Chloroplast evidence for geographic stasis of the Australian bird‐dispersed shrub Tasmannia lanceolata (Winteraceae)

Few chloroplast‐based genetic studies have been undertaken for plants of mesic temperate forests in the southern hemisphere and fossil‐based models have provided evidence of vegetation history only at the broadest scales in this region. This study investigates the chloroplast DNA phylogeography of Tasmannia lanceolata (Winteraceae), a fleshy‐fruited, bird‐dispersed shrub that is widespread in the mountains of southeastern Australia and Tasmania. Thirty haplotypes were identified after sequencing 3206 bp of chloroplast DNA in each of 244 individuals collected across the species’ range. These haplotypes showed unexpectedly strong phylogeographic structuring, including a phylogeographic break within a continuous part of the species’ range, with the distribution of four major clades mostly not overlapping, and geographic structuring of haplotypes within these clades. This strong geographic patterning of chloroplast DNA provided evidence for the survival of T. lanceolata in multiple putative wet forest refugia as well as evidence for additional wet forest species refugia in southeastern Australia. In western Tasmania lower haplotype diversity below the LGM tree line compared to above the LGM tree line suggests that glacial refugia at high altitudes may have been important for T. lanceolata. The level of geographic structuring in T. lanceolata is similar to gravity dispersed southern hemisphere plants such as Nothofagus and Eucalyptus. Behavioural traits of the birds transporting seed may have had a strong bearing on the limited transport of T. lanceolata seed, although factors limiting establishment, possibly including selection, may also have been important.     

Mitochondrial DNA of pre‐last glacial maximum red deer from NW Spain suggests a more complex phylogeographical history for the species

The major climatic oscillations that characterized the Quaternary had a great influence on the evolution and distribution of several species. During cold periods, the distribution of temperate‐adapted species became fragmented with many surviving in southern refugia (Iberian, Italian, and Balkan Peninsulas). Red deer was one of the species that contracted its original range to southern refugia. Currently, two main lineages have been described for the species: western and eastern. We have analyzed fossils pre‐dating the last glacial maximum (LGM) from Liñares cave (NW Spain) that belongs to the peripheral range of the western clade, and fossils from the Danish Holocene belonging to the central part of the same clade. Phylogenetic analyses place our samples in the western clade. However, some specimens from Liñares represent an early split in the tree along with other pre‐LGM western samples from previous studies. Despite low bootstrap values in the Bayesian phylogenies, haplotype networks connect these foreign haplotypes to the eastern clade. We suggest a mixed phylogeographical model to explain this pattern with range expansions from the east during the expansion phase after the cold periods in marine isotope stage 3. We find slight isolation by distance in post‐LGM populations that could be a consequence of the recolonization from southern refugia after the LGM.     

History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

How Quaternary climatic oscillations affected range distributions and intraspecific divergence of alpine plants on the Qinghai‐Tibetan Plateau (QTP) remains largely unknown. Here, we report a survey of chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variation aimed at exploring the phylogeographical history of the QTP alpine endemic Aconitum gymnandrum. We sequenced three cpDNA fragments (rpl20–rps12 intergenic spacer, the trnV intron and psbA‐trnH spacer) and also the nuclear (ITS) region in 245 individuals from 23 populations sampled throughout the species’ range. Two distinct lineages, with eastern and western geographical distributions respectively, were identified from a phylogenetic analysis of ITS sequence variation. Based on a fast substitution rate, these were estimated to have diverged from each other in the early Pleistocene approximately 1.45 Ma. The analysis of cpDNA variation identified nine chlorotypes that clustered into two major clades that were broadly congruent in geographical distribution with the two ITS lineages. The east–west split of cpDNA divergence was supported by an amova which partitioned approximately half of the total variance between these two groups of populations. Analysis of the spatial distribution of chlorotypes showed that each clade was subdivided into two groups of populations such that a total of four population groups existed in the species. It is suggested that these different groups derive from four independent glacial refugia that existed during the Last Glacial Maximum (LGM), and that three of these refugia were located at high altitude on the QTP platform itself at that time. Coalescent simulation of chlorotype genealogies supported both an early Pleistocene origin of the two main cpDNA clades and also the ‘four‐refugia’ hypothesis during the LGM. Two previous phylogeographical studies of QTP alpine plants indicated that such plants retreated to refugia at the eastern/south‐eastern plateau edge during the LGM and/or previous glacial maxima. However, the results for A. gymnandrum suggest that at least some of these cold‐tolerant species may have also survived centrally on the QTP platform throughout the Quaternary.     

