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The 10th International Conference on Serpentine Ecology was held in Nancy, France on June 12–16, 2023. The main goals of the conference were to create a platform for the exchange of ideas and experiences and to promote scientific dialogue among scientists from numerous fields who share expertise in the study of ultramafic habitats worldwide. The proceedings of the conference are being published as two Special Issues of Ecological Research, of which this is the second. In this article, we present the major topics and provide some highlights of the contributions to the 10th International Conference on Serpentine Ecology. [ABSTRACT FROM AUTHOR]

The overabundance of sika deer has become a significant threat to plant communities across Japan. As a result of the deer overgrazing, rare plants are undergoing a demographic bottleneck, leading to a loss of genetic diversity. Genetic diversity is crucial for the reproductive success of self‐incompatible plants, and it also provides evolutionary potential, which increases their long‐term population viability. Therefore, it is essential to appropriately manage the remaining genotypes to conserve local genetic resources. In this study, we exemplify this, via a conservation genetic analysis of Parasenecio peltifolius populations impacted by deer. Genetic data revealed that the small populations confined to isolated refugial sites consisted of effectively single genets. Recent reproductive failures in these populations may be attributed to the loss of genotypic diversity. Despite the bottlenecks, the remaining genets exhibited high individual heterozygosity, which is a good indicator that they have not been affected by severe inbreeding. Hybrid simulations suggested that interpopulation outbreeding between the unique genotypes can be a viable option to promote sexual reproduction and re‐establish genetic diversity within the local populations. Establishing artificial progenies in botanical gardens can serve as a vital genetic resource for the long‐term viability of threatened P. peltifolius populations. [ABSTRACT FROM AUTHOR]

The 10th International Conference on Serpentine Ecology was held in Nancy, France on 12–16 June, 2023. As a major international scientific forum in the field of serpentine (ultramafic) ecology, this conference brings together botanists, zoologists, microbiologists, physiologists, geneticists, geologists, soil scientists, and other applied specialists studying the ecology of ultramafic rocks and soil. A notable aspect of these meetings is the multidisciplinary nature of research on ultramafic biota, including diversity, ecology, evolution, physiology, and applied research in phytotechnologies and conservation. The main goals of the conference were to create a platform for the exchange of ideas and experiences and to promote scientific dialogue among scientists from numerous fields who share expertise in the study of ultramafic habitats worldwide. In this Special Issue we present the major topics and provide some highlights of the contributions to the 10th International Conference on Serpentine Ecology. [ABSTRACT FROM AUTHOR]

Recent phylogeographical studies have revealed that refugia sometimes retain high levels of genetic heterogeneity due to multiple colonization events, a phenomenon defined as 'refugia within refugium'. In previous research, we reported a complex genetic structure within the Geranium yesoense complex, an alpine plant found in an interglacial refugium at high elevation in Central Japan, probably resulting from multiple colonization and hybridization events. However, we were unable to evaluate instances of introgression due to limited sample size. In the present study, we performed additional chloroplast genome sequencing, along with Sanger sequencing of selected chloroplast DNA regions, to elucidate the phylogenetic relationships among the refugial populations. The chloroplast genome sequence of a sample from Mt. Asama (an important refugium) was nested within the northern lineage (i.e. var. yesoense and var. pseudopratense), and haplotypes from Mt. Asama and Mt. Ibuki were also grouped with those of the northern lineage. Although our previous study suggested hybridization events between northern and southern lineages (i.e. var. nipponicum) at Mt. Asama, haplotypes from the southern lineage were not detected at range margins. This suggests that directional introgression occurred in these regions. Overall, our results further support that genetic heterogeneity within these refugia was amplified by recolonization and hybridization during past climate oscillations. [ABSTRACT FROM AUTHOR]

Plant species with overlapping distributions are expected to experience the same historical events. In contrast, species with different preferred habitat types may exhibit incongruent phylogeographic patterns because of their habitat‐dependent demographic changes in spite of their overlapping distributions. On the western side of the Japanese Archipelago, boreal forest and non‐forest vegetation were dominant during the last glacial period; subsequently, temperate forests expanded, and open vegetation (e.g., grasslands) decreased. Such vegetation shifts can result in incongruent phylogeographic patterns among temperate forest and grassland species; however, few phylogeographic studies have investigated this hypothesis. Here, we evaluated the phylogeographic structure of two related Geranium species that occur in grassland (Geranium krameri) and temperate forest (Geranium shikokianum) habitats using chloroplast genome sequencing and nuclear genome‐wide single‐nucleotide polymorphisms genotyping. The phylogeographic structure was stronger for the temperate forest species than the grassland species, despite its currently scattered distribution for grassland species. The observed patterns indicate that the phylogeographic histories of these species were influenced by their habitat configurations since the last glacial period. During the ice age, grasslands in Japan were much more widespread than today; this would have enabled the grassland species to form a continuous distribution, leading to low divergence among regional populations. In contrast, the significant genetic divergence within the forest species can be attributed to the glacial isolation of regional populations. Our genetic results suggest that vegetation transitions have variously controlled the population dynamics of two species with overlapping distributions. [ABSTRACT FROM AUTHOR]

Geranium erianthum is an alpine plant growing in dry habitats, which is distributed from East Asia to northern coastal regions of the northern Pacific. The ice-free area around the current Bering Strait (i.e., Beringia) had played an important role in range expansion into neighboring regions such as East Asia and North America for some alpine plants. However, recent studies suggest that some alpine plants in snowbed environment spread from East Asia to northern coastal regions of the northern Pacific. In this study, we investigated phylogenetic relationships and genetic differentiations among populations of G. erianthum and the related species using the chloroplast genome and single-nucleotide polymorphisms, to evaluate the alternative biogeographic hypotheses in which region of Beringia, British Columbia or East Asia is probable for its distributional origin. Range reconstruction based on phylogenetic tree of chloroplast genome indicated G. erianthum and related species originated in East Asia, from where G. erianthum migrated eastward into Beringia and British Columbia. In addition, nuclear genome-wide SNPs indicated that no significant genetic differentiation was detected between Japanese and Beringian populations. The lack of genetic differentiation suggests that the current range of G. erianthum resulted from rapid range expansion during the latter period of the last glacial era. Overall, the East Asian refugium hypothesis was applicable to the alpine plant G. erianthum in dry habitat, indicating that range expansion pattern from East Asia into the northern Pacific may be more common rather than limited for snowbed species. [ABSTRACT FROM AUTHOR]

Aim: The Sino‐Japanese Floristic Region has extremely high species diversity with respect to temperate plants; however, the reasons for this diversity are poorly understood because most studies have only considered geographic isolation caused by climatic oscillations. In some plant groups, high floral trait diversity and uneven species diversity between insular systems and the continental area suggest other factors may have important roles too. The primary purpose of this study is to reveal how abiotic and biotic factors have shaped the species diversity anomaly of Heterotropa between the insular systems and the continental area. Location: The Sino‐Japanese Floristic Region. Taxon: Section Heterotropa (genus Asarum; Aristolochiaceae). Methods: Using ddRAD‐seq and chloroplast genome data, we built a time‐calibrated phylogenetic tree including 79 species. We estimated the patterns of floral traits (flowering time and floral size) evolution using macroevolutionary modelling, and tested the correlation of speciation rate with the trait evolution rates. Finally, we estimated the isolation factors of all taxa pairs and sister‐taxa pairs based on distribution range and floral traits. Results: Phylogenetic analysis indicated that Heterotropa was diverged into two clades (continental clade and insular clade) in the Miocene, and the major subclades corresponded to geographic entities. Most rate shifts accelerating floral trait's evolution occurred during the Pleistocene period. Evolution rate of floral traits showed positive correlation with the speciation rate. Large proportion of taxa in the insular clade are distributed allopatrically. Several sister pairs showed floral trait divergence with geographic overlap. Main Conclusions: The diversification of Heterotropa appears to have been triggered by geographic and climatic events, and subsequent repeated floral trait evolution with and without geographic isolation. Furthermore, the high species diversity in the insular systems would have been formed by the repeated range fragmentations and contractions. Our study demonstrates the importance of multidimensional studies to understand the diversification process of temperate plants in the Sino‐Japanese Floristic Region. [ABSTRACT FROM AUTHOR]

