Measurement of Diversity and Dissimilarity for Stochastic Populations

The existing measures of diversity within a population and of dissimilarity between two populations postulate a static population with unchanging probabilistic structure. We assume that the measurements associated with an individual change with time according to a stochastic process. General measures of diversity and of dissimilarity when the underlying process is a finite Markov chain are developed. An aportionment of these measures based on a partition of the state-space is provided. Their asymptotic behaviour is investigated. The spectral analysis of measures of diversity is carried out. Some specific measures of diversity and dissimilarity are obtained when the underlying stochastic process is a general vector-valued process. An indication of directions for future work is provided.     

Conceptual analysis of methods applied to assessment of diversity within and distance between populations with asexual or mixed mode of reproduction

Measures of diversity within populations, and distance between populations, are compared for organisms with an asexual or mixed mode of reproduction. Examples are drawn from studies of plant pathogenic fungi based on binary traits including presence/absence of DNA bands or virulence/avirulence to differential hosts. Commonly used measures of population diversity or genetic distance consider either genotype frequencies or allele frequencies. Kosman's diversity and distance measures are the most suitable for populations with an asexual or mixed mode of reproduction, because by considering genetic patterns of all individuals they take into account not just the genotype frequencies but also the genetic similarities between genotypes in the populations. The Kosman distance and diversity measures for populations can be calculated using different measures of dissimilarity between individuals (the simple mismatch, Jaccard and Dice coefficients of dissimilarity). Kosman's distances based on the simple mismatch and Jaccard dissimilarities are metrics. Comparisons of diversity indices for hypothetical examples as well as for actual data sets are presented to demonstrate that inferences from diversity analysis of populations can be driven by techniques of diversity and distance assessments and not only data driven.     

Dispersal ecology of the endangered woodland lichen Lobaria pulmonaria in managed hemiboreal forest landscape

Changes in the forest management practices have strongly influenced the distribution of species inhabiting old-growth forests. The epiphytic woodland lichen Lobaria pulmonaria is frequently used as a model species to study the factors affecting the population biology of lichens. We sampled 252 L. pulmonaria individuals from 12 populations representing three woodland types differing in their ecological continuity and management intensity in Estonia. We used eight mycobiont-specific microsatellite loci to quantify genetic diversity among the populations. We calculated the Sørensen distance to estimate genetic dissimilarity among individuals within populations. We revealed that L. pulmonaria populations have significantly higher genetic diversity in old-growth forests than in managed forests and wooded meadows. We detected a significant woodland-type-specific pattern of genetic dissimilarity among neighbouring L. pulmonaria individuals, which suggests that in wooded meadows and managed forests dominating is vegetative reproduction. The vegetative dispersal distance between the host trees of L. pulmonaria was found to be only 15–30 m. Genetic dissimilarity among individuals was also dependent on tree species and trunk diameter. Lobaria pulmonaria populations in managed forests included less juveniles compared to old-growth forests and wooded meadows, indicating that forest management influences life stage structure within populations. We conclude that as intensive stand management reduces the genetic diversity of threatened species in woodland habitats, particular attention should be paid to the preservation of remnant populations in old-growth habitats. Within managed habitats, conservation management should target on maintenance of the stand’s structural diversity and availability of potential host trees.     

Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species

Determining true genetic dissimilarity between individuals is an important and decisive point for clustering and analysing diversity within and among populations, because different dissimilarity indices may yield conflicting outcomes. We show that there are no acceptable universal approaches to assessing the dissimilarity between individuals with molecular markers. Different measures are relevant to dominant and codominant DNA markers depending on the ploidy of organisms. The Dice coefficient is the suitable measure for haploids with codominant markers and it can be applied directly to (0,1)-vectors representing banding profiles of individuals. None of the common measures, Dice, Jaccard, simple mismatch coefficient (or the squared Euclidean distance), is appropriate for diploids with codominant markers. By transforming multiallelic banding patterns at each locus into the corresponding homozygous or heterozygous states, a new measure of dissimilarity within locus was developed and expanded to assess dissimilarity between multilocus states of two individuals by averaging across all codominant loci tested. There is no rigorous well-founded solution in the case of dominant markers. The simple mismatch coefficient is the most suitable measure of dissimilarity between banding patterns of closely related haploid forms. For distantly related haploid individuals, the Jaccard dissimilarity is recommended. In general, no suitable method for measuring genetic dissimilarity between diploids with dominant markers can be proposed. Banding patterns of diploids with dominant markers and polyploids with codominant markers represent individuals' phenotypes rather than genotypes. All dissimilarity measures proposed and developed herein are metrics.     

