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.     

Shared phylogeographic patterns and widespread chloroplast haplotype sharing in Eucalyptus species with different ecological tolerances

We examined the phylogeography of three south-east Australian trees (Eucalyptus delegatensis, Eucalyptus obliqua, and Eucalyptus regnans) with different tolerances, in terms of cold, drought, fire and soil to explore whether species with different ecologies share major phylogeographic patterns. A second aim of this study was to examine geographic patterns of chloroplast DNA (cpDNA) haplotype sharing among the three study species. Trees of E. delegatensis (n?=?120), E. obliqua (n?=?265) and E. regnans (n?=?270) were genotyped with five cpDNA microsatellite markers. The species shared major phylogeographic disjunctions, and common patterns at proposed glacial refugia (generally high haplotype diversity) and areas thought to have been treeless during the Last Glacial Maximum (LGM) (low diversity). Inter-specific sharing of haplotypes was extensive, and fixation of shared, regional haplotypes was more frequent in areas postulated as having been treeless at the LGM. Despite ecological differences, chloroplast microsatellite data suggest the three species have responded to past climatic changes in a similar way, by persisting in multiple, generally common refugia. We suggest that the natural ability of eucalypt species to hybridise with others with quite different or broader ecological tolerances may provide an “insurance policy” for response to rapidly changing abiotic conditions.     

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.     

Genetic evidence for the origins of range disjunctions in the Australian dry sclerophyll plant Hardenbergia violacea

Aim The distribution of genetic variation in the Australian dry sclerophyll plant Hardenbergia violacea (Fabaceae) is examined in the context of Pleistocene climate change in order to identify likely refugia. Particular consideration is given to the origin of range disjunctions in South Australia and Tasmania, and to determining whether the Tasmanian population is indigenous or recently introduced from mainland Australia. Location Southeastern Australian mainland and Tasmania. Methods A combination of chloroplast polymerase chain reaction–restriction fragment length polymorphism and genomic amplified fragment length polymorphism (AFLP) marker systems was used to examine the genetic structure of 292 individuals from 13 populations across the range of H. violacea in southeastern Australia. Results Hardenbergia violacea populations in Tasmania and southern Victoria were characterized by low, almost monotypic chloroplast diversity. New South Wales showed higher haplotype diversity and haplotype sharing among widely distributed populations. Principal coordinates analysis (PCoA) of the AFLP data found a strong latitudinal cline in AFLP variation from northern New South Wales south to Tasmania. The Tasmanian population formed an isolated and somewhat disjunct genetic cluster at one end of this cline. However, the South Australian population was an exception to the clinal variation shown by all other populations, forming a highly disjunct cluster in the PCoA. Within‐population genetic diversity was low in both disjunct populations. Main conclusions The genetic evidence indicates that the Tasmanian population is likely to be indigenous and probably the product of vicariance, which was followed by range contraction at the Last Glacial Maximum or an earlier glacial event. The deep phylogenetic disjunction in South Australia is evidence of a much earlier separation on mainland Australia. The chloroplast structure indicates that, during the Pleistocene, H. violacea underwent broad‐scale recolonization in southern Victoria and Tasmania, possibly from a large continental refugium in eastern New South Wales. We conclude that H. violacea, and presumably the sclerophyll communities in which it occurs, have undergone multiple range contractions to large continental refugia during different Pleistocene glaciations in southeastern Australia.     

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

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

Phylogeographic analyses suggest that a deciduous species (Ostryopsis davidiana Decne., Betulaceae) survived in northern China during the Last Glacial Maximum