Premise: The genetic structure between plant populations is facilitated by the spatial population arrangement and limited dispersal of seed and pollen. Saxifraga acerifolia, a local endemic species in Japan, is a habitat specialist that is confined to waterfalls in riparian environments. Its sister species, Saxifraga fortunei, is a generalist that is widely distributed along riverbanks. Here, we examined sympatric populations of the two Saxifraga species to test whether the differences in habitat preference and colonization process influenced regional and local genetic structures. Methods: To reveal genetic structures, we examined chloroplast microsatellite variations and genome‐wide nucleotide polymorphisms obtained by genotyping by sequencing. We also estimated the gene flow among and within populations and performed landscape genetic analyses to evaluate seed and pollen movement and the extent of genetic isolation related to geographic distance and/or habitat differences. Results: We found strong genetic structure in the specialist S. acerifolia, even on a small spatial scale (<1 km part); each population on a different waterfall in one river system had a completely different predominant haplotype. By contrast, the generalist S. fortunei showed no clear genetic differentiation. Conclusions: Our findings suggest that the level of genetic isolation was increased in S. acerifolia by the spatially fragmented habitat and limited seed and pollen dispersal over waterfalls. Habitat differentiation between the sister taxa could have contributed to the different patterns of gene flow and then shaped the contrasting genetic structures. [ABSTRACT FROM AUTHOR]

Recent studies have found that geographical fragmentation and recurrent colonization result in complex genetic structures in refugial areas. This phenomenon, known as 'refugia within refugium', has been identified from many geographical locations. In Japan, the high-elevation mountains of central Honshu provided an interglacial refugium for alpine plants. Here we focused on the Geranium yesoense complex, which exhibits increased morphological variation in the refugial area, to determine whether this variation was shaped by recurrent colonization, range fragmentation or phenotypic changes independent of population history. We analysed single nucleotide polymorphism data and chloroplast genome sequences. Diversification in the G. yesoense species complex occurred in the mid-Pleistocene. The varieties are distinct entities and suggest the presence of a genetic cluster with highly disjunct distributions, occurring both in northern Japan and in southern refugial areas in central Honshu. Demographic analysis suggests that a single ancestral variety (var. nipponicum) evolved in the alpine region of central Honshu, and that subsequent migration from one of the two diverged northern varieties (var. pseudopratense) led to secondary contact with var. nipponicum during the last glacial period. Recolonization into refugial populations in central Honshu and hybridization between diverged populations have resulted in complex genetic structures among refugial populations. [ABSTRACT FROM AUTHOR]

Background and Aims Contrasting life-history traits can evolve through generations of dwarf plant ecotypes, yet such phenotypic changes often involve decreased plant size and reproductive allocation, which can configure seed dispersal patterns and, subsequently, population demography. Therefore, evolutionary transitions to dwarfism can represent good study systems to test the roles of life-history traits in population demography by comparing genetic structure between related but phenotypically divergent ecotypes. Methods In this study, we examined an ecotypic taxon pair of the world's smallest goldenrod (stem height 2.6 cm) in alpine habitats and its closely related lowland taxon (30–40 cm) found on Yakushima Island, Japan. Genetic variation in chloroplast DNA sequences, nuclear microsatellites and genome-wide single-nucleotide polymorphisms were used to investigate 197 samples from 16 populations, to infer the population genetic demography and compare local genetic structure of the ecotypes. Key Results We found a pronounced level of genetic differentiation among alpine dwarf populations, which were much less geographically isolated than their lowland counterparts. In particular, several neighbouring dwarf populations (located ~500 m apart) harboured completely different sets of chloroplast haplotypes and nuclear genetic clusters. Demographic modelling revealed that the dwarf populations have not exchanged genes at significant levels after population divergence. Conclusions These lines of evidence suggest that substantial effects of genetic drift have operated on these dwarf populations. The low-growing stature and reduced fecundity (only 3.1 heads per plant) of the dwarf plants may have reduced gene flow and rare long-distance seed dispersal among habitat patches, although the effects of life-history traits require further evaluation using ecological approaches. [ABSTRACT FROM AUTHOR]

Premise: Light is essential for plants, and local populations exhibit adaptive photosynthetic traits depending on their habitats. Although plastic responses in morphological and/or physiological characteristics to different light intensities are well known, adaptive divergence with genetic variation remains to be explored. This study focused on Saxifraga fortunei (Saxifragaceae) growing in sun‐exposed and shaded habitats. Methods: We measured the leaf anatomical structure and photosynthetic rate of plants grown in their natural habitats and in a common greenhouse (high‐ and low‐intensity light experimental sites). To assess differences in ecophysiological tolerance to high‐intensity light between the sun and shade types, we evaluated the level of photoinhibition of photosystem II and the leaf mortality rate under high‐intensity light conditions. In addition, population genetic analysis was conducted to investigate phylogenetic origins. Results: Clear phenotypic differences were found between the sun and shade types despite their recent phylogenetic origin. The leaf anatomical structure and photosynthetic rate showed plastic changes in response to growing conditions. Moreover, the sun type had a well‐developed palisade parenchyma and a higher photosynthetic rate, which were genetically fixed, and a lower level of photoinhibition under high‐intensity light. Conclusions: Our findings demonstrate that light intensity is a selective pressure that can rapidly promote phenotypic divergence between the sun and shade types. While phenotypic changes in multiple photosynthetic traits were plastic, genetic divergence in specific traits related to adaptation to high‐intensity light would be fundamental for ecotypic divergence to different light regimes. [ABSTRACT FROM AUTHOR]

