Chloroplast Fragments Research Articles

High effects of climate oscillations on population diversity and structure of endangered Myricaria laxiflora.

Exploring the effects of climate oscillations on the population diversity and structure of endangered organisms in the Three Gorges Reservoir (TGR) area is essential for hydrological environment changes on endangered organism evolution. Myricaria laxiflora is an endemic and endangered shrub restricted to the TGR along the banks of Yangtze River, China. Recently, six natural populations of this species were newly found upstream and downstream of the TGR, whose habitats have been dramatically changed by the summer flooding regulated by large dams. To study the water level fluctuations and climatic shifts on the genetic diversity and genetic differentiation of the six natural populations, 303 individuals from six populations were analyzed based on one nuclear DNA (ITS) and four chloroplast fragments (trnL-F, psbA-trnH, rps16, and rpl16). The phylogenetic tree and significant genetic divergence identified in the cpDNA and ITS with genetic isolation and limited gene flow among regions suggested that the six populations separated well to two groups distributed upstream and downstream. The MaxEnt modeling results indicated that obvious unidirectional eastward migration via Yangtze River gorges watercourse mediated from Last Interglacial to Last Glacial Maximum were showed with the narrow scale distributions of six remnant populations and nine extirpated populations. The initial habitat fragmentation could be triggered by the accumulation of local habitat loss of the impoundment of the TGR during the Present period and might remain stable restoration with bidirectional diffusion in the Future. Divergences among M. laxiflora populations might have been induced by the drastic changes of the external environment and limited seed/pollen dispersal capacity, as the results of long-term ecological adaptability of summer flooding stress. The haplotypes of nuclear gene could be used for population's differentiation and germplasm protection. This identified gene flow and range dynamics have provided support for the gene-flow and geology hypothesis. It is also crucial for rescuing conservation to understand the impact of environmental dynamics on endangered organism evolution.

Effects of climatic fluctuations on the fragmented distribution pattern of a Tertiary relict plant, Pseudotaxus chienii (Taxaceae), in subtropical China

Abstract Habitat fragmentation can facilitate local adaptation of species to heterogeneous environments and affect population demographic history. To understand the factors influencing evolutionary dynamics, such as climatic fluctuations and complex geomorphological features, we used 18 chloroplast microsatellites, 15 nuclear microsatellites, three chloroplast fragments, and two nuclear regions to explore the genetic structure and phylogeographical history of Pseudotaxus chienii. Furthermore, its current and past distributions were constructed based on ecological niche modelling. Moderate to high levels of genetic diversity were found at the species level. Precipitation was a decisive factor influencing the genetic structure of P. chienii. In addition, local adaptation to heterogeneous environments also contributed to maintain the fragmented distribution. Finally, incomplete lineage sorting led to the cyto-nuclear discordance. Overall, we show that pre-Quaternary and Quaternary climatic fluctuations and restricted gene flow exerted significant effects on the formation and maintenance of the fragmented distribution of P. chienii. The study provides new insights into the evolutionary history of plants in subtropical China.

Phylogenetic Diversity of Prokaryotic Communities of the Upper Sediment Layers of the Kandalaksha Gulf, White Sea

Abstract—Microbial communities of the sediments of the Kandalaksha Gulf (White Sea) remain insufficiently studied. While the data on the rates of some microbial processes are available, very little is known of the microorganisms inhabiting these sediments. In the present work, high-throughput sequencing of variable regions of the 16S rRNA genes was used to characterize the microbial communities of 47 Kandalaksha Gulf sediment samples, collected at 10 cm below from the bottom surface. Pseudomonadota and Desulfobacterota were the most abundant phyla, which together comprised about a half of all prokaryotes. Determination of the dominant genus-level taxon proved impossible. The most represented chemoorganotrophic microorganisms were uncultured Sandaracinaceae (up to 10.8%) and Woeseia (up to 7.5%). Sulfate-reducing bacteria were important community components in the studied upper sediment layers, with uncultured groups SEEP-SRB1 (up to 7.0%) and Sva0081 (up to 5.9%) among the most abundant. In some samples, the genera Sulfurovum (up to 15.5%) and Thiohalophilus (up to 7.0%), involved in the oxidation of sulfur compounds, were important components of the community. Among the archaeal ASVs, the genus Nitrosopumilus, oxidizing ammonium to nitrite, exhibited the highest relative abundance (up to 6.9% of the total number of prokaryotes). Numerous sequences identified as the 16S rRNA gene fragments of chloroplasts were found in the samples, indicating that the rate of organic matter delivery to the upper sediment layers exceeded the rate of its degradation.

