Lack of genetic structure in endangered large yellow croaker Larimichthys crocea from China inferred from mitochondrial control region sequence data

The large yellow croaker Larimichthys crocea is an important commercial marine fish species in China. However, information about the population structure of this species is limited. In the present study, mitochondrial DNA (mtDNA) control region was sequenced from four populations of the yellow croaker in the southern Yellow Sea, East China Sea and South China Sea to investigate the genetic structure of this species. A total of 54 haplotypes were detected among 62 individuals of large yellow croaker. High levels of population genetic diversity were observed. Among the four populations, the haplotype diversity was between 0.9895 ± 0.0193 (Xiamen) and 1.0000 ± 0.0524 (Lvsi, Zhoushan). The nucleotide diversity ranged from 0.0208 ± 0.0108 (Xuwen) to 0.0246 ± 0.0138 (Lvsi). The results of AMOVA detected no significant differences among populations. The conventional F_ST statistics were negative and insignificant values. These indicated lack of population genetic structure throughout the Yellow Sea, East China Sea and South China Sea, and random mixing of individuals among the samples. Biological characters of large yellow croaker and lack of physical barrier in the studied area could be the reasons for lack of genetic structure in this species.     

Genetic diversity and population structure of miiuy croaker populations in East China Sea revealed by the mitochondrial DNA control region sequence

The genetic diversity and population structure of the miiuy croaker (Miichthys miiuy) were investigated. Seventy-six individuals were sampled from six localities of the East China Sea. Genetic variation in DNA sequences was examined from the 5′-end of the mitochondrial DNA control region. High levels of haplotype diversity (h = 0.99333) in the control region were detected, indicating a high level of genetic diversity. A total of 81 polymorphic sites were found, and 65 haplotypes were defined. The results of AMOVA analysis indicated that 97.9% of the genetic variation contained within populations and 2.14% occurred among populations. No significant genealogical branches or clusters were recognized on the NJ tree. Tests of neutral evolution and analysis of mismatch distribution suggested that miiuy croaker might have undergone a population expansion. The knowledge on genetic diversity and genetic structure will be crucial to establish appropriate fishery management stocks for the species.     

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.     

Microsatellite diversity and population genetic structure of yellowcheek, Elopichthys bambusa (Cyprinidae) in the Yangtze River

Yellowcheek carp (Elopichthys bambusa) is the only species of genus Elopichthys. It is widely distributed in Chinese freshwaters but currently its populations have declined to threatening level. We examined the genetic diversity and population structure of E. bambusa in the Yangtze River basin. A total of nine polymorphic microsatellite markers were employed to study five populations occurring in middle and lower reaches of the river. The results revealed low-to-moderate genetic diversity. The number of alleles per locus varied between 3 and 8 with an average of 4.8. Observed heterozygosity ranged from 0.15 to a maximum of 1.00. Significant deviations (P < 0.01) from Hardy–Weinberg equilibrium were observed for all the tested locus-population combinations with clear heterozygosity deficits. AMOVA indicated that majority of the variance lies within populations (93.81%) than among the populations (7.05%). Pairwise F_ST and unbiased genetic distance pointed out significant differentiation among the samples from populations with different connections to the Yangtze River. In the UPGMA dendrogram, clustering pattern of populations indicated that most of the populations are reproductively isolated due to anthropogenic interventions. Clustering of PYL and DTL populations shows ongoing gene flow through the mainstream. The recent hydrological alterations and overfishing are major factors shaping the current genetic structure. These results can be helpful for effective management and sustainable conservation of E. bambusa populations.     

