Persistent history of the bird-dispersed arctic-alpine plant Vaccinium vitis-idaea L. (Ericaceae) in Japan

Fine-scale clonal structure of the lingonberry Vaccinium vitis-idaea under the nurse plant Pinus pumila vegetation in an alpine region, Mt. Norikura

The nurse effect is a positive interaction in which a nurse plant improves the abiotic environment for another species (beneficiary plant) and facilitates its establishment. The evergreen shrub Vaccinium vitis-idaea (a beneficiary plant) grows mainly under the dwarf shrub Pinus pumila (a nurse plant) in the alpine regions of central Japan. However, whether V. vitis-idaea shrubs under various P. pumila shrubs spread through clonal growth and/or seeds remains unclear. We investigated the clonal structure of V. vitis-idaea under the nurse plant P. pumila in Japanese alpine regions. MIG-seq analysis was conducted to clarify the clonal diversity of V. vitis-idaea in isolated and patchy P. pumila plots on a ridge (PATs), and in a plot covered by dense P. pumila on a slope adjacent to the ridge (MAT) on Mt. Norikura, Japan. We detected 28 multilocus genotypes in 319 ramets of V. vitis-idaea across 11 PATs and MAT. Three genets expanded to more than 10 m in the MAT. Some genets were shared among neighboring PATs or among PATs and MAT. These findings suggest that the clonal growth of V. vitis-idaea plays an important role in the sustainability of populations. The clonal diversity of V. vitis-idaea was positively related with the spatial size of PATs and was higher in MAT than in PATs at a small scale. Therefore, the spatial spread of the nurse plant P. pumila might facilitate the nurse effect on the genetic diversity of beneficiary plants, leading to the sustainability of beneficiary populations.

Chloroplast genome-based genetic resources via genome skimming for the subalpine forests of Japan and adjacent regions

The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold-tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole-genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis-idaea) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast-based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA.

Phylogeographical evidence for historical long-distance dispersal in the flightless stick insect Ramulus mikado

Exploring how organisms overcome geographical barriers to dispersal is a fundamental question in biology. Passive long-distance dispersal events, although infrequent and unpredictable, have a considerable impact on species range expansions. Despite limited active dispersal capabilities, many stick insect species have vast geographical ranges, indicating that passive long-distance dispersal is vital for their distribution. A potential mode of passive dispersal in stick insects is via the egg stage within avian digestive tracts, as suggested by experimental evidence. However, detecting such events under natural conditions is challenging due to their rarity. Therefore, to indirectly assess the potential of historical avian-mediated dispersal, we examined the population genetic structure of the flightless stick insect Ramulus mikado across Japan, based on a multifaceted molecular approach [cytochrome oxidase subunit I (COI) haplotypes, nuclear simple sequence repeat markers and genome-wide single nucleotide polymorphisms]. Subsequently, we identified unique phylogeographic patterns, including the discovery of identical COI genotypes spanning considerable distances, which substantiates the notion of passive long-distance genotypic dispersal. Overall, all the molecular data revealed the low and mostly non-significant genetic differentiation among populations, with identical or very similar genotypes across distant populations. We propose that long-distance dispersal facilitated by birds is the plausible explanation for the unique phylogeographic pattern observed in this flightless stick insect.

Virtual issue: phylogeographic studies in the Japanese Archipelago: from geographic patterns of genetic variation to biodiversity in plants

Phylogeographic studies have investigated genetic variation and structure within species or closely related lineages and are fundamental for understanding factors and processes of genetic divergence as well as speciation. This virtual issue collects 35 papers on phylogeographic studies published in the Journal of Plant Research and focuses on three major topics in biodiversity: (1) biogeography, (2) systematics, and (3) evolution.