Revealing biogeographic patterns in genetic diversity of native and invasive plants and their association with soil community diversity in the Chinese coast

Within‐species genetic diversity is shaped by multiple evolutionary forces within the confines of geography, and has cascading effects on the biodiversity of other taxa and levels. Invasive species are often initially limited in genetic diversity but still respond rapidly to their new range, possibly through ‘pre‐adapted' genotypes or multiple sources of genetic diversity, but little is known about how their genetic structure differs from that of native species and how it alters the genetic‐species diversity relationship. Here, we selected a widespread native species Phragmites australis and its co‐occurring invasive competitor Spartina alterniflora as our model plant species. We investigated the genetic structure of P. australis using two chloroplast fragments and ten nuclear microsatellites in 13 populations along the Chinese coastal wetlands. We discovered a distinct geographical differentiation, showing that the northern and southern populations harbored unique genotypes. We also found a significant increase in genetic diversity (allelic richness and expected heterozygosity) from south to north. Combined with previous studies of S. alterniflora, the Mantel tests revealed a significant correlation of genetic distances between P. australis and S. alterniflora even when controlling for geographic distance, suggesting that the invasive species S. alterniflora might exhibit a phylogeographic pattern similar to that of the native species to some extent. Furthermore, our results suggest that the S. alterniflora invasion has altered the relationship between the genetic diversity of the dominant native plant and the associated species richness of soil nematodes. The reason for the alteration of genetic‐species diversity relationship might be that the biological invasion weakens the environmental impact on both levels of biodiversity. Our findings contribute to understanding the latitudinal patterns of intraspecific genetic diversity in widespread species. This work on the genetic diversity analysis of native species also provides significant implications for the invasion stage and ecological consequences of biological invasions.

Phylogeography and ecological niche modeling implicate multiple microrefugia of Swertia tetraptera during quaternary glaciations

BackgroundClimate fluctuations during the Pleistocene and mountain uplift are vital driving forces affecting geographic distribution. Here, we ask how an annual plant responded to the Pleistocene glacial cycles.MethodsIn this study, we analyzed the population demographic history of the annual herb Swertia tetraptera Maxim (Gentianaceae) endemic to Qinghai-Tibetan Plateau (QTP). A total of 301 individuals from 35 populations of S. tetraptera were analyzed based on two maternally inherited chloroplast fragments (trnL-trnF and trnS-trnG). Phylogeographic analysis was combined with species distribution modeling to detect the genetic variations in S. tetraptera.ResultsThe genetic diversity of S. tetraptera was high, likely due to its wide natural range, high proportion of endemic haplotypes and evolutionary history. Fifty-four haplotypes were identified in S. tetraptera. Only a few haplotypes were widespread (Hap_4, Hap_1, Hap_3), which were dispersed throughout the present geographical range of S. tetraptera, while many haplotypes were confined to single populations. The cpDNA dataset showed that phylogeographic structuring was lacking across the distribution range of S. tetraptera. Analyses of molecular variance showed that most genetic variation was found within populations (70.51%). In addition, the relationships of the haplotypes were almost completely unresolved by phylogenetic reconstruction. Both mismatch distribution analysis and neutrality tests showed a recent expansion across the distribution range of S. tetraptera. The MaxEnt analysis showed that S. tetraptera had a narrow distribution range during the Last Glacial Maximum (LGM) and a wide distribution range during the current time, with predictions into the future showing the distribution range of S. tetraptera expanding.ConclusionOur study implies that the current geographic and genetic distribution of S. tetraptera is likely to have been shaped by Quaternary periods. Multiple microrefugia of S. tetraptera existed during Quaternary glaciations. Rapid intraspecific diversification and hybridization and/or introgression may have played a vital role in shaping the current distribution patterns of S. tetraptera. The distribution range of S. tetraptera appeared to have experienced contraction during the LGM; in the future, when the global climate becomes warmer with rising carbon dioxide levels, the distribution of S. tetraptera will expand.

