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

Across two phylogeographic breaks: Quaternary evolutionary history of a mountain aspen (Populus rotundifolia) in the Hengduan Mountains

Biogeographical barriers to gene flow are central to plant phylogeography. In East Asia, plant distribution is greatly influenced by two phylogeographic breaks, the Mekong-Salween Divide and Tanaka-Kaiyong Line, however, few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both. Here we used 14 microsatellite loci and four chloroplast DNA fragments to examine genetic diversity and distribution patterns of 49 populations of Populus rotundifolia, a species that spans both the Mekong-Salween Divide and the Tanaka-Kaiyong Line in southwestern China. Demographic and migration hypotheses were tested using coalescent-based approaches. Limited historical gene flow was observed between the western and eastern groups of P. rotundifolia, but substantial flow occurred across both the Mekong-Salween Divide and Tanaka-Kaiyong Line, manifesting in clear admixture and high genetic diversity in the central group. Wind-borne pollen and seeds may have facilitated the dispersal of P. rotundifolia following prevalent northwest winds in the spring. We also found that the Hengduan Mountains, where multiple genetic barriers were detected, acted on the whole as a barrier between the western and eastern groups of P. rotundifolia. Ecological niche modeling suggested that P. rotundifolia has undergone range expansion since the last glacial maximum, and demographic reconstruction indicated an earlier population expansion around 600 Ka. The phylogeographic pattern of P. rotundifolia reflects the interplay of biological traits, wind patterns, barriers, niche differentiation, and Quaternary climate history. This study emphasizes the need for multiple lines of evidence in understanding the Quaternary evolution of plants in topographically complex areas.

Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai-Tibetan plateau

KEY MESSAGE

Positive selection genes are related to metabolism, while differentially expressed genes are related to photosynthesis, suggesting that genetic adaptation and expression regulation may play independent roles in different gene classes. Genome-wide investigation of the molecular mechanisms for high-altitude adaptation is an intriguing topic in evolutionary biology. The Qinghai-Tibet Plateau (QTP) with its extremely variable environments is an ideal site for studying high-altitude adaptation. Here, we used transcriptome data of 100 individuals from 20 populations collected from various altitudes on the QTP to investigate the adaptive mechanisms of the aquatic plant Batrachium bungei at both the genetic and transcriptional level. To explore genes and biological pathways that may contribute to QTP adaptation, we employed a two-step approach, in which we identified positively selected genes and differentially expressed genes using the landscape genomic and differential expression approaches. The positive selection analysis showed that genes involved in metabolic regulation played a crucial role in B. bungei adaptation to the extreme environments of the QTP, especially intense ultraviolet radiation. Altitude-based differential expression analysis suggested that B. bungei could increase the rate of energy dissipation or reduce the efficiency of light energy absorption by down regulating the expression of photosynthesis-related genes to adapt to the strong ultraviolet radiation. Weighted gene co-expression network analysis identified ribosomal genes as hubs of altitude adaptation in B. bungei. Only a small part of genes (about 10%) overlapped between positively selected genes and differentially expressed genes in B. bungei, suggesting that genetic adaptation and gene expression regulation might play relatively independent roles in different categories of functional genes. Taken together, this study enriches our understanding of the high-altitude adaptation mechanism of B. bungei on the QTP.

Clear phylogeographical structures shed light on the origin and dispersal of the aquatic boreal plant Hippuris vulgaris

Aquatic plants are an important ecological group in the arctic flora; however, their evolutionary histories remain largely unknown. In order to deepen our understanding of the evolution of these plants, we explored the phylogeographical structure of an aquatic boreal plant Hippuris vulgaris in a broad geographical sampling from Eurasia and North America using the chloroplast intergenic spacer psbA-trnH and seven nuclear microsatellite loci. Two closely-related species H. lanceolata and H. tetraphylla were also included because of their taxonomic controversy. Both chloroplast DNA sequences and nuclear microsatellite data revealed three genetic lineages with distinct distribution ranges. Incongruence between nuclear and chloroplast DNA lineages occurred in 14 samples from Russian Far East and Europe caused by inter-lineage hybridization. No private haplotypes or independent genetic clusters were evident in H. lanceolata or H. tetraphylla, suggesting that these two species should be considered conspecific ecotypes of H. vulgaris. Analysis using Approximate Bayesian Computation-Random Forest approach suggests that Hippuris vulgaris originated in China, followed by dispersal into Russia plus Northeast China, then successively westwards into Europe and North America, and finally into the Russian Far East from both North America and Russia plus Northeast China. This study is the first to elucidate the historical dispersal processes of a circumarctic aquatic plant across the entirety of its range.