Phylogeography of Pulsatilla vernalis (L.) Mill. (Ranunculaceae): chloroplast DNA reveals two evolutionary lineages across central Europe and Scandinavia

Aim The aim of this study was to test hypotheses regarding some of the main phylogeographical patterns proposed for European plants, in particular the locations of glacial refugia, the post‐glacial colonization routes, and genetic affinities between southern (alpine) and northern (boreal) populations. Location The mountains of Europe (Alps, Balkans, Carpathians, Central Massif, Pyrenees, Scandinavian chain, Sudetes), and central European/southern Scandinavian lowlands. Methods As our model system we used Pulsatilla vernalis, a widely distributed European herbaceous plant occurring both in the high‐mountain environments of the Alps and other European ranges and in lowlands north of these ranges up to Scandinavia. Based on a distribution‐wide sampling of 61 populations, we estimated chloroplast DNA (cpDNA) variation along six regions using polymerase chain reaction–restriction fragment‐length polymorphisms (PCR–RFLPs) (trnH–trnK, trnK–trnK, trnC–trnD, psbC–trnS, psaA–trnS, trnL–trnF) and further sequencing of trnL–trnF and trnH–psbA. In addition, 11 samples of other European species of Pulsatilla were sequenced to survey the genus‐scale cpDNA variation. Results Eleven PCR–RFLP polymorphisms were detected in P. vernalis, revealing seven haplotypes. They formed two distinct genetic groups. Three haplotypes representing both groups dominated and were widely distributed across Europe, whereas the others were restricted to localized regions (central Alps, Tatras/Sudetes mountains) or single populations. Sequencing analysis confirmed the reliability of PCR–RFLPs and homology of haplotypes across their distribution. The chloroplast DNA variation across the section Pulsatilla was low, but P. vernalis did not share haplotypes with other species. Main conclusions The genetic distinctiveness of P. vernalis populations from the south‐western Alps with respect to other Alpine populations, as well as the affinities between the former populations and those from the eastern Pyrenees, is demonstrated, thus providing support for the conclusions of previous studies. Glacial refugia in the Dolomites are also suggested. Isolation is inferred for the high‐mountain populations from the Tatras and Sudetes; this is in contrast to the case for the Balkans, which harboured the common haplotype. Specific microsatellite variation indicates the occurrence of periglacial lowland refugia north of the Alps, acting as a source for the post‐glacial colonization of Scandinavia. The presence of different fixed haplotypes in eastern and western Scandinavia, however, suggests independent post‐glacial colonization of these two areas, with possible founder effects.     

Northern glacial refugia for the pygmy shrew Sorex minutus in Europe revealed by phylogeographic analyses and species distribution modelling

The southern European peninsulas (Iberian, Italian and Balkan) are traditionally recognized as glacial refugia from where many species colonized central and northern Europe after the Last Glacial Maximum (LGM). However, evidence that some species had more northerly refugia is accumulating from phylogeographic, palaeontological and palynological studies, and more recently from species distribution modelling (SDM), but further studies are needed to test the idea of northern refugia in Europe. Here, we take a rarely implemented multidisciplinary approach to assess if the pygmy shrew Sorex minutus, a widespread Eurasian mammal species, had northern refugia during the LGM, and if these influenced its postglacial geographic distribution. First, we evaluated the phylogeographic and population expansion patterns using mtDNA sequence data from 123 pygmy shrews. Then, we used SDM to predict present and past (LGM) potential distributions using two different training data sets, two different algorithms (Maxent and GARP) and climate reconstructions for the LGM with two different general circulation models. An LGM distribution in the southern peninsulas was predicted by the SDM approaches, in line with the occurrence of lineages of S. minutus in these areas. The phylogeographic analyses also indicated a widespread and strictly northern‐central European lineage, not derived from southern peninsulas, and with a postglacial population expansion signature. This was consistent with the SDM predictions of suitable LGM conditions for S. minutus occurring across central and eastern Europe, from unglaciated parts of the British Isles to much of the eastern European Plain. Hence, S. minutus likely persisted in parts of central and eastern Europe during the LGM, from where it colonized other northern areas during the late‐glacial and postglacial periods. Our results provide new insights into the glacial and postglacial colonization history of the European mammal fauna, notably supporting glacial refugia further north than traditionally recognized.     

