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

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

Cryptic diversity within the Moroccan endemic day geckos Quedenfeldtia (Squamata: Gekkonidae): a multidisciplinary approach using genetic,morphological and ecological data

Quedenfeldtia (Boettger, 1883) is a genus of diurnal geckos, endemic to the Atlas Mountains in Morocco, with two species being recognized: Quedenfeldtia moerens and Quedenfeldtia trachyblepharus. Quedenfeldtia moerens is found across a wide variety of habitats, from sea level to 3000 m a.s.l., whereas Q. trachyblepharus occupies exclusively high mountain regions reaching up to 4000 m a.s.l. This differentiation, offers an interesting model for study biogeographical patterns and evolutionary scenarios in a North African endemic. Analysis of two mitochondrial (12S rRNA and ND4) and four nuclear (ACM4, MC1R, PDC, and Rag1) DNA markers revealed high genetic variation, consistent with other recent phylogeographical studies, and with the two currently described species. However, within each species, a subdivision into two groups with geographical consistence was found. Multivariate morphological analyses confirmed the existence of two main phenotypes, whereas ecological niche modelling identified various environmental variables associated with the distribution of each species, and helped to predict occurrences outside the confirmed ranges. The results obtained in the present study indicate the possible existence of additional ‘cryptic’ species within this genus, a condition found in many North African reptiles, and particularly common in geckos. In general, North African montane fauna appears to reflect the occurrence of diverse palaeoendemics, as seen in Central Africa Mountain systems, rather than the pattern of recent postglacial recolonization observed in Europe. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Phylogeography of southern Asian Dolly Varden char <Emphasis Type="Italic">Salvelinus malma krascheninnikovi</Emphasis>: Genealogical analysis of mitochondrial DNA

Phylogeography of southern Asian Dolly Varden char was studied using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D loop) obtained using PCR-RFLP analysis. Analysis of contemporary population genetic structure showed that Salvelinus malma krascheninnikovi throughout the whole species range was characterized by high population differentiation in combination with rather small differences between the populations from remote regions. The genealogy of mtDNA haplotypes was reconstructed and nested clade analysis of geographical distances was performed. Geographical distribution of mtDNA haplotypes of S. m. krascheninnikovi was explained by population genetic processes (restricted gene flow), as well as by historical demographic events (range expansion and fragmentation). It was demonstrated that the main demographic events were associated with cyclic processes of the geological formation of the Sea of Japan and adjacent territories. Furthermore, genealogical tree of S. m. krascheninnikovi contained the traces of secondary contact between isolated phylogeographical lineages.     

Phylogeographical patterns in Coenosia attenuata (Diptera: Muscidae): a widespread predator of insect species associated with greenhouse crops

The tiger‐fly Coenosia attenuata is a globally widespread predatory fly which is not only associated with greenhouse crops, but also occurs in open fields. It is a potential control agent against some of the more common pests in these crops. Assessing the genetic structure and gene flow patterns may be important for planning crop protection strategies and for understanding the historical processes that led to the present distribution of genetic lineages within this species. In the present study, the phylogeographical patterns of this species, based on mitochondrial cytochrome oxidase I and nuclear white and elongation factor‐1α genes, are described, revealing relatively low genetic diversity and weak genetic structure associated with a recent and sudden population expansion of the species. The geographical distribution of mitochondrial haplotypes indicates the Mediterranean as the most likely region of origin of the species. Some dispersal patterns of the species are also revaled, including at least three independent colonizations of North and South America: one from Middle East to North America with a strong bottleneck event, another from Europe to South America (Chile), with both likely to be a result of unintentional introduction, and a third one of still undetermined origin to South America (Ecuador). © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 308–326.     

