Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration

Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri within and between adjacent streams in Belize. The genetic data were complemented by a tagging study of movement within one stream. In the absence of physical dispersal barriers (waterfalls), population structure followed an isolation by distance (IBD) pattern. Genetic differentiation (F_ST up to 0.07) was significant between and within creeks, despite high dispersal in the latter as judged by the tagging data. Such heterogeneity apparently was a result of genetic drift in local demes, due to small population sizes and highly skewed paternity. The IBD pattern was interrupted by waterfalls, boosting F_ST above 0.30 between adjacent samples across these barriers. Overall, our results are helpful in understanding the interplay of evolutionary forces and population dynamics in a small fish living in a changeable habitat.     

Genetic differentiation among populations of Caridinazebra (Decapoda: Atyidae) in tropical rainforest streams, northern Australia

1. Caridina zebra is a common atyid shrimp in some tropical rainforest streams in far north Queensland, Australia. Genetic variation at five allozyme loci was used to estimate the level of dispersal among populations of this species, within and between stream systems. Shrimps were sampled from nine streams in the Tully River catchment and two headwater streams in the adjacent Herbert River catchment in an area under consideration for extensive hydroelectric development.
2. High levels of genetic differentiation were recorded among most populations which suggests that, like other fully aquatic species, movement is limited to a very small spatial scale.
3. In the Tully catchment, populations of shrimp from streams with confluences at high altitude showed less genetic differentiation than those from streams which directly entered the lower river. Dispersal between the latter streams is clearly limited by the presence of large waterfalls and cascades.
4. Adjacent stream populations were often highly differentiated, despite their close proximity, suggesting that overland dispersal is unlikely. However, populations of shrimp in the two streams in the Herbert catchment were strikingly similar in genetic structure to those in adjacent headwater streams of the Tully. Such similarity may reflect relatively recent changes in drainage patterns.     

Reconciling patterns of genetic variation with stream structure, earth history and biology in the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae)

We examined the consequences of barriers, stream architecture and putative dispersal capability on levels of genetic differentiation among populations of the freshwater fish Craterocephalus stercusmuscarum. Seven polymorphic allozyme loci and sequences of a 498-bp fragment of the ATPase 6 mitochondrial DNA (mtDNA) gene were used to assess patterns of genetic variation among 16 populations from upland and lowland streams of five drainages in northern Queensland, Australia. Concordant patterns at both genetic markers revealed that there were significant levels of genetic subdivision among all populations, while an analysis of molecular variation showed that the distribution of genetic diversity was not consistent with contemporary drainage structure. There were reciprocally monophyletic mtDNA clades and fixed or large frequency differences at allozyme loci either side of instream barriers such as waterfalls. This implied barriers were effective in restricting gene flow between upland and lowland populations separated by waterfalls. However, there were two genetically distinct groups in upland areas, even within the same subcatchment, as well as high levels of genetic subdivision among lowland populations, suggesting barriers alone do not explain the patterns of genetic diversity. The data revealed a complex phylogeographic pattern, which we interpreted to be the result of one or more invasion events of independent lineages to different sections of each drainage, possibly mediated by well documented geomorphological changes. Our results highlight the importance of earth structure and history in shaping population genetic structure in stream organisms where dispersal capability may be limited, and reveal that the contemporary structure of drainages is not necessarily a good indicator of genetic relationships among populations.     

How river structure and biological traits influence gene flow: a population genetic study of two stream invertebrates with differing dispersal abilities

