The causes of species richness patterns across space, time, and clades and the role of "ecological limits"

A major goal of research in ecology and evolution is to explain why species richness varies across habitats, regions, and clades. Recent reviews have argued that species richness patterns among regions and clades may be explained by "ecological limits" on diversity over time, which are said to offer an alternative explanation to those invoking speciation and extinction (diversification) and time. Further, it has been proposed that this hypothesis is best supported by failure to find a positive relationship between time (e.g., clade age) and species richness. Here, I critically review the evidence for these claims, and propose how we might better study the ecological and evolutionary origins of species richness patterns. In fact, ecological limits can only influence species richness in clades by influencing speciation and extinction, and so this new "alternative paradigm" is simply one facet of the traditional idea that ecology influences diversification. The only direct evidence for strict ecological limits on richness (i.e., constant diversity over time) is from the fossil record, but many studies cited as supporting this pattern do not, and there is evidence for increasing richness over time. Negative evidence for a relationship between clade age and richness among extant clades is not positive evidence for constant diversity over time, and many recent analyses finding no age-diversity relationship were biased to reach this conclusion. More comprehensive analyses strongly support a positive age-richness relationship. There is abundant evidence that both time and ecological influences on diversification rates are important drivers of both large-scale and small-scale species richness patterns. The major challenge for future studies is to understand the ecological and evolutionary mechanisms underpinning the relationships between time, dispersal, diversification, and species richness patterns.     

物种丰富度垂直分布格局及影响机制

物种丰富度分布格局是一定地域内物种丰富度沿三维空间的立体分布,包括物种丰富度在经度、纬度和垂直梯度(海拔高度和海水深度)三个维度上的空间分异。近年来物种多样性的垂直分布格局与机制研究得到了生物地理学家和生态学家的重视。物种丰富度的垂直分布格局存在多种类型,但随海拔增加而物种数减少的单调递减模型和中海拔物种丰富度最高的单峰模型较为常见。目前在机制研究中验证较多的是气候稳定性、生物因子(种间相互作用)、能量、生境异质性、干扰、进化时间、物种分化速率、面积、中域效应(mid-domain effect)、生态位保守性(niche conservatism)等假说和机制。物种丰富度的分布格局是多方面因素综合作用的结果;由于地理、地形、气候、地质演化历史、物种库和进化历史、物种分化速率、干扰等差异,在不同地区存在着特别的物种丰富度空间分布格局和机制;处于同一地区的不同类群的物种也因进化扩散历史和生态适应能力不同而呈现多样化的分布格局。因此,对不同地区和类群的物种丰富度格局和机制进行研究应具体分析后才能得到可信结论。     

Evolutionary and ecological causes of the latitudinal diversity gradient in hylid frogs: treefrog trees unearth the roots of high tropical diversity

Why are there more species in the tropics than in temperate regions? In recent years, this long-standing question has been addressed primarily by seeking environmental correlates of diversity. But to understand the ultimate causes of diversity patterns, we must also examine the evolutionary and biogeographic processes that directly change species numbers (i.e., speciation, extinction, and dispersal). With this perspective, we dissect the latitudinal diversity gradient in hylid frogs. We reconstruct a phylogeny for 124 hylid species, estimate divergence times and diversification rates for major clades, reconstruct biogeographic changes, and use ecological niche modeling to identify climatic variables that potentially limit dispersal. We find that hylids originated in tropical South America and spread to temperate regions only recently (leaving limited time for speciation). There is a strong relationship between the species richness of each region and when that region was colonized but not between the latitudinal positions of clades and their rates of diversification. Temperature seasonality seemingly limits dispersal of many tropical clades into temperate regions and shows significant phylogenetic conservatism. Overall, our study illustrates how two general principles (niche conservatism and the time-for-speciation effect) may help explain the latitudinal diversity gradient as well as many other diversity patterns across taxa and regions.     

EVOLUTIONARY AND BIOGEOGRAPHIC ORIGINS OF HIGH TROPICAL DIVERSITY IN OLD WORLD FROGS (RANIDAE)

Differences in species richness between regions are ultimately explained by patterns of speciation, extinction, and biogeographic dispersal. Yet, few studies have considered the role of all three processes in generating the high biodiversity of tropical regions. A recent study of a speciose group of predominately New World frogs (Hylidae) showed that their low diversity in temperate regions was associated with relatively recent colonization of these regions, rather than latitudinal differences in diversification rates (rates of speciation–extinction). Here, we perform parallel analyses on the most species-rich group of Old World frogs (Ranidae; ∼1300 species) to determine if similar processes drive the latitudinal diversity gradient. We estimate a time-calibrated phylogeny for 390 ranid species and use this phylogeny to analyze patterns of biogeography and diversification rates. As in hylids, we find a strong relationship between the timing of colonization of each region and its current diversity, with recent colonization of temperate regions from tropical regions. Diversification rates are similar in tropical and temperate clades, suggesting that neither accelerated tropical speciation rates nor greater temperate extinction rates explain high tropical diversity in this group. Instead, these results show the importance of historical biogeography in explaining high species richness in both the New World and Old World tropics.     

