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.
Fagus could have originated in the North Pacific region in late early Eocene. Both subgenera (Fagus and Engleriana) are monophyletic and they diverged at the Eocene/Oligocene boundary (32.7 Ma). The late Miocene accelerated global cooling and the Pleistocene glaciation would have driven beeches into East Asia, North America, and West Eurasia and most lineages split during this period.
White cypress pine (
Callitris glaucophylla
) is a drought-tolerant evergreen conifer, which is a member of the Australian
C. columellaris
species complex. The complex is comprised of five closely ...related morphospecies that occur in a wide range of bioclimatic regions in Australia. Ecological genomics of the complex provides an opportunity to identify markers associated with environmental adaptation and is expected to broaden our understanding of its speciation process. We adopted a single-tree linkage mapping approach combined with high-throughput restriction site associated DNA (RAD) sequencing and expressed sequence tag-simple sequence repeat (EST-SSR) genotyping to set up a baseline genetic map for
C. glaucophylla
. The generated linkage map consisted of 4284 markers positioned on 11 linkage groups, corresponding to the haploid chromosome number of
Callitris
(2
n
= 22). The spatial distribution of markers was uneven compared to random expectation with significant clustering in central positions of some linkage groups, which may be associated with recombination cold spots of pericentromere regions. Allelic segregation was shown to be distorted in particular regions of four linkage groups, where selection may have operated on viability genes, leaving allelic distortion in surrounding linked markers. We then tested RAD single nucleotide polymorphisms (RAD-SNP) marker recovery and transferability of the linkage map to population genomic data collected for a related species,
Callitris gracilis
. Of the linkage map markers, 1257 markers (ca. 30 %) were recovered in independent RAD sequencing of population samples of
C. glaucophylla
. Genetic diversity and differentiation evaluated using mapped markers reflected ascertainment bias slightly; a decrease in
H
s (absolute difference of −0.018) for a related species (
C. gracilis
) and an increase in
F
ST
between
C. glaucophylla
and
C. gracilis
(+0.018) were detected. Although care should be taken given such biases in cross-species transfer, this study demonstrated that the RAD-SNP-based linkage map is essentially useful when combined with population genomic analysis of this conifer lineage.
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.
Tricyrtis macropoda var. bulbifera, a new variety from northwestern Kyushu, Japan, is describe. It is characterized by bulbils in the leaf axils, asexually generated offspring and sexual reproduction ...via seeds. Variety bulbifera resembles var. macropoda in its flowers, but differs in producing many apical and axillary cymose inflorescences in addition to the bulbils.
The warm‐temperate and subtropical climate zones of East Asia are a hotspot of plant species richness and endemism, including a noticeable number of species‐poor Tertiary relict tree genera. However, ...little is understood about when East Asian Tertiary relict plants diversified, how they responded demographically to past environmental change, and to what extent their current genomic composition (and adaptive capacity) might mitigate the effects of global warming. Here, we obtained genomic (RAD‐SNP) data for 171 samples from two extant species of Euptelea in China (24 E. pleiosperma populations) and Japan (11 E. polyandra populations) to elucidate their divergence and demographic histories, genome‐wide associations with current environmental variables, and genomic vulnerability to future climate change. Our results indicate that Late Miocene changes in climate and/or sea level promoted species divergence, whereas Late Pliocene uplifting in southwest China likely fostered lineage divergence within E. pleiosperma. Its subsequent range expansion into central/east (CE) China bears genomic signatures of climate‐driven selection, yet extant CE populations are predicted to be most vulnerable to future climate change. For E. polyandra, geography was the only significant predictor of genomic variation. Our findings indicate a profound impact of Late Neogene geological and climate change on the evolutionary history of Euptelea, with much stronger signals of local adaptation left in China than in Japan. This study deepens our understanding of the complex evolutionary forces that influence the distribution of genetic variation of Tertiary relict trees, and provides insights into their susceptibility to global change and potential for adaptive responses. Our results lay the groundwork for future conservation and restoration programs for Euptelea.
A set of twelve EST-SSR markers were developed to evaluate the genetic diversity and genetic structure of Hemerocallis middendorffii Trautv. & C. A. Mey (Asphodelaceae) in Japan. The total number of ...alleles for each locus ranged from 3 to 19, with an average of 10.25; the mean values of HO and HE were 0.567 and 0.648, respectively. Versatility of the markers was evaluated for two additional species of the same genus, H. lilioasphodelus L. var. thunbergii (Baker) M. Hotta and H. hakuunensis Nakai to show that all the EST-SSR markers are transferrable between them.
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.
The Sino-Japanese Floristic Region (SJFR) is a key area for plant phylogeographical research, due to its very high species diversity and disjunct distributions of a large number of species and ...genera. At present, the root cause and temporal origin of the discontinuous distribution of many plants in the Sino-Japanese flora are still unclear.
(Caprifoliaceae; Linnaeoideae) is a genus endemic to Asia, mostly in Japan, but two recent discoveries in China raised questions over the role of the East China Sea (ECS) in these species' disjunctions. Chloroplast DNA sequence data were generated from 402 population samples for two regions (
32-
L, and
H-
A) and 11 nuclear microsatellite loci were screened for 549 individuals. Haplotype, population-level structure, combined analyses of ecological niche modeling, and reconstruction of ancestral state in phylogenies were also performed. During the Last Glacial Maximum (LGM) period after the Tertiary,
was potentially widely distributed in southeastern China, the continental shelf of the East China Sea and Japan (excluding Hokkaido). After LGM, all populations in China have disappeared except those in Zhejiang which may represent a Glacial refuge. Populations of
in Japan have not experienced significant bottleneck effects, and populations have maintained a relatively stable state. The observed discontinuous distribution of
species between China and Japan are interpreted as the result of relatively ancient divergence. The phylogenetic tree of chloroplast fragments shows the characteristics of multi-origin evolution (except for
). STRUCTURE analysis of nuclear Simple Sequence Repeat (nSSR) showed that the plants of the
were divided into five gene pools:
(
var.
-Korea), and populations of
var.
in Yamagata prefecture, northern Japan. Molecular evidence provides new insights of
into biogeography, a potential glacial refuge, and population-level genetic structure within species. In the process of species differentiation, ECS acts as a corridor for two-way migration of animals and plants between China and Japan during glacial maxima, providing the possibility of secondary contact for discontinuously distributed species between China and Japan, or as a filter (creating isolation) during glacial minima. The influence of the ECS in speciation and biogeography of
in the Tertiary remains unresolved in this study. Understanding origins, evolutionary histories, and speciation will provide a framework for the conservation and cultivation of
.
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.
We developed 19 EST‐SSR markers for Rhododendron section Brachycalyx. The EST‐SSR markers developed in this study will be useful for elucidating population genetic structure and breeding systems in section Brachycalyx.
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.
Nuclear microsatellite markers were developed for the threatened plant Geranium soboliferum var. kiusianum. 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.
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