华北地区小丛红景天种群的AFLP遗传多样性

利用扩增片段长度多态性(AFLP)标记, 对分布于华北地区5个山脉的25个小丛红景天(Rhodiola dumulosa)自然种群的776个样品进行了遗传多样性和遗传结构的研究。结果表明: 华北地区小丛红景天种群具有较高的遗传多样性, 4对选择扩增引物共扩增出398条清晰的条带, 其中多态带312条, 种群的平均多态位点百分率为78.46%, 种群总的Nei’s基因多样性为0.364 9, 总Shannon多态性信息指数为0.542 2。华北地区小丛红景天种群间的遗传分化系数G_st = 0.150 7, 基因流Nm = 2.817 9, 表明种群间遗传分化较低, 有一定的基因交流。AMOVA分析结果也表明: 华北地区小丛红景天的遗传变异主要存在于种群内, 地理单元间有一定的遗传分化, 而种群间的遗传分化较低。STRUCTURE的分析和UPGMA聚类分析结果一致, 结果显示地理分布距离相近的种群优先聚在一起。Mantel检验也进一步证实, 华北地区小丛红景天种群的遗传距离与地理距离间呈显著的正相关关系(r = 0.512 9, p < 0.001)。种群的遗传多样性与海拔呈显著的负相关关系(p < 0.05), 而与坡向没有显著相关性。用Dfdist软件分析海拔对遗传多样性的影响, 结果表明没有显著的受选择位点。     

Genetic Structure of the Carnivorous Plant Pinguicula moranensis (Lentibulariaceae) on the Transvolcanic Mexican Belt

Most species of Pinguicula present a montane distribution with populations located at high altitudes. In this context, we proposed that populations of Pinguicula species could be genetically differentiated even at a local scale. This study supported that prediction, as a RAPD-based analysis of molecular variance revealed a high degree of genetic structure (Φ (st) = 0.157, P = 0.001) and low gene flow (Nm = 1.0) among four central populations of Pinguicula moranensis in Mexico, with a maximum geographic separation of about 140 km. The four populations also exhibited high levels of genetic diversity (mean Nei's genetic diversity = 0.3716; % polymorphism = 95.45%). The evolutionary implications of the genetic structure found in P. moranensis for other species in the genus are discussed in the context of the naturally fragmented distribution and a set of life history traits shared by most Pinguicula species that could promote geographic isolation and limited gene flow.     

白皮松的保育遗传学研究I．基因保护分析

在白皮松主要分布区抽取了10个天然群体进行酶电泳分析,共测定了16种酶系统,得到31个清晰酶位点和53个等位基因。按照基因频率进行分类,53个基因中有32个全局基因、14个广域基因、6个局域基因和1个特异基因。通过计算机模拟建立基因捕获曲线的结果表明,随机抽取5个群体可平均捕获99．9％的基因。群体的等位基因频率与地理生态因子的相关分析表明,Idh与Pgi—2两个位点的基因频率呈现明显的梯度变异。该项研究为有效保护白皮松天然群体的基因资源提供了依据。     

白皮松的保育遗传学研究Ⅰ.基因保护分析

在白皮松主要分布区抽取了10个天然群体进行酶电泳分析,共测定了16种酶系统,得到31个清晰酶位点和53个等位基因。按照基因频率进行分类,53个基因中有32个全局基因、14个广域基因、6个局域基因和1个特异基因。通过计算机模拟建立基因捕获曲线的结果表明,随机抽取5个群体可平均捕获99.9%的基因。群体的等位基因频率与地理生态因子的相关分析表明,Idh与Pgi^-2两个位点的基因频率呈现明显的梯度变异。该项研究为有效保护白皮松天然群体的基因资源提供了依据。     

Genetic structure and seed-mediated dispersal rates of an endangered shrub in a fragmented landscape: a case study for Juniperus communis in northwestern Europe

Background

Population extinction risk in a fragmented landscape is related to the differential ability of the species to spread its genes across the landscape. The impact of landscape fragmentation on plant population dynamics will therefore vary across different spatial scales. We quantified successful seed-mediated dispersal of the dioecious shrub Juniperus communis in a fragmented landscape across northwestern Europe by using amplified fragment length polymorphism (AFLP) markers. Furthermore we investigated the genetic diversity and structure on two spatial scales: across northwestern Europe and across Flanders (northern Belgium). We also studied whether seed viability and populations size were correlated with genetic diversity.