Testing the ‘Pleistocene species pump’ in alpine habitats: lineage diversification of flightless ground beetles (Coleoptera: Carabidae: Nebria) in relation to altitudinal zonation

Alpine species often have similar demographic responses to Pleistocene climate changes, but exhibit different spatial patterns of genetic diversity. Using a comparative phylogeographical approach, we examined the factors influencing lineage formation in three alpine carabid beetles of the genus Nebria Latreille inhabiting the California Sierra Nevada. These flightless beetles differ in altitudinal zonation and habitat preferences, but overlap spatially, have limited dispersal capacities and share life history characteristics. Species distribution modelling predicted decreasing population connectivity in relation to increasing altitudinal preferences. Diversity patterns at the cytochrome oxidase subunit I gene revealed north–south genetic structure and recent population growth in all three species. The high‐elevation‐restricted species, Nebria ingens Horn, exhibited a deep phylogeographical split, morphological divergence and evidence of limited, unidirectional gene flow towards the south. This was supported by additional data from three nuclear genes and isolation with migration analysis. Nebria spatulata Van Dyke, inhabiting an intermediate altitudinal range, exhibited fixed morphological differences between northern and southern populations, but showed limited structure. The broadly distributed Nebria ovipennis LeConte showed less structure and lacked morphological variation. Diversification of these Nebria species supports the role of altitudinal zonation in lineage formation and is consistent with the Pleistocene species pump model. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Phylogeography and species limits in the green woodpecker complex (Aves: Picidae): multiple Pleistocene refugia and range expansion across Europe and the Near East

The green woodpecker complex consists of the green woodpecker (Picus viridis), distributed from Western Europe to the Caucasus and Iran, and the related LeVaillant's woodpecker (P. vaillantii), distributed in north‐western Africa from central Morocco to Tunisia. Much of the habitat of green woodpeckers in Central and Northern Europe was covered by ice, tundra, steppe or other unsuitable habitat during the Pleistocene; consequently, they must have come to occupy most of their current range during the past 20 000 years. We used complete mitochondrial ND2 sequences from populations throughout the range to investigate the genetic structure and evolutionary history of this complex. Three well‐differentiated clades, corresponding to three biogeographical regions, were recovered; 89% of the total genetic variance was distributed among these three regions. The populations in North Africa were sister to those of Europe and, within Europe, Iberia was sister to the rest of Europe and the Near East. This suggests that the post‐glacial colonization of most of Europe occurred from a refuge east of Iberia, probably in Italy or the Balkans; there was no substantial divergence among these regions. In addition, a population sample from Iran was genetically distinct from those of Western Europe, indicating a history of genetic isolation and an additional Pleistocene refuge east of the well‐known Balkan refugia and south of the Caucasus. Within Europe, northern populations were less genetically variable than southern ones, consistent with recent colonization. There was significant isolation‐by‐distance across Europe, indicating restricted gene flow; this was particularly apparent between western populations and those of the Caucasus and Iran. We recognize four species in the complex. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 710–723.     

Limited phylogeographical structure across Eurasia in two red wood ant species Formica pratensis and F. lugubris (Hymenoptera, Formicidae)

The phylogeography and demographic history of two closely related species of the red wood ant (Formica pratensis and F. lugubris) were examined across Eurasia. The phylogeny based on a 1.5-kilobase mitochondrial DNA fragment, including the cytochrome b gene and part of the ND6 gene, showed one phylogeographical division in F. pratensis. This division (0.7% of nucleotide divergence) suggests postglacial colonization of western Europe and of a wide area ranging from Sweden on the west to Lake Baikal on the east from separate forest refugia. In two localities, mitochondrial DNA has been transferred from F. lugubris to F. pratensis and all the individuals of F. pratensis sampled from the Pyrenees had haplotypes clustering in the lugubris clade. No phylogeographical divisions were detected in F. lugubris. Comparison of species-wide phylogeography between the two sympatrically distributed species of ant demonstrates a difference in phylogeographical structure that implies different vicariant histories. However, over most of the species' distribution ranges, similar signs of demographic expansion predating the last glaciation and the lack of phylogeographical structure were found in both the eastern phylogroup of F. pratensis and F. lugubris. This finding is highly consistent with the results reported for all other boreal forest animal species studied to date in Eurasia. Contraction of the distribution range of each species to a single refugial area at different times during the late Pleistocene and a subsequent population expansion seem to be an explanation for the lack of phylogeographical structure across most of Eurasia in species that are ecologically associated with the boreal forest.     

