Population genetic structure of Vitex negundo (Verbenaceae) in Three-Gorge Area of the Yangtze River: The riverine barrier to seed dispersal in plants

Previous studies have demonstrated that large rivers can influence inter- and intra-specific gene flow for many animals. The effects of large rivers on the genetics of plant populations have focused on either hydrochoric impacts of water current on gene flow or genetic differentiation among populations from different watersheds. Few studies have explicitly tested the barrier effects on plant gene flow across banks of large rivers, especially their relative effects on pollen and seed dispersals. The Yangtze River (Changjiang River), one of the major rivers of the world, provides an excellent model to evaluate the impacts of rivers on gene flow in plants. Using RAPD (random amplified polymorphic DNA) and cpDNA (chloroplast DNA) markers, we investigated the genetic structure of 10 populations of Vitex negundo in two regions of Three-Gorge Area along the Yangtze River. Each region contained two populations on the north bank, two on the south bank and one island population along the river. The analyses indicated low RAPD between banks, and similar or a little higher differentiation between populations within the same bank. In contrast, a large proportion of chloroplast polymorphism was ascribed to among-bank variation but much lower cpDNA differentiation was among populations within the same bank. These results indicate that the Yangtze River represents a general barrier to the dispersal of seeds but not to the movement of pollen in V. negundo. The cpDNA genetic distances or differentiations between the island populations and those on either bank of the river are intermediate to those between the banks across the river, implying that the islands in the Yangtze River may serve as a stepping-stone for seed dispersal. Our results suggest that large rivers may serve as a general barrier, not only for the movement of animals, but also for the dispersal of plants, which should be of great significance for the conservation of biodiversity around the rivers.     

Spatio-temporal effects of stray hatchery-reared Atlantic salmon Salmo salar on population genetic structure within a 21 km-long Icelandic river system

Although the tendency of Atlantic salmon Salmo salar to form differentiated populations among rivers and among tributaries within large river systems (>100 km-long) is well documented, much less is known about population structure within small river systems (<30 km-long). In the present study, we investigated the genetic effects of straying of hatchery-reared salmon on population structure and genetic composition within the Ellidaár river system, a small system (21 km total length) in SW Iceland. We analyzed spatial and temporal variation of wild and domesticated samples (farmed and ranched; n = 931) using seven microsatellite loci. Estimates of population differentiation [F _ST, genetic tree (D _A)] and Bayesian cluster analysis (STRUCTURE) revealed a significant population structure as well as relative long-term temporal stability of the genetic composition in the main river from 1948 to 2005. However, the genetic composition of the tributary populations was unstable and genetically homogenized in recent years. Wild-hatchery hybrids were detected during the influx of strays as well as few years after, suggesting that introgression has changed the genetic composition of the wild populations. More investigations are needed in Iceland and elsewhere on possible fine-scale population differentiation and factors leading to it. Fine-scale population differentiation as observed in the present study has implications for the resolution with which harvest and habitat management of salmon should be conducted. In addition, farming and ranching operations should be located to minimize potential negative effects of strays on wild fish.     

Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.     

Genetic diversity in population of largemouth bronze gudgeon (Coreius guichenoti Sauvage et Dabry) from Yangtze River determined by microsatellite DNA analysis

Largemouth bronze gudgeon (Coreius guichenoti Sauvage et Dabry 1874), one of the endemic fish species in the upper reaches of the Yangtze River in China, is a benthic and potamodromous fish that is typically found in rivers with torrential flow. Three dams in the Yangtze River, Ertan Dam, Three Gorges Dam and Gezhouba Dam, may have had vital impacts on the habitat and spawning behaviors of largemouth bronze gudgeon, and could ultimately threaten the survival of this fish. We studied the population genetic diversity of C. guichenoti samples collected at seven sites (JH, GLP, BX, HJ, MD, SDP and XB) within the Yangtze River and one of its tributaries, the Yalong River. Genetic diversity patterns were determined by analyzing genetic data from 11 polymorphic microsatellite loci. A high genetic diversity among these largemouth bronze gudgeon populations was indicated by the number of microsatellite alleles (A) and the expected heterozygosity (HE). No significant population variation occurred among GLP, BX, HJ and MD populations, but dramatic population differentiation was observed among JH and XB, two dam-blocked populations, versus other populations. Tests for bottlenecks did not indicate recent dramatic population declines and concurrent losses of genetic diversity in any largemouth bronze gudgeon populations. To the contrary, we found that dams accelerated the population differentiation of this fish.     