Phylogeny and Flow Cytometry of the Genus Kalidium Moq. (Amaranthaceae s.l.) in Kazakhstan.

The article presents data on phylogeny, genome size, and ploidy of species of the genus Kalidium Moq. in the flora of Kazakhstan. Genus Kalidium belongs to the tribe Salicornieae of the subfamily Salicornioideae of the family Chenopodiaceae and unites eight species, the main range of which covers the Iranian-Turanian and Central Asian deserts. There are four species in the flora of Kazakhstan: K. foliatum, K. caspicum, K. schrenkianum, and the recently described K. juniperinum. Populations of species of the genus Kalidium in the saline deserts of Kazakhstan occupy large areas, often forming monodominant communities. Sometimes there is a joint growth of two and very rarely three species of the genus. During the period of fieldwork (2021-2022), populations were identified in which these species grew together with a predominance, in most cases, of K. caspicum. Samples of representatives from 15 populations were collected for research. Selected plant samples were studied by flow cytometry to determine plant ploidy. Sequencing of nrITS and two chloroplast fragments were used to build a phylogenetic tree, including sequences from the NCBI database., A phylogenetic tree of species of the genus Kalidium was compiled, which takes previously published data into consideration. In the valley of the middle reaches of the Syrdarya River, tetraploid populations of K. caspicum were found. A hybrid between K. foliatum and K. caspicum was found in the Ili River valley (Almaty region, Uigur district). To identify phylogenetic processes at the intraspecific level, the SCoT (Start codon targeted) fingerprinting method was used.

Chloroplast DNA Markers on the Phylogeography Study of Roburoid Oaks (<i>Quercus</i> L. sect. <i>Quercus</i>, Fagaceae) in the Crimean-Caucasian Region

The variability of five fragments of chloroplast DNA (ASq, CDq, TFq, trnH-psbA and trnK-matK) with a total length of more than 10,000 bp in three species of roburoid oaks of the Crimean-Caucasian region (Q. robur, Q. petraea, Q. pubescens) was studied. A total of 11 haplotypes were found in 290 individuals from 20 populations, 10 of which differed from the haplotypes of the main range. The obtained results show a pronounced structure of the geographical distribution of haplotypes of roburoid oaks in the Crimea and the Caucasus, and the chloroplast haplotypes of the region belong to several divergent phylogenetic lines. A comparison with data from other studies was carried out, with an assessment of the degree of effectiveness of the use of various chloroplast fragments and markers. The isolated phylogenetic position of the haplotypes of the Crimean-Caucasian populations and deep differences from the haplotypes of the main area allows us to conclude that robouroid oaks have historically been isolated for a long time in the Caucasus and Crimea. At the same time, the presence of common haplotypes indicates closer historical ties between the Crimean-Caucasian populations with Asia Minor and the Balkans. All haplotypes are identified by three fragments (ASq, CDq and TFq), with a sufficient level of variability and suitable for solving problems of oak phylogeography in the Crimean-Caucasian region. The trnH-psbA and trnK-matK markers had a low level of variability and did not reveal additional haplotypes. Optimized genotyping options have been proposed, including both step by step sequencing, and a combination of analysis of chloroplast DNA microsatellite loci (cpSSR), restriction analysis (PCR-RFLP), and sequencing. To assess the variability of markers in a larger taxonomic range, representatives of other sections of the genus Quercus were included in the analysis. It was shown that the oak-specific primers proposed for ASq, CDq, and TFq fragments are suitable for species of other sections.

