The homogenous genetic structure and inferred unique history of range shifts during the Pleistocene climatic oscillations of Arcterica nana (Maxim.) Makino (Ericaceae)

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.

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.

Yalongjiang River Has Had an Important Role in the Dispersal and Divergence of Rosa soulieana in the Hengduan Mountains of China

The Hengduan Mountains are the core of the Sino-Himalayan Floristic Region. Rosa soulieana Crép. is an important wild rose species that is widely distributed in the Hengduan Mountains. To provide better future utilization of this wild rose, and also to add some possible proof of the effect of geomorphological and ecological characteristics of the Hengduan Mountains on the current spatial distribution and genetic diversity of local species, the genetic diversity and genetic structure of 556 individuals from 37 populations of R. soulieana were studied using fluorescent amplified fragment length polymorphisms (AFLPs). R. soulieana showed a moderately high level of genetic diversity and a high level of genetic differentiation at the species level. The total percentage of polymorphic loci, total heterozygosity (Ht), Shannon index (I), and heterozygosity value within populations (Hs) were 97.8%, 0.253, 0.339, and 0.139, respectively. More than half of the total genetic variation (54.0%) occurred within populations, and the overall gene differentiation coefficient (Gst) was 0.451. The genetic differentiation among populations was positively and significantly correlated with geographic distance. The neighbor-joining cluster and the Bayesian analysis divided all the populations and individuals into 3 groups, and did not support the morphology based intraspecific varieties. The results confirmed that the ancient R. soulieana of the third group survived in northwestern Yunnan and Yalongjiang valley and then moved upnorth along the valley. The spatial distribution of the other two groups was the result of allopatric divergence due to long period of adaptation to the different climatic conditions of its distribution at either side of the Yalongjiang River.

Origins, genetic structure, and systematics of the narrow endemic peatmosses (Sphagnum): S. guwassanense and S. triseriporum (Sphagnaceae)

PREMISE OF THE STUDY

Sphagnum dominates vast expanses of wetland habitats throughout the northern hemisphere and species delimitation within the genus is important because floristic changes associated with a warming global climate may have measureable impacts on large-scale ecological processes. Most northern hemisphere peatmoss species (Sphagnum) have circumboreal ranges, but the Japanese species generally known as S. calymmatophyllum is endemic to Honshu Island. This prompted a population genetic and phylogenetic analysis to resolve the origin(s), population structure, and phylogenetic relationships of this morphologically variable species. •

METHODS

Sixty plants collected from Mt. Gassan and Mt. Hakkoda were genotyped for 12 microsatellite loci. Two plastid loci and three anonymous nuclear loci were sequenced in a subset of the plants, plus representatives from 10 closely related species. •

KEY RESULTS

Gametophytes exhibited fixed or nearly fixed heterozygosity at 9-10 of the 12 microsatellite loci. Two genetic groups were resolved by the microsatellite data, individuals showed no evidence of admixture, and the two groups of plants differ in morphology. They are heterozygous for different sets of alleles. The two taxa share plastid DNA sequences with two species that are common in Alaska. •

CONCLUSIONS

Two taxa were distinguished: S. guwassanense and S. triseriporum. Both are allopolyploids; they originated independently from different but closely related progenitors. The maternal progenitor was likely either S. orientale or S. inexspectatum. The two allopolyploid taxa are heterozygous for (different) private microsatellite alleles, and one progenitor could be extinct.

Molecular evolution of cryptochrome genes and the evolutionary manner of photoreceptor genes in Cardamine nipponica (Brassicaceae)

Various photoreceptors in plants are used to monitor important environmental light signals and regulate plant development. Despite their functional importance, recent studies have demonstrated that red/far-red absorbing phytochromes or blue/UV-A absorbing cryptochromes are involved in local adaptation within a species' range. In the present study, to exemplify the intraspecific photoreceptor evolutionary pattern, the genetic structures of cryptochrome genes (CRY1 and CRY2) in Cardamine nipponica (Brassicaceae), of which PHYE, a gene coding one of the phytochromes, was found to be involved in local adaptation between central and northern Japanese populations. Although clear genetic differentiations between central and northern Japan were detected (CRY1: F (ST) = 0.63, CRY2: F (ST) = 0.53), overall nucleotide diversity was very low (CRY1: π (Total) = 0.0014, CRY2: π (Total) = 0.0013), and the polymorphism patterns were neutral (CRY1: Tajima's D = 0.084, P = 0.32, CRY2: D = -0.014, P = 0.39). Therefore, the involvement of cryptochromes in the adaptation to local environments is difficult to postulate. Consequently, this study along with our previous findings suggest that intraspecific photoreceptor gene polymorphisms in C. nipponica were mostly suppressed by purifying selection due to their functional importance as photoreceptors, while some of the photoreceptors may play substantial roles in adaptation to local environments.