Aim Palaeontologial data suggest that all temperate forest species in northern China migrated southwards during the Last Glacial Maximum (LGM) and recolonized post‐glacially within the Holocene. We tested this assumption using phylogeographical studies of a temperate deciduous shrub species (Ostryopsis davidiana Decne., Betulaceae), which has a wide distribution in northern China. Location Northern China. Methods We sequenced two chloroplast DNA (cpDNA) fragments (trnL–trnF and psbA–trnH, together about 1300 bp in length) of 294 plants from 21 populations across the total distribution range of this species. We used maximum parsimony and haplotype network methods to construct phylogenetic relationships among haplotypes. Results The analysis of cpDNA variation identified eight haplotypes. A single haplotype was fixed in all populations except for one population that was polymorphic, having two haplotypes. The population subdivisions were extremely high (G_ST = 0.972 and N_ST = 0.974), suggesting very low gene flow between populations. Haplotypes clustered into two tentative clades, both of which occur in the southern region of the species’ range but only one of which occurs in the northern region. Across the sampled populations, the haplotype distributions were differentiated geographically. Main conclusions Our analyses suggest that multiple refugia were maintained across the range of O. davidiana in both northern (north of the Qing Mountains) and southern (south of the Qing Mountains) regions during the LGM rather than that the species survived only in the south and subsequently colonized northwards. The extremely low within‐population diversity of this species suggests strong bottleneck or founder effects within each fragmented region during the Quaternary climatic oscillations. These findings provide important clues for understanding range shifts and changes in within‐ and/or between‐population genetic diversity of temperate forests in response to past climatic oscillations in northern China.     

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.     

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

The genetic diversity and phylogeography of maternal lineages in Ursus arctos Linnaeus, 1758 (the brown bear) have been studied extensively over the last two decades; however, sampling has largely been limited to the northern Holarctic, and was possibly biased towards lineages that recolonized the vast expanses of the north as the Last Glacial Maximum (LGM) ended. Here we report the genetic diversity and phylogeography of U. arctos from Turkey based on 35 non‐invasive samples, including five from captive individuals. Bayesian phylogenetic analyses based on a 269‐bp fragment of the mitochondrial DNA control region revealed 14 novel haplotypes belonging to three major lineages. The most widespread lineage was found to be the Eastern clade 3a, whereas geographically more restricted Western and Middle Eastern lineages were reported for the first time in Turkey. A specimen from the Taurus mountain range carried a haplotype closely related to the presumably extinct bears in Lebanon. Moreover, we identify a unique new lineage that appears to have split early within the Middle Eastern clade. Despite limited sampling, our study reveals a high level of mitochondrial diversity in Turkish U. arctos, shows that the ranges of both European and Middle Eastern clades extend into Turkey, and identifies a new divergent lineage of possibly wider historical occurrence. Obtaining these results with 35 samples also demonstrates the value of proper sampling from regions that have not been significantly affected by the LGM. © 2015 The Linnean Society of London     

Searching for the glacial refugia of Erebia euryale (Lepidoptera,Nymphalidae) – insights from mtDNA‐ and nDNA‐based phylogeography in the Western Carpathians

The refugial history and postglacial re‐colonization routes of Western Carpathian insects are insufficiently understood. Therefore, we investigated the spatio‐genetic structure (phylogeography) of Western Carpathian populations of Erebia euryale (Esper, 1805) (Lepidoptera, Nymphalidae) and inferred their colonization routes over the postglacial period. Our results provide new insights into the phylogeography and origin of Erebia euryale in the rarely studied region of the Western Carpathian Mountains. Their phylogeography, including glacial refugia and Pleistocene expansion routes, was reconstructed based on two mitochondrial (COI and CR) and three nuclear markers (CAD, MDH and IDH). Statistical parsimony networks showed the following geographic coherences: (1) populations from Romania and the Bukovské Mountains (Kremenec) grouped together; (2) a ?ergov group containing populations only from the ?ergov Mountains; (3) a Volovské Mountains group with populations from Koj?ovská ho?a and Slovak Paradise grouped together, most likely due to the lack of geographic isolation between the areas; (4) haplotypes characterized from the Volovské Mountains populations were widespread. Comparisons of Western Carpathian E. euryale COI‐haplotypes with haplotypes from the Southern Carpathians and Balkans suggest that the refugial areas were located in south‐eastern Europe in the Balkan region and Southern Carpathians. We also hypothesize possible central European contact zones in Slovakia for E. euryale in the Western Carpathians. Our results indicate that the Western Carpathians could have served as one of the contact zones between Eastern and Western populations, and additionally as an extra refugium in the southern part of the Volovské Mountains for populations also occurring in Czech mountain regions.     