1. Determined by landscape structure as well as dispersal‐related traits of species, connectivity influences various key aspects of population biology, ranging from population persistence to genetic structure and diversity. Here, we investigated differences in small‐scale connectivity in terms of gene flow between populations of two ecologically important invertebrates with contrasting dispersal‐related traits: an amphipod (Gammarus fossarum) with a purely aquatic life cycle and a mayfly (Baetis rhodani) with a terrestrial adult stage. 2. We used highly polymorphic markers to estimate genetic differentiation between populations of both species within a Swiss pre‐alpine catchment and compared these results to the broader‐scale genetic structure within the Rhine drainage. Landscape genetic approaches were used to test for correlations of genetic and geographical structures and in‐stream barrier effects. 3. We found overall very weak genetic structure in populations of B. rhodani. In contrast, G. fossarum showed strong genetic differentiation, even at spatial scales of a few kilometres, and a clear pattern of isolation by distance. Genetic diversity decreased from downstream towards upstream populations of G. fossarum, suggesting asymmetric gene flow. Correlation of genetic structure with landscape topography was more pronounced in the amphipod. Our study also indicates that G. fossarum might be capable of dispersing overland in headwater regions and of crossing small in‐stream barriers. 4. We speculate that differences in dispersal capacity but also habitat specialisation and potentially the extent of local adaptation could be responsible for the differences in genetic differentiation found between the two species. These results highlight the importance of taking into account dispersal‐related traits when planning management and conservation strategies.     

Water availability strongly impacts population genetic patterns of an imperiled Great Plains endemic fish

Genetic, demographic, and environmental processes affect natural populations synergistically, and understanding their interplay is crucial for the conservation of biodiversity. Stream fishes in metapopulations are particularly sensitive to habitat fragmentation because persistence depends on dispersal and colonization of new habitat but dispersal is constrained to stream networks. Great Plains streams are increasingly fragmented by water diversion and climate change, threatening connectivity of fish populations in this ecosystem. We used seven microsatellite loci to describe population and landscape genetic patterns across 614 individuals from 12 remaining populations of Arkansas darter (Etheostoma cragini) in Colorado, a candidate species for listing under the U.S. Endangered Species Act. We found small effective population sizes, low levels of genetic diversity within populations, and high levels of genetic structure, especially among basins. Both at- and between-site landscape features were associated with genetic diversity and connectivity, respectively. Available stream habitat and amount of continuous wetted area were positively associated with genetic diversity within a site, while stream distance and intermittency were the best predictors of genetic divergence among sites. We found little genetic contribution from historic supplementation efforts, and we provide a set of management recommendations for this species that incorporate a conservation genetics perspective.     

Extensive long-distance pollen dispersal in a fragmented landscape maintains genetic diversity in white spruce

Conifers are among the most genetically diverse plants but show the lowest levels of genetic differentiation, even among geographically distant populations. High gene flow among populations may be one of the most important factors in maintaining these genetic patterns. Here, we provide empirical evidence for extensive pollen-mediated gene dispersal between natural stands of a widespread northern temperate/boreal conifer, Picea glauca. We used 6 polymorphic allozyme loci to quantify the proportion of seeds sired by pollen originating from different sources in a landscape fragmented by agriculture in North Central Ontario, Canada. In 7 stands, a small proportion of seeds were sired by self-pollen or neighboring trees but 87.1% (+/-1.7% standard error [SE]) of seeds were sired by pollen from at least 250 to 3000 m away. In 4 single isolated trees, self-fertilization rates were low and more than 96% (+/-1.3% SE) of seeds were sired by immigrant pollen. The average minimum pollen dispersal distance in outcrossed matings was 619 m. These results provide strong evidence that extensive long-distance pollen dispersal plays a primary role in maintaining low genetic differentiation among natural populations of P. glauca and helps maintain genetic diversity and minimize inbreeding in small stands in a fragmented landscape.     

Spatial genetic structure among and within populations of Primula sieboldii growing beside separate streams

We investigated the hierarchical genetic structure of SSR (simple sequence repeats) and cpDNA (chloroplast DNA) polymorphisms among and within populations of Primula sieboldii, a heterostylous clonal herb. Seven out of eight populations at the study site, located in a mountainous region of Nagano Prefecture, had each developed alongside a different stream, and the other occurred on a flat area 70 m from the nearest stream. The magnitude of genetic differentiation among streamside populations in maternally inherited cpDNA (Phi = 0.341) was much higher than that in biparentally inherited SSRs (Phi = 0.011). This result suggests that seed dispersal among streams was restricted, and pollen was the primary agent of gene flow among streamside populations. In contrast, genetic differentiation among subpopulations within streams were low at both markers (Phi = 0.053 for cpDNA, Phi = 0.025 for SSR). This low differentiation among subpopulations in cpDNA compared with that among streamside populations suggest that seed dispersal occur along the stream probably during flooding. This hypothesis was supported by the fact that in cpDNA haplotypes, no clear genetic structure was detected within the streamside population, while a significant genetic structure was found within 20 m in the nonstreamside population. Furthermore, within the streamside populations, two pairs of ramets with identical multilocus genotypes for eight SSR loci were distantly (> 50 m) distributed along the same streamside, suggesting dispersal of clonal propagule. Our study showed that the heterogeneity of the landscape can influence gene flow and hence spatial genetic structure.     

