Environmental change and rates of evolution: the phylogeographic pattern within the hartebeest complex as related to climatic variation

Global climate fluctuated considerably throughout the Pliocene-Pleistocene period, influencing the evolutionary history of a wide array of species. Using the phylogeographic patterns within the hartebeest (Alcelaphus buselaphus (Pallas, 1766)) complex, we evaluated the evolutionary consequences of such environmental change for a typical large mammal ranging on the African savannah. Our results, as generated from two mitochondrial DNA markers (the D-loop and cytochrome b), suggest an origin of the hartebeest in eastern Africa from where the species has colonized other parts of the continent. Phylogenetic analyses revealed an early diversification into southern and northern hartebeest lineages, an event that may be related to the formation of the Rift Valley lakes. The northern lineage has further diverged into eastern and western lineages, most probably as a result of the expanding central African rainforest belt and subsequent contraction of savannah habitats during a period of global warming. The diversification events appear to have coincided with major climatic changes and are highly correlated in time. These observations strongly suggest that large-scale climatic fluctuations have been a major determinant for the species' evolutionary history and that hartebeest evolution has mainly taken place in isolated yet environmentally favourable refugia during periods of global warming. Indications of sudden population expansion for two putative ancestral hartebeest populations provide further support for a refugia-based explanation of the diversification events. Reciprocal monophyly between southern and northern lineages may suggest that reproductive barriers exist and that the hartebeest complex comprises two different species.     

Isolation and characterization of species-specific microsatellite markers for blue and black wildebeest (<Emphasis Type="BoldItalic">Connochaetes taurinus</Emphasis> and <Emphasis Type="BoldItalic">C. gnou</Emphasis>)

The blue wildebeest (Connochaetes taurinus) is distributed throughout southern and east Africa while the black wildebeest (Connochaetes gnou) is endemic to South Africa and was driven to near extinction in the early 1900s due to hunting pressure and disease outbreaks. Extensive translocation of both species throughout South Africa is threatening the genetic integrity of blue and black wildebeest. To effectively manage these species, genetic tools that can be used to detect hybrid individuals, identify genetically unique subpopulations and determine the levels of genetic diversity are required. In this study, 11 microsatellite markers were developed for wildebeest through next-generation sequencing. The microsatellite loci displayed 2.00–4.14 alleles, unbiased heterozygosity values ranged from 0.32 to 0.60 and observed heterozygosity values ranged from 0.26 to 0.52. The comparatively high level of polymorphism observed in the microsatellite markers indicates that these markers can contribute significantly to our knowledge of population genetic structure, relatedness, genetic diversity and hybridization in these species.     

Ancient forest fragmentation or recent radiation? Testing refugial speciation models in chameleons within an African biodiversity hotspot

Aim East Africa is one of the most biologically diverse regions, especially in terms of endemism and species richness. Hypotheses put forward to explain this high diversity invoke a role for forest refugia through: (1) accumulation of new species due to radiation within refugial habitats, or (2) retention of older palaeoendemic species in stable refugia. We tested these alternative hypotheses using data for a diverse genus of East African forest chameleons, Kinyongia. Location East Africa. Methods We constructed a dated phylogeny for Kinyongia using one nuclear and two mitochondrial markers. We identified areas of high phylogenetic diversity (PD) and evolutionary diversity (ED), and mapped ancestral areas to ascertain whether lineage diversification could best be explained by vicariance or dispersal. Results Vicariance best explains the present biogeographic patterns, with divergence between three major Kinyongia clades (Albertine Rift, southern Eastern Arc, northern Eastern Arc) in the early Miocene/Oligocene (> 20 Ma). Lineage diversification within these clades pre‐dates the Pliocene (> 6 Ma). These dates are much older than the Plio‐Pleistocene climatic shifts associated with cladogenesis in other East African taxa (e.g. birds), and instead point to a scenario whereby palaeoendemics are retained in refugia, rather than more recent radiations within refugia. Estimates of PD show that diversity was highest in the Uluguru, Nguru and East Usambara Mountains and several lineages (from Mount Kenya, South Pare and the Uluguru Mountains) stand out as being evolutionarily distinct as a result of isolation in forest refugia. PD was lower than expected by chance, suggesting that the phylogenetic signal is influenced by an unusually low number of extant lineages with long branch lengths, which is probably due to the retention of palaeoendemic lineages. Main conclusions The biogeographic patterns associated with Kinyongia are the result of long evolutionary histories in isolation. The phylogeny is dominated by ancient lineages whose origins date back to the early Miocene/Oligocene as a result of continental wide forest fragmentation and contraction due to long term climatic changes in Africa. The maintenance of palaeoendemic lineages in refugia has contributed substantially to the remarkably high biodiversity of East Africa.     

