ploidyfrost: Reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graphs.

Polyploidy is ubiquitous and its consequences are complex and variable. A change of ploidy level generally influences genetic diversity and results in morphological, physiological and ecological differences between cells or organisms with different ploidy levels. To avoid cumbersome experiments and take advantage of the less biased information provided by the vast amounts of genome sequencing data, computational tools for ploidy estimation are urgently needed.

The rediscovery of (Juglandaceae) after 63 years reveals a new record from China.

Despite having been first published in 1941, (A.Chev.) J.

Dead-End Hybridization in Walnut Trees Revealed by Large-Scale Genomic Sequence Data.

Although hybridization plays a large role in speciation, some unknown fraction of hybrid individuals never reproduces, instead remaining as genetic dead-ends. We investigated a morphologically distinct and culturally important Chinese walnut, Juglans hopeiensis, suspected to have arisen from hybridization of Persian walnut (J. regia) with Asian butternuts (J.

Different rates of pollen and seed gene flow cause branch-length and geographic cytonuclear discordance within Asian butternuts.

Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance. We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance. Our findings indicate that the chloroplast genome had substantially deeper divergence (branch-length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome.

Recent demographic histories of temperate deciduous trees inferred from microsatellite markers.

Background: Accurate inference of demographic histories for temperate tree species can aid our understanding of current climate change as a driver of evolution. Microsatellites are more suitable for inferring recent historical events due to their high mutation rates. However, most programs analyzing microsatellite data assume a strict stepwise mutation model (SMM), which could cause false detection of population shrinkage when microsatellite mutation does not follow SMM.

Do annual and perennial populations of an insect-pollinated plant species differ in mating system?

Background And Aims: Theory predicts that outcrossing should be more prevalent among perennials than annuals, a pattern confirmed by comparative evidence from diverse angiosperm families. However, intraspecific comparisons between annual and perennial populations are few because such variation is uncommon among flowering plants. Here, we test the hypothesis that perennial populations outcross more than annual populations by investigating Incarvillea sinensis, a wide-ranging insect-pollinated herb native to China.

Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut.

Persian walnut (Juglans regia) is cultivated worldwide for its high-quality wood and nuts, but its origin has remained mysterious because in phylogenies it occupies an unresolved position between American black walnuts and Asian butternuts. Equally unclear is the origin of the only American butternut, J. cinerea.

Demographically idiosyncratic responses to climate change and rapid Pleistocene diversification of the walnut genus Juglans (Juglandaceae) revealed by whole-genome sequences.

Whether species demography and diversification are driven primarily by extrinsic environmental changes such as climatic oscillations in the Quaternary or by intrinsic biological interactions like coevolution between antagonists is a matter of active debate. In fact, their relative importance can be assessed by tracking past population fluctuations over considerable time periods. We applied the pairwise sequentially Markovian coalescent approach on the genomes of 11 temperate Juglans species to estimate trajectories of changes in effective population size (N ) and used a Bayesian-coalescent based approach that simultaneously considers multiple genomes (G-PhoCS) to estimate divergence times between lineages.

Phylogeography of postglacial range expansion in Juglans mandshurica (Juglandaceae) reveals no evidence of bottleneck, loss of genetic diversity, or isolation by distance in the leading-edge populations.

The past studies of postglacial recolonization patterns in high latitude regions have revealed a significant role of dispersal capacity in shaping the genetic diversity and population structure of temperate trees. However, most of these studies have focused on species with long-distance dispersal followed by exponential population growth and were therefore unable to reveal the patterns in the case of a gradual expansion. Here we studied the impacts of postglacial range expansions on the distribution of genetic diversity in the Manchurian walnut (Juglans mandshurica), a common tree of East Asian cool-temperate deciduous forests that apparently lacks long-distance seed dispersal ability.

Seasonal variation in the mating system of a selfing annual with large floral displays.