Relationship between genetic, chemical, and bacterial diversity in the Atlanto-Mediterranean bath sponge Spongia lamella

Does diversity beget diversity? Diversity includes a diversity of concepts because it is linked to variability in and of life and can be applied to multiple levels. The connections between multiple levels of diversity are poorly understood. Here, we investigated the relationships between genetic, bacterial, and chemical diversity of the endangered Atlanto-Mediterranean sponge Spongia lamella. These levels of diversity are intrinsically related to sponge evolution and could have strong conservation implications. We used microsatellite markers, denaturing gel gradient electrophoresis and quantitative polymerase chain reaction, and high performance liquid chromatography to quantify genetic, bacterial, and chemical diversity of nine sponge populations. We then used correlations to test whether these diversity levels covaried. We found that sponge populations differed significantly in genetic, bacterial, and chemical diversity. We also found a strong geographic pattern of increasing genetic, bacterial, and chemical dissimilarity with increasing geographic distance between populations. However, we failed to detect significant correlations between the three levels of diversity investigated in our study. Our results suggest that diversity fails to beget diversity within a single species and indicates that a diversity of factors regulates a diversity of diversities, which highlights the complex nature of the mechanisms behind diversity.     

CLUSTERING POPULATIONS BY MIXED LINEAR MODELS

INTRODUCTIONInevolutionstudiesandplant(oranimal)breedingresearch,clusteranalysesarewidelyusedforgroupingpopulations.Therehavebeenalotofmethodsdevelopedforgroupingpopulations(SneathandSokal,1973;Eve-ritt,1993).Variousmethodsaredifferedinthewaysfordistance(…     

Positive correlation between vegetation dissimilarity and genetic differentiation of Carex sempervirens

Synthesizing genetic data at population level and vegetation data at community level may give insight into how ecological and evolutionary processes associated with different vegetation influence genetic diversity and differentiation of plant populations. We correlated population genetic patterns of Carex sempervirens with community vegetation patterns in abandoned subalpine grassland in the Swiss Alps. Within-population genetic diversity (percentage of polymorphic bands and Nei's gene diversity) of C. sempervirens was not significantly correlated with plant richness, evenness or Shannon's diversity index (Pearson correlation coefficient |r|<0.32, P>0.10). However, the genetic distance (F_ST) between C. sempervirens populations was significantly positively correlated with the vegetation dissimilarity between communities (Mantel's r=0.23, P<0.01). The correlation between the population genetic differentiation and the vegetation dissimilarity was not due to the parallel effects of geographic isolation or site conditions, because F_ST was not correlated with the geographic distance or the pairwise differences in any of the measured site condition parameters. One likely mechanism is that different plant communities were associated with different selective forces, which, in turn, influenced the genetic differentiation between C. sempervirens populations. Another possibility is that the vegetation heterogeneity (dissimilarity) generated ecological barriers against gene flow and thus enhanced the genetic differentiation between C. sempervirens populations.     

Bolete diversity in two relict forests of the Mexican beech (Fagus grandifolia var. mexicana; Fagaceae)

The current distribution of the endangered Mexican beech [Fagus grandifolia var. mexicana (Martinez) Little] is restricted to relict isolated populations in small remnants of montane cloud forest in northeastern Mexico, and little is known about its associated biota. We sampled bolete diversity in two of these monospecific forests in the state of Hidalgo, Mexico. We compared alpha diversity, including species richness and ensemble structure, and analyzed beta diversity (dissimilarity in species composition) between forests. We found 26 bolete species, five of which are probably new. Species diversity and evenness were similar between forests. Beta diversity was low, and the similarities of bolete samples from within and between forests were not significantly different. These results support the idea that the two forests share a single bolete ensemble with a common history. In contrast, cumulative species richness differed between the forests, implying that factors other than the mere presence of the host species have contributed to shaping the biodiversity of ectomycorrhizal fungi in relict Mexican beech forests.     

