to it as Pristurus sp. 1. The phylogenetic tree of Pristurus supports the hypothesis that P. celerrimus is sister to all the other species in the analyses and that the Socotra Archipelago was independently colonized a minimum of two times.

A phylogeographic survey of the pygmy mouse Mus minutoides in South Africa: taxonomic and karyotypic inference from cytochrome b sequences of museum specimens.

The African pygmy mice (Mus, subgenus Nannomys) are a group of small-sized rodents that occur widely throughout sub-Saharan Africa. Chromosomal diversity within this group is extensive and numerous studies have shown the karyotype to be a useful taxonomic marker. This is pertinent to Mus minutoides populations in South Africa where two different cytotypes (2n = 34, 2n = 18) and a modification of the sex determination system (due to the presence of a Y chromosome in some females) have been recorded. This chromosomal diversity is mirrored by mitochondrial DNA sequences that unambiguously discriminate among the various pygmy mouse species and, importantly, the different M. minutoides cytotypes. However, the geographic delimitation and taxonomy of pygmy mice populations in South Africa is poorly understood. To address this, tissue samples of M. minutoides were taken and analysed from specimens housed in six South African museum collections. Partial cytochrome b sequences (400 pb) were successfully amplified from 44% of the 154 samples processed. Two species were identified: M. indutus and M. minutoides. The sequences of the M. indutus samples provided two unexpected features: i) nuclear copies of the cytochrome b gene were detected in many specimens, and ii) the range of this species was found to extend considerably further south than is presently understood. The phylogenetic analysis of the M. minutoides samples revealed two well-supported clades: a Southern clade which included the two chromosomal groups previously identified in South Africa, and an Eastern clade that extended from Eastern Africa into South Africa. Congruent molecular phylogenetic and chromosomal datasets permitted the tentative chromosomal assignments of museum specimens within the different clades as well as the correction of misidentified museum specimens.

Phylogeography and Pleistocene refugia of the Little OwlAthene noctuainferred 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.

Taxonomic reassessment of Blanus strauchi (Bedriaga, 1884) (Squamata: Amphisbaenia: Blanidae), with the description of a new species from southeast Anatolia (Turkey).

The study of mitochondrial and nuclear DNA sequences reveals that the polytypic Blanus strauchi is a species complex including three well-defined allopatric clades, one of which consists of two sub-clades. Only the two sub-clades of the Western clade are morphologically diagnosable in the field, whereas obvious characters to distinguish the Central and the Eastern clades are lacking. However, all four clades show significant statistical differentiation on meristic traits, as well as in morphometric characters of the head when compared by means of the geometric morphometrics. The genetic distance between the three major mitochondrial clades is comparable to the p-distances for the same markers observed between Blanus species-pairs from Morocco and the Iberian Peninsula, respectively. The nuclear marker confirms the mitochondrial clades, and shows that the three major clades do not share any haplotypes, as an indication of restricted gene flow among them. On the basis of this evidence, the taxonomy of Blanus strauchi is re-assessed: the Western clade corresponds to B. strauchi, with two subspecies: B. s. strauchi and B. s. bedriagae. The Central clade corresponds to B. aporus, here elevated at the species rank. For the eastern clade there are no available names, and therefore it is described here as Blanus alexandri sp. nov.

A new species of lutrine opossum, genusLutreolinaThomas (Didelphidae), from the South American Yungas

Abstract This study presents the most comprehensive systematic revision of the genus Lutreolina to date, by means of genetic (mitochondrial DNA of 22 specimens) and morphologic (assessment of 262 specimens) evidence. Molecular analyses were based on cytochrome-b gene sequences from 22 individuals collected at 18 localities from Argentina, Bolivia, Brazil, Paraguay, and Uruguay, which are currently allocated to L. crassicaudata. Results indicate that Lutreolina has sharp phylogeographic structure, with 2 reciprocally monophyletic groups (2.7% divergent, whereas intraclade variation is minimal) occurring east and west of the Dry Chaco, where Lutreolina is absent. The eastern clade includes populations from eastern Paraguay, northeastern central Argentina, southern Brazil, and Uruguay. These populations were traditionally allocated to the subspecies L. c. crassicaudata and L. c. paranalis, whose monophyly is not supported in our study. Therefore, eastern populations are all assigned here to the nominotypic s...

Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe.

After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human-induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present-day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000 years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting-associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction.

Contemporary Genetic Structure, Phylogeography and Past Demographic Processes of Wild Boar Sus scrofa Population in Central and Eastern Europe

The wild boar (Sus scrofa) is one of the most widely distributed mammals in Europe. Its demography was affected by various events in the past and today populations are increasing throughout Europe. We examined genetic diversity, structure and population dynamics of wild boar in Central and Eastern Europe. MtDNA control region (664 bp) was sequenced in 254 wild boar from six countries (Poland, Hungary, Belarus, Ukraine, Moldova and the European part of Russia). We detected 16 haplotypes, all known from previous studies in Europe; 14 of them belonged to European 1 (E1) clade, including 13 haplotypes from E1-C and one from E1-A lineages. Two haplotypes belonged respectively to the East Asian and the Near Eastern clade. Both haplotypes were found in Russia and most probably originated from the documented translocations of wild boar. The studied populations showed moderate haplotype (0.714±0.023) and low nucleotide diversity (0.003±0.002). SAMOVA grouped the genetic structuring of Central and Eastern European wild boar into three subpopulations, comprising of: (1) north-eastern Belarus and the European part of Russia, (2) Poland, Ukraine, Moldova and most of Belarus, and (3) Hungary. The multimodal mismatch distribution, Fu's Fs index, Bayesian skyline plot and the high occurrence of shared haplotypes among populations did not suggest strong demographic fluctuations in wild boar numbers in the Holocene and pre-Holocene times. This study showed relatively weak genetic diversity and structure in Central and Eastern European wild boar populations and underlined gaps in our knowledge on the role of southern refugia and demographic processes shaping genetic diversity of wild boar in this part of Europe.