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.     

Similarity of contemporary and historical gene flow among highly fragmented populations of an endangered rattlesnake

Populations of endangered taxa in recently fragmented habitats often show high levels of genetic structure, but the role that contemporary versus historical processes play in generating this pattern is unclear. The eastern massasauga rattlesnake (Sistrurus c. catenatus) is an endangered snake that presently occurs throughout central and eastern North America in a series of populations that are isolated because of habitat fragmentation and destruction. Here, we use data from 19 species-specific microsatellite DNA loci to assess the levels of genetic differentiation, genetic effective population size, and contemporary and historical levels of gene flow for 19 populations sampled across the range of this snake. Eastern massasaugas display high levels of genetic differentiation (overall θ(Fst) = 0.21) and a Bayesian clustering method indicates that each population represents a unique genetic cluster even at regional spatial scales. There is a twofold variation in genetically effective population sizes but little genetic evidence that populations have undergone recent or historical declines in size. Finally, both contemporary and historical migration rates among populations were low and similar in magnitude even for populations located <7 km apart. A test of alternate models of population history strongly favours a model of long-term drift-migration equilibrium over a recent isolation drift-only model. These results suggest that recent habitat fragmentation has had little effect on the genetic characteristics of these snakes, but rather that this species has historically existed in small isolated populations that may be resistant to the long-term negative effects of inbreeding.     

群体遗传结构中的基因流

群体遗传结构上的差异是遗传多样性的一种重要体现,对群体遗传结构的研究已有较久的历史,而其中的基因流研究近些年来越来越受到重视。它对群体遗传学、进化生物学、保护生物学、生态学有着极其重要的作用。虽然传统的群体遗传学能估测基因流大小,但它的精确性还有很大局限性。随着生物技术的进步,对基因流的研究逐渐向分子水平过渡,应用蛋白质电泳技术、分子标记技术(RAPD、RFLP、VNTR、ISSR、DNA测序等)方法对群体间基因流的流动水平进行了深入细致的研究。通过综述群体遗传结构的几种模式:陆岛模式、海岛模式、阶石模式、距离隔离模式、层次模式,以及在群体遗传结构的几种模式基础上的基因流的研究方法、作用、地位和近些年来研究者的研究成果,并指出了这些方法的局限性。     

Genetic structure in large, continuous mammal populations: the example of brown bears in northwestern Eurasia

Knowledge of population structure and genetic diversity and the spatio-temporal demographic processes affecting populations is crucial for effective wildlife preservation, yet these factors are still poorly understood for organisms with large continuous ranges. Available population genetic data reveal that widespread mammals have for the most part only been carefully studied at the local population scale, which is insufficient for understanding population processes at larger scales. Here, we provide data on population structure, genetic diversity and gene flow in a brown bear population inhabiting the large territory of northwestern Eurasia. Analysis of 17 microsatellite loci indicated significant population substructure, consisting of four genetic groups. While three genetic clusters were confined to small geographical areas-located in Estonia, southern Finland and Leningrad oblast, Russia-the fourth cluster spanned a very large area broadly falling between northern Finland and the Arkhangelsk and Kirov oblasts of Russia. Thus, the data indicate a complex pattern where a fraction of the population exhibits large-scale gene flow that is unparalleled by other wild mammals studied to date, while the remainder of the population appears to have been structured by a combination of demographic history and landscape barriers. These results based on nuclear data are generally in good agreement with evidence previously derived using mitochondrial markers, and taken together, these markers provide complementary information about female-specific and population-level processes. Moreover, this study conveys information about spatial processes occurring over multiple generations that cannot be readily gained using other approaches, e.g. telemetry.     

Microgeographic genetic structure and gene flow in Hibiscus moscheutos (Malvaceae) populations

Microgeographic genetic variation in populations of a wetland macrophyte, Hibiscus moscheutos L. (Malvaceae), was investigated using allozyme polymorphism. The species is a self-compatible insect-pollinated perennial, and seeds are water dispersed (hydrochory). Six hundred plants were analyzed from eight brackish and two freshwater populations within the Rhode River watershed/estuarine system. The genetic structure of the populations was assessed by fixation indices and spatial autocorrelation analyses. The degree of genetic differentiation among sites and gene flow between all paired combinations of sites (M ) was analyzed using three hypothetical gene flow models. Fixation indices indicated almost complete panmixia within populations, and spatial autocorrelations showed that genotypes were randomly distributed within sites, most likely the result of water dispersal of seeds. Allele frequencies were significantly different among sites, and estimated FST indicated moderate genetic differentiation (_ = 0.062). Genetic differences between populations were mostly explained by a gene flow model that accounted for the location of populations relative to the tidal stream. The importance of hydrochory in affecting spatial genetic structure was thus suggested both within and among H. moscheutos populations.     