Phylogeography of the marine isopod Stenosoma nadejda (Rezig, 1989) in North African Atlantic and western Mediterranean coasts reveals complex differentiation patterns and a new species

The transition zone between the Mediterranean and Atlantic basins has been extensively addressed in phylogeographical studies of marine species. However, biases exist towards the analysis of highly dispersive species, and there is a higher sampling effort in European coasts compared to North Africa. This may be hindering a detailed understanding of the historical and contemporary processes that shaped patterns of population genetic structure in the region. In the present study, we investigated the phylogeographical and phylogenetic patterns of mitochondrial cytochrome c oxidase subunit I sequences from a species with direct development and low dispersal abilities, Stenosoma nadejda (Rezig, 1989). The study area included 13 localities along the Atlantic and Mediterranean North African coasts, as well as the Alboran Sea. A new Stenosoma species, from the coasts of Algeria and Alboran Island, was discovered. For S. nadejda, phylogeographical analyses revealed three distinct clades: one in the Iberian Atlantic plus the Alboran Sea, one in the western Mediterranean, and another in the Atlantic coast of Africa. Haplotypes from the Alboran Island were more related to those from the western Mediterranean coast (east of the Almeria–Oran Front). Given the strong differentiation, it is probable that this species survived in multiple glacial refugia during the Pleistocenic glaciations. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 419–431.     

Small‐scale genetic structuring in a tropical cave snail and admixture with its above‐ground sister species†

We analyse the phylogeographical structure in the cave snail Georissa filiasaulae Haase & Schilthuizen, 2007 (Gastropoda: Hydrocenidae) and its above‐ground sister species G. saulae (van Benthem‐Jutting, 1966) at limestone outcrops in Sabah, Malaysian Borneo. Morphometric and 16S mitochondrial DNA data for some 220 individuals reveal strong morphological differentiation, despite ongoing unidirectional gene flow from the epigean into the hypogean environment, strong, small‐scale genetic structuring within the cave and underground dispersal between caves that were previously thought to be isolated. We discuss these results – which constitute the first phylogeographical analysis of a terrestrial cave snail – in the light of speciation in cave organisms and across ecotones in general. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 727–740.     

Mitochondrial phylogeography and population history of finless porpoises in Sino‐Japanese waters

Phylogeographical patterns of intraspecific variation can provide insights into the population‐level processes responsible for speciation and yield information useful for conservation purposes. In the present study, three hundred and forty‐five base pairs of the mitochondrial DNA control region were sequenced to analyse the genetic diversity, population structure and history, and phylogeography of finless porpoises (Neophocaena phocaenoides) in Chinese and Japanese waters of the North Pacific. Nucleotide and haplotype diversities were 0.44% and 0.79 ± 0.01 for Chinese and Japanese waters, respectively, but varied significantly among populations. Analysis of molecular variance showed a high level of genetic structure between populations (Φ_ST = 0.61, P < 0.001; F_ST = 0.52, P < 0.001). Eleven of 18 haplotypes were restricted to a single population, common haplotypes were found in two to four populations, but no haplotype was found throughout Sino‐Japanese waters, suggesting multiple colonization events followed by limited gene flow. The inferred age of demographic expansion was from the end stage of the last ice age to the Holocene. No obvious phylogeographical pattern was revealed, including between saline and fresh water populations. A low level of genetic diversity for each population and high among‐population differentiation in haplotype frequency were revealed, which suggest a role for random genetic drift, recent demographic bottlenecks, and reduced or limited gene flow in these populations. Some conservation considerations, with special reference to the unique Yangtze population, are discussed. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 193–204.     

Mitochondrial DNA haplogrouping of the brown bear,Ursus arctos (Carnivora: Ursidae) in Asia,based on a newly developed APLP analysis

Sequence analyses of the complete brown bear, Ursus arctos, mitochondrial DNA (mtDNA) genome have detected scattered single nucleotide polymorphisms (SNPs) that define distinct mtDNA haplogroups in phylogeographical studies. The degraded DNA in historical samples, such as stuffed or excavated specimens, however, is often not suitable for sequence analyses. To address this problem, we developed an amplified product length polymorphism (APLP) analysis for mtDNA‐haplogrouping U. arctos specimens by detecting haplogroup‐specific SNPs. We verified the validity and utility of this method by analysing up to 170‐year‐old skin samples from U. arctos specimens collected widely across continental Eurasia. We detected some of the same haplogroups as those occurring in eastern Hokkaido (Japan) and eastern Alaska in continental Eurasia (the Altai and the Caucasus). Our results show that U. arctos in eastern Hokkaido and eastern Alaska descended from a common ancestor in continental Eurasia, and suggest that U. arctos occupied several refugia in southern Asia during the Last Glacial Maximum. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 627–635.     

