Allozyme variation of the endangered endemic plant Myricaria laxiflora: Implications for conservation

Myricaria laxiflora, a riparian plant that naturally occurs in the riverbanks of the Yangtze River Valley, has become extinct across its entire geographical distribution range in the wild due to the construction of the Three Gorges Dam. The allozyme variation of M. laxiflora populations was investigated in the present study. Mean number of alleles per locus (A) was 2.35, and the observed heterozygosity (H_o) and expected heterozygosity (H_e) were 0.35 and 0.30, respectively. Six populations showed significant excesses of heterozygotes based on the examination of a multilocus fixation index (F_IS). The population genetic divergence of M. laxiflora is high (G_ST = 0.144 and ?_B = 0.131) and the analysis of molecular variance analysis shows that 19.71% of the total genetic variation is caused by the difference between populations. Based on the obtained genetic information, six management units have been identified, all of which are expected to enhance the effective management of the remaining and transplanted individuals of this endangered species in the future.     

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 structure of Pyrenophora teres net and spot populations as revealed by microsatellite analysis

The population structure of the fungal pathogen Pyrenophora teres, collected mainly from different regions of the Czech and Slovak Republics, was examined using a microsatellite analyses (SSR). Among 305 P. teres f. teres (PTT) and 82 P. teres f. maculata (PTM) isolates that were collected, the overall gene diversity was similar (? = 0.12 and ? = 0.13, respectively). A high level of genetic differentiation (F_ST = 0.46; P < 0.001) indicated the existence of population structure. Nine clusters that were found using a Bayesian approach represent the genetic structure of the studied P. teres populations. Two clusters consisted of PTM populations; PTT populations formed another seven clusters. An exact test of population differentiation confirmed the results that were generated by Structure. There was no difference between naturally infected populations over time, and genetic distance did not correlate with geographical distance. The facts that all individuals had unique multilocus genotypes and that the hypothesis of random mating could not be rejected in several populations or subpopulations serve as evidence that a mixed mating system plays a role in the P. teres life cycle. Despite the fact that the genetic differentiation value between PTT and PTM (F_ST = 0.30; P < 0.001) is lower than it is between the populations within each form (F_ST = 0.40 (PTT); F_ST = 0.35 (PTM); P < 0.001) and that individuals with mixed PTT and PTM genomes were found, the two forms of P. teres form genetically separate populations. Therefore, it can be assumed that these populations have most likely undergone speciation.     

Genetic diversity of the threatened aquatic plant Ottelia alismoides in the Yangtze River

Ottelia alismoides is a threatened submerged macrophyte in China. Genetic variation and population structure of 11 O. alismoides populations from lakes in mid-lower reaches of the Yangtze River were assessed by inter-simple sequence repeat (ISSR) markers. Eleven primer combinations produced a total of 130 unambiguous bands of which 57 (43.9%) were polymorphic. O. alismoides exhibited a very low level of intra-population genetic diversity (P_p = 13.0%, H_E = 0.042, I = 0.063). The main factors responsible for that were its short life history and high degree of autogamy in the reproductive system of the species. The F statistics calculated by different approaches consistently revealed a high genetic differentiation among populations, contributing >55% of the total gene diversity. The evident population structure of O. alismoides could be due to self-fertilizing reproduction, restricted gene flow and genetic drift. Estimates of gene flow by F_ST and coalescent-based simulation analysis indicated a restricted recurrent gene exchange among populations (Nm = 0.180, M = 0.190). Genetic drift played a more important role than gene flow in the current population genetic structure of O. alismoides because its habitat range was fragmented and highly influenced by environment changes. The results are discussed in relation to both in situ and ex situ conservation efforts of the species. A conservation strategy for conserving all extant populations to maximize genomic representation of the species is recommended.     

Genetic differentiation and species cohesion in two widespread Central American Begonia species