Background And Aims: Flowering plants display considerable variation in mating system, specifically the relative frequency of cross- and self-fertilization. The majority of estimates of outcrossing rate do not account for temporal variation, particularly during the flowering season. Here, we investigated seasonal variation in mating and fertility in Incarvillea sinensis (Bignoniaceae), an annual with showy, insect-pollinated, 'one-day' flowers capable of delayed selfing.

Phylogeographic breaks within Asian butternuts indicate the existence of a phytogeographic divide in East Asia.

East Asia has been hypothesized to be subdivided into two distinct northern and southern areas, separated by a band of dry climate that was far more severe in the early Tertiary but still exists today. However, this biogeographic hypothesis has rarely been tested using a molecular phylogeographic approach. We genotyped 70 populations throughout the distributional range of Asian butternuts (Juglans section Cardiocaryon) using eight chloroplast DNA regions, one single-copy nuclear gene, and 17 nuclear microsatellite loci, supplemented with paleodistribution modeling of the major genetic clades.

Evolutionary history of a widespread tree species Acer mono in East Asia.

East Asia has the most diverse temperate flora in the world primarily due to the lack of Pleistocene glaciation and the geographic heterogeneity. Although increasing phylogeography studies in this region provided more proofs in this issue, discrepancies and uncertainty still exist, especially in northern temperate deciduous broad-leaved and coniferous mixed forest region (II). And a widespread plant species could reduce the complexity to infer the relationship between diversity and physiographical pattern.

Contrasts between the phylogeographic patterns of chloroplast and nuclear DNA highlight a role for pollen-mediated gene flow in preventing population divergence in an East Asian temperate tree.

Plant phylogeographic studies in East Asia have provided support for the biogeographic hypothesis that the complex landforms and climate of this region have provided substantial opportunities for allopatric speciation. However, most of these studies have been based on maternally inherited chloroplast DNA (cpDNA) markers and were therefore unable to reveal the role of pollen-mediated gene flow in preventing population divergence. Here, we investigate the phylogeography of the Chinese walnut Juglans cathayensis, a temperate deciduous tree widely distributed across disjunct montane sites in subtropical China.

Influence of asymmetrical mating patterns and male reproductive success on the maintenance of sexual polymorphism in Acer pictum subsp. mono (Aceraceae).

Populations of Acer species often contain more than three sex phenotypes with complex sexual polymorphism including duodichogamy, protandry and protogyny. We identified the mechanisms that maintain sexual polymorphism in Acer pictum subsp. mono, a temperate tree from northern China, by investigating maternal mating patterns and male reproductive success.

Development of polymorphic microsatellite markers for Incarvillea sinensis (Bignoniaceae).

Premise Of The Study: Microsatellite markers were developed for Incarvillea sinensis var. sinensis (Bignoniaceae), an annual herb endemic to Inner Mongolia, to study the degree to which delayed self-fertilization is favored.

Methods And Results: Eight polymorphic primer sets were isolated and characterized in two Inner Mongolia populations of I.

Nuclear and chloroplast DNA phylogeography reveal two refuge areas with asymmetrical gene flow in a temperate walnut tree from East Asia.

• Recently, there has been a debate about whether the temperate forests of East Asia merged or fragmented during glacial periods in the Pleistocene. Here, we tested these two opposing views through phylogeographical studies of the temperate-deciduous walnut tree, Juglans mandshurica (Juglandaceae) in northern and northeastern China, as well as Japan and Korea. • We assessed the genetic structure of 33 natural populations using 10 nuclear microsatellite loci and seven chloroplast DNA (cpDNA) fragments.

Variation in floral sex allocation and reproductive success in sequentially flowering inflorescence of Corydalis remota var. lineariloba (Fumariaceae).

In hermaphroditic plants, female reproductive success often varies among different positions within an inflorescence. However, few studies have evaluated the relative importance of underlying causes such as pollen limitation, resource limitation or architectural effect, and few have compared male allocation. During a 2-year investigation, we found that female reproductive success of an acropetally flowering species, Corydalis remota Fisch.