Fat-tailed gene flow in the dioecious canopy tree species Fraxinus mandshurica var. japonica revealed by microsatellites

Pollen flow, seed dispersal and individual reproductive success can be simultaneously estimated from the genotypes of adults and offspring using stochastic models. Using four polymorphic microsatellite loci, gene flow of the wind-pollinated and wind-seed-dispersed dioecious tree species, Fraxinus mandshurica var. japonica, was quantified in a riparian forest, in northern Japan. In a 10.5-ha plot, 74 female adults, 76 male adults and 292 current-year seedlings were mapped and genotyped, together with 200 seeds. To estimate dispersal kernels of pollen and seeds, we applied normal, exponential power, Weibull, bivariate t-distribution kernels, and two-component models consisting of two normal distribution functions, one with a small and one with a large variance. A two-component pollen flow model with a small contribution (26.1%) from short-distance dispersal (sigma = 7.2 m), and the rest from long-distance flow (sigma = 209.9 m), was chosen for the best-fitting model. The average distance that integrated pollen flows inside and outside the study plot was estimated to be 196.8 m. Tree size and flowering intensity affected reproduction, and there appeared to be critical values that distinguished reproductively successful and unsuccessful adults. In contrast, the gene flow model that estimated both pollen and seed dispersal from established seedlings resulted in extensive seed dispersal, and the expected spatial genetic structures did not satisfactorily fit with the observations, even for the selected model. Our results advanced small-scale individual-based parentage analysis for quantifying fat-tailed gene flow in wind-mediated species, but also clarified its limitations and suggested future possibilities for gene flow studies.     

Fragmentation can increase spatial genetic structure without decreasing pollen-mediated gene flow in a wind-pollinated tree

Fragmentation reduces population sizes, increases isolation between habitats and can result in restricted dispersal of pollen and seeds. Given that diploid seed dispersal contributes more to shaping fine-scale spatial genetic structure (SGS) than haploid pollen flow, we tested whether fine-scale SGS can be sensitive to fragmentation even if extensive pollen dispersal is maintained. Castanopsis sclerophylla (Lindley & Paxton) Schottky (Fagaceae), a wind-pollinated and gravity seed-dispersed tree, was studied in an area of southeast China where its populations have been fragmented to varying extents by human activity. Using different age classes of trees in areas subject to varying extents of fragmentation, we found no significant difference in genetic diversity between prefragmentation vs. postfragmentation C. sclerophylla subpopulations. Genetic differentiation among postfragmentation subpopulations was also only slightly lower than among prefragmentation subpopulations. In the most fragmented habitat, selfing rates were significantly higher than zero in prefragmentation, but not postfragmentation, cohorts. These results suggest that fragmentation had not decreased gene flow among these populations and that pollen flow remains extensive. However, significantly greater fine-scale SGS was found in postfragmentation subpopulations in the most fragmented habitat, but not in less fragmented habitats. This alteration in SGS reflected more restricted seed dispersal, induced by changes in the physical environments and the prevention of secondary seed dispersal by rodents. An increase in SGS can therefore result from more restricted seed dispersal, even in the face of extensive pollen flow, making it a sensitive indicator of the negative consequences of population fragmentation.     

Using parentage analysis to examine gene flow and spatial genetic structure

Numerous approaches have been developed to examine recent and historical gene flow between populations, but few studies have used empirical data sets to compare different approaches. Some methods are expected to perform better under particular scenarios, such as high or low gene flow, but this, too, has rarely been tested. In this issue of Molecular Ecology , Saenz-Agudelo et   al . (2009 ) apply assignment tests and parentage analysis to microsatellite data from five geographically proximal (2–6 km) and one much more distant (1500 km) panda clownfish populations, showing that parentage analysis performed better in situations of high gene flow, while their assignment tests did better with low gene flow. This unusually complete data set is comprised of multiple exhaustively sampled populations, including nearly all adults and large numbers of juveniles, enabling the authors to ask questions that in many systems would be impossible to answer. Their results emphasize the importance of selecting the right analysis to use, based on the underlying model and how well its assumptions are met by the populations to be analysed.     