Effects of highland environments on clonal diversity in aquatic plants: An interspecific comparison study on the Qinghai-Tibetan Plateau

Clonal reproduction is one of the most distinctive characteristics of plants and is common and diverse in aquatic macrophytes. The balance between sexual and asexual reproduction is affected by various conditions, especially adverse environments. However, we know little about clonal diversity of aquatic plants under suboptimal conditions, such as at high altitudes, and having this information would help us understand how environmental gradients influence patterns of clonal and genetic variation in freshwater species. The microsatellite data of four aquatic taxa in our previous studies were revisited to estimate clonal and genetic diversity on the Qinghai-Tibetan Plateau. Clonal diversity among different genetic groups was compared. Local environmental features were surveyed. Beta regressions were used to identify the environmental factors that significantly explained clonal diversity for relative taxon. The level of clonal diversity from high to low was Stuckenia filiformis > Hippuris vulgaris > Myriophyllum species > Ranunculus section Batrachium species. A positive correlation between clonal and genetic diversity was identified for all taxa, except H. vulgaris. Clonal diversity was affected by climate in S. filiformis and by the local environment in H. vulgaris. For Myriophyllum spp., low elevation and high sediment nutrition were significant for sexual recruitment. The environmental effects on clonal diversity were not significant in R. sect. Batrachium spp. Clonal diversity of aquatic plants is moderate to high and varies greatly in highlands. The effects of breeding systems and environmental factors on the patterns of clonal variation were identified. Elevational gradients, climates and local conditions play different roles in clonal diversity among relative taxon. Our results highlight the importance of sexual recruitment in alpine aquatic plant populations and the influence of environmental factors on the genetic patterns in freshwater species at local and regional scales.

Phylogeography and genetic diversity of the widespread katydid Ducetia japonica (Thunberg, 1815) across China

Habitat fragmentation can lower migration rates and genetic connectivity among remaining populations of native species. Ducetia japonica is one of the most widespread katydids in China, but little is known about its genetic structure and phylogeographic distribution. We combined the five-prime region of cytochrome c oxidase subunit I (COI-5P), 11 newly developed microsatellite loci coupled with an ecological niche model (ENM) to examine the genetic diversity and population structure of D. japonica in China and beyond to Laos and Singapore. Both Bayesian inference (BI) and haplotype network methods revealed six mitochondrial COI-5P lineages. The distribution of COI-5P haplotypes may not demonstrate significant phylogeographic structure (N ST > G ST, p > .05). The STRUCTURE analysis based on microsatellite data also revealed six genetic clusters, but discordant with those obtained from COI-5P haplotypes. For both COI-5P and microsatellite data, Mantel tests revealed a significant positive correlation between geographic and genetic distances in mainland China. Bayesian skyline plot (BSP) analyses indicated that the population size of D. japonica's three major mitochondrial COI-5P lineages were seemingly not affected by last glacial maximum (LGM, 0.015-0.025 Mya). The ecological niche models showed that the current distribution of D. japonica was similar to the species' distribution during the LGM period and only slightly extended in northern China. Further phylogeographic studies based on more extensive sampling are needed to identify specific locations of glacial refugia in northern China.

The complete chloroplast genome of Hippuris vulgaris (Plantaginaceae)

Hippuris vulgaris is an aquatic perennial herb distributed worldwide. In this research, the complete chloroplast genome of H. vulgaris was sequenced and assembled. Its complete genome size was 152,698 bp in length. The typical quadripartite structure was shown, which contained a large single-copy region (82,940 bp), a small single-copy region (18,262 bp), and a pair of inverted repeat regions (25,748 bp). The CG content of this genome was 37.6%. A total of 114 genes have been identified in the genome, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. In addition, 18 genes possessed at least one intron. The phylogenetic analysis indicated that H. vulgaris was nested in Plantaginaceae with 100% bootstrap value and was a sister to Digitalis, Plantago, Hemiphragma, Veronica and Veronicastrum.

The complete chloroplast genome sequences of Hippuris vulgaris (Plantaginaceae)

Two complete chloroplast genomes of Hippuris vulgaris (H. vulgaris_A and H. vulgaris_B), representing two distinct clades in China, were sequenced and assembled in this study. The circular genomes were 152,763 and 152,713 bp in length and exhibit a typical quadripartite structure of the large single-copy (LSC, 82,983/82,949 bp) and small single-copy (SSC, 18,294/18,278 bp) regions, separated by a pair of inverted repeats (IRs, both 25,743 bp). Both two cp genomes identically contain 133 genes, including 88 protein-coding genes, 37 tRNA, and eight rRNA genes. The phylogenetic analysis within Plantaginaceae demonstrated Hippuris an independent clade included in the expanded Plantaginaceae.