Ice holes microrefugia harbor genetically and functionally distinct populations of Vaccinium vitis-idaea (Ericaceae)

In the mountain terrain, ice holes are little depressions between rock boulders that are characterized by the exit of cold air able to cool down the rock surface even in summer. This cold air creates cold microrefugia in warmer surroundings that preserve plant species probably over thousands of years under extra-zonal climatic conditions. We hypothesized that ice hole populations of the model species Vaccinium vitis-idaea (Ericaceae) show genetic differentiation from nearby zonal subalpine populations, and high functional trait distinctiveness, in agreement with genetic patterns. We genotyped almost 30,000 single nucleotide polymorphisms using restriction site-associated DNA sequencing and measured eight functional traits indicative of individual performance and ecological strategies. Genetic results showed high differentiation among the six populations suggesting isolation. On siliceous bedrock, ice hole individuals exhibited higher levels of admixture than those from subalpine populations which could have experienced more bottlenecks during demographic fluctuations related to glacial cycles. Ice hole and subalpine calcareous populations clearly separated from siliceous populations, indicating a possible effect of bedrock in shaping genetic patterns. Trait analysis reflected the bedrock effect on populations' differentiation. The significant correlation between trait and genetic distances suggests the genetic contribution in shaping intraspecific functional differentiation. In conclusion, extra-zonal populations reveal a prominent genetic and phenotypic differentiation determined by history and ecological contingency. Therefore, microrefugia populations can contribute to the overall variability of the species and lead to intraspecific-driven responses to upcoming environmental changes.

The evolutionary history of rice azaleas (Rhododendron tschonoskii alliance) involved niche evolution to a montane environment

PREMISE

The formation of isolated montane geography on islands promotes evolution, speciation, and then radiation if there are ecological changes. Thus, investigating evolutionary histories of montane species and associated ecological changes may help efforts to understand how endemism formed in islands' montane floras. To explore this process, we investigated the evolutionary history of the Rhododendron tschonoskii alliance, which grows in montane environments of the Japanese archipelago and the Korean Peninsula.

METHODS

We studied the five species in the R. tschonoskii alliance and 30 outgroup species, using genome-wide single-nucleotide polymorphisms and cpDNA sequences, in association with environmental analyses.

RESULTS

The monophyletic R. tschonoskii alliance diverged since the late Miocene. Species in the alliance currently inhabit a cold climatic niche that is largely different from that of the outgroup species. We observed clear genetic and niche differentiations between the taxa of the alliance.

CONCLUSIONS

The association of the alliance's evolution with the formation of cooler climates on mountains indicates that it was driven by global cooling since the mid-Miocene and by rapid uplift of mountains since the Pliocene. The combination of geographic and climatic isolation promoted high genetic differentiation between taxa, which has been maintained by climatic oscillations since the Quaternary.

Decades-long phylogeographic issues: complex historical processes and ecological factors on genetic structure of alpine plants in the Japanese Archipelago

Mountain regions are important places for biodiversity, where organisms could persist throughout prolonged periods and accumulate genetic divergence as well as promote speciation. Roles of mountains for biodiversity have been exclusively discussed in regions that have specifically diverse species or covered with ice-sheets during the Pleistocene glacial periods, whereas the importance of mountainous regions in East Asia has been less disputed. High mountains in the Japanese Archipelago, located at the eastern edge of the Eurasia continent, have one of southernmost populations of alpine and arctic-alpine plants that are also distributed in the northern Pacific and/or the circumarctic regions. Phylogeographic studies on the Japanese alpine plants have excluded their possible ephemeral occurrence during the current warm period, and rather, suggest persistence of alpine plants throughout several cycles of climate changes in the Pleistocene on high mountains in central Honshu, the main island of the Japanese Archipelago. In this review, I look through decade long phylogeographic studies and show complicated patterns of range dynamics of Japanese alpine plants. In addition, I note recent findings of genetic relationships of Japanese populations of alpine and/or arctic-alpine plants with those in northern regions and their possible ecological divergence in the Japanese Archipelago. Taken together, I provide several issues for understanding historical processes that established distribution of alpine plants following climate changes as well as their diversification and propose importance of Japanese populations of alpine plants on biodiversity in alpine communities across broader range, especially in the northern Pacific region.