A long‐standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope

Aim Previous genetic studies of African savanna ungulates have indicated Pleistocene refugial areas in East and southern Africa, and recent palynological, palaeovegetation and fossil studies have suggested the presence of a long‐standing refugium in the south and a mosaic of refugia in the east. Phylogeographic analysis of the common eland antelope, Taurotragus oryx (Bovidae), was used to assess these hypotheses and the existence of genetic signatures of Pleistocene climate change. Location The sub‐Saharan savanna biome of East and southern Africa. Methods Mitochondrial DNA control‐region fragments (414 bp) from 122 individuals of common eland were analysed to elucidate the phylogeography, genetic diversity, spatial population structuring, historical migration and demographic history of the species. The phylogeographic split among major genetic lineages was dated using Bayesian coalescent‐based methods and a calibrated fossil root of 1.6 Ma for the split between the common eland and the giant eland, Taurotragus derbianus. Results Two major phylogeographic lineages comprising East and southern African localities, respectively, were separated by a net nucleotide distance of 4.7%. A third intermediate lineage comprised only three haplotypes, from Zimbabwe in southern Africa. The estimated mutation rate of 0.097 Myr^?1 revealed a more recent common ancestor for the eastern lineage (0.21 Ma; 0.07–0.37) than for the southern lineage (0.35 Ma; 0.10–0.62). Compared with the latter, the eastern lineage showed pronounced geographic structuring, lower overall nucleotide diversity, higher population differentiation, and isolation‐by‐distance among populations. Main conclusions The data support the hypothesis of Pleistocene refugia occurring in East and southern Africa. In agreement with palynological, palaeovegetation and fossil studies, our data strongly support the presence of a longer‐standing population in the south and a mosaic of Pleistocene refugia in the east, verifying the efficacy of genetic tools in addressing such questions. The more recent origin of the common eland inhabiting East Africa could result from colonization following extinction from the region. Only two other dated African ungulate phylogenies have been published, applying different methods, and the similarity of dates obtained from the three distinct approaches indicates a significant event c. 200 ka, which left a strong genetic signature across a range of ungulate taxa.     

Birth of a hotspot of intraspecific genetic diversity: notes from the underground

Hotspots of intraspecific diversity have been observed in most species, often within areas of putative Pleistocene refugia. They have thus mostly been viewed as the outcome of prolonged stability of large populations within the refugia. However, recent evidence has suggested that several other microevolutionary processes could also be involved in their formation. Here, we investigate the contribution of these processes to current range-wide patterns of genetic diversity in the Italian endemic mole Talpa romana, using both nuclear (30 allozyme loci) and mitochondrial markers (cytochrome b sequences). Southern populations of this species showed an allozyme variation that is amongst the highest observed in small mammals (most populations had an expected heterozygosity of 0.10 or above), which was particularly unexpected for a subterranean species. Population genetic, phylogeographic and historical demographic analyses indicated that T. romana populations repeatedly underwent allopatric differentiations followed by secondary admixture within the refugial range in southern Italy. A prolonged demographic stability was reliably inferred from the mitochondrial DNA data only for a population group located north and east of the Calabrian peninsula, showing comparatively lower levels of allozyme variability, and lacking evidence of secondary admixture with other groups. Thus, our results point to the admixture between differentiated lineages as the main cause of the higher levels of diversity of refugial populations. When compared with the Pleistocene evolutionary history recently inferred for species from both the same and other geographic regions, these results suggest the need for a reappraisal of the role of gene exchange in the formation of intraspecific hotspots of genetic diversity.     