Begonia is one of the ten largest plant genera, with over 1500 species. This high species richness may in part be explained by weak species cohesion, which has allowed speciation by divergence in allopatry. In this study, we investigate species cohesion in the widespread Central American Begonia heracleifolia and Begonia nelumbiifolia, by genotyping populations at microsatellite loci. We then test for post-zygotic reproductive barriers using experimental crosses, and assess whether sterility barriers are related to intraspecific changes in genome size, indicating major genome restructuring between isolated populations. Strong population substructure was found for B. heracleifolia (F_ST=0.364, F′_ST=0.506) and B. nelumbiifolia (F_ST=0.277, F′_ST=0.439), and Bayesian admixture analysis supports the division of most populations into discrete genetic clusters. Moderate levels of inferred selfing (B. heracleifolia s=0.40, B. nelumbiifolia s=0.62) and dispersal limitation are likely to have contributed to significant genetic differentiation (B. heracleifolia Jost''s D=0.274; B. nelumbiifolia D=0.294). Interpopulation crosses involving a divergent B. heracleifolia population with a genome size ∼10% larger than the species mean had a ∼20% reduction in pollen viability compared with other outcrosses, supporting reproductive isolation being polymorphic within the species. The population genetic data suggest that Begonia populations are only weakly connected by gene flow, allowing reproductive barriers to accumulate between the most isolated populations. This supports allopatric divergence in situ being the precursor of speciation in Begonia, and may also be a common speciation mechanism in other tropical herbaceous plant groups.     

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.     

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.     

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.     

Population genetic structure of the Korean threadsail filefish (Stephanolepis cirrhifer) based on microsatellite marker analysis

The threadsail filefish Stephanolepis cirrhifer is one of the most important commercial fish resources in Korea. However, its natural populations have declined drastically over the last several decades. To investigate the genetic characteristics of the threadsail filefish for conservation and management purposes, its genetic variation was analyzed in Korean fishing grounds using 11 microsatellite loci. All populations showed moderate genetic diversity (mean number of alleles (N_A) = 8.6, expected heterozygosity (He) = 0.73), representing a slightly lower level of genetic variability than other congeneric species. The presence of a weak genetic population substructure was detected (F_ST = 0.023, R_ST = 0.030, P < 0.001), but this substructure did not feature significant isolation based on the distance between populations. This differentiation may be primarily attributable to genetic differences between populations from Geomundo and other localities, based on relative low level of gene flow, a high level of pairwise F_ST and R_ST or the position of this population in a phylogenetic tree. An analysis of molecular variance (AMOVA) also revealed a greater part of the variation within the population and genetic differentiation among the samples analyzed and identified two genetic clusters. The possibility of a recent genetic bottleneck was observed in some populations of S. cirrhifer. Given the prevailing ocean currents and the intensity of threadsail filefish harvesting activities in Korea, the possibility that human harvest and stock enhancement activities may have partially contributed to our detected genetic pattern cannot be excluded. Management strategies that take these findings into account might lower the risk of harmful genetic change in the species.     

Population genetic structure in the endemic cyprinid fish Microphysogobio alticorpus in Taiwan: Evidence for a new phylogeographical area

The Formosa Bank is a significant zoogeographical barrier for the freshwater fish in Southern Taiwan. Here, we present population genetic structure analyses on Microphysogobio alticorpus populations in Taiwan, and biogeographic pattern to infer the relationship between historic dispersal geological dynamics. A total of 24 haplotypes were genotyped for mitochondrial CR + cyt b region in 134 specimens collected from 9 populations. Relatively high levels of haplotype diversity (h = 0.896) and low levels of nucleotide diversity (π = 0.005) were detected in M. alticorpus. Two major phylogenetic haplotype groups, Clade N1+N2 and S, were revealed and estimated to diverge about 0.121 myr (million years) ago. Haplotype network and population genetic analyses indicated significant genetic structure (F_ST = 0.876), largely concordant with the geographical location of the populations. According to SAMOVA analysis, M. alticorpus populations were divided into five units that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow. The results of the topological pattern and network suggested that the Kaoping River was the first habitat colonized by the ancestor of M. alticorpus, before the northward dispersal.     

Genetic diversity of the traditional Chinese medicinal plant Ypsilandra thibetica (Melanthiaceae): Applications for conservation

Twelve microsatellite markers were developed to determine the genetic diversity and genetic structure of Ypsilandra thibetica, represented by a total of 90 individuals from six natural populations. All twelve microsatellite loci were polymorphic, and the results indicated that a high genetic diversity was present within populations (mean R_S = 4.996; mean H_E = 0.615), with high levels of genetic structure (mean F_ST = 0.165; mean F_IS = 0.692) among populations. This pattern is likely attributable to consanguineous mating, and this hypothesis is supported by a low relatedness coefficient. Our study suggested that environment factors might restrict gene flow among populations. In addition, physical distances between populations were not related to genetic distances, implying that ancestral populations might have been distributed over a wider area. These results suggest that Y. thibetica should be a high priority for conservation managers.     

