Phylogeographic analyses of a widely distributed Populus davidiana: Further evidence for the existence of glacial refugia of cool-temperate deciduous trees in northern East Asia

A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of Populus davidiana

Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the Populus davidiana southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate the contributions of the ancestral-state bases (ASBs) relative to derived bases (DBs) in the local adaptation of P. davidiana in the Yunnan-Guizhou Plateau from a quantitative perspective using whole-genome re-sequencing data from 90 P. davidiana samples from three regions across the species range. Our results showed that the uplift of the Qinghai-Tibet Plateau during the Neogene and associated climate fluctuations during the Middle Pleistocene were likely an important factor in the early divergence of P. davidiana. Highly differentiated genomic regions between populations were inferred to have undergone strong linked natural selection, and ASBs are the chief means by which populations of P. davidiana adapt to novel environmental conditions; however, when adapting to regions with high environmental differences relative to the ancestral range, the proportion of DBs was significantly higher than that of background regions, as ASBs are insufficient to cope with these environments. Finally, a number of genes were identified in the outlier region.

Genetic diversity and population dynamic of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow in Central China

Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single-copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θ w = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (F st = 0.197). Relatively low long-distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction-expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high-latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.

Genome-scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky)

Human-assisted movement has allowed the Asian longhorned beetle (ALB, Anoplophora glabripennis (Motschulsky)) to spread beyond its native range and become a globally regulated invasive pest. Within its native range of China and the Korean peninsula, human-mediated dispersal has also caused cryptic translocation of insects, resulting in population structure complexity. Previous studies used genetic methods to detangle this complexity but were unable to clearly delimit native populations which is needed to develop downstream biosurveillance tools. We used genome-wide markers to define historical population structure in native ALB populations and contemporary movement between regions. We used genotyping-by-sequencing to generate 6102 single-nucleotide polymorphisms (SNPs) and amplicon sequencing to genotype 53 microsatellites. In total, we genotyped 712 individuals from ALB's native distribution. We observed six distinct population clusters among native ALB populations, with a clear delineation between northern and southern groups. Most of the individuals from South Korea were distinct from populations in China. Our results also indicate historical divergence among populations and suggest limited large-scale admixture, but we did identify a restricted number of cases of contemporary movement between regions. We identified SNPs under selection and describe a clinal allele frequency pattern in a missense variant associated with glycerol kinase, an important enzyme in the utilization of an insect cryoprotectant. We further demonstrate that small numbers of SNPs can assign individuals to geographic regions with high probability, paving the way for novel ALB biosurveillance tools.

Ancient volcanos as species pumps: A case study of freshwater amphipods in Northeast Asia

Volcano-tectonic processes have been viewed as primary drivers in the formation of present-day diversity. Volcanos associated with mountain uplifts drive allopatric speciation through vicariance and may impact the surrounding areas like species pump or species attractor. However, the application of these hypotheses to aquatic fauna has rarely been tested explicitly. We tested these hypotheses in the Changbai Mountains (Mts), which are one of the most typical, active volcanic ranges in Northeast (NE) Asia with a long and turbulent geological history. The Gammarus nekkensis species complex of amphipod crustaceans, widely distributed throughout NE Asia with poor dispersal abilities and a long evolutionary history, is a suitable model for testing hypotheses of species pump or species attractor. Phylogenetic and ancestral range reconstructions demonstrated that the studied amphipod originated from the Changbai Mts ~27 Ma and diverged into eastern (Clade I) and western (Clade II) clades, which corresponds well with the initial volcanic eruption of the Changbai Mts in the Late Oligocene. The subsequent diversifications of subclades CI-3, CII-1a and CII-2a were probably driven by second and third eruptions of the Changbai Mts during the Miocene. In particular, the Changbai lineages had spread to the Russian Far East multiple times since the Early Miocene, and widely colonized the region during the Pleistocene. Our discoveries suggest that the ancient volcanos of the Changbai Mts act as species pumps in NE Asia, resulted in burst of diversification around the Changbai Mts and subsequent dispersals into adjacent regions.

