The decoupling of abundance and species richness in lizard communities

1. Patterns of species richness often correlate strongly with measures of energy. The more individuals hypothesis (MIH) proposes that this relationship is facilitated by greater resources supporting larger populations, which are less likely to become extinct. Hence, the MIH predicts that community abundance and species richness will be positively related. 2. Recently, Buckley & Jetz (2010, Journal of Animal Ecology, 79, 358-365) documented a decoupling of community abundance and species richness in lizard communities in south-west United States, such that richer communities did not contain more individuals. They predicted, as a consequence of the mechanisms driving the decoupling, a more even distribution of species abundances in species-rich communities, evidenced by a positive relationship between species evenness and species richness. 3. We found a similar decoupling of the relationship between abundance and species richness for lizard communities in semi-arid south-eastern Australia. However, we note that a positive relationship between evenness and richness is expected because of the nature of the indices used. We illustrate this mathematically and empirically using data from both sets of lizard communities. When we used a measure of evenness, which is robust to species richness, there was no relationship between evenness and richness in either data set. 4. For lizard communities in both Australia and the United States, species dominance decreased as species richness increased. Further, with the iterative removal of the first, second and third most dominant species from each community, the relationship between abundance and species richness became increasingly more positive. 5. Our data support the contention that species richness in lizard communities is not directly related to the number of individuals an environment can support. We propose an alternative hypothesis regarding how the decoupling of abundance and richness is accommodated; namely, an inverse relationship between species dominance and species richness, possibly because of ecological release.     

Comparative phylogeography of three endemic rodents from the Albertine Rift, east central Africa

The major aim of this study was to compare the phylogeographic patterns of codistributed rodents from the fragmented montane rainforests of the Albertine Rift region of east central Africa. We sampled individuals of three endemic rodent species, Hylomyscus denniae, Hybomys lunaris and Lophuromys woosnami from four localities in the Albertine Rift. We analysed mitochondrial DNA sequence variation from fragments of the cytochrome b and control region genes and found significant phylogeographic structuring for the three taxa examined. The recovered phylogenies suggest that climatic fluctuations and volcanic activity of the Virunga Volcanoes chain have caused the fragmentation of rainforest habitat during the past 2 million years. This fragmentation has played a major role in the diversification of the montane endemic rodents of the region. Estimation of the divergence times within each species suggests a separation of the major clades occurring during the mid to late Pleistocene.     

Tree species distribution in forests of the Albertine Rift, western Uganda

The distribution of trees of diameter ≥ 10 cm was assessed in twelve 1‐ha (20 × 500 m) plots of Bwindi Impenetrable National Park (BINP), Kasyoha‐Kitomi Forest Reserve (KKFR), Kibale National Park (KNP) and Budongo Forest Reserve (BFR) in the Albertine Rift, western Uganda. Distribution was analysed at three spatial scales: local (1 ha plots), within individual forests (>300 km² each) and regional (>56,000 km²). The aim was to classify tree species into Rabinowitz's seven forms of rarity. We recorded 5747 trees in 53 families, 159 genera, and 212 species. Twenty‐two families had one species each while the rest had between two and 25 species. Number of species was highest in the family Euphorbiaceae (25 species) followed by Meliaceae and Rubiaceae with sixteen species each. Based on Rabinowitz's forms of rarity, 93% of the species were geographically widespread, 47% were restricted to a single forest type, while 41% occurred at densities of <1 individual ha^?1. Ubiquitous common species with high frequency and high local abundance occurred in the Meliaceae, Flacourtiaceae, Moraceae and Apocynaceae families. Conservation of geographically widespread species should focus on landscape rather than site specific approaches. The rarest species would benefit from species‐specific strategies.     

