Impact of mountain chains, sea straits and peripheral populations on genetic and taxonomic structure of a freshwater turtle, Mauremys leprosa (Reptilia, Testudines, Geoemydidae)

Mauremys leprosa, distributed in Iberia and North‐west Africa, contains two major clades of mtDNA haplotypes. Clade A occurs in Portugal, Spain and Morocco north of the Atlas Mountains. Clade B occurs south of the Atlas Mountains in Morocco and north of the Atlas Mountains in eastern Algeria and Tunisia. However, we recorded a single individual containing a clade B haplotype in Morocco from north of the Atlas Mountains. This could indicate gene flow between both clades. The phylogenetically most distinct clade A haplotypes are confined to Morocco, suggesting both clades originated in North Africa. Extensive diversity within clade A in south‐western Iberia argues for a glacial refuge located there. Other regions of the Iberian Peninsula, displaying distinctly lower haplotype diversities, were recolonized from within south‐western Iberia. Most populations in Portugal, Spain and northern Morocco contain the most common clade A haplotype, indicating dispersal from the south‐western Iberian refuge, gene flow across the Strait of Gibraltar, and reinvasion of Morocco by terrapins originating in south‐western Iberia. This hypothesis is consistent with demographic analyses, suggesting rapid clade A population increase while clade B is represented by stationary, fragmented populations. We recommend the eight, morphologically weakly diagnosable, subspecies of M. leprosa be reduced to two, reflecting major mtDNA clades: Mauremys l. leprosa (Iberian Peninsula and northern Morocco) and M. l. saharica (southern Morocco, eastern Algeria and Tunisia). Peripheral populations could play an important role in evolution of M. leprosa because we found endemic haplotypes in populations along the northern and southern range borders. Previous investigations in another western Palearctic freshwater turtle (Emys orbicularis) discovered similar differentiation of peripheral populations, and phylogeographies of Emys orbicularis and Mauremys rivulata underline the barrier status of mountain chains, in contrast to sea straits, suggesting common patterns for western Palearctic freshwater turtles.     

Biogeography and contemporary climatic differentiation among Moroccan Salamandra algira

The opening of the Gibraltar land bridge occurred at the end of the Messinian Salinity Crisis approximately 5.3 Mya, and was one of the main causes of vicariance between European and north‐west African amphibians, resulting in the origin of several new species. However, little is currently known about the causes for post‐Messinian amphibian differentiation in the Maghreb, although it is acknowledged that the Pleistocene glaciations probably had considerable influence on several species. The current study uses both species distribution modelling (MAXENT) and information from a total of 694 bp of mitochondrial data (351 from cytochrome b and 342 from 12S rRNA) from 36 representatives of all three recognized subspecies of Moroccan Salamandra to infer the phylogeny and biogeography of Salamandra algira tingitana, which is characterized by both viviparous and ovoviviparous populations. According to the results, the split between S. a. tingitana and S. a. algira from the Rif and Middle Atlas mountains took place approximately 1.6 Mya, and could have been caused by a shift towards a colder and drier climate that occurred during the upper Pliocene, which may have resulted in the isolation of Salamandra at increasingly higher altitudes, or in other climatically favourable areas. Several lineages within S. a. tingitana originated during the Pleistocene climatic oscillations, one of which gave rise to the viviparous populations north of the Oued Martil. It is suggested that the origin of viviparity in S. a. tingitana occurred during the last 600 000 years. In order to further understand the origin of the unique viviparous population of S. algira from North Africa, predictive distribution models of the viviparous and ovoviviparous populations of S. a. tingitana were created using MAXENT to assess environmental differences. Niche divergence was subsequently determined using Schoener's D and Warren et al.'s I niche similarity metrics. Predictive modelling and niche divergence analyses revealed significant environmental differences between the two reproductive types, which could have influenced the transition from ovoviviparity to viviparity. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 626–641.     