Gene flow of the canker pathogen Botryosphaeria australis between Eucalyptus globulus plantations and native eucalypt forests in Western Australia

Abstract The eucalypt plantation industry in Western Australia provides a unique opportunity to study the movement of pathogens between closely related host taxa. Eucalyptus globulus, a native to Tasmania and south‐eastern Australia, is the predominant species in Western Australian plantations, often being planted adjacent to native forest containing Eucalyptus marginata and Eucalyptus diversicolor. Since the commencement of the plantation industry 20 years ago, several fungal species, previously known only to eastern Australia or overseas, have been reported on E. globulus in Western Australia. Botryosphaeria australis is a newly described species, recently found causing cankers on Acacia spp. in eastern Australia. However, during a routine survey, B. australis was found to be the predominant species associated with E. globulus plantations and native Eucalyptus spp. in Western Australia. In this study, six short simple repeat markers were used to evaluate genetic diversity and gene flow between collections of B. australis from native eucalypt forest and E. globulus plantations at two locations in south‐western Australia. In both cases, there was no restriction to gene flow between the plantations and the adjacent native forest. Botryosphaeria australis has now been isolated from a wide range of hosts across south‐western Australia and was not isolated from E. globulus in Tasmania or South Australia. This extensive distribution and host range suggests B. australis is native to Western Australia. This study demonstrates the ability of a pathogen to move between plantation and forests.     

Plio‐Pleistocene diversification and genetic population structure of an endangered lizard (the Blue Mountains water skink,Eulamprus leuraensis) in south‐eastern Australia

Aim Although climatic fluctuations occurred world‐wide during the Pleistocene, the severity of glacial and drought events – and hence their influence on animal and plant biogeography – differed among regions. Many Holarctic species were forced to warmer‐climate refugia during glacial periods, leaving the genetic signature of recent expansion and gene flow among modern‐day populations. Montane south‐eastern Australia experienced less extreme glaciation, but the effects of drier and colder climatic conditions over this period on biotic distributions, and hence on the present‐day genetic structure of animal and plant populations, are poorly known. Location South‐eastern Australia. Methods The endangered Blue Mountains water skink (Eulamprus leuraensis) is a viviparous lizard known from fewer than 40 isolated small swamps at 560–1060 m elevation in south‐eastern Australia. We conducted molecular phylogenetic, dating and population genetics analyses using the mitochondrial NADH dehydrogenase 4 (ND4) of 224 individuals of E. leuraensis sampled across the species’ distribution. Results Ancient divergences in haplotype groups between lizards from the Blue Mountains and the Newnes Plateau, and strong genetic differences, even between swamps separated by only a few kilometres, suggest that the species has persisted as a series of relatively isolated populations within its current distribution for about a million years. Presumably, habitat patches similar to current‐day swamps persisted throughout glacial–interglacial cycles in this region, allowing the development of high levels of genetic structuring within and among present‐day populations. Main conclusions Our results suggest that less extreme glacial conditions occurred in the Southern Hemisphere compared with the Northern Hemisphere, allowing cold‐adapted species (such as E. leuraensis) to persist in montane areas. However, additional studies are needed before we can assemble a comprehensive view of the impact of Pleistocene climatic variation on the phylogeography of Southern Hemisphere taxa.     

Molecular relationships within Bostrychia tenuissima (Rhodomelaceae, Rhodophyta)

Bostrychia tenuissima King and Puttock is restricted to southern Australia and New Zealand. Previous studies in Australia have revealed two distinct patterns in the presence of osmotically active polyols. Southern populations only have D-sorbitol whereas northern populations have both D-sorbitol and D-dulcitol. These polyol patterns lead to speculation on the ecotypic differentiation of these two population types. Using single-stranded confirmation polymorphism to rapidly score plastid haplotypes, plus DNA sequencing, a 100% congruence was found between polyol patterns and plastid haplotype. Analysis of 33 B. tenuissima isolates shows that the plastid relationships closely follow biogeo-graphic regions, with south-eastern Australia (southern NSW and Victoria) and South Australia and Tasmania having one haplotype and central and northern NSW having two alternate haplotypes. There is an overlap at the haplotype boundary just south of Sydney, New South Wales.     