Migratory behaviour shapes spatial genetic structure of cyprinid fishes within the Lake Malawi catchment

• Genetic differences among freshwater fish populations are dependent on life‐history characteristics of the species, including the range of adult dispersal and the extent of homing to natal breeding grounds. However, the effects of variation in such characteristics on population genetic connectivity are rarely studied comparatively among closely related species.
• We studied population genetic structure within three congeneric cyprinid species from the Lake Malawi catchment that differ substantially in life‐history traits and conservation status, using a combination of microsatellite and mitochondrial DNA markers. Mpasa (Opsaridium microlepis) is a large (70 cm total length) migratory species that spawns in rivers, but as an adult is exclusively known from the main lake body. Sanjika (Opsaridium microcephalum), is a medium size (30 cm total length) species that exists in lake breeding, river‐lake migratory and apparently landlocked populations. Dwarf sanjika (Opsaridium tweddleorum) is a small non‐migratory species (15 cm total length) that persists in small tributaries surrounding the main lake and adjoining rivers.
• The results revealed striking differences among the three species in spatial genetic structuring. The river‐lake migratory mpasa showed only weak yet significant population genetic structure within the main Lake Malawi catchment, suggesting that there is no strong natal homing. The habitat‐generalist sanjika showed only weak spatial genetic differentiation at microsatellite loci within the Lake Malawi catchment, but moderate structure in mitochondrial DNA, potentially reflecting male‐biased dispersal. The river‐restricted dwarf sanjika showed strong genetic structure in both microsatellite and mitochondrial DNA, suggesting strictly limited dispersal at both adult and juvenile stages.
• We conclude that contrasting migration life histories have resulted in dramatically different patterns of population genetic structure among these congeneric species. The observed patterns demonstrate how divergent life‐history evolution may strongly influence broader patterns of population genetic connectivity in freshwater fish, with consequences for management and conservation. Specifically the results suggesting gene flow among Lake Malawi populations of mpasa, an IUCN red‐listed ‘Endangered’ species endemic to the lake catchment, imply that conservation initiatives operating at both local and catchment scales are needed to reverse local population decline.

     

Population genetic structure of three major river Populations of rohu,Labeo rohita (Cyprinidae: Cypriniformes) using microsatellite DNA markers

Determining the genetic structure is essential for developing conservation and stock improvement plans. Four dinucleotide microsatellite loci were analysed to reveal population genetic structure of the Indian major carp,Labeo rohita collected from three major rivers namely the Halda, the Jamuna, and the Padma in Bangladesh. The four loci were polymorphic (P ₉₅) in all the populations. The populations varied in the number and frequencies of alleles as well as heterozygosities in the loci analyzed. Population differentiation (F _ST) value between the Halda and the Jamuna population was significant (P<0.05). Relatively high level of gene flow and low level ofF _ST values were found between the Padma and the Jamuna population. The unweighted pair group method with averages (UPGMA) dendrogram based on genetic distance resulted in two clusters: the Halda population was alone in one cluster whereas the Jamuna and the Padma made another cluster. The results revealed a relatively low level of genetic variability in the river populations ofL. rohita in Bangladesh.     

An observation of the loss of genetic variability in prenant’s schizothoracin,Schizothorax prenanti,inhabiting a plateau lake

Prenant’s schizothoracin (Schizothorax prenanti) was found naturally distributed in a plateau lake (Lake Wuxu) in upper reaches of the River Jiulong. The genetic diversities of the populations from L. Wuxu and R. Jiulong were investigated according to analysis of mtDNA control region and compared against three other reported river populations. The L. Wuxu population showed lower haplotype (h = 0.74) and nucleotide (π = 0.001) diversities compared to the R. Jiulong population (h = 0.87; π = 0.012); the lake population had suffered from a bottleneck, which might contribute to its low genetic diversity; the lake population significantly differentiated from the river populations, and significant gene flow was hardly found between river populations and L. Wuxu population, suggesting that there is a strong population structure between the lake and river populations. The L. Wuxu population was ecologically isolated from the R. Jiulong population, while the relatively low genetic variability had not affected its viability.     