Phylogeographic analysis of North American populations of the parasitic herbaceous plant Monotropa hypopitys L. reveals a complex history of range expansion from multiple late glacial refugia

Aim We carried out a phylogeographic study across the range of the herbaceous plant species Monotropa hypopitys L. in North America to determine whether its current disjunct distribution is due to recolonization from separate eastern and western refugia after the Last Glacial Maximum (LGM). Location North America: Pacific Northwest and north‐eastern USA/south‐eastern Canada. Methods Palaeodistribution modelling was carried out to determine suitable climatic regions for M. hypopitys at the LGM. We analysed between 155 and 176 individuals from 39 locations spanning the species’ entire range in North America. Sequence data were obtained for the chloroplast rps2 gene (n = 168) and for the nuclear ITS region (n = 158). Individuals were also genotyped for eight microsatellite loci (n = 176). Interpolation of diversity values was used to visualize the range‐wide distribution of genetic diversity for each of the three marker classes. Minimum spanning networks were constructed showing the relationships between the rps2 and ITS haplotypes, and the geographical distributions of these haplotypes were plotted. The numbers of genetic clusters based on the microsatellite data were estimated using Bayesian clustering approaches. Results The palaeodistribution modelling indicated suitable climate envelopes for M. hypopitys at the LGM in both the Pacific Northwest and south‐eastern USA. High levels of genetic diversity and endemic haplotypes were found in Oregon, the Alexander Archipelago, Wisconsin, and in the south‐eastern part of the species’ distribution range. Main conclusions Our results suggest a complex recolonization history for M. hypopitys in North America, involving persistence in separate eastern and western refugia. A generally high degree of congruence between the different marker classes analysed indicated the presence of multiple refugia, with at least two refugia in each area. In the west, putative refugia were identified in Oregon and the Alexander Archipelago, whereas eastern refugia may have been located in the southern part of the species’ current distribution, as well as in the ‘Driftless Area’. These findings are in contrast to a previous study on the related species Orthilia secunda, which has a similar disjunct distribution to M. hypopitys, but which appears to have recolonized solely from western refugia.     

Late Neogene history of the laurel tree (Laurus L., Lauraceae) based on phylogeographical analyses of Mediterranean and Macaronesian populations

Aim The post‐glacial range dynamics of many European plant species have been widely investigated, but information rapidly diminishes as one moves further back in time. Here we infer the historical range shifts of Laurus, a paradigmatic tree of the Tethyan flora that has covered southern Eurasia since the Oligo‐Miocene, by means of phylogenetic and phylogeographical analyses. Location Mediterranean Basin, Black Sea and Macaronesian archipelagos (Azores, Madeira, Canary Islands). Methods We analysed plastid DNA (cpDNA) sequence (trnK–matK, trnD–trnT) variation in 57 populations of Laurus and three Lauraceae genera. Phylogenetic methods (maximum parsimony and Bayesian inference) and statistical parsimony networks were used to reconstruct relationships among haplotypes. These results were contrasted with the fossil record and bioclimatic niche‐based model predictions of past distributions to infer the migration routes and location of refugia. Results The phylogenetic tree revealed monophyly for Laurus. Overall sequence variability was low within Laurus, but six different haplotypes were distinguished and a single network retrieved, portraying three lineages primarily related to geography. A strongly divergent eastern lineage occupied Turkey and the Near East, a second clade was located in the Aegean region and, lastly, a western clade grouped all Macaronesian and central and western Mediterranean populations. A close relationship was observed between the Macaronesian populations of L. azorica and the western populations of L. nobilis. Main conclusions The phylogeographical structure of Laurus preserves the imprints of an ancient contraction and break‐up of the range that resulted in the evolution of separate cpDNA lineages in its western‐ and easternmost extremes. Intense range dynamics in the western Mediterranean and multiple glacial refugia contributed to the generation and long‐term conservation of this phylogeographical pattern, as shown by the fit between the haplotype ranges and past suitable areas inferred from bioclimatic models. Finally, our results challenge the taxonomic separation of Laurus into two distinct species.     