Genetic diversity and relationships among wild and cultivated Stenocereus queretaroensis populations in western Mexico

Stenocereus queretaroensis is an endemic, chiropterophilous, columnar cactus of economic importance in Mexico. To investigate the effect of artificial selection on genetic diversity, inter-simple sequence repeat (ISSR) markers were used to estimate the genetic variation of wild, orchard, and backyard populations of S. queretaroensis from two regions in western Mexico. Six primers were used to generate 62 bands, of which 39 were polymorphic (62.9%). The total genetic diversity was similar in the wild (H_T = 0.296) and orchard (H_T = 0.291) groups, and slightly lower in the backyard group (H_T = 0.281). Wild populations (F_ST = 0.13) were less differentiated than backyard (F_ST = 0.17) and orchard (F_ST = 0.21) populations. The wild and backyard groups were genetically closer (0.015) than the wild and orchard (0.018) groups. A Mantel test revealed a positive correlation between genetic and geographic distances (r = 0.433, p = 0.002). In conclusion, gene flow and the prevailing management system have efficiently maintained genetic diversity and facilitated inter-population differentiation in S. queretaroensis.     

Genetic differences between continuous and disjunct populations: some insights from sal (<Emphasis Type="Italic">Shorea robusta</Emphasis> Roxb.) in Nepal

Sal (Shorea robusta Gaertn., Dipterocarpaceae) is a wind-pollinated tropical tree species found in southern Asia. We investigated the genetic diversity and structure at four microsatellites of 15 populations comprising continuous-peripheral and disjunct-peripheral populations in Nepal. Estimates of genetic diversity (N _A = 8.98, H _O = 0.62, H _E = 0.69) were similar when compared with those of other tropical tree species. A higher level of genetic diversity was observed in continuous-peripheral populations (N _A = 9.61, H _O = 0.67, H _E = 0.72) as compared to disjunct-peripheral (N _A = 8.04, H _O = 0.55, H _E = 0.64). Population differentiation was higher among disjunct-peripheral populations (F _ST = 0.043) than among continuous peripherals (F _ST = 0.012). There was a significant association between gene flow distances and genetic differentiation (r ² = 0.128, P ≤ 0.007). No spatial arrangement of populations according to their geographical locations was found. Based on observed genetic diversity protection of some populations in continuous-peripheral range are suggested for the sustainable conservation of genetic resources of the species while protection of some disjunct-peripheral populations are also recommended for conserving rare alleles.     

Population structure and genetic diversity of Dysosma versipellis (Berberidaceae), a rare endemic from China

Dysosma versipellis (Berberidaceae) is an endangered and endemic species in China. To provide scientific foundation for formulating conservation strategies, we sampled six extant populations of this species and assessed the levels and patterns of genetic diversity using ISSR markers (11 primers). Of 144 bands detected 57.64% were polymorphic, but on average only 20.72% were polymorphic within populations. Our results revealed a low level of intraspecific genetic diversity (at population level: H_pop = 0.082, H_B = 0.177, SI = 0.1194; at species level: H_pop = 0.207, H_B = 0.378, SI = 0.3069). A high level of genetic differentiations among populations was detected based on Nei's genetic diversity analysis (60%), AMOVA analysis (65%), and Bayesian analysis (53%). The low levels of heterozygosity and high genetic differentiation observed in D. versipellis may be the consequence of low rate of natural recruitment, clonal growth, gene drift, and habitat fragmentation. Based on this, we suggest that in situ conservation be an important and practical measure for maintaining the genetic diversity of this species. Ex situ conservation should sample from different populations across the distribution range of the species to conserve high genetic diversity.     

Genetic diversity and population structure of Opisthopappus longilobus and Opisthopappus taihangensis (Asteraceae) in China determined using sequence related amplified polymorphism markers

The genetic diversity and structure of four Opisthopappus longilobus and nine Opisthopappus taihangensis populations from Mts. Taihang were analyzed using SRAP markers. The results showed that O. longilobus (PPB = 95.16%, H = 0.349, I = 0.517) and O. taihangensis populations (PPB = 94.58%, H = 0.332, I = 0.504) had high genetic diversity. The genetic diversity within populations varied according to two species. Low genetic differentiation was detected among O. longilobus (Φ_ST = 0.105) and O. taihangensis (Φ_ST = 0.188) populations, respectively. Significantly genetic variation was found between O. longilobus and O. taihangensis (Φ_ST = 0.232). The dendrogram generated from pairwise genetic distance among all populations showed two distinct clusters, each corresponding to one species. A Mantel test revealed insignificant positive correlation between genetic distances and geographic distances (r_{O. longilobus} = 0.3021; r_{O. taihangensis} = 0.3658; P > 0.05). Those results indicated that self-compatibility, effective gene flow, biological traits, and historical factors may be the main factors causing geographical differentiation in the structure of O. longilobus and O. taihangensis populations.     

