Connections between species diversity and genetic diversity

Species diversity and genetic diversity remain the nearly exclusive domains of community ecology and population genetics, respectively, despite repeated recognition in the literature over the past 30 years of close parallels between these two levels of diversity. Species diversity within communities and genetic diversity within populations are hypothesized to co‐vary in space or time because of locality characteristics that influence the two levels of diversity via parallel processes, or because of direct effects of one level of diversity on the other via several different mechanisms. Here, we draw on a wide range of studies in ecology and evolution to examine the theoretical underpinnings of these hypotheses, review relevant empirical literature, and outline an agenda for future research. The plausibility of species diversity–genetic diversity relationships is supported by a variety of theoretical and empirical studies, and several recent studies provide direct, though preliminary support. Focusing on potential connections between species diversity and genetic diversity complements other approaches to synthesis at the ecology–evolution interface, and should contribute to conceptual unification of biodiversity research at the levels of genes and species.     

Relational diversity

In biology, the measurement of diversity traditionally focusses on reporting number of unambiguously distinguishable types, thus referring to qualitative (discontinuously varying) traits. Inclusion of frequencies or other weights has produced a large variety of diversity indices. Quantitative (continuously varying) traits do not readily fit into this perspective. In fact, in the context of quantitative traits, the concept of diversity is not always clearly distinguished from the (statistical) notion of dispersion. In many cases the ambiguity even extends to qualitative traits. This is at variance with the broad spectrum of diversity issues ranging, e.g., from ecological and genetic aspects of diversity to functional, structural, systematic, or evolutionary (including phylogenetic) aspects. In view of the urgent need for a more consistent perspective, it is called to attention that all of these aspects, whether of qualitative or quantitative nature, can be gathered under the common roof of binary relations (for qualitative traits two objects are related, for example, if they share the same trait state). A comprehensive concept of (relational) diversity can be developed in two steps: (1) determine the number of unrelated pairs of objects among all admissible pairs as a measure of implicit (relative) diversity, (2) invoke the concept of effective number to transform the implicit measure of diversity into an explicit (absolute) measure. The transformation operates by equating the observed implicit diversity to the implicit diversity obtained for the ideal model of an equivalence relation with classes of equal size. The number of these classes specifies the effective number as an explicit measure of diversity. The wealth of problems that can be treated from this unified perspective is briefly addressed by classifying and interpreting established diversity indices in the light of relational diversity. Desirable applications to the above-mentioned aspects are specified with the help of types of relations such as order, hierarchical, and tree relations. Corresponding biological issues including taxonomic community diversity, mating system, food web, sociological, cladistic and phylogenetic, or hypercycle diversity are suggested for future consideration.     

On hierarchical diversity decomposition

Abstract. Question: According to Whittaker's proposal, ecologists have traditionally viewed β‐diversity as the ratio between γ‐diversity and average α‐diversity. More recently, an alternative way of partitioning diversity has been ‘rediscovered’for which β‐diversity is obtained as the difference between γ‐diversity and average α‐diversity. This additive way of partitioning diversity has rapidly become a very popular framework for hierarchical diversity decomposition at various spatial scales. The question for this study is: Can we highlight any relation between these two ways of partitioning diversity, or do these methods really capture different facets of spatial turnover in species composition? Methods: First the properties that a diversity measure should possess for enabling additive decomposition into α‐, β‐, and γ‐components are reviewed. Next, attention is drawn to the relationships between additive and multiplicative diversity decomposition. Results: It is shown that the additive model is closely related to its multiplicative counterpart through a simple logarithmic transformation. Conclusions: Contrary to the current assumption, both methods for partitioning diversity are not as different as they appear. Hence, the supposed superiority of additive diversity partition over multiplicative diversity decomposition is largely unjustified.     

Plant genotypic diversity does not beget root-fungal species diversity

The number of genetically distinct individuals within a community is a key component of biodiversity and yet its impact at different trophic levels, especially upon the diversity of functionally important soil microorganisms is poorly understood. Here, we test the hypothesis that plant communities that are genetically impoverished will support fewer species of root-associated fungi. We used established grassland mesocosms comprising non-sterile natural soil supporting defined communities of 11 clonally-propagated plant species. Half of the mesocosms contained one genotype per species and half 16 genotypes per species. After 8 years growth, we sampled roots from the mesocosms and measured root-associated fungal richness and diversity using terminal restriction fragment length polymorphism (T-RFLP). Contrary to our hypothesis, we found that the roots of genetically impoverished communities contained more species of fungi and had greater diversity compared to genetically rich communities. Analysis of the plant species composition of the mesocosm communities indicated that genotypic diversity affects root-fungal diversity indirectly through its influence upon plant species diversity. Our findings highlight the need to include feedbacks with plant intraspecific diversity into existing models describing the maintenance of soil biodiversity.     