The often patchy distribution of serpentine geology can lead to abrupt changes in soil and microclimates. Thus, serpentine areas provide an ideal natural setting to understand how divergent selection drives the process of local adaptation in edaphically specialized plants. When the serpentine ecotype is surrounded by a related nonserpentine ecotype, a balance of natural selection and potential gene flow should maintain the different ecotypes over very short distances. We aimed to reveal the mechanisms allowing soil ecotypes of a goldenrod species to co‐occur sympatrically in Japan.We performed field surveys to characterize microenvironments and flowering phenology of each ecotype, common garden and reciprocal transplant experiments and artificial crossing, and population genetic analysis to investigate the levels of genetic differentiation between ecotypes.Growth chamber experiments show that serpentine plants showed lower specific leaf area (SLA) and greater resource allocation to their root systems than did their nonserpentine counterparts, a potential adaptation to drier and less fertile soil condition in serpentine habitats. Reciprocal transplant studies demonstrated a clear pattern of local adaptation in the plant growth rate. Importantly, serpentine populations completed flowering by midsummer versus late summer in nonserpentine plants. This pattern is consistent with the hypothesis that early flowering ensures reproductive success, before the microclimatic conditions becomes severe in open habitats. Although prezygotic isolation was a strong barrier to gene flow, genetic differentiation was very low, indicating a recent origin for the serpentine ecotypes and/or gene flow at low frequencies.Synthesis. The findings indicate that the early flowering times of serpentine ecotypes, which would have been selected for by microclimates in serpentine areas, can play roles in local adaptation, but also population isolation via a by‐product of diverged reproductive timings. This study contributes to general understanding of the initial stages of plant ecological speciation under potential gene flow in very small geographic scales. Without any effective geographic barriers, the Solidago soil ecotypes were maintained by divergent selection imposed by microclimatic conditions in alternative habitats. Importantly, the divergent flowering time played dual roles of a local adaptation to each habitat and assortative mating to further restrict gene flow between populations. [ABSTRACT FROM AUTHOR]

The eastern Australian temperate biota harbours many plants with fragmented geographic ranges distributed over 1000s of kilometres, yet the spatial genetic structure of their populations remains largely unstudied. In this study, we investigated genetic variation of the nuclear internal transcribed spacer (ITS) and chloroplast DNA sequences to disentangle the phylogeography of two widely distributed but highly fragmented eastern Australian fire-sensitive temperate conifers: Callitris oblonga (12 populations and 121 individuals) and C. rhomboidea (22 populations and 263 individuals). The three highly disjunct populations of C. oblonga all had unique chloroplast and ITS haplotypes consistent with the classification of these three populations as distinct subspecies. Molecular dating indicates that divergences of these populations occurred pre- to mid- Pleistocene (2.66 to 1.08 mya). Callitris rhomboidea showed greater diversity of chloroplast haplotypes which was strongly phylogeographically structured (Gst = 0.972), with haplotypes unique to specific geographic regions. ITS haplotype diversity was far higher than in C. oblonga with 38 haplotypes displaying high geographic structuring (Gst = 0.387) with many population-specific haplotypes. A phylogeographic break was identified between populations north and south of eastern Victoria dated at 0.43–0.47 mya. In both species, the strong genetic structuring of both chloroplast and ITS haplotypes provides evidence that their widespread ranges have resulted from long term persistence in low fire frequency refugia combined with poor dispersal. Any loss of populations due to increasing fire frequency or habitat loss is likely to result in a reduction of genetic diversity. [ABSTRACT FROM AUTHOR]

Serpentine, a chemically extreme substrate with a discontinuous distribution, supports a high proportion of endemic plant species. The evolutionary pathway of edaphic endemics in isolated areas may be of parallel origin (convergence), but this can be difficult to detect due to similar sets of phenotypic traits repeatedly selected for by the extreme conditions of serpentine environments. Testing the alternative histories of single origin vs. parallel evolution in serpentine plant populations provides insight into the ability of plants to adapt to extreme serpentine environments and to disperse between isolated serpentine areas. In this study, we focused on the herb Picris hieracioides L. (Asteraceae), which includes early-flowering serpentine populations surrounded by later flowering, non-serpentine populations on Hokkaido Island, Japan. We performed population genetic analysis based on genome-wide SNPs markers and quantified temporal overlap of flowering times under natural conditions. Phylogeographic analysis confirmed the occurrence of two genetic groups, corresponding to the serpentine and non-serpentine races. Although the two races were found to occur in close parapatry over multiple paired soil sites, little evidence for hybridization was detected. The flowering times of the two races showed significant divergence, with flowering peaks separated by more than 1 month. Overall, this study supported the single origin of serpentine Picris populations, and showed the role of divergent flowering time as a strong prezygotic barrier to maintain the edaphic races over short spatial distances. [ABSTRACT FROM AUTHOR]

• Background and Aims The processes and mechanisms underlying lineage diversification are major topics in evolutionary biology. Eurasian goldenrod species of the Solidago virgaurea complex show remarkable morphological and ecological diversity in the Japanese Archipelago, with ecotypic taxa well adapted to specific environments (climate, edaphic conditions and disturbance regimes). The species complex is a suitable model to investigate the evolutionary processes of actively speciating plant groups, due to its ability to evolve in relation to environmental adaptation and its historical population dynamics. • Methods Two chloroplast markers, 18 nuclear microsatellite markers and ddRAD-sequencing were used to infer population genetic demography of S. virgaurea complex with its related species/genera. • Key Results Our analysis showed that populations in Japan form an evolutionary unit, which was genetically diverged from adjacent continental populations. The phylogenetic structure within the archipelago strongly corresponds to the geography, but interestingly there is no concordance between genetic structure and ecotypic boundaries; neighbouring populations of distinct ecotypes share a genetic background. • Conclusions We propose that the traits specific to the ecotypic entities are maintained by natural selection or are very recently generated and have little effect on the genomes, making genome-wide genetic markers unsuitable for detecting ecotypic differentiation. Furthermore, some sporadically distributed taxa (found as rheophytes and alpine plants) were repeatedly generated from a more widespread taxon in geographically distant areas by means of selection. Overall, this study showed that the goldenrod complex has a high ability to evolve, enabling rapid ecological diversification over a recent timeframe. [ABSTRACT FROM AUTHOR]

The genus Tanakaea is a plant genus that consists of one or two evergreen herbaceous species in Japan and China. As rithophytic plant species occur on shaded rocks, the populations are usually isolated and sporadically found in disjunct areas. To evaluate the genetic structure of the species at multiple spatial scales, 10 nuclear and mitochondrial microsatellite markers were developed. The novel markers showed high genetic variations (two to 15 alleles and He from 0.400 to 0.894). Clonal samples were identified with the probability of identity of 9.0E-8. When evaluated with 11 populations in Japan, significant genetic differentiation between regional population groups was detected ( FST = 0.313 between Shikoku and Honshu islands), suggesting they have long been isolated from each other. Overall, these markers will be useful for population genetic research to investigate clonal structure and genetic diversity and levels of genetic differentiation between the geographically isolated populations. [ABSTRACT FROM AUTHOR]

Early stages of ecological speciation can create populations with an ecology and reproduction timing distinct from those of related populations. Landscape genetic models incorporating environmental heterogeneity and population-specific reproductive traits enable the processes of population genetic differentiation to be inferred., We investigated genome-wide genetic variation in ecotypic populations of Solidago virgaurea sensu lato, a herbaceous plant inhabiting a wide range of habitats (woodlands, serpentine barrens and alpine grasslands) and displaying remarkable variation in flowering time., Simultaneous evaluation of environmental factors revealed an overwhelming effect of soil type differences on neutral genetic differentiation, compared with elevational differences. This result probably reflects the abrupt environmental changes generated by geological boundaries, whereas mountain slopes exhibit clinal changes, facilitating gene exchange between neighbouring populations. Temporal isolation was positively associated with genetic differentiation, with some early-flowering serpentine populations having allele frequencies distinct from adjacent nonserpentine populations., Overall, this study highlights the importance of ecological processes and of evolution of flowering time to promote genetic differentiation of S. virgaurea populations in a complex landscape. [ABSTRACT FROM AUTHOR]