Convergence, divergence, and homogenization in the ecological structure of emydid turtle communities: the effects of phylogeny and dispersal

Studies that have explored the origins of patterns of community structure from a phylogenetic perspective have generally found either convergence (similarity) in community structure between regions through adaptive evolution or lack of convergence (dissimilarity) due to phylogenetic conservatism in the divergent ecological characteristics of lineages inhabiting different regions. We used a phylogenetic approach to document a third pattern in the structure of emydid turtle communities. Emydid communities in southeastern North America tend to have a higher proportion of aquatic species than those in the northeast. This pattern reflects phylogenetic conservatism in the ecology and biogeography of two basal emydid clades, limiting convergence in community structure between these regions. However, differences in community structure between northeastern and southeastern North America have also been homogenized considerably by the dispersal of species with phylogenetically conserved ecological characteristics between regions. This pattern of ecologically conservative dispersal may be important in many continental and oceanic systems.     

What explains patterns of species richness? The relative importance of climatic‐niche evolution,morphological evolution,and ecological limits in salamanders

A major goal of evolutionary biology and ecology is to understand why species richness varies among clades. Previous studies have suggested that variation in richness among clades might be related to variation in rates of morphological evolution among clades (e.g., body size and shape). Other studies have suggested that richness patterns might be related to variation in rates of climatic‐niche evolution. However, few studies, if any, have tested the relative importance of these variables in explaining patterns of richness among clades. Here, we test their relative importance among major clades of Plethodontidae, the most species‐rich family of salamanders. Earlier studies have suggested that climatic‐niche evolution explains patterns of diversification among plethodontid clades, whereas rates of morphological evolution do not. A subsequent study stated that rates of morphological evolution instead explained patterns of species richness among plethodontid clades (along with “ecological limits” on richness of clades, leading to saturation of clades with species, given limited resources). However, they did not consider climatic‐niche evolution. Using phylogenetic multiple regression, we show that rates of climatic‐niche evolution explain most variation in richness among plethodontid clades, whereas rates of morphological evolution do not. We find little evidence that ecological limits explain patterns of richness among plethodontid clades. We also test whether rates of morphological and climatic‐niche evolution are correlated, and find that they are not. Overall, our results help explain richness patterns in a major amphibian group and provide possibly the first test of the relative importance of climatic niches and morphological evolution in explaining diversity patterns.     

Patterns of species diversity and phylogenetic structure of vascular plants on the Qinghai‐Tibetan Plateau

Large-scale patterns of species richness and the underlying mechanisms regulating these patterns have long been the central issues in biogeography and macroecology. Phylogenetic community structure is a result of combined effects of contemporary ecological interactions, environmental filtering, and evolutionary history, and it links community ecology with biogeography and trait evolution. The Qinghai-Tibetan Plateau provides a good opportunity to test the influence of contemporary climate on shaping species richness because of its unique geological history, cold climate, and high biodiversity. In this study, based on high-resolution distributions of ˜9000 vascular plant species, we explored how species richness and phylogenetic structure of vascular plants correlate with climates on the highest (and species rich) plateau on the Earth. The results showed that most of the vascular plants were distributed on the eastern part of the plateau; there was a strong association between species richness and climate, even after the effects of habitat heterogeneity were controlled. However, the responses of richness to climate remarkably depended on life-forms. Richness of woody plants showed stronger climatic associations than that of herbaceous plants; energy and water availability together regulated richness pattern of woody plants; whereas water availability predominantly regulated richness pattern of herbaceous plants. The phylogenetic structure of vascular species clustered in most areas of the plateau, suggesting that rapid speciation and environment filtering dominated the assembly of communities on the plateau. We further propose that biodiversity conservation in this area should better take into account ecological features for different life-forms and phylogenetic lineages.     

