Деякі міркування щодо характерних рис оселищ популяцій, а також про біотопи у реальних умовах їхнього існування

What is the influence of the seed bank on the persistence and genetic structure of plant populations that experience a high level of disturbance?

SummaryIt is generally accepted that kelp populations have a metapopulation structure. Most zoospores settle near to their parent individual, and infrequent but long‐distance dispersal of zoospores contributes to gene flow between local populations. Population genetic analysis of single nucleotide polymorphism genotyping by MIG‐seq (i.e. multiplexed inter‐simple sequence repeats genotyping by sequencing) was performed on the dominant kelp, Eisenia bicyclis, in two areas: Kitsunezaki (a sheltered area) and Shimoda (an exposed site). Regional scale analysis of genetic structure was conducted at six sites in Kitsunezaki and three sites in Shimoda. When viewed on a regional scale based on the inbreeding coefficient within the local population, the inbreeding ratio was higher in Shimoda than in Kitsunezaki, probably as a result of the limited vertical zonal distribution in the exposed environment. Vertically wide distribution in the sheltered environment apparently enabled frequent crossing among individuals in Kitsunezaki. By contrast, when viewed on a local scale based on the pairwise kinship coefficient (FST) between populations, gene flow among local populations in Shimoda occurred over a wide area, but was limited in Kitsunezaki. In Shimoda, genetic exchange between local populations, even if inbreeding is locally active, is likely to support metapopulation maintenance and rapid recovery of local populations. In Kitsunezaki, however, genetic exchange among local populations is limited within few 100 m, and the metapopulation structure will decline in the long term because of inbreeding depression. Local dispersal distance of zoospores was investigated based on parent–offspring analysis in the Kitsunezaki population, which revealed that zoospores mainly settled within 5 m of their parent. However, some zoospores traveled over 27 m within the 4 × 30 m study area. The present study shows the importance of examination at different spatial scales when investigating zoospore dispersal of laminarialean kelps.

Summary 1 Long‐distance dispersal events are biologically very important for plants because they affect colonization probabilities, the probabilities of population persistence in a fragmented habitat, and metapopulation structure. They are, however, very difficult to investigate because of their low frequency. We reviewed the use of molecular markers in the population genetics approach to studying dispersal. With these methods the consequences of long‐distance dispersal are studied, rather than the frequency of the dispersal events themselves. 2 Molecular markers vary, displaying different amounts of variation and different modes of inheritance: they may be either dominant or codominant, and may or may not be subjected to genetic recombination. Use of markers has inspired the development of maximum likelihood techniques that take the evolutionary history of alleles into account while estimating gene flow. 3 Inferring seed dispersal rates from indirect measurements of gene flow involves three steps: (i) quantifying genetic differentiation among populations and using this to estimate the rate of gene flow; (ii) producing a genetic dispersal curve by regressing geographical distance among populations against the amount of gene flow; and (iii) separating seed‐mediated from pollen‐mediated gene flow, by comparing differentiation in nuclear vs. cytoplasmic molecular markers. In this way, potentially very low levels of gene flow can be detected. 4 The indirect approach is based on a number of assumptions. The validity of each assumption should be assessed by independent methods or the estimates of gene flow and dispersal should be mainly used in a comparative context. In metapopulations, with frequent extinction and colonization, the relationship between genetic differentiation and gene flow is not straightforward, and other methods should be used. 5 Highly variable molecular markers, especially microsatellites, have facilitated a direct genetic approach to measuring gene flow, based on parental analyses. 6 The population genetic approach provides different information about dispersal than ecological methods. Thus population genetic and ecological methods may supplement each other, and together lead to a better insight into the dispersal process than either of the methods on its own.

Habitat fragmentation is one of the major threats to amphibian species. In a previous study, population genetic analyses of the Japanese brown frog Rana japonica were conducted using a mitochondrial DNA (mtDNA) marker in a typical Japanese agricultural landscape (known as satoyama) in Chiba, Japan. This previous study revealed that gene flow was restricted by the roads and cement-walled urban river that divide this site. In the present study, we reanalyzed the genetic structure of the same meta-population using microsatellite markers in comparison with the mtDNA results and elucidated fine-scale gene flow. The genetic structure derived from the microsatellite clustering analysis was almost identical to that of the mtDNA results, although some important details differed. We recognized boundaries of genetic structure are consistent with the major roads and cement-walled river, however, we also detected gene flow across those artificial barriers. We concluded that the current genetic structure was formed in the past when gene flow was strongly restricted. Gene flow among breeding populations is now being restored by the maintenance of breeding sites, although it is not sufficient to erase the signature of historical isolation.