Maximal ecological diversity exceeds evolutionary diversity in model ecosystems

Understanding community saturation is fundamental to ecological theory. While investigations of the diversity of evolutionary stable states (ESSs) are widespread, the diversity of communities that have yet to reach an evolutionary endpoint is poorly understood. We use Lotka–Volterra dynamics and trait-based competition to compare the diversity of randomly assembled communities to the diversity of the ESS. We show that, with a large enough founding diversity (whether assembled at once or through sequential invasions), the number of long-time surviving species exceeds that of the ESS. However, the excessive founding diversity required to assemble a saturated community increases rapidly with the dimension of phenotype space. Additionally, traits present in communities resulting from random assembly are more clustered in phenotype space compared to random, although still markedly less ordered than the ESS. By combining theories of random assembly and ESSs we bring a new viewpoint to both the saturation and random assembly literature.     

Climate and food diversity as drivers of mammal diversity in Inner Mongolia

Traditionally, geographical distribution of biodiversity is assumed to be codetermined by multiple factors, for example, temperature, precipitation, environmental heterogeneity, and biotic interactions. However, few studies have simultaneously compared the relative roles of these factors in shaping the mammal diversity patterns for different feeding groups, that is, herbivores, insectivores, and carnivores. In this study, we assessed the relations between mammal diversity and current climate (mean annual temperature and precipitation), altitudinal range as well as mammal's food diversity in Inner Mongolia. Our results showed that the species richness for the three feeding guilds of mammals consistently increased with their food diversity, that is, species richness of plants, insects, and rodents. Mammal diversity also significantly decreased with mean annual temperature and precipitation. Random Forest models indicated that climate and food diversity were always included in the combinations of variables most associated with mammal diversity. Our findings suggest that while climate is an important predictor of large scale distribution of mammal diversity, biotic interactions, that is, food diversity, could also play important roles.     

Experimental tests of the dependence of arthropod diversity on plant diversity

ABSTRACT Because a diversity of resources should support a diversity of consumers, most models predict that increasing plant diversity increases animal diversity. We report results of a direct experimental test of the dependence of animal diversity on plant diversity. We sampled arthropods in a well-replicated grassland experiment in which plant species richness and plant functional richness were directly manipulated. In simple regressions, both the number of species planted ([Formula: see text] transformed) and the number of functional groups planted significantly increased arthropod species richness but not arthropod abundance. However, the number of species planted was the only significant predictor of arthropod species richness when both predictor variables were included in ANOVAs or a MANOVA. Although highly significant, arthropod species richness regressions had low [Formula: see text] values, high intercepts (24 arthropod species in monocultures), and shallow slopes. Analyses of relations among plants and arthropod trophic groups indicated that herbivore diversity was influenced by plant, parasite, and predator diversity. Furthermore, herbivore diversity was more strongly correlated with parasite and predator diversity than with plant diversity. Together with regression results, this suggests that, although increasing plant diversity significantly increased arthropod diversity, local herbivore diversity is also maintained by, and in turn maintains, a diversity of parasites and predators.     