Assessing the accuracy of species distribution models to predict amphibian species richness patterns

1. Evaluating the distribution of species richness where biodiversity is high but has been insufficiently sampled is not an easy task. Species distribution modelling has become a useful approach for predicting their ranges, based on the relationships between species records and environmental variables. Overlapping predictions of individual distributions could be a useful strategy for obtaining estimates of species richness and composition in a region, but these estimates should be evaluated using a proper validation process, which compares the predicted richness values and composition with accurate data from independent sources. 2. In this study, we propose a simple approach to estimate model performance for several distributional predictions generated simultaneously. This approach is particularly suitable when species distribution modelling techniques that require only presence data are used. 3. The individual distributions for the 370 known amphibian species of Mexico were predicted using maxent to model data on their known presence (66,113 presence-only records). Distributions were subsequently overlapped to obtain a prediction of species richness. Accuracy was assessed by comparing the overall species richness values predicted for the region with observed and predicted values from 118 well-surveyed sites, each with an area of c. 100 km(2), which were identified using species accumulation curves and nonparametric estimators. 4. The derived models revealed a remarkable heterogeneity of species richness across the country, provided information about species composition per site and allowed us to obtain a measure of the spatial distribution of prediction errors. Examining the magnitude and location of model inaccuracies, as well as separately assessing errors of both commission and omission, highlights the inaccuracy of the predictions of species distribution models and the need to provide measures of uncertainty along with the model results. 5. The combination of a species distribution modelling method like maxent and species richness estimators offers a useful tool for identifying when the overall pattern provided by all model predictions might be representing the geographical patterns of species richness and composition, regardless of the particular quality or accuracy of the predictions for each individual species.     

Mammal density and patterns of ectoparasite species richness and abundance

Patterns of species richness, prevalence and abundance of ectoparasites have rarely been investigated at both the levels of populations and species of hosts. Here, we investigated the effects in changes in small mammal density on species richness, abundance and prevalence of ectoparasitic fleas. The comparative analyses were conducted for different small mammal species and among several populations during a long-term survey. We tested the hypothesis that an increase in host density should be linked with an increase in parasite species richness both among host species and among populations within host species, as predicted by epidemiological models. We also used host species density data from literature. We found that host density has a major influence on the species richness of ectoparasite communities of small mammals among host populations. We found no relationship between data of host density from the literature and parasite species richness. In contrast with epidemiological hypotheses, we found no relationships between abundance, or prevalence, and host density, either among host species or among host populations. Moreover, a decrease in abundance of fleas in relation with an increase in host density was observed for two mammal species (Apodemus agrarius and A. flavicollis). The decrease or the lack of increase in flea abundance in relation with an increase in host density suggests anti-parasitic behavioural activities such as grooming.     

Habitat selection determines abundance, richness and species composition of beetles in aquatic communities

Distribution and abundance patterns at the community and metacommunity scale can result from two distinct mechanisms. Random dispersal followed by non-random, site-specific mortality (species sorting) is the dominant paradigm in community ecology, while habitat selection provides an alternative, largely unexplored, mechanism with different demographic consequences. Rather than differential mortality, habitat selection involves redistribution of individuals among habitat patches based on perceived rather than realized fitness, with perceptions driven by past selection. In particular, habitat preferences based on species composition can create distinct patterns of positive and negative covariance among species, generating more complex linkages among communities than with random dispersal models. In our experiments, the mere presence of predatory fishes, in the absence of any mortality, reduced abundance and species richness of aquatic beetles by up to 80% in comparison with the results from fishless controls. Beetle species' shared habitat preferences generated distinct patterns of species richness, species composition and total abundance, matching large-scale field patterns previously ascribed to random dispersal and differential mortality. Our results indicate that landscape-level patterns of distribution and species diversity can be driven to a large extent by habitat selection behaviour, a critical, but largely overlooked, mechanism of community and metacommunity assembly.     

Non-neutral patterns of species abundance in grassland communities

Although the distribution of plant species abundance in a Minnesota grassland was consistent with neutral theory, niche but not neutral mechanisms were supported by the ability of species traits to predict species abundances in three experimental grassland communities. In particular, data from 27 species grown in monoculture showed that species differed in a trait, R *, which is the level to which each species reduced the concentration of soil nitrate, the limiting soil nutrient and which is predicted to be inversely associated with competitive ability for nitrogen (N). In these N-limited habitats, species abundance ranks correlated with their predicted competitive ranks: low R * species, on average dominated. These correlations were significantly different than expected for neutral theory, which assumes the exchangeability of species traits. Additionally, we found that changes in relative abundance after environmental change (N-addition or disturbance) were not neutral but also were significantly associated with R *.     