Allozyme diversity and genetic structure of the leafy cactus (Pereskia guamacho [Cactaceae])

We examined levels of genetic variation and genetic structure in the leafy cactus (Pereskia guamacho) in arid and semiarid zones in Venezuela. We surveyed genetic diversity within 17 populations using 19 allozyme loci. Genetic diversity was relatively high at both the species (P(s) = 89%, A(s) = 3.26, AP(s) = 3.53, H(es) = 0.24) and population (P(p) = 63%, A(p) = 1.90, AP(p) = 2.42, H(ep) = 0.20) levels. A significant deficit of heterozygote individuals was detected within populations in the Paraguana Peninsula region (F(IS) = 0.301). Relatively low levels of population differentiation were detected at macrogeographic (G(ST) = 0.112) and regional levels (G(ST) = 0.044 for peninsula region and G(ST) = 0.074 for mainland region), suggesting substantial genetic exchange among populations; however, gene flow in this species seems to be regulated by the distance among populations. Overall, estimates of genetic diversity found in P. guamacho are concordant with the pattern observed for other cacti surveyed, namely high levels of polymorphism and genetic diversity with one common allele and several rare alleles per locus. Differences in gene dispersal systems between this species and other cacti studied were not reflected in the patterns of genetic diversity observed. The concentration of the highest estimates of genetic variation in northwestern Venezuela suggests a potential reservoir of plant genetic diversity within xerophilous ecosystems in northern South America.     

Regional gene flow and population structure of the wind-dispersed plant species Hypochaeris radicata (Asteraceae) in an agricultural landscape

Using microsatellites, we investigated population structure and gene flow of the short-lived, wind-dispersed plant species Hypochaeris radicata in a fragmented agricultural landscape where more than 99% of the nutrient-poor grasslands have disappeared over the last century. We sampled populations in the few remaining high density populations in conservation areas, as well as individuals that occurred, with lower densities, in linear landscape elements, at two spatial scales. In a re-inventory of the landscape, after 3 years, both extinctions and colonizations of populations were observed. Contrary to expectations, no differences in genetic diversity between high and low density populations were observed. Both types of populations had relatively high levels of diversity. Overall genetic differentiation (theta) was 0.04 and significantly different from zero (P < 0.01). A significant isolation-by-distance pattern was found when all populations were simultaneously analysed (r = 0.24, P = 0.013). Isolation by distance was (marginally) significant at the small scale (r = 0.32, P = 0.06), whereas nonsignificant at the large spatial scale (r = -0.05, P = 0.66). A maximization-of-explained-variance procedure resulted in a threshold distance of 3.5 km above which populations were effectively genetically isolated. An additional partial exclusion Bayesian-based assignment test showed that overall 32.3% of the individuals were assigned to their population of origin, 48% were assigned to another population in the area and 19.7% were not assigned. Together, these results suggest high levels of gene flow. Seed dispersal contributes to the observed gene flow up to several hundred metres, which is higher than previously modelled using aerodynamic models on seed dispersal of H. radicata. We discuss the consequences of these results for an evaluation of the probability of persistence of this species in the fragmented landscape.     