Environmental correlates of anuran beta diversity in the Brazilian Cerrado

Evolutionary processes are known to influence contemporary patterns of biological diversity, yet disentangling the effects of current and historical drivers of biodiversity patterns remain challenging. We use spatial analyses of community dissimilarity to generate hypotheses about the current and historical processes underlying patterns of beta diversity in anuran species in the Brazilian Cerrado. Specifically, we use a generalized dissimilarity modeling (GDM) approach to model compositional dissimilarity of anuran species and endemics as a function of geographic separation and local (within‐Cerrado) environmental conditions. To gain insight about potential historical processes, we incorporate information from biomes adjacent to the Cerrado to investigate whether environmental conditions in neighboring areas can help explain patterns of beta diversity within the Cerrado. Patterns of anuran beta diversity of both endemics and all species in the Cerrado appear to be strongly influenced by local environmental gradients, with elevation as one of the most important variables in all models. However, in models using endemic species only, environmental conditions of adjacent biomes were related to beta‐diversity patterns, and more strongly so, than to total species models. These results suggest that phylogenetic niche conservatism within species groups that invaded the Cerrado from adjacent biomes may cause these species to be restricted to environmental conditions within the Cerrado that are most similar to the conditions in the adjacent biome where they originated. Time‐calibrated phylogenies of Cerrado endemics and studies of ancestral and current ranges of Cerrado species are needed to test this hypothesis.     

Spatial and temporal homogenisation of freshwater macrofaunal communities in ditches

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Patterns of chemical diversity in the Mediterranean sponge Spongia lamella

The intra-specific diversity in secondary metabolites can provide crucial information for understanding species ecology and evolution but has received limited attention in marine chemical ecology. The complex nature of diversity is partially responsible for the lack of studies, which often target a narrow number of major compounds. Here, we investigated the intra-specific chemical diversity of the Mediterranean sponge Spongia lamella. The chemical profiles of seven populations spreading over 1200 km in the Western Mediterranean were obtained by a straightforward SPE-HPLC-DAD-ELSD process whereas the identity of compounds was assessed by comparison between HPLC-MS spectra and literature data. Chemical diversity calculated by richness and Shannon indexes differed significantly between sponge populations but not at a larger regional scale. We used factor analysis, analysis of variance, and regression analysis to examine the chemical variability of this sponge at local and regional scales, to establish general patterns of variation in chemical diversity. The abundance of some metabolites varied significantly between sponge populations. Despite these significant differences between populations, we found a clear pattern of increasing chemical dissimilarity with increasing geographic distance. Additional large spatial scale studies on the chemical diversity of marine organisms will validate the universality or exclusivity of this pattern.     

Genetic variation in Costa Rican populations of the tropical timber species Cedrela odorata L., assessed using RAPDs

Cedrela odorata L. (Spanish cedar), an economically important timber species native to the American tropics, is the focus of increasing conservation concern due to high rates of deforestation within its native range. To assess the extent of the genetic diversity within and between populations of this species, samples were obtained from 10 widely dispersed populations within Costa Rica and analysed for random amplified polymorphic DNA (RAPD) variation. Fourteen 10-mer primers were used to generate 97 polymorphic RAPD bands. Presence/absence data for all bands were subjected to a pairwise genetic distance analysis, according to Jaccard's coefficient, then neighbour-joining cluster analysis was performed on these distances, as was an analysis of molecular variance ( AMOVA ), to assess levels of differentiation between populations and regions, and Shannon's Diversity Index was used to quantify levels of diversity within and between populations. Results indicated highly significant genetic differentiation ( P < 0.004, AMOVA ) between populations originating from the North Pacific and Atlantic/South Pacific regions of Costa Rica, with 35.3% of the total variation attributable to a difference between these areas. Little differentiation was recorded between populations from within the same region ( P = 0.757, AMOVA ), and 65.1% of the total variance was attributable to variation within populations. Estimated values for within-population diversity, calculated as H _pop/ H _sp by means of Shannon's Diversity Index, were found to vary greatly between primers, but the overall within-population component of genetic diversity was 0.45. Possible reasons for the high degree of intraspecific genetic variation within this species are discussed and the implications of these results for the conservation and use of its genetic resources are described.     

Genetic diversity of a dominant C4 grass is altered with increased precipitation variability

Climate change has the potential to alter the genetic diversity of plant populations with consequences for community dynamics and ecosystem processes. Recent research focused on changes in climatic means has found evidence of decreased precipitation amounts reducing genetic diversity. However, increased variability in climatic regimes is also predicted with climate change, but the effects of this aspect of climate change on genetic diversity have yet to be investigated. After 10 years of experimentally increased intra-annual variability in growing season precipitation regimes, we report that the number of genotypes of the dominant C₄ grass, Andropogon gerardii Vitman, has been significantly reduced in native tallgrass prairie compared with unmanipulated prairie. However, individuals showed a different pattern of genomic similarity with increased precipitation variability resulting in greater genome dissimilarity among individuals when compared to unmanipulated prairie. Further, we found that genomic dissimilarity was positively correlated with aboveground productivity in this system. The increased genomic dissimilarity among individuals in the altered treatment alongside evidence for a positive correlation of genomic dissimilarity with phenotypic variation suggests ecological sorting of genotypes may be occurring via niche differentiation. Overall, we found effects of more variable precipitation regimes on population-level genetic diversity were complex, emphasizing the need to look beyond genotype numbers for understanding the impacts of climate change on genetic diversity. Recognition that future climate change may alter aspects of genetic diversity in different ways suggests possible mechanisms by which plant populations may be able to retain a diversity of traits in the face of declining biodiversity.     