Complex fine‐scale phylogeographical patterns in a putative refugial region for Fagus sylvatica (Fagaceae)

Broad‐scale plastid (chloroplast) DNA studies of beech (Fagus sylvatica) populations suggest the existence of glacial refugia and introgression zones in south‐eastern Europe. We choose a possible refugium of beech in northern Greece, Mt. Paggeo, which hosts a private plastid haplotype for beech, to conduct a fine‐scale genetic study. We attempt to confirm or reject the hypothesis of the existence of a small‐scale refugium and to gain an understanding of the ecological and topographical factors affecting the spatial distribution of plastid haplotypes in the area. Our results reveal a high haplotype diversity on Mt. Paggeo, but the overall distribution of haplotypes shows no significant correlation with the ecological characteristics of the beech forests. However, the private haplotype is found at high frequencies in beech forests located in or near ravines, having a high spatial overlap with a relict vegetation type occurring in ecological conditions found mainly in ravines. This result emphasizes the importance of topography in the existence of glacial refugia in the wider area. Furthermore, haplotypes originating from two more widespread beech lineages in Greece are found on Mt. Paggeo, indicating a possible mixing of populations originating from a local refugium with populations from remote refugia that possibly migrated into the area after the last glaciation. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 516–528.     

Chloroplast DNA diversity associated with protected slopes and valleys for hybridizing Eucalyptus species on isolated ranges in south‐eastern Australia

Aim To relate genetic diversity to topographic features and to investigate genetic interactions between Eucalyptus species in a local centre of endemism and diversity in south‐eastern Australia. Location Grampian Ranges, Victoria, Australia. Methods We documented chloroplast DNA (cpDNA) variation for a group of endemic Eucalyptus species (E. serraensis, E. verrucata and E. victoriana) that dominate rocky, high‐elevation ridgelines of the Grampian Ranges and for one closely‐related, widespread species (E. baxteri) occupying flanking slopes and valleys. We documented genetic patterns across the landscape using cpDNA microsatellites, and related them to topographic features (exposed west‐facing versus protected east‐facing slopes and valleys). We also determined the extent of local haplotype sharing between populations of endemic species and neighbouring E. baxteri downslope with cpDNA microsatellites, and haplotype sharing between the endemic group and more distantly related species (E. obliqua, E. pauciflora and E. willisii) with sequences of the J_LA+ chloroplast region. Results We detected 26 cpDNA microsatellite haplotypes in a relatively small area of c. 20 km × 50 km. Populations of E. baxteri on east‐facing slopes and valleys had greater cpDNA microsatellite diversity than E. baxteri and endemic species on exposed west‐facing slopes. Endemic species frequently shared chloroplast haplotypes with E. baxteri downslope. Sharing of J_LA+ haplotypes with species outside the endemic group was mostly restricted to E. victoriana, which had cpDNA more similar to the species from other sections of Eucalyptus (E. obliqua, E. willisii and E. pauciflora). Main conclusions Intensive sampling of related species on small isolated mountain ranges allowed us to relate genetic diversity to fine‐scale habitats and to document extensive local haplotype sharing between species. This study contributes to a general understanding of the environmental conditions that enable plant population persistence by linking concentrations of genetic diversity to particular habitats.     

Contrasting genetic patterns between two coexisting Eleutherococcus species in northern China