The evolutionary history of Afrocanarian blue tits inferred from genomewide SNPs

A common challenge in phylogenetic reconstruction is to find enough suitable genomic markers to reliably trace splitting events with short internodes. Here, we present phylogenetic analyses based on genomewide single‐nucleotide polymorphisms (SNPs) of an enigmatic avian radiation, the subspecies complex of Afrocanarian blue tits (Cyanistes teneriffae). The two sister species, the Eurasian blue tit (Cyanistes caeruleus) and the azure tit (Cyanistes cyanus), constituted the out‐group. We generated a large data set of SNPs for analysis of population structure and phylogeny. We also adapted our protocol to utilize degraded DNA from old museum skins from Libya. We found strong population structuring that largely confirmed subspecies monophyly and constructed a coalescent‐based phylogeny with full support at all major nodes. The results are consistent with a recent hypothesis that La Palma and Libya are relic populations of an ancient Afrocanarian blue tit, although a small data set for Libya could not resolve its position relative to La Palma. The birds on the eastern islands of Fuerteventura and Lanzarote are similar to those in Morocco. Together they constitute the sister group to the clade containing the other Canary Islands (except La Palma), in which El Hierro is sister to the three central islands. Hence, extant Canary Islands populations seem to originate from multiple independent colonization events. We also found population divergences in a key reproductive trait, viz. sperm length, which may constitute reproductive barriers between certain populations. We recommend a taxonomic revision of this polytypic species, where several subspecies should qualify for species rank.     

Genetic diversity and phylogeography of Siberian roe deer,Caproulus pygargus,in central and peripheral populations

Current understanding of phylogeographical structure and genetic diversity of Siberian roe deer remains limited mainly due to small sample size and/or low geographical coverage in previous studies. Published data suggest at least two phylogroups: western (Ural Mountains and Western Siberia) and eastern (east from lake Baikal, including the Korean peninsula), but their phylogenetic relationship remains unclear. Combined sequences of cytochrome b (1140 bp) and the mtDNA control region (963 bp) were analyzed from 219 Siberian roe deer from 12 locations in Russia, Mongolia, and South Korea, which cover a large part of its range, to assess genetic diversity and phylogeographical status. Special emphasis was placed on the demographic history and genetic features of central, peripheral, and isolated populations. Results of median‐joining network and phylogenetic tree analyses indicate that Siberian roe deer from the Urals to the Pacific Ocean are genetically diverse and that geographical distribution and composition of haplogroups coincide with previously described ranges of the subspecies Capreolus pygargus pygargus and Capreolus pygargus tianschanicus. We found that peripheral populations in the northwestern parts of the species range (Urals), as well as the isolated population from Jeju Island, are genetically distinct from those in the core part of the range, both in terms of genetic diversity and quantitative composition of haplogroups. We also found that northwestern (Urals) and northern (Yakutia) peripheral populations share the same haplogroup and fall into the same phylogenetic clade with the isolated population from Jeju Island. This finding sheds light on the taxonomic status of the Jeju Island population and leads to hypotheses about the discordance of morphological and genetic evolution in isolated populations and specific genetic features of peripheral populations.     

Phylogeography of the pademelons (Marsupialia: Macropodidae: Thylogale) in New Guinea reflects both geological and climatic events during the Plio‐Pleistocene