Global patterns of terrestrial assemblage turnover within and among land uses

Land use has large effects on the diversity of ecological assemblages. Differences among land uses in the diversity of local assemblages (alpha diversity) have been quantified at a global scale. Effects on the turnover of species composition between locations (beta diversity) are less clear, with previous studies focusing on particular regions or groups of species. Using a global database on the composition of ecological assemblages in different land uses, we test for differences in the between‐site turnover of species composition, within and among land‐use types. Overall, we show a strong impact of land use on assemblage composition. While we find that compositional turnover within land uses does not differ strongly among land uses, human land uses and secondary vegetation in an early stage of recovery are poor at retaining the species that characterise primary vegetation. The dissimilarity of assemblages in human‐impacted habitats compared with primary vegetation was more pronounced in the tropical than temperate realm. An exploratory analysis suggests that this geographic difference might be caused primarily by differences in climate seasonality and in the numbers of species sampled. Taken together the results suggest that, while small‐scale beta diversity within land uses is not strongly impacted by land‐use type, compositional turnover between land uses is substantial. Therefore, land‐use change will lead to profound changes in the structure of ecological assemblages.     

Genotypic richness and dissimilarity opposingly affect ecosystem functioning

Biodiversity is an essential determinant of ecosystem functioning. Numerous studies described positive effects of diversity on the functioning of communities arising from complementary resource use and facilitation. However, high biodiversity may also increase competitive interactions, fostering antagonism and negatively affecting community performance. Using experimental bacterial communities we differentiated diversity effects based on genotypic richness and dissimilarity. We show that these diversity characteristics have opposite effects on ecosystem functioning. Genotypic dissimilarity governed complementary resource use, improving ecosystem functioning in complex resource environments. Contrastingly, genotypic richness drove allelopathic interactions, mostly reducing ecosystem functioning. The net biodiversity effect on community performance resulted from the interplay between the genetic structure of the community and resource complexity. These results demonstrate that increasing richness, without concomitantly increasing dissimilarity, can decrease ecosystem functioning in simple environments due to antagonistic interactions, an effect insufficiently considered so far in mechanistic models of the biodiversity-ecosystem functioning relationship.     

Multiple site dissimilarity quantifies compositional heterogeneity among several sites,while average pairwise dissimilarity may be misleading

Several measures of multiple site dissimilarity have been proposed to quantify the overall heterogeneity in assemblage composition among any number of sites. It is also a common practice to quantify such overall heterogeneity by averaging pairwise dissimilarities between all pairs of sites in the pool. However, pairwise dissimilarities do not account for patterns of co‐occurrence among more than two sites. In consequence, the average of pairwise dissimilarities may not accurately reflect the overall compositional heterogeneity within a pool of more than two sites. Here I use several idealized examples to illustrate why pairwise dissimilarity measures fail to properly quantify overall heterogeneity. Thereafter, the effect of this potential problem in empirical patterns is exemplified with data of world amphibians. In conclusion, when the attribute of interest is the overall heterogeneity in a pool of sites (i.e. beta diversity) or its turnover or nestedness components, only multiple site dissimilarity measures are recommended.     

