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•Genomic RAD and SSR data supported the monophyly of three Cardiocrinum species.•Late Neogene tectonic/climatic events triggered the speciation of Cardiocrinum.•Pleistocene climatic ...fluctuations had limited influence on species divergence.•All three species experienced population expansions from LIG to LGM.
The Sino-Japanese Floristic Region (SJFR) in East Asia is one of the most diverse temperate floras in the world. However, the relative influence of Neogene palaeogeographical changes and Quaternary climatic fluctuations as causal mechanisms on species diversification remains largely controversial, because most divergence time estimates were inferred from single-locus data and have limited geographic or taxonomic sampling. To evaluate these influences, we use SNP markers from restriction site-associated DNA sequencing (RAD-Seq) loci and expressed sequence tags-simple sequence repeat (EST-SSR) markers to investigate the levels of genetic variation, speciation and demographic history of the temperate-deciduous forest (TDF) endemic Cardiocrinum (Endlicher) Lindley (Liliaceae), a genus comprising three species in China (C. giganteum, C. cathayanum) and Japan (C. cordatum). Phylogenomic and population genomic coalescent-based analyses demonstrated that Late Neogene tectonic/climatic events triggered speciation of Cardiocrinum, and Pleistocene climatic fluctuations had limited influence on its divergence history. Population demographic inference using Approximate Bayesian Computation from EST-SSRs and palaeoclimatic niche models both indicated that all three Cardiocrinum species experienced population expansions during the transition from the LIG to the LGM. We also discussed the implications of these results on the conservation of montane TDF species in the SJFR under ongoing environmental change. Our results improve our understanding of how the constituents of montane TDF across the SJFR responded to previous periods of rapid climate and environmental change in terms of speciation and population demographic processes.
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
.
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.
The evolutionary origin and historical demography of extant Arcto-Tertiary forest species in East Asia is still poorly understood. Here, we reconstructed the evolutionary and population demographic ...history of the two extant Euptelea species in China (E. pleiosperma) and Japan (E. polyandra). Chloroplast/nuclear DNA sequences and microsatellite loci were obtained from 36 Euptelea populations to explore molecular structure and diversity in relation to past and present distributions based on ecological niche modelling (ENM). Time-calibrated phylogenetic/phylogeographic inferences and niche-identity tests were used to infer the historical process of lineage formation.
Euptelea pleiosperma diverged from E. polyandra around the Late Miocene and experienced significant ecological differentiation. A near-simultaneous diversification of six phylogroups occurred during the mid-to-late Pliocene, in response to the abrupt uplift of the eastern Tibetan Plateau and an increasingly cooler and drier climate. Populations of E. pleiosperma seem to have been mostly stationary through the last glacial cycles, while those of E. polyandra reflect more recent climate-induced cycles of range contraction and expansion.
Our results illustrate how Late Neogene climatic/tectonic changes promoted speciation and lineage diversification in East Asia's Tertiary relict flora. They also demonstrate for the first time a greater variation in such species' responses to glacial cycles in Japan when compared to congeners in China.
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.
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.
This study investigated whether phenotypic variations of the Solidago virgaurea complex along an elevational gradient are maintained despite active gene flow by efficient dispersal ecology of the species. This study suggests that genome regions of adaptive traits differed among the populations by strong selection pressures despite the existence of gene flow and that phenotypic variations of the S. virgaurea complex along the elevational gradient are maintained by strong selection pressures.
Nuclear microsatellite markers were developed for Geranium thunbergii, an herbaceous plant characterized by petal color polymorphism. Utilizing RNA sequencing data obtained by next-generation ...sequencing techniques, we developed and characterized 19 polymorphic microsatellite markers with two to 12 alleles in the nuclear genome. These markers will be used to reveal the genetic structure and demographic history of G. thunbergii in the Japanese archipelago, which will elucidate the genetic background of flower color polymorphism among populations.
Abstract
Flowering is an important step in the life cycle of plants and indicates adaptability to external climatic cues such as temperature and photoperiod. We investigated the expression patterns ...of core genes related to flowering-time regulation in Japanese wild radish (Raphanus sativus var. raphanistroides) with different vernalization requirements (obligate and facultative) and further identified climatic cues that may act as natural selective forces. Specifically, we analysed flowering-time variation under different cold and photoperiod treatments in Japanese wild radish collected from the Hokkaido (northern lineage) and Okinawa (southern lineage) islands, which experience contrasting climatic cues. The cultivation experiment verified the obligate and facultative vernalization requirements of the northern and southern wild radish accessions, respectively. The expression of major genes involved in flowering time indicated that RsFLC and RsCOL5 (A&B) may interact to regulate flowering time. Notably, floral initiation in the northern lineage was strongly correlated with RsFLC expression, whereas flowering in the southern linage was correlated with induction of RsCOL5-A expression, despite high RsFLC transcript levels. These results suggested that the northern accessions are more sensitive to prolonged cold exposure, whereas the southern accessions are more sensitive to photoperiod. These different mechanisms ultimately confer an optimal flowering time in natural populations in response to locally contrasting climatic cues. This study provides new insights into the variant mechanisms underlying floral pathways in Japanese wild radish from different geographic locations.
To identify climate cues that might act as natural selective forces shaping the genetic variation for flowering initiation, we conducted analyses of the flowering-time variation in response to cold treatment and day length in wild radish collected from Hokkaido and Okinawa islands with vernalization requirements. Our results collectively offer a hint that accessions with obligate vernalization requirements might exhibit a higher sensitivity to prolonged cold exposure, whereas in accessions with facultative vernalization requirements the photoperiod pathway predominates, and these mechanisms confer an optimal flowering time in natural populations, in response to their contrasting climate cues.
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.
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