Genetic monitoring and effects of stocking practices on small <Emphasis Type="Italic">Cyprinus carpio</Emphasis> populations

The ability to detect genetic differences both in space and time is crucial for conserving genetic variation. It can reveal genetic diversity and genetic composition changes of declining native populations that are supported through stocking with captive bred individuals. The present study was designed to analyse the temporal stability of a declining common carp (Cyprinus carpio) population from Lake Volvi (North Greece). Polymorphism was evaluated using seven microsatellite loci at two sampling time points (separated by 12 years). The genetic variability of four additional populations (from two rivers and two lakes) in Northern Greece was also investigated for comparison. Heterozygosity values (0.692–0.868) and allelic richness (8.530–11.148) were high for all studied populations and comparable to other European populations. However, the analysis of temporal common carp samples from Lake Volvi revealed a significant change in their genetic composition and admixture analysis demonstrated significant introgression of stocked individuals into the native population. Both temporal and point estimate methods revealed low effective size (Ne = 61–171.3) for this population, possibly a result of an ancient genetic bottleneck that led to population decline and/or recent anthropogenic interventions. This low Ne has rendered the native population vulnerable to alteration of its genetic composition. Our study demonstrates that enhancement programs should be applied cautiously, especially for small populations. Moreover, it underlines the need for temporal analyses, which may contribute to the evaluation of previous management policies and to future decision making.     

基于线粒体D-loop区和Cyt b基因分析广西禾花鲤三个群体遗传结构

研究基于线粒体D-loop区和Cyt b基因部分序列, 分析了广西全州、融水、环江三地禾花鲤(Cyprinus carpio)的遗传结构。在3个群体中共鉴定到19种D-loop与Cyt b序列的组合单倍型, 总的单倍型多样性(H_d)和核苷酸多样性(π)分别为0.916±0.010和0.008±0.004, 禾花鲤线粒体DNA具有单倍型多样性高和核苷酸多样性低的特点。环江群体单倍型多样性最低, 但是核苷酸多样性却最高, 反映了环江群体存在最明显的谱系混杂。分子方差分析(AMOVA)显示遗传变异主要来源于群体内部(71.54%), 禾花鲤三个群体间有显著的遗传分化(F_st=0.285; P<0.01)。系统发育分析表明, 多数样本的线粒体单倍型属于华南鲤(C. carpio rubrefusus)类型, 同时三地禾花鲤中均检测到一定频率的西鲤(C. carpio carpio)或远东鲤(C. carpio haematopterus)类型的线粒体单倍型, 提示禾花鲤可能受到鲤养殖品种的杂交渐渗。研究初步揭示了广西禾花鲤的种质资源现状, 为禾花鲤这一地方特色“稻鱼共作”品种的选育和苗种管理提供了必要的依据。     

Could an Asian carp population establish in the Great Lakes from a small introduction?

Bighead (Hypothalmichthys nobilis) and Silver carp (Hypothalmichthys molitrix) have established populations in the Mississippi, Illinois, Missouri and Maumee rivers, and because of the hydrological connections, there is now a risk that these species may establish in the Great Lake basins. It has been suggested this risk is minimal because of the small number of fish that breach containment measures, and possible mating-finding difficulties as a consequence. Using literature data, we parameterize a stage- and river-structured population model and examine the probability of a small number of fish establishing a population in one of the Great Lakes. We find that for sexual maturity earlier than age 5, there can be a significant risk of establishment with a very small number of fish (<20) in a lake basin with 10 or fewer spawning rivers. If all fish locate spawning rivers, mating is quite probable for very few spawning rivers. The subdivision of a few spawning adults across a large number rivers does reduce the probability of successful mating, but once a threshold number of fish is reached (dependent on the number of spawning rivers and the probability of fish locating a river), then mating success is very likely. Environmental stochasticity that reduces spawning success and juvenile survival predictably reduces establishment probability, but if spawning rivers have environmental conditions that fluctuate out of phase, this impact is much reduced. As expected, the most hazardous containment breach scenario is if barriers are continually leaky, and a small number of fish are introduced into the lake basin each year. In contrast, a single introduction represents a lower risk of establishment. Overall, the model suggests that establishment is quite likely (>75 % probability) for a large number of scenarios involving a small number of founding individuals (<20 fish). We conclude that while propagule pressure does increase risk in this system, it is not the most important consideration. Instead, probable age at first maturity in a given Great Lake basin may be critical to determining risk.     