Plant species distributed along wide elevational or latitudinal gradients show phenotypic variation due to their heterogeneous habitats. This study investigated whether phenotypic variation in populations of the Solidago virgaurea complex along an elevational gradient is caused by genetic differentiation. A common garden experiment was based on seeds collected from nine populations of the S. virgaurea complex growing at elevations from 1,597 m to 2,779 m a.s.l. on Mt. Norikura in central Japan. Population genetic analyses with microsatellite markers were used to infer the genetic structure and levels of gene flow between populations. Leaf mass per area was lower, while leaf nitrogen and chlorophyll concentrations were greater for higher elevations at which seeds were originally collected. For reproductive traits, plants derived from higher elevations had larger flower heads on shorter stems and flowering started earlier. These elevational changes in morphology were consistent with the clines in the field, indicating that phenotypic variation along the elevational gradient would have been caused by genetic differentiation. However, population genetic analysis using 16 microsatellite loci suggested an extremely low level of genetic differentiation of neutral genes among the nine populations. Analysis of molecular variance also indicated that most genetic variation was partitioned into individuals within a population, and the genetic differentiation among the populations was not significant. This study suggests that genome regions responsible for adaptive traits may differ among the populations despite the existence of gene flow and that phenotypic variation of the S. virgaurea complex along the elevational gradient is maintained by strong selection pressure. [ABSTRACT FROM AUTHOR]

EST-SSR markers were developed for A sarum sakawanum var. stellatum to evaluate the genetic diversity and genetic structure of series S akawanum and assess their utility in other series in the genus Asarum. A total of 1864 primer pairs, including 1864 tri-nucleotide SSR motifs, were designed based on transcriptome data. Of the 96 primers tested, 17 loci were successfully amplified and polymorphic in series S akawanum taxa. Furthermore, all these loci were successfully amplified in A. takaoi, whereas only 10 loci were amplified in the more phylogenetically distant A . pellucidum. For populations of A . sakawanum var. stellatum, the values of observed and expected heterozygosity ranged from 0.261 to 0.957 and 0.317 to 0.881, respectively. These newly developed EST-SSR markers will be used in population genetic studies of series S akawanum to infer the evolutionary history and genetic diversity of these series, many of which are endangered in Japan. [ABSTRACT FROM AUTHOR]

Premise of the study: High‐throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms. Methods: Chloroplasts were enriched using a high‐salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high‐throughput sequencing. Results: Using this simple method, significant enrichment of chloroplast DNA‐derived reads was attained, allowing deep sequencing of chloroplast genomes. As an example, the chloroplast genome of the conifer Callitris sulcata was assembled, from which polymorphic microsatellite loci were isolated successfully. Discussion: This chloroplast enrichment method from small amounts of plant tissue will be particularly useful for studies that use sequencers with relatively small throughput and that cannot use large amounts of tissue (e.g., for endangered species). [ABSTRACT FROM AUTHOR]

Decreases in pollinator abundance may particularly constrain plants that lack floral rewards, since they are poor competitors for pollinators in the plant community. Here, we documented the pollination ecology of a rewardless orchid, Calanthe reflexa Maxim., and examined effects of forest understory degradation by deer browsing on pollination success of the species in the light of a change in the abundance of neighboring flowering plants in 2010 and 2011. Bombus species were the only pollinators at each site and the flowering phenology of C. reflexa did not overlap with that of other rewarding plants. Pollinator visit rates (assessed by time-lapse photography), and pollinia removal rate were higher in the undegraded understory site than the degraded site in both years, while the fruit set ratio did not differ between the sites in 2011. Coverage by neighboring flowering plants was extremely low in the degraded site. Our results suggest that, although its flowering phenology and consequently lower interspecific competition of C. reflexa with rewarding plants for attracting bumblebees, neighboring flowering plants may play an important role for maintaining the visitation frequency of bumblebees of C. reflexa and contribute to its pollination success. [ABSTRACT FROM AUTHOR]

Climate and fire are the key environmental factors that shape the distribution and demography of plant populations in Australia. Because of limited palaeoecological records in this arid continent, however, it is unclear as to which factor impacted vegetation more strongly, and what were the roles of fire regime changes owing to human activity and megafaunal extinction (since ca 50 kya). To address these questions, we analysed historical genetic, demographic and distributional changes in a widespread conifer species complex that paradoxically grows in fire-prone regions, yet is very sensitive to fire. Genetic demographic analysis showed that the arid populations experienced strong bottlenecks, consistent with range contractions during the Last Glacial Maximum (ca 20 kya) predicted by species distribution models. In southern temperate regions, the population sizes were estimated to have been mostly stable, followed by some expansion coinciding with climate amelioration at the end of the last glacial period. By contrast, in the flammable tropical savannahs, where fire risk is the highest, demographic analysis failed to detect significant population bottlenecks. Collectively, these results suggest that the impact of climate change overwhelmed any modifications to fire regimes by Aboriginal landscape burning and megafaunal extinction, a finding that probably also applies to other fire-prone vegetation across Australia. [ABSTRACT FROM AUTHOR]

Range shifts during the Pleistocene shaped the unique phylogeographical structures of numerous species. Accompanying species migration, sister taxa may have experienced multiple introgression events. Here, we report the signature of introgression events in multiple areas in Schizocodon, herbs endemic to Japan, using amplified fragment length polymorphism ( AFLP) fingerprinting and plastid DNA haplotyping in 48 populations. Although the present distributions of S. soldanelloides and S. ilicifolius are mainly allopatric, the species share plastid DNA haplotypes in each region (north-eastern, north-central, south-central and south-western Japan); in contrast, the specific groups were highly supported by AFLP analyses. These results support the occurrence of multiple introgression events in Schizocodon. Notably, the disjunct plastid haplotypes found only in S. ilicifolius var. intercedens suggest complete plastid DNA replacement at local areas from S. soldanelloides into S. ilicifolius var. ilicifolius. Furthermore, we found that S. soldanelloides experienced range contraction and expansion during glacial and interglacial cycles based on mismatch distribution analysis and ecological niche modelling. Based on several pieces of evidence, our study supports the idea that historical range shifts associated with Pleistocene climatic oscillations favoured multiple and regional introgression events in Schizocodon. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173, 46-63. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We investigated the biogeographic history of Kalopanax septemlobus, one of the most widespread temperate tree species in East Asia, using a combined phylogeographic and palaeodistribution modelling approach. Range-wide genetic differentiation at nuclear microsatellites ( G′ST = 0.709; 2205 samples genotyped at five loci) and chloroplast DNA ( GST = 0.697; 576 samples sequenced for 2055 bp at three fragments) was high. A major phylogeographic break in Central China corresponded with those of other temperate species and the spatial delineation of the two temperate forest subkingdoms of East Asia, consistent with the forests having been isolated within both East and West China for multiple glacial-interglacial cycles. Evidence for multiple glacial refugia was found in most of its current range in China, South Japan and the southernmost part of the Korean Peninsula. In contrast, lineage admixture and absence of private alleles and haplotypes in Hokkaido and the northern Korean Peninsula support a postglacial origin of northernmost populations. Although palaeodistribution modelling predicted suitable climate across a land-bridge extending from South Japan to East China during the Last Glacial Maximum, the genetic differentiation of regional populations indicated a limited role of the exposed sea floor as a dispersal corridor at that time. Overall, this study provides evidence that differential impacts of Quaternary climate oscillation associated with landscape heterogeneity have shaped the genetic structure of a wide-ranging temperate tree in East Asia. [ABSTRACT FROM AUTHOR]

