A comparison of four methods for detecting weak genetic structure from marker data

Genetic structure is ubiquitous in wild populations and is the result of the processes of natural selection, genetic drift, mutation, and gene flow. Genetic drift and divergent selection promotes the generation of genetic structure, while gene flow homogenizes the subpopulations. The ability to detect genetic structure from marker data diminishes rapidly with a decreasing level of differentiation among subpopulations. Weak genetic structure may be unimportant over evolutionary time scales but could have important implications in ecology and conservation biology. In this paper we examine methods for detecting and quantifying weak genetic structures using simulated data. We simulated populations consisting of two putative subpopulations evolving for up to 50 generations with varying degrees of gene flow (migration), and varying amounts of information (allelic diversity). There are a number of techniques available to detect and quantify genetic structure but here we concentrate on four methods: F(ST), population assignment, relatedness, and sibship assignment. Under the simple mating system simulated here, the four methods produce qualitatively similar results. However, the assignment method performed relatively poorly when genetic structure was weak and we therefore caution against using this method when the analytical aim is to detect fine-scale patterns. Further work should examine situations with different mating systems, for example where a few individuals dominate reproductive output of the population. This study will help workers to design their experiments (e.g., sample sizes of markers and individuals), and to decide which methods are likely to be most appropriate for their particular data.     

干扰对动物传播森林植物种子有效性影响的研究进展

干扰在森林生态系统中普遍存在,并影响森林的更新和演替.动物传播种子是种子更新的必经阶段,其对森林干扰的响应在一定程度上能够预测未来的森林群落组成和结构变化,对于明确森林演替方向具有重要意义.本文论述了森林干扰对动物传播种子有效性(包括动物传播种子的数量和质量)影响研究的生态学意义,全面揭示了自然干扰(火干扰、林窗干扰等)和人为干扰(生境破碎化、狩猎、采伐等)对动物传播种子数量、传播距离以及传播后幼苗更新影响的研究进展,指出干扰通过影响动物种群动态,进而造成动物传播种子数量发生了改变,动物传播种子的距离对干扰的响应基本表现出轻微负相关;干扰对传播后幼苗更新的影响结果因干扰类型的不同而复杂多变,干扰迹地环境因子的变化也影响着传播后的种子萌发和幼苗更新.干扰对动物传播种子有效性影响研究中存在的问题,主要表现为火干扰迹地恢复过程、增益性的干扰(如抚育、间伐、林窗)等对种子传播有效性影响研究的匮乏,以及忽略了温带森林内的干扰对动物传播种子的影响等.今后,应开展干扰对种子传播有效性的长期研究;对于干扰多发地带的森林,应高度重视增益性干扰影响动物传播植物种子的研究.     

Spatial genetic structure in populations of the terrestrial orchid Orchis cyclochila (Orchidaceae)

Orchid seeds are minute, dust-like, wind-borne and, thus, would seem to have the potential for long-distance dispersal. Based on this perception, one may predict near-random spatial genetic structure within orchid populations. In reality we do not know much about seed dispersal in orchids and the few empirical studies of fine-scale genetic structure have revealed significant genetic structure at short distances (< 5m), suggesting that most seeds of orchids fall close to the maternal plant. To obtain more empirical data on dispersal, Ripley’s L(d)-statistics, spatial autocorrelation analyses (coancestry, f_ij analyses) and Wright’s F statistics were used to examine the distribution of individuals and the genetic structure within two populations of the terrestrial orchid Orchis cyclochila in southern Korea. High levels of genetic diversity (H_e = 0.210) and low between-population variation were found (F_ST = 0.030). Ripley’s L(d)-statistics indicated significant aggregation of individuals, and patterns varied depending on populations. Spatial autocorrelation analysis revealed significant positive genetic correlations among individuals located <1 m, with mean f_ij values expected for half sibs. This genetic structure suggests that many seeds fall in the immediate vicinity of the maternal plant. The finding of significant fine-scale genetic structure, however, does not have to preclude the potential for the long distance dispersal of seeds. Both the existence of fine-scale genetic structure and low F_ST are consistent with a leptokurtic distribution of seed dispersal distances with a very flat tail.     

