Fragmented habitat drives significant genetic divergence in the Chinese endemic plant,Urophysa henryi (Ranuculaceae)

Urophysa henryi (Oliv.) Ulbr., endemic to China with small populations, is known as a medicinal plant. In this study, ISSR markers were used to assess the genetic diversity and population structure throughout its entire distribution areas. Twelve primers revealed high genetic diversity at the species level (PPB = 95.6%; H = 0.3441; I = 0.5111), as well as high level of genetic differentiation (F_ST = 0.659, p < 0.001; G_ST = 0.677) and restricted gene flow (Nm = 0.239) among populations. According to the UPGMA and PCoA analysis, the 9 populations were clustered into three main groups, which were roughly in accordance with their geographical regions. In addition, a significant correlation between the genetic difference and geographic distances among populations was detected from the IBD analysis (r = 0.516, p = 0.003). These results indicated that the habitat heterogeneity and physical barriers play important roles in the modern distribution pattern and population divergence of U. henryi. However, human activities have posed serious threat to its living environment and continued survival. It is necessary to adopt some measures to restrict anthropogenic disturbances and preserve the existing populations.     

Genetic diversity and population structure of endangered endemic Paeonia jishanensis in China and conservation implications

Paeonia jishanensis, one of the most important ancestral species of cultivated tree peonies, is an endangered ornamental and medicinal plant endemic to China. A total of 236 individuals of P. jishanensis from 10 extant populations were analysed using 21 EST-SSR markers to assess their genetic diversity and population structure. Moderate genetic diversity levels (H_E = 0.340) and high genetic differentiation among populations (F_ST = 0.335) were revealed. Combining the results of STRUCTURE, PCoA and neighbour-joining analyses, the 10 populations were divided into four genetic groups that were significantly related to their geographical origins, which was further supported by hierarchical AMOVA showing the highest variation of 17.9% among groups. The Mantel test showed a significant positive correlation between genetic distance and geographic distance among populations (r = 0.873, P < 0.0001). The genetic structure of P. jishanensis may be due to limited gene flow hindered by vicariance and its breeding system: facultative vegetative reproduction. This study carries significant implications for the conservation and utilization of this endangered species.     

Genetic variation of wild litchi (<Emphasis Type="Italic">Litchi chinensis</Emphasis> Sonn. subsp. <Emphasis Type="Italic">chinensis</Emphasis>) revealed by microsatellites

Understanding the amount and distribution of genetic diversity in natural populations can inform the conservation strategy for the species in question. In this study, genetic variation at eight nuclear microsatellite loci was used to investigate genetic diversity and population structure of wild litchi (Litchi chinensis Sonn. subsp. chinensis). Totally 215 individuals were sampled, representing nine populations of wild litchi. All eight loci were polymorphic, with a total of 51 alleles. The expected heterozygosity in the nine populations ranged from 0.367 to 0.638 with an average value of 0.526. Inbreeding within wild litchi populations was indicated by a strong heterozygote defect. Significant bottleneck events were detected in the populations from Yunnan and Vietnam, which could be responsible for lower levels of genetic diversity in these populations. Measures of genetic differentiation (F _ST = 0.269) indicated strong differentiation among wild litchi populations. Significant correlation was found between genetic differentiation and geographical distance (r = 0.655, P = 0.002), indicating a strong isolation by distance in these populations. Bayesian clustering suggested genetic separation among three regional groups, namely, the western group, the central group and the eastern group. Some conservation strategies for wild litchi populations were also proposed based on our results.     