Pollinator diversity and specialization in relation to flower diversity

In the face of global decline in biodiversity, the relationship between diversity and species interactions deserves particular attention. If pollinators are strongly dependent on floral diversity due to mutual specialization, declines in plant diversity, e.g. caused by land use intensification, may be associated with linked extinctions of pollinators. However, the general extent of pollinator specialization is still poorly known. To explore the dependence of local bee and hoverfly communities on flower diversity, we recorded flower supply and flower‐visiting insects on 27 meadows with varying flower diversity in southern Germany and analyzed (a) whether the diversity of flower visitors is correlated with flower diversity, (b) whether the degree of dietary specialization of flower visitors changes with flower diversity and (c) whether flower preferences of individual flower visitor species are constant or variable between different communities. Flower–visitor interaction webs were compiled during a single day on each meadow. This approach prevents relating pollinator species to flowers they never encounter because of non‐overlapping phenology or spatial segregation. (a) Flower diversity and flower visitor diversity were positively correlated. (b) Flower visitor assemblies were significantly specialized at a relatively high level, contrasting to the opinion that plant–pollinator webs are highly generalized, and providing a possible explanation for the positive diversity correlation. However, the level of specialization did not change significantly across the gradient of flower diversity, suggesting that pollinators are partitioned to a similar extent in each meadow. (c) In the analysis of ten common flower visitor species previously categorized as generalists, strong evidence was found for both, consistent preferences and preferences that differ between sites. These results indicate a flexibility in flower preferences and a dynamic resource partitioning among pollinators. Generally, our findings highlight the complexity of plant–pollinator interactions and confirm the importance of flower diversity for bee and hoverfly communities.     

Viral diversity limits immune diversity in asymptomatic phase of HIV infection

We propose a new diversity threshold theory which states that the specific CTLs to the viral strain become inactivated (that is, some HIV strain can escape from its specific immune response) when the diversity of HIV strains exceeds some threshold number. We call this number “immune diversity threshold”. Our theory can explain the inactivation of specific immune response and a limit of maximum immune diversity. We can conclude that the accumulation of viral diversity eventually leads to AIDS.     

Structural type diversity: measuring structuredness of communities by type diversity

Recently, the notion of diversity, which is directed towards (effective) numbers of types (states of a trait such as species and genotypes), is increasingly used as an umbrella term akin to “variation”, thus including classical metrics of dispersion among others. This is probably due to the growing interest in functional aspects of variation which involve variable differences between types. Though the traditional notion of diversity does not cover these aspects, it shows up in many interpretations. To overcome this ambiguity, the traditional notion of diversity is extended in this paper to include variable differences with emphasis on their general significance as structuring features. For this purpose, structure is conceived to be captured by the representation of types via variable differences and abundances. Structural diversity then results from application of traditional measures of diversity to the relative structural representations of types in addition to their relative abundances. Since diversity as effective number of types alone provides no information about their mutual distinctness and the range covered by them, connections to measures of dispersion are indispensable. This is considered via two approaches that rely on dispersion characteristics and one approach that allows for an assessment of structural diversity for controlled levels of type distinctness. Effects of structure on dispersion and diversity are analyzed. The use of the approaches for discovering rarely considered characteristics of phylogenetic structure is demonstrated.     

Resource availability controls fungal diversity across a plant diversity gradient

Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales.     

Size diversity and species diversity relationships in fish assemblages of Western Palearctic lakes

Body size, coupled with abundance and taxonomy, may help to understand the mechanisms shaping community structure. Since the body size of fish is closely related to their trophic niche, size diversity (based on individual body size) of fish communities may capture intraspecific variations in fish trophic niches that are not detected by species diversity. Thus, the relationship between size diversity and species diversity may help to integrate variation at both intraspecific and interspecific levels. We studied the relationship between species diversity and size diversity as a measure of the degree of overlap in size among species and thereby the potential overlap in niches in a community. We hypothesized that the relationship between size diversity and species would be different across the European continent due to different levels of size overlap in fish communities. The data were derived from samplings of fish communities using standardised benthic gill nets in 363 lakes. At the continental scale, size diversity increased with species diversity; at the ecoregion scale, the slope of the relation changed across the continent, with the greatest mismatch occurring in northern Europe where communities comprised only one or a few species, but each of which exhibited a great range in size. There was an increase in slope towards the south with significant relations for four out of six ecoregions. The steeper size diversity‐species diversity slope at lower latitudes is attributable to a lower overlap in fish size and thus likely to finer niche separation. Our results also suggest that size diversity is not a strong surrogate for species diversity in European lake fish communities. Thus, particularly in fish communities composed of few species, measuring size diversity may help to detect potential functional variation which may be neglected by measuring species diversity alone.     