The complete chloroplast genome sequence of Populus tremula (Salicaceae)

The complete chloroplast genome sequence of Populus tremula was characterized from Illumina pair-end sequencing. The chloroplast genome of P. tremula was 156,862 bp in length, containing a large single-copy region (LSC) of 84,971 bp, a small single-copy region (SSC) of 16,605 bp, and two inverted repeat (IR) regions of 27,640 bp. The overall GC content is 30.69%, while the correponding values of the LSC, SSC, and IR regions are 64.5%, 69.3%, and 60.1%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. tremula and Populus davidiana clustered together as sisters to other Populus species.

Phylogeographic analyses of poplar revealed potential glacial refugia and allopatric divergence in southwest China

The distribution pattern and genetic structure of plant species have been profoundly influenced by climate oscillations. Phylogeographic analyses have been numerously conducted in biodiversity hotspot regions and some general conclusions have been documented. However, other regions have received less attentions and these places may serve as potential glacial refugia for plant species to survive the Quaternary glaciation. Here, we used six nuclear and three cpDNA markers to estimate the phylogeographic pattern of Populus davidiana, a widespread species distributed in southwest China. As a widely distributed species in southwest China, the nucleotide diversity of P. davidiana was relatively high (N _a = 6.28, H _O = 0.534, and H _E = 0.658). Genetic differentiation (F _ST) between the two main distribution regions, Yunnan and Guizhou provinces, was 0.21221. According to the composition of chloroplast haplotypes and the result of structure in these populations, we clearly distinguished two distantly sublineages corresponding to two distribution regions. Results of the Mantel test showed that there was a significant correlation between genetic distance and geographical distance (R ² = 0.8252, p<.05). The topographically heterogeneous regions and the low dispersal ability of seed and pollen may lead to high genetic differentiation between these two regions. A potential glacial refugia for P. davidiana located in adjacent regions to the Hengduan range was revealed and allopatric divergence in separated glacial refugia may directly lead to the present phylogeographic pattern of this species.

Genetic architecture, demographic history, and genomic differentiation of Populus davidiana revealed by whole-genome resequencing

Forest trees are an excellent resource from which to understand population differentiation and heterogeneous genome variation patterns due to the majority of forest trees being distributed widely and able to adapt to different climates and environments. Populus davidiana is among the most geographically widespread and ecologically important tree species in China. Whole-genome resequencing data of 75 individual examples of P. davidiana throughout China were conducted, finding that all examples from different regions were clearly divided into either Northeast (N), Central (C), and South (S) populations. The ancestors of P. davidiana diverged into Northern group, comprising both N and C and Southern populations approximately 792,548 years ago. This time point of differentiation suggests that divergence of P. davidiana populations might have been triggered by the mid-Pleistocene transition. The three populations experienced considerable periods of bottleneck following divergence, with population expansion beginning around 5,000 years ago after the end of the last glacial maximum. We found N to be the center of origin of P. davidiana in China. The migration route of P. davidiana in China was from N to S. Although the majority of the regions of genomic differentiation between N and S populations can be explained by neutral processes, a number of tested outlier regions were also found to have been significantly influenced by natural selection. Our results highlight that linked selection and rates of recombination were important factors in genomic differentiation between the N and S populations. Finally, we identified a substantial number of functional genes related to climate change during population differentiation and adaptive evolution.

