Reconstructing community relationships: the impact of sampling error, ordination approach, and gradient length

Effectively summarizing complex community relationships is an important feature in studies such as biodiversity, global change, and invasion ecology. The reliability of such community summaries depends on the degree of sampling variability that is present in the data, the structure of the data, and the choice of ordination method, but the relative importance of these factors is not understood. We compared the validity of results from different ordination methods by applying five levels of sampling error to a simulated coenoplane model at two gradient lengths using two types of data (abundance and presence–absence). The multivariate methods we compared were correspondence analysis (CA), detrended correspondence analysis (DCA), non-metric multidimensional scaling (NMDS), principal component analysis (PCA) and principal coordinates analysis (PCoA). Our results showed CA and PCA using presence–absence data were the most successful methods regardless of sampling error and gradient length, closely followed by the other methods using presence–absence data. With abundance data, PCA and CA were the most successful approaches with the short and long gradients, respectively. Approaches based on PCoA and NMDS using abundance data did not perform well regardless of the choice of distance measure used in the analysis. Both of these methods, along with the PCA using abundance data, were strongly affected by the longer gradient, leading to more distorted results.     

Food habits of the longnose skate, <Emphasis Type="Italic">Raja rhina</Emphasis> (Jordan and Gilbert, 1880), in central California waters

Feeding studies can provide researchers with important insights towards understanding potential fishery impacts on marine systems. Raja rhina is one of the most common elasmobranch species landed in central and northern California demersal fisheries, yet life history information is extremely limited for this species and aspects of its diet are unknown. Specimens of R. rhina were collected between September, 2002 and August, 2003 from fisheries-independent trawl surveys. Percent Index of Relative Importance values indicated that the five most important prey items in 618 stomachs of R. rhina were unidentified teleosts (31.6% IRI), unidentified shrimps (19.6% IRI), unidentified euphausiids (10.9% IRI), Crangonidae (7.4% IRI), and Neocrangon resima (6.0% IRI). There were significant dietary shifts with increasing skate total length and with increasing depths. Smaller skates ate small crustaceans and larger skates ate larger fishes and cephalopods. With increasing depths, diet included bentho-pelagic teleosts and more cephalopods and euphausiids. The findings of this study are consistent with previous researchers that report similar diet shifts in skate species with size and depth.     

Microsatellite null alleles and estimation of population differentiation

Microsatellite null alleles are commonly encountered in population genetics studies, yet little is known about their impact on the estimation of population differentiation. Computer simulations based on the coalescent were used to investigate the evolutionary dynamics of null alleles, their impact on F(ST) and genetic distances, and the efficiency of estimators of null allele frequency. Further, we explored how the existing method for correcting genotype data for null alleles performed in estimating F(ST) and genetic distances, and we compared this method with a new method proposed here (for F(ST) only). Null alleles were likely to be encountered in populations with a large effective size, with an unusually high mutation rate in the flanking regions, and that have diverged from the population from which the cloned allele state was drawn and the primers designed. When populations were significantly differentiated, F(ST) and genetic distances were overestimated in the presence of null alleles. Frequency of null alleles was estimated precisely with the algorithm presented in Dempster et al. (1977). The conventional method for correcting genotype data for null alleles did not provide an accurate estimate of F(ST) and genetic distances. However, the use of the genetic distance of Cavalli-Sforza and Edwards (1967) corrected by the conventional method gave better estimates than those obtained without correction. F(ST) estimation from corrected genotype frequencies performed well when restricted to visible allele sizes. Both the proposed method and the traditional correction method have been implemented in a program that is available free of charge at http://www.montpellier.inra.fr/URLB/. We used 2 published microsatellite data sets based on original and redesigned pairs of primers to empirically confirm our simulation results.     

Phenology of Zamia boliviana (Zamiaceae), a threatened species from a seasonally dry biodiversity hotspot in South America