Rhytidium rugosum (Bryophyta) colonized Scandinavia from at least two glacial refugial source populations

The Scandinavian post‐glacial history of the moss Rhytidium rugosum is traced on the basis of information from the nuclear markers ITS and gpd for 229 Scandinavian and 81 other specimens. Some haplotypes, groups or lineages identified in a NeighborNet split network are predominantly northern Scandinavian, whereas others are southern. With the distributions of individual haplotypes and the timing of the deglaciation in different parts of Scandinavia, this implies colonization from the south and from the north or north‐east. High haplotype and nucleotide diversity and the occurrence of certain private haplotypes in the north suggest that the species may have survived the Last Glacial Maximum in local refugia. Slightly higher numbers of private haplotypes in Scandinavia than in central or north‐eastern Europe also favour an explanation with at least some local glacial survival. Low diversity in the southernmost contiguous region of the Scandinavian mountain range is probably a result of recent land uplift and late colonization. The Scandinavian lowland regional populations probably represent remains of an earlier widespread population that became increasingly restricted to small and isolated areas when the vegetation closed during the post‐glacial period. Some of the lowland populations require extensive management to survive. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 635–657.     

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.     

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.     

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.     

A multi-compartmented glacial refugium in the northern Rocky Mountains: Evidence from the phylogeography of <Emphasis Type="Italic">Cardamine constancei</Emphasis> (Brassicaceae)

The age and origin of the mesic coniferous forest ecosystem of the Pacific Northwest of North America have long been the subject of debate by biogeographers. Cardamine constancei, an endemic of the Rocky Mountain segment of this ecosystem, was subjected to phylogeographic analysis to test explicit hypotheses on the age of the ecosystem. We have predicted genetic homogeneity among river drainages if C. constancei and other associated species migrated into the region after glaciation, in contrast to the genetic differentiation that may have accrued if the species and its ecosystem have long survived in the relatively warm river canyons south of glaciation. We detected 19 haplotypes with divergence up to 1.5%, and they comprise 4 well-differentiated cpDNA clades. These clades are allopatric except for two haplotypes from the lower Clearwater clade that appear to have dispersed north into partial sympatry with the clade endemic to St.␣Joe River. The divergence and distribution of these clades is consistent with the existence of a complex glacial refugium with at least four compartments. The surprisingly high cpDNA diversity within this species suggests that conservation of mesic coniferous forest ecosystems in the region warrant a conservation plan that accounts for the historically imposed spatial structure of genetic diversity. We are currently testing our phylogeographic hypotheses by the comparative analyses of a suite of plants, animals and fungi.     

Phylogeography and palaeodistribution modelling of Nassauvia subgenus Strongyloma (Asteraceae): exploring phylogeographical scenarios in the Patagonian steppe