Aim Alternative hypotheses concerning genetic structuring of the widespread endemic New Guinean forest pademelons (Thylogale) based on current taxonomy and zoogeography (northern, southern and montane species groupings) and preliminary genetic findings (western and eastern regional groupings) are investigated using mitochondrial sequence data. We examine the relationship between the observed phylogeographical structure and known or inferred geological and historical environmental change during the late Tertiary and Quaternary. Location New Guinea and associated islands. Methods We used primarily museum specimen collections to sample representatives from Thylogale populations across New Guinea and three associated islands. Mitochondrial cytochrome b and control region sequence data were used to construct phylogenies and estimate the timing of population divergence. Results Phylogenetic analyses indicated subdivision of pademelons into ‘eastern’ and ‘western’ regional clades. This was largely due to the genetic distinctiveness of north‐eastern and eastern peninsula populations, as the ‘western’ clade included samples from the northern, southern and central regions of New Guinea. Two tested island groups were closely related to populations north of the Central Cordillera; low genetic differentiation of pademelon populations between north‐eastern New Guinea and islands of the Bismarck Archipelago is consistent with late Pleistocene human‐mediated translocations, while the Aru Islands population showed divergence consistent with cessation of gene flow in the mid Pleistocene. There was relatively limited genetic divergence between currently geographically isolated populations in subalpine and nearby mid‐montane or lowland regions. Main conclusions Phylogeographical structuring does not conform to zoogeographical expectations of a north/south division across the cordillera, nor to current species designations, for this generalist forest species complex. Instead, the observed genetic structuring of Thylogale populations has probably been influenced by geological changes and Pleistocene climatic changes, in particular the recent uplift of the north‐eastern Huon Peninsula and the lowering of tree lines during glacial periods. Low sea levels during glacial maxima also allowed gene flow between the continental Aru Island group and New Guinea. More work is needed, particularly multi‐taxon comparative studies, to further develop and test phylogeographical hypotheses in New Guinea.     

Mitochondrial DNA variation and the phylogeography of the grey partridge (Perdix perdix) in Europe: from Pleistocene history to present day populations

Abstract For a phylogeographical analysis of European grey partridge (Perdix perdix) we sequenced 390 nucleotides of the 5′ end of the mitochondrial control region (CR) of 227 birds from several localities. The birds were divided into two major clades (western and eastern) which differed in control region 1 (CR1) by 14 nucleotide substitutions (3.6%). For estimation of the time of divergence, the whole CR of 14 specimens was sequenced. The major clades differed by 2.2%, corresponding to an estimated coalescence time of c. 1.1 million years. On CR1, 45 haplotypes were found. Western clade haplotypes were found in France, England, Germany, Poland, Italy and Austria. Eastern clade haplotypes were found in Finland, Bulgaria, Greece, and Ireland. One Finnish population and all Bulgarian and Irish populations were mixed, but only in Bulgaria was the mixing assumed to be natural. Nucleotide and haplotype diversities varied between populations, and both clades showed geographical structuring. The distribution of pairwise nucleotide differences in the eastern clade fitted the expectations of an expanding population. About 80% of the genetic structure in the grey partridge could be explained by the clades. The western clade presumably originates on the Iberian Peninsula (with related subtypes in Italy), and the eastern clade either on the Balkan or Caucasian refugia. Large‐scale hand‐rearing and releasing of western partridges have introduced very few mtDNA marks into the native eastern populations in Finland.     

The role of demography and climatic events in shaping the phylogeography of Amazona aestiva (Psittaciformes, Aves) and definition of management units for conservation

Aim The blue‐fronted amazon (Amazona aestiva) is a widely distributed Neotropical parrot with two recognized sub‐species, which are mainly characterized by the colour of the shoulder. We explored mitochondrial DNA variability to determine how demographic processes and historical climatic fluctuations may have contributed to phylogeographical pattern and morphological variation of A. aestiva, and how this information could be useful to understand the evolutionary relationship of this species and the Amazona ochrocephala complex and to determine management units for conservation purposes. Location Brazil and north‐eastern Argentina. Methods We analysed a fragment of COI gene of 78 A. aestiva and 27 A. ochrocephala. We computed a median‐joining network, and the population structure of A. aestiva populations was assessed using a hierarchical analysis of nucleotide diversity. The mismatch distribution, Fu's F_s‐test of neutrality and R² test were used to detect past population expansion. Results All A. aestiva haplotypes and A. ochrocephala subspecies from north‐eastern and southern South America were recovered within the South American clade. Hierarchical analysis of nucleotide diversity of A. aestiva populations detected two geographical groups as obtained by median‐joining network. These two A. aestiva groups showed evidence of a recent population expansion. The time of populations splitting estimated corresponding to the Middle Pleistocene. Main conclusions The two A. aestiva genetic groups identified in our analyses agree with the morphological variation, corresponding to named subspecies. These two A. aestiva groups have undergone a recent population expansion, with low gene flow between them. The expansion of savannah areas may have contributed to the population expansion of these two groups. We concluded that introgression after isolated diversification may better explain haplotype sharing between A. aestiva and A. ochrocephala subspecies. We suggest that management and conservation strategies should consider these two A. aestiva groups (or subspecies) as different management units and should maintain viable populations of these two management units.     