Genetic variability and gene flow in the globally, critically-endangered Taita thrush

Analysis of 155 individuals with seven polymorphicmicrosatellite DNA markers showed significant genetic differentiationbetween the only three remaining subpopulations of the globally,critically-endangered Taita thrush. Small, recently-disturbedsubpopulations such as studied here may violate the assumptions ofmutation-drift and gene flow-drift equilibrium inherent to mostpopulation genetic tools that estimate gene flow. We thereforeidentified putative dispersers using two recently-developed assignmenttests based on individual genotypes. Previous-generation and currentmigration rates between any two subpopulations were estimated at one andzero individuals per generation, respectively. Strong congruence withnon-genetic estimates of between-fragment dispersal provided indirectevidence for the accuracy of the assignment test. From a conservationperspective, the available demographic and genetic data suggest asubstantial threat to the long-term survival of at least the smallestsubpopulation.     

Genetic diversity and multilocus structure in sexual Otiorhynchus alpicola populations (Goleoptera: Gurculionidae)

Otiorhynchus alpicola Boh. (Coleoptera: Curculionidae) is distributed on high mountains of central, southern and south-eastern Europe. On the Balkan peninsula, this species is patchily distributed on mountain peaks at heights over 1800 m. To examine the organization of isoenzyme variation of the ten sexual (diploid) populations, starch gel electrophoresis of enzymes was used. The average heterozygosity over 14 gene loci was 0.11. For diploid O. alpicola, F-statistics were used to assess population heterogeneity and substructuring. The data indicate that, compared with other insects, this high-altitude weevil species is genetically very differentiated (the average F _ST= 0.35). In addition, gene-flow among populations was extremely low (the estimates of N_em from Wright's F _ST and Slatkin private-allele methods were 0.47 and 0.83, respectively). Pairwise linkage disequilibrium (LD) parameters were estimated from zygotic frequencies using Burrows' method. The average rate of significant LD in analysed populations of O. alpicola was about 27%. The pattern of LD over the diploid populations indicates that stochastic factors might be a primary cause of the observed multilocus associations.     

Gene flow among small populations of a self-incompatible plant: an interaction between demography and genetics

We assessed the effects of population size and genetic relatedness on rates of pollen gene flow into experimental populations of the insect-pollinated, self-incompatible plant Raphanus sativus. We created synthetic populations of sizes 2, 5, 10, and 20 with three genetic structures (full siblings, half siblings, and unrelated plants). Following pollination in a natural setting, we conducted a simple paternity exclusion analysis using the allozyme genotypes of progeny to measure apparent gene flow and Monte Carlo simulations to estimate total gene flow. Estimates of apparent pollen gene flow rates ranged from 0 to 100% and were similar in rank to estimates of total gene flow. There were significant effects of population size and relatedness on the rate of apparent gene flow, and there were significant population size by relatedness interactions. Populations of size 2 had higher gene flow rates than larger populations, gene flow being negatively associated with the level of cross-compatibility (as measured by hand pollinations). Gene flow into populations of size 2 was also negatively associated with the distance to the nearest population of size 10 or 20. These results suggest that interactions among demography (population size), genetics (cross-compatibility), and ecology (pollinator behavior) are important influences on pollen gene flow rates into small plant populations.     

Contemporary gene flow and the spatio-temporal genetic structure of subdivided newt populations (Triturus cristatus, T. marmoratus)

Gene flow and drift shape the distribution of neutral genetic diversity in metapopulations, but their local rates are difficult to quantify. To identify gene flow between demes as distinct from individual migration, we present a modified Bayesian method to genetically test for descendants between an immigrant and a resident in a nonmigratory life stage. Applied to a metapopulation of pond-breeding European newts (Triturus cristatus, T. marmoratus) in western France, the evidence for gene flow was usually asymmetric and, for demes of known census size (N), translated into maximally seven reproducing immigrants. Temporal sampling also enabled the joint estimation of the effective demic population size (Ne) and the immigration rate m (including nonreproductive individuals). Ne ranged between 4.1 and 19.3 individuals, Ne/N ranged between 0.05 and 0.65 and always decreased with N; m was estimated as 0.19-0.63, and was possibly biased upwards. We discuss how genotypic data can reveal fine-scale demographic processes with important microevolutionary implications.     

