The Kuroshio Current influences genetic diversity and population genetic structure of a tropical seagrass,Enhalus acoroides

Information on genetic diversity and differentiation of seagrass populations is essential for the conservation of coastal ecosystems. However, little is known about the seagrasses in the Indo‐West Pacific Ocean, where the world's highest diversity of seagrasses occurs. The influence of sea currents on these populations is also unknown. We estimated the genetic diversity and population genetic structure and identified reproductive features in Enhalus acoroides populations from the Yaeyama Islands, Hainan Island and the Philippines. The Philippines are situated at the centre of the E. acoroides range, Yaeyama and Hainan are peripheral populations, and the Yaeyama population is at the northern limit of the species range. The powerful Kuroshio Current flows from the Philippines to Yaeyama. Genetic analyses using nine microsatellite markers indicated that reproduction of E. acoroides is mostly sexual. Clonal diversity does not decrease in northern populations, although genetic diversity does. However, the genetic diversity of the Yaeyama populations is greater than that of the Hainan populations. Significant genetic differentiation among most populations was evident; however, the Yaeyama and north‐east Philippines populations were genetically similar, despite being separated by ~1100 km. An assignment test suggested that recruitment occurs from the north‐east Philippines to Yaeyama. The strong current in this region is probably responsible for the extant genetic diversity and recruitment patterns.     

Population structure and colonization of Bactrocera dorsalis (Diptera: Tephritidae) in China,inferred from mtDNA COI sequences

The oriental fruit fly, Bactrocera dorsalis, is a serious pest of fruits and vegetables in South‐east Asia, and, because of quarantine restrictions, impedes international trade and economic development in the region. Revealing genetic variation in oriental fruit fly populations will provide a better understanding of the colonization process and facilitate the quarantine and management of this species. The genetic structure in 15 populations of oriental fruit fly from southern China, Laos and Myanmar in South‐east Asia was examined with a 640‐bp sequence of the mitochondrial cytochrome oxidase subunit I (COI) gene. The highest levels of genetic diversity were found in Laos and Myanmar. Low to medium levels of genetic differentiation (F_ST ≤ 0.134) were observed among populations. Pooled populations from mainland China differed from those in Laos and Myanmar (F_ST = 0.024). Genetic structure across the region did not follow the isolation‐by‐distance model. The high genetic diversity observed in Laos and Myanmar supports the South‐east Asian origin of B. dorsalis. High genetic diversity and significant differentiation between some populations within mainland China indicate B. dorsalis populations have been established in the region for an extended period of time. High levels of genetic diversity observed among the five populations from Hainan Island and similarity between the Island and Chinese mainland populations indicate that B. dorsalis was introduced to Hainan from the mainland and has been on the island for many years. High genetic diversity in the recently established population in Shanghai (Pudong) suggests multiple introductions or a larger number of founders.     

濒危植物海南龙血树的种群结构与动态

了解种群的生存现状与动态趋势对濒危植物的保护至关重要。为了更好地保护濒危海南龙血树种群,对海南岛不同生境的11个海南龙血树(Dracaena cambodiana)种群进行了调查;并利用个体基径数据建立各种群的年龄结构和静态生命表,得到种群年龄结构动态指数,绘制种群存活曲线和生存函数曲线,从而获得海南龙血树的种群结构与动态。结果表明:海南龙血树种群年龄结构与种群所处的生境关系密切,海边的NS和YL种群结构为衰退型,LN和CH居群为稳定型,而非海边种群为增长型,没有老龄个体;11个种群中,EXL种群显示出最高的增长趋势和最好的种群稳定性,NS和YL种群稳定性最差,种群抗干扰能力极低;11个种群的存活曲线均属于Deevey-Ⅰ型,但生存函数分析显示海南龙血树种群生活史早期和晚期脆弱,中期稳定,这表明海南龙血树种群所处的生境更适合成年个体生存,现有的生境对幼龄个体的环境筛作用较强。海南龙血树属于退偿物种,针对其种群的生存现状,应采取多种方法相结合的方式进行保护与复壮。     