Extensive spatial genetic structure revealed by AFLP but not SSR molecular markers in the wind-pollinated tree, Fagus sylvatica

Studies of fine-scale spatial genetic structure (SGS) in wind-pollinated trees have shown that SGS is generally weak and extends over relatively short distances (less than 30-40 m) from individual trees. However, recent simulations have shown that detection of SGS is heavily dependent on both the choice of molecular markers and the strategy used to sample the studied population. Published studies may not always have used sufficient markers and/or individuals for the accurate estimation of SGS. To assess the extent of SGS within a population of the wind-pollinated tree Fagus sylvatica, we genotyped 200 trees at six microsatellite or simple sequence repeat (SSR) loci and 250 amplified fragment length polymorphisms (AFLP) and conducted spatial analyses of pairwise kinship coefficients. We re-sampled our data set over individuals and over loci to determine the effect of reducing the sample size and number of loci used for SGS estimation. We found that SGS estimated from AFLP markers extended nearly four times further than has been estimated before using other molecular markers in this species, indicating a persistent effect of restricted gene flow at small spatial scales. However, our SSR-based estimate was in agreement with other published studies. Spatial genetic structure in F. sylvatica and similar wind-pollinated trees may therefore be substantially larger than has been estimated previously. Although 100-150 AFLP loci and 150-200 individuals appear sufficient for adequately estimating SGS in our analysis, 150-200 individuals and six SSR loci may still be too few to provide a good estimation of SGS in this species.     

Patterns and levels of gene flow in Rhododendron metternichii var. hondoense revealed by microsatellite analysis

Parentage analysis was conducted to elucidate the patterns and levels of gene flow in Rhododendron metternichii Sieb. et Zucc. var. hondoense Nakai in a 150 x 70 m quadrant in Hiroshima Prefecture, western Japan. The population of R. metternichii occurred as three subpopulations at the study site. Seventy seedlings were randomly collected from each of three 10 x 10 m plots (S1, S2, and S3) on the forest floor of each subpopulation (A1, A2, and A3). Almost all parents (93.8%) of the 70 seedlings were unambiguously identified by using 12 pairs of microsatellite markers. Within the quadrant, adult trees less than 5 m from the centre of the seedling bank (plots S1, S2, and S3) produced large numbers of seedlings. The effects of tree height and distance from the seedling bank on the relative fertilities of adult trees were highly variable among subpopulations because of the differences in population structure near the seedling bank: neither distance nor tree height had any significant effect in subpopulation A1; distance from the seedling bank had a significant effect in subpopulation A2; and tree height had a significant effect in subpopulation A3. Although gene flow within each subpopulation was highly restricted to less than 25 m and gene flow among the three subpopulations was extremely small (0-2%), long-distance gene flow from outside the quadrant reached 50%. This long-distance gene flow may be caused by a combination of topographical and vegetational heterogeneity, differences in flowering phenology, and genetic substructuring within subpopulations.     

Variogram analysis of the spatial genetic structure of continuous populations using multilocus microsatellite data

A geostatistical perspective on spatial genetic structure may explain methodological issues of quantifying spatial genetic structure and suggest new approaches to addressing them. We use a variogram approach to (i) derive a spatial partitioning of molecular variance, gene diversity, and genotypic diversity for microsatellite data under the infinite allele model (IAM) and the stepwise mutation model (SMM), (ii) develop a weighting of sampling units to reflect ploidy levels or multiple sampling of genets, and (iii) show how variograms summarize the spatial genetic structure within a population under isolation-by-distance. The methods are illustrated with data from a population of the epiphytic lichen Lobaria pulmonaria, using six microsatellite markers. Variogram-based analysis not only avoids bias due to the underestimation of population variance in the presence of spatial autocorrelation, but also provides estimates of population genetic diversity and the degree and extent of spatial genetic structure accounting for autocorrelation.     

Chromosome-specific spatial periodicities in gene expression revealed by spectral analysis

Recent years have seen an unprecedented surge of research activity in studies of gene expression. This extensive work, however, has been almost uniformly focused on genome-wide gene expression and has largely ignored the fundamental fact that every gene has a specific chromosome location. We propose a novel method of spectral analysis for detecting hidden periodicities in gene expression signals ordered along the length of each chromosome. Using this method, we have discovered that each chromosome in rodents and humans has a unique periodic pattern of gene expression. The uncovered spatial periodicities in gene expression are tissue-specific in the sense that the largest differences in humans were observed between two normal tissues (brain and mammary gland) as well as between their tumor counterparts (glioma and breast cancer). The smallest differences resulted from the comparison of tumors (glioma and breast cancer) with their normal counterparts. All such effects do not extend to all chromosomes but are limited to only some of them. The estimated periods and amplitudes are identical for the genes located on the positive and negative DNA strands. While precise molecular mechanisms of chromosome-specific periodicities in gene expression have yet to be unraveled, their universal presence in different tissues adds another dimension to the current understanding of the genome organization.     