Dioecy, a character common to all cycads, requires obligatory outcrossing. The absence of potential reproductive mates of the opposite sex renders individuals effectively sterile. Therefore, reproductive synchrony is essential for the reproductive success of cycads. Here, we describe the reproductive phenology, morphology, and lifespan of strobili of Zamia boliviana (Cycadales, Zamiaceae), an endemic cycad in South America. We examined the variation in timing of maturation between polliniferous and ovuliferous individuals in two Z. boliviana populations. Lifespan of polliniferous and ovuliferous strobili was based on direct observations and systematic measurements of strobili development. Phenological study covered three reproductive cohorts in two distinct cycad populations. Lifespan of polliniferous strobili was comprised of four phases and lasted 50 days until the cycle's completion, while ovuliferous strobili underwent seven phases that extended over 330 days until seed dehiscence. Both sexes produced strobili during the dry season. We identified a seasonally synchronous pattern in the reproductive phenology of Z. boliviana, with a major overlap in the phases of emergence, pollen release, and strobili receptivity between sexes, populations, and subsequent years. Reproductive events of Z. boliviana followed the seasonality of the Cerrado vegetation and climate. Synchrony between the period of strobili production and reproductive activity peaks was found in both sexes, but seed dehiscence occurred in the dry season. Our study provides relevant and new biological data for Z. boliviana in its natural habitat, demonstrating a temporal distinction between the lifespan of polliniferous and ovuliferous strobili and the necessary overlap between the release and receptivity of pollen.     

祁连山青海云杉林群落结构的空间异质性

以动态监测样地(340 m×300 m)的网格(5 m×5 m)为基本单元,选择5个群落结构属性变量,采用分形几何学和地统计学方法对祁连山大野口流域青海云杉林群落结构的空间异质性进行研究.结果表明: 青海云杉林5个结构属性的变异程度大小依次为:密度＞平均冠幅＞显著度＞盖度＞平均树高,变异系数为43.7%～79.6%.Moran I系数表明,各个结构属性均有不同程度的空间自相关性,自相关大小顺序为:密度＞平均树高＞盖度＞平均冠幅＞显著度,变化范围为-0.047～0.382.指数理论变异函数模型能很好地拟合不同结构属性的空间变异,变程为24.6～68.1 m,各属性变量的结构比除盖度表现为中等空间相关,其他指标均为强烈空间相关,各属性指标分维数接近2,空间依赖性较小.植被密度和盖度空间分布呈带状结构和斑块结构叠加的特点,其他指标呈较强的斑块状空间结构,密度和盖度对平均冠幅、显著度和平均树高有一定的空间依赖性.青海云杉林群落结构空间异质性适宜的采样间隔和采样面积分别为10 m和0.5 hm².     

Measuring population differentiation using GST or D? A simulation study with microsatellite DNA markers under a finite island model and nonequilibrium conditions

The genetic differentiation of populations is a key parameter in population genetic investigations. Wright's F(ST) (and its relatives such as G(ST) ) has been a standard measure of differentiation. However, the deficiencies of these indexes have been increasingly realized in recent years, leading to some new measures being proposed, such as Jost's D (Molecular Ecology, 2008; 17, 4015). The existence of these new metrics has stimulated considerable debate and induced some confusion on which statistics should be used for estimating population differentiation. Here, we report a simulation study with neutral microsatellite DNA loci under a finite island model to compare the performance of G(ST) and D, particularly under nonequilibrium conditions. Our results suggest that there exist fundamental differences between the two statistics, and neither G(ST) nor D operates satisfactorily in all situations for quantifying differentiation. D is very sensitive to mutation models but G(ST) noticeably less so, which limits D's utility in population parameter estimation and comparisons across genetic markers. Also, the initial heterozygosity of the starting populations has some important effects on both the individual behaviours of G(ST) and D and their relative behaviours in early differentiation, and this effect is much greater for D than G(ST) . In the early stages of differentiation, when initial heterozygosity is relatively low (<0.5, if the number of subpopulations is large), G(ST) increases faster than D; the opposite is true when initial heterozygosity is high. Therefore, the state of the ancestral population appears to have some lasting impacts on population differentiation. In general, G(ST) can measure differentiation fairly well when heterozygosity is low whatever the causes; however, when heterozygosity is high (e.g. as a result of either high mutation rate or high initial heterozygosity) and gene flow is moderate to strong, G(ST) fails to measure differentiation. Interestingly, when population size is not very small (e.g. N ≥ 1000), G(ST) measures differentiation quite linearly with time over a long duration when gene flow is absent or very weak even if mutation rate is not low (e.g. μ = 0.001). In contrast, D, as a differentiation measure, performs rather robustly in all these situations. In practice, both indexes should be calculated and the relative levels of heterozygosities (especially H(S) ) and gene flow taken into account. We suggest that a comparison of the two indexes can generate useful insights into the evolutionary processes that influence population differentiation.     

Junker: An Intergenic Explorer for Bacterial Genomes

In the past few decades, scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs, small open reading frames, pseudogenes, transposons, integrase binding attB/attP sites, repeat elements within the bacterial intergenic regions (IGRs) and in the analysis of those junk regions for ge- nomic complexity. Here we have developed a web server, named Junker, to facilitate the in-depth analysis of IGRs for examining their length distribution, four-quadrant...