The niche, biogeography and species interactions

In this paper, I review the relevance of the niche to biogeography, and what biogeography may tell us about the niche. The niche is defined as the combination of abiotic and biotic conditions where a species can persist. I argue that most biogeographic patterns are created by niche differences over space, and that even ‘geographic barriers’ must have an ecological basis. However, we know little about specific ecological factors underlying most biogeographic patterns. Some evidence supports the importance of abiotic factors, whereas few examples exist of large-scale patterns created by biotic interactions. I also show how incorporating biogeography may offer new perspectives on resource-related niches and species interactions. Several examples demonstrate that even after a major evolutionary radiation within a region, the region can still be invaded by ecologically similar species from another clade, countering the long-standing idea that communities and regions are generally ‘saturated’ with species. I also describe the somewhat paradoxical situation where competition seems to limit trait evolution in a group, but does not prevent co-occurrence of species with similar values for that trait (called here the ‘competition–divergence–co-occurrence conundrum’). In general, the interface of biogeography and ecology could be a major area for research in both fields.     

An intercontinental comparison of dung beetle diversity between two mediterranean-climatic regions: local versus regional and historical influences

The species richness of biological communities is influenced by both local ecological, regional ecological, and historical factors. The relative importance of these factors may be deduced by comparison between communities in climatically and ecologically equivalent, but geographically and historically separate regions of the world. This claim is based on the hypothesis that community processes driven by similar local ecological factors lead to convergence in species richness whereas those driven by differing regional or historical factors lead to divergence. An intercontinental comparison between the winter rainfall regions of South Africa and the Iberian Peninsula showed that overall species richness of dung beetles was dissimilar at local, subregional and regional scales in Scarabaeidae s. str. but similar at all scales in Aphodiinae. Removal of species widespread in the summer rainfall region of Africa or the temperate region of Europe (regional component) resulted in dissimilarity in species richness of mediterranean endemics at all scales in both dung beetle taxa. However, the lines joining each set of species richness values were parallel which may indicate similarities in processes between different mediterranean climatic regions despite slight differences in latitudinal range. The dominant pattern of dissimilarity or non-convergence may be related primarily to intercontinental differences in regional biogeographical and evolutionary history (faunal dispersal, glaciation effects in relation to geographical barriers to dispersal, speciation history, long-term disturbance history). The limited pattern of similarity or convergence in overall species richness of Aphodiinae may be a chance result or primarily related to intercontinental similarities in local ecological factors.     

Can the tropical conservatism hypothesis explain temperate species richness patterns? An inverse latitudinal biodiversity gradient in the New World snake tribe Lampropeltini

Aim  A latitudinal gradient in species richness, defined as a decrease in biodiversity away from the equator, is one of the oldest known patterns in ecology and evolutionary biology. However, there are also many known cases of increasing poleward diversity, forming inverse latitudinal biodiversity gradients. As only three processes (speciation, extinction and dispersal) can directly affect species richness in areas, similar factors may be responsible for both classical (high tropical diversity) and inverse (high temperate diversity) gradients. Thus, a modified explanation for differential species richness which accounts for both patterns would be preferable to one which only explains high tropical biodiversity.
Location  The New World.
Methods  We test several proposed ecological, temporal, evolutionary and spatial explanations for latitudinal diversity gradients in the New World snake tribe Lampropeltini, which exhibits its highest biodiversity in temperate regions.
Results  We find that an extratropical peak in species richness is not explained by latitudinal variation in diversification rate, the mid-domain effect, or Rapoport's rule. Rather, earlier colonization and longer duration in the temperate zones allowing more time for speciation to increase biodiversity, phylogenetic niche conservatism limiting tropical dispersal and the expansion of the temperate zones in the Tertiary better explain inverse diversity gradients in this group.
Main conclusions  Our conclusions are the inverse of the predictions made by the tropical conservatism hypothesis to explain higher biodiversity near the equator. Therefore, we suggest that the processes invoked are not intrinsic to the tropics but are dependent on historical biogeography to determine the distribution of species richness, which we refer to as the 'biogeographical conservatism hypothesis'.     

Integrating the effects of area, isolation, and habitat heterogeneity on species diversity: a unification of island biogeography and niche theory

We present an analytical model that unifies two of the most influential theories in community ecology, namely, island biogeography and niche theory. Our model captures the main elements of both theories by incorporating the combined effects of area, isolation, stochastic colonization and extinction processes, habitat heterogeneity, and niche partitioning in a unified, demographically based framework. While classical niche theory predicts a positive relationship between species richness and habitat heterogeneity, our unified model demonstrates that area limitation and dispersal limitation (the main elements of island biogeography) may create unimodal and even negative relationships between species richness and habitat heterogeneity. We attribute this finding to the fact that increasing heterogeneity increases the potential number of species that may exist in a given area (as predicted by niche theory) but simultaneously reduces the amount of suitable area available for each species and, thus, increases the likelihood of stochastic extinction. Area limitation, dispersal limitation, and low reproduction rates intensify the latter effect by increasing the likelihood of stochastic extinction. These analytical results demonstrate that the integration of island biogeography and niche theory provides new insights about the mechanisms that regulate the diversity of ecological communities and generates unexpected predictions that could not be attained from any single theory.     