Results

Unexpectedly, estimated seed-mediated dispersal rates were quite high and ranged between 3% and 14%. No population differentiation and no spatial genetic structure were detected on the local, Flemish scale. A significant low to moderate genetic differentiation between populations was detected at the regional, northwest European scale (PhiPT = 0.10). In general, geographically nearby populations were also genetically related. High levels of within-population genetic diversity were detected but no correlation was found between any genetic diversity parameter and population size or seed viability.

Conclusions

In northwestern Europe, landscape fragmentation has lead to a weak isolation-by-distance pattern but not to genetic impoverishment of common juniper. Substantial rates of successful migration by seed-mediated gene flow indicate a high dispersal ability which could enable Juniperus communis to naturally colonize suitable habitats. However, it is not clear whether the observed levels of migration will suffice to counterbalance the effects of genetic drift in small populations on the long run.     

Microsatellite analysis reveals interpopulation differentiation and gene flow in the endangered tree Changiostyrax dolichocarpa (Styracaceae) with fragmented distribution in central China

Polymorphic simple sequence repeat (SSR) markers were used to investigate the impact of habitat fragmentation on the population structure and gene flow of Changiostyrax dolichocarpa, a critically endangered tree in central China. Intrapopulation genetic diversity, population structure and gene flow in the five extant populations of this species were analysed by eight SSR markers. Intrapopulation genetic diversity results suggest that C. dolichocarpa remnants maintained a relatively high degree of genetic diversity despite severe fragmentation. Low genetic differentiation among populations was found based on Wright's F(ST) and amova analysis. Both the F(ST)-based estimate and private allele method revealed high historical gene flow among the remnant populations. Recent immigrants, detected by assignment tests, tend to decrease from the grandparent generation to the current generation. The potentially highly restricted current gene flow among fragments may render the fragmented populations of C. dolichocarpa at a higher risk of local extinction several generations after fragmentation. Both in situ and ex situ conservation management for the remnant populations of C. dolichocarpa are therefore urgently needed to rescue remaining genetic diversity.     

Stepping-stone expansion and habitat loss explain a peculiar genetic structure and distribution of a forest insect

It is challenging to unravel the history of organisms with highly scattered populations. Such species may have fragmented distributions because extant populations are remnants of a previously more continuous range, or because the species has narrow habitat requirements in combination with good dispersal capacity (naturally or vector borne). The northern pine processionary moth Thaumetopoea pinivora has a scattered distribution with fragmented populations in two separate regions, northern and south-western Europe. The aims of this study were to explore the glacial and postglacial history of T. pinivora, and add to the understanding of its current distribution and level of contemporary gene flow. We surveyed published records of its occurrence and analysed individuals from a representative subset of populations across the range. A 633 bp long fragment of the mtDNA COI gene was sequenced and nine polymorphic microsatellite loci were genotyped. Only nine nucleotide sites were polymorphic in the COI gene and 90% of the individuals from across its whole range shared the same haplotype. The microsatellite diversity gradually declined towards the north, and unique alleles were found in only three of the northern and three of southern sites. Genetic structuring did not indicate complete isolation among regions, but an increase of genetic isolation by geographic distance. Approximate Bayesian model choice suggested recent divergence during the postglacial period, but glacial refugia remain unidentified. The progressive reduction of suitable habitats is suggested to explain the genetic structure of the populations and we suggest that T. pinivora is a cold-tolerant relict species, with situation-dependent dispersal.     

大王马先蒿云南五个居群遗传变异研究

采用随机扩增多态DNA(RAPD)分子标记方法,对大王马先蒿(PedicularisrexL.)分布在云南中甸、丽江、大理、武定和昆明的5个居群(其中中甸居群有3个亚居群)的遗传多样性和遗传结构进行了研究。结果表明,大王马先蒿居群具有较高的遗传多样性,多态位点百分率P、Shannon表型多样性指数I和Nei的基因多样性指数h分别为82.0%、0.361和0.240,遗传多样性水平与居群的地理分布范围相关;大王马先蒿居群间的遗传变异较高,遗传变异主要发生在居群之间,而不是居群内部;居群间遗传分化系数Gst为0.747,遗传分化明显,居群间基因交流较少。居群间的遗传距离与居群间的相对地理距离具有一定的相关性。对云南西北部中甸居群的3个亚居群的遗传多样性分析表明,居群的遗传多样性水平与海拔高度有一定的相关性。居群间遗传变异较高可能是由于大王马先蒿为短命多年生植物,繁育系统为混交型,且自交占较大比例等原因造成的。     