Genetic diversity and genetic structure of Decalobanthus boisianus in Hainan Island,China

Decalobanthus boisianus is a native plant of Hainan Island, China, which has caused considerable damage to tropical forest ecosystems in recent decades. Understanding the genetic diversity and structure of this species can facilitate uncovering the molecular mechanism of its invasive ability. Here, we collected 77 individuals of D. boisianus spanning 8 distribution areas with a gradient of human disturbance intensity (i.e., low, moderate, and high disturbance intensity groups) to assess patterns of genetic diversity and structure using inter simple sequence repeat (ISSR) markers. We found that a total of 220 loci were scored with 13 primers using ISSR methods, and that 198 loci were polymorphic. The genetic diversity of D. boisianus among these eight forests decreased with increasing human disturbance intensity. Over 70% of the total genetic variation was present within populations, while less than 30% of variation was found among populations. There was a high gene flow (1.27) among them due to a lack of effective geographic barriers. The mean Nei's genetic distance of D. boisianus populations was found to be relatively small (i.e., 0.07), and the average genetic similarity of the eight populations was high (i.e., 0.93). Our findings indicate that the genetic diversity of D. boisianus correlated to human disturbance density, and that D. boisianus populations in Hainan Island have frequent gene exchange. We suggest that reduce deforestation to decrease human disturbance may be a good way to prevent the invasion of D. boisianus.     

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small N_e (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high F_ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high F_ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small N_e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.     

Past population history versus recent population decline – founder effects in island species and their genetic signatures

Island populations are mostly characterized by low genetic diversity if compared with their mainland conspecifics. This is often explained as a consequence of founder effects in the wake of island colonization and concomitant bottlenecks. In a recent contribution, Stuessy et al. (Journal of Biogeography, 2012, 39, 1565–1566) point out that the genetic imprint of past founder effects is no longer visible today, as most island colonizations occurred millions of generations ago. The authors argue that low genetic diversity detectable today is mainly caused by recent environmental factors such as anthropogenic habitat destruction. This scenario should be complemented by the influence of long‐term isolation and small habitat size, which often lead to strong population fluctuations and repeated bottlenecks. In consequence, inbreeding and genetic drift, coupled with the potential effects of purging in small populations, may also result in genetic diversity remaining low for a long time after colonization.     

Population genetic structure,migration, and polyploidy origin of a medicinal species Gynostemma pentaphyllum (Cucurbitaceae)

Gynostemma pentaphyllum, a member of family Cucurbitaceae, is a perennial creeping herb used as a traditional medicinal plant in China. In this study, six polymorphic nSSR and four EST‐SSR primers were used to genotype 1,020 individuals in 72 wild populations of G. pentaphyllum. The genetic diversity and population structure were investigated, and ecological niche modeling was performed to reveal the evolution and demographic history of its natural populations. The results show that G. pentaphyllum has a low level of genetic diversity and high level of variation among populations because of pervasive asexual propagation, genetic drift, and long‐term habitat isolation. Results of the Mantel test demonstrate that the genetic distance and geographic distance are significantly correlated among G. pentaphyllum natural populations. The populations can be divided into two clusters on the basis of genetic structure. Asymmetrical patterns of historical gene flow were observed among the clusters. For the contemporary, almost all the bidirectional gene flow of the related pairs was symmetrical with slight differences. Recent bottlenecks were experienced by 34.72% of the studied populations. The geographic range of G. pentaphyllum continues to expand northward and eastward from Hengduan Mountains. The present distribution of G. pentaphyllum is a consequence of its complex evolution. Polyploidy in G. pentaphyllum is inferred to be polygenetic. Finally, G. pentaphyllum is a species in need of protection, so in situ and ex situ measures should be considered in the future.     