Influence of environmental factors on the genetic variation of the aquatic macrophyte Ranunculus subrigidus on the Qinghai-Tibetan Plateau

BACKGROUND

Due to the environmental heterogeneity along elevation gradients, alpine ecosystems are ideal study objects for investigating how ecological variables shape the genetic patterns of natural species. The highest region in the world, the Qinghai-Tibetan Plateau, is a hotspot for the studies of evolutionary processes in plants. Many large rivers spring from the plateau, providing abundant habitats for aquatic and amphibious organisms. In the present study, we examined the genetic diversity of 13 Ranunculus subrigidus populations distributed throughout the plateau in order to elucidate the relative contribution of geographic distance and environmental dissimilarity to the spatial genetic pattern.

RESULTS

A relatively low level of genetic diversity within populations was found. No spatial genetic structure was suggested by the analyses of molecular variance, Bayesian clustering analysis and Mantel tests. Partial Mantel tests and multiple matrix regression analysis showed a significant influence of the environment on the genetic divergence of the species. Both climatic and water quality variables contribute to the habitat heterogeneity of R. subrigidus populations.

CONCLUSIONS

Our results suggest that historical processes involving long-distance dispersal and local adaptation may account for the genetic patterns of R. subrigidus and current environmental factors play an important role in the genetic differentiation and local adaptation of aquatic plants in alpine landscapes.

Evolutionary History of Rhus chinensis (Anacardiaceae) From the Temperate and Subtropical Zones of China Based on cpDNA and Nuclear DNA Sequences and Ecological Niche Model

To explore the origin and evolution of local flora and vegetation, we examined the evolutionary history of Rhus chinensis, which is widely distributed in China’s temperate and subtropical zones, by sequencing three maternally inherited chloroplast DNAs (cpDNA: trnL-trnF, psbA-trnH, and rbcL) and the biparentally inherited nuclear DNA (nuDNA: LEAFY) from 19 natural populations of R. chinensis as well as the ecological niche modeling. In all, 23 chloroplast haplotypes (M1–M23) and 15 nuclear alleles (N1–N15) were detected. The estimation of divergence time showed that the most recent common ancestor dated at 4.2 ± 2.5 million years ago (Mya) from cpDNA, and the initial divergence of genotypes occurred at 4.8 ± 3.6 Mya for the nuDNA. Meanwhile, the multimodality mismatch distribution curves and positive Tajima’s D values indicated that R. chinensis did not experience population expansion after the last glacial maximum. Besides, our study was also consistent with the hypothesis that most refugia in the temperate and subtropical zones of China were in situ during the glaciation.

Association analysis uncovers the genetic basis of general combining ability of 11 yield-related traits in parents of hybrid rice

Association analysis between constructed single nucleotide polymorphism linkage disequilibrium blocks (SNPLDBs) and general combining ability (GCA) effects is a novel approach to uncover the genetic basis of GCA within the sequence genomes of parents of hybrid rice. Here, we calculated the GCA effect values of 33 parents of hybrid rice and sequenced them to identify genome-wide single nucleotide polymorphisms (SNPs). In total, 64.6 % of the uniquely mapped paired-end short reads revealed a final total of 291 959 SNPs between the 33 parental genomes and the Nipponbare reference genome. The identified SNPs were non-randomly distributed among all chromosomes of rice, whereas one-fourth of the SNPs were situated in the exonic regions with 16 % being non-synonymous. Further, the identified SNPs were merged and optimized for construction of 2612 SNPLDB markers, using linkage disequilibrium information. The single-factor analysis of variance-based association method between the constructed SNPLDB markers and GCA effects values detected 99 significant SNPLDBs for GCA of 11 yield-related traits. The associated SNPLDB markers explained 26.4 % of phenotypic variations with traits, on average. We mined 50 favourable GCA alleles at the associated SNPLDBs regions, distributed across the 33 parental genomes. The parental genomes possessed a small number of favourable GCA alleles for studied traits, with the exception of days to heading and plant height. Our results suggest that the identified GCA alleles could be used to improve the GCA performance of parents of hybrid rice through optimal crossing design. Moreover, favourable GCA alleles should be incorporated in the parental genomes through marker-assisted selection experiments, and the parental lines carrying more alleles could be utilized in breeding as superior parents for developing rice hybrids of desirable characteristics.