Plant neighbour diversity

Abstract. Neighbour diversity is the diversity of other plant species contacting a reference species. The expected value and confidence intervals of neighbour diversity assuming random contacts can be found using bootstrapping. In general, frequent species have higher expected neighbour diversities with narrow confidence intervals than infrequent species. In fixed sand dunes dominated by lichens and bryophytes most species have lower than expected neighbour diversity. However, the fixed sand dunes seem to be a mixture of two patch types, with the species in lichen-rich patches having higher diversities than the species in bryophyte-rich patches. In hay pastures, nearly all species have lower than expected neighbour diversities. The more frequent the species is, the less is its expected neighbour diversity. This implies that its frequent species are selective as to their neighbours, and so they drive a biological formation of spatial pattern.     

Land-use diversity index: a new means of detecting diversity at landscape level

Preservation of ecological diversity is a guiding principle of landscape management and planning. Although diversity is often quantified with measurable indices, common approaches used to measure diversity, for example the Shannon–Weaver index, are not adequate for many landscape studies, because they are affected by scale and sampling efforts. A robust index for measurement of landscape diversity should be able to quantify distinctive components of a landscape mosaic. This paper provides a new diversity index for landscape studies that improves the measurement of diversity at landscape level. The key features of the method are inclusion of an implication of physical moment and quantification of diversity by placing greater weight on the structure and composition of a patch. We have named the new index the land-use diversity index, or LUDI, and have concluded that the LUDI is the preferred measure of diversity at landscape level.     

高寒草地植物物种多样性与功能多样性的关系

物种多样性与功能多样性的关系是生态学当前研究的热点问题之一,不同区域典型生态系统物种多样性和功能多样性的关系研究有利于生物多样性保护理论的全面发展。以青藏高原地区的主要草地生态系统—高寒草甸和高寒草原为研究对象,采用4个物种多样性指数(Patrick丰富度指数、Shannon-Weiner多样性指数、Pielou均匀度指数和Simpson优势度指数)和9个功能多样性指数(FAD功能性状距离指数、MFAD功能性状平均距离指数、基于样地的FDp和基于群落的FDc功能树状图指数、FRic功能体积指数、FEve功能均匀度指数、Rao功能离散度常二次熵指数、FDiv功能离散指数、FDis功能分散指数),分析了高寒草地植物物种多样性、功能多样性关系及其与初级生产力的关系,以期阐明3个科学问题:不同草地类型的高寒草地生态系统植物物种多样性和功能多样性有何差异?高寒草地生态系统的植物物种多样性和功能多样性有何关系?高寒草地生态系统物种多样性、功能多样性对生态系统功能的影响有何异同?研究结果表明:(1)与高寒草原相比,高寒草甸具有更高的物种多样性、功能丰富度和功能离散度;(2)高寒草甸中,Patrick丰富度与功能丰富度指数(FAD、MFAD、FDp、FDc)和功能离散度指数(FDiv)的具有较强的相关性,最优拟合方程分别为幂函数和二次多项式函数;(3)高寒草原中,Patrick丰富度与功能丰富度指数(FAD、MFAD、FDp、FDc、FRic)、Shannon指数和Simpson指数与FEve指数的相关性较强,最优拟合方程为二次多项式函数,Pielou指数与FEve指数的相关性较强,最优拟合方程为指数函数;(4)高寒草甸的初级生产力分别与物种丰富度指数Patrick、功能离散指数FDiv具有较强的相关性;而高寒草原的初级生产力与4个物种多样性指数间均具有较强的相关性,与功能离散指数FDiv具有较强的相关性,最佳拟合方程均为二次多项式函数。研究的总体结论为:物种多样性、功能多样性、二者之间的关系以及二者与生态系统服务功能(以初级生产力为例)之间的关系在高寒草甸和高寒草原群落中表现迥异,因此在研究青藏高原高寒草地的生态功能时,不能仅仅测度传统的物种多样性,还应测度与物种多样性、生态功能密切相关的功能多样性。     

The application of gene diversity analyses to surname diversity data

The use in the literature of statistics and measures derived for the measurement and the analysis of inbreeding from data on gene frequency diversity and applied to data on surname diversity is discussed. To overcome the difficulties encountered with this approach, a simple mathematical model for analysing isonymy data is proposed. Finally some further measures of surname diversity are given based on measures developed for gene diversity analysis and for community diversity analysis in ecology.     