Genetic diversity and population connectivity of the Asian green mussel Perna viridis in South China Sea,inferred from mitochondria DNA markers

The Asian green mussel Perna viridis is ecologically and economically important in the coastal regions of China. In order to characterize the genetic diversity and population connectivity of P. viridis in South China Sea, a 664 bp region of mitochondrial COI gene and a 293 bp region of 16S rRNA gene were sequenced and analyzed for 78 and 92 individuals from four populations in South China Sea, respectively. A total of 15 haplotypes were defined by 14 variable nucleotide sites in COI gene, and 7 haplotypes by 6 variable nucleotide sites in 16S rRNA gene. High haplotype diversity and low nucleotide diversity were observed in COI gene, while moderate haplotype diversity and low nucleotide diversity were observed in 16S rRNA gene. Pairwise F_ST values of COI gene were all negative and those of 16S rRNA gene ranged from −0.01409 to 0.10289. The results showed that no significant genetic divergence (or shallow genetic structure) and high levels of population connectivity among the four populations of P. viridis in South China Sea.     

Genetic diversity and population structure of Swertia tetraptera (Gentianaceae), an endemic species of Qinghai-Tibetan Plateau

Swertia tetraptera Maxim is an annual alpine herb endemic to the Qinghai-Tibetan Plateau (QTP). Its populations are locally scattered as isolated patches throughout this region. Genetic variation within and among thirty-four populations of this species was assessed using ISSR fingerprinting with 10 primers. High levels of genetic diversity exist within species (P = 98.9%, I = 0.3475; He = 0.2227), while the within-population diversity is low (P = 32.7%, I = 0.177; He = 0.12). High levels of genetic differentiation were detected among populations based on various statistics, including Nei’s genetic diversity analysis (G_ST = 0.4608), Bayesian analysis (θ^B = 0.476) and AMOVA (F_ST = 0.57). That is, populations shared low levels of genetic identity (I = 0.2622–0.0966). This genetic structure was probably due to severe genetic drift, breeding system and limited gene flow. The observed genetic structure of the populations implies that different populations across the distribution range of the species should be sampled to maintain high genetic diversity when a conservation strategy is implemented.     

Genetic diversity of Astragalus nitidiflorus, a critically endangered endemic of SE Spain,and implications for its conservation

Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population structure in five populations of Astragalus nitidiflorus, a critically endangered species endemic to southeast Spain. Eight primers amplified 78 bands with 40 (51.3%) being polymorphic. Statistical results indicated a low genetic diversity at the population and species level, with percentages of polymorphic bands (PPB) ranging from 28.2 to 37.2% (an average of 31.8%), and means of gene diversity (H_E) of 0.129 and 0.171 respectively. The Shannon’s index (SI) ranged from 0.160 to 0.214 at the population level and was 0.260 at the species level. A low level of genetic differentiation among populations was detected, based on the Shannon’s information index (0.297), the coefficient of genetic differentiation between populations (G_ST = 0.2418) and AMOVA analysis (Φ_ST = 0.255). The estimated gene flow (Nm) was 0.789. The high genetic connectivity found among populations of A. nitidiflorus is an evidence of a recent habitat fragmentation. In addition, a bottleneck event in the past has been revealed, with a subsequent reduction of population size and a loss of genetic variation. Based on these results, the conservation strategy of A. nitidiflorus was proposed.     

Genetic variation and Phylogeography of Sinibrama Macrops (Teleostei: Cyprinidae) in Qiantang River Basin,China

A 924 bp segment of the mitochondrial control region (d-loop) was sequenced and analyzed in 334 specimens of Sinibrama macrops from 13 sites in Qiantang River Basin, China. Haplotype diversity (h = 0.724 ± 0.063) and nucleotide diversity (π = 0.00263 ± 0.00027) were lowest in Shengzhou population which had been separated from mainstream of Qiantang River Basin by seawater. The results of pairwise Fst values and average genetic distance revealed significant divergence between Shengzhou and other populations. No geographic clustering was observed in haplotype network, suggesting that there were gene flow among populations except Shengzhou. Pairwise mismatch distributions and Tajima's d-test showed demographic history of Shengzhou population was different from others. Base on the analysis of mitochondrial control region, the differentiation of Shengzhou population was considered to be the result of the transgression and regression in the last interglacial period.     

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.     