籽蒿的地理分布与遗传分化

 对籽蒿(Artemisia sphaerocephala)的分布地点进行了调查,发现了籽蒿在浑善达克沙地的新分布, 绘制了籽蒿的分布图。在籽蒿集中分布的地区取了5个种群,新分布点取了一个种群,利用随机扩增多态性DNA（RAPD）方法进行了遗传分化的研究。15个引物共扩增出255条带,其中多态带232条,多态位点百分率为91%。各种群以乌海流动沙地种群最低, 多态位点百分率为66.7%, 沙坡头种群最高,多态位点百分率为83.4%。籽蒿种群间有着一定的遗传分化,遗传分化系数（Gst）为0.234 8, 表明76.52%的遗传变异存在于种群内。聚类分析显示,籽蒿种群之间的遗传距离与地理距离有着一定的相关性。而相隔很远的浑善达克沙地的锡林浩特种群与毛乌素沙地的榆林种群间的遗传距离较小,且被聚到了一起,表明两个草原区沙地籽蒿种群间的关系密切。     

Population genetics and breeding system of Tupistra pingbianensis (Liliaceae),a naturally rare plant endemic to SW China

The levels and partitioning of genetic diversity and inbreeding depression were investigated in Tupistra pingbianensis, a narrow endemic of southeast Yunnan, China, characterized by a naturally fragmented distribution due to extreme specialization on a rare habitat type. Here genetic diversity and patterns of genetic variation within and among 11 populations were analyzed using amplified fragment length polymorphism markers with 97 individuals across its whole geographical range. High levels of genetic variation were revealed both at the species level (P_(99)=96.012%; H_t=0.302) and at the population level (P_(99)=51.41%; H_8= 0.224). Strong genetic differentiation among populations was also detected (F_(ST)= 0.2961; θ~Ⅱ= 0.281), which corresponded to results reported for typical animal-pollinated, mixed selfing, and outcrossing plant species. This result was consistent with mating patterns detected by our pollination experiments. The indirect estimate of gene flow based on θ~Ⅱwas low (N_m=0.64). Special habitat and its life history traits might play an important role in shaping the genetic diversity and the genetic structure of this species. A pollination experiment also failed to detect significant inbreeding depression upon F_1 fruit set, seed weight, and germinate rate fitness-traits. As a naturally rare species, T. pingbianensis is not seriously genetically impoverished and likely to have adapted to tolerating a high level of inbreeding early in its history, we propose this species need only periodic monitoring to ensure their continued persistence, but not intervention to remain viable.     

Habitat fragmentation versus fragmented habitats

Habitats often show similar present structuring, but contrasting histories: habitats occur naturally fragmented due to abiotic or biotic factors over long time periods, but may also have become fragmented only recently through transformation from interconnected to highly fragmented habitats within short time periods. Species and populations being faced with such contrasting habitat scenarios also show contrasting responses at species and intraspecific level. Organisms and populations from naturally fragmented habitats may show a reduction in their genetic load (purging) due to purifying selection in isolation. In contrast, sudden habitat transformations from interconnected to highly fragmented structures and the resulting transition from gene flow or panmixia to strong population differentiation often have negative effects on biota; while species occur in interconnected population networks (maintaining a high proportion of genetic diversity), a sudden breakdown of gene flow may lead to a severe loss of genetic diversity and the manifestation of weakly deleterious alleles. In consequence, fragmented habitats need not have a negative impact on species per se, but the history of habitat structures, particularly fast transformation processes, may severely affect the persistence and fitness of species.     