Mitochondrial differentiation and biogeography of Hyla meridionalis (Anura: Hylidae): an unusual phylogeographical pattern

Aim To study the patterns of genetic variation and the historical events and processes that influenced the distribution and intraspecific diversity in Hyla meridionalis Boettger, 1874. Location Hyla meridionalis is restricted to the western part of the Mediterranean region. In northern Africa it is present in Tunisia, Algeria and Morocco. In south‐western Europe it is found in the south of France, north‐western Italy and north‐eastern and south‐western Iberian Peninsula. There are also insular populations, as in the Canaries and Menorca. Methods Sampling included 112 individuals from 36 populations covering the range of the species. We used sequences of mitochondrial DNA Cytochrome Oxidase I (COI) for the phylogeographical analysis (841 bp) and COI plus a fragment including part of tRNA lysine, ATP synthase subunits 6 and 8 and part of Cytochrome Oxidase III for phylogenetic analyses (2441 bp). Phylogenetic analyses were performed with paup *4.0b10 (maximum likelihood, maximum parsimony) and Mr Bayes 3.0 (Bayesian analysis). Nested clade analysis was performed using tcs 1.18 and Geo Dis 2.2. A dispersal‐vicariant analysis was performed with diva 1.0 to generate hypotheses about the geographical distribution of ancestors. Results We found little genetic diversity within samples from Morocco, south‐western Europe and the Canary Islands, with three well‐differentiated clades. One is distributed in south‐western Iberia and the High Atlas, Anti‐Atlas and Massa River in Morocco. The second is restricted to the Medium Atlas Mountains. The third one is present in northern Morocco, north‐eastern Iberia, southern France and the Canaries. These three groups are also represented in the nested clade analysis. Sequences from Tunisian specimens are highly divergent from sequences of all other populations, suggesting that the split between the two lineages is ancient. diva analysis suggests that the ancestral distribution of the different lineages was restricted to Africa, and that an explanation of current distribution of the species requires three different dispersal events. Main conclusions Our results support the idea of a very recent colonization of south‐western Europe and the Canary Islands from Morocco. South‐western Europe has been colonized at least twice: once from northern Morocco probably to the Mediterranean coast of France and once from the western coast of Morocco to southern Iberia. Human transport is a likely explanation for at least one of these events. Within Morocco, the pattern of diversity is consistent with a model of mountain refugia during hyperarid periods within the Pleistocene. Evaluation of the phylogenetic relationships of Tunisian haplotypes will require an approach involving the other related hylid taxa in the area.     

Complex phylogeography in the Southern Smooth Snake (Coronella girondica) supported by mtDNA sequences

Palearctic reptiles with wide distribution through the Western Mediterranean are expected to display genetic substructuring because of the combining effects of current or past geographic barriers and climate fluctuations. We have examined this issue by sequencing cytochrome b and 16S rRNA mitochondrial fragments of 80 individuals of the snake Coronella girondica from 71 localities, covering the range of the species across Tunisia, Algeria, Morocco, Spain, Portugal, southern France and north‐western Italy. According to the obtained genealogy, C. girondica is structured into three divergent and well‐supported clades (north‐western Africa, Betic range and Iberia–France–Italy), which greatly match other phylogeographies already published for this region. Our estimations suggest that the divergence among the three clades took place approximately 1.4‐2.0 Ma, which roughly coincides with the Plio‐Pleistocene transition, characterized by an increase in climate variability. The existence of a clade in a narrow belt of south‐eastern Iberia represents another example of the high endemism rate of the region, with a key geographical situation and an important role in vicariant processes. Since the split among the three major lineages would be take place after the opening of the Strait of Gibraltar, overwater dispersal is here suggested. The subsequent genetic substructuring of these clades during the Pleistocene fits within the refugia‐within‐refugia model, highlighting the importance of the region as a scenario for multiple vicariant events.     