* Premise of the study: We developed simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) for Callitris columellaris sensu lato (s.l.) to elucidate population genetic structure and detect outlier loci by genome scan. * Methods and Results: mRNA from an individual seedling was subjected to cDNA synthesis and then de novo pyrosequencing. Two hundred and nineteen primer pairs bordering sequence regions were designed from the obtained sequence data. In total, 52 showed polymorphism within 16 individuals representative of the species' entire range, with the number of alleles per locus and expected heterozygosity ranging from two to 10 and 0.06 to 0.84, respectively. * Conclusions: The EST-SSR markers developed in this study will be useful for evaluating the range-wide genetic structure of C. columellaris s.l. and detecting outlier loci under selection, as well as providing useful markers to investigate the conservation genetics and reproductive ecology of the species. [ABSTRACT FROM AUTHOR]

We attempted to clarify how coastal lands temporarily exposed during the last glacial maximum (LGM) contributed to the northward colonisation of Kalopanax septemlobus (Thunb. ex Murray) Koidzumi during the postglacial period in the Japanese Archipelago. Distribution records in 30-arc-s pixels were related to bioclimate variables using the maximum entropy technique to model the ecological niche of this species. Bioclimatic conditions in the exposed coastal lands during the LGM were reconstructed based on simulated palaeoclimate and fine-resolution marine topography. Potential distribution ranges were then estimated under the climatic conditions during the LGM, mid-Holocene and the present. The ecological niche of this species was influenced mainly by the temperature component of the bioclimates, leading to northward range shift after the LGM as the climate warmed. On average, 26% of the potential range of K. septemlobus during the LGM was located on the exposed seafloor. The northern edges of the species range on both sides of Honshu Island were estimated by up to several hundred kilometres farther north, when compared to the prediction assuming no sea level change. Application of ecological niche modelling provided new insight into the role of exposed seafloor as cryptic glacial refugia for this species, which has never been evidenced by fossil records. In a temperate island system characterised by long coastlines, the northern exposed seafloor would have been more important in terms of harbouring the putative source populations for northward directional colonisation during the postglacial period. [ABSTRACT FROM AUTHOR]

[Display omitted] • The Japanese population diverged from the Eurasian population in the late Miocene. • Northern and Southern regional clades were identified in Japan. • Ecotypic taxa specialized in the various habitats belonged to the southern clade. • Phenotypic diversification occurred especially in the leading-edge populations. • Alpine and riverside ecotypic taxa appeared to have developed in parallel. Phenotypic polymorphism within a species is a notable phenomenon in evolutionary biology to understand the process of adaptive speciation and other historical events. The Saxifraga fortunei complex is a widespread herb found in East Asia. It includes several ecotypic taxa corresponding to their habitat environments. The distribution of the various ecotypes in a limited area of the Japanese Archipelago makes the species a suitable model to investigate the impact of population demographic history and natural selection on lineage diversification. Here, Sanger-based sequencing was used to estimate the divergence timeframe between populations of the Eurasian continent and Japan. Genome-wide SNPs obtained by ddRAD sequencing were used to investigate the phylogeographic origins of ecotypic taxa. The phylogenetic analyses revealed the divergence of the Japanese population from the continental population in the late Miocene. Two distinct regional clades of North and South Japan were identified; phenotypic diversification was evident only in the southern clade. The South Japan clades displayed a historical distribution expansion from north to south. The phenotypic variations appeared to have generated during the expansion. The ecotypic boundaries were incongruent with the genetic grouping. We propose that morphological and ecological specialization in Japanese populations was repeatedly generated by local natural selection. [ABSTRACT FROM AUTHOR]

Callitris sulcata (Parl.) Schltr. (Cupressaceae) is a conifer species endemic to the ultramafic massif of southern New Caledonia. This species occurs on lowland gallery rainforests, usually close to rivers, and grows as thickets or scattered with other tree species (Farjon, 2005). Total population size is estimated to be less than 2500 individuals, and the species is recognized as endangered by the International Union for Conservation of Nature (IUCN) Red List (Thomas, 2010). An ex situ propagation program is being undertaken to secure the wild populations, but there is no genetic information on how much species-wide genetic diversity the ex situ populations can capture and how one can manage plants derived from different river systems. Thus, there is an urgent need for development of genetic markers useful for conservation genetics. [ABSTRACT FROM AUTHOR]

The article presents a case study related to 61-year-old man with an 18-year history of gout has presented to our hospital with left knee pain. Topics include the physical examination has revealed inflammatory changes in the left knee, large subcutaneous nodules in the first metatarsophalangeal (MTP) joints bilaterally, and the radiography of the feet revealed bone erosion, overhanging has calcified edges in first MTP joints, and spurs in first metatarsal bones with soft tissue thickening.

Aim: Although the evolution of island endemic plants has long been investigated, the majority of such studies have focused on species with remarkable levels of morphological variation and on islands substantially far from the mainland. Endemic plants on nearshore oceanic islands have received less attention. We investigate the population genetic structure and dynamics in plants endemic to nearshore and recently formed oceanic islands and examined the possibility of multiple colonizations onto the islands. Location: Japanese mainland Honshu and the adjacent Izu Islands. Taxon Solidago virgaurea (Asteraceae). Methods: Sixteen and nine populations of S. virgaurea complex were sampled from the mainland and islands respectively; phylogeographical and population genetics analyses, including Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis and Discrete Phylogeographic Approach (DPA) to trace the history of colonization events onto the islands, were performed using plastid DNA and nuclear microsatellite DNA variations. Results: Phylogenetically close plastid DNA haplotypes were shared between the mainland and islands, although the populations of S. virgaurea from different islands tended to exhibit phylogenetically distinct haplotypes. Admixture analyses based on nuclear DNA variations revealed distinct genetic structures between the mainland and island populations. Gene flow among islands is restricted but may partially offset genetic drift on each island. Main conclusions The genetic structure observed in this study may not have originated from a single dispersal event and successive expansion but rather from at least three colonization events and subsequent gene flow among island populations. Based on the nuclear DNA variations, the Izu Island populations of S. virgaurea are genetically distinct from the mainland ones. Repeated colonization events may have provided sufficient genetic diversity, which would generally be susceptible to founder effects and exert a driving force for evolutionary adaptation, to these oceanic island populations. [ABSTRACT FROM AUTHOR]

Plant dwarfism, a syndrome characterised by a significant reduction in plant height and organ size, is a widely observed pattern of stress‐tolerant life‐form evolution that results from local adaptation to harsh environmental conditions. The drivers of assemblage‐level dwarfism have primarily been attributed to abiotic factors, such as low temperature, aridity, poor soil fertility or frequent fires. While biotic factors such as grazing pressure from herbivores can contribute to the establishment of plant dwarfism, these factors have rarely been tested at assemblage levels.Focusing on a dwarf plant assemblage comprising over 80 taxa on a small continental island in Japan with a high deer density, we hypothesised that historical deer grazing could also be a factor contributing to the large‐scale convergent evolution of dwarfism.To test this hypothesis, we measured the size of 1908 individual plants of 40 taxa pairs, comprising both palatable and unpalatable pairs from the island and their counterpart taxa from neighbouring regions, and sought to assess which factors (i.e. low solar radiation, estimated divergence time, low nutrient conditions and grazing pressure from deer) may have contributed to the formation of the dwarf plant assemblage on the island. We also performed genetic analysis to infer the time frames for the establishment of dwarf taxa.Statistical analyses revealed that plant size was significantly reduced mainly among the palatable taxa growing on the island, with preferential grazing by deer being identified as the most significant factor influencing plant size. Furthermore, genetic analyses revealed that dwarf ecotypes may have evolved over tens of thousands of years.Synthesis: To the best of our knowledge, this study is the first to demonstrate that interactions with herbivores can shape the assemblage‐level convergence of plant dwarfism. These findings enhance our current understanding of the formation of plant functional diversity. [ABSTRACT FROM AUTHOR]