Environmental correlates of vegetation patterns and species richness in the northern Grampians,Victoria

Abstract Plant species cover-abundance and density data were collected for 94 sample plots across a gradient from rocky uplands to sandy outwash plains in the northern part of Grampians (Gariwerd) National Park in western Victoria. Detrended correspondence analysis (DCA) was used to identify dominant gradients in species composition. A range of static (e.g. substrate type, soil depth, microclimate indicators) and dynamic (e.g. elapsed time since last fire) environmental variables were measured. Correlations were sought between these variables and vegetation patterns including those for richness (R) and Shannon-Weiner diversity (H′). The dominant gradient of vegetation change identified by DCA separated rocky sites and sites near ephemeral streams, from well-drained, sandy sites. Secondary gradients identified time since last fire as important for sandy sites, and altitude and aspect-related microclimate for rocky sites. Diversity was highest in the first 2 years after fire but showed no further decline in older sites. Overall, R and H' were negatively correlated with soil nutrient concentrations. On sandy sites R was high, but was low on rocky sites and near streams. Within the rocky sites, R was highest on cool, moist south and east slopes, and lowest on hot, dry north and west slopes. Explanations of diversity patterns based on inhibition of competitive exclusion due to stress and recurrent disturbance best fit the results presented here.     

Predicting patterns of plant species richness in megadiverse South Africa

Using new tools (boosted regression trees) in predictive biogeography, with extensive spatial 23 distribution data for >19 000 species, we developed predictive models for South African plant species richness patterns. Further, biome level analysis explored possible functional determinants of country‐wide regional species richness. Finally, to test model reliability independently, we predicted potential alien invasive plant species richness with an independent dataset. Amongst the different hypotheses generally invoked to explain species 30 diversity (energy, favorableness, topographic heterogeneity, irregularity and seasonality), results revealed topographic heterogeneity as the most powerful single explanatory variable for indigenous South African plant species richness. Some biome‐specific responses were observed, i.e. two of the five analyzed biomes (Fynbos and Grassland) had richness best explained by the “species‐favorableness” hypothesis, but even in this case, topographic heterogeneity was also a primary predictor. This analysis, the largest conducted on an almost exhaustive species sample in a species‐rich region, demonstrates the preeminence of topographic heterogeneity in shaping the spatial pattern of regional plant species richness. Model reliability was confirmed by the considerable predictive power for alien invasive species richness. It thus appears that topographic heterogeneity controls species richness in two main ways: firstly, by providing an abundance of ecological niches in contemporary space (revealed by alien invasive species richness relationships) and secondly, by facilitating the persistence of ecological niches through time. The extraordinary richness of the South African Fynbos biome, a world‐renowned hotspot of biodiversity with the steepest environmental gradients in South Africa, may thus have arisen through both mechanisms. Comparisons with similar regions of the world outside South Africa are needed to confirm the generality of topographic heterogeneity and favorableness as predictors of plant richness.     

Randomvs non-random sampling: Effects on patterns of species abundance, species richness and vegetation-environment relationships