栌菊木的等位酶分析及其在生物地理和保护生物学上的意义

对我国西南特有的菊科单种属植物栌菊木10个居群、149个个体、11个酶系统及16个酶位点的水平淀粉凝胶电泳分析表明,栌菊木的遗传多样性水平在特有种中较高,在居群水平上,平均每个位点的等位基因数A=1．1—1．4,多态位点百分数P=6．3％—43．8％,实际杂合度Ho=0．063～0．250,期望杂合度He=0．043～0．194;物种水平上A=1．6,P=37．5％,Ho=0．143,He=0．141。居群间遗传一致度I=0．902—1．000,杂合性基因多样度比率FST为0．2395。栌菊木居群间分化程度较大,云南南盘江流域碧云寺居群遗传多样性较低,明显低于金沙江流域的居群。栌菊木可能是来自冈瓦纳古陆祖先的后裔,可能是古地中海退却以后在金沙江干热河谷分化出来的特有属,并且可能由于湿度等生态因子的限制,其分布区未能进一步扩大,仅在南盘江流域形成零散分布。等位酶分析结果还表明栌菊木遗传多样性总体水平较高,建议对遗传多样性较高的金沙江流域的居群加以保护。     

Gene flow, dispersal, and nested clade analysis among populations of the stonefly Peltoperla tarteri in the southern Appalachians

We examined the genetic structure and phylogeography of populations of the stonefly Peltoperla tarteri in the Southern Appalachians to determine the extent and likely mechanism for dispersal of this stream insect. A 454-base-pair (bp) portion of the mitochondrial control region was sequenced from a minimum of 20 individuals from eight populations. Pairwise FST and exact tests showed high levels of differentiation among almost all populations except those on the same stream. amova analysis detected significant genetic differentiation between streams within drainages (phi(SD) = 0.14, P < 0.001), and there was a slight positive correlation between aquatic distance and genetic distance (r = 0.295, P = 0.03). According to nested clade analysis, the present day pattern of genetic variation in P. tarteri is the result of a historical range expansion coupled with restricted gene flow with isolation by distance. Together, these analyses suggest that adult dispersal is limited and that movement by larvae is the primary dispersal mechanism for P. tarteri.     

Spatial genetic structure in a metapopulation of the land snail Cepaea nemoralis (Gastropoda: Helicidae)

Habitat fragmentation is a major force affecting demography and genetic structure of wild populations, especially in agricultural landscapes. The land snail Cepaea nemoralis (L.) was selected to investigate the impact of habitat fragmentation on the spatial genetic structure of an organism with limited dispersal ability. Genetic and morphological patterns were investigated at a local scale of a 500 m transect and a mesoscale of 4 x 4 km in a fragmented agricultural landscape while accounting for variation in the landscape using least-cost models. Analysis of microsatellite loci using expected heterozygosity (HE), pairwise genetic distance (FST/1-FST) and spatial autocorrelograms (Moran's I) as well as shell characteristics revealed spatial structuring at both scales and provided evidence for a metapopulation structure. Genetic diversity was related to morphological diversity regardless of landscape properties. This pointed to bottlenecks caused by founder effects after (re)colonization. Our study suggests that metapopulation structure depended on both landscape features and the shape of the dispersal function. A range of genetic spatial autocorrelation up to 80 m at the local scale and up to 800 m at the mesoscale indicated leptokurtic dispersal patterns. The metapopulation dynamics of C. nemoralis resulted in a patchwork of interconnected, spatially structured subpopulations. They were shaped by gene flow which was affected by landscape features, the dispersal function and an increasing role of genetic drift with distance.     

海南粗榧(Cephalotaxus mannii Hk.f.) 5个种群遗传多样性及分化研究

采用垂直板型聚丙烯酰胺凝胶电泳测定了海南粗榧5个种群遗传多样性和遗分化程度。结果表明：海南粗榧种群遗传多样性水平较低,多态位点比率P＝0．33,等位基因平均数A＝1．33,平均期望杂合度为He=0．135,观察杂合度为Ho＝0139。种群间遗传分化程度较低,基因分化系数Gst=0.123,种群间遗传一致度和遗传距离的均值分别为0．9719、9．0288。黎母山种群与其它种群分化最大,其原因可能与传粉时盛行的风向有关。     

Population structure and genetic diversity of trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>) above and below natural and man-made barriers in the Russian River,California