Eleven native Geranium species have been reported in Japan, several of which include infraspecific taxa. Although phylogenetic analyses have been conducted using conventional methods (i.e., chloroplast fragment and ribosomal DNA sequencing), relationships at the infraspecific level have not been elucidated due to a lack of genetic polymorphisms. We collected specimens of 22 Geranium taxa from Japan and peripheral areas (e.g., mainland China, South Korea, Russia, and Taiwan), and performed detailed phylogenetic analyses using chloroplast genome sequencing and genome-wide single-nucleotide polymorphisms. Some discrepancies were observed between the current taxonomy and the phylogenetic relationships elucidated in our analyses. The Geranium tripartitum complex was found to be paraphyletic, and Geranium onoei f. yezoense, which is synonym of Geranium reinii, was found to be more closely related to Geranium erianthum than to G. reinii. In particular, G. tripartitum var. hastatum located at intermediate position between Geranium thunbergii and Geranium wilfordii in the network analysis. Therefore, we suggest that G. tripartitum var. hastatum should be treated as an independent species, and that G. onoei f. yezoense should be transferred to G. erianthum. [ABSTRACT FROM AUTHOR]

Aim: Description of the driving forces for genetic divergence is important for understanding spatial pattern of biodiversity and development of conservation plans. Paleo‐climate, geographical barriers and habitat heterogeneity are considered to be the main influential factors; however, an integrative study is still lacking to reveal their interactions. Location: Eastern North America. Methods: Here, we generated MIG‐seq SNPs of 403 Sanguinaria canadensis samples and seven plastome data. The methods of phylogeography and landscape genomics were applied to infer their genetic divergence, demography, species distribution modelling, ecological differentiation and local adaptation. Results: We identified three distinct genetic lineages corresponding to geographical distributions isolated by the Appalachian Mountains and the Mississippi River. Ecological niche modelling and population demographic inference demonstrated that the response of S. canadensis to Pleistocene climate changes was consistent with the pattern of southward contraction during the ice age and northward recolonization during the inter−/postglacial period. Isolation in multiple southern refugia was a key factor resulting in the genetic divergence, whereas secondary contact triggered by repeated range shifts allowed gene flow among different lineages. A greater effect of isolation‐by‐environment than isolation‐by‐distance was founded, which suggested heterogeneous environment was also a promotor of genetic differentiation. Candidate adaptive loci related to transposable elements were identified under the influence of divergent environmental selection. Ecological niche divergence also reflected adaptation to different environments. Main Conclusions: This study revealed that genetic divergence has occurred within S. canadensis populations under the combined effect of paleo‐climate, geographical barriers and habitat heterogeneity, and emphasized the necessity of establishing different conservation units in future biological conservation and management work. [ABSTRACT FROM AUTHOR]

The tribe Neottieae (Orchidaceae subfam. Epidendroideae) represents an excellent potential system for understanding plastome evolution in orchids. The tribe includes about 100 species with six recognized genera and includes both chlorophyllous and achlorophyllous taxa. Previously published Neottieae plastomes have revealed a complicated history of gene loss, particularly ndh gene loss, as well as plastome structural changes in achlorophyllous taxa. However, the plastome structure of most Neottieae taxa remains unknown. Here we investigate plastome structure in two newly sequenced Neottia species (N. suzukii and N. japonica) and characterize sequence divergence among Neottieae plastomes. We sequenced and analysed the complete plastomes of three individuals of two Neottia species (two individuals of N. japonica and one individual of N. suzukii) and compared them to seven additional published Neottia plastomes. The total genome lengths of the plastomes of N. japonica and N. suzukii ranged from 156,978 to 157,326 bp. The newly sequenced plastomes possessed the typical structure and gene content of angiosperm plastomes. Phylogenetic analyses based on complete plastomes and the nuclear internal transcribed spacer (ITS) showed that N. japonica and N. suzukii form a clade, but the two accessions of N. japonica were in phylogenetically incongruent positions in ITS vs plastome trees. Among all three newly sequenced Neottia plastomes, five regions (ndhH-ndhA spacer, ndhA intron, ycf3 intron, atpF intron, and trnL-ndhB spacer) showed high nucleotide divergence values (> 0.15), and are therefore considered useful molecular markers for future phylogenetic and phylogeographic studies of Neottia. [ABSTRACT FROM AUTHOR]

Premise: Snow is an important environmental factor affecting plant distribution. Past changes in snowfall regimes may have controlled the demographies of snow‐dependent plants. However, our knowledge of changes in the distribution and demographies of such plants is limited because of the lack of fossil records. Methods: Population genetic and landscape genetic analyses were used to investigate the response of population dynamics of Arnica mallotopus (Asteraceae)—a plant confined to heavy‐snow areas of Japan—to changes in snowfall regimes from the Last Glacial Period to the Holocene. Results: The population genetic analysis suggested that the four geographic lineages diverged during the Last Glacial Period. The interaction between reduced snowfall and lower temperatures during this period likely triggered population isolation in separate refugia. Subpopulation differentiation in the northern group was lower than in the southern group. Our ecological niche model predicted that the current distribution was patchy in the southern region; that is, the populations were isolated by topologically flat and climatically unsuitable lowlands. The landscape genetic analysis suggested that areas with little snowfall acted as barriers to the Holocene expansion of species distribution and continued limiting gene flow between local populations. Conclusions: These findings indicate that postglacial population responses vary among regions and are controlled by environmental and geographic factors. Thus, changes in snowfall regime played a major role in shaping the distribution and genetic structure of the snow‐dependent plant. [ABSTRACT FROM AUTHOR]

Nuclear microsatellite markers were developed for the threatened plant Geranium soboliferum var. kiusianum, which has decreased its population size as a result of loss of its wetland habitat in Kyushu, Japan. Utilizing RNA-seq data obtained by next-generation sequencing techniques, 10 polymorphic microsatellite markers with 3-16 alleles in a nuclear genome were developed and characterized. Two to 15 alleles were observed in G. soboliferum. These markers will be used to investigate the genetic circumstance of remnant populations of G. soboliferum var. kiusianum and their phylogenetic relationship with G. soboliferum. [ABSTRACT FROM AUTHOR]

Simple sequence repeat ( SSR) markers were developed from expressed sequence tags ( ESTs) for Rhododendron section Brachycalyx in order to elucidate its evolutionary processes and reproductive ecology. Nineteen polymorphic EST-SSR markers were developed from EST libraries of R. amagianum and R. hyugaense. Polymorphisms for these markers were assessed using four species of section Brachycalyx. The number of alleles ranged from 1 to 14, and the observed and expected heterozygosity ranged from 0.000 to 0.931 and 0.000 to 0.904, respectively. The EST-SSR markers developed in this study will be useful for elucidating population genetic structure and breeding systems in section Brachycalyx. [ABSTRACT FROM AUTHOR]