Relatedness structure in Rhododendron metternichii var. hondoense revealed by microsatellite analysis

The relatedness structure of Rhododendron metternichii Sieb. et Zucc. var. hondoense Nakai was analysed in a 150 x 70-m quadrat in Hiroshima Prefecture, western Japan. The population of R. metternichii occurred as three subpopulations at the study site (A1-A3). Pairwise relatedness based on microsatellite genotypes at eight loci and Mantel tests revealed a hierarchical structure of relatedness within and among subpopulations: (i) relatedness between individuals within 10 m of one another was significantly positive; (ii) relatedness between individuals in the same subpopulation was significantly positive, but negative between individuals in distant subpopulations; and (iii) relatedness was not significantly different from zero among neighbouring subpopulations. In detail, however, relatedness within each subpopulation was significantly positive in subpopulation A1, relatively weak but significantly positive in subpopulation A2, and not significantly different from zero in subpopulation A3. Relatedness within each subpopulation was inversely related to correlations between interindividual distance and relatedness. The aggregation of related individuals at short distances from one another may lead to decreasing relatedness within subpopulations as a whole. Moreover, negative correlations between interindividual distance and relatedness corresponded to high flowering densities at less than 10-m distance, implying that high flowering densities reduce pollinator foraging distance and lead to stronger genetic structure within subpopulations. Small individuals (< 2.0 m in height) showed stronger genetic structure compared with that of large individuals (> or = 2.0 m in height). The different relatedness structure within and among subpopulations may be caused by various degrees of gene flow affected by distribution patterns of individuals and population density.     

Demographic spatial genetic structure of the Neotropical tree, Jacaranda copaia

We used genotypes from six microsatellite loci and demographic data from a large mapped forest plot to study changes in spatial genetic structure across demographic stages, from seed rain to seedlings, juveniles, and adult diameter classes in the Neotropical tree, Jacaranda copaia. In pairwise comparisons of genetic differentiation among demographic classes, only seedlings were significantly differentiated from the other diameter classes; F(ST) values ranged from 0.006 to 0.009. Furthermore, only seedlings showed homozygote excess suggesting biparental inbreeding in the large diameter reproductive adults. We found very low levels of relatedness in the first distance class of trees, 1-26 cm diameter (F(ij) = 0.011). However, there was a 5- to 10-fold rise in relatedness in the smallest distance class, from the smallest to the largest tree diameter classes (F(ij) = 0.110 for individuals > 56 cm diameter). A variety of non-mutually exclusive mechanisms have been invoked perviously to explain such a pattern, including natural selection, history, or nonequilibrium population dynamics. The long-term demographic data available for this species allow us to evaluate these mechanisms. Jacaranda is a fast-growing, light-demanding species with low recruitment rates and high mortality rates in the smaller diameter classes. It successfully regenerates only in large light gaps, which occur infrequently and stochastically in space and time. These factors contribute to the nonequilibrium population dynamics and observed low genetic structure in the small size classes. We conclude that the pattern of spatial genetic transitions in Jacaranda is consistent with overlapping related generations and strong but infrequent periods of high recruitment, followed by long periods of population decline.     

Global population genetic structure and male-mediated gene flow in the green sea turtle (Chelonia mydas): analysis of microsatellite loci

We assessed the degree of population subdivision among global populations of green sea turtles, Chelonia mydas, using four microsatellite loci. Previously, a single-copy nuclear DNA study indicated significant male-mediated gene flow among populations alternately fixed for different mitochondrial DNA haplotypes and that genetic divergence between populations in the Atlantic and Pacific Oceans was more common than subdivisions among populations within ocean basins. Even so, overall levels of variation at single-copy loci were low and inferences were limited. Here, the markedly more variable microsatellite loci confirm the presence of male-mediated gene flow among populations within ocean basins. This analysis generally confirms the genetic divergence between the Atlantic and Pacific. As with the previous study, phylogenetic analyses of genetic distances based on the microsatellite loci indicate a close genetic relationship among eastern Atlantic and Indian Ocean populations. Unlike the single-copy study, however, the results here cannot be attributed to an artifact of general low variability and likely represent recent or ongoing migration between ocean basins. Sequence analyses of regions flanking the microsatellite repeat reveal considerable amounts of cryptic variation and homoplasy and significantly aid in our understanding of population connectivity. Assessment of the allele frequency distributions indicates that at least some of the loci may not be evolving by the stepwise mutation model.     