Managing diversity: Domestication and gene flow in Stenocereus stellatus Riccob. (Cactaceae) in Mexico

Microsatellite markers (N = 5) were developed for analysis of genetic variation in 15 populations of the columnar cactus Stenocereus stellatus, managed under traditional agriculture practices in central Mexico. Microsatellite diversity was analyzed within and among populations, between geographic regions, and among population management types to provide detailed insight into historical gene flow rates and population dynamics associated with domestication. Our results corroborate a greater diversity in populations managed by farmers compared with wild ones (H_E = 0.64 vs. 0.55), but with regional variation between populations among regions. Although farmers propagated S. stellatus vegetatively in home gardens to diversify their stock, asexual recruitment also occurred naturally in populations where more marginal conditions have limited sexual recruitment, resulting in lower genetic diversity. Therefore, a clear‐cut relationship between the occurrence of asexual recruitment and genetic diversity was not evident. Two managed populations adjacent to towns were identified as major sources of gene movement in each sampled region, with significant migration to distant as well as nearby populations. Coupled with the absence of significant bottlenecks, this suggests a mechanism for promoting genetic diversity in managed populations through long distance gene exchange. Cultivation of S. stellatus in close proximity to wild populations has led to complex patterns of genetic variation across the landscape that reflects the interaction of natural and cultural processes. As molecular markers become available for nontraditional crops and novel analysis techniques allow us to detect and evaluate patterns of genetic diversity, genetic studies provide valuable insights into managing crop genetic resources into the future against a backdrop of global change. Traditional agriculture systems play an important role in maintaining genetic diversity for plant species.     

Colonization patterns and genetic structure of peripheral populations of the trumpeter finch (Bucanetes githagineus) from Northwest Africa, the Canary Islands and the Iberian Peninsula

Aim This paper has three aims: (1) to reconstruct the colonization history of two peripheral populations of the trumpeter finch (Bucanetes githagineus) presumably originating from the same source, one the result of an ancient expansion process and the other recently established and still expanding; (2) to estimate the importance of key events, such as past and current gene flow and bottlenecks, in both expansion processes and their contribution to the present population structure and genetic diversity; and (3) to find out whether two peripheral populations that established at widely differing times also differ in terms of genetic diversity. Location Northwest Africa (assumed source population), Canary Islands (long‐established peripheral) and south‐eastern Iberian Peninsula (recently established peripheral). Methods Bayesian analysis of population structure, individual assignment tests, F‐statistics, maximum likelihood migration estimates, genetic diversity indices and bottleneck tests were calculated with microsatellite data from 194 trumpeter finches from five breeding and two seasonal non‐breeding sites. Results Our data support the existence of two subpopulations (Canary Island and Ibero‐African) as the most likely population structure. Seasonal sites in the Iberian Peninsula had the highest percentage of birds assigned to other, mainly Iberian, sites. Pairwise F_ST values showed that the Canary Island localities were very similar to each other, but differed from the rest. Gene flow estimates within subpopulations were only slightly higher in the Canary Island population than in the Ibero‐African one. Gene diversity indices were similar at all localities. Canary Island sites show evidence of bottlenecks, whereas the Ibero‐African sites do not. Main conclusions Our data show that, at present, birds from the Canary Islands are genetically differentiated from those in North Africa and continental Spain. We could not unequivocally confirm the African origin of Canary populations because the contrary is also plausible. The Iberian Peninsula seems to have repeatedly received individuals from North Africa, which would have led to the relatively high genetic diversity found in these recently established localities and prevented bottlenecks. Movements of individuals towards sites outside their current range during the non‐breeding season are likely to precede the establishment of new breeding sites at the periphery of the distribution range.     