• The wild-ginger, series Sakawanum shows clinal floral variation. • Evolutionary history of four taxa was inferred by molecular markers. • Two admixture events may have occurred between morphologically distinct taxa. • Geographic range shift to glacial refugia could have allowed secondary contact. • A complicated demographic history may have shaped intertaxonomic clinal variation. Clinal variation is a major pattern of observed phenotypic diversity and identifying underlying demographic processes is a necessary step to understand the establishment of clinal variation. The wild ginger series Sakawanum (genus Asarum) comprises four taxa, which exhibit intertaxonomic clinal variation in calyx lobe length across two continental islands isolated by a sea strait. To test alternative hypotheses of the evolutionary history and to determine the implications for the formation of clinal variation, we conducted approximate Bayesian computation (ABC) analysis and ecological niche modeling (ENM). ABC analysis indicated that the scenario assuming multiple admixture events was strongly supported. This scenario assumed two admixture events occurred between morphologically distinct taxa, likely leading to the generation of intermediate taxa. One of the admixture events was estimated to have occurred during the last glacial maximum (LGM), during which the taxa were estimated to have formed a common refugia in southern areas by ENM analysis. Although four taxa are currently distributed allopatrically on different islands and trans-oceanic dispersal appears unlikely, the formation of a land bridge and the geographic range shift to refugia would have allowed secondary contact between previously isolated taxa. This study suggests that clinal variation can be shaped by demographic history including multiple admixtures due to climatic oscillations. [ABSTRACT FROM AUTHOR]

• Background and Aims Clines, the gradual variation in measurable traits along a geographical axis, play a major role in evolution and can contribute to our understanding of the relative roles of selective and neutral process in trait variation. Using genetic and morphological analyses, the relative contributions of neutral and non-neutral processes were explored to infer the evolutionary history of species of the series Sakawanum (genus Asarum), which shows significant clinal variation in calyx lobe length. • Methods A total of 27 populations covering the natural geographical distribution of the series Sakawanum were sampled. Six nuclear microsatellite markers were used to investigate genetic structure and genetic diversity. The lengths of calyx lobes of multiple populations were measured to quantify their geographical and taxonomic differentiation. To detect the potential impact of selective pressure, morphological differentiation was compared with genetic differentiation (QCT-FST comparison). • Key Results Average calyx lobe length of A. minamitanianum was 124.11 mm, while that of A. costatum was 13.80 mm. Though gradually changing along the geographical axis within series, calyx lobe lengths were significantly differentiated among the taxa. Genetic differentiation between taxa was low (FST = 0.099), but a significant geographical structure along the morphological cline was detected. Except for one taxon pair, pairwise QCT values were significantly higher than the neutral genetic measures of FST and G'ST. • Conclusions Divergent selection may have driven the calyx lobe length variation in series Sakawanum taxa, although the underlying mechanism is still not clear. The low genetic differentiation indicates recent divergence and/or gene flows between geographically close taxa. These neutral processes would also affect the clinal variation in calyx lobe lengths. Overall, this study implies the roles of population history and divergent selection in shaping the current cline of a flower trait in the series Sakawanum. [ABSTRACT FROM AUTHOR]

The article presents a case study of a 75-year-old woman with rheumatoid arthritis and who was hospitalized due to fever and nausea. Using non-enhanced abdominal computed tomography, hyperdense fluid was found in the urinary bladder of the patient. The patient was diagnosed with urinary tract infection (UTI) and was treated with antibiotics.

A set of expressed sequence tag (EST) simple sequence repeat (SSR) markers were developed and characterized using next-generation sequencing technology for the genus Diabelia (Caprifoliaceae). De novo assembly of RNA-seq reads resulted in 58 669 contigs with the N50 length of 1211 bp. A total of 2746 contigs were identified to harbor SSR motifs, of which 48 primer pairs were designed and 11 were shown to be polymorphic across three morphospecies of Diabelia. When evaluated with 30 individuals, the number of alleles per locus ranged from 2 to 11 and the expected heterozygosity varied from 0.399 to 0.873, respectively. Distance-based clustering indicated that the EST-SSR markers can provide sufficient power to distinguish the three species (or populations). These markers will be useful for evaluating the range-wide genetic diversity of each species and examining genetic divergence and gene flow between the three species. [ABSTRACT FROM AUTHOR]

Continental islands provide opportunities for testing the effects of isolation and migration on genetic variation in plant populations. In characteristic of continental islands is that the geographic connections between these islands, which are currently distinguished by seaways, have experienced fluctuations caused by sea-level changes due to climate oscillations during the Quaternary. Plant populations on the islands have migrated between these islands via the exposed seafloors or been isolated. Here, we examined the demographic history of a temperate shrub, Rhododendron weyrichii, which is distributed in the southwestern parts of the Japanese archipelago and on an island of South Korea, using statistical phylogeographic approaches based on the DNA sequences of two chloroplast and eight nuclear loci in samples analyzed from 18 populations on eight continental islands, and palaeodistribution modeling. Time estimates for four island populations indicate that the durations of vicariance history are different between these populations, and these events have continued since the last glacial or may have predated the last glacial. The constancy or expansion of population sizes on the Japanese islands, and in contrast a bottleneck in population size on the Korean island Jeju, suggests that these islands may have provided different conditions for sustaining populations. The result of palaeodistribution modeling indicates that the longitudinal range of the species as a whole has not changed greatly since the last glacial maximum. These results indicate that exposed seafloors during the glacial period formed both effective and ineffective migration corridors. These findings may shed light on the effects of seafloor exposure on the migration of plants distributed across continental islands. [ABSTRACT FROM AUTHOR]

Aims: Quaternary climate changes dramatically affected species' distributions and thus impacted genetic diversity patterns, particularly for rear‐edge populations. Empirical studies have shown the southernmost (rear‐edge), fragmented populations of Japanese woody plants can harbour high genetic diversity owing to their origin in southern glacial refugia. The effect of Holocene climate warming on rear‐edge populations has, however, rarely been demonstrated. We assessed whether the genetic structure of populations of temperate plants in Japan can be interpreted to show legacies of both icy (Last Glacial Maximum, LGM) and warm (Holocene) climates. Location: Japanese Archipelago. Taxon: Hemerocallis middendorffii (Asphodelaceae). Methods: Population genetic profiles of 737 individuals from 41 populations were analysed to examine population structure and past population demography, using 12 EST‐SSR markers. Present and past suitable habitat areas during the LGM and the Holocene climatic optimum were estimated by ecological niche modelling (ENM). Reconstructed palaeodistribution was combined with population genetics to statistically predict population demographics in relation to past climate changes. Results: Genetic analysis of the 41 populations revealed 6 regional population groups. Four groups widely dominating the northern–central ranges harboured high genetic diversity, whereas genetic divergence within the groups was low. In contrast, the two groups at the southwestern edge were geographically and genetically isolated, and they showed the lowest genetic diversity. The estimated palaeodistributions showed a decrease in the suitable range during the Holocene in comparison with that at the LGM, and only habitat suitability in the Holocene was able to predict the genetic diversity across the range. Main conclusions Populations at the centre of the current distribution harbour high genetic diversity because they remained stable during both cold and warm periods. However, habitat fragmentation and population decline in relation to climate warming during the Holocene resulted in genetic isolation and impoverishment of the rear‐edge populations. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY: Homoploid hybrid speciation is receiving growing attention due the increasing recognition of its role in speciation. We investigate if individuals intermediate in morphology between the two species of the conifer genus Athrotaxis represent a homoploid hybrid species, A. laxifolia, or are spontaneous F1 hybrids. METHODS: A total of 1055 individuals of Athrotaxis cupressoides and A. seiaginoides, morphologically intermediate individuals, and two putative hybrid swarms were sampled across the range of the genus and genotyped with 13 microsatellites. We used simulations to test the power of our data to identify the pure species, F1 s, F2 s, and backcross generations. KEY RESULTS: We found that Athrotaxis cupressoides and A. seiaginoides are likely the most divergent congeneric conifers known, but the intermediates are F, hybrids, sharing one allele each from A. cupressoides and A. seiaginoides at six loci with completely species specific alleles. The hybrid swarms contain wide genetic variation with stronger affinities to the locally dominant species, A. seiaginoides and A. seiaginoides backcrosses outnumbering A cupressoides backcrosses. In addition, we observed evidence for isolated advanced generation backcrosses within the range of the pure species. CONCLUSIONS: We conclude that, even though they can be large and long-lived, Athrotaxis hybrid swarms are on a trajectory of decline and will eventually be reabsorbed by the parental species. However, this process may take millennia and fossil evidence suggests that such events have occurred repeatedly since the early Quaternary. Given this timeline, our study highlights the many obstacles to homoploid hybrid speciation. [ABSTRACT FROM AUTHOR]