The Patagonian steppe is an immense, cold, arid region, yet phylogeographically understudied. Nassauvia subgen. Strongyloma is a characteristic element of the steppe, exhibiting a continuum of morphological variation. This taxon provides a relevant phylogeographical model not only to understand how past environmental changes shaped the genetic structure of its populations, but also to explore phylogeographical scenarios at the large geographical scale of the Patagonian steppe. Here, we (1) assess demographic processes and historical events that shaped current geographic patterns of haplotypic diversity; (2) analyze hypotheses of isolation in refugia, fragmentation of populations, and/or colonization of available areas during Pleistocene glaciations; and (3) model extant and palaeoclimatic distributions to support inferred phylogeographical patterns. Chloroplast intergenic spacers, rpl32–trnL and trnQ–5′rps16, were sequenced for 372 individuals from 63 populations. Nested clade analysis, analyses of molecular variance, and neutrality tests were performed to assess genetic structure and range expansion. The present potential distribution was modelled and projected onto a last glacial maximum (LGM) model. Of 41 haplotypes observed, ten were shared among populations associated with different morphological variants. Populations with highest haplotype diversity and private haplotypes were found in central‐western and south‐eastern Patagonia, consistent with long‐term persistence in refugia during Pleistocene. Palaeomodelling suggested a shift toward the palaeoseashore during LGM; new available areas over the exposed Atlantic submarine platform were colonized during glaciations with postglacial retraction of populations. A scenario of fragmentation and posterior range expansion may explain the observed patterns in the center of the steppe, which is supported by palaeomodelling. Northern Patagonian populations were isolated from southern populations by the Chubut and the Deseado river basins during glaciations. Pleistocene glaciations indirectly impacted the distribution, demography, and diversification of subgen. Strongyloma through decreased winter temperatures and water availability in different areas of its range.     

Caucasus Mountains divide postulated postglacial colonization routes in the white‐breasted hedgehog,Erinaceus concolor

For many European species, the mountains of the Alps and the Pyrenees have acted as significant barriers to northwards colonization from southern glacial refugia. To the east, the Caucasus Mountains would seem to have been a similar barrier to the white‐breasted hedgehog (Erinaceus concolor). A deep divergence among hedgehog mitochondrial sequences to the north and south of the Caucasus Mountains suggests two colonization routes, originating from separate refugial regions and divided by this mountain barrier. From a Balkan refugium, hedgehogs have colonized northwards into Russia and to the northern foothills of the Caucasus Mountains. The origins of hedgehogs colonizing the southern parts of the Caucasus are not entirely clear, although fossil and climatic data suggest a glacial refugium on the southern shores of the Black Sea. Divergence within the southern group indicates a long‐standing fragmentation within such a refugium or the presence of further cryptic refugia in Turkey and the Near East. The Caucasus barrier would seem to have been an important factor in structuring the late Pleistocene distribution of species.     

Phylogeography of Eastern Grey Kangaroos,Macropus giganteus,Suggests a Mesic Refugium in Eastern Australia

Phylogeographic studies around the world have identified refugia where fauna were able to persist during unsuitable climatic periods, particularly during times of glaciation. In Australia the effects of Pleistocene climate oscillations on rainforest taxa have been well studied but less is known about the effects on mesic-habitat fauna, such as the eastern grey kangaroo (Macropus giganteus). The eastern grey kangaroo is a large mammal that is common and widespread throughout eastern Australia, preferring dry mesic habitat, rather than rainforest. As pollen evidence suggests that the central-eastern part of Australia (southeast Queensland and northern New South Wales) experienced cycles of expansion in mesic habitat with contraction in rainforests, and vice versa during glacial and interglacial periods, respectively, we hypothesise that the distribution of the eastern grey kangaroo was affected by these climate oscillations and may have contracted to mesic habitat refugia. From 375 mitochondrial DNA control region sequences from across the distribution of eastern grey kangaroos we obtained 108 unique haplotypes. Phylogenetic analysis identified two clades in Queensland, one of which is newly identified and restricted to a small coastal region in southern Queensland north of Brisbane, known as the Sunshine Coast. The relatively limited geographic range of this genetically isolated clade suggests the possibility of a mesic habitat refugium forming during rainforest expansion during wetter climate cycles. Other potential, although less likely, reasons for the genetic isolation of the highly distinct clade include geographic barriers, separate northward expansions, and strong local adaptation.     