A Disjunctive Marginal Edge of Evergreen Broad-Leaved Oak (Quercus gilva) in East Asia: The High Genetic Distinctiveness and Unusual Diversity of Jeju Island Populations and Insight into a Massive, Independent Postglacial Colonization

Jeju Island is located at a marginal edge of the distributional range of East Asian evergreen broad-leaved forests. The low genetic diversity of such edge populations is predicted to have resulted from genetic drift and reduced gene flow when compared to core populations. To test this hypothesis, we examined the levels of genetic diversity of marginal-edge populations of Quercus gilva, restricted to a few habitats on Jeju Island, and compared them with the southern Kyushu populations. We also evaluated their evolutionary potential and conservation value. The genetic diversity and structure were analyzed using 40 polymorphic microsatellite markers developed in this study. Ecological Niche Modeling (ENM) has been employed to develop our insights, which can be inferred from historical distribution changes. Contrary to our expectations, we detected a similar level of genetic diversity in the Jeju populations, comparable to that of the southern Kyushu populations, which have been regarded as long-term glacial refugia with a high genetic variability of East Asian evergreen trees. We found no signatures of recent bottlenecks in the Jeju populations. The results of STRUCTURE, neighbor-joining phylogeny, and Principal Coordinate Analysis (PCoA) with a significant barrier clearly demonstrated that the Jeju and Kyushu regions are genetically distinct. However, ENM showed that the probability value for the distribution of the trees on Jeju Island during the Last Glacial Maximum (LGM) converge was zero. In consideration of these results, we hypothesize that independent massive postglacial colonization from a separate large genetic source, other than Kyushu, could have led to the current genetic diversity of Jeju Island. Therefore, we suggest that the Jeju populations deserve to be separately managed and designated as a level of management unit (MU). These findings improve our understanding of the paleovegetation of East Asian evergreen forests, and the microevolution of oaks.

The complete chloroplast genome sequence of Populus davidiana, and a comparative analysis with other Populus species

Populus davidiana plays an important ecological role in boreal and temperate forests, serving as wildlife habitats and watersheds. The complete chloroplast genome sequence of P. davidiana was characterized from Illumina pair-end sequencing. The chloroplast genome of P. davidiana was 155,325 bp in length, containing a large single-copy region (LSC) of 84,679 bp, a small single-copy region (SSC) of 16,862 bp, and two inverted repeat (IR) regions of 26,892 bp. The overall GC content is 36.80%, while the corresponding values of the LSC, SSC, and IR regions are 34.5%, 30.5%, and 42.5%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species), and 8 rRNA genes (4 rRNA species). The neighbour-joining phylogenetic analysis showed that P. davidiana and P. hopeiensis clustered together as sisters to other Populus species.

The complete chloroplast genome sequence of Populus rotundifolia, and a comparative analysis with other Populus species

Populus rotundifolia, which is an endemic of the Himilayas and adjacent regions, is the species that occupy the highest habitat in the Populus genus. The complete chloroplast genome sequence of Populus rotundifolia was characterized from Illumina pair-end sequencing. The chloroplast genome of P. rotundifolia was 155,212 bp in length, containing a large single-copy region (LSC) of 84,545 bp, a small single-copy region (SSC) of 16,859 bp, and two inverted repeat (IR) regions of 26,904 bp. The overall GC content is 36.80%, while the correponding values of the LSC, SSC, and IR regions are 34.5%, 30.5%, and 42.3%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. rotundifolia and Populus davidiana clustered together as sisters to other Populus species.

The complete chloroplast genome sequence of Artemisia ordosica

The complete chloroplast genome sequence of Artemisia ordosica was characterized from Illumina pair-end sequencing. The chloroplast genome of A. ordosica was 151,209 bp in length, containing a large single-copy region (LSC) of 80,975 bp, a small single-copy region (SSC) of 16,002 bp, and two inverted repeat (IR) regions of 27,116 bp. The overall GC content is 30.71%, while the correponding values of the LSC, SSC, and IR regions are 64.2%, 69.3%, and 60.0%, respectively. The genome contains 138 complete genes, including 91 protein-coding genes (62 protein-coding gene species), 39 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that A. ordosica and Artemisia scoparia clustered together as sisters to other Artemisia species.