Migration patterns of Gentiana crassicaulis, an alpine gentian endemic to the Himalaya-Hengduan Mountains.

The Himalaya–Hengduan Mountain region is one of the hotspots of biodiversity research. The uplift of the Qinghai–Tibetan Plateau (QTP) and the Quaternary glaciation caused great environmental changes in this region, and the responses of many species in the QTP to the Quaternary climate are still largely unknown. The genetic structure and phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an endemic Chinese alpine species in this area, were investigated based on four chloroplast fragments and internal transcribed spacer region of the nuclear ribosomal DNA (nrITS) sequences of 11 populations. The populations with highly diverse chloroplast haplotypes were mainly found at the edge of the QTP. There were two main haplotypes of nrITS clones, one shared by the Yunnan and Guizhou populations, and the other by the remaining populations. The population with the highest diversity was the Gansu population, located at the edge of the plateau. Based on molecular dating, the diversification of G. crassicaulis at the edge of the plateau occurred before the Last Glacial Maximum (LGM), and the species may have completed its expansion from the edge to the platform. Ecological niche models were conducted to predict the distributional ranges of G. crassicaulis at present, during the LGM, and during the last interglacial (LIG) period. The results demonstrated that G. crassicaulis survived on the QTP platform and at the edge during the LGM but afterward retreated from the platform to the southern edge, followed by expansion to the platform.

Cytotype distribution and chloroplast phylogeography of the Actinidia chinensis complex

BackgroundPlant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA (ndhF-rpl132, rps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes.ResultsThe ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa. Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties’ ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM).ConclusionsPliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.

Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence of Chamaesium (Apiaceae).

Exploring the effects of orographic events and climatic shifts on the geographic distribution of organisms in the Himalayas-Hengduan Mountains (HHM) region and Qinghai-Tibetan Plateau (QTP) is crucial to understand the impact of environmental changes on organism evolution. To gain further insight into these processes, we reconstructed the evolutionary history of nine Chamaesium species distributed across the HHM and QTP regions. In total, 525 individuals from 56 populations of the nine species were analyzed based on three maternally inherited chloroplast fragments (rpl16, trnT-trnL, and trnQ-rps16) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-two chloroplast DNA (cpDNA) and 47 ITS haplotypes were identified in nine species. All of the cpDNA and ITS haplotypes were species-specific. Phylogenetic analysis suggested that all nine species form a monophyletic clade with high support. Dating analysis and ancestral area reconstruction revealed that the ancestral group of Chamaesium originated in the southern Himalayan region at the beginning of the Paleogene (60.85 Ma). The nine species of Chamaesium then separated well during the last 25 million years started in Miocene. Our maxent modeling indicated the broad-scale distributions of all nine species remained fairly stable from LIG to the present and predicted that it will remain stable into the future. The initial split of Chamaesium was triggered by climate changes following the collision of the Indian plate with the Eurasia plate during the Eocene. Subsequently, divergences within Chamaesium may have been induced by the intense uplift of the QTP, the onset of the monsoon system, and Central Asian aridification. Long evolutionary history, sexual reproduction, and habitat fragmentation could contribute to the high level of genetic diversity of Chamaesium. The higher genetic differentiation among Chamaesium populations may be related to the drastic changes of the external environment in this region and limited seed/pollen dispersal capacity.

