Importance of demographic history for phylogeographic inference on the arctic–alpine plant Phyllodoce caerulea in East Asia

Arctic–alpine plants have enormous ranges in the Northern Hemisphere. Phylogeographic studies have provided insights into their glacial survival as well as their postglacial colonization history. However, our understanding of the population dynamics of disjunct alpine populations in temperate regions remains limited. During Pleistocene cold periods, alpine populations of arctic–alpine species in East Asia were either connected to an ice-free Beringia refugium or they persisted with prolonged isolation after their establishment. To estimate which of these scenarios is more likely, we elucidated the genetic structure of Phyllodoce caerulea (Ericaceae) in Beringia and northern Japan, East Asia. Sequence variation in multiple nuclear loci revealed that P. caerulea can be distinguished into northern and southern groups. A demographic analysis demonstrated that the north–south divergence did not predate the last glacial period and detected introgression from Phyllodoce aleutica, relative widely distributed in East Asia, exclusively into the southern group. Therefore, although there has been genetic divergence between northern Japan and Beringia in P. caerulea, the divergence is unlikely to have resulted from their prolonged geographic separation throughout several cycles of glacial and interglacial periods. Instead, our study suggests that the introgression contributed to the genetic divergence of P. caerulea and that the range of P. caerulea was plausibly connected between northern Japan and Beringia during the last glacial period. Overall, our study not only provides a biogeographic insight into alpine populations of arctic–alpine plants in East Asia but also emphasizes the importance of careful interpretation of genetic structure for inferring phylogeographic history.     

High mountains of the Japanese archipelago as refugia for arctic–alpine plants: phylogeography of Loiseleuria procumbens (L.) Desvaux (Ericaceae)

According to previous phylogeographic studies, high mountains at low latitudes are important areas for the study of the evolutionary history of arctic–alpine plants in surviving the Pleistocene climatic oscillations. To evaluate this hypothesis, we elucidated the genetic structure of the arctic–alpine plant, Loiseleuria procumbens , in the Japanese archipelago, which corresponds to one of the southernmost limits of its distribution, using 152 individuals from 17 populations that covered the entire distribution of the Japanese archipelago and Sakhalin, in addition to samples from Sweden. Based on 854 bp of chloroplast DNA, we detected eight haplotypes. Along with haplotype distribution, strong genetic differentiation between populations in central and northern Japan was elucidated by a neighbour-joining tree (100%) and spatial analysis of molecular variance (79%), which is consistent with other alpine plants in Japan, regardless of the species' range. In addition, the southernmost populations from northern Japan showed specific genetic structure, although the remaining areas of northern Japan and Sakhalin harboured an homogenous genetic structure. Our results suggest that the populations in central Japan persisted for a long time during the Pleistocene climatic oscillation and that genetic divergence occurred in situ , supporting our hypothesis in conjunction with a previous study of another arctic–alpine plant, Diapensia lapponica subsp. obovata .  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 403–412.     

The homogenous genetic structure and inferred unique history of range shifts during the Pleistocene climatic oscillations of <Emphasis Type="Italic">Arcterica nana</Emphasis> (Maxim.) Makino (Ericaceae)

Previous phylogeographic studies of alpine plants in Japan have inferred that populations in central Honshu persisted during the Pleistocene climatic oscillations and suggested interglacial survival in high mountains. However, Arcterica nana (Maxim.) Makino (Ericaceae) exhibits a homogenous genetic structure throughout Japan and may therefore have a unique phylogeographic history. This inconsistency could have resulted from insufficient resolution of previously analyzed chloroplast DNA sequences. Therefore, we conducted a phylogeographic investigation based on amplified fragment length polymorphisms. Using 176 individuals from 21 populations, the relationships among individuals and populations were determined by principal coordinate analysis and a neighbor-joining tree, respectively. In addition, genetic differentiation was estimated using analysis of molecular variance and spatial autocorrelation analysis. These analyses demonstrate a homogenous structure throughout the entire Japanese range, supporting the previous cpDNA phylogeography. Although this genetic structure is inconsistent with those of other alpine plants, it is difficult to postulate that pre-existing genetic differentiation was swamped exclusively within A. nana. Therefore, this homogenous genetic structure may have been caused by the distinct history of populations of A. nana. Specifically, the southern-ward migration and the subsequent continuous populations enabled gene flow throughout the Japanese archipelago during the last glacial period. Thus, our data suggest that alpine plants in the Japanese archipelago did not always experience a shared distribution change following climatic oscillations.     