Bergmanns's size cline in New Zealand marine spray zone spiders (Araneae: Anyphaenidae: Amaurobioides)

Members of the spider genus Amaurobioides are restricted to the spray zone of rocky marine coasts, where they construct and hunt from silk retreats. Collecting for this study shows these spiders to be distributed around the entire New Zealand coast. A Templeton, Crandall, and Sing (TCS) analysis of the ND1 mitochondrial gene places specimens from the North Island and the northern half of the South Island into a group distinct from Amaurobioides maritima O.P.‐Cambridge, 1883, which is restricted to the southern half of the South Island. Females of this northern group exhibit latitude‐ and temperature‐related clines in body length, body mass, and residual index of condition, with larger individuals with greater indices of condition being found at cooler, southern sites. This size cline also appeared in a broader geographical analysis that included Amaurobioides piscator Hogg, 1909 from the sub‐Antarctic Auckland and Campbell Islands. Thirteen ND1 haplotypes are represented in the northern group. Both independent contrast analyses and standard regressions of the mean body lengths and mean masses of these haplotypes, and the mean latitudes and temperatures of the sites where haplotypes were present, document a Bergmann's size cline, and provide evidence for an underlying genetic component. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 78–92.     

Inferring the evolutionary history of divergence despite gene flow in a lizard species,Scincella lateralis (Scincidae), composed of cryptic lineages

Although recent radiations are fruitful for studying the process of speciation, they are difficult to characterize and require the use of multiple loci and analytical methods that account for processes such as gene flow and genetic drift. Using multilocus sequence data, we combine hierarchical cluster analysis, coalescent species tree inference, and isolation‐with‐migration analysis to investigate evolutionary relationships among cryptic lineages of North American ground skinks. We also estimate the extent that gene flow has accompanied or followed diversification, and also attempt to account for and minimize the influence of gene flow when reconstructing relationships. The data best support seven largely parapatric populations that are broadly concordant with mitochondrial (mt)DNA phylogeography throughout most of the species range, although they fail to fully represent extensive mtDNA divergence along the Gulf Coast. Relationships within and among three broad geographical groups are well supported, despite evidence of gene flow among them. Rejection of an allopatric divergence model partially depends on the inclusion of samples from near parapatric boundaries in the analyses, suggesting that allopatric divergence followed by recent migration may best explain migration rate estimates. Accounting for geographical variation in patterns of gene flow can improve estimates of migration–divergence parameters and minimize the influence of contemporary gene flow on phylogenetic inference. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Phylogeographic structure of brown trout Salmo trutta in Britain and Ireland: glacial refugia,postglacial colonization and origins of sympatric populations

The phylogeographical structure of brown trout Salmo trutta in Britain and Ireland was studied using polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis of four mitochondrial DNA segments (16S/ND1, ND5/6, COXIII/ND5 and ND5/12S). Analysis of 3636 individuals from 83 sites–morphotypes revealed a total of 25 haplotypes. These haplotypes were nested in seven two‐step clades. Although there was a clear geographical patterning to the occurrence of derived clades, admixture among ancestral clades was extensive throughout the studied area. A relevant feature of the data was that some populations contained mixtures of highly divergent clades. This type II phylogeographic pattern is uncommon in nature. Clade intermixing is likely to have taken place during earlier interglacials as well as since the Last Glacial Maximum. The anadromous life history of many S. trutta populations has probably also contributed to clade mixing. Based on the data presented here and published data, postglacial colonization of Britain and Ireland most likely involved S. trutta from at least five potential glacial refuges. Probable locations for such refugia were: south of England–western France, east of the Baltic Sea, western Ireland, Celtic Sea and North Sea. Ferox S. trutta, as defined by their longevity, late maturation and piscivory, exhibited a strong association with a particular clade indicating that they share a common ancestor. Current evidence indicates that the Lough Melvin gillaroo S. trutta and sonaghen S. trutta sympatric types diverged prior to colonization of Lough Melvin and, although limited gene flow has occurred since secondary contact, they have remained largely reproductively isolated due to inlet and outlet river spawning segregation. Gillaroo S. trutta may reflect descendents of a previously more widespread lineage that has declined due to habitat alterations particularly affecting outlet rivers. The mosaic‐like distribution of mtDNA lineages means that conservation prioritization in Britain and Ireland should be based on the biological characteristics of local populations rather than solely on evolutionary lineages.     