Population genetic structure and dispersal across a fragmented landscape in cerulean warblers (<Emphasis Type="Italic">Dendroica cerulea</Emphasis>)

Cerulean warblers (Dendroica cerulea) have experienced significant declines across their breeding range and presently exist in disjunct populations, largely because of extensive loss and fragmentation of their breeding and wintering habitat. Despite this overall decline, a recent north-eastern expansion of the breeding range has been proposed, and some researchers have suggested that the eastern Ontario population may be acting as a source population maintaining sink populations elsewhere. However, little is known about either the geographic distribution of genetic variation or dispersal in these birds. We assayed variation in five microsatellite loci and a 366 base-pair fragment of the mitochondrial control region among 154 cerulean warblers from five populations throughout the breeding range. No evidence of population genetic structure was found. Assignment tests suggested that six individuals were either inter-population migrants or descendants of recent migrants. The lack of population genetic structure is probably due to a combination of historical association and contemporary dispersal. Population decline does not appear to have reduced genetic variation yet. Overall results suggest that cerulean warblers from Ontario, Illinois, Arkansas and Tennessee should be considered a single genetic management unit for conservation.     

POPULATION GENETIC STRUCTURE OF CECROPIA OBTUSIFOLIA,A TROPICAL PIONEER TREE SPECIES

Theoretical analyses of the genetic organization of pioneer species have postulated two very different scenarios. Some models have predicted that such species would show strong population substructuring, whereas other models have suggested that extinction and recolonization can augment gene flow and reduce interpopulation differentiation. We tested these alternative scenarios by analyzing the genetic structure of eight loci from populations of the pioneer dioecious tree, Cecropia obtusifolia, in the tropical rain forest region of Los Tuxtlas, México. The populations studied exhibit low overall F_ST values, no clear pattern of isolation by distance, and high estimates of gene flow. These results suggest either that the species is not at a genetic equilibrium under present levels of gene flow with populations derived from each other in the recent past, or that pollen and seed dispersal in this species occur over long distances (up to more than 100 km). Mating among relatives appears higher than expected by chance based on significantly positive fixation indices (F) and F_IS values at some loci. However, no direct evidence for biparental inbreeding was found. The multilocus and single-locus outcrossing rates for C. obtusifolia were estimated at t_m = 0.974 (SE = 0.024) and t_s = 0.980 (SE = 0.035), respectively. These are not significantly different from 1, and the difference, t_m — t_s = — 0.006 (SE = 0.018), is not significantly different from 0. These estimates, however, could be biased because in all enzymes, except PGM-1, we found statistically significant departures from the mixed-mating model used to estimate them. Two rare alleles were found only in seeds collected from the soil, and the greatest number of different alleles were found also in soil seeds. It is hypothesized that the seed bank may play an important role in the genetic buffering of C. obtusifolia. Significantly positive or negative fixation indices in adults at some loci and significantly different heterozygosities among different life stages (from seeds to adults) suggest the action of selection at some loci.     

Pollen and seed flow patterns of Carapa guianensis Aublet. (Meliaceae) in two types of Amazonian forest

Various factors affect spatial genetic structure in plant populations, including adult density and primary and secondary seed dispersal mechanisms. We evaluated pollen and seed dispersal distances and spatial genetic structure of Carapa guianensis Aublet. (Meliaceae) in occasionally inundated and terra firme forest environments that differed in tree densities and secondary seed dispersal agents. We used parentage analysis to obtain contemporary gene flow estimates and assessed the spatial genetic structure of adults and juveniles. Despite the higher density of adults (diameter at breast height ≥ 25 cm) and spatial aggregation in occasionally inundated forest, the average pollen dispersal distance was similar in both types of forest (195 ± 106 m in terra firme and 175 ± 87 m in occasionally inundated plots). Higher seed flow rates (36.7% of juveniles were from outside the plot) and distances (155 ± 84 m) were found in terra firme compared to the occasionally inundated plot (25.4% and 114 ± 69 m). There was a weak spatial genetic structure in juveniles and in terra firme adults. These results indicate that inundation may not have had a significant role in seed dispersal in the occasionally inundated plot, probably because of the higher levels of seedling mortality.     

Population substructure in Alkanna orientalis (Boraginaceae) in the Sinai Desert, in relation to its pollinator behaviour

Subpopulation genetic structure was studied in a population of the short-lived perennial plant Alkanna orientalis from the Sinai Desert, Egypt. The population investigated was subdivided for sampling into four subpopulations, which were located within three steep-sided wadis and a central plain area. Results from previous studies suggested that bee pollinator behaviour was likely to cause limited gene dispersal within the population and that subpopulations might have diverged from each other genetically. Seven RAPD primers were used to detect polymorphisms in the population. Differences between sub-populations in fragment frequency were found for several of the 45 polymorphic RAPD fragments scored. Population subdivision was evident from cluster analysis, and an analysis of genetic distances showed that there was significant genetic differentiation between all subpopulations. Nevertheless, more extensive gene flow appears to take place within the population than was expected, as demonstrated by a higher level of genetic similarity between subpopulations from two of the narrow wadis and the interconnecting plain. It is suggested that seed transport mediated by periodic flash floods is responsible for this pattern.