The effects of landscape features on gene flow in threatened and endangered species play an important role in influencing the genetic structure of populations. We examined genetic variation of trout in the species Oncorhynchus mykiss at 22 microsatellite loci from 20 sites in the Russian River basin in central California. We assessed relative patterns of genetic structure and variation in fish from above and below both natural (waterfalls) and man-made (dams) barriers. Additionally, we compared sites sampled in the Russian River with sites from 16 other coastal watersheds in California. Genetic variation among the 20 sites sampled within the Russian River was significantly partitioned into six groups above natural barriers and one group consisting of all below barrier and above dam sites. Although the below-barrier sites showed moderate gene flow, we found some support for sub-population differentiation of individual tributaries in the watershed. Genetic variation at all below-barrier sites was high compared to above-barrier sites. Fish above dams were similar to those from below-barrier sites and had similar levels of genetic diversity, indicating they have not been isolated very long from below-barrier populations. Population samples from above natural barriers were highly divergent, with large F _st values, and had significantly lower genetic diversity, indicating relatively small population sizes. The origins of populations above natural barriers could not be ascertained by comparing microsatellite diversity to other California rivers. Finally, below-barrier sites farther inland were more genetically differentiated from other watersheds than below-barrier sites nearer the river’s mouth.     

Conservation genetics of the endangered Iberian steppe plant Ferula loscosii (Apiaceae)

Ferula loscosii (Lange) Willk (Apiaceae) is a threatened endemic species native to the Iberian Peninsula. The plant has a narrow and disjunct distribution in three regions, NE, C and SE Spain. Genetic variability within and among 11 populations from its natural distribution was assessed using allozymes. Intermediate levels of genetic diversity were detected in F. loscosii (P(99%) = 36.83; H(E) = 0.125; H(T) = 0.152). However, the highest genetic diversity (58%) corresponded to the threatened populations from SE and C Spain (H(T) = 0.169) rather than the more abundant and larger populations from NE Spain (Ebro valley) (H(T) = 0.122). Low to moderate levels of genetic structure were found among regional ranges (G(ST) = 0.134), and several statistical spatial correlation analyses corroborated substantial genetic differentiation among the three main regional ranges. However, no significant genetic differentiation was found among the NE Spain populations, except for a northernmost population that is geographically isolated. Outcrossing mating and other biological traits of the species could account for the maintenance of the present values of genetic diversity within populations. The existence of an ancestral late Tertiary wider distribution of the species in SE and C Spain, followed by the maintenance of different Quaternary refugia in these warmer areas, together with a more recent and rapid post-glacial expansion towards NE Spain, are arguments that could explain the low genetic variability and structure found in the Ebro valley and the higher levels of diversity in the southern Iberian populations.     

The patterns of genetic diversity in Carpentaria acuminata (Arecaceae), and rainforest history in northern Australia

Carpentaria acuminata occurs in monsoon rainforest and is endemic to the Northern Territory, Australia. The genetic diversity of C. acuminata populations was surveyed across the geographical range of the species using isozyme analysis. Genetic diversity within C. acuminata populations ( H _E = 0.143) was typical of rainforest species and woody angiosperms generally. Genetic diversity was not correlated with rainforest patch size. However, there was significant heterogeneity among populations ( F _ST = 0.379), with infrequent effective gene flow among populations ( Nm = 0.39). Genetic diversity was negatively correlated with increasing distance between neighbouring C. acuminata populations, but geographical distance was not a good predictor of genetic similarity. C. acuminata is a favoured food of mobile frugivores such as Torres Strait pigeons and flying foxes. The decreased diversity with decreasing density of populations indicated that seed dispersal by frugivores has been important for the maintenance of diversity in this species. Populations known to have originated on relatively young, Holocene landforms were not necessarily genetically depauperate. Gene flow by pollen is apparently limited because C. acuminata populations are significantly inbred regardless of genetic diversity ( F = 0.641). The distribution and diversity of rare alleles, i.e. those occurring in few populations, is consistent with the theory of rainforest contraction during the Pleistocene.     