Genetic Differentiation Among Populations of the Roseate Spoonbill (Platalea ajaja; Aves: Pelecaniformes) in Three Brazilian Wetlands

Effective population size, levels of genetic diversity, gene flow, and genetic structuring were assessed in 205 colonial Roseate spoonbills from 11 breeding colonies from north, central west, and south Brazil. Colonies and regions exhibited similar moderate levels of diversity at five microsatellite loci (mean expected heterozygosity range 0.50–0.62; allelic richness range 3.17–3.21). The central west region had the highest Ne (59). F _ST values revealed low but significant genetic structuring among colonies within the north and within the south regions. Significant global genetic structuring was found between the northern and central western populations as well as between the northern and southern populations. An individual-based Bayesian clustering method inferred three population clusters. Assignment tests correctly allocated up to 64% of individuals to their source regions. Collectively, results revealed complex demographic dynamics, with ongoing gene flow on a local scale, but genetic differentiation on a broader scale. Populations in the three regions may all be conserved, but special concern should be given to central western ones, which can significantly contribute to the species’ gene pool in Brazil.     

Multi-scale genetic analysis of Uniola paniculata (Poaceae): a coastal species with a linear, fragmented distribution

Geographic and fine-scale population genetic structures of Uniola paniculata, the dominant coastal dune grass in the southeastern USA, were examined. The linear, naturally fragmented distribution of this native perennial was hypothesized to lead to high genetic structure and lower genetic diversity at the margin of the species range. The extensive ramet production and low seed germination of this species were also expected to cause populations to be dominated by a few large clones. At 20 sites throughout the range of the species, leaf tissue was collected from 48 individuals. Clonal structure was examined using leaf tissue collected from an additional 60 individuals, each in four patches at two sites. Starch gel electrophoresis was used to resolve 27 allozyme loci. The results indicated that Uniola had greater genetic structure (G(ST) = 0.304) than most other outcrossing species, indicating moderate barriers to gene flow. There was a weak but significant positive relationship between genetic distance and geographic distance, supporting an isolation-by-distance model of gene flow. There were no obvious disjunctions between regions. Genetic diversity (H(e)) was relatively uniform throughout most of the range of the species but was lower in all western Gulf of Mexico populations. Clonal diversity varied both within and among sites, but clones were often small, suggesting that sexual reproduction and recruitment from seeds are important factors maintaining genetic diversity.     

Geographical structuring of genetic diversity across the whole distribution range of Narcissus longispathus, a habitat-specialist, Mediterranean narrow endemic

Background and Aims

High mountain ranges of the Mediterranean Basin harbour a large number of narrowly endemic plants. In this study an investigation is made of the levels and partitioning of genetic diversity in Narcissus longispathus, a narrow endemic of south-eastern Spanish mountains characterized by a naturally fragmented distribution due to extreme specialization on a rare habitat type. By using dense sampling of populations across the species'' whole geographical range, genetic structuring at different geographical scales is also examined.

Methods

Using horizontal starch-gel electrophoresis, allozyme variability was screened at 19 loci for a total of 858 individuals from 27 populations. The data were analysed by means of standard statistical approaches in order to estimate gene diversity and the genetic structure of the populations.

Key Results

Narcissus longispathus displayed high levels of genetic diversity and extensive diversification among populations. At the species level, the percentage of polymorphic loci was 68 %, with average values of 2·1, 0·11 and 0·14 for the number of alleles per locus, observed heterozygosity and expected heterozygosity, respectively. Southern and more isolated populations tended to have less genetic variability than northern and less-isolated populations. A strong spatial patterning of genetic diversity was found at the various spatial scales. Gene flow/drift equilibrium occurred over distances <4 km. Beyond that distance divergence was relatively more influenced by drift. The populations studied seem to derive from three panmictic units or ‘gene pools’, with levels of admixture being greatest in the central and south-eastern portions of the species'' range.

Conclusions

In addition to documenting a case of high genetic diversity in a narrow endemic plant with naturally fragmented populations, the results emphasize the need for dense population sampling and examination of different geographical scales for understanding population genetic structure in habitat specialists restricted to ecological islands.Key words: Allozymes, genetic diversity, geographical scale, habitat isolation, Narcissus longispathus, Mediterranean endemism, mountain range, natural fragmented distribution     