Mitochondrial DNA reveals multiple Northern Hemisphere introductions of Caprella mutica (Crustacea, Amphipoda)

Caprella mutica (Crustacea, Amphipoda) has been widely introduced to non-native regions in the last 40 years. Its native habitat is sub-boreal northeast Asia, but in the Northern Hemisphere, it is now found on both coasts of North America, and North Atlantic coastlines of Europe. Direct sequencing of mitochondrial DNA (cytochrome c oxidase subunit I gene) was used to compare genetic variation in native and non-native populations of C. mutica . These data were used to investigate the invasion history of C. mutica and to test potential source populations in Japan. High diversity (31 haplotypes from 49 individuals), but no phylogeographical structure, was identified in four populations in the putative native range. In contrast, non-native populations showed reduced genetic diversity (7 haplotypes from 249 individuals) and informative phylogeographical structure. Grouping of C. mutica populations into native, east Pacific, and Atlantic groups explained the most among-region variation (59%). This indicates independent introduction pathways for C. mutica to the Pacific and Atlantic coasts of North America. Two dominant haplotypes were identified in eastern and western Atlantic coastal populations, indicating several dispersal routes within the Atlantic. The analysis indicated that several introductions from multiple sources were likely to be responsible for the observed global distribution of C. mutica , but the pathways were least well defined among the Atlantic populations. The four sampled populations of C. mutica in Japan could not be identified as the direct source of the non-native populations examined in this study. The high diversity within the Japan populations indicates that the native range needs to be assessed at a far greater scale, both within and among populations, to accurately assess the source of the global spread of C. mutica .     

Pattern of population genetic structure revealed by nuclear simple sequence repeat markers in the understory perennial Veratrum album ssp. oxysepalum (Melanthiaceae) with a disjunct pattern of chloroplast DNA haplotypes

Compared to tree species, there still remains a very limited number of phylogeographical studies on temperate forest perennials. In the present study, we used nuclear microsatellite markers to detect extant patterns of population genetic structure of the perennial plant Veratrum album ssp. oxysepalum in the understory of temperate forests, aiming to provide insights into the post‐glacial history of the species and the reasons for the disjunct distribution of chloroplast DNA (cpDNA) haplotypes found in a previous study. We examined eight polymorphic nuclear microsatellite loci to examine genetic variation within and among 32 populations of V. album ssp. oxysepalum and seven populations of Veratrum stamineum. The population of V. album ssp. oxysepalum was split into two groups: those in the northern part of the Japanese Archipelago and all others. In addition, each population group was split into two subgroups. Only one population of V. stamineum included a substantial number of individuals categorized as V. album ssp. oxysepalum. The population genetic structure revealed by nuclear microsatellites suggests that V. album ssp. oxysepalum migrated from Eurasia into the Japanese Archipelago at least twice before the last glacial era through two different land bridges: the Korean Peninsula and Sakhalin. In addition, there appeared to be at least two refugia of V. album ssp. oxysepalum in each of the areas, dominated by the two different lineages from Eurasia during the last glacial era. The disjunct geographical pattern found in cpDNA variation in a previous study was blurred in the genetic structure as revealed by microsatellite markers, probably as a result of extensive gene flow via pollen. Currently, one‐directional introgressive hybridization occurs from V. album ssp. oxysepalum to V. stamineum at only one locality; there is no evidence of the opposite pattern. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 108 , 278–293.     