Effective size in management and conservation of subdivided populations

A numerical method for computing the eigenvalue variance effective size of a subdivided population connected by any fixed pattern of migration is described. Using specific examples it is shown that total effective size of a subdivided population can become less than the sum of the subpopulation sizes as a result of directionalities in the pattern of migration. For an extension of the model with threshold harvesting and local deterministic logistic population dynamic we consider the problem of maximizing the total harvesting yield with constraints on the total effective size. For some simple source-sink systems and more complicated population structures where subpopulations differ in their degree of isolation, it is shown to be optimal, for a given total effective size, to raise the harvesting thresholds relatively more in small and in isolated populations. Finally, we show how the method applies to populations which are supplemented, either intentionally or unintentionally. It is shown that the total effective size can be reduced by several orders of magnitude if the captive component of a population is much smaller than the wild component, even with symmetric backward migration.     

Loss of historical immigration and the unsuccessful rehabilitation of extirpated salmon populations

Comprehensive evaluations of multiple genetic factors are rarely undertaken in rehabilitation attempts of extirpated populations, despite a growing need to address why some rehabilitation projects succeed and others fail. Using temporally-spaced samples of microsatellite DNA, we tested several genetic hypotheses that might explain an unsuccessful attempt to re-establish Atlantic salmon populations (Salmo salar) in two rivers of the inner Bay of Fundy, Canada. Census sizes (N) in both populations plummeted to near zero from initial increases after reintroduction/human-mediated recolonization occurred. Over the same period (1974–1996), both populations were characterized by low or relatively low effective sizes (N _e ) and temporally unstable genetic structuring, whereas neighbouring populations, known historically for their significant salmon production, were not. Despite evidence for genetic bottlenecking and continual linkage disequilibrium over time in both populations, neither exhibited detectable inbreeding or a significant loss of allelic diversity or heterozygosity relative to known donor/source populations. Ratios of N _e to N also increased with decreasing N in both populations, implying a buffering capacity against losses of genetic diversity at depressed abundances. Most significantly, multiple lines of evidence were consistent with the hypothesis that there has been substantial and recurrent asymmetric migration (migration rate, m) from neighbouring areas into both populations even after initial rehabilitation. This included migration from a historically productive population that became extirpated during the course of rehabilitation efforts, indicating that both populations might have naturally depended on immigration from neighbouring areas for persistence. Our results highlight the value of incorporating temporal genetic data beyond commonly used metrics of neutral genetic diversity (F _ST, allelic richness, heterozygosity) to evaluate rehabilitation successes or failures. They also illustrate how the joint evaluation of multiple genetic concerns in rehabilitation attempts, at spatial scales beyond donor and rehabilitated populations, is useful for focusing future rehabilitation efforts.     

Asymmetric gene flow and the evolutionary maintenance of genetic diversity in small,peripheral Atlantic salmon populations

Small populations may be expected to harbour less genetic variation than large populations, but the relation between census size (N), effective population size (N _e), and genetic diversity is not well understood. We compared microsatellite variation in four small peripheral Atlantic salmon populations from the Iberian peninsula and three larger populations from Scotland to test whether genetic diversity was related to population size. We also examined the historical decline of one Iberian population over a 50-year period using archival scales in order to test whether a marked reduction in abundance was accompanied by a decrease in genetic diversity. Estimates of effective population size (N _e) calculated by three temporal methods were consistently low in Iberian populations, ranging from 12 to 31 individuals per generation considering migration, and from 38 to 175 individuals per generation if they were regarded as closed populations. Corresponding N _e/N ratios varied from 0.02 to 0.04 assuming migration (mean=0.03) and from 0.04 to 0.18 (mean=0.10) assuming closed populations. Population bottlenecks, inferred from the excess of heterozygosity in relation to allelic diversity, were detected in all four Iberian populations, particularly in those year classes derived from a smaller number of returning adults. However, despite their small size and declining status, Iberian populations continue to display relatively high levels of heterozygosity and allelic richness, similar to those found in larger Scottish populations. Furthermore, in the R. Asón no evidence was found for a historical loss of genetic diversity despite a marked decline in abundance during the last five decades. Thus, our results point to two familiar paradigms in salmonid conservation: (1)␣endangered populations can maintain relatively high levels of genetic variation despite their small size, and (2) marked population declines may not necessarily result in a significant loss of genetic diversity. Although there are several explanations for such results, microsatellite data and physical tagging suggest that high levels of dispersal and asymmetric gene flow have probably helped to maintain genetic diversity in these peripheral populations, and thus to avoid the negative consequences of inbreeding.     