The Distribution and Host Shifts of Cotton-Melon Aphids in Northern China

Aphis gossypii Glover (Hemiptera: Aphididae) is a serious pest of cotton in northern China. A microsatellite analysis was used to characterize the genetic structure of A. gossypii populations from different geographic, host plant, and seasonal populations in 2014. Among 906 individuals, 507 multilocus genotypes were identified, with genotypic richness values of 0.07–1.00 for the populations. We observed moderate levels of genetic differentiation among geographic populations (F_ST = 0.103; 95% confidence interval: 0.065–0.145) and host plant populations (F_ST = 0.237; 95% confidence interval: 0.187–0.296). A Mantel test of isolation by distance revealed no significant correlations between Slatkin’s linearized F_ST and the natural logarithm of geographic distance. A Bayesian analysis of population genetic structures identified three clusters. An analysis of molecular variance revealed significant differences among the three clusters (F = 0.26596, P < 0.0001), among seasons (F = 0.04244, P = 0.00381), and among host populations (F = 0.12975, P = 0.0029). Thus, the A. gossypii populations in northern China exhibit considerable genotypic diversity. Additionally, our findings indicated that the 31 analyzed populations could be classified as one of three host biotypes (i.e., cotton, cucumber, and pomegranate biotypes). There were also clear seasonal effects on population genetic structure diversity among aphids collected from Anyang.     

Microsatellite diversity and mating system of Sinojackia xylocarpa (Styracaceae), a species extinct in the wild

Sinojackia xylocarpa is a Chinese endemic species that is extinct in the wild but extant in botanical gardens. Microsatellites were used to investigate the genetic diversity and mating system of this species for future use in a reintroduction program. Ex situ conserved populations of S. xylocarpa maintain intermediate levels of genetic diversity (H_E = 0.570–0.640). However, a general and significant heterozygote excess was found, with a mean F_IS of −0.103. S. xylocarpa was determined to be predominantly outcrossing (t_m = 0.992; t_s = 1.092). Population size and genetic diversity were found to be positively correlated (r = 0.991; P = 0.084). Principal coordinate analysis (PCA) suggests that all extant individuals are derived from two source populations. Reintroduction strategies of S. xylocarpa were proposed on the basis of these results.     

Conservation genetics of Heritiera littoralis (Sterculiaceae), a threatened mangrove in China,based on AFLP and ISSR markers

AFLP and ISSR markers were used to determine the genetic variations in eight mangrove and non-mangrove populations of Heritiera littoralis (Sterculiaceae), a threatened species in China. Our results showed a moderate to high level of genetic variation in this species (P = 63.69%, H_T = 0.20 for AFLP; P = 76.07%, H_T = 0.22 for ISSR), and a relatively high level of genetic differentiation among populations (G_ST = 0.24 for AFLP and 0.27 for ISSR). Life history traits, long-distance dispersal of floating seeds, and local environments may play important roles in shaping the genetic diversity and genetic structure of this species. Investigation of the plant’s reproductive capacity showed that the natural seed production of H. littoralis was low, as was the germination rate and the transformation rate from juvenile to adult. H. littoralis is seriously threatened and is in urgent need of conservation in China.     

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.     

Highly differentiated populations of the narrow endemic and endangered species Primula cicutariifolia in China,revealed by ISSR and SSR

The perennial herb Primula cicutariifolia Pax is an endangered and endemic species with narrow distribution in eastern Anhui and Zhejiang provinces of China. In this study, the levels of genetic variation and the pattern of genetic structure in five natural populations of P. cicutariifolia were assessed by inter-simple sequence repeats (ISSR) and simple sequence repeat (SSR) markers. Both markers revealed that there was remarkably low genetic variation within populations (e.g., H_e = 0.19 and 0.18, for ISSR and SSR respectively) and high differentiation among populations (G_ST = 0.714 and 0.611; Φ_ST = 0.698 and 0.599, for ISSR and SSR respectively). The level of population genetic diversity was correlated to population size only detected by ISSR markers. The genetic structure of P. cicutariifolia may be explained by limited gene flow that was caused by habitat fragmentation and limited seeds and pollen dispersal ability, self breeding system and biennial life form. To protect and avoid disappearance of P. cicutariifolia, much more attentions should be paid to protect all the remnant populations and their habitats, and three management units, i.e. Tianmushan, Damodao, and Panan units, were proposed.