Leopard tortoises in southern Africa have greater genetic diversity in the north than in the south (Testudinidae)

In contrast to mammals, little is known about the phylogeographic structuring of widely distributed African reptile species. With the present study, we contribute data for the leopard tortoise (Stigmochelys pardalis). It ranges from the Horn of Africa southward to South Africa and westwards to southern Angola. However, its natural occurrence is disputed for some southern regions. To clarify the situation, we used mtDNA sequences and 14 microsatellite loci from 204 individuals mainly from southern Africa. Our results retrieved five mitochondrial clades; one in the south and two in the north‐west and north‐east of southern Africa, respectively, plus two distributed further north. Using microsatellites, the southern clade matched with a well‐defined southern nuclear cluster, whilst the two northern clades from southern Africa corresponded to another nuclear cluster with three subclusters. One subcluster had a western and central distribution, another occurred mostly in the north‐east, and the third in a small eastern region (Maputaland), which forms part of a biodiversity hotspot. Genetic diversity was low in the south and high in the north of our study region, particularly in the north‐east. Our results refuted that translocations influenced the genetic structure of leopard tortoises substantially. We propose that Pleistocene climatic fluctuations caused leopard tortoises to retract to distinct refugia in southern and northern regions and ascribe the high genetic diversity in the north of southern Africa to genetic structuring caused by the survival in three refuges and subsequent admixture, whereas tortoises in the south seem to have survived in only one continuous coastal refuge.     

Assessing introgressive hybridization between blue wildebeest (<Emphasis Type="Italic">Connochaetes taurinus</Emphasis>) and black wildebeest (<Emphasis Type="Italic">Connochaetes gnou</Emphasis>) from South Africa

Introgressive hybridization poses a threat to the genetic integrity of black wildebeest (Connochaetes gnou) and blue wildebeest (Connochaetes taurinus) populations in South Africa. Black wildebeest is endemic to South Africa and was driven to near extinction in the early 1900s due to habitat destruction, hunting pressure and disease outbreaks. Blue wildebeest on the other hand are widely distributed in southern and east Africa. In South Africa the natural distribution ranges of both species overlap, however, extensive translocation of black wildebeest outside of its normal distribution range in South Africa have led to potential hybridization between the two species. The molecular identification of pure and admixed populations is necessary to design viable and sustainable conservation strategies, since phenotypic evidence of hybridization is inconclusive after successive generations of backcrossing. The aim of this study was to assess levels of hybridization in wildebeest using both species-specific and cross-species microsatellite markers. Black wildebeest (157) and blue wildebeest (122) from provincial and national parks and private localities were included as reference material, with 180 putative hybrid animals also screened. A molecular marker panel consisting of 13 cross-species and 11 species-specific microsatellite markers was developed. We used a Bayesian clustering model to confirm the uniqueness of blue- and black wildebeest reference groups, assign individuals to each of the two clusters, and determine levels of admixture. Results indicated a clear partition between black wildebeest and blue wildebeest (the average proportions of membership to black wildebeest and blue wildebeest clusters were QI?=?0.994 and QI?=?0.955 respectively). From the putative hybrid samples, only five hybrid individuals were confirmed. However, high levels of linkage disequilibrium were observed in the putative hybrid populations which may indicate historical hybridization. Measures of genetic diversity in the black wildebeest populations were found to be lower than that of the blue wildebeest. The observed lower level of genetic diversity was expected due to the demographic history of the specie. This study will make a significant contribution to inform a national conservation strategy to conserve the genetic integrity of both species.     