The complete chloroplast genome sequence of Populus trinervis, and a comparative analysis with other Populus species

Populus trinervis, which is a unique plant for China. The complete chloroplast genome sequence of Populus trinervis was characterized from Illumina pair-end sequencing. The chloroplast genome of P. trinervis was 156,415 bp in length, containing a large single-copy region (LSC) of 84,805 bp, a small single-copy region (SSC) of 16,505 bp, and two inverted repeat (IR) regions of 27,554 bp. The overall GC content is 36.70%, while the corresponding values of the LSC, SSC, and IR regions are 34.5, 30.5, and 42.0%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species), and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. trinervis and P. hopeiensis clustered together as sisters to other Populus species.

The complete chloroplast genome sequence of Populus davidiana (Salicaceae)

The complete chloroplast genome sequence of Populus davidiana was characterized from Illumina pair-end sequencing. The chloroplast genome of P. davidiana was 156,868 bp in length, containing a large single-copy region (LSC) of 84,976 bp, a small single-copy region (SSC) of 16,606 bp, and two inverted repeat (IR) regions of 27,643 bp. The overall GC content is 30.70%, while the correponding values of the LSC, SSC, and IR regions are 64.6%, 69.2%, and 60.1%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. davidiana and Populus rotundifolia clustered together as sisters to other Populus species.

The complete chloroplast genome sequence of medicinal plant, Artemisia gmelinii

The complete chloroplast genome sequence of Artemisia gmelinii was characterized from Illumina pair-end sequencing. The chloroplast genome of A. gmelinii was 151,050 bp in length, containing a large single-copy region (LSC) of 80,976 bp, a small single-copy region (SSC) of 16,006 bp, and two inverted repeat (IR) regions of 27,034 bp, each. The overall GC content is 30.70%, while the correponding values of the LSC, SSC, and IR regions are 64.6, 69.2, and 60.1%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that A. gmelinii and Artemisia scoparia clustered together as sisters to other Artemisia species.

The complete chloroplast genome sequence of Populus tremuloides (Salicaceae)

The complete chloroplast genome sequence of Populus tremuloides was characterized from Illumina pair-end sequencing. The chloroplast genome of P. tremuloides was 155,816 bp in length, containing a large single-copy region (LSC) of 85,804 bp, a small single-copy region (SSC) of 16,489 bp, and two inverted repeat (IR) regions of 26,962 bp. The overall GC content is 36.71%, while the correponding values of the LSC, SSC, and IR regions are 64.9%, 69.2%, and 60.3%, respectively. The genome contains 167 complete genes, including 86 protein-coding genes (77 protein-coding gene species), 73 tRNA genes (29 tRNA species) and 8 rRNA genes(4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. tremuloides and Populus tremula clustered together as sisters to other Populus species.

Phylogeographic analyses of a widely distributed Populus davidiana: Further evidence for the existence of glacial refugia of cool-temperate deciduous trees in northern East Asia

Despite several phylogeographic studies had provided evidence to support the existence of glacial refugia of cool-temperate deciduous trees in northeast China, the species used in these studies were limited by the species ranges, which could not exclude the possibility that northern populations were the colonists from southern refugial populations during the last glacial maximum (LGM). Here, we estimated the nucleotide variation in Populus davidiana, a widespread species distributed in Eurasia. Three groups in northeast, central, and southwest China were constructed according to the simulation results from SAMOVA, composition of chloroplast haplotypes and structure results. We revealed that the northeast China had endemic haplotypes, the haplotypes and nucleotide diversity in northern regions were not lower than that in southern China, and this species has not experienced population expansion base on the estimation of Bayesian skyline plots. Ecological niche modeling (ENM) indicated that the northeast China had a high suitability score during the last glacial maximum. The combined evidence clearly demonstrated that northeastern and southwestern refugia were maintained across the current distributional range of P. davidiana during the LGM. The genetic differentiation between these two refugia might be mainly caused by differences of climate among these areas. The phylogeographic analyses of a widely distributed P. davidiana provided robust evidence to clarify the issue of refugia in northeast China, and these results are of great importance for understanding the influence of Quaternary glaciations on the distribution and evolution of species in East Asia.