Reduced genetic structure of north Ethiopian cattle revealed by Y-chromosome analysis

Ethiopia is considered to be a putative migratory corridor for both Near-East Bos taurine and Arabian and Indian B. indicus cattle into East Africa. African pastoralism, which is associated with adaptation to specific habitats and farming systems, has contributed to the composite constitution of Ethiopian cattle. We analyse, for the first time, five Y-chromosome microsatellite markers from seven north Ethiopian cattle populations, using a European Holstein-Friesian population as a reference, to assess the paternal gene pool and to explore the mechanisms behind the genetic structure. Our results reveal that the indicine alleles predominate in the present populations, with only one animal in the Arado carrying the taurine alleles. The north Ethiopian cattle populations with one exception (Abergelle) are characterized by a general low Y-chromosome haplotype diversity, as well as by a reduced interpopulation variance (Phi(ST)=4.0%), which can be a result of strong male-mediated selective sweeps. Population structure revealed by multidimensional-scaling analysis differentiates two populations (Arado and Abergelle) from the rest. Analysis of molecular variance does not lend support to the traditional classification for the populations, which is mainly based on physical characteristics. A network analysis indicates two closely related founding haplotypes accounting for a large proportion (50.0% in Abergelle and 85.0-94.7% in others) of north Ethiopian cattle Y-chromosomes. Our findings point to a common, but limited, paternal origin of the north Ethiopian cattle populations and strong male-mediated gene flow among them. The findings also provide insight into the historical immigration of cattle into East Africa.     

Optimal sampling strategy for estimation of spatial genetic structure in tree populations

Fine-scale spatial genetic structure (SGS) in natural tree populations is largely a result of restricted pollen and seed dispersal. Understanding the link between limitations to dispersal in gene vectors and SGS is of key interest to biologists and the availability of highly variable molecular markers has facilitated fine-scale analysis of populations. However, estimation of SGS may depend strongly on the type of genetic marker and sampling strategy (of both loci and individuals). To explore sampling limits, we created a model population with simulated distributions of dominant and codominant alleles, resulting from natural regeneration with restricted gene flow. SGS estimates from subsamples (simulating collection and analysis with amplified fragment length polymorphism (AFLP) and microsatellite markers) were correlated with the 'real' estimate (from the full model population). For both marker types, sampling ranges were evident, with lower limits below which estimation was poorly correlated and upper limits above which sampling became inefficient. Lower limits (correlation of 0.9) were 100 individuals, 10 loci for microsatellites and 150 individuals, 100 loci for AFLPs. Upper limits were 200 individuals, five loci for microsatellites and 200 individuals, 100 loci for AFLPs. The limits indicated by simulation were compared with data sets from real species. Instances where sampling effort had been either insufficient or inefficient were identified. The model results should form practical boundaries for studies aiming to detect SGS. However, greater sample sizes will be required in cases where SGS is weaker than for our simulated population, for example, in species with effective pollen/seed dispersal mechanisms.     

Relationship between population genetic structure and riparian habitat as revealed by RAPD analysis of the rheophyte Acorus gramineus Soland. (Araceae) in Taiwan

Acorus gramineus Soland. (Araceae) is a rheophyte and is distributed in southeastern Asia. Its populations are restricted to riparian habitats. The discontinuous distribution might result in high genetic diversification among plants of different river systems. In the present study, leaf samples were collected from populations along six river systems in western Taiwan and the genetic variation was investigated by employing RAPD markers. A total of 255 samples from 17 sampling sites was studied. Eighty random 10-mer primers were screened and six of them, which showed better amplification results, were selected to analyse all of the samples. Data of 34 high-intensity and highly reproducible polymorphic fragments were used in statistical analyses. The results of AMOVA analyses indicated that, of the total variation, 46.84% was attributable to differences among river systems, 16.88% to differences among sampling sites within river systems, and 36.28% to differences among individuals within sampling sites. The results of cluster analysis and principal coordinate analysis revealed that sampling sites of each river system formed distinct clusters and the sampling sites of six river systems were clustered into three main groups according to latitudinal relationships. The results of the present study indicated that the population genetic structure of the plants of different river systems is highly diversified, which seems to imply that the gene flow among them is very limited.     