Mitochondrial DNA phylogeography of Lissotriton boscai (Caudata, Salamandridae): evidence for old, multiple refugia in an Iberian endemic

In Europe, southern peninsulas served as refugia during cold periods in the Pleistocene, acting both as centres of origin of endemisms and as sources from which formerly glaciated areas were recolonized during interglacial periods. Previous studies have revealed that within the main refugial areas, intraspecific lineages often survived in allopatric refugia. We analysed two mitochondrial markers (nad4, control region, approximately 1.4 kb) in 103 individuals representing the entire distribution of Lissotriton boscai, a newt endemic to the western Iberian Peninsula. We inferred the evolutionary history of the species through phylogenetic, phylogeographic and historical demographic analyses. The results revealed unexpected, deep levels of geographically structured genetic variability. We identified two main evolutionary lineages, each containing three well-supported clades. The first historical split involved populations from central-southwestern coastal Portugal and the ancestor of all the remaining populations around 5.8 million years ago. Both lineages were subsequently fragmented into different population groups between 2.5 and 1.2 million years ago. According to nested clade analysis, at lower hierarchical levels the patterns suggest restricted gene flow with isolation by distance, whereas at higher levels the clades exhibit signatures of contiguous range expansion. Bayesian Skyline Plots show recent bottlenecks, followed by demographic expansions in all lineages. The significant genetic structure found is consistent with long-term survival of populations in allopatric refugia, supporting the 'refugia-within-refugia' scenario for southern European peninsulas. The comparison of our results with other co-distributed species highlights the generality of this hypothesis for the Iberian herpetofauna and suggests that Mediterranean refuges had more relevance for the composition and distribution of present biodiversity patterns than currently acknowledged. We briefly discuss the taxonomic and conservation implications of our results.     

Population genetic structure and diversity of the Apennine endemic stream frog, Rana italica--insights on the Pleistocene evolutionary history of the Italian peninsular biota

For most species in the Western Palaearctic region, southern Mediterranean peninsulas have been identified as major Quaternary refugia and hotspots of intraspecific diversity, and thus, as areas of particular relevance for the conservation of the evolutionary potential. We analysed the patterns of geographical variation among 26 populations of the Italian stream frog, using both nuclear (allozymes) and mitochondrial (partial cytochrome b sequences) markers. Phylogenetic, phylogeographical and population genetic analyses suggested that the species survived the last glacial–interglacial cycles in two distinct refugia, one restricted to the tip of the Calabrian peninsula, at the extreme south of the species' range, the other spanning from central Calabria to central Apennines and showing evidences for further population subdivision therein. Historical demographic tests suggested a significant population expansion from the latter, which most likely began around the last pleniglacial. This expansion would have led to the rapid colonization of the northern Apennines to the north, and to a secondary contact and population admixture with the population from the southern refugium in southern central Calabria. A comparison of the evolutionary history inferred for the Italian stream frog with the data emerging for other codistributed species suggests: (i) the generality of a multiple-refugia scenario for the Italian peninsula, (ii) the possible occurrence of at least one suture zone in southern Italy, and (iii) that for most species, this Pleistocene refugium is not only a hotspot, but also a melting pot of intraspecific genetic diversity. Finally, the conservation implications of these results are also briefly highlighted.     

Regional genetic structuring and evolutionary history of the impala Aepyceros melampus

Samples of 162 impala antelope (Aepyceros melampus) from throughout its distribution range in sub-Saharan Africa were surveyed using eight polymorphic microsatellite loci. Furthermore, 155 previously published mitochondrial DNA (mtDNA) sequences from the same localities were reanalyzed. Two subspecies of impala are presently recognized--the isolated black-faced impala (Aepyceros melampus petersi) in southwest Africa and the common impala (Aepyceros melampus melampus) abundant in southern and east Africa. All tests performed indicated significant genetic differentiation at the subspecific level. Furthermore, individual-based analyses split the common impala subspecies into two distinct genetic groups, conforming with regional geographic affiliation to southern or east Africa. This was supported by assignment tests, genetic distance measures, pairwise theta values, and analysis of molecular variance. We suggest that the presence of such previously unknown regional structuring within the subspecies reflects a pattern of colonization from a formerly large panmictic population in southern Africa toward east Africa. This scenario was supported by a progressive decline in population diversity indices toward east Africa and a significant increase in the quantity theta/(1 - theta). Both microsatellite and mtDNA data indicated a genetic distinctiveness of the Samburu population in Kenya.     