Effect of the Aegean Sea barrier between Europe and Asia on differentiation in Juniperus drupacea (Cupressaceae)

Juniperus drupacea is an eastern Mediterranean mountain tree with a disjunct geographical range. We hypothesized that this disjunct occurrence (the Peloponnese in Europe and the Taurus and Lebanon Mountains in Asia) should be reflected in the patterns of genetic and morphological diversity and differentiation. Nuclear microsatellite markers (nSSR) and biometric variables of the cones and seeds were examined on material sampled from four populations in Europe and eight in Asia. The Asian populations were characterized by a higher level of genetic diversity than the European populations. The genetic differentiation among populations was moderate but significant (F_ST = 0.101, P < 0.001). According to the clustering performed with BAPS, six genetically and geographically groups of populations were found: I and II from the Peloponnese; III from the Taurus Mountains; IV and V from the Anti‐Taurus Mountains; and VI from the Lebanon Mountains. The level of genetic differentiation among these six groups (4.30%, P = 0.012) probably reflects long‐lasting genetic isolation during the Pleistocene, as limited genetic admixture was found. In accordance with genetic analysis, the biometric investigations indicated a high level of morphological divergence between the European and Asian populations of the species, with further differentiation between the populations from the Taurus and Lebanon Mountains.     

Genetic diversity and structure of natural Pinus tabulaeformis populations in North China using amplified fragment length polymorphism (AFLP)

Chinese pine (Pinus tabulaeformis carr.), endemic to China, is a conifer species with extensive and fragmented distribution in North China. In this study, the genetic diversity and structure of 20 natural populations of this species were investigated using amplified fragment length polymorphism (AFLP) markers. A total of 445 fragments were revealed with 8 pairs of primers, 379 (85.17%) of which were polymorphic. A moderate level of genetic diversity was detected at the species level (Shannon's information index I = 0.356, Nei's gene diversity H_E = 0.271) and at the population level (I = 0.219, H_E = 0.206). Most of genetic variation was within populations while a considerable level of genetic differentiation was detected (G_ST = 0.352, Ф_ST = 0.304). The high differentiation could be attributed to the complex and fragmented habitats, and a limited gene flow among populations (N_m = 0.572). The Mantel test indicated that there was significant correlation (r = 0.455, P < 0.001) between Nei's genetic distance and geographical distance among all the populations. The results suggested that proper countermeasures should be taken to prevent the habitat further deterioration and maintain the genetic diversity of this species.     

The effect of past climatic oscillations on spatial genetic structure of Atraphaxis manshurica (Polygonoideae) in the Horqin sandlands,northern China

To investigate the effect of past climate oscillations on the genetic diversity and demographic history of organisms in the Horqin sandlands, at the margin of the monsoonal zone in northern China. We selected Atraphaxis manshurica as a model and examined the spatial genetic structure in populations of this species across most of its covered range. Five haplotypes were identified on the basis of two chloroplast DNA sequences (psbK-psbI and psbB-psbH) in 127 individuals from 11 natural populations. The total genetic diversity (H_T = 0.437) of A. manshurica is low compared with species to the west in arid northwestern China, outside of monsoonal influence. Analysis of molecular variance (AMOVA) indicates that genetic differentiation primarily occurred among two geographical groups distinguished by spatial analysis of molecular variance (SAMOVA). The BEAST molecular clock approach revealed that genetic divergence of the species mostly occurred in middle-late Pleistocene, in accordance with the periodic glacial periods and accompanying monsoonal changes. From species distribution modeling (SDM), we found that the species experienced range contraction and southward retreat during the Last Glacial Maximum (LGM). The current genetic pattern and demographic history may have thus been shaped by glacial–interglacial cycles and changes of habitat since the middle Pleistocene.     

Genetic diversity and population structure of the endangered conifer Taxus wallichiana var. mairei (Taxaceae) revealed by Simple Sequence Repeat (SSR) markers

Taxus wallichiana var. mairei is an endangered conifer with important medicinal value in southern China. Nuclear SSR markers were employed to assess genetic diversity and structure of 13 geographically disjunct populations. The present study revealed a moderate genetic diversity (H_E = 0.538) and low genetic differentiation (F_ST = 0.159). And most populations encountered in severe inbreeding and bottleneck effect. No significant genetic structure was detected by IBD and Structure analysis, which was supported by AMOVA analysis. The present results could be ascribed to an earlier period of more pronounced gene flow when the species had a more continuous distribution. However, the 13 studied populations were divided into four clusters based on the UPGMA dendrogram; these clusters were almost congruent with their geographical distributions. Vital areas such as southern mountains of Sichuan basin, Nanling Mts. and the margin of this yew's distribution range had a high priority for conservation.     