From a strictly statistical perspective, most of the commonly used statistical tests cannot be performed on vegetation data obtained using a non-random sampling design. Despite this, non-randomly sampled plots such as phytosociological relevés still make sense: because they may focus on objectives not appropriately addressed by random sampling, such as the study of rare plant communities or species; and because random sampling is often more time-demanding and expensive. Considering the huge body of phytosociological data available, an interesting question arises: if we compare randomly and non-randomly sampled data sets, to what extent do the results of our analyses differ with respect to various species and vegetation parameters? We present an attempt to tackle this question by comparing two data sets collected in a 25 km² area close to the city of Bremen, northwestern Germany: the first data set consisted of 30 subjectively (non-randomly) placed, homogeneous plots across different plant communities, each of which was laid out in a nested design including 9 sizes from 0.5 m² to 1,000 m². The second data set consisted of 30 (again nested) plots randomly selected and located with a GPS device; plots were rejected only if they for some reason were inaccessible. The data collection was the same for both data sets: presence-absence of all vascular plants was recorded for the different plot sizes, and soil samples were collected for the determination of the values of some important environmental variables. For the comparison of the two data sets, we used either the complete data sets or sub-sets of those plots located in woodlands. The main results included the following: (1) Species abundance patterns: Random sampling resulted in a larger number of common and a smaller number of rare species than non-random sampling. (2) Species richness at different spatial scales: For the small plot sizes, the number of species in the non-randomly placed plots was higher than in the randomly placed plots, while the differences were less pronounced at larger spatial scales. As a consequence, also the parameters of species-area curves differed between the data sets, especially in the sub-set including woodland plots. (3) Vegetation differentiation: In random sampling, there was considerable redundancy, i.e., there were several plots with high floristic similarity. (4) Vegetation-environment relationships: The ordination scores of the non-randomly placed plots showed a larger number of significant correlations to soil parameters than the scores of randomly placed plots. The results suggest that conclusions drawn from the analysis of non-randomly placed plots such as phytosociological relevés may be biased, especially regarding estimates of species abundance and species richness patterns.     

中国陆栖哺乳动物物种丰富度的地理格局及其与环境因子的关系

物种丰富度的大尺度地理格局及其成因是宏观生态学和生物地理学的中心议题之一。本文利用中国陆栖哺乳动物分布数据, 结合高分辨率的气候、地形、植被等环境信息, 探讨了中国陆栖哺乳动物及主要类群的物种丰富度格局及其影响因素。结果显示, 中国陆栖哺乳动物物种丰富度具有显著的纬度梯度格局, 总体上呈现出由低纬度向高纬度逐渐减少的趋势, 并与宏观地形具有良好的对应关系; 其中, 亚热带、热带西部山区的物种丰富度最高, 而东部平原地区、西北干旱区和青藏高原腹地则是丰富度的低值区。各主要类群的物种丰富度格局既有相似性, 又存在差异。最优线性模型的分析结果显示, 由归一化植被指数(NDVI)、生态系统类型数和气温年较差构成的回归模型对哺乳动物物种丰富度格局的解释率最高, 其中NDVI对模型解释率的贡献最大, 这表明中国陆栖哺乳动物物种丰富度的地理分异受多种环境因素的共同影响, 其中植被生产力起主导作用。各主要类群的最优线性模型显示, 影响物种丰富度格局的主要环境因子因类群而异, 这可能反映了各类群进化历史及生理适应的差异。     

中国蛇类物种丰富度地理格局及其与生态因子的关系

物种丰富度地理格局成因是生态学和生物地理学研究重要目标之一。生态假说在解释物种丰富度地理格局的成因上受到广泛关注。该文基于100km×100km空间分辨率研究中国蛇类物种丰富度的地理分布格局,并结合生态假说探讨影响蛇类分布格局的因素。该研究采用主轴邻距法获得基于特征值的空域数据,并同生态因子进行多元回归分析,结果表明:(1)中国蛇类物种丰富度在经、纬度上呈现多峰分布格局,物种丰富度最高的地区位于东洋界亚热带、热带,丰富度较低的地区位于青藏高原、北方草原荒漠、黄淮平原、两湖平原及鄱阳湖平原等;(2)多元回归分析能解释56.5%的蛇类物种丰富度变化,分析得出蛇类物种丰富度格局的主要影响因子是归一化植被指数、最冷季降水量和年温差。(3)模型选择结果显示,在多元回归分析中,P<0.05的变量(归一化植被指数、最冷季降水量和年温差)组成的模型是解释蛇类物种丰富度格局的最优模型。这说明蛇类物种丰富度格局是由不同生态因子共同作用的结果。基于中国蛇类物种丰富度地理格局成因研究的复杂性,该文提出在进一步研究中,需重视各假说中影响因子的选择和人类活动的影响,并在不同空间尺度上对蛇类物种丰富度地理格局进行综合分析。     

Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history

Phylogenetic information is increasingly being used to understand the assembly of biological communities and ecological processes. However, commonly used metrics of phylogenetic diversity (PD) do not incorporate information on the relative abundances of individuals within a community. In this study, we develop three indices of PD that explicitly consider species abundances. First, we present a metric of phylogenetic-abundance evenness that evaluates the relationship between the abundance and the distribution of terminal branch lengths. Second, we calculate an index of hierarchical imbalance of abundances at the clade level encapsulating the distribution of individuals across the nodes in the phylogeny. Third, we develop an index of abundance-weighted evolutionary distinctiveness and generate an entropic index of phylogenetic diversity that captures both information on evolutionary distances and phylogenetic tree topology, and also serves as a basis to evaluate species conservation value. These metrics offer measures of phylogenetic diversity incorporating different community attributes. We compare these new metrics to existing ones, and use them to explore diversity patterns in a typical California annual grassland plant community at the Jasper Ridge biological preserve.
Ecology Letters (2010) 13: 96–105     

Plio-Pleistocene Carnivora of eastern Africa: species richness and turnover patterns

This paper presents an up-to-date and detailed overview of the Plio-Pleistocene fossil record of Carnivora in eastern Africa. Major events in the carnivoran lineages present in the region are discussed and stratigraphic ranges of all species-level taxa are provided. The compiled data are used for quantitative analyses of species richness and turnover. Sampling is considered to be adequate for the interval 3.6–1.5 Mya, and poorer in the half-million-year time slices before and after this interval. Species richness peaks around 3.6–3.0 Mya and declines gradually from that time until the end of the time period analysed. Calculation of origination and extinction rates indicate that there are two peaks of origination: at 3.9–3.3 Mya (although the earlier half of this interval is biased through poor sampling) and at 2.1–1.8 Mya. The origination rate is zero in the interval 3.0–2.4 Mya. The extinction rate peaks at around 3.0 Mya after which it falls slightly, remaining nearly constant until 1.8 Mya, after which it increases considerably. The data support the hypothesis that the modern carnivoran guild of eastern Africa originated relatively recently, mostly within the last million years. There is no support in these data for a turnover pulse in Carnivora between 3 and 2 Mya.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 121–144.     

Relative abundance distributions in plant communities: effects of species richness and of spatial scale

Abstract. Relative abundance distributions (RADs) are an important feature of community structure, but little is known of the factors affecting which type of RAD is observed in a particular community. We examined the influences of species richness and of spatial scale on the RAD of plant communities. The effect of species richness was examined by analysing simulated communities generated under the Broken stick model, the Sequential breakage model, and a randomized version of Niche pre-emption model. In all cases, when there were few species in the community the data only occasionally gave the best fit to the model that was used to generate it. With 40–65 species, a best fit was obtained for the correct model in about 75 % of cases, almost irrespective of the model. Effects of spatial scale were examined in data from four dune slacks and from two semi-arid grasslands, by analysing biomass values at a range of sample sizes. The model that best fitted the whole sample differed between the four slacks and between the slacks and the semi-arid grasslands. The change in which model of RAD fitted best, as sample size was reduced, varied between sites and between habitat types. At the smallest sample sizes, the Zipf-Mandelbrot model often fitted, and in the slack sites the Broken stick also, though neither fitted (in the vegetation examined) at larger spatial scales. It is concluded the RAD is affected by species richness and by spatial scale, in ways that currently do not enable simple prediction. RADs can theoretically give information on the processes such as resource partitioning, immigration and competition that have structured the community, but they are a blunt tool for this purpose.     