Characterization of variability of the intergenic spacers cpDNA trnH–psbA, trnY–trnT AND rpoB–trnC in representatives of Pisum L. (Tribe Fabeae)

Background. Plant chloroplast genome have conservative structure, but its nucleotide sequence is polymorphous due to which cpDNA fragments are often used in taxonomic and phylogenetic studies. Despite the widespread distribution and use of Fabeae species, mainly peas (Pisum), data on the intraspecific diversity of cpDNA fragments are almost absent. The aim of the work was to analyze the intraspecific variability of three cpDNA spacers in Pisum.
 Materials and methods. As a result of the work, intergenic spacers trnYtrnT, trnHpsbA and rpoBtrnC in 38 accessions of the Pisum and related Fabeae species were sequenced. Despite the fact that the selected chloroplast fragments are generally considered to be sufficiently variable in plants and are often used for phylogenetic studies, Pisum accessions have been found to have no intraspecific differences in two of the three spacers sequences analyzed.
 Results and conclusion. A total 97 SNPs were detected in Pisum accessions, seven of them distinguished P. sativum from P. fulvum. The most variable of the analyzed fragments was the intergenic spacer rpoBtrnC. Based on rpoBtrnC sequence 17 haplotypes in P. sativum and four haplotypes in P. fulvum were revealed. The cpDNA sequencing data were used for a phylogenetic analysis. On the obtained tree Vavilovia formosa accession formed a separate branch from pea accessions. All Pisum accessions fall in one cluster, split into distinct P. sativum and P. fulvum subclusters (BI = 99%).

Blow to the Northeast? Intraspecific differentiation of Populus davidiana suggests a north‐eastward skew of a phylogeographic break in East Asia

AbstractAimThere is increasing interest in the role that biological traits, and historical and biogeographic processes, play in the formation of phylogeographic patterns. An arid belt that once existed in northern China might have affected many plants, but this has yet to be tested in an arid‐tolerant, wind‐dispersed species. Here, we tested how intrinsic and extrinsic factors have affected the phylogeography of Populus davidiana.LocationEast Asia.MethodsGenetic variation was surveyed across 40 populations (555 individuals) covering the Chinese range of P. davidiana, using 16 nuclear microsatellite loci (nSSRs) and four chloroplast fragments (cpDNA). Demographic and migration hypotheses were tested using coalescent‐based approaches, and the present and past potential distributions were predicted using species distribution modelling.ResultsMolecular data divide P. davidiana into two lineages, north‐eastern China (NECR) and central and northern China (CNCR); however, the dividing line is around 118ºE for nSSRs, but 122ºE for cpDNA. The range and habitat of the two lineages barely overlap at present, and their ecological separation may have initiated around the Pliocene‐Quaternary boundary, when major intraspecific cpDNA clades diverged. NECR and CNCR experienced post‐glacial north‐eastward and northward range shifts respectively. Bi‐directional historical gene flow was detected between NECR and CNCR for both bi‐parentally inherited nSSRs and maternally inherited cpDNA. Demographic inferences suggest a severe bottleneck for CNCR and especially NECR, around the latest Pleistocene.Main conclusionsThe phylogeographic break within P. davidiana reflects the impacts of biogeographic history, climate and biological traits. Its plumed, wind‐dispersed seeds might be especially significant because prevailing south‐western spring winds may have moved the NECR‐CNCR boundary further east than similar phylogenetic breaks in other species, and also moved the cpDNA boundary relative to that for nuclear markers. Biological traits, therefore, should also be considered when examining the genetic and ecological differentiation between closely related taxa.

Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification.