Landscape genetics of the widespread ground-beetle Carabus auratus in an agricultural region

The brachypterous carabid beetle Carabus auratus was chosen as an indicator organism for analysing the relationship between landscape composition and population genetic structure (AFLP) in an agricultural region. We selected eight landscape sections with different landscape composition. The landscapes were analysed in 7 radii ranging from 500 to 2000 m (step size: 250 m). It is shown that the population as a whole exhibits a moderate genetic differentiation with geographically restricted genetic exchange. Genetic diversity of local populations is high. It is positively associated with increasing numbers of migrants estimated from the molecular data. This indicates that even widespread species with a presumed low dispersal capacity may exhibit high levels of genetic exchange at larger spatial scales. The availability of grassland within the landscape sections enhanced genetic diversity of local populations at larger spatial scales and explained over 50% of the observed genetic diversity. Thus, the unexpectedly high genetic exchange of C. auratus critically depends on the availability of suitable landscape features. Our results emphasise the need to take into account the adverse effects of ongoing changes in landscape composition on the genetic diversity even of widespread species when aiming at conserving genetic and functional diversity in agricultural landscapes.     

Genetic diversity and differentiation in Dalbergia sissoo (Fabaceae) as revealed by RAPD

Dalbergia sissoo, a wind-dispersed tropical tree, is one of the most preferred timber tree species of South Asia. Genetic diversity and differentiation among natural populations of D. sissoo were examined for the first time. We found a relatively high level of genetic diversity in D. sissoo, both at the species level (percentage of polymorphic bands = 89.11%; H = 0.2730; I = 0.4180) and the population level (percentage of polymorphic bands = 68.7%; H = 0.239; I = 0.358), along with a relatively low degree of differentiation among populations (GST = 0.1311; AMOVA = 14.69%). Strong gene flow among populations was estimated, N(m) = 3.3125. The Mantel test suggested that genetic distances between populations were weakly correlated with geographic distances (R = 0.3702, P = 0.1236). The high level of genetic diversity, low degree of differentiation, strong gene flow, and weak correlation between genetic and geographic distances can be explained by its biological character and wide-spread planting. This information will be useful for the introduction, conservation and further studies of D. sissoo and related species.     

Population genetic structure of Venezuelan chiropterophilous columnar cacti (Cactaceae)

We conducted allozyme surveys of three Venezuelan self-incompatible chiropterophilous columnar cacti: two diploid species, Stenocereus griseus and Cereus repandus, and one tetraploid, Pilosocereus lanuginosus. The three cacti are pollinated by bats, and both bats and birds disperse seeds. Population sampling comprised two spatial scales: all Venezuelan arid zones (macrogeographic) and two arid regions in northwestern Venezuela (regional). Ten to 15 populations and 17-23 loci were analyzed per species. Estimates of genetic diversity were compared with those of other allozyme surveys in the Cactaceae to examine how bat-mediated gene dispersal affects the population genetic attributes of the three cacti. Genetic diversity was high for both diploid (P(s) = 94.1-100, P(p) = 56.7-72.3, H(s) = 0.182-0.242, H(p) = 0.161-0.205) and tetraploid (P(s) = 93.1, P(p) = 76.1, H(s) = 0.274, H(p) = 0.253) species. Within-population heterozygote deficit was detected in the three cacti at macrogeographic (F(IS) = 0.145-0.182) and regional (F(IS) = 0.057-0.174) levels. Low genetic differentiation was detected at both macrogeographic (G(ST) = 0.043-0.126) and regional (G(ST) = 0.009-0.061) levels for the three species, suggesting substantial gene flow among populations. Gene exchange among populations seems to be regulated by distance among populations. Our results support the hypothesis that bat-mediated gene dispersal confers high levels of genetic exchange among populations of the three columnar cacti, a process that enhances levels of genetic diversity within their populations.     

西鄂尔多斯特有种四合木种群遗传多样性及遗传分化研究

利用垂直板聚丙烯酰胺凝胶电泳技术,对西鄂尔多斯高原特有种四合木（Tetraena mogolica）4个种群遗传多样性和遗传分化进行了初步研究。电泳结果表明,四合木在种和种群水平维持较高的遗传多样性,1多态位点百分率P＝60％,等位基因平均数A＝1.6,平均期望杂合度He=0.245。4个种群之间遗传分化很小,基因分化系数GST只有0.052,明不同于其它濒危物种。四合木种较高的遗传多样性和极低的种群间分化,说明不同的种群可能有共同的起源,随机遗传漂变和近交衰退不是影响遗传多样性的主要过程。