Anthropogenic fragmentation may not alter pre‐existing patterns of genetic diversity and differentiation in perennial shrubs

Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no prefragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird‐pollinated shrub Grevillea caleyi R.Br., by comparing current patterns of genetic structure and diversity with those of the closely related G. longifolia R.Br. that has a similar life history but has not experienced anthropogenic fragmentation. Grevillea caleyi and G. longifolia showed similar and substantial population subdivision at all spatial levels (global F′_ST = 0.615 and 0.454; S_p = 0.039 and 0.066), marked isolation by distance and large heterozygous deficiencies. These characteristics suggest long‐term effects of inbreeding in self‐compatible species that have poor seed dispersal, limited connectivity via pollen flow and undergo population bottlenecks because of periodic fires. Highly structured allele size distributions, most notably in G. caleyi, imply historical processes of drift and mutation were important in isolated subpopulations. Genetic diversity did not vary with population size but was lower in more isolated populations for both species. Through this comparison, we reject the hypothesis that anthropogenic fragmentation has impacted substantially on the genetic composition or structure of G. caleyi populations. Our results suggest that highly self‐compatible species with limited dispersal may be relatively resilient to the genetic changes predicted to follow habitat fragmentation.     

Population genetic structure and migration patterns of Dendrothrips minowai (Thysanoptera: Thripidae) in Guizhou,China

Dendrothrips minowai Priesner (Thysanoptera: Thripidae) is one of the most destructive insect pests on tea plants. Although outbreaks of this pest occur annually in South China, especially in Guizhou Province, little is known about its population genetics, such as genetic diversity and gene flow. To investigate its population genetic structure and migration routes in Guizhou Province, we analyzed 24 D. minowai populations across Guizhou using six microsatellite loci. We detected the moderate genetic diversity and the population genetic structure of this thrip species. Neighbor‐joining (NJ) phylogenetic tree and STRUCTURE analyses recognized two clusters within the studied populations. No correlation between genetic and geographical distances (r = 0.0139, P = 0.5830) was detected and more than 89% of the variation occurred among samples within populations. Gene flow analysis revealed high migration rates (74.0 – 894.1) among D. minowai populations. Overall, the trend of asymmetrical gene flow was from northeast to southwest. Our analyses demonstrated that D. minowai derived or originated from multiple sites and could be eventually divided into two groups in Guizhou.     

Genetic diversity and structure of Pinus dabeshanensis revealed by expressed sequence tag-simple sequence repeat (EST-SSR) markers

Assessing patterns of genetic variation in rare endangered species is critical for developing both in situ and ex situ conservation strategies. Pinus dabeshanensis Cheng et Law is an endangered species endemic to the Dabieshan Mountains of eastern China. To obtain fundamental information of genetic diversity, population history, effective population size, and gene flow in this species, we explored patterns of genetic variation of natural populations, in addition to an ex situ conserved population, using expressed sequence tag-simple sequence repeats (EST-SSR) markers. Our results revealed moderate levels of genetic diversity (e.g., H_E = 0.458 vs. H_E = 0.423) and a low level of genetic differentiation (F_ST = 0.028) among natural and conserved populations relative to other conifers. Both contemporary and historical migration rates among populations were high. Bayesian coalescent-based analyses suggested that 3 populations underwent reductions in population size ca. 10,000 yr ago, and that two populations may have experienced recent genetic bottlenecks under the TPM. Bayesian clustering revealed that individuals from the ex situ population were largely assigned to the ‘red’ cluster. Additionally, our results identified private alleles in the natural populations but not in the ex situ population, suggesting that the ex situ conserved population insufficiently represents the genetic diversity present in the species. Past decline in population size is likely to be due to Holocene climate change. Based on the genetic information obtained for P. dabeshanensis, we propose some suggestions for the conservation and efficient management of this endangered species.     