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     

Phylogeography and diversification of an Amazonian understorey hummingbird: paraphyly and evidence for widespread cryptic speciation in the Plio‐Pleistocene

Straight‐billed Hermit Phaethornis bourcieri inhabits the understorey of upland terra firme forest throughout most of the Amazon basin. Currently, two allopatric taxa regarded as subspecies are recognized: P. b. bourcieri and P. b. major. However, the validity, interspecific limits and evolutionary history of these taxa are not yet fully elucidated. We use molecular characters to propose a phylogenetic hypothesis for populations and taxa grouped under Phaethornis bourcieri. Our results showed that P. bourcieri is part of the ‘Ametrornis’ clade, along with Phaethornis philippii and Phaethornis koepckeae, and that the subspecies major is more closely related to the latter two species than to populations grouped under nominate bourcieri. Our phylogenetic hypotheses recovered three main reciprocally monophyletic clades under nominate bourcieri separated by the lower Negro River and the Branco River or the Branco–Negro interfluve (clades B and C) and the upper Amazon (Solimões) or lower Marañon/Ucayali Rivers (clades C and D). Based on multi‐locus phylogeographic and population genetics approaches, we show that P. b. major is best treated as a separate species, and that P. b. bourcieri probably includes more than one evolutionary species, whose limits remain uncertain. The diversification of the ‘Ametrornis’ clade (P. bourcieri, P. philippii and P. koepckeae) is centred in the Amazon and appears to be closely linked to the formation of the modern Amazon drainage during the Plio‐Pleistocene.     

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

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

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

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

Biogeographic barriers in south‐eastern Australia drive phylogeographic divergence in the garden skink,Lampropholis guichenoti

Aim To investigate the impact of climatic oscillations and recognized biogeographic barriers on the evolutionary history of the garden skink (Lampropholis guichenoti), a common and widespread vertebrate in south‐eastern Australia. Location South‐eastern Australia. Methods Sequence data were obtained from the ND4 mitochondrial gene for 123 individuals from 64 populations across the entire distribution of the garden skink. A range of phylogenetic (maximum likelihood, Bayesian) and phylogeographic analyses (genetic diversity, Tajima’s D, Φ_ST, mismatch distribution) were conducted to examine the evolutionary history and diversification of the garden skink. Results A deep phylogeographic break (c. 14%), estimated to have occurred in the mid–late Miocene, was found between ‘northern’ and ‘southern’ populations across the Hunter Valley in northern New South Wales. Divergences among the geographically structured clades within the ‘northern’ (five clades) and ‘southern’ (seven clades) lineages occurred during the Pliocene, with the location of the major breaks corresponding to the recognized biogeographic barriers in south‐eastern Australia. Main conclusions Climatic fluctuations and the presence of several elevational and habitat barriers in south‐eastern Australia appear to be responsible for the diversification of the garden skink over the last 10 Myr. Further molecular and morphological work will be required to determine whether the two genetic lineages represent distinct species.     

Molecular phylogeography of the fruit bat genus Melonycteris in northern Melanesia

Aim To investigate patterns of genetic divergence between populations of the fruit bat genus Melonycteris Dobson 1877 in relation to the possible effects on dispersal of the geological history of water barriers within and between northern Melanesian archipelagos. Location The genus is found only in the Bismarck Archipelago and Solomon Islands of northern Melanesia. Methods Up to 935 aligned bases of cytochrome b and cytochrome c oxidase subunit I DNA sequences were determined for specimens of most species and subspecies of Melonycteris. Measures of genetic distance, analysis of molecular variation and phylogenetic investigations (using maximum parsimony, maximum likelihood and Bayesian approaches) were conducted to assess the evolutionary relationships amongst populations. Results The deepest divergences within Melonycteris separate the genus into two reciprocally monophyletic clades from first, the Bismarck Archipelago, and secondly, the Solomon Islands. Within the Solomon Islands, five major clades received strong support. Listed in a generally north‐western to south‐eastern direction these were: (1) specimens from Choiseul and Santa Isabel; (2) specimens from New Georgia and Kolombangara; (3) specimens from Malaita; (4) specimens from Guadalcanal; and (5) specimens from Makira. Outgroup rooting suggested that the clade from Makira was the most basal within the Solomon Islands, being shown as the sister group to all other Melonycteris from this archipelago. Main conclusions Patterns of genetic variation within Melonycteris were generally consistent, given current knowledge of northern Melanesian geological history, with the hypothesis that the dispersal of these fruit bats is strongly inhibited by water barriers. Within the Solomon Islands the main genetic clades were each restricted to a single island or to a group of islands that are thought to have belonged to larger landmasses (Greater Gatumbangara and Greater Bukida) formed by land bridges during the Pleistocene. The high genetic distance between specimens from the Bismarck Archipelago and from the Solomon Islands reflects the persistently large geographic distance between these archipelagos. The unexpected phylogenetic position of the Makira specimens suggests either that this island was the first colonized by Melonycteris in the Solomon Islands or that this population is the relict of a clade that was previously more widely distributed.     