五条河流青海湖裸鲤的同工酶变异

为全面了解青海湖裸鲤遗传多样性现状,采用水平淀粉凝胶电泳技术分析了青海湖裸鲤[样品采自青海湖的五条支流,分别为泉吉河(QJ)、沙柳河(SL)、哈尔盖河(HEG)、布哈河(BH)以及甘子河(GZ)]的13种同工酶,共记录26个位点,统计了基因频率,计算了其遗传多样性。结果表明:26个基因位点中多态位点6个,分别为Pgm、Hk、Cat、Gdh、Es-t1、S-Mdh,多态位点比例(P0.99)为23.08%,表明青海湖裸鲤的五个群体皆具有较高的遗传多样性水平;分别计算了五个群体的平均杂合度(H)为0.1161(HEG)、0.1178(GZ)、0.1304(SL)、0.1305(BH)、0.1287(QJ),多态位点比例(Ae)分别为1.3112(BH)、1.3069(SL)、1.2542(GZ)、1.2492(HEG)、1.2453(QJ);除泉吉河群体外,其它四个群体的遗传偏离指数均为负数,表明多数群体处于一定程度的杂合子缺失状态;计算了五个群体间的遗传距离以及遗传相似度,结果显示群体间遗传距离与遗传相似度与各个河流的地理位置具有很强的相关性;根据五个群体的遗传距离进行了聚类分析,通过构建系统树图将其基本分为两大种群,甘子河与哈尔盖河两群体为一类群,另外三个群体分为一个类群;计算群体间的基因流(Nm)为7.2013,说明河道之间具有较为广泛的基因交流,并计算了两两群体间的基因流,其中布哈河群体与其它群体间的基因交流都较为广泛。     

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.     

Environmental transition zone and rivers shape intraspecific population structure and genetic diversity of an Amazonian rain forest tree frog

Diversification processes acting across geographically continuous populations have been rarely documented in Amazonia, because of the lack of fine-scale sampling over extensive areas. We aimed to determine the geographic effects of an environmental transition zone and large rivers on the intraspecific population structure of the Manaus slender-legged tree frog (Osteocephalus taurinus) along a ~ 900 km transect of tropical rain forest. Using one mitochondrial (16S), two nuclear genes (TYR, POMC) and three microsatellites, we estimated the population structure, phylogenetic relationships and geographic variation of 262 O. taurinus and 5 O. oophagus (a close relative) along the Purus–Madeira interfluve (PMI) and opposite banks of the central Amazon and upper Madeira rivers, at central-southern Amazonia, Brazil. Six genetic clusters were identified: two corresponding to sympatric populations of O. taurinus and O. oophagus from their type locality, north of Amazon river. Within PMI, there were three distinct O. taurinus genetic clusters distributed along the geographic gradient with one main phylogeographic break found (concordant between 16S and TYR), that corresponds to a transition zone (ecotone) between dense and open rain forest ecotypes. The sixth cluster was an O. taurinus population isolated at the east bank of the upper Madeira river. In addition, restricted haplotype sharing was identified from the west to east banks at upper Madeira river. Within PMI, parapatric genetic structure is explained by a potential association of the genetic clusters to the different forest ecotypes they inhabit coupled with isolation by distance, thus supporting the gradient hypothesis for diversification. Differentiation of populations that are external to the PMI is most likely explained by the barrier effect of the Madeira and Amazon rivers. Our findings provide new evidence on diversification processes across continuous Amazonian landscapes; however, the specific mechanisms underlying the origin and maintenance of the identified phylogeographic break need to be further studied.     

Geographic differentiation of <Emphasis Type="Italic">Cobitis shikokuensis</Emphasis> inferred from mtDNA RFLP analysis

Mitochondrial DNA divergence among populations of the Japanese spinous loach Cobitis shikokuensis, endemic to Shikoku Island, was investigated by restricted fragment length polymorphism analysis. A total of 68 restriction sites on DNA fragments from the cytochrome b to D-loop regions and from the 12S rRNA to 16S rRNA regions, amplified by PCR, were analyzed. A total of 12 haplotypes (plus 6 in outgroups) were detected in 268 specimens collected from 19 localities in seven rivers (and 41 specimens from four localities in three rivers in outgroups). Three of the seven river populations of C. shikokuensis were shown to have unique haplotypes, and four of the seven river populations were monomorphic. The nested structure of the haplotype network for populations of C. shikokuensis exhibited two large clades corresponding to (1) populations from the Shimanto River and its neighbors and (2) two genetically divergent populations in the Shigenobu and Iwamatsu Rivers. The population from the Shimanto River, the largest river inhabited by C. shikokuensis, maintains great haplotype diversity as well as the allozyme diversity previously reported. On the other hand, populations from the Hiji River, the second largest river, which exhibited the highest allozyme diversity, were monomorphic in their mtDNA. The nested clade analysis (NCA) revealed that past fragmentation between the above two clades could occur in the initial distribution process of C. shikokuensis. The large genetic divergence of two river populations from the Shigenobu and Iwamatsu Rivers was inferred to be caused by a process of long distance colonization and fragmentation. MtDNA introgression into the Hiji River population from southern river populations was suggested. Taking genetic divergence into consideration, each river population of C. shikokuensis should be conserved separately as like a distinct species, and conservation programs for the small populations showing less genetic variability should be invoked as soon as possible.     