Phylogenetic,Demographic and Dating Analyses of Bufo gargarizans Populations from the Zhoushan Archipelago and Mainland China

Relatively little is known about the relationship between Bufo gargarizans populations from Zhoushan Archipelago and nearby continental regions on the Pacific coast of eastern China.In this paper,155 new specimens of B.gargarizans from Zhoushan Archipelago and adjacent continents and 71 published specimens of B.gargarizans from mainland China were studied.Phylogeographical and dating analyses of B.gargarizans were performed using mitochondrial DNA sequencing with a length of 1436 bp.A mt DNA tree that indicated seven major clades was obtained.The earliest split in the mt DNA tree corresponding to the divergence of populations from the western highland region occurred approximately 4.0 million years ago(mya).A subsequent clade occurred about 3.4 mya,with cladogenesis continuing toward the end of the Pleistocene.The continental clades were distributed in the western,central and northeastern regions of China.Zhoushan Archipelago clades consisted of two largely geographically overlapping subclades with the mt DNA divergence time of 0.73 mya.These results indicated there was extensive dispersal after vicariance.The B.gargarizans populations on Zhoushan Archipelago most probably originated from populations in nearby eastern continental regions of China.It was concluded that geological uplifting during the Pliocene and several sea-level changes in Pleistocene might have influenced the divergence and population demographical history of this species.     

Population fragmentation causes randomly fixed genotypes in populations of <Emphasis Type="Italic">Arabidopsis kamchatica</Emphasis> in the Japanese Archipelago

Populations of arctic alpine plants likely disappeared and re-colonised several times at the southern edge of their distributions during glacial and interglacial cycles throughout the Quaternary. Range shift and population fragmentation after a glacial period would affect the genetic structure of such plants in southernmost populations. We aimed to elucidate how climatic oscillations influenced the population subsistence of alpine plants in the Japanese Archipelago as one of the southernmost populations, by inferring the genetic structure of Arabidopsis kamchatica subsp. kamchatica and the intraspecific littoral taxon, subsp. kawasakiana. We identified genotypes based on the haplotypes of five nuclear genes and two chloroplast DNA spacers for 164 individuals from 24 populations. Most populations harboured only one private genotype, whereas few polymorphisms were found in each population. Two genetic genealogies were found, suggesting that northern Japanese populations of alpine subsp. kamchatica, subsp. kawasakiana and the northerly subsp. kamchatica in eastern Russia and Alaska clustered and differentiated from populations in central Honshu, western Japan and Taiwan. During climatic oscillations, the genetic structure of extant southernmost populations would have been shaped by strong genetic drift under population fragmentation and randomly fixed to a single genotype among their ancestral polymorphisms.     

Intraspecific molecular phylogeny, genetic variation and phylogeography of Reticulitermes speratus (Isoptera: Rhinotermitidae)

Population structure was investigated in Reticulitermes speratus populations in the Korean Peninsula and the Japanese Archipelago. All trees derived from analyses of the combined sequence dataset of two mitochondrial genes, COII and COIII, showed that R. speratus populations cluster into two major clades comprising the Korean/southern Japanese populations and the north-ern Japanese populations. Analysis of population ge-netic structure showed strong genetic partitioning between populations of the two clades. To understand historical migration routes and current distributions, the phylogeographic history of R. speratus was inferred from intra-/interspecific phylogeny and diver-gence times estimated between the clades of the phylogenetic tree. The estimated migration route and divergence time of ancestral R. speratus are congruent with recent paleogeographic hypotheses involving land-bridge connections between the Asian continent and the Japanese Archipelago. We suggest that ancestral R. speratus separated into northern and southern Japanese populations after its migration into the Japanese main islands from East China during the early Pleistocene via the East China Sea basin, which may have been exposed during that period. The Korean populations seem to have diverged recently from southern Japanese populations; this may explain the current distribution of R. speratus in the Japanese Arachipelago, and account for why it is restricted to northern areas of the Tokara Strait.     