The increasing fragmentation of natural habitats may strongly affect patterns of dispersal and gene flow among populations, and thus alter evolutionary dynamics. We examined genetic variation at twelve microsatellite loci in the Agile frog (Rana dalmatina) from 22 breeding ponds in the Iberian Peninsula, the southwest limit of its range, where populations of this species are severely fragmented and are of conservation concern. We investigated genetic diversity, structure and gene flow within and among populations. Diversity as observed heterozygosities ranged from 0.257 to 0.586. The mean number of alleles was 3.6. Just one population showed a significant FIS value. Four populations show evidence of recent bottlenecks. Strong pattern of structure was observed due to isolation by distance and to landscape structure. The average degree of genetic differentiation among populations was FST = 0.185. Three operational conservation units with metapopulation structure were identified. Additionally, there are some other isolated populations. The results reinforce the view that amphibian populations are highly structured even in small geographic areas. The knowledge of genetic structure pattern and gene flow is fundamental information for developing programmes for the preservation of R. dalmatina at the limits of its geographic distribution.

Anthropogenic habitat fragmentation often restricts gene flow and results in small populations that are at risk of inbreeding. However, some endangered species naturally occupy patchy habitat where local population extinction and recolonization are normal. We investigated population fragmentation in the range-restricted New Zealand small-scaled skink (Oligosoma microlepis), documenting changes in habitat occupancy and analyzing mitochondrial, microsatellite, and morphological variation sampled across the geographical range of the species (approximately 100 km2). Small-scaled skinks have a strong preference for rocky outcrops that exist in a mosaic of other habitat types. A metapopulation structure was indicated by both local extinction and colonization of new sites. We found relatively high mtDNA nucleotide site diversity within this narrow range (π = 0.004; 16S), evidence of inter-patch gene flow, and no statistical support for inbreeding. Gene flow was limited by geographical distance, although the existence of pasture between habitat patches apparently has not prevented skink dispersal. Generalized linear models indicated an association between body size and location suggesting a local environmental influence on phenotype. Prior to human-induced habitat modification, native forest probably separated preferred sites and, less than 2000 years ago, volcanic activity devastated much of the area currently occupied by O. microlepis. This skink appears able to re-establish populations if other human-linked factors such as agricultural intensification and introduced predators are limited. Although in contrast to expectations for a scarce and localized species living in a highly modified landscape, this lizard may have previously adapted to a dynamic, mosaic environment mediated by volcanism.

Genetic diversity and metapopulation structure of the brown swimming crab (Callinectes bellicosus) along the coast of Sonora, Mexico: Implications for fisheries management

Metapopulation structure generated by recurrent extinctions and recolonizations plays an important role in the evolution of species but is rarely considered in agricultural systems. In this study, generation and mechanism of metapopulation structure were investigated by microsatellite assaying 725 isolates of Alternaria alternata sampled from potato hosts at 16 locations across China. We found a single major cluster, no isolate-geography associations and no bottlenecks in the A. alternata isolates, suggesting a metapopulation genetic structure of the pathogen. We also found weak isolation-by-distance, lower among than within cropping region population differentiation, concordant moving directions of potato products and net gene flow and the highest gene diversity in the region with the most potato imports. These results indicate that in addition to natural dispersal, human-mediated gene flow also contributes to the generation and dynamics of the metapopulation genetic structure of A. alternata in China. Metapopulation structure increases the adaptive capacity of the plant pathogen as a result of enhanced genetic variation and reduced population fragmentation. Consequently, rigid quarantine regulations may be required to reduce population connectivity and the evolutionary potential of A. alternata and other pathogens with a similar population dynamics for a sustainable plant disease management.

BackgroundUnderstanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in connectivity throughout the SCS is seldom studied. In this study, we aim to evaluate the role of DANP in conserving regional marine biodiversity.MethodsIn total, 206 samples across nine marine species were collected and sequenced from Dongsha Atoll, and these data were combined with available sequence data from each of these nine species archived in the Genomic Observatories Metadatabase (GEOME). Together, these data provide the most extensive population genetic analysis of a single marine protected area. We evaluate metapopulation structure for each species by using a coalescent sampler, selecting among panmixia, stepping-stone, and island models of connectivity in a likelihood-based framework. We then completed a heuristic graph theoretical analysis based on maximum dispersal distance to get a sense of Dongsha’s centrality within the SCS.ResultsOur dataset yielded 111 unique haplotypes across all taxa at DANP, 58% of which were not sampled elsewhere. Analysis of metapopulation structure showed that five out of nine species have strong regional connectivity across the SCS such that their gene pools are effectively panmictic (mean pelagic larval duration (PLD) = 78 days, sd = 60 days); while four species have stepping-stone metapopulation structure, indicating that larvae are exchanged primarily between nearby populations (mean PLD = 37 days, sd = 15 days). For all but one species, Dongsha was ranked within the top 15 out of 115 large reefs in the South China Sea for betweenness centrality. Thus, for most species, Dongsha Atoll provides an essential link for maintaining stepping-stone gene flow across the SCS.ConclusionsThis multispecies study provides the most comprehensive examination of the role of Dongsha Atoll in marine connectivity in the South China Sea to date. Combining new and existing population genetic data for nine coral reef species in the region with a graph theoretical analysis, this study provides evidence that Dongsha Atoll is an important hub for sustaining connectivity for the majority of coral-reef species in the region.

Biological invasions constitute major threats to global biodiversity. Eco‐evolutionary considerations highlight the importance of contemporary evolution in community responses to bioinvasions. However, effects of metapopulation structure on invasion success have been mostly overlooked even though metapopulation structure determines gene flow and is likely to affect evolutionary processes. Here, we investigate a stepping‐stone model with evolving alien native interaction strengths. We demonstrate analytically that the site of invasion can determine the success of an invading consumer because gene flow and demography of a local resource species interact to obstruct local resource adaptation. Our main results are 1) that invasion success is more likely in genetic sink populations of the native species and 2) that invasion is more likely to occur against the migrational flow of native species. These findings suggest that invasibility is best regarded as an emergent property not only of communities but of entire metapopulations. Since migration networks of aliens and natives are often mismatched due to anthropogenic interference, our results indicate how population structure eases the spread of invasives against the migrational flow of natives.

We discuss the roles of gene flow, genetic drift, and selection in determining the distribution of genetic variation in complex, real-world landscapes. A metapopulation is a group of populations that experience some degree of gene flow among them. Metapopulation structure can have complex effects on patterns of genetic variation within and among populations. For species that do not naturally occur in discrete habitat patches, a landscape genetics framework is more appropriate. Landscape genetics combines population genetics, landscape ecology, and spatial statistics to understand how environmental heterogeneity affects gene flow and genetic variation. Habitat loss and fragmentation have severed connectivity among populations of many formerly continuous species, isolating populations that then lose genetic variation due to reduced gene flow. Genetic rescue, the supplementation of small inbred populations with immigrants from larger more genetically diverse populations, can be used to increase genetic diversity and reduce extinction probabilities of populations isolated by habitat fragmentation.

Isolation by distance is usually tested by the correlation of genetic and geographic distances separating all pairwise populations' combinations. However, this method can be significantly biased by only a few highly diverged populations and lose the information of individual population. To detect outlier populations and investigate the relative strengths of gene flow and genetic drift for each population, we propose a decomposed pairwise regression analysis. This analysis was applied to the well-described one-dimensional stepping-stone system of stream-dwelling Dolly Varden charr (Salvelinus malma). When genetic and geographic distances were plotted for all pairs of 17 tributary populations, the correlation was significant but weak (r(2) = 0.184). Seven outlier populations were determined based on the systematic bias of the regression residuals, followed by Akaike's information criteria. The best model, 10 populations included, showed a strong pattern of isolation by distance (r(2) = 0.758), suggesting equilibrium between gene flow and genetic drift in these populations. Each outlier population was also analysed by plotting pairwise genetic and geographic distances against the 10 nonoutlier populations, and categorized into one of the three patterns: strong genetic drift, genetic drift with a limited gene flow and a high level of gene flow. These classifications were generally consistent with a priori predictions for each population (physical barrier, population size, anthropogenic impacts). Combined the genetic analysis with field observations, Dolly Varden in this river appeared to form a mainland-island or source-sink metapopulation structure. The generality of the method will merit many types of spatial genetic analyses.