Comparative phylogeography of African savannah ungulates

The savannah biome of sub-Saharan Africa harbours the highest diversity of ungulates (hoofed mammals) on Earth. In this review, we compile population genetic data from 19 codistributed ungulate taxa of the savannah biome and find striking concordance in the phylogeographic structuring of species. Data from across taxa reveal distinct regional lineages, which reflect the survival and divergence of populations in isolated savannah refugia during the climatic oscillations of the Pleistocene. Data from taxa across trophic levels suggest distinct savannah refugia were present in West, East, Southern and South-West Africa. Furthermore, differing Pleistocene evolutionary biogeographic scenarios are proposed for East and Southern Africa, supported by palaeoclimatic data and the fossil record. Environmental instability in East Africa facilitated several spatial and temporal refugia and is reflected in the high inter- and intraspecific diversity of the region. In contrast, phylogeographic data suggest a stable, long-standing savannah refuge in the south.     

Across the southern Andes on fin: glacial refugia,drainage reversals and a secondary contact zone revealed by the phylogeographical signal of Galaxias platei in Patagonia

We employed DNA sequence variation at two mitochondrial (control region, COI) regions from 212 individuals of Galaxias platei (Pisces, Galaxiidae) collected throughout Patagonia (25 lakes/rivers) to examine how Andean orogeny and the climatic cycles throughout the Quaternary affected the genetic diversity and phylogeography of this species. Phylogenetic analyses revealed four deep genealogical lineages which likely represent the initial division of G. platei into eastern and western lineages by Andean uplift, followed by further subdivision of each lineage into separate glacial refugia by repeated Pleistocene glacial cycles. West of the Andes, refugia were likely restricted to the northern region of Patagonia with small relicts in the south, whereas eastern refugia appear to have been much larger and widespread, consisting of separate northern and southern regions that collectively spanned most of Argentinean Patagonia. The retreat of glacial ice following the last glacial maximum allowed re‐colonization of central Chile from nonlocal refugia from the north and east, representing a region of secondary contact between all four glacial lineages. Northwestern glacial relicts likely followed pro‐glacial lakes into central Chilean Patagonia, whereas catastrophic changes in drainage direction (Atlantic → Pacific) for several eastern palaeolakes were the likely avenues for invasions from the east. These mechanisms, combined with evidence for recent, rapid and widespread population growth could explain the extensive contemporary distribution of G. platei throughout Patagonia.     

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.     

Population genomic evidence for plant glacial survival in Scandinavia

Quaternary glaciations have played a major role in shaping the genetic diversity and distribution of plant species. Strong palaeoecological and genetic evidence supports a postglacial recolonization of most plant species to northern Europe from southern, eastern and even western glacial refugia. Although highly controversial, the existence of small in situ glacial refugia in northern Europe has recently gained molecular support. We used genomic analyses to examine the phylogeography of a species that is critical in this debate. Carex scirpoidea Michx subsp. scirpoidea is a dioecious, amphi‐Atlantic arctic–alpine sedge that is widely distributed in North America, but absent from most of Eurasia, apart from three extremely disjunct populations in Norway, all well within the limits of the Weichselian ice sheet. Range‐wide population sampling and variation at 5,307 single nucleotide polymorphisms show that the three Norwegian populations comprise unique evolutionary lineages divergent from Greenland with high between‐population divergence. The Norwegian populations have low within‐population genetic diversity consistent with having experienced genetic bottlenecks in glacial refugia, and host private alleles that probably accumulated in long‐term isolated populations. Demographic analyses support a single, pre‐Weichselian colonization into Norway from East Greenland, and subsequent divergence of the three populations in separate refugia. Other refugial areas are identified in North‐east Greenland, Minnesota/Michigan, Colorado and Alaska. Admixed populations in British Columbia and West Greenland indicate postglacial contact. Taken together, evidence from this study strongly indicates in situ glacial survival in Scandinavia.     