Phylogeography and historical demography of the anadromous fish Leucopsarion petersii in relation to geological history and oceanography around the Japanese Archipelago

Phylogeographical patterns of marine and diadromous organisms are often influenced by dynamic ocean histories. For example, the marine realm around the Japanese Archipelago is an interesting area for phylogeographical research because of the wide variation in the environments driven by repeated shifts in sea level in the Quaternary. We analysed mitochondrial cyt b gene and nuclear myh6 gene sequences for individuals collected from throughout the range of the anadromous fish Leucopsarion petersii to assess the lineage divergence, phylogeographical pattern and historical demography in relation to geological history and oceanographic features around the archipelago. Leucopsarion petersii has two major lineages (the Japan Sea and Pacific Ocean lineages), which diverged during the late-early to middle Pleistocene. Geographical distributions of the two lineages were closely related to the pathways of the two warm currents, the Tsushima Current and the Kuroshio Current, that flow past the archipelago. Evidence of introgressive hybridization between these lineages was found at two secondary contact zones. Demographic tests suggested that the Japan Sea and Pacific Ocean lineages carried the genetic signal of different historical demographic processes, and these signals are probably associated with differences in habitat stability during recent glacial periods. The Japan Sea lineage has a larger body-size and more vertebrae, probably in relation to severe habitat conditions through Pleistocene climatic oscillations. Thus, the two lineages have long independent evolutionary histories, and the phylogeographical structure and demography of this species have been influenced both by historical events and the present-day oceanography around the Japanese Archipelago.     

Late Pleistocene origin of the entire circumarctic range of the arctic‐alpine plant Kalmia procumbens

The circumarctic ranges of arctic‐alpine plants are thought to have been established in the late Pliocene/early Pleistocene, when the modern arctic tundra was formed in response to climate cooling. Previous findings of range‐wide genetic structure in arctic‐alpine plants have been thought to support this hypothesis, but few studies have explicitly addressed the temporal framework of the genetic structure. Here, we estimated the demographic history of the genetic structure in the circumarctic Kalmia procumbens using sequences of multiple nuclear loci and examined whether its genetic structure reflects prolonged isolation throughout the Pleistocene. Both Bayesian clustering and phylogenetic analyses revealed genetic distinction between alpine and arctic regions, whereas detailed groupings were somewhat discordant between the analyses. By assuming a population grouping based on the phylogenetic analyses, which likely reflects a deeper intraspecific divergence, we conducted model‐based analyses and demonstrated that the intraspecific genetic divergence in K. procumbens likely originated during the last glacial period. Thus, there is no need to postulate range separation throughout the Pleistocene to explain the current genetic structure in this species. This study demonstrates that range‐wide genetic structure in arctic‐alpine plants does not necessarily result from the late Pliocene/early Pleistocene origin of their circumarctic ranges and emphasizes the importance of a temporal framework of the current genetic structure for understanding the biogeographic history of the arctic flora.     

Divergence and diversity: lessons from an arctic-alpine distribution (Pardosa saltuaria group, Lycosidae)