Microsatellite‐based analysis of genetic structure and gene flow of Mythimna separata (Walker) (Lepidoptera: Noctuidae) in China

The oriental armyworm, Mythimna separata, is a serious agricultural pest in China. Seasonal and roundtrip migration has recently led to sudden, localized outbreaks and crop losses. To evaluate genetic differentiation between populations in eastern and western China and elucidate gene flow, the genetic structure of 20 natural populations from nine provinces was examined using seven microsatellite markers. The results indicated high genetic diversity. However, little to moderate (0 < F_ST < 0.15) genetic differentiation was detected, and there was no correlation between genetic distance and geographical distance. Bayesian clustering analysis identified three groups whereas discriminant analysis of principal components identified ten clusters that were considered as two clear‐cut clusters and one admixed group. Gene flow occurred frequently in most population pairs, and an asymmetrical migration rate was detected in several pairwise population comparisons. The bottleneck test showed that few populations had experienced recent bottlenecks. Correspondingly, large‐scale and long‐distance migration of M. separata has caused low genetic differentiation and frequent gene exchange. Our findings are important for studying genetic evolution and help to improve predictions of M. separata outbreaks in China.     

Low genetic variability and strong differentiation among isolated populations of the rare steppe grass Stipa capillata L. in Central Europe

Stipa capillata L. (Poaceae) is a rare grassland species in Central Europe that is thought to have once been widespread in post‐glacial times. Such relict species are expected to show low genetic diversity within populations and high genetic differentiation between populations due to bottlenecks, long‐term isolation and ongoing habitat fragmentation. These patterns should be particularly pronounced in selfing species. We analysed patterns of random amplified polymorphic DNA (RAPD) variation in the facultatively cleistogamous S. capillata to examine whether genetic diversity is associated with population size, and to draw initial conclusions on the migration history of this species in Central Europe. We analysed 31 S. capillata populations distributed in northeastern, central and western Germany, Switzerland and Slovakia. Estimates of genetic diversity at the population level were low and not related to population size. Among all populations, extraordinarily high levels of genetic differentiation (amova : φ_ST = 0.86; Bayesian analysis: θ^B = 0.758) and isolation‐by‐distance were detected. Hierarchical amova indicated that most of the variability was partitioned among geographic regions (59%), or among populations between regions when the genetically distinct Slovakian populations were excluded. These findings are supported by results of a multivariate ordination analysis. We also found two different groups in an UPGMA cluster analysis: one that contained the populations from Slovakia, and the other that combined the populations from Germany and Switzerland. Our findings imply that S. capillata is indeed a relict species that experienced strong bottlenecks in Central Europe, enhanced by isolation and selfing. Most likely, populations in Slovakia were not the main genetic source for the post‐glacial colonization of Central Europe.     

海南岛油茶种质资源遗传多样性的SRAP分析

为了解海南岛油茶(Camellia oleifera)种质资源的遗传多样性,采用SRAP分子标记,对海南岛油茶主要分布区的31个居群进行了遗传多样性和亲缘关系分析。结果表明,海南岛油茶资源的遗传多样性低,物种水平的多态性百分率(PPB)为98.30%,Nei’s基因多样性(H)为0.222 8,Shannon信息指数(I)为0.353 8;居群水平的PPB=40.96%,观测等位基因数(Na)为1.409 6,有效等位基因数(Ne)为1.237 1, H=0.138 5, I=0.208 3,这与海南岛油茶丰富的表型多样性水平不一致。海南岛油茶资源遗传分化较大,居群间基因交流有限,不同居群间的遗传分化指数(Gst)为0.380,基因流(Nm)为0.813 91。遗传变异主要发生在居群内,有38.05%的变异存在居群间,61.95%存在于居群内。遗传距离为0.022 6～0.276 4,平均为0.107 7,居群间的亲缘关系较近。UPGMA聚类分析表明,在遗传距离为0.11处,可将31个油茶居群聚为6类,表现出明显的行政区域性,而与地理距离关系不大。因此,海南岛油茶资源遗传多样性低,亲缘关系近可能导致自交或近交不亲和,可能是海南油茶林分花量大而结实低的主要内在原因。     

Contrasting patterns of population structure and demographic history in cryptic species of Bostrychia intricata (Rhodomelaceae,Rhodophyta) from New Zealand