青藏高原特有属——固沙草属表型变异及其对环境因子的响应

该研究通过测量固沙草属(Orinus)3个物种(青海固沙草、固沙草和居间固沙草)的40个天然居群145个个体的22个表型性状,依据VIF膨胀系数筛选得到年平均降雨(MAP)等9个气候因子和海拔等因子,并采用冗余分析(db-RDA)考察不同物种、不同居群植物表型多样性与多元地理气候环境的关系,探讨该属植物表型多样性驱动机理。结果显示:(1)基于22个植物表型性状,固沙草属天然居群在组内最小方差(Ward)55时可归为2类,居群间表型性状不存在显著的空间自相关性(P 0.05),植物表型多样性高(Shannon-Wiener index,H:1.045～2.734),17个定量的表型性状变异系数(CV)平均值47.84%,而居群间小穗颜色多样性最低(H:0.170),证明固沙草属植物表型性状具有独特的环境响应模式。(2)巢式方差分析显示,固沙草属植物表型在居群间和居群内均存在丰富的变异(F 10,P0.01),旗叶、颖片和外稃分别是主成分分析中表型总变异的重要组成部分,表型分化系数居群间变异(71.10%)大于居群内(28.90%),固沙草属植物表型变异来源于居群间。(3)冗余分析结果表明,海拔(ALT)和年平均风速(Wind)是决定青海固沙草(O.kokonoricus)和固沙草(O.thoroldii)居群间表型差异性的主要影响因子;极端气候条件[最冷季平均温度(Bio9)和最干季降雨量(Bio14)]对固沙草居群间表型相似性起促进作用,相反干燥度指数(AI)与水气压(Vapr)对其差异性起促进作用;居间固沙草(O.intermedius)居群间表型差异受年均降雨(MAP)、潜在蒸散(PET)和水气压(Vapr)影响。研究认为,固沙草属植物天然居群之间表型变异反映出明显的地理气候变化趋势,这些表型变异是高山植物环境适应性的重要标志。     

A quantitative review of MHC‐based mating preference: the role of diversity and dissimilarity

Sexual selection hypotheses stipulate that the major histocompatibility complex genes (MHC) constitute a key molecular underpinning for mate choice in vertebrates. The last four decades saw growing empirical literature on the role of MHC diversity and dissimilarity in mate choice for a wide range of vertebrate animals, but with mixed support for its significance in natural populations. Using formal phylogenetic meta‐analysis and meta‐regression techniques, we quantitatively review the existing literature on MHC‐dependent mating preferences in nonhuman vertebrates with a focus on the role of MHC diversity and dissimilarity. Overall, we found small, statistically nonsignificant, average effect sizes for both diversity‐ and dissimilarity‐based mate choice (r = 0.113 and 0.064, respectively). Importantly, however, meta‐regression models revealed statistically significant support regarding female choice for diversity, and choice for dissimilarity (regardless of choosy sex) only when dissimilarity is characterized across multiple loci. Little difference was found among vertebrate taxa; however, the lack of statistical power meant statistically significant effects were limited to some taxa. We found little sign of publication bias; thus, our results are likely to be robust. In light of our quantitative assessment, methodological improvements and fruitful future avenues of research are highlighted.     

Life in the desert: The impact of geographic and environmental gradients on genetic diversity and population structure of Ivesia webberi

For range‐restricted species with disjunct populations, it is critical to characterize population genetic structure, gene flow, and factors that influence functional connectivity among populations in order to design effective conservation programs. In this study, we genotyped 314 individuals from 16 extant populations of Ivesia webberi, a United States federally threatened Great Basin Desert using six microsatellite loci. We assessed the effects of Euclidean distance, landscape features, and ecological dissimilarity on the pairwise genetic distance of the sampled populations, while also testing for a potential relationship between I. webberi genetic diversity and diversity in the vegetative communities. The results show low levels of genetic diversity overall (H _e = 0.200–0.441; H _o = 0.192–0.605) and high genetic differentiation among populations. Genetic diversity was structured along a geographic gradient, congruent with patterns of isolation by distance. Populations near the species’ range core have relatively high genetic diversity, supporting in part a central‐marginal pattern, while also showing some evidence for a metapopulation dynamic. Peripheral populations have lower genetic diversity, significantly higher genetic distances, and higher relatedness. Genotype cluster admixture results suggest a complex dispersal pattern among populations with dispersal direction and distance varying on the landscape. Pairwise genetic distance strongly correlates with elevation, actual evapotranspiration, and summer seasonal precipitation, indicating a role for isolation by environment, which the observed phenological mismatches among the populations also support. The significant correlation between pairwise genetic distance and floristic dissimilarity in the germinated soil seed bank suggests that annual regeneration in the plant communities contribute to the maintenance of genetic diversity in I. webberi.     

Population genetical investigations on Indian tribals. Preliminary report

Data on the distribution of genetic markers in Indian tribal populations as well as in Southwest and Southeast Asiatic populations have been recorded in order to study comparatively the extent of genetic similarity and dissimilarity, respectively, 1. within the various regional tribal groups, and 2. among tribals and the populations from Southwest and Southeast Asia. The--preliminary--results of these comparisons are discussed considering the racial history of the Indian subcontinent.