Non‐concordant phylogeographical patterns of three widely codistributed endemic Western Balkans lacertid lizards (Reptilia,Lacertidae) shaped by specific habitat requirements and different responses to Pleistocene climatic oscillations

The Balkan Peninsula is a hot spot for European herpetofaunal biodiversity and endemism. The rock climbing lizards Dalmatolacerta oxycephala and Dinarolacerta mosorensis and the ground‐dwelling Dalmatian wall lizard Podarcis melisellensis are endemic to the Western Balkans, and their ranges largely overlap. Here, we present a comparative phylogeographical study of these three species in the area of their codistribution in order to determine the level of concordance in their evolutionary patterns. Phylogenetic analyses were performed based on two mitochondrial genes (cytochrome b and 16S rRNA), and a molecular clock approach was used to date the most important events in their evolutionary histories. We also tested for correlations regarding genetic differentiation among populations and their geographical distances. For all three species, a significant correlation between genetic and geographical distances was found. Within D. oxycephala, two deeply separated clades (‘island’ and ‘mainland clade’), with further subdivision of the ‘mainland clade’ into two subclades (‘south‐eastern’ and ‘north‐western’), were found. High sequence divergences were observed between these groups. From our data, the time of separation of the two main clades of D. oxycephala can be estimated at about 5 mya and at about 0.8 mya for the two subclades of the mainland clade. Within D. mosorensis, coalescence time may be dated at about 1 mya, while D. mosorensis and D. montenegrina separated around 5 mya. The results imply the existence of complex palaeo‐biogeographical and geological factors that probably influenced the observed phylogeographical patterns in these lacertid species, and point to the presence of numerous glacial/interglacial refugia. Furthermore, the observed cryptic genetic diversity within the presently monotypic species D. oxycephala prompts for a revision of its taxonomic and conservation status.     

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.     

Phylogeography of the Common Pheasant Phasianus colchicus

The Common Pheasant Phasianus colchicus is widely distributed in temperate to subtropical regions of the Palaearctic realm. Populations of Common Pheasant have been classified into five subspecies groups based on morphological variations in male plumage. Previous phylogeographical studies have focused on limited sets of subspecies groups in the eastern Palaearctic and knowledge on subspecies in the western Palaearctic region is still poor. In this study, we undertake the first comprehensive analysis of subspecies from all five defined subspecies groups across the entire Palaearctic region. Two mitochondrial (CYTB and CR) and two nuclear (HMG and SPI) loci were used to investigate genetic relationships of these subspecies groups and to infer their dispersal routes. Our results revealed that the subspecies elegans, with its range in northwestern Yunnan, China, was in the basal position among 17 studied subspecies, supporting a previous hypothesis that the Common Pheasant most probably originated in forests in southeastern China. Subspecies in the western Palaearctic region nested within the most subspecies‐rich torquatus group (‘Grey‐rumped Pheasants’), indicating that the torquatus group is not a clade but instead forms a gradation with other subspecies and subspecies groups. Our dating analysis suggested that the initial divergence among populations of Common Pheasant originated around 3.4 Mya with subsequent dispersal into the Western Palaearctic region during the Late Pliocene–Lower Pleistocene approximately 2.5–1.8 Mya. We propose two possible east‐to‐west colonization routes for the Common Pheasant and suggest conservation implications for some regional subspecies. Overall, this study demonstrates the lack of concordance between morphology‐based subspecies delimitation and their genetic relationships. This is likely to be a consequence of initial isolation due to historical vicariance followed by population admixture due to recent range expansion of Common Pheasant in the western Palaearctic region.     