Although the medicinal properties of Coelogyne spp. have been previously studied, there is little genomic information providing a valuable tool for the plant taxonomy, conservation, and utilization of this genus. This study used the next-generation MiSeq sequencing platform to characterize the chloroplast (cp) genomes of Coelogyne fimbriata and Coelogyne ovalis. The Maximum Likelihood (ML) and Bayesian (BI) methods were employed to confirm the phylogenetic position of two Coelogyne species based on the whole chloroplast genome sequences. Additionally, we developed eight new primers based on the two cp genomes’ medium variable regions and evaluated the transferability to another 16 Coelogyne species. We constructed phylogenetic trees including 18 Coelogyne species and four outgroup species using the chloroplast fragments with the ML method. Our results showed that the cp genomes of C. fimbriata and C. ovalis contained a small single-copy region (18,839 and 18,851 bp, respectively) and a large single-copy region (87,606 and 87,759 bp, respectively), separated by two same-length inverted-repeat regions (26,675 bp in C. fimbriata and 26,715 bp C. ovalis, respectively). They all contained 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, revealing strong structure and gene content similarities. The phylogenetic analysis indicated a close relationship between the genera Coelogyne and Pleione. The newly developed primers revealed good transferability among the Coelogyne taxa and provided enough variable sites to distinguish C. fimbriata and C. ovalis. The two complete cp genomes and the eight new primers of Coelogyne provide new genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Coelogyne taxa.

Phylogeographic investigation of Elaeagnus mollis revealed potential glacial refugia and allopatric divergence in central China

Climate and geography oscillations in the Quaternary profoundly influenced the distribution pattern and genetic structure of plant species. Phylogeographic investigations have been numerously conducted in biodiversity hotspot regions. However, other regions have received less attention and these places may serve as potential glacial refugia for plant species. In the study presented here, phylogeographic pattern of Elaeagnus mollis, a plant species exclusively distributed in central China, was investigated using multiple nSSR loci and chloroplast fragments. As an endangered species in China, the genetic diversity of E. mollis was relatively high (Na = 7.82, HO = 0.532, and HE = 0.623). Genetic differentiation (FST) between the two main distribution regions, Shanxi and Shaanxi provinces, was 0.23177. STRUCTURE analysis of nSSR data as well as phylogenetic construction of chloroplast haplotypes clearly distinguished two distantly sublineages, corresponding well with two distribution regions. Multiple factors such as outcrossing were thought to contribute to the high level of genetic diversity. The topographically heterogeneous regions and the low dispersal ability of seed and pollen may lead to high genetic differentiation between these two regions. Two potential glacial refugia for E. mollis located in adjacent regions to the Qinling Mountains and south of the Loess Plateau were revealed, and allopatric divergence in separated glacial refugia may directly lead to the present phylogeographic pattern of this species. This study set a solid foundation for future protection and sustainable utilization of this important germplasm resource.

Spatial genetic structuring in a widespread wetland plant on a plateau: Effects of elevation‐driven geographic isolation and environmental heterogeneity

Abstract Highlands are ideal research areas for improving our understanding of the influence of ecological factors on the diversity and spatial patterns of natural species. Elevation‐driven physical and environmental isolation greatly affect the evolution of plants. The mechanisms and essential drivers underlying these processes may differ among research scales, habitats and landscapes. Wetlands are important elements of the Qinghai–Tibetan Plateau, which is the highest plateau in the world, and these habitats harbour high aquatic organismal diversity. However, how the environments shape the genetic variation and structure of hydrophilous plants is poorly understood. Using microsatellite markers and a chloroplast fragment, we quantified the genetic diversity and spatial genetic pattern of Stuckenia filiformis, one of the most widespread aquatic plants on the plateau. The relative contributions of geography, climate and local conditions to intra‐ and interpopulation variation were estimated. The results showed that intrapopulation genetic variation of the plant is moderate to high and not constrained by high‐altitude environments. Topographical isolation mainly contributes to the genetic structure of S. filiformis, as inferred by simple sequence repeats and chloroplast DNA data. Significant effects of environmental variables on the spatial genetic patterns of this freshwater species were also suggested by landscape genetic analysis. Infrequent long‐distance dispersal, sexual recruitment and annual growth are probably important for the maintenance and distribution of this variation. Our findings imply a combined effect of geography and elevation‐driven environmental heterogeneity on the evolution of aquatic organisms in highlands.