Allopatric divergence and regional range expansion of Juniperus sabina in China

In this study, we aimed to study the phylogeographic pattern of Juniperus sabina, a shrub species commonly occurring in the northern, northwestern and western China. We sequenced three chloroplast DNA fragments (trnL-trnF, trnS-trnG, and trriD-trriT) for 137 individuals from 16 populations of this species. Five chloroplast DNA chlorotypes (A, B, C, D, and E) were identified and they showed no overlapping distribution. The population subdivision is very high (GST = 0.926, NST= 0.980), suggesting a distinct phylogeographic structure (NST > GST, P < 0.05). Phylogenetic analyses of the five chlorotypes were clustered into three clades, consistent with their respective distributions in three separate regions: northern Xinjiang, western Xinjiang, and northern-northwestern China. However, within each region, the interpopulation differentiation is extremely low. These results as well as statistical tests suggested distinct allopatric differentiations between regional populations and independent glacial refugia for postglacial recolonization. The deserts that developed during the late Quaternary might have acted as effective barriers to promote genetic differentiation among these regions. However, the low diversity dominated by the single chlorotype within each fragmented region suggested that all current populations were derived from a common regional range expansion.     

The combined role of glaciation and hybridization in shaping the distribution of genetic variation in a Patagonian southern beech

Aim The distribution of the genetic variation in long‐lived species is a combination of both, historical and current processes. In Nothofagus nervosa (Phil.) Dim. et Mil., the possible existence of multiple glacial refugia, the unidirectional gene flow along fragmented areas and the natural hybridization with the related species Nothofagus obliqua (Mirb.) Oerst. highlights as the most important factors responsible for modelling its genetic structure. The present study aims to find out the relative importance of these evolutionary processes in determining the distribution pattern of the genetic variation in N. nervosa. Location The study was carried out in north‐western Patagonia, Argentina. Twenty populations covering the entire distribution range of N. nervosa in Argentina were analysed. For comparison purposes, three populations from Chile were also included. Methods Genetic variation was detected using isozyme gene markers; diversity and differentiation parameters were calculated. A cluster analysis was performed and the correlation between genetic and geographical distances was tested. Results Levels of genetic variation were relatively high given the small distribution range of the species in Argentina. Genetic and geographical distances were not correlated and a longitudinal trend in the genetic variation was evident. Hotspots of diversity with rare and private alleles were observed among western populations, while hybrid seeds were found almost exclusively among eastern populations. Main conclusions The higher level of diversity observed in western populations could be related with the location of glacial refugia. Furthermore, it should also reflect low levels of gene flow given the eastward unidirectional winds. On the contrary, ancient and current interspecific hybridization processes would mainly cause the particular genetic constitution of the eastern populations. Evidence is presented supporting that glaciations and hybridization were the main factors shaping the distribution of the genetic variation in N. nervosa.     

Conservation Genetics of the Endemic Mexican Heliconia uxpanapensis in the Los Tuxtlas Tropical Rain Forest

Heliconia uxpanapensis (Heliconiaceae) is an outcrossing endemic herb that grows within continuous and fragmented areas of the tropical rain forest of southeast Veracrúz (México). The genetic diversity, population differentiation, and genetic structure of seven populations of the studied species were assessed using inter‐simple sequence repeat) markers. Population differentiation was moderately high (F_ST range: 0.18–0.22) and indirect estimates of gene flow were rather low (Nm=0.65–0.83). Analysis of molecular variance indicated that the populations explained 22.2 percent of the variation, while individuals within the populations accounted for 77.8 percent. The similar and high level of genetic diversity found within populations of the continuous and fragmented forest suggests that H. uxpanapensis has not suffered yet the expected negative effect of fragmentation. Genetic structure analyses indicated the presence of fewer genetic clusters (K=4) than populations (N=7). Three of the four fragmented forest populations were assigned each to one of the clusters found within the continuous forest, suggesting the absence of a negative fragmentation effect on the amount and distribution of genetic variation. Given the significant genetic structure combined with high genetic diversity and low levels of gene flow, theoretical simulations indicated that H. uxpanapensis might be highly susceptible to changes in the mating system, which promotes inbreeding within fragmented populations. Thus, future conservation efforts in this species should be directed to ensure that levels of gene flow among populations are sufficient to prevent an increment in the magnitude of inbreeding within fragments.     