Genetic divergence in nuclear genomes between populations of <Emphasis Type="Italic">Fagus crenata</Emphasis> along the Japan Sea and Pacific sides of Japan

Genetic diversity and structure in Fagus crenata were studied by analyzing 14 nuclear microsatellite loci in 23 populations distributed throughout the species’ range. Although population differentiation was very low (F _ST = 0.027; R _ST = 0.041), both neighbor-joining tree and Bayesian clustering analyses provided clear evidence of genetic divergence between populations along the Japan Sea (Japan Sea lineage) and Pacific (Pacific lineage) sides of Japan, indicating that physical barriers to migration and gene flow, notably the mountain ranges separating the populations along the Japan Sea and Pacific sides, have promoted genetic divergence between these populations. The two lineages of the nuclear genome are generally consistent with those of the chloroplast genome detected in a previous study, with several discrepancies between the two genomes. Within-population genetic diversity was generally very high (average H _E = 0.839), but decreased in a clinal fashion from southwest to northeast, largely among populations of the Japan Sea lineage. This geographical gradient may have resulted from the late-glacial and postglacial recolonization to the northeast, which led to a loss of within-population genetic diversity due to cumulative founder effects.     

Assessing the genetic diversity and population structure of Culter alburnus in China based on mitochondrial 16S rRNA and COI gene sequences

The genetic diversity and population genetic structure of Culter alburnus were investigated using mitochondrial cytochrome c oxidase subunit I (COI) and ribosomal 16S subunit (16S rRNA) gene sequences. A total of 89 individuals from four localities were included in the analysis. Overall, 12 polymorphic sites were observed and 10 haplotypes were defined. The C. alburnus populations were characterized by high haplotype diversity (0.587 ± 0.047) and low nucleotide diversity (0.00197 ± 0.00073). Pairwise fixation index (F_ST) analysis indicated significant genetic differentiation among different populations. The hierarchical analysis of molecular variance (AMOVA) analysis also showed significant genetic divergence (φ_ST = 0.3792, P < 0.01) among these populations. The present results suggest that subdivisions exist among four C. alburnus populations, and should be considered as different management unit for effective conservation and management purposes. This study provides new information for genetic assessment and will be crucial for establishing fisheries management and strategies for this species.     

Genetic diversity of Shiraia bambusicola from East China assessed using ISSR markers

To understand the genetic differentiation of the medicinal fungus Shiraia bambusicola, the genetic diversity of 107 individuals from eight populations collected from Jiangsu, Anhui and Zhejiang provinces were studied using inter-simple sequence repeat (ISSR) analysis. The results revealed that the 11 employed primers produced a total of 241 ISSR loci, of which 240 loci (PPB = 99.6%) were polymorphic. Both Nei's gene diversity indexes and Shannon's gene diversity indexes showed that the genetic differentiation of S. bambusicola primarily occurred within the populations. AMOVA revealed that the variation among populations was 40.0%, and the variation within populations was 60.0%. The results of an unweighted pair group method arithmetic average (UPGMA) analysis and a principal coordinate analysis (PCA) revealed that the populations with minimal geographic separations frequently exhibited regional characteristics. These findings revealed that the relationship between sibship and geographical distribution was intensive.     

Host-associated genetic differentiation in rice grasshopper, Oxya japonica, on wild vs. cultivated rice

Rice grasshopper, Oxya japonica, is one of the most important pests in south China, mainly inhabiting fields of wild rice (Oryza rufipogon) and cultivated rice (Oryza sativa). In this study, we used AFLP marker to investigate the genetic diversity and population structure of rice grasshoppers collected from south China, with emphasis on testing the hypothesis that there was significant genetic differentiation among grasshopper populations associated with different hosts (i.e. wild vs. cultivated rice). Seven populations consisting of 104 individuals were sampled from Hainan Island and the mainland of south China. Eight primer combinations produced 564 reliable bands, of which 563 were polymorphic. O. japonica showed considerable genetic variation at population level, with gene diversity (H_E) ranging from 0.1103 to 0.2035. Genetic diversity were studied on seven populations, and generally three populations from wild rice had higher levels of genetic diversity (H_E = 0.1635) than the other four populations feeding on cultivated rice (H_E = 0.1327). We observed high population differentiation, with F_st ranging from 0.4172 to 0.7652 among the seven populations. However, Mantel test detected no significant correlation between genetic distance and geographical distance (r = 0.3541; p = 0.0689). By contrast, we found significant genetic differentiation between groups collected from different hosts. These data suggested that the anthropogenic activity in cultivated rice fields (i.e. pesticides, fertilization and cultivation) could have played an important role in shaping the genetic structure of O. japonica.     