The relationship of interpopulation genetic divergence and within-population diversity has been studied for many temperate species in Europe, but not for the cold-adapted fauna. Here we present the first European-wide phylogeographical study of an arctic-alpine distribution in invertebrates, focusing on wolf spiders of the Pardosa saltuaria group. One hundred twenty-seven (127) specimens from 14 populations were examined. Within Europe, these populations were distributed among six high mountain ranges and Scandinavia. We sequenced the whole 921 base pair mitochondrial (mt) ND1 gene. The resulting 55 unique haplotypes form three monophyletic phylogroups of deep divergence: a Pyrenean, a Balkan and a 'northern' clade. Genetic distances (3.6-4.0%) between the major clades indicate that the arctic-alpine range disjunction was initiated by vicariance events, which precede the four major Alpine glaciations. However, low divergence and incomplete lineage sorting within the 'northern clade' suggest a late Pleistocene separation of the Alpine, Scandinavian, Carpathian and Sudetian populations. Thus, we provide evidence for a multiglacial origin of arctic-alpine distributions in Europe, i.e. the current disjunction results from range fragmentation in several glacial cycles. The pattern of genetic diversity within populations seems predominantly determined by historical factors, but is modified by contemporary aspects. Overall, diversity and divergence are negatively correlated. We suggest that low diversity values might result from (i) ancient bottlenecking during warm interglacial periods, as seen in the Pyrenees and Balkans; (ii) recent bottlenecking in small modern areas, as seen in the Giant Mountains and Bohemian Forest; and (iii) dispersal bottlenecking in northern Scandinavia.     

Divergence among arctic and alpine populations of the annual, Koenigia islandica: morphology, life-history, and phenology

Arctic and alpine habitats occur along complex environmental gradients, and over an extensive geographical range. Despite some selective forces common to these habitats, evolutionary divergence among populations of arctic and alpine plants along this gradient is expected. Of particular significance, both in the context of life-history theory and for implications of climate change, are the few annual species that have adapted to the constraints of an unpredictable, short growing season. In this study, morphological, life-history and phenological characters were found to differ significantly among six widely distributed populations of the arctic-alpine annual Koenigia islandica. On the basis of morphology and life-history traits, populations from high latitudes, with the exception of Svalbard, performed better in simulated arctic conditions, whereas the low latitude alpine plants from Colorado showed enhanced performance under simulated alpine conditions. On the basis of phenology, the six populations can be clearly grouped into arctic, high latitude alpine and alpine populations: arctic plants were found to develop and flower earliest; alpine plants latest. Because these results were obtained using seeds harvested from plants first grown through a complete generation in growth chambers, they indicate strong genetic differentiation. We discuss possible adaptive explanations for observed differences among the six geographically divergent populations.     

Three times out of Asia Minor: the phylogeography of Arabis alpina L. (Brassicaceae)

Arabis alpina is a characteristic plant in arctic-alpine habitats and serves as a classical example to demonstrate biology, ecology and biogeography of arctic-alpine disjuncts. It has a wider distribution than most other arctic-alpine plants, covering all European mountain systems, the Canary Islands, North Africa, the high mountains of East Africa and Ethiopia, the Arabian Peninsula and mountain ranges of Central Asia in Iran and Iraq. Additionally it is found in the northern amphi-Atlantic area including northeastern North America, Greenland, Iceland, Svalbard and northwestern Europe. We used markers from the nuclear (internal transcribed spacer of ribosomal DNA) and chloroplast genome (trnL-F region) to reconstruct its phylogeographic history. Both markers revealed clear phylogeographic structure. We suggest that A. alpina originated in Asia Minor less than 2 million years ago based on synonymous mutation rates of different genes (plastidic matK, nuclear adh and chs). From the Asian ancestral stock one group migrated via the Arabian Peninsula to the East African high mountains. A second group gave rise to all European and northern populations, and also served as source for the northwest African populations. A third group, which is still centred in Asia, migrated independently southwards and came into secondary contact with the East African lineage in Ethiopia, resulting in high genetic diversity in this area. In the Mediterranean regions, the genetic diversity was relatively high with numerous unique haplotypes, but almost without geographic structure. In contrast, the populations in the northern amphi-Atlantic area were extremely depauperate, suggesting very recent (postglacial) expansion into this vast area from the south.     