Mitochondrial genetic diversity and population structure of a vulnerable freshwater fish,rock carp (Procypris rabaudi) in upper Yangtze River drainage

Rock carp (Procypris rabaudi (Tchang)) is an endemic species in the upper Yangtze River drainage. The genetic variability and population structure of eight populations (Mudong (MD), Hejiang (HJ), Wanzhou (WZ), Xishui (XS), Nantan (NT), Cangxi (CX), Tongjiang (TJ) and Wulong (WL)) were investigated based on mitochondrial DNA control region. According to the river dimensions, MD, HJ, WZ, WL and CX were defined as large river populations, while TJ, XS and NT were defined as small. The total genetic diversity level of rock carp was moderate (h = 0.858, π = 0.0079). Genetic differentiations among populations in small rivers were greater than those among populations in large rivers, and small rivers showed significant differentiation from large rivers. Analysis from the coalescent-based method showed that there were asymmetric gene flows among four large river populations (CX, HJ, MD and WZ). Demographic analyses suggested that the species as a whole and the WZ population experienced population expansion, while the HJ, NT, and MD populations experienced bottlenecks. The analysis of genetic diversity and population structure suggested that the WL, TJ, CX, NT and XS populations should be protected and managed separately, and that the HJ, MD and WZ populations should be considered as a genetic management unit.     

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.     

Assessment of genetic diversity and chemical composition among seven black locust populations from Northern China

Black locust (Robinia pseudoacacia L.) is one of the important biomass sources used to produce bioenergy and bioethanol. In this study, we examined variations in chemical composition as well as genetic diversity and differentiation among 165 black locust plants from seven populations in five provinces (Beijing, Hebei, Gansu, Shanxi, Shandong) of Northern China using microsatellite markers(SSR). The contents of cellulose, hemicellulose, lignin varied widely among seven populations. Of the microsatellite markers analysed, 14 showed polymorphisms, and 45 alleles were identified. The polymorphism information content (PIC) ranged from 0.2885 (Rops4) to 0.6837 (Rp200), and most of the microsatellite loci had PIC values > 0.5. Expected heterozygosity (He), observed heterozygosity (Ho), and Shannon's information index (I) detected relatively high genetic variation among populations. The percentage of polymorphic loci in three populations was 100%, and the average among all populations were 95.92%. Analysis of molecular variance (AMOVA) indicated that the degree of genetic differentiation among the seven populations was low (G_ST = 0.058; N_m = 4.05), and chemical compositions had no relationship with genetic or geographic distance. This study demonstrates that microsatellite markers efficiently assess of genetic diversity and genetic differentiation in black locust populations, and all seven populations exhibit high genetic diversity. The population from Feixian has the potential to be lingo-cellulosic biomass for bioenergy and bioethanol.     

Low genetic diversity and significant structuring in the endangered Mentha cervina populations and its implications for conservation

Eighteen populations of the endangered aromatic and medicinal plant Mentha cervina (Lamiaceae) were sampled across its natural range, in the western half of the Iberian Peninsula, and inter-simple sequence repeats (ISSRs) markers were used to assess genetic diversity and population structure. M. cervina populations exhibited a relatively low genetic diversity (percentage of polymorphic loci PPB = 14.2–58.3%, Nei's genetic diversity H_e = 0.135–0.205, Shannon's information index I = 0.08 − 0.33). However, the genetic diversity at species level was relatively high (PPB = 98.3%; H_e = 0.325; I = 0.23). The results of the analysis of molecular variance indicated very structured populations, with 50% of the variance within populations, 44% among populations and 6% between regions defined by hydrographic basins, in line with the gene differentiation coefficient (G_ST = 0.532). A Mantel test did not find significant correlation between genetic and geographic distance matrices (r = 0.064), indicating that isolation by distance is not shaping the present genetic structure. The levels and patterns of genetic diversity in M. cervina populations were assumed to result largely from a combination of evolutionary history and its unique biological traits, such as breeding system, low capacity of dispersion, small effective size and habitat fragmentation. The high genetic differentiation among populations indicates the necessity of conserving the maximum possible number of populations. The results also provide information to select sites for ex situ conservation. Optimal harvesting strategies, cultivation and tissue culture should also be developed as soon as possible to guarantee sustainable use of the species under study.     