Evolutionary history of the Maltese wall lizard Podarcis filfolensis: insights on the ‘Expansion–Contraction’ model of Pleistocene biogeography

The expansion–contraction (EC) model predicts demographic and range contraction of temperate species during Pleistocene glaciations as a consequence of climate‐related habitat changes, and provides a paradigm for explaining the high intraspecific diversity found in refugia in terms of long‐term demographic stability. However, recent evidence has revealed a weak predictive power of this model for terrestrial species in insular and coastal settings. We investigated the Pleistocene EC dynamics and their evolutionary consequences on temperate species using the Maltese archipelago and its endemic lizard Podarcis filfolensis as a model system. The evolutionary and demographic history of P. filfolensis as inferred from mitochondrial and nuclear sequences data does not conform to the EC model predictions, supporting (i) demographic and spatial stability or expansion, rather than contraction, of the northern and southern lineages during the last glacial period; and (ii) a major role for allopatric differentiation primed by sea‐level dynamics, rather than prolonged demographic stability, in the formation of the observed genetic diversity. When combined with evidence from other Mediterranean refugia, this study shows how the incorporation of Pleistocene sea‐level variations in the EC model accounts for a reverse demographic and range response of insular and coastal temperate biotas relative to continental ones. Furthermore, this cross‐archipelago pattern in which allopatric diversity is formed and shaped by EC cycles resembles that seen between isolated populations within mainland refugia and suggests that the EC model, originally developed to explain population fluctuations into and out‐of refugia, may be appropriate for describing the demographic and evolutionary dynamics driving the high genetic diversity observed in these areas.     

Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum

Aim We examine several hypotheses emerging from biogeographical and fossil records regarding glacial refugia of a southern thermophilic plant species. Specifically, we investigated the glacial history and post‐glacial colonization of a forest understorey species, Trillium cuneatum. We focused on the following questions: (1) Did T. cuneatum survive the Last Glacial Maximum (LGM) in multiple refugia, and (if so) where were they located, and is the modern genetic structure congruent with the fossil record‐based reconstruction of refugia for mesic deciduous forests? (2) What are the post‐glacial colonization patterns in the present geographical range? Location South‐eastern North America. Methods We sampled 45 populations of T. cuneatum throughout its current range. We conducted phylogeographical analyses based on maternally inherited chloroplast DNA (cpDNA haplotypes) and used TCS software to reconstruct intraspecific phylogeny. Results We detected six cpDNA haplotypes, geographically highly structured into non‐overlapping areas. With one exception, none of the populations had mixed haplotype composition. TCS analysis resulted in two intraspecific cpDNA lineages, with one clade subdivided further by shallower diversification. Main conclusions Our investigation revealed that T. cuneatum survived the LGM in multiple refugia, belonging to two (western, eastern) genealogical lineages geographically structured across south‐eastern North America. The western clade is confined to the south‐western corner of T. cuneatum’s modern range along the Lower Mississippi Valley, where fossil records document a major refugium of mesic deciduous forest. For the eastern clade, modern patterns of cpDNA haplotype distribution suggest cryptic vicariance, in the form of forest contractions and subsequent expansions associated with Pleistocene glacial cycles, rather than simple southern survival and subsequent northward colonization. The north–south partitioning of cpDNA haplotypes was unexpected, suggesting that populations of this rather southern thermophilic species may have survived in more northern locations than initially expected based on LGM climate reconstruction, and that the Appalachian Mountains functioned as a barrier to the dispersal of propagules originating in more southern refugia. Furthermore, our results reveal south‐west to north‐east directionality in historical migration through the Valley and Ridge region of north‐west Georgia.     

Pleistocene extinctions and recent expansions in an anguid lizard of the genus Pseudopus

Climatic changes during the Pleistocene played an instrumental role in the shaping recent distribution and diversity of the Western Palearctic biota. Range oscillations often lead to allopatric differentiation followed by the establishment of secondary contact zones. As a result, many species are composed of complex networks of phylogenetic lineages with different histories. Pseudopus apodus is the only surviving member of an ancient genus of Western Palearctic anguid lizards (Anguidae) distributed from the Balkans through Anatolia and Caucasus to central Asia. Here, we used mitochondrial and nuclear DNA sequences to reconstruct the evolutionary history of the species in phylogeographic and demographic frameworks. Our analyses revealed three main phylogenetic lineages that diverged during or shortly before the Pleistocene. Two of them more or less correspond to the known subspecies, and their low genetic variability suggests relatively recent dispersal and colonization of vast parts of the range. The third, southern, lineage is more geographically restricted and diversified than the other two. This pattern shows that the Quaternary climatic oscillations presumably caused repeated large‐scale population extinctions of the species, depleting most of its diversity. Only a few refugia located in Anatolia, Levant, and Transcaucasia served as sources for subsequent recolonization to the areas of the recent distribution. This is in contrast to many other Western Palearctic reptiles that survived unfavorable climatic conditions in numerous local refugia and sanctuaries, which resulted in more complex phylogenetic structure.     