Molecular genetic evidence for the post-Pleistocene divergence of populations of the arctic-alpine ground beetle Amara alpina (Paykull) (Coleoptera: Carabidae)

Aim This study examines the hypothesis that the biogeographic history of a species is reflected in the distribution of molecular genetic diversity and the phylogenies of extant populations. Location Populations of arctic-alpine ground beetle Amara alpina were analysed from Beringia (Alaska and northernmost British Columbia), the Hudson Bay region, the northern Appalachian Mountains, and the central Rocky Mountains of North America. Methods Mitochondrial restriction site variation of specimens from twenty-two populations were assayed by using radioactively labelled mtDNA to probe Southern membranes containing restriction enzyme digested total DNA. Restriction sites were mapped and genetic distances were calculated by pairwise comparison of presence and absence of restriction sites. Genetic distances were used in a molecular analysis of variance and to construct a minimal spanning tree. Parsimony methods were used to investigate the phylogenetic relationships between the haplotypes. These results were compared to an existing model for postglacial dispersal based on fossil and modern occurrences of arctic-alpine beetles. Results Among the twenty-two populations, fifteen haplotypes were detected. Genetic variation within each of the four regions corresponded to that expected from the palaeontologically based model. Beringian populations were the most genetically diverse. In contrast, no restriction site variation was observed in populations from the Hudson Bay region. Intermediate amounts of variation were observed in alpine populations of the Rocky and Appalachian Mountains. Maximum parsimony and cluster analysis provide evidence that at least two ancestral haplotypes existed in the Southern refugium from which the Rocky and the Appalachian Mountains populations were founded. Main conclusions The genetic results are generally consistent with the palaeontologically based model. The diversity of Beringian populations is consistent with this region having been continuously inhabited by Amara alpina throughout the Pleistocene. The Hudson Bay region was not deglaciated until about 6000 years, and its populations have no restriction site variation. The molecular genetic data support the interpretation that the Hudson Bay region was colonized from Beringia based on the occurrence of the same haplotype in both regions.     

Phylogeography of a pearl oyster (Pinctada maxima) across the Indo‐Australian Archipelago: evidence of strong regional structure and population expansions but no phylogenetic breaks

This study investigates the genetic structure and phylogeography of a broadcast spawning bivalve mollusc, Pinctada maxima, throughout the Indo‐West Pacific and northern Australia. DNA sequence variation of the mitochondrial cytochrome oxidase subunit I (COI) gene was analysed in 367 individuals sampled from nine populations across the Indo‐West Pacific. Hierarchical AMOVA indicated strong genetic structuring amongst populations (Φ_ST = 0.372, P < 0.001); however, sequence divergence between the 47 haplotypes detected was low (maximum 1.8% difference) and no deep phylogenetic divergence was observed. Results suggest the presence of genetic barriers isolating populations of the South China Sea and central Indonesian regions, which, in turn, show patterns of historical separation from northern Australian regions. In P. maxima, historical vicariance during Pleistocene low sea levels is likely to have restricted planktonic larval transport, causing genetic differentiation amongst populations. However, low genetic differentiation is observed where strong ocean currents are present and is most likely due to contemporary larval transport along these pathways. Geographical association with haplotype distributions may indicate signs of early lineage sorting arising from historical population separations, yet an absence of divergent phylogenetic clades related to geography could be the consequence of periodic pulses of high genetic exchange. We compare our results with previous microsatellite DNA analysis of these P. maxima populations, and discuss implications for future conservation management of this species. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 632–646.     

Comparative phylogeography of three codistributed stomatopods: origins and timing of regional lineage diversification in the Coral Triangle

The Indonesian-Australian Archipelago is the center of the world's marine biodiversity. Although many biogeographers have suggested that this region is a "center of origin," criticism of this theory has focused on the absence of processes promoting lineage diversification in the center. In this study we compare patterns of phylogeographic structure and gene flow in three codistributed, ecologically similar Indo-West Pacific stomatopod (mantis shrimp) species. All three taxa show evidence for limited gene flow across the Maluku Sea with deep genetic breaks between populations from Papua and Northern Indonesia, suggesting that limited water transport across the Maluku Sea may limit larval dispersal and gene flow across this region. All three taxa also show moderate to strong genetic structure between populations from Northern and Southern Indonesia, indicating limited gene flow across the Flores and Java Seas. Despite the similarities in phylogeographic structure, results indicate varied ages of the genetic discontinuities, ranging from the middle Pleistocene to the Pliocene. Concordance of genetic structure across multiple taxa combined with temporal discordance suggests that regional genetic structures have arisen from the action of common physical processes operating over extended time periods. The presence in all three species of both intraspecific genetic structure as well as deeply divergent lineages that likely represent cryptic species suggests that these processes may promote lineage diversification within the Indonesian-Australian Archipelago, providing a potential mechanism for the center of origin. Efforts to conserve biodiversity in the Coral Triangle should work to preserve both existing biodiversity as well as the processes creating the biodiversity.     