物种与物种多样性

本文首先讨论生物物种的科学概念和生物学本质，分析物种客观存在的自然属性和物种概念的局限性，认为物种的生物学属性和物种多样性的科学属性之间有着本质联系。物种多样性研究的实质是研究生物物种的生物学多样性。度量物种多样性程度有多种方法，但物种数目是物种多样性程度最直接、也是最基本的表达，估计物种多样性数目是当前国际上物种多样性研究的核心与热点内容。物种多样性产生的根源是物种形成，物种绝灭速率是维持物种多样性的关键因素。本文简要总结了物种形成与绝灭的基本模式和机制，通过分析生物地理区系与物种多样性研究的密切关系，说明物种的区系成份分析是物种多样性大尺度格局研究的重要内容。     

Nucleotide diversity in gorillas

Comparison of the levels of nucleotide diversity in humans and apes may provide valuable information for inferring the demographic history of these species, the effect of social structure on genetic diversity, patterns of past migration, and signatures of past selection events. Previous DNA sequence data from both the mitochondrial and the nuclear genomes suggested a much higher level of nucleotide diversity in the African apes than in humans. Noting that the nuclear DNA data from the apes were very limited, we previously conducted a DNA polymorphism study in humans and another in chimpanzees and bonobos, using 50 DNA segments randomly chosen from the noncoding, nonrepetitive parts of the human genome. The data revealed that the nucleotide diversity (pi) in bonobos (0.077%) is actually lower than that in humans (0.087%) and that pi in chimpanzees (0.134%) is only 50% higher than that in humans. In the present study we sequenced the same 50 segments in 15 western lowland gorillas and estimated pi to be 0.158%. This is the highest value among the African apes but is only about two times higher than that in humans. Interestingly, available mtDNA sequence data also suggest a twofold higher nucleotide diversity in gorillas than in humans, but suggest a threefold higher nucleotide diversity in chimpanzees than in humans. The higher mtDNA diversity in chimpanzees might be due to the unique pattern in the evolution of chimpanzee mtDNA. From the nuclear DNA pi values, we estimated that the long-term effective population sizes of humans, bonobos, chimpanzees, and gorillas are, respectively, 10,400, 12,300, 21,300, and 25,200.     

Determinants of web spider species diversity: Vegetation structural diversity vs. prey availability

Summary The hypotheses that vegetation structural diversity and prey availability determine alpha diversity were examined for scrub- and meadow-inhabiting web spider species assemblages along elevational gradients in Costa Rica and California. Prey availabilities were estimated by sticky trap catches, using only the orders and size classes of insects actually captured by the spiders. The measured component of vegetation structural diversity was the maximum tip height in 20 cm increments from 0 to 2.0 m. Spider species diversity and vegetation tip height diversity were both expressed by the Inverse Simpson Index. Web spider species diversity is highly significantly correlated with vegetation tip height diversity. Prey availability is not a significant predictor of web spider species diversity in these habitats.U.S. Department of Agriculture, Biological Control of Insects Research Laboratory, Agriculture Research Service, Columbia, MO 65205, USA     

Tree diversity drives diversity of arthropod herbivores,but successional stage mediates detritivores

The high tree diversity of subtropical forests is linked to the biodiversity of other trophic levels. Disentangling the effects of tree species richness and composition, forest age, and stand structure on higher trophic levels in a forest landscape is important for understanding the factors that promote biodiversity and ecosystem functioning. Using a plot network spanning gradients of tree diversity and secondary succession in subtropical forest, we tested the effects of tree community characteristics (species richness and composition) and forest succession (stand age) on arthropod community characteristics (morphotype diversity, abundance and composition) of four arthropod functional groups. We posit that these gradients differentially affect the arthropod functional groups, which mediates the diversity, composition, and abundance of arthropods in subtropical forests. We found that herbivore richness was positively related to tree species richness. Furthermore, the composition of herbivore communities was associated with tree species composition. In contrast, detritivore richness and composition was associated with stand age instead of tree diversity. Predator and pollinator richness and abundance were not strongly related to either gradient, although positive trends with tree species richness were found for predators. The weaker effect of tree diversity on predators suggests a cascading diversity effect from trees to herbivores to predators. Our results suggest that arthropod diversity in a subtropical forest reflects the net outcome of complex interactions among variables associated with tree diversity and stand age. Despite this complexity, there are clear linkages between the overall richness and composition of tree and arthropod communities, in particular herbivores, demonstrating that these trophic levels directly impact each other.