Wildlife managers are challenged to manage spatially structured populations efficiently and effectively, therefore dispersal and gene flow are vital to understand and manage, particularly for a harvested species. We used a genetic approach to describe the metapopulation structure of Rocky Mountain elk (Cervus elaphus) in Idaho to assess past patterns of population distribution and influences of harvest. We used elk tissue and DNA samples (n ¼ 216) to examine genetic dissimilarity between 7 regions and 9 elk management zones throughout Idaho using microsatellite loci (n ¼ 11). Using 5 approaches, including pairwise FST-values, assignment tests, and a Bayesian model–based clustering of genotypes, we examined the distribution of genetic variation. The distribution of genetic variation between elk populations indicated low levels of genetic differentiation among regions (expected heterozygosity [HE] ¼ 0.55–0.61, overall FST ¼ 0.011) and elk management zones (HE ¼ 0.54–0.60, overall FST ¼ 0.017). Assignment tests and migration rates indicated directional gene flow between elk populations. A patchy metapopulation best describes the distribution of genetic variation among Idaho elk populations because likely enough individual interchange occurs between geographically separated populations. The elk populations we sampled could be part of a geographically larger patchy metapopulation potentially stretching from Yellowstone National Park through Idaho into western Canada. Because of historical translocations of elk from Yellowstone National Park, insufficient time may have passed to detect differences in genetic variation. Subtle differences in the distribution of genetic variation were observed in 2 of the 9 elk management zones within 2 different regions of the state. Our findings indicate management of Idaho elk populations and dispersal are maintaining sufficient gene flow. Metapopulation structure of a harvested species based on the distribution of genetic variation is an indicator of potential genetic consequences of harvesting and sustainable harvest levels.

Gene products of 18 allozyme loci from 1268 individuals of a Japanese freshwater goby called donko, Odontobutis obscura (Odontobutidae; Gobioidei), from 33 localities in the Koya River, Yamaguchi Prefecture, Japan, were investigated to determine the extent of genetic divergence and gene flow within a river metapopulation. Genetic indices including GST(mean FST 0.182), FIT(mean 0.192) and D(mean 0.015) indicated a considerable divergence of local populations in the river. The genetic distance (D) and channel distance between pairs of populations did not show a good correlation, and geographical neighbors were not always genetic neighbors. Therefore, the genetic divergence of populations is attributable to independent genetic drift with restricted gene flow among populations. The agricultural dams and weirs constructed across the river must be responsible for the restricted gene flow. The metapopulation structure of O. obscura in the Koya River may be barely sustained by one-way gene flow only from the upper to the lower populations. An occasional artificial transplantation of some individuals from the lower to the upper populations may be one alternative to maintain a river metapopulation structure safely.

2 ) using polymorphic microsatellite markers. Both species were found in approximately 60% of sites formerly known to harbour the aphids, although, generally when they did occur, they occurred singly (MA ~50%; ME ~60%) and rarely together on the same plant at the same time (approximately 10%) and then usually only in the early part of the growing season. This difference may be a result of quasi-apparent competition effects elicited by ants farming ME aphids, and preferentially actively eliminating or disturbing MA aphids. In terms of population genetics, both aphids showed extreme genetic heterogeneity within a metapopulation structure, with ME more than MA (i.e. higher FST values, approximately 0.4 versus 0.15, respectively), and limited levels of interpopulation gene flow. Subpopulations often deviated from Hardy-Weinberg equilibrium and showed linkage disequilibria, as expected in animals with extended parthenogenetic reproduction, and had positive FIS values for most large samples, suggesting inbreeding, and possibly philopatry, certainly in ME. Hierarchical analysis (allele range and number per locus, analysis of molecular variance and FST) strongly suggested that the plant rather than site governs the level of genetic variation. Bayesian clustering analysis revealed that both species had heterogeneous historical genetic patterning, with K (number of subgroups) in the range 3-7. Evidence is also provided from isolation-by-distance and private allele analyses indicating that, in MA, the presence of winged autumn males, absent in ME where males are wingless, influences comparative population genetic structuring, such that ME subpopula- tions are comparatively more inbred and genetically differentiated than MA subpopulations. Lastly, additional spatial arrangement (ALLELES-IN-SPACE) analysis showed that, in both species, certain subpopulations were genetically isolated from the remainder, probably as a result of geographical barriers, including intervening buildings and woods. As such, the biology of these tansy aphids living in semi-natural habitats is very different from many pest aphid species examined within agro-ecosystems and infesting ephemeral crops. This is because the former appear to be much more reluctant to fly and hence show contrastingly much higher levels of interpopulation divergence, even at small spatial scales as investigated in the present study. Indeed, the number of genotypic clusters found for tansy aphids using Bayesian approaches is similar to that globally for the major pest, the peach-potato aphid, Myzus persicae. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 838-865. ADDITIONAL KEYWORDS: gene flow - genetic variation - historical patterns - inbreeding - migration - population divergence.