Genetic structure in peripheral Western European populations of the endangered species Cochlearia pyrenaica (Brassicaceae)

Cochlearia pyrenaica is one of the most endangered plant species in Europe, listed in many European and regional conservation policy documents (e.g. Spain, France, Belgium, Switzerland). To study its genetic structure, define its conservation units and propose a management strategy for this species, amplified fragment length polymorphism markers were used to analyse the genetic diversity within and between five representative populations of the species distribution in Western Europe (Cantabrian Range, North of Spain; Pyrenees, France; Wallonia, Belgium). Low levels of genetic diversity were revealed by the population percentage of polymorphic bands (PPB?=?36.56%), average within-population diversity (H _S?=?0.0990) and genetic diversity within populations (H _pop?=?0.1541), although high levels were reported at species level (PPB?=?81.16%; total genetic diversity for the species, H _T?=?0.0990; and genetic diversity within whole species, H _sp?=?0.2515). The coefficient of genetic differentiation among populations (G _ST) was 0.3869. The analysis of Shannon diversity index in population and for the total data set partitioned (38.72%) and AMOVA (53%) detected a high level of interpopulation diversity, in broad agreement with the result of genetic differentiation analysis. NeighborNet network and principal coordinate analyses clustered the populations in three major groups congruent with geographical regions. Bayesian clustering also confirmed these three distinct genetic clusters. The level of gene flow (Nm) was estimated as 0.3961 individuals per generation among populations, with the genetic identity (I) and genetic distance (D) among populations ranging from 0.8679 to 0.9651 and from 0.0355 to 0.1417, respectively. Therefore, the low levels of genetic variation and high divergence of regional gene pools indicate that there is a need to protect each disjunct region of Western Europe.     

Remarkable genetic divergence of Gymnodiptychus dybowskii between south and north of Tianshan Mountain in northwest China

Gymnodiptychus dybowskii is endemic to Xinjiang, China and has been locally listed as protected animals. To investigate its genetic diversity and structure, specimens were collected from six localities in Yili River system and Kaidu River. Fragments of 1092bp Cyt b gene were sequenced for 116 individuals. A total of 21 haplotypes were found in all samples, and no haplotype was shared between Yili River system and Kaidu River population. Sequence comparisons revealed 123 variable sites, with eight singleton sites and 115 parsimony informative sites. For all the populations examined, the haplotype diversity (h) was 0.8298 ± 0.0226, nucleotide diversity (π) was 0.2521 ± 0.1202, and average number of pairwise nucleotide differences (k) was 275.3369 ± 118.5660. AMOVA analysis showed that the differences were significant for total populations except for Yili River system populations. The pairwise F_st values revealed same conclusion with AMOVA analysis: Kaidu River population was divergent from Yili River system populations. The genetic distance between two groups was 0.108 and the divergence time was estimated at 5.4–6.6 Ma, the uplift of Tianshan Mountain might have separated them and resulted in the genetic differentiation. The neutrality test and mismatch analysis indicated that both two groups of G. dybowskii had went through population expansion, the expansion time of Yili River system and Kaidu River population was estimated at 0.5859–0.7146 Ma and 0.5151–0.6282 Ma, respectively. The climate changes of Qinghai-Tibetan Plateau might have influenced the demographic history of G. dybowskii.     