Phylogeography of the world's tallest angiosperm, Eucalyptus regnans: evidence for multiple isolated Quaternary refugia

Aim There is a need for more Southern Hemisphere phylogeography studies, particularly in Australia, where, unlike much of Europe and North America, ice sheet cover was not extensive during the Last Glacial Maximum (LGM). This study examines the phylogeography of the south‐east Australian montane tree species Eucalyptus regnans. The work aimed to identify any major evolutionary divergences or disjunctions across the species’ range and to examine genetic signatures of past range contraction and expansion events. Location South‐eastern mainland Australia and the large island of Tasmania. Methods We determined the chloroplast DNA haplotypes of 410 E. regnans individuals (41 locations) based on five chloroplast microsatellites. Genetic structure was examined using analysis of molecular variance (AMOVA), and a statistical parsimony tree was constructed showing the number of nucleotide differences between haplotypes. Geographic structure in population genetic diversity was examined with the calculation of diversity parameters for the mainland and Tasmania, and for 10 regions. Regional analysis was conducted to test hypotheses that some areas within the species’ current distribution were refugia during the LGM and that other areas have been recolonized by E. regnans since the LGM. Results Among the 410 E. regnans individuals analysed, 31 haplotypes were identified. The statistical parsimony tree shows that haplotypes divided into two distinct groups corresponding to mainland Australia and Tasmania. The distribution of haplotypes across the range of E. regnans shows strong geographic patterns, with many populations and even certain regions in which a particular haplotype is fixed. Many locations had unique haplotypes, particularly those in East Gippsland in south‐eastern mainland Australia, north‐eastern Tasmania and south‐eastern Tasmania. Higher haplotype diversity was found in putative refugia, and lower haplotype diversity in areas likely to have been recolonized since the LGM. Main conclusions The data are consistent with the long‐term persistence of E. regnans in many regions and the recent recolonization of other regions, such as the Central Highlands of south‐eastern mainland Australia. This suggests that, in spite of the narrow ecological tolerances of the species and the harsh environmental conditions during the LGM, E. regnans was able to persist locally or contracted to many near‐coastal refugia, maintaining a diverse genetic structure.     

Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn.

Traditionally, information on the postglacial history of plant species has been gained from the analysis of fossil pollen data. More recently, surveys of present patterns of genetic variation have given valuable insights into species phylogeography. The genus Alnus , based on fossil data, is known to have had at least four glacial refugia. A survey of chloroplast DNA (cpDNA) diversity in populations of black alder ( A. glutinosa ) was undertaken in order to gain more insight into its postglacial history. This revealed a high degree of structuring of 13 cpDNA haplotypes on a European scale which indicated that most of northern and central Europe was colonized from a refuge in the Carpathian Mountains. Based on the distribution of two common cpDNA haplotypes, colonization routes from this refuge can be determined. The locations of other previously identified refugia are confirmed and two formerly unconfirmed refugial areas for alder (southern Spain and Turkey) are proposed.     

The role of disjunction and postglacial population expansion on phylogeographical history and genetic diversity of the circumboreal plant Chamaedaphne calyculata

In the last decade a number of studies has illustrated quite different phylogeographical patterns amongst plants with a northern present‐day geographical distribution, spanning the entire circumboreal region and/or circumarctic region and southern mountains. These works, employing several marker systems, have brought to light the complex evolutionary histories of this group. Here I focus on one circumboreal plant species, Chamaedaphne calyculata (leatherleaf), to unravel its phylogeographical history and patterns of genetic diversity across its geographical range. A survey of 29 populations with combined analyses of chloroplast DNA (cpDNA), internal transcribed spacer (ITS) and AFLP markers revealed structuring into two groups: Eurasian/north‐western North American, and north‐eastern North American. The present geographical distribution of C. calyculata has resulted from colonization from two putative refugial areas: east Beringia and south‐eastern North America. The variation of chloroplast DNA (cpDNA) and ITS sequences strongly indicated that the evolutionary histories of the Eurasian/north‐western North American and the north‐eastern North American populations were independent of each other because of a geographical disjunction in the distribution area and ice‐sheet history between north‐eastern and north‐western North America. Mismatch analysis using ITS confirmed that the present‐day population structure is the result of rapid expansion, probably since the last glacial maximum. The AFLP data revealed low genetic diversity of C. calyculata (P = 19.5%, H = 0.085) over the whole geographical range, and there was no evidence of loss of genetic diversity within populations in the continuous range, either at the margins or in formerly glaciated and nonglaciated regions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 761–775.     