Population genetics of the aquatic fungus Tetracladium marchalianum over space and time

Aquatic hyphomycete fungi are fundamental mediators of energy flow and nutrient spiraling in rivers. These microscopic fungi are primarily dispersed in river currents, undergo substantial annual fluctuations in abundance, and reproduce either predominantly or exclusively asexually. These aspects of aquatic hyphomycete biology are expected to influence levels and distributions of genetic diversity over both spatial and temporal scales. In this study, we investigated the spatiotemporal distribution of genotypic diversity in the representative aquatic hyphomycete Tetracladium marchalianum. We sampled populations of this fungus from seven sites, three sites each in two rivers in Illinois, USA, and one site in a Wisconsin river, USA, and repeatedly sampled one population over two years to track population genetic parameters through two seasonal cycles. The resulting fungal isolates (N = 391) were genotyped at eight polymorphic microsatellite loci. In spite of seasonal reductions in the abundance of this species, genotypic diversity was consistently very high and allele frequencies remarkably stable over time. Likewise, genotypic diversity was very high at all sites. Genetic differentiation was only observed between the most distant rivers (∼450 km). Clear evidence that T. marchalianum reproduces sexually in nature was not observed. Additionally, we used phylogenetic analysis of partial β-tubulin gene sequences to confirm that the fungal isolates studied here represent a single species. These results suggest that populations of T. marchalianum may be very large and highly connected at local scales. We speculate that large population sizes and colonization of alternate substrates in both terrestrial and aquatic environments may effectively buffer the aquatic populations from in-stream population fluctuations and facilitate stability in allele frequencies over time. These data also suggest that overland dispersal is more important for structuring populations of T. marchalianum over geographic scales than expected.     

Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems

Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (H_S = 0.68), which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G” _ST = 0.269 and 0.164 and D _EST = 0.190 and 0.124, respectively) and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.     

长江水系钱草鱼遗传结构及变异性的RAPD研究

采用随机扩增多态性DNA（RAPD）技术对长江中游的湖北嘉鱼与江西瑞昌两个地理群体和中游的汉江和湘江两大水系的鲢和草鱼的群体进行了遗传学研究。发现长江水系链的遗传变异要高于草鱼,与现今生物量成反比的反常现象。鲢遗传多样性从大到小的分布是嘉鱼→湘江→瑞昌→汉江。草鱼遗传多样性从大到小的分布是瑞昌→汉江→湘江→嘉鱼,鲢和草鱼的遗传多样性地理分布并不一致。遗传分化指数Gst分别为12.3%和17.5%,表明鲢和草鱼的四个地理群体的遗传分化度较低,可能与地理较近和基因交流频繁有关。     

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.     

Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus F_ST = 0.32, F_ST’ = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R² = 0.51) and higher local inbreeding (R² = 0.22). Populations varied greatly in levels of local inbreeding (F_IS = 0.2–0.9) and F_IS increased in more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.     

Validation of eDNA Surveillance Sensitivity for Detection of Asian Carps in Controlled and Field Experiments

In many North American rivers, populations of multiple species of non-native cyprinid fishes are present, including black carp (Mylpharyngodon piceus), grass carp (Ctenopharyngodon idella), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), common carp (Cyprinus carpio), and goldfish (Carassius auratus). All six of these species are found in the Mississippi River basin and tracking their invasion has proven difficult, particularly where abundance is low. Knowledge of the location of the invasion front is valuable to natural resource managers because future ecological and economic damages can be most effectively prevented when populations are low. To test the accuracy of environmental DNA (eDNA) as an early indicator of species occurrence and relative abundance, we applied eDNA technology to the six non-native cyprinid species putatively present in a 2.6 river mile stretch of the Chicago (IL, USA) canal system that was subsequently treated with piscicide. The proportion of water samples yielding positive detections increased with relative abundance of the six species, as indicated by the number of carcasses recovered after poisoning. New markers for black carp, grass carp, and a common carp/goldfish are reported and details of the marker testing to ensure specificity are provided.