Genetic structure of a native cyprinid in a reservoir‐altered stream network

1. Reservoirs modify riverine ecosystems worldwide, and often with deleterious impacts on native biota. The immediate effects of reservoirs on native fish species below dams and in impounded reaches have received considerable attention, but it is unclear how reservoirs may affect fish species at larger spatial and temporal scales. Documented declines of stream fish populations in direct tributaries of reservoirs suggest reservoir pools may reduce gene flow among historically connected populations. 2. Because of increased predator densities in reservoirs and the extent of habitat alteration in impounded reaches, I predicted reservoir habitats would reduce gene flow among small‐bodied fish populations separated by reservoir habitat. I used microsatellite markers to assess the spatial genetic structure of populations of the red shiner (Cyprinella lutrensis), in a reservoir‐fragmented stream network (Lake Texoma, U.S.A.). I also tested the prediction that populations in two direct tributaries that have experienced population declines would have low genetic diversity. Individuals were collected from six sites upstream of the reservoir, three sites in the reservoir and three sites in direct tributaries of the reservoir during 2008 and 2009. 3. Results indicate that most populations were isolated by distance with little divergence among populations. In one direct tributary population, however, there was substantial genetic divergence, and genetic diversity was significantly lower than in other populations. Gene flow also seemed to be lower in reservoir habitats than in intact stream habitats, suggesting reservoir habitats may be reducing gene flow among the reservoir‐separated populations. These results indicate that reservoirs may reduce gene flow among reservoir‐fragmented stream fish populations, altering the evolutionary trajectories of fragmented populations.     

Holocene re‐colonisation,central–marginal distribution and habitat specialisation shape population genetic patterns within an Atlantic European grass species

Corynephorus canescens (L.) P.Beauv. is an outbreeding, short‐lived and wind‐dispersed grass species, highly specialised on scattered and disturbance‐dependent habitats of open sandy sites. Its distribution ranges from the Iberian Peninsula over Atlantic regions of Western and Central Europe, but excludes the two other classical European glacial refuge regions on the Apennine and Balkan Peninsulas. To investigate genetic patterns of this uncommon combination of ecological and biogeographic species characteristics, we analysed AFLP variation among 49 populations throughout the European distribution range, expecting (i) patterns of SW European glacial refugia and post‐glacial expansion to the NE; (ii) decreasing genetic diversity from central to marginal populations; and (iii) interacting effects of high gene flow and disturbance‐driven genetic drift. Decreasing genetic diversity from SW to NE and distinct gene pool clustering imply refugia on the Iberian Peninsula and in western France, from where range expansion originated towards the NE. High genetic diversity within and moderate genetic differentiation among populations, and a significant pattern of isolation‐by‐distance indicate a gene flow drift equilibrium within C. canescens, probably due to its restriction to scattered and dynamic habitats and limited dispersal distances. These features, as well as the re‐colonisation history, were found to affect genetic diversity gradients from central to marginal populations. Our study emphasises the need for including the specific ecology into analyses of species (re–)colonisation histories and range centre–margin analyses. To account for discontinuous distributions, new indices of marginality were tested for their suitability in studies of centre–periphery gradients.     

Allozyme diversity and history of distribution expansion in the maritime perennial plant Hedyotis strigulosa (Rubiaceae), distributed over the wide latitudes in the Japanese Archipelago

Allozyme diversity was examined in 30 populations of the maritime perennial plant Hedyotis strigulosa var. parviflora , which is distributed from subtropical islands to the central mainland of Japan. Genetic diversity within populations tended to be larger in southern island populations than in northern mainland populations. In the southern part of the distribution, the population size is generally large and populations are distributed more continuously than in the northern area, resulting in the larger effective size of southern populations as a whole. These factors play a major role in maintaining greater genetic diversity in the southern populations. By contrast, genetic diversity in the northern populations is very low, probably resulting from bottlenecks of population establishments during recolonization from refugial area to the northern areas. Geographically close populations were located near each other in the multidimensional scaling and the phenogram based on genetic distances, suggesting that gene flow among remote populations is rather limited. The pattern of genetic diversity in H. strigulosa var. parviflora is likely caused by the distribution expansion of the species; in the last glacier era, the species was restricted to the southern area; its advance to the northern area is relatively recent. Another variety endemic only to the Daito Islands, H. strigulos a var. luxurians , has lower genetic diversity than H. strigulosa var. parviflora and has genetically diverged from H. strigulosa var. parviflor a.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 679–688.