Tertiary relicts often show evolutionary stasis in morphology and ecology and have been hypothesized to retain stable population sizes in refugia. However, recent studies have reported that some relicts evolutionarily shifted their physiology, ecology, and morphology and experienced various patterns of demography. To understand the historical survival of relict plants, a multidimensional study investigating the evolution of ecological and morphological traits as well as population demographic history is needed. The genus Tanakaea (Saxifragaceae) comprises two species in China and Japan. These species share most vegetative characteristics and are sometimes treated as a single species. The distribution pattern is relictual, as the populations are confined to small areas in mesic warm temperate forests less influenced by Quaternary glacial climates. Focusing on the relictual plant group, this study tested the hypotheses of evolutionary stasis and population stability in long‐term refugia. Genetic analyses using plastome sequences and genome‐wide single‐nucleotide polymorphisms revealed divergence of the two species approximately 6.8 million years ago and strong genetic differentiation of the regional populations. Demographic analysis revealed that almost all populations retained stable population sizes during glacial–interglacial climate changes, supporting the traditional view. However, morphological assessments revealed a simultaneous shift in breeding systems (from hermaphrodite to dioecy/non‐clonal to clonal reproduction) in Japanese species and intraspecific differentiation of leaf traits. Therefore, the relict species do not show evolutionary stasis in every aspect. Changes in reproductive characteristics may have contributed to their long‐term in situ survival. [ABSTRACT FROM AUTHOR]

Fagus L. is a key component in temperate deciduous broadleaf forests of the Northern Hemisphere. However, its biogeographic history has not been examined under the framework of a fully resolved and reasonably time‐calibrated phylogeny. In this study, we sequenced 28 nuclear single/low‐copy loci (18 555 bp in total) of 11 Fagus species/segregates and seven outgroups. Phylogenetic trees were reconstructed using both concatenation‐based (maximum parsimony, maximum likelihood, and Bayesian inference) and coalescent‐based methods (StarBEAST2, ASTRAL). The monophyly of two subgenera (Fagus and Engleriana) and most sections was well supported, except for sect. Lucida, which was paraphyletic with respect to sect. Longipetiolata. We also found a major phylogenetic conflict among North American, East Asian, and West Eurasian lineages of subgen. Fagus. Three segregates that have isolated distribution (F. mexicana, F. multinervis, and F. orientalis) were independent evolutionary units. Biogeographic analysis with fossils suggested that Fagus could have originated in the North Pacific region in late early Eocene. Major diversifications coincided with a climate aberration at the Eocene/Oligocene boundary and the global cooling since mid‐Miocene. The late Miocene accelerated global cooling and the Pleistocene glaciations would have driven beeches into East Asia, North America, and West Eurasia. Meanwhile, range reduction and extinction in high latitudes, central Asia, and western North America converged to form the beech modern distribution pattern. This study provides a first attempt to disentangle the biogeographic history of beeches in the context of a nearly resolved and time‐calibrated phylogeny, which could shed new insights into the formation of the temperate biome in the Northern Hemisphere. [ABSTRACT FROM AUTHOR]

Aim Many predictions of responses to future climate change utilize ecological niche models ( ENMs). We assess the capacity of these models to predict species distributions under conditions that differ from the current environment by testing whether they can predict past distributions of species. Location From 43° S to 31° S in south-eastern Australia (including Tasmania). Methods We studied three dominant tree species of temperate Australian mesic forests, Atherosperma moschatum, Eucalyptus regnans and Nothofagus cunninghamii. Phylogeographic evidence indicates that these species each survived the Last Glacial Maximum ( LGM) in multiple refugia. We modelled the current distribution of each species and projected those models onto LGM climates under six palaeoclimatic scenarios. The support for phylogeographic-based glacial refugia was estimated under each scenario using three different thresholds for inferring species presence/absence. Results The LGM models under scenarios that allowed for a realistic level of rainfall failed to predict survival of the study species in refugia identified from genetic evidence, apart from those in perhumid western Tasmania. Main conclusions Correct prediction of nearly all modern occurrences of the species suggests that this failure of ENMs to predict refugial survival was not methodological. Rather we conclude that the existing realized niches of these species may have changed since the LGM. Such niche changes may have involved the occurrence of non-analogue climates in the LGM and some significant alteration of fundamental niche (for at least E. regnans). Our results emphasize that predictions of future impacts of climate change on biodiversity will benefit from awareness of the limitations of ENMs in predicting the extinction of populations/species. Greater knowledge of how niches have changed through time and how this relates to the characteristics of species is needed to improve the reliability of ENMs. Niche changes in plants may also affect palaeoclimatic estimates based on fossil pollen. [ABSTRACT FROM AUTHOR]

Capsicum peppers are among the oldest domesticated crops in the Americas. Columbus introduced them to Europe, from where they spread to the Far East via Africa, South Asia, and Southeast Asia. However, the details of how Capsicum peppers were introduced into the Asia–Pacific region and their subsequent dispersal remain unknown. Therefore, we investigated the genetic diversity and relationships of Capsicum frutescens in the Asia–Pacific region through restriction site-associated DNA sequencing (RAD-seq) and the sequencing of a variable chloroplast genome locus. The RAD-seq analysis showed that three accessions from Japan are most closely related to those from the Americas and Micronesia, and are distant from most of those from islands and continental Southeast Asia. Although C. frutescens has two chloroplast haplotypes (T and TC), only the T type was found in the Americas and Japan, whereas both types were distributed in other regions. Therefore, we postulate that some C. frutescens accessions were introduced into the Asia–Pacific region from the Americas via the Pacific dispersal route, whereas only the T type was introduced into Japan. Evidence for this Pacific dispersal route of C. frutescens could lead to a reconsideration of the dispersal routes of other crops native to the Americas. [ABSTRACT FROM AUTHOR]