Vicariance and dispersal effects on phylogeographic structure and speciation in a widespread estuarine invertebrate

Vicariance and dispersal can strongly influence population genetic structure and allopatric speciation, but their importance in the origin of marine biodiversity is unresolved. In transitional estuarine environments, habitat discreteness and dispersal barriers could enhance divergence and provide insight to evolutionary mechanisms underlying marine and freshwater biodiversity. We examined this by assessing phylogeographic structure in the widespread amphipod Gammarus tigrinus across 13 estuaries spanning its northwest Atlantic range from Quebec to Florida. Mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 1 phylogenies supported deep genetic structure consistent with Pliocene separation and cryptic northern and southern species. This break occurred across the Virginian-Carolinian coastal biogeographic zone, where an oceanographic discontinuity may restrict gene flow. Ten estuarine populations of the northern species occurred in four distinct clades, supportive of Pleistocene separation. Glaciation effects on genetic structure of estuarine populations are largely unknown, but analysis of molecular variance (AMOVA) supported a phylogeographic break among clades in formerly glaciated versus nonglaciated areas across Cape Cod, Massachusetts. This finding was concordant with patterns in other coastal species, though there was no significant relationship between latitude and genetic diversity. This supports Pleistocene vicariance events and divergence of clades in different northern glacial refugia. AMOVA results and private haplotypes in most populations support an allopatric distribution across estuaries. Clade mixture zones are consistent with historical colonization and human-mediated transfer. An isolation-by-distance model of divergence was detected after we excluded a suspected invasive haplotype in the St. Lawrence estuary. The occurrence of cryptic species and divergent population structure support limited dispersal, dispersed habitat distribution, and historical factors as important determinants of estuarine speciation and diversification.     

Types of oreal and oreotundral disjunctions in the western Palearctic

The cyclic changes of the Pleistocene between cold and warm periods resulted in antagonistic responses within two different groups of organisms: one expanding during the warm periods and retracting during the cold phases and another with opposed responses. The latter group is composed of so-called arctic and alpine species. These species have recently become the focus of phylogeographical research. However, we still lack a comprehensive characterization of the different types of alpine and arctic-alpine disjunctions in the western Palearctic. Such an overview might facilitate the selection of different model species to test the different patterns of disjunctions for congruences revealing their past distribution. Therefore, we list all alpine and arctic-alpine disjunction types of the western Palearctic using butterflies and moths as a model group. We distinguish between (1) endemics of the Alps (α) with strongly restricted and (β) with broader distributions; (2) alpine disjunct species (α) with perialpine disjunctions and (β) with a wide western Palearctic distribution; (3) oro-Mediterranean species; and (4) arctic-alpine disjunct species. These types of distributions and further subtypes are exemplified using chorological data of butterfly and moth species. In this context, we discuss the intraspecific differentiation and the differentiation among sibling-species within and among disjunct parts of the distribution area. We also formulate hypotheses of the distribution patterns during the last ice age which might best explain the actual patterns. Finally, we suggest some case studies of genetic analyses to test the above mentioned hypotheses.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 415–430.     