黄河流域被子植物和陆栖脊椎动物丰富度格局及其影响因子

生物多样性的大尺度空间分布格局及其形成机制一直是生态学和生物地理学的核心内容。黄河流域是我国重要的生态屏障, 明确该区域动植物多样性分布格局及其影响因素, 对我国黄河流域生态保护和高质量发展具有重要意义。本研究通过收集黄河流域被子植物和陆栖脊椎动物分布数据, 结合气候、环境异质性和人类活动等信息, 探讨了黄河流域被子植物和陆栖脊椎动物物种丰富度格局及其主要影响因素。结果表明, 黄河流域被子植物和陆栖脊椎动物物种丰富度在区域尺度具有相似的分布格局: 南部山地动植物物种丰富度最高, 而东部高寒区和北部干旱区物种丰富度最低。回归树模型表明, 冠层高度范围和净初级生产力范围分别是黄河流域被子植物和陆栖脊椎动物物种丰富度最重要的预测因子; 当移除空间自相关影响后, 环境异质性和气候因子依然对区域尺度的动植物物种丰富度具有较高且相似的解释度。表明环境异质性和气候共同决定了黄河流域被子植物和陆栖脊椎动物物种丰富度格局, 而人类使用土地面积并不是影响黄河流域动植物物种丰富度格局的主要因子。因此, 在未来的研究中若针对不同区域筛选出更精准的环境驱动因子或选用更多不同类别的环境异质性因子进行分析, 将有助于更深入理解物种多样性格局的成因。     

Relative role of contemporary environment versus history in shaping diversity patterns of China's woody plants

What determines large‐scale patterns of species diversity is a central and controversial topic in biogeography and ecology. In this study, we compared the effects of contemporary environment and historical contingencies on species richness patterns of woody plants in China, using fine‐resolution geographic databases of the distributions of 11 405 woody species and climate, topography, and vegetation information. Residuals of species richness‐environment generalized linear models were significantly different from 0 in the majority of seven biogeographical regions, and also differed significantly between these regions, indicating significant deviation from the predicted species richness based on contemporary environment. Additionally, species richness of a given biogeographical region deviated substantially from the predictions of species richness‐environment models developed for the remaining regions combined. This suggests different richness‐environment relationships among regions. These results indicate important historical signals in the species richness patterns of woody plants across China. The signals are especially pronounced in the eastern Himalayas, the Mongolian Plateau, and the Tibetan Plateau, perhaps reflecting their special geological features and history. Nevertheless, partial regression indicated that historical effects were less important relative to contemporary environment. In conclusion, contemporary environment (notably climate) determines the general trend in woody‐plant species richness across China, while historical contingencies generate regional deviations from this trend. Our findings imply that both species diversity and regional evolutionary and ecological histories should be taken into account for future nature conservation.     

Toward molecular trait‐based ecology through integration of biogeochemical,geographical and metagenomic data

Using metagenomic ‘parts lists’ to infer global patterns on microbial ecology remains a significant challenge. To deduce important ecological indicators such as environmental adaptation, molecular trait dispersal, diversity variation and primary production from the gene pool of an ecosystem, we integrated 25 ocean metagenomes with geographical, meteorological and geophysicochemical data. We find that climatic factors (temperature, sunlight) are the major determinants of the biomolecular repertoire of each sample and the main limiting factor on functional trait dispersal (absence of biogeographic provincialism). Molecular functional richness and diversity show a distinct latitudinal gradient peaking at 20°N and correlate with primary production. The latter can also be predicted from the molecular functional composition of an environmental sample. Together, our results show that the functional community composition derived from metagenomes is an important quantitative readout for molecular trait‐based biogeography and ecology.     

The impact of population processes on patterns of species richness: Lessons from elevational gradients

In the last few years, considerable headway has been made towards understanding patterns of species richness along latitudinal and elevational gradients, mostly by focussing on the influences of surface area, climatic factors, evolutionary history, and stochastic processes. However, the potential impact of population-level processes in determining or modifying patterns of species richness has largely been neglected, partly due to the difficulty of gathering such data for numerous species along geographical or ecological gradients. Based on two empirical examples, I here show that dispersal and the resulting source-sink effects modify patterns of plant species richness along elevation gradients, and that the inclusion or exclusion of such sink populations alters the perception of the diversity patterns and hence our interpretation of them. I argue that population processes should be taken into account when studying patterns of species richness, especially at scales at which dispersal is common in the taxon under consideration.     