Climate oscillations are the key factors to understand the patterns in modern biodiversity. East Asia harbors the most diverse temperate flora, largely because an extensive terrestrial ice cap was absent during repeated Pleistocene glaciation–interglacial cycles. Comparing the demographic histories of species that are codistributed and are close relatives may provide insight into how the process of climate change influences species ranges. In this study, we compared the spatial genetic structure and demographic histories of two coexisting Eleutherococcus species, Eleutherococcus senticosus and E. sessiliflorus. Both species are distributed in northern China, regions that are generally considered to be sensitive to climatic fluctuations. These regions once hosted temperate forest, but this temperate forest was replaced by tundra and taiga forest during the Last Glacial Maximum (LGM), according to pollen records. Using three chloroplast DNA fragments, we assessed the genetic structure of 20 and 9 natural populations of E. senticosus and E. sessiliflorus, respectively. Extremely contrasting genetic patterns were found between the two species; E. sessiliflorus had little genetic variation, whereas E. senticosus had considerably higher levels of genetic variation (15 haplotypes). We speculated that a recent severe bottleneck may have resulted in the extremely low genetic diversity in E. sessiliflorus. In E. senticosus, populations in Northeast China (NEC) harbored all of the haplotypes found in this species and included private haplotypes. The populations in NEC had higher levels of genetic diversity than did those from North China (NC). Therefore, we suggest that both the NC and NEC regions can sustain LGM refugia and that lineage admixture from multiple refugia took place after the LGM elevated the local genetic diversity in NEC. In NEC, multiple genetic hot spots were found in the Changbai Mountains and the Xiaoxing'an Range, which implied that multiple locations in NEC may sustain LGM refugia, even in the Xiaoxing'an Range.     

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.     

Northern richness and southern poverty: contrasting genetic footprints of glacial refugia in the relictual tree Sciadopitys verticillata (Coniferales: Sciadopityaceae)

Sciadopitys verticillata is amongst the most relictual of all plants, being the last living member of an ancient conifer lineage, the Sciadopityaceae, and is distributed in small and disjunct populations in high rainfall regions of Japan. Although mega‐fossils indicate the persistence of the species within Japan through the Pleistocene glacial–interglacial cycles, how the species withstood the colder and drier climates of the glacials is not well known. The present study utilized phylogeography and palaeodistribution modelling to test whether the species survived within pollen‐based coastal temperate forest glacial refugia or within previously unidentified refugia close to its current range. Sixteen chloroplast haplotypes were found that displayed significant geographical structuring. Unexpectedly, northern populations in central Honshu most distant from coastal refugia had the highest chloroplast diversity and were differentiated from the south, a legacy of glacial populations possibly in inland river valleys close to its current northern range. By contrast, populations near putative coastal refugia in southern Japan, harboured the lower chloroplast diversity and were dominated by a single haplotype. Fragment size polymorphism at a highly variable and homoplasious mononucleotide repeat region in the trnT‐trnL intergenic spacer reinforced the contrasting patterns of diversity observed between northern and southern populations. The divergent histories of northern and southern populations revealed in the present study will inform the management of this globally significant conifer. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 108 , 263–277.     

No obvious genetic erosion,but evident relict status at the westernmost range edge of the Pontic‐Pannonian steppe plant Linum flavum L. (Linaceae) in Central Europe

We investigate patterns of genetic variation along an east–west transect of Central European populations of Linum flavum and interpret the Quaternary history of its peripheral populations, especially those at the westernmost isolated range edge, discussing their migrations and possible relict status. We defined our peripheral transect across three study regions from Central Hungary, eastern Austria to southwestern Germany. Using AFLP fingerprinting and cpDNA sequence variation (rpL16 intron, atpI‐H), we analyzed 267 and 95 individuals, respectively, representing each study region by four populations. Hierarchical AMOVA (AFLPs) indicated significant variation among study regions (12% of total variance) and moderate differentiation between populations (10%). Population differentiation was high at the westernmost range edge (11.5%, Germany), but also in the east (13.4%, Hungary), compared to the Austrian study region (8.6%). Correspondingly, AFLP diversity was highest in the center of the study transect in eastern Austria. CpDNA haplotypes support a pattern of regional structuring with the strongest separation of the westernmost range edge, and some haplotype sharing among Austrian and Hungarian individuals. Equilibrating nucleotide versus haplotype diversity patterns, the highly diverse populations at the Pannonian range edge (Austria) indicate long‐term persistence, while Central Pannonian populations are obviously effected by recent bottlenecks. Intermediate nucleotide, but high haplotype diversity within the westernmost exclave (Swabian Alb), is indicative of a founder bottleneck during its pre‐LGM or early postglacial migration history, followed by sufficient time to accumulate cpDNA variation. The not obviously reduced genetic diversity and distinctiveness of L. flavum at the westernmost range edge suggest a long‐term persistence (relict status) of populations in this region, where the species has survived probably even the Würm glaciation in extra‐Mediterranean refugia. This genetic relict variation represents an important part of the overall genetic diversity found in the western periphery of this steppe plant and highlights the high conservation priority of respective gene pools.     