American marten (Martes americana) in the Pacific Northwest: population differentiation across a landscape fragmented in time and space

American marten (Martes americana) have a close association with mature temperate forests, a habitat that expanded throughout the Pacific Northwest as glaciers receded at the end of the Pleistocene. Similar to several other forest-associated mammals in North America (e.g. black bear), genetic analysis of the marten shows a deep phylogeographical subdivision that reflects populations with distinctive evolutionary histories. Using a suite of 14 microsatellite markers, we explored the genetic structure of marten populations in two reciprocally monophyletic clades in the Pacific Northwest identified previously as M. caurina and M. americana by mitochondrial haplotypes and morphology. Microsatellite phylogeographical patterns were congruent with mitochondrial analyses. These independent data sets shed light upon hybridization patterns, population structure and evolutionary histories. Hybridization between M. caurina and M. americana individuals was documented in two regions of sympatry (Kuiu Island in southeastern Alaska and southern Montana). Northern insular populations of M. caurina exhibited higher differentiation and lower variability relative to northern populations of M. americana. Greater divergence among M. caurina populations may reflect longer isolation and persistence in coastal forest habitat that was fragmented by rising sea level in the early Holocene. Lower differentiation among northern M. americana populations and close relationship to other continental M. americana populations may reflect more recent expansion into the Pacific Northwest and/or continued gene flow among populations. Differentiation among M. caurina populations was attributed to habitat fragmentation (i.e. rising sea level), as opposed to isolation-by-distance; oceanic straits pose significant barriers to gene flow among M. caurina populations and between populations of M. caurina and M. americana.     

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

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

Genetic consequences of Pleistocene range shifts: contrast between the Arctic, the Alps and the East African mountains

In wide-ranging species, the genetic consequences of range shifts in response to climate change during the Pleistocene can be predicted to differ among different parts of the distribution area. We used amplified fragment length polymorphism data to compare the genetic structure of Arabis alpina, a widespread arctic-alpine and afro-alpine plant, in three distinct parts of its range: the North Atlantic region, which was recolonized after the last ice age, the European Alps, where range shifts were probably primarily altitudinal, and the high mountains of East Africa, where the contemporary mountain top populations result from range contraction. Genetic structure was inferred using clustering analyses and estimates of genetic diversity within and between populations. There was virtually no diversity in the vast North Atlantic region, which was probably recolonized from a single refugial population, possibly located between the Alps and the northern ice sheets. In the European mountains, genetic diversity was high and distinct genetic groups had a patchy and sometimes disjunct distribution. In the African mountains, genetic diversity was high, clearly structured and partially in accordance with a previous chloroplast phylogeography. The fragmented structure in the European and African mountains indicated that A. alpina disperses little among established populations. Occasional long-distance dispersal events were, however, suggested in all regions. The lack of genetic diversity in the north may be explained by leading-edge colonization by this pioneer plant in glacier forelands, closely following the retracting glaciers. Overall, the genetic structure observed corresponded to the expectations based on the environmental history of the different regions.     

Phylogeography of Arabis serrata (Brassicaceae) in the Japanese Archipelago based on chloroplast DNA variations

Arabis serrata (Brassicaceae), a perennial plant widely distributed along the Japanese Archipelago, occurs in various habitats: for example, limestone zones, serpentine barrens, volcanic soils, and roadsides. It likely survived by adapting to its surrounding environment, resulting in great morphological and ecological variation. In this study, we performed a phylogeographic analysis to examine past changes in the distribution of A. serrata following climate oscillations during the Pleistocene. To cover most of A. serrata's range, leaves were collected from eight to ten individuals randomly selected from each of 37 populations in the Japanese Archipelago. Two chloroplast noncoding regions of the samples were amplified and sequenced: trnT(GGU)‐psbD and trnH(GUG)‐psbA spacers. Twenty‐five haplotypes were detected and distinguished by 31 substitutions. Four main haplotypes were observed in many populations distributed throughout the Japanese Archipelago. According to the genetic boundaries detected using the Monmonier algorithm, A. serrata is clustered into four groups, each including several populations: Hokkaido Island, northern mainland Honshu, central Japan, and western Japan. The boundaries, however, were not robust because all genetic parameters did not support the differentiation among groups. These results indicate the absence of an obvious geographic structure in the distribution of A. serrata, suggesting that this species has experienced a rapid range expansion in postglacial times.