云南西花蓟马rDNA-ITS2遗传多态性及其种群扩张

应用rDNA-ITS2基因序列对云南各地理种群西花蓟马Frankliniella occidentalis(Pergande)的遗传结构和遗传分化程度进行初步研究。经过比对112条序列,共发现了59个变异位点,定义了30种单倍型。云南省西花蓟马的单倍型多态性较高(Hd=0.90219),而核酸多态性较低(Pi=0.00891)。各地理种群西花蓟马的遗传分化指数Fst为0.00810,基因流Nm为30.61,表明各地理种群间遗传分化程度非常低,种群间存在充分的基因交流。对群体进行中性检验、错配分析表明西花蓟马群体曾经历过近期的种群扩张。分子方差分析(AMOVA)表明,云南西花蓟马的遗传变异主要来自于种群内部,种群间的遗传变异水平还非常低。从分子生物学的角度上也证实了西花蓟马近期入侵云南的事实。     

Genetic structure of mountain lion (Puma concolor) populations in California

Analysis of 12 microsatellite loci from431 mountain lions (Puma concolor)revealed distinct genetic subdivision that wasassociated with geographic barriers andisolation by distance in California. Levels ofgenetic variation differed among geographicregions, and mountain lions that inhabitedcoastal areas exhibited less heterozygositythan those sampled inland. The San FranciscoBay and Sacramento-San Joaquin River Delta, theCentral Valley, and the Los Angeles Basinappeared to be substantial barriers to geneflow, and allele frequencies of populationsseparated by those features differedsubstantially. A partial barrier to gene flowappeared to exist along the crest of the SierraNevada. Estimated gene flow was high amongmountain lions inhabiting the Modoc Plateau,the western Sierra Nevada, and northern sectionof the eastern Sierra Nevada. SouthernCalifornia mountain lion populations mayfunction as a metapopulation; however, humandevelopments threaten to eliminate habitat andmovement corridors. While north-south geneflow along the western Sierra Nevada wasestimated to be very high, projected loss andfragmentation of foothill habitat may reducegene flow and subdivide populations. Preservation of existing movement corridorsamong regions could prevent population declinesand loss of genetic variation. This studyshows that mountain lion management andconservation efforts should be individualizedaccording to region and incorporatelandscape-level considerations to protecthabitat connectivity.     

Islands and streams: clusters and gene flow in wild barley populations from the Levant

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter‐mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analysing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication.     

Genetic structure of the stonefly, Yoraperla brevis, populations: the extent of gene flow among adjacent montane streams

1. Gene flow in populations of stream insects is expected to depend on the distance between and the connectedness of sites in stream networks, and on dispersal ability (i.e. larval drift and adult flight).
2. Yoraperla brevis (Banks) is an abundant and characteristic stonefly of smaller streams in the northern Rocky Mountains. The present authors analysed genetic structure at 27 sites in sevenz streams flowing into the Bitterroot River in western Montana, USA. Cellulose acetate electrophoresis identified five variable loci with 16 alleles.
3. Genotype frequencies conformed to Hardy–Weinberg expectations. Within-stream differentiation was low and among-stream variation ( F _st) was an order of magnitude higher.
4. UPGMA grouped sites within streams and also grouped adjacent streams. The tree produced by the Neighbour Joining Method was similar although not quite so clear cut.
5. This orderly pattern (i.e. Hardy–Weinberg proportions, homogeneity within streams and geographical structure) contrasts strongly with patterns observed in invertebrates from subtropical streams in Australia. Yoraperla brevis maintains large populations in predictable environments, has a long life-cycle with a likelihood of cohort mixing, emerges synchronously in large breeding populations and occupies streams separated by areas of high relief; the Australian situation is the opposite in most respects.
6. Further analysis of a range of species is required to determine whether the different genetic structure in Y. brevis compared to the Australian species occurs more generally in North American stream insects.     

Genetic structure in northeastern populations of the Alpine newt (Triturus alpestris): evidence for post-Pleistocene differentiation

Genetic variation in 13 populations of the Alpine newt, Triturus alpestris, was assessed at the northeastern margin of its range (southern Poland). Variation at six microsatellite loci was scored in 354 newts, and two mitochondrial DNA fragments (c. 2000 bp) were sequenced in a subset of 27 individuals. Significant differences in allele frequencies and the presence of private alleles determined genetic units corresponding to three separate mountain ranges, i.e. the Carpathian, Sudetes and Holy Cross Mountains. F(ST)'s were three times greater in among than in within mountain range pairwise comparisons. An assignment test and pairwise F(ST)'s suggested relatively high levels of gene flow at the local level, although the Sudetes populations revealed some subtle structuring. Genetic variation was lower in the Carpathians and Holy Cross Mountains. The geographic pattern of mitochondrial DNA variation indicated that these newt populations originated from a single glacial refugium/founder population, and that the colonization of southern Poland took place in an easterly direction. The data show that substantial neutral variation and between group divergence has accumulated relatively quickly in these low-vagility organisms. The Alpine newt case exemplifies species history as a factor determining patterns of genetic diversity in marginal populations.