Spatial patterns of genetic diversity provide insight into the demography and history of species. Morphologically similar but genetically distinct “cryptic” species are increasingly being recognized in marine organisms through molecular analyses. Such species are, on closer inspection, often discovered to display contrasting life histories or occasionally minor morphological differences; molecular tools can thus be useful indicators of diversity. Bostrychia intricata, a marine red alga, is widely distributed throughout the Southern Hemisphere and comprises many cryptic species. We used mitochondrial cytochrome c oxidase I gene sequences to assess the genetic variation, population genetic structure, and demographic history of B. intricata in New Zealand. Our results supported the existence of three cryptic species of B. intricata (N2, N4, and N5) in New Zealand. Cryptic species N4, which was found throughout New Zealand, showed a higher genetic diversity and wider distribution than the other two species, which were only found in the North Island and northern South Island. Our analyses showed low to moderate genetic differentiation among eastern North Island populations for cryptic species N2, but high differentiation among North and South Island populations for N4, suggesting different population structure between these cryptic species. Data also indicated that N2 has recently undergone population expansion, probably since the Last Glacial Maximum (LGM), while the higher genetic diversity in N4 populations suggests persistence in situ through the LGM. The contrasting population structures and inferred demographic histories of these species highlight that life history can vary greatly even among morphologically indistinguishable taxa.     

Population structure and biogeography of Hemiphaga pigeons (Aves: Columbidae) on islands in the New Zealand region

Aim The New Zealand avifauna includes lineages that lack close relatives elsewhere and have low diversity, characteristics sometimes ascribed to long geographic isolation. However, extinction at the population and species levels could yield the same pattern. A prominent example is the ecologically important pigeon genus Hemiphaga. In this study, we examined the population structure and phylogeography of Hemiphaga across islands in the region. Location New Zealand, Chatham Islands and Norfolk Island. Methods Mitochondrial DNA was sequenced for all species of the genus Hemiphaga. Sixty‐seven individuals from mainland New Zealand (Hemiphaga novaeseelandiae novaeseelandiae), six of the Chatham Islands sister species (Hemiphaga chathamensis), and three of the extinct Norfolk Island subspecies (Hemiphaga novaeseelandiae spadicea) were included in this study. Novel D‐loop and cytochrome b primers were designed to amplify DNA from museum samples. Additionally, five other mitochondrial genes were used to examine placement of the phylogenetic root. Results Analyses of mitochondrial DNA sequences revealed three Hemiphaga clades, consistent with the allopatric populations of recognized (sub)species on oceanic islands. Of the 23 D‐loop haplotypes among 67 New Zealand pigeons (Hemiphaga n. novaeseelandiae), 19 haplotypes were singletons and one haplotype was common and widespread. Population genetic diversity was shallow within and between New Zealand populations, indicating range expansion with high inter‐population exchange. Tentative rooting of the Hemiphaga clade with cyt b data indicates exchange between mainland New Zealand and the Chatham Islands prior to colonization of Norfolk Island. We found low genetic divergence between populations on New Zealand, the Chatham Islands and Norfolk Island, but deep phylogenetic divergence from the closest living relatives of Hemiphaga. Main conclusions The data are consistent with the hypothesis of population reduction during the Pleistocene and subsequent expansion from forest refugia. Observed mobility of Hemiphaga when feeding helps explain the shallow diversity among populations on islands separated by many hundreds of kilometres of ocean. Together with comparison of distribution patterns observed among birds of the New Zealand region, these data suggest that endemicity might represent not long occupancy of an area, but descent from geologically recent colonizations. We consider the role of lineage pruning in creating the impression of old endemicity.     