Differentiation between populations of Japanese grenadier anchovy (Coilia nasus) in Northwestern Pacific based on ISSR markers: Implications for biogeography

Northwestern Pacific provides unique scenarios for studying the roles of geography and ecology in driving population divergence and speciation. To elucidate the phylogeographic pattern of Coilia nasus in Northwestern Pacific, we examined ninety individuals from five localities along the coastal regions of China and the Ariake Bay of Japan by using seven ISSR markers. Analyses of molecular variance (AMOVA) showed that genetic differentiation among groups is relatively high (F_CT = 0.1904; P = 0.000). Bayesian analysis of ISSR data also revealed significant population structuring between Chinese and Japanese locations. Phylogenetic reconstructions show reciprocal monophyly in populations between China and the Ariake Bay of Japan. We conclude that the present-day phylogeographic pattern is the result of genetic isolation between Japanese and Chinese populations in the Northwestern Pacific following the glacial retreat, and that life-history traits and ecology may play a pivotal role in shaping the realized geographical distribution pattern of this species.     

Genetic diversity and geographical differentiation of Dipteronia Oliv. (Aceraceae) endemic to China as revealed by AFLP analysis

The genus Dipteronia Oliv. endemic to central and southern China consists of two species, Dipteronia sinensis Oliv. and Dipteronia dyeriana Henry, both of them are rare and endangered. AFLP markers were used to characterize the genetic diversity and geographical differentiation of the genus. Eight out of 32 PstI + 3/MseI + 3 selective primer combinations screened were applied to the analysis on 142 individuals of 17 D. sinensis and 4 D. dyeriana populations, respectively. A total of 324 fragments with 316 polymorphic were amplified. The proportion of polymorphic loci (PPB) was 97.53%. The Nei's gene diversity in D. sinensis and D. dyeriana was 0.3319 and 0.3047, respectively. About 43.6% (G_ST = 0.4356) of the genetic variation occurred among the populations, indicating a relatively high genetic differentiation among the populations. Cluster analysis grouped the 21 populations into two groups according to their species delimitation. The populations of D. sinensis were further divided into three subgroups corresponding to their geographical distributions. Correlation analysis revealed a significant correlation (p < 0.05) between geographical distance and genetic distance of these populations, suggesting that the relatively high genetic differentiation among the populations of D. sinensis might be caused by geographical isolation.     

High genetic differentiation and variation as revealed by ISSR marker in Pseudotaxus chienii (Taxaceae), an old rare conifer endemic to China

Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China, with a historically disjunct distribution pattern. Eleven populations sampled throughout its range were examined using inter-simple sequence repeats (ISSR) markers. Twenty primers generated 242 bands, and each detected polymorphic loci, with 73.14% of polymorphic loci overall. The estimate for θ^B was 0.5306, whereas G_ST and Φ_ST values were 0.6146 and 0.6401, respectively. 50.62% of the total diversity based on Shannon's index of phenetic diversity was attributed to among populations, which was consistent with the θ^B estimation. Compared with other conifers, remarkable genetic differentiation occurred among P. chienii populations. A Mantel test indicated that pairwise values of θ^B were significantly related with geographical distances between populations (r = 0.676, P = 0.001). In terms of the above results, conservation strategies and maintenance plans of P. chienii were recommended.     

Characterization of genetic variance within and among five populations of Sperata seenghala (Skyes, 1839) revealed by random amplified polymorphic DNA markers

The genetic diversity among five populations (Bhadbada reservoir, Mohinisagar reservoir, Bansagar reservoir, Bargi reservoir and Gandhisagar reservoir) was revealed using random amplified polymorphic DNA markers. 10 random primers screened, 5 primers revealed various banding patterns and yielded 71 total loci as an average of which 39.60 (55.77%) were polymorphic between the population and 86.84% within the population of Sperata seenghala. Population wise the highest genetic polymorphism was obtained in Bhadbada reservoir as 67.61% whereas the lowest was in Gandhisagar reservoir as 49.30%. However, Analysis of Molecular Variance indicated low genetic diversity (H_pop = 0.0921 ± 0.1249; I = 0.1584 ± 0.1942) in Bansagar reservoir. Relative genetic differentiation (G_ST = 0.3993) and restricted gene flow (N_m = 0.7523) as an average indicated low gene diversity among the fish populations. The un-weighted pair group method with averages (UPGMA) dendrogram showed 05 major clusters, each cluster representing a population. Fish population of Mohinisagar reservoir showed high genetic distance (0.3981) with respective Bargi reservoir population and highest genetic identity (0.8846) reflected between Bansagar and Gandhisagar reservoir. Highest genetic distance between Mohinisagar and Bargi reservoir fish populations shows no significant correlation between genetic and geographical distance of the genotypes collected from different lentic and geographical isolated water bodies. This investigation indicated that lowest genetic diversity existed in different geographic populations of S. seenghala. All the five populations were found to be low in genetic variation, which is useful information for future conservation measures of S. seenghala confined in natural water bodies of Madhya Pradesh.     