Mitochondrial phylogeography of the moor frog, Rana arvalis

The moor frog Rana arvalis is a lowland species with a broad Eurasiatic distribution, from arctic tundra through forest to the steppe zone. Its present-day range suggests that glacial refugia of this frog were located outside southern European peninsulas. We studied the species-wide phylogeographical pattern using sequence variation in a 682 base pairs fragment of mtDNA cytochrome b gene; 223 individuals from 73 localities were analysed. Two main clades, A and B, differing by c. 3.6% sequence divergence were detected. The A clade is further subdivided into two subclades, AI and AII differing by 1.0%. All three lineages are present in the Carpathian Basin (CB), whereas the rest of the species range, including huge expanses of Eurasian lowlands, are inhabited solely by the AI lineage. We infer that AII and B lineages survived several glacial cycles in the CB but did not expand, at least in the present interglacial, to the north. The geographical distribution and genealogical relationships between haplotypes from the AI lineage indicate that this group had two glacial refugia, one located in the eastern part of the CB and the other probably in southern Russia. Populations from both refugia contributed to the colonization of the western part of the range, whereas the eastern part was colonized from the eastern refugium only. The effective population size as evidenced by theta(ML) is an order of magnitude higher in the AI lineage than in the AII and B lineages. Demographic expansion was detected in all three lineages.     

Second Sahelian amphibian endemism suggested by phylogeography of Groove crowned Bullfrog (Hoplobatrachus occipitalis) in western Sahel and hints of polyploid species formation

Several studies have assessed the phylogeographic patterns of vertebrates in North Africa and Sahara–Sahel, but most of the phylogeographic knowledge on amphibians comes from the Mediterranean region while the southern Sahara and Sahel remain poorly studied. Here, we assess the phylogeography of the African Groove crowned frog Hoplobatrachus occipitalis, with a focus on western Sahel in order to better understand the biogeographic patterns of semi-aquatic species in this arid region. Using mitochondrial and nuclear markers, we have assessed the species’ genetic structure, distribution of genetic diversity, and the presence of cryptic diversity. We found evidence of a recent (re-)colonization of the mountains in its northernmost distribution, but also for the role of southern Mauritanian mountains and large rivers as refugia. Two major lineages were detected, one perhaps endemic to Mauritania and the other widespread in Africa. The first lineage possibly constitutes the second Sahelian amphibian endemic; the latter may have originated through an allopolyploidy event, with the Mauritanian lineage being one of the parental ones.     

Phylogeographic insights of the lowland species Cheirolophus sempervirens in the southwestern Iberian Peninsula

The southwestern Iberian Peninsula is an important biogeographic region, showing high biodiversity levels and hosting several putative glacial refugia for European flora. Here, we study the genetic diversity and structure of the Mediterranean, thermophilous plant Cheirolophus sempervirens (Asteraceae) across its whole distribution range in SW Iberia, as a tool to disentangle some of the general biogeographic patterns shaping this southern refugia hotspot. Null genetic diversity was observed in the cpDNA sequencing screening. Nonetheless, AFLP data revealed high levels of among-population genetic differentiation correlated to their geographic location. Our results suggest longer species persistence in southern Iberian refugia during glacial periods and subsequent founder effects northwards due to colonizations in warmer stages (i.e., the southern richness to northern purity pattern). Additionally, our phylogeographic analyses indicate the presence of two separate genetic lineages within Ch. sempervirens, supporting the hypothesis of multiple minor refugia for SW Iberia in agreement with the refugia within refugia model.