Rethinking long‐term vegetation dynamics: multiple glacial refugia and local expansion of a species complex

Evidence is accumulating that some arcto‐boreal plant taxa persisted through the last glacial maximum (LGM) in Alaska and adjacent Canada. However, the spatial patterns of glacial persistence and associated postglacial colonization remain largely unknown. In this study, we investigated the LGM refugia of an alder (Alnus) species complex (n = 3 taxa) and assess the spatiotemporal dynamics of Alnus in this vast region. Specifically, we conducted high‐throughput DNA sequencing (ddRADseq) on Alnus foliar samples collected from a dense population network to investigate patterns of genetic structure and infer the presence of glacial lineages. Species distribution modeling (SDM) was used to investigate the probability and possible locations of glacial persistence. These analyses were integrated and then compared with fossil pollen data to identify the locations of refugial populations and spatial patterns of postglacial colonization. Our genetic analyses revealed two glacial lineages with separate geographic origins for each Alnus taxon, suggesting that the genus persisted in multiple LGM refugia. Non‐overlapping hindcast distributions based on SDMs further support the presence of multiple, spatially distinct refugia. These ddRADseq and SDM results, in conjunction with reassessment of fossil pollen records, suggest that Alnus expanded from several population nuclei that existed during the LGM and coalesced during the Holocene to form its present range. These results challenge the unidirectional model for postglacial vegetation expansion, implying that climate buffering associated with landscape heterogeneity and adaptation to millennial‐scale environmental variability played important roles in driving late‐Quaternary population dynamics.     

Resilient forest faunal communities in South Africa: a legacy of palaeoclimatic change and extinction filtering?

Aim To examine the influence of climatic extinction filtering during the last glacial maximum (LGM; c. 18,000 yr bp ) and of the subsequent recolonization of forest faunas on contemporary assemblage composition in southern African forests. Location South Africa, Mozambique, Swaziland, Zimbabwe. Methods Data comprised presence/absence by quarter‐degree grid cell for forest‐dependent and forest‐associated birds, non‐volant mammals and frogs. Twenty‐one forest subregions were assigned to one of three previously identified forest types: Afrotemperate, scarp, and Indian Ocean coastal belt. Differences among forest types were examined through patterns and gradients of species richness and endemism, assemblage similarity, species turnover, and coefficients of species dispersal direction. The influence of contemporary environment on assemblage composition was investigated using partial canonical correspondence analysis. Several alternative biogeographical hypotheses for the recolonization of forest faunas were tested. Results Afrotemperate faunas are relatively species‐poor, have low species turnover, and are unsaturated and infiltrated by generalist species. In northern and central regions, communities are supplemented by recolonization from scarp forest refugia, and among frogs by autochthanous speciation in localized refugia. Scarp faunas are relatively species‐rich, contain many forest‐dependent species, have high species turnover, and overlap with coastal and Afrotemperate faunas. Coastal forests are relatively species‐rich with high species turnover. Main conclusions Afrotemperate communities were affected most by climatic extinction filtering events. Scarp forests were Afrotemperate refugia during the LGM and are a contemporary overlap zone between Afrotemperate and coastal forest. Coastal faunas derive from post‐LGM colonization along the eastern seaboard from tropical East African refugia. The greatest diversity is achieved in scarp and coastal forest faunas in northern KwaZulu–Natal province. This historical centre of diversity has influenced the faunal diversity of nearly all other forests in South Africa. The response of vertebrate taxa to large‐scale, historical processes is dependent on their relative mobility: forest birds best illustrate patterns resulting from post‐glacial faunal dispersal, while among mammals and frogs the legacy of climatic extinction filtering remains stronger.