The phylogeography of palm cockatoos, Probosciger aterrimus, in the dynamic Australo-Papuan region

Aims We aimed to investigate the effects of historical land–sea boundary and vegetation dynamics in the Australo‐Papuan region on the genetic structure of palm cockatoo populations. In doing so, we also sought to clarify the intraspecific taxonomic status of palm cockatoos, and to examine the potential conservation implications of our results. Location New Guinea and northern Australia. Methods We examined mtDNA (domain III, control region) genetic structure in 71 palm cockatoos from 17 locations across their Australo‐Papuan range. Results Twenty polymorphic sites over 242‐base pairs defined 12 haplotypes that were arranged in a 95% confidence parsimony network of six one‐step clades. Half of these were linked in one clade that included birds from eastern New Guinea–Australia, and the other half included birds from western New Guinea. Nested clade analyses revealed strong and significant genetic structure between these two clades. The average nucleotide divergence between eastern and western birds is c. 3.3%. Within the western clade there was a non‐random distribution of haplotypes according to sampling location alone, but the locations did not cluster significantly, probably due to low sample sizes. A non‐random distribution of haplotypes emerged within one of the one‐step clades from the east of the range (once rare haplotypes were removed), although the historic mechanism that may have created this pattern is unclear. The underlying low nucleotide divergence (0.39%) among haplotypes within the eastern clade suggests relatively recent common ancestry. Main conclusions Our results suggest genetic isolation of the eastern and western clades sometime during the Pleistocene. The continual reappearance of land bridges associated with Pleistocene glacio‐eustatic cycles within the eastern part of the range provides an explanation for our results. We suggest that the occurrence of two deep marine troughs maintained a narrow mountainous barrier between eastern and western birds throughout much of the Pleistocene at a time when extensive land bridges formed elsewhere in the species’ range, and that this has maintained their genetic distinctiveness. Our results provide little support for the current accepted subspecies; the western clade is roughly congruent with Probosciger aterrimus goliath (with caveats), but the otherwise unstructured small genetic distances cast considerable doubt on the remaining subspecies. The eastern and western lineages are endemic to each area and should therefore be considered for independent conservation status and management.     

Divergent mitochondrial lineages arose within a large,panmictic population of the Savannah sparrow (Passerculus sandwichensis)

Unusual patterns of mtDNA diversity can reveal interesting aspects of a species’ biology. However, making such inferences requires discerning among the many alternative scenarios that could underlie any given mtDNA pattern. Next‐generation sequencing methods provide large, multilocus data sets with increased power to resolve unusual mtDNA patterns. A mtDNA‐based phylogeography of the Savannah sparrow (Passerculus sandwichensis) previously identified two sympatric, but divergent (~2%) clades within the nominate subspecies group and a third clade that consisted of birds sampled from northwest Mexico. We revisited the phylogeography of this species using a population genomic data set to resolve the processes leading to the evolution of sympatric and divergent mtDNA lineages. We identified two genetic clusters in the genomic data set corresponding to (a) the nominate subspecies group and (b) northwestern Mexico birds. Following divergence, the nominate clade maintained a large, stable population, indicating that divergent mitochondrial lineages arose within a panmictic population. Simulations based on parameter estimates from this model further confirmed that this demographic history could produce observed levels of mtDNA diversity. Patterns of divergent, sympatric mtDNA lineages are frequently interpreted as admixture of historically isolated lineages. Our analyses reject this interpretation for Savannah sparrows and underscore the need for genomic data sets to resolve the evolutionary mechanisms behind anomalous, locus‐specific patterns.