Ecotypic differentiation of a circumpolar Arctic-alpine species at mid-latitudes: variations in the ploidy level and reproductive system of Vaccinium vitis-idaea

Although plant species originated from Arctic regions commonly grow in alpine habitats at mid-latitudes, some populations of these species exist also in some specific habitats below the treeline. Local populations at lower elevations may have different origins, ploidy levels, mating systems and/or morphological traits from alpine populations, but comparative studies between alpine and low-elevation populations are scarce. We aimed to reveal the ecological and genetic differentiations between higher and lower populations of Vaccinium vitis-idaea in Hokkaido, northern Japan by comparing 22 populations growing in diverse environments. We analysed the ploidy level of individual populations using flow cytometry. Genetic differentiation among populations, and genetic diversity within populations were calculated using microsatellite markers. Fruit and seed production were recorded under natural conditions, and a pollination experiment was conducted to reveal the variations in mating system across populations. Furthermore, we compared shoot growth and leaf characteristics among populations. Most of the low-elevation populations were tetraploid, whereas all but one of the alpine populations were diploid. Tetraploid populations were clearly differentiated from diploid populations. Some tetraploid populations formed huge clonal patches but genetic diversity was higher in tetraploids than in diploids. Alpine diploids were self-incompatible and produced more seeds per fruit than tetraploid populations. In contrast, tetraploids showed high self-compatibility. Leaf size and foliar production were greater in tetraploid populations. Our results indicate that the genetic compositions of low-elevation tetraploid populations are different from those of alpine diploid populations. Most populations at lower elevations contained unique ecotypes suited to persistence in isolated situations. Local, low-elevation populations of typical alpine species maintain ecologically and genetically specific characteristics and could be valuable in terms of evolutionary and conservation biology. The present study demonstrates the biological importance of small and isolated populations at the edges of species distribution.

Refugia within refugium of Geranium yesoense (Geraniaceae) in Japan were driven by recolonization into the southern interglacial refugium

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.

Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (HE = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: FST = 0.165***; cpDNA: FST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000-100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex.

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.

Genetic and geographical structure of boreal plants in their southern range: phylogeography of Hippuris vulgaris in China

BACKGROUND

Our current understanding of the evolutionary history of boreal and arctic-alpine plants in their southern range in Asia remains relatively poor. Using three cpDNA non-coding regions and nine nuclear microsatellite (nSSR) loci, we examine the phylogeographic pattern in a broad geographic sampling of the boreal plant Hippuris vulgaris to infer its dispersal and diversification in China. In addition, the species distributions at the Last Glacial Maximum (LGM) and at present were predicted using ecological niche modeling (ENM).

RESULTS

The cpDNA results revealed two distinct lineages, A and B. A is restricted to Northeast China; B is distributed in Northwest China, the Qinghai-Tibet Plateau (QTP) and North and Northeast (NNE) China; and A and B diverged ca. 1.36 Ma. The nSSR data revealed two genetic clusters corresponding to the two cpDNA lineages and nonreciprocal hybridization with lineage A as the maternal lineage in Northeast China. Cluster B further divided into three subclusters: I, mainly in NNE China and the northeastern border of the QTP; II, in Northwest China and the QTP; and III, on the QTP. ENM predicted a marked range shift on the QTP at the LGM, retreating from the platform to the northeast and southeast edges.

CONCLUSIONS

Hippuris vulgaris probably diverged into lineages A and B in high latitudes and then immigrated into Northeast China and Northwest China, respectively. Lineage A persisted and diversified in Northeast China. Lineage B reached the QTP during the mid-Pleistocene, diversified in that region due to the influence of climatic oscillations, migrated into Northeast China and subsequently hybridized with lineage A. Our findings give empirical evidence that boreal plants display complex evolutionary history in their southern range in Asia and provide new insights into the evolution of boreal and arctic-alpine plants.