稀有种和常见种对植物群落物种丰富度格局的相对贡献

物种丰富度格局的形成不仅依赖于群落的构建过程, 同样也依赖于群落中的物种组成(如稀有种和常见种)。本文以黄土高原子午岭林区的辽东栎(Quercus wutaishanica)林为研究对象, 根据频度大小对物种进行排序, 形成稀有-常见种和常见-稀有种两条物种序列, 通过逐一添加(去除)物种, 分析引起的总体物种丰富度及其成分(α多样性和β多样性)的变化, 确定稀有种和常见种对物种丰富度格局的相对贡献。结果表明: (1)常见-稀有种序列与群落总体物种丰富度的相关性呈先剧增后平稳的对数增长曲线, 而稀有-常见种序列与群落总体的相关性与前者刚好相反, 呈先平稳后剧增的指数增长曲线; (2) α多样性在常见-稀有种序列中呈明显的对数变化曲线, 而在稀有-常见种序列中呈指数增长曲线; (3)与α多样性变化相反, β多样性在常见-稀有种序列中随物种的进入先迅速降低后逐渐平稳, 而在稀有-常见种序列中先平稳后急剧降低。可以看出, 常见种不仅主导群落的总体物种丰富度格局, 同时也是α多样性和β多样性格局的重要贡献者。因此, 常见种是群落物种丰富度格局的指示者, 也应该是优先保护的物种。     

How species richness and total abundance constrain the distribution of abundance

The species abundance distribution (SAD) is one of the most intensively studied distributions in ecology and its hollow‐curve shape is one of ecology's most general patterns. We examine the SAD in the context of all possible forms having the same richness (S) and total abundance (N), i.e. the feasible set. We find that feasible sets are dominated by similarly shaped hollow curves, most of which are highly correlated with empirical SADs (most R² values > 75%), revealing a strong influence of N and S on the form of the SAD and an a priori explanation for the ubiquitous hollow curve. Empirical SADs are often more hollow and less variable than the majority of the feasible set, revealing exceptional unevenness and relatively low natural variability among ecological communities. We discuss the importance of the feasible set in understanding how general constraints determine observable variation and influence the forms of predicted and empirical patterns.     

Multi-scale altitudinal patterns in species richness of land snail communities in south-eastern France

Aim Species richness is an important feature of communities that varies along elevational gradients. Different patterns of distribution have been described in the literature for various taxonomic groups. This study aims to distinguish between species density and species richness and to describe, for land snails in south‐eastern France, the altitudinal patterns of both at different spatial scales. Location The study was conducted on five calcareous mountains in south‐eastern France (Etoile, Sainte Baume, Sainte Victoire, Ventoux and Queyras). Methods Stratified sampling according to vegetation and altitude was undertaken on five mountains, forming a composite altitudinal gradient ranging from 100 to 3100 m. Visual searching and analysis of turf samples were undertaken to collect land snail species. Species density is defined as the number of species found within quadrats of 25 m². Species richness is defined as the number of species found within an elevation zone. Different methods involving accumulation curves are used to describe the patterns in species richness. Elevation zones of different sizes are studied. Results Eighty‐seven species of land snails were recovered from 209 samples analysed during this study. Land snail species density, which can vary between 29 and 1 species per 25 m², decreases logarithmically with increasing altitude along the full gradient. However, on each mountain separately, only a linear decrease is observable. The climatic altitudinal gradient can explain a large part of this pattern, but the great variability suggests that other factors, such as heterogeneity of ground cover, also exert an influence on species density. The altitudinal pattern of species richness varies depending on the spatial resolution of the study. At fine resolution (altitudinal zones of 100 m) land snail species richness forms a plateau at altitudes below 1000 m, before decreasing with increasing altitude. At coarse resolution (altitudinal zones of 500 and 1000 m) the relationship becomes linear. Main conclusions This study reveals that land snail species density and land snail species richness form two different altitudinal patterns. Species density exhibits strong variability between sites of comparable altitude. A large number of samples seem necessary to study altitudinal patterns of species density. Species density decreases logarithmically with increasing altitude. Above a critical altitudinal threshold, this decrease lessens below the rate seen in the first 1500 m. Different methods exist to scale‐up species density to species richness but these often produce different patterns. In this study, the use of accumulation curves has yielded a pattern of species richness showing a plateau at low altitude, whereas simple plotting of known altitudinal ranges from single mountains would have produced stronger mid‐altitudinal peaks. This study shows that not only factors such as temperatures and habitat heterogeneity, but also an ecotone effect, are responsible for the observed patterns.