Genetic diversity and population structure of the medicinal orchid Gastrodia elata revealed by microsatellite analysis

The wild resources of Gastrodia elata are currently threatened with extinction due to over-harvesting because of their high medicinal value. Genetic diversity plays a key role in the survival of endangered orchid species. In this study we investigated the genetic pattern in eight microsatellite loci within eight G. elata populations from central China. Compared with the other orchids, G. elata showed a low level of genetic variation within populations (H_E = 0.356–0.622). The main factors responsible for the genetic pattern were the plant's inbreeding system due to mating within clone patches, and the genetic bottlenecks and genetic drift caused by a long-history over-collecting. The significant heterozygote deficit was detected in all the populations. The F statistics calculated by different approaches consistently revealed a clear genetic differentiation among populations, contributing about 20% of the total gene diversity. The results are discussed in relation to both in situ and ex situ conservation efforts of the species. The populations with a high level of genetic diversity or with great genetic distinction were identified, which should be a high priority for conservation managers.     

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。     

Movements of adult fish in a hybrid zone revealed by microsatellite genetic analysis and capture-recapture data

• 1 Barbus barbus and Barbus meridionalis (Cyprinidae) form a hybrid zone in the Lergue river (southern France). We attempted to characterise the pattern of adult dispersal with the aim of understanding the evolutionary interactions maintaining this hybrid zone. In a previous capture/recapture study, movements between localities at a distance of 2.5 km or more appeared extremely rare. We therefore decided to investigate adult movement using a different method, based on genetic markers.
• 2 As this hybrid zone has produced allele frequency clines, massive population movements would produce temporal variations in genetic composition at a given locality. In order to determine the relationship between gene frequency and position, we surveyed four diagnostic or semidiagnostic microsatellite loci over the hybrid zone and estimated the cline produced by introgression. Then, we focused on a single locality at the centre of the hybrid zone and established its introgression index over 11 periods during two years.
• 3 The introgression index varied between periods producing significant Fst. A synthetic hybrid index, based on principal component analysis of the logit frequencies, was used for regression analyses and appeared significantly correlated with the river flow. This may be explained by displacement of adult fishes in response to flow increase. Using the information from the cline, we estimate that the most important gene frequency changes among dates, if created exclusively by population movement, correspond to a distance of 1500 m.
• 4 Additionally, we performed recaptures on a finer geographic scale than previously, around the central locality. No recaptured fishes were observed at 1875 m or more downstream, and at 875 m or more upstream, from the central locality. A high proportion of recaptured fishes (20% and 12%) was found in the nearest points (312 m downstream and 437 m upstream, respectively).
• 5 Thus, we established that (i) individual movements appear limited to a few hundred metres and (ii) individuals in a location tend to move in the same direction at the same time, probably in response to the same environmental factor.

     

Coexistence of three canopy tree species in a riparian forest in the Chichibu Mountains, central Japan

Three canopy tree species (Fraxinus platypoda, Pterocarya rhoifolia, andCercidiphyllum japonicum) coexist in riparian forests in the Chichibu Mountains of central Japan. We compared the forest structure and the reproductive characteristics of these species.F. platypoda was the dominant canopy species. It produced many saplings and grew in abandoned channels and floodplains, and was able to invade both large and small disturbance sites.P. rhoifolia was a subdominant species that occurred on the deposits of large-scale landslides and grew in patches containing even-aged trees.C. japonicum was the other subdominant species that produced few saplings and invaded large disturbance sites together withP. rhoifolia. Establishment sites ofC. japonicum were restricted to fine mineral soils and fallen logs. We found tradeoffs in reproductive characteristics (seed size, seed number, irregular seed production, and sprouting) among the three canopy species.F. platypoda andP. rhoifolia had large seeds and produced fruits irregularly.C. japonicum produced many small seeds every year and sprouted prolifically around the main stem. The causes of the coexistence mechanism of the three riparian canopy tree species may be both niche- and chance-determined to varying degrees. In riparian areas, the three canopy species were well-adapted to disturbances throughout their life-history.