Roads to isolation: Similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes

Freshwater species often show high levels of endemism and risk of extinction owing to their limited dispersal abilities. This is exemplified by the stenotopic freshwater crab, Johora singaporensis which is one of the world's 100 most threatened species, and currently inhabits less than 0.01 km² of five low order hill streams within the highly urbanized island city‐state of Singapore. We compared populations of J. singaporensis with that of the non‐threatened, widespread, abundant, and eurytopic freshwater crab, Parathelphusa maculata, and found surprisingly high congruence between their population genomic histories. Based on 2,617 and 2,470 genome‐wide SNPs mined via the double‐digest restriction‐associated DNA sequencing method for ~90 individuals of J. singaporensis and P. maculata, respectively, the populations are strongly isolated (F_ST = 0.146–0.371), have low genetic diversity for both species (also for COI), and show signatures of recent genetic bottlenecks. The most genetically isolated populations for both species are separated from other populations by one of the oldest roads in Singapore. These results suggest that anthropogenic developments may have impacted stream‐dependent species in a uniform manner, regardless of ubiquity, habitat preference, or dispersal modes of the species. While signs of inbreeding were not detected for the critically endangered species, the genetic distinctiveness and low diversity of the populations call for genetic rescue and connecting corridors between the remaining fragments of the natural habitat.     

Effect of Yangtze River on population genetic structure of the relict plant Parrotia subaequalis in eastern China

Parrotia subaequalis (Hamamelidaceae) is a Tertiary relic species endemic in eastern China. We used inter‐simple sequence repeat (ISSR) markers to access genetic diversity and population genetic structure in natural five populations of P. subaequalis. The levels of genetic diversity were higher at species level (H = 0.2031) but lower at population level (H = 0.1096). The higher genetic diversity at species levels might be attributed to the accumulation of distinctive genotypes which adapted to the different habitats after Quaternary glaciations. Meanwhile, founder effects on the early stage, and subsequent bottleneck of population regeneration due to its biological characteristics, environmental features, and human activities, seemed to explain the low population levels of genetic diversity. The hierarchical AMOVA revealed high levels (42.60%) of among‐population genetic differentiation, which was in congruence with the high levels of Nei's genetic differentiation index (G_ST = 0.4629) and limited gene flow (N_m = 0.5801) among the studied populations. Mantel test showed a significant isolation‐by‐distance, indicating that geographic isolation has a significant effect on genetic structure in this species. Unweighted pair‐group method with arithmetic average clustering, PCoA, and Bayesian analyses uniformly recovered groups that matched the geographical distribution of this species. In particular, our results suggest that Yangtze River has served as a natural barrier to gene flow between populations occurred on both riversides. Concerning the management of P. subaequalis, the high genetic differentiation among populations indicates that preserving all five natural populations in situ and collecting enough individuals from these populations for ex situ conservation are necessary.     

Conservation genetics of the Critically Endangered Saint Croix ground lizard (<Emphasis Type="Italic">Ameiva polops</Emphasis> Cope 1863)

The Saint Croix ground lizard (Ameiva polops) is a Critically Endangered species endemic to Saint Croix, U.S. Virgin Islands. Although it is completely extirpated from Saint Croix Island (last seen in 1968), two small natural satellite populations survive on two islets off St. Croix: one on Protestant Cay (estimated at ~30 individuals in 2002); and one on Green Cay (estimated at ~180 individuals in 2002). Two additional small populations exist that were founded with individuals translocated from the two surviving natural populations. One is on Ruth Island, a man-made islet off St. Croix, founded in 1990 with 10 individuals from Protestant Cay. The other is on Buck Island, ~2.5 km from Saint Croix, founded in 2008 with 57 individuals from Green Cay. All populations are vulnerable to catastrophic events such as hurricanes, sea level rise, introduction of exotic species, and landscape transformation. Herein, we used mitochondrial and nuclear-microsatellite markers to examine levels of genetic diversity within extant populations of A. polops and the degree of genetic differentiation among them. We also conducted analyses to search for signatures of recent bottlenecks in these populations and to estimate their effective population size (N _e ). We found low genetic variability within populations of this lizard, comparable to that observed in other threatened vertebrates. We also found significant genetic differentiation among the three populations examined, as well as signatures of recent bottlenecks and critically low N _e values in all populations. Based on our results, we suggest two different conservation units for A. polops: (1) Green Cay and its replicate population at Buck Island; and (2) Protestant Cay and its replicate population at Ruth Island. We discuss the implications of our findings on the conservation and management of A. polops.