A climate change context for the decline of a foundation tree species in south-western Australia: insights from phylogeography and species distribution modelling

Background and Aims A worldwide increase in tree decline and mortality has been linked to climate change and, where these represent foundation species, this can have important implications for ecosystem functions. This study tests a combined approach of phylogeographic analysis and species distribution modelling to provide a climate change context for an observed decline in crown health and an increase in mortality in Eucalyptus wandoo, an endemic tree of south-western Australia.Methods Phylogeographic analyses were undertaken using restriction fragment length polymorphism analysis of chloroplast DNA in 26 populations across the species distribution. Parsimony analysis of haplotype relationships was conducted, a haplotype network was prepared, and haplotype and nucleotide diversity were calculated. Species distribution modelling was undertaken using Maxent models based on extant species occurrences and projected to climate models of the last glacial maximum (LGM).Key Results A structured pattern of diversity was identified, with the presence of two groups that followed a climatic gradient from mesic to semi-arid regions. Most populations were represented by a single haplotype, but many haplotypes were shared among populations, with some having widespread distributions. A putative refugial area with high haplotype diversity was identified at the centre of the species distribution. Species distribution modelling showed high climatic suitability at the LGM and high climatic stability in the central region where higher genetic diversity was found, and low suitability elsewhere, consistent with a pattern of range contraction.Conclusions Combination of phylogeography and paleo-distribution modelling can provide an evolutionary context for climate-driven tree decline, as both can be used to cross-validate evidence for refugia and contraction under harsh climatic conditions. This approach identified a central refugial area in the test species E. wandoo, with more recent expansion into peripheral areas from where it had contracted at the LGM. This signature of contraction from lower rainfall areas is consistent with current observations of decline on the semi-arid margin of the range, and indicates low capacity to tolerate forecast climatic change. Identification of a paleo-historical context for current tree decline enables conservation interventions to focus on maintaining genetic diversity, which provides the evolutionary potential for adaptation to climate change.     

Historical biogeography of Australian Rhamnaceae, tribe Pomaderreae

Aim To discover the pattern of relationships of areas of endemism for Australian genera in the plant family Rhamnaceae tribe Pomaderreae for comparison with other taxa and interpretation of biogeographical history. Location Australian mainland, Tasmania and New Zealand. Methods A molecular phylogeny and geographic distribution of species within four clades of Pomaderreae are used as a basis for recognition of areas of endemism and analysis of area relationships using paralogy‐free subtrees. The taxon phylogeny is the strict consensus tree from a parsimony analysis of 54 taxa, in four clades, and sequence data for the internal transcribed spacer regions of ribosomal DNA (ITS1‐5.8S‐ITS2) and the plastid DNA region trnL‐F. Results The biogeographical analysis identified five subtrees, which, after parsimony analysis, resulted in a minimal tree with 100% consistency and seven resolved nodes. Three sets of area relationships were identified: the areas of Arnhem and Kimberley in tropical north Australia are related based on the phylogeny of taxa within Cryptandra; the moister South‐west of Western Australia, its sister area the coastal Geraldton Sandplains, the semi‐arid Interzone region and arid Western Desert are related, based on taxa within Cryptandra, Spyridium, Trymalium and Pomaderris; and the eastern regions of Queensland, McPherson‐Macleay, south‐eastern New South Wales (NSW), Victoria, southern Australia, Tasmania and New Zealand are related based on Cryptandra, Pomaderris and Spyridium. Tasmania and NSW are related based entirely on Cryptandra, but the position of New Zealand relative to the other south‐eastern Australian regions is unresolved. Main conclusions The method of paralogy‐free subtrees identified a general pattern of geographic area relationships based on Australian Pomaderreae. The widespread distribution of clades, the high level of endemicity and the age of fossils for the family, suggest that the Pomaderreae are an old group among the Australian flora. Their biogeographical history may date to the early Palaeogene with subsequent changes through to the Pleistocene.