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

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

Global phylogeography in Sanionia uncinata (Amblystegiaceae: Bryophyta)

Global phylogeographic patterns in Sanionia uncinata are addressed based on information in internal transcribed spacer (ITS) (214 specimens) and the plastid markers trnL‐trnF (221) and rpl16 (217). ITS suggests a monophyletic Sanionia and a paraphyletic S. uncinata; this was neither supported nor rejected by plastid data. Northern or Eastern Eurasia and Alaska appear important in the early evolution of Sanionia and some populations dispersed into the Southern Hemisphere relatively early. Some haplotypes or groups of haplotypes are morphologically and ecologically distinct, biologically meaningful units that correspond with S. orthothecioides, S. symmetrica and S. georgicouncinata s.l. The latter includes two species that are indistinguishable by morphology, S. georgicouncinata s.s. (Southern Hemisphere) and S. nivalis (Northern Hemisphere). Tropical African and South American S. uncinata populations have separate origins and the Southern Hemisphere was colonized at least twice. In the northern circum‐Arctic region, the haplotype composition differs between the North Atlantic and Beringian areas. Eastern Eurasia has a higher S. uncinata haplotype diversity than other Holarctic regions, implying less devastating effects of recurrent glacial periods. For Eastern and Western Eurasia, North America and the Southern Hemisphere, most of the haplotype variation was found within the regions, but 14–18% can be referred to among region variation. Plastid haplotype diversity was lower in the Southern Hemisphere than in the Arctic to subarctic, possibly attributable to founder effects. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 19–42.     

Genetic divergences pre-date Pleistocene glacial cycles in the New Zealand speckled skink, Oligosoma infrapunctatum

Aim To examine the hypothesis raised by Graham S. Hardy that Pleistocene glacial cycles suffice to explain divergence among lineages within the endemic New Zealand speckled skink, Oligosoma infrapunctatum Boulenger. Location Populations were sampled from across the entire range of the species, on the North and South Islands of New Zealand. Methods We sequenced the mitochondrial genes ND2 (550 bp), ND4 + tRNAs (773 bp) and cytochrome b (610 bp) of 45 individuals from 21 locations. Maximum likelihood, maximum parsimony and Bayesian methods were used for phylogenetic reconstruction. The Shimodaira–Hasegawa test was used to examine hypotheses about the taxonomic status of morphologically distinctive populations. Results Our analysis revealed four strongly supported clades within O. infrapunctatum. Clades were largely allopatric, except on the west coast of the South Island, where representatives from all four clades were found. Divergences among lineages within the species were extremely deep, reaching over 5%. Two contrasting phylogeographical patterns are evident within O. infrapunctatum. Main conclusions The deep genetic divisions we found suggest that O. infrapunctatum is a complex of cryptic species which diverged in the Pliocene, contrary to the existing Pleistocene‐based hypothesis. Although Pleistocene glacial cycles do not underlie major divergences within this species, they may be responsible for the shallower phylogeographical patterns that are found within O. infrapunctatum, which include a radiation of haplotypes in the Nelson and Westland regions.     

Phylogeographical structure of the boreal‐montane orchid Malaxis monophyllos as a result of multi‐directional gene flow

We investigated the phylogeographical structure of the boreal‐montane orchid Malaxis monophyllos in its Eurasian geographical range. We analysed four sequences of plastid DNA (trnL, trnL–trnF, rps16 and accD‐psaI), resulting in 19 haplotypes and revealing a high level of intraspecific diversity (H_D = 0.702 and π = 0.196 × 10⁻²), but showing a lack of phylogeographical structure. This pattern might be caused by multiple phenomena and processes, e.g. broad‐fronted recolonization with accompanying multi‐directional gene flow between populations and expansion from at least two refugial areas. Despite the lack of phylogeographical structure, three centres of haplotype diversity were indicated in the European part of the range of M. monophyllos. According to these data, alpine and lowland glacial refugia located between the ice sheets in the European Alps and the Scandinavian glaciers seem most likely to be in Europe. Moreover, models of climatically suitable areas during the Last Glacial Maximum (LGM) confirmed the Alps as a possible refuge, and indicated an opportunity for the persistence of M. monophyllos populations in Beringia and parts of Siberia. Using two models [Model for Interdisciplinary Research on Climate (MIROC) and Community Climate System Model (CCSM)], we predicted a significant reduction in climatically suitable areas for M. monophyllos in the future (2080). Our study also demonstrated that the biological features of M. monophyllos, including breeding system and dispersal mode, seem to be crucial in understanding its phylogeographical pattern. Our results also highlighted the importance of anthropogenic habitats as reservoirs of genetic diversity and alternative habitats for this species in the context of declining natural populations. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 138–154.