Natural selection on PHYE by latitude in the Japanese archipelago: insight from locus specific phylogeographic structure in Arcterica nana (Ericaceae)

Phytochromes play a key role in allowing plants to monitor their surrounding environment and, conversely, adaptation to local environments has driven the evolutionary history of phytochromes. As a result of natural selection, polymorphisms in phytochrome genes would thus be expected to exhibit locus-specific phylogeographic structure. To evaluate this hypothesis, we conducted a phylogeographic investigation based on four nuclear genes, including two phytochrome genes (PHYB and PHYE) using 155 samples of Arcterica nana from the entire range of the Japanese archipelago. Bayesian clustering revealed geographic differentiation between northern and southern Japan when all four genes were included. However, this geographic differentiation is inconsistent with previously reported genetic structure of genome-wide polymorphisms based on amplified fragment length polymorphisms, as these did not show geographic differentiation throughout the Japanese archipelago. In contrast, the north-south differentiation was not apparent when PHYE was excluded. This indicates that PHYE alone could be responsible for the north-south differentiation (F(CT) = 0.15, P < 0.001). Furthermore, a single nonsynonymous polymorphism (C360T) strongly contributed to geographic differentiation (F(CT) = 0.57, P < 0.001) and its corresponding amino acid replacement (P120L) was significantly under positive selection based on maximum likelihood analysis (P = 0.98). Consequently, the locus-specific geographic differentiation in PHYE could be caused by natural selection, suggesting the involvement of PHYE in local adaptation between populations of A. nana in northern and southern Japan. This finding is consistent with a previous study on Cardamine nipponica, indicating the importance of PHYE for local adaptation in Japanese alpine plants.

Application of the isolation with migration model demonstrates the pleistocene origin of geographic differentiation in Cardamine nipponica (Brassicaceae), an endemic Japanese alpine plant

The Pleistocene was characterized by a cyclic pattern of cold and warm climatic periods, or climatic oscillations, which caused fluctuations in the distributions of organisms. This resulted in drastic changes in demography, thereby accelerating the genetic divergence of populations. Phylogeographic studies have elucidated the history of populations during the Pleistocene. However, given the lack of model-based analysis of population histories, previous phylogeographic studies could not adequately evaluate the effect of these Pleistocene climatic oscillations on the genetic divergence and migration events between populations. Populations of Japanese alpine plants in central and northern Japan are highly differentiated, and a history of isolation between regions during the Pleistocene was inferred. Using sequences of 10 nuclear genes (ca. approximately 7,000 bp in total) from Cardamine nipponica (Brassicaceae), we applied an isolation with migration (IM) model to test the significance of the isolation history between central and northern Japan and to assess whether range shifts during the Pleistocene climatic oscillations were involved in the genetic differentiation between regions. The estimated divergence time indicates that the two regions were separated about 100,000-110,000 years ago. The exclusive occurrence of closely related haplotypes within each region (parsimony network) and the high level of genetic differentiation between the regions (mean F(ST) = 0.417) indicate that genetic divergence occurred following the isolation of the two regions. Therefore, the genetic differentiation between regions was shaped during the Pleistocene, especially during the last glacial and inter and postglacial periods. In addition, our multilocus analysis showed that populations in central and northern Japan were completely isolated after they split. Geographic separation and subsequent restricted migration events among mountains could explain this isolation history between regions. Furthermore, genetic drift in the reduced populations would remove evidence of occasional migration, emphasizing the isolation history. Therefore, our application of a demographic model demonstrated the Pleistocene origin of geographic differentiation statistically and provided a plausible migration history for C. nipponica.

Molecular evolution of phytochromes in Cardamine nipponica (Brassicaceae) suggests the involvement of PHYE in local adaptation

Given that plants are sessile organisms, traits involved in adapting to local environments and/or in monitoring the surrounding environment, such as having photoreceptors, are significant targets of natural selection in plant evolution. To assess the intraspecific adaptive evolution of photoreceptors, we investigated sequence variations in four phytochrome genes (PHYA-C and PHYE) of Cardamine nipponica (Brassicaceae), an endemic Japanese alpine plant. The genealogies of haplotypes and genetic differentiations showed inconsistent patterns of evolution across phytochromes, suggesting that evolutionary forces were distinct in phytochromes of C. nipponica. An overall low level of nucleotide diversity in phytochrome genes suggests that the evolution of phytochromes is constrained by purifying selection within C. nipponica, which is consistent with previous findings on phytochromes. However, PHYE alone exhibited a non-neutral pattern of polymorphisms (Tajima's D = 1.91, P < 0.05) and an accumulation of nonsynonymous substitutions between central and northern Japan. In particular, the PHY domain, which plays an important role in stabilizing the active form (Pfr) of phytochromes, harbored a specific nonsynonymous fixation between regions. Thus, our finding indicates that local adaptation is involved in the evolution of PHYE in C. nipponica and is the first to suggest the involvement of PHYE in local adaptation.