Genetic diversity and population structure of the endangered ripon barbel,Barbus altianalis (Boulenger, 1900) in Lake Victoria catchment,Kenya based on mitochondrial DNA sequences

Approximately 850 bp of the mitochondrial control region was used to assess the genetic diversity, population structure and demographic expansion of the endangered cyprinid Barbus altianalis, a species known to be potamodramous in the Lake Victoria drainage system. The 196 samples taken from the four main rivers draining the Lake Victoria catchment (Nzoia, Yala, Nyando and Sondu–Miriu) yielded 49 mitochondrial DNA haplotypes; 83.7% thereof were private haplotypes restricted to particular rivers. The overall mean haplotype diversity was high (0.93663 ± 0.008) and ranged between 0.566 (Sondu – Miriu) and 0.944 (Nzoia). The overall mean nucleotide diversity was low (0.01322 ± 0.00141), ranging from 0.0342 (Sondu – Miriu) to 0.0267 (Nzoia). Population differentiation tests revealed strong and highly significant (P ≤ 0.001) segregation of populations in the four river basins. F_ST values among the four river‐based populations ranged from 0.05202 to 0.44352. The samples formed two main haplotype networks based on a 95% parsimony criterion, each exhibiting a strong signature of past population expansion. The smaller network was restricted to the River Nzoia, whereas the larger network contained representatives from all four rivers; within this the central haplotypes were found in more than one river, whereas the peripheral haplotypes tended to be river‐specific. The degree of population differentiation and the number of river‐specific haplotypes are too high to be explained by recent anthropogenic impacts alone and suggest that the species has probably existed in the Lake Victoria catchment as two populations: the now ‘extinct’ migratory population and the extant river restricted non‐migratory populations.     

Genetic diversity and population structure of Chrysichthys nigrodigitatus from Niger Delta based on AFLP analysis

The silver catfish, Chrysichthys nigrodigitatus is an important food fish in the Niger Delta. To understand the genetic variations and population structure in Nigeria’s Niger Delta, eighty-eight individuals collected from 7 locations were analyzed based on amplified fragment length polymorphism (AFLP) analysis. A total of 243 bands were identified using 4 AFLP primer combinations. The average gene diversity was 0.1708 ± 0.1547 and Shannon’s information index was 0.2792 ± 0.2224. The pairwise F_st values ranged from 0.133 to 0.796. The results of AMOVA analysis indicated that 19.03% of the genetic variation was contained among three groups. The gene flow estimates (Nm) demonstrated that different degrees of gene flow existed among populations ranging from 0.064 to 1.630. Two clades were recognized on the UPGMA tree. The results supported that freshwater or brackishwater habitat, limited long-distance dispersal of the adult and juveniles and physical barriers may be responsible for the current genetic structure.     

Genetic diversity and population structure of the endangered alpine quillwort Isoetes hypsophila (Isoetaceae) revealed by SSR analysis

Isoetes hypsophila Hand.-Mazz. (Isoetaceae) is an endangered alpine quillwort endemic to the Qinghai-Tibetan Plateau (QTP). A total of 247 individuals of I. hypsophila from 11 populations were analyzed using ten pairs simple sequence repeats (SSR) markers. Seventy-seven alleles were recorded, with an average of 7.7 alleles per locus (ranging from 3 to 12) and the expected heterozygosity (H_E) ranged from 0.392 to 0.536 (average 0.471). Clear population structure among I. hypsophila populations was found and the proportion of genetic differentiation among populations accounted for about 20% of total genetic diversity (F_ST = 0.178; probability of allelic co-ancestory F_coal = 0.238). This genetic structure was probably due to limited gene flow hindered by complex terrains, bottlenecks resulting from water fluctuation in habitats, and repeated population retreat and recolonization during the ice ages. In conservation, four management units corresponding to four geographic regions were suggested, and the populations from different management units with higher genetic variation should be the priority targets of both in situ and ex situ conservation.     