Pollen morphology of Leptodermis (Rubiaceae) and its systematic implications

Leptodermis is a taxonomically problematic genus, and little information about its palynology was known previously. In order to find taxonomic informative characters for species delimitation and their systematic implications, 105 pollen samples, representing 28 species and four varieties, were observed and analyzed. Phylogenetic inference was also conducted based on six chloroplast fragments from 32 taxa to trace the evolutionary trend of pollen characters in Leptodermis. Results showed that two types of pollen can be identified based on the aperture number and position, viz. zonoaperturate pollen with 3 or 4 colpi situated equatorially and pantoaperturate pollen with 6 to 15 apertures evenly spread over the surface forming a polygonal platelike pattern. Pollen polymorphism was rarely observed in a few Leptodermis species. Pollen dimorphism also occurs in Leptodermis, in which the muri are smooth in pollen from pin flowers whereas have minute granules in pollen from thrum flowers. Phylogenetic mapping demonstrated that each of the nine clades matched well with aperture number and position and the 3-colpate condition was plesiomorphic. In Leptodermis, pantoaperturate grains evolved three times independently and were apomorphic. In addition, the frequent occurrence of pollen polymorphism in some species might be explained by shifts among 3-colpate, 4-colpate, and pantoaperturate pollen grains. The pollen-type mapping to the phylogenetic tree revealed that the aperture number and position could well match different phylogenetic clades, suggesting that pollen morphology could provide useful information for taxonomic and systematic studies in Leptodermis.

Mitochondrial genome sequencing and phylogenetic analysis of Cynodondactylon × Cynodontransvaalensis

Cynodon dactylon × Cynodon transvaalensis is one of the most important turfgrasses. Sequencing the C. dactylon × C. transvaalensis mitochondrial genome can help us learn more about its genomic composition and allow further study of the population genetics, taxonomy, and evolutionary biology of Poaceae plants and other related species. Here the C. dactylon × C. transvaalensis mitochondrial genome was sequenced using Illumina HiSeq combined with PacBio sequencing technology, and the map of the mitochondrial genome was constructed after de novo assembly and annotation. The C. dactylon × C. transvaalensis mitochondrial genome has 366,612 bp and contains 53 genes, including 31 protein-coding genes, 3 rRNA genes, and 16 tRNA genes. The result of relative synonymous codon usage (RSCU) showed an A or U preference at the third position of the codons. Thirty-three chloroplast DNA fragments were found in C. dactylon × C. transvaalensis mitochondrial DNA, ranging from 72 to 3003 bp. Phylogenetic trees built based on the chloroplast genome were congruent with the plant taxonomy and NCBI taxonomy common tree, while the phylogenetic trees built based on 9 mitochondrial genes showed some differences from the common tree.

基于叶绿体DNA片段的槭属鸡爪槭组系统进化和生物地理学研究

基于叶绿体DNA片段的槭属鸡爪槭组系统进化和生物地理学研究

Chloroplast and nuclear DNA analyses provide insight into the phylogeography and conservation genetics of Camellia nitidissima (Theaceae) in southern Guangxi, China

Camellia nitidissima is a high-value endemic ornamental plant with a limited distribution in the south of Guangxi, China. This plant is classified as ‘vulnerable’, and the particular variety (var.) known as microcarpa is classified as ‘endangered’. In this study, we used phylogeographic analysis of one chloroplast fragment and two single-copy nuclear DNA sequences to study the genetic structure of C. nitidissima samples from nine populations distributed across four regions in Guangxi. We carried out this study to facilitate the development of appropriate conservation strategies for the protection of this plant. Analysis of nuclear DNA showed that the genetic variation in var. microcarpa was distinct from that in var. nitidissima. Chloroplast and nuclear markers showed high levels of genetic variation among three disjunct geographical regions of var. nitidissima, indicating that the current genetic structure of this variety reflects long-term isolation and limited gene flow across the regions investigated. We recommend that conservation programmes recognise var. microcarpa and that the three disjunct geographical population groups of var. nitidissima be treated as three separate management units.