Phylogeography of Lagochilus ilicifolius (Lamiaceae) in relation to Quaternary climatic oscillation and aridification in northern China

Using two chloroplast DNA intergenic spacers, a phylogeographical study of Lagochilus ilicifolius with 168 individuals from 14 populations was performed to assess geographical patterns and genetic variation in relation to past climate change. Population structure and history were inferred by nested clade analysis, neutrality tests, divergence time estimates, and mismatch distribution analysis. Twelve haplotypes were identified. Genetic differentiation among populations within groups was also elevated (F_SC = 0.772), suggesting restricted gene flow among populations within groups. Divergence time was at approximately 0.71 Ma, consistent with aridification and desert expansion during the middle Pleistocene. The Helan Mountains contained a large proportion of the haplotypes, which implies that the region may be the center of diversification for the species, whereas the Loess Plateau as a dispersal corridor for postglacial re-colonization northward. Climatic oscillation, aridification, and desert expansion within these regions have molded current distribution and biodiversity of L. ilicifolius.     

Population genetics of the common long-armed octopus Octopus minor (Sasaki, 1920) (Cephalopoda: Octopoda) in Chinese waters based on microsatellite analysis

Octopus minor (Sasaki, 1920) is a commercially important cephalopod in Chinese waters. To provide a theoretical basis for resource protection and sustainable management, we investigated genetic structure of ten O. minor populations in Chinese waters using microsatellite DNA markers. Eight microsatellite loci revealed high allelic diversity with 11–26 alleles per locus. Observed and expected heterozygosity varied from 0.412 to 0.900 and from 0.337 to 0.845, respectively. The overall F_ST value was 0.198, indicating great genetic differentiation among populations. The F_ST value between Yilan and other populations reached more than 0.3 that may be indicative of subspecies rank. Mantel test showed significant correlations between genetic and geographic distance (R = 0.383, P = 0.004) indicating that genetic differentiation of O. minor conformed to a pattern of isolation-by-distance. Using the Neighbor-joining method, cluster analysis divided nine populations into three groups and divided ten populations into two groups wherein Yilan was distinguished from the other populations. Analysis based on F_ST, D_c values and clustering highlighted the heterogeneity of Yilan and the relative homogeneity between Yilan and Ganyu. The significant population genetic structure of O. minor is related to the combined effects of geographical barriers, current features and life history characteristics.     

Chloroplast microsatellite diversity of Clintonia udensis (Liliaceae) populations in East Asia

Nineteen populations of Clintonia udensis Trautv. & Mey. were examined to quantify genetic diversity and genetic structure by chloroplast DNA microsatellites (cpSSR). Significant cpSSR genetic diversity (PPB = 63.64%) was detected in this species. Tetraploid populations demonstrated approximately the same level of genetic diversity as the diploid ones. A significant differentiation, however, was found between tetraploids and diploids. Most of the sixteen chloroplast haplotypes were limited to a single population. The level of haplotype diversity was high (Hd = 0.915). AMOVA, PCA and Bayesian clustering analysis revealed that there were significant genetic differences among populations. Inter-population genetic distances among population sites correlated significantly with geographic distances. These results indicate that the mixed-mating – breeding system, limited gene flow, environmental stress, and historical factors may be the main factors causing geographical differentiation in the genetic structure of C. udensis.