Genetic diversity of natural populations of Larix principis-rupprechtii in Shanxi Province,China

Prince Rupprecht's Larch (Larix principis-rupprechtii Mayr.) is one of dominant components of middle and high elevation forests in North China. Shanxi Province is well known as “the Hometown of Prince Rupprecht's Larch” in China. In this study, six natural populations of this species across Shanxi were selected to investigate the genetic variation of the species using amplified fragment length polymorphism (AFLP) markers. Results showed that in comparison with some other species of Larix, higher genetic diversity was revealed at the species level for L. principis-rupprechtii (percentage of polymorphic loci PPL = 71.9%, Nei's gene diversity H_E = 0.225, Shannon information index I = 0.341). Most of genetic variation existed within populations (80.5%), while the genetic differentiation among populations was significant (p < 0.001) and higher (G_st = 0.194) than most other species of Larix. The differentiation can be attributed to the limited gene flow (N_m = 1.035) among populations, which could be due to the spatial isolation and habitat fragmentation. The six populations can be divided into three groups based on the Nei's genetic distances between populations (from 0.033 to 0.076). There was no significant correlation (r = 0.268, p > 0.05) between genetic distance and geographic distance among populations. The measures for in-situ or ex-situ conservation should be taken to preserve the genetic diversity of this species.     

Genetic diversity of the cultured giant freshwater prawn (Macrobrachium rosenbergii) in China based on microsatellite markers

The Giant freshwater prawn (GFP), Macrobrachium rosenbergii, is one of the most important crustacean species cultured in China, but information on the genetic diversity of GFP in China is still limited. In this study we analyzed the genetic diversity of 6 cultured GFP populations collected in China, and 2 wild populations from Viet Nam. The wild populations were included as a reference so that the genetic diversity of the introduced cultured GFP populations could be evaluated. We used six polymorphic primer pairs to estimate genetic diversity. Results showed that the number of alleles per locus ranged from 6 to 19. The mean observed heterozygosity (0.364 ± 0.090) was less than the expected heterozygosity (0.893 ± 0.016); highly significant deficiencies in heterozygotes were detected (100%). The polymorphism information content (PIC) of 8 populations at 6 loci was greater than 0.5 (varying from 0.616 to 0.912). Pair-wise genetic differentiation (F_ST) varied from 0.006 to 0.129 among the eight populations. The dendrogram based on genetic distance showed six populations distributed on the same major branch, suggesting that they have closely genetic distance and two populations (ZJC and GDB) distributed on the other branch, so they also have closely genetic distance. The results of study provide a baseline assessment of genetic diversity in some populations in China and Viet Nam that will be useful for the development of breeding programmes in the future.     

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 Taxus cuspidata in the Changbai Mountains assessed by chloroplast DNA sequences and microsatellite markers

Taxus cuspidata, a tree species with high economic value because of its anticancer properties, is experiencing severe reduction in populations across its range in China. We examined one chloroplast DNA (cpDNA) region (petA-psbE) and 9 nuclear simple sequence repeats (SSRs) loci variations among seven populations in the Changbai Mountains of China to investigate the levels of genetic diversity and population structure. A moderate level of haplotype diversity (H_T = 0.625), low nuclear microsatellite diversity (H_E = 0.261 ± 0.028), significant genetic differences (F_ST = 0.065) and substantial gene flow (Nm = 2.806) were observed. Most of the total genetic variation was partitioned within the population (87.8% and 94.0% for cpDNA and SSRs, respectively). Our haplotype identification permutation tests revealed that G_ST > N_ST, indicating an absence of phylogeographic structure in T. cuspidata. Neither STRUCTURE nor UPGMA analyses showed any geographic pattern in T. cuspidata populations. By comparatively analyzing the genetic diversity and survival situation of T. cuspidata, our results provide a theoretical foundation for the resource protection, utilization cultivation and breeding of this valuable plant.