Historical stability of diversity patterns in African estrildid finches (Aves: Estrildidae)?

Studying shifts in species diversity through time and space is an essential component of many aspects of biogeography and ecology. In this study, we predict the potential distribution of 61 species of African estrildid finches in order to assess current and past diversity patterns. Models were projected onto two climatic scenarios (Community Climate System Model, CCSM, and Model for Interdisciplinary Research on Climate, MIROC) representing past climate conditions, as might be expected during the Last Glacial Maximum 21 000 years BP. Subsequent overlays of the resulting potential distributions were conducted under different dispersal assumptions and compared with expert maps. Our results suggest highly similar current distribution patterns obtained by both methods. Projections onto Pleistocene scenarios showed similar patterns, with only small differences under limited and unlimited dispersal assumptions. Looking separately at diversity patterns predicted for forest and savannah species, diversity hot spots of forest species under MIROC conditions were consistent with suggested forest refugia, but were inconsistent under CCSM conditions. According to our models, savannah species were more widely distributed during the cooler and drier conditions of the Pleistocene. By using ecological niche models we show that current diversity patterns of a whole species group may have changed only slightly since the Pleistocene, suggesting a pattern of general spatial stability. However, we emphasize the importance of using different climatic scenarios as well as including the supposed dispersal of organisms in the modelling, as these factors influence results on a broad scale. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 455–470.     

Time and environment explain the current richness distribution of non‐marine turtles worldwide

Ecological, historical, and evolutionary hypotheses are important to explain geographical diversity gradients in many clades, but few studies have combined them into a single analysis allowing a comparison of their relative importance. This study aimed to evaluate the relative importance of ecological, historical, and evolutionary hypotheses in explaining the current global distribution of non‐marine turtles, a group whose distribution patterns are still poorly explored. We used data from distribution range maps of 336 species of non‐marine turtles, environmental layers, and phylogeny to obtain richness estimates of these animals in 2° × 2° cells and predictors related to ecological, evolutionary and historical hypotheses driving richness patterns. Then we used a path analysis to evaluate direct and indirect effects of the predictors on turtle richness. Ancestral area reconstruction was also performed in order to evaluate the influence of time‐for‐speciation in the current diversity of the group. We found that environmental variables had the highest direct effects on non‐marine turtle richness, whereas diversification rates and area available in the last 55 million yr minimally influenced turtle distributions. We found evidence for the time‐for‐speciation effect, since regions colonized early were generally richer than recently colonized regions. In addition, regions with a high number of colonization events had a higher number of turtle species. Our results suggested that ecological processes may influence non‐marine turtle richness independent of diversification rates, but they are probably related to dispersal abilities. However, colonization time was also an important component that must be taken into account. Finally, our study provided additional support for the importance of ecological (climate and productivity) and historical (time‐for‐speciation and dispersal) processes in shaping current biodiversity patterns.     

Climate, niche conservatism, and the global bird diversity gradient

We tested the proposition that there are more species in the tropics because basal clades adapted to warm paleoclimates have been lost in regions now experiencing cool climates. Molecular phylogenies were used to classify species as "basal" and "derived" based on their family, and their richness patterns were contrasted. Path models also evaluated environmental predictors of richness patterns. As predicted, basal clades are more diverse in the lowland tropics, whereas derived clades are more diverse in the extratropics and high-altitude tropics. Seventy-four percent of the variation in bird richness was explained by environmental variables, but models differed for basal and derived groups. The overall gradient is described by the spatial pattern of basal clades, although there are differences in the Old and New Worlds. We conclude that in ecological time, the global richness gradient reflects birds' responses to climatic gradients, partially operating via plants. Over evolutionary time, the gradient primarily reflects the extirpation of species in older clades from parts of the world that have become cooler in the present. A strong secondary effect arises from dispersal of clades from centers of origin and subsequent radiations. Overall, the diversity gradient is well explained by niche conservatism and the "time-for-speciation" hypothesis.     

Species richness and evolutionary niche dynamics: a spatial pattern-oriented simulation experiment

Evolutionary processes underlying spatial patterns in species richness remain largely unexplored, and correlative studies lack the theoretical basis to explain these patterns in evolutionary terms. In this study, we develop a spatially explicit simulation model to evaluate, under a pattern-oriented modeling approach, whether evolutionary niche dynamics (the balance between niche conservatism and niche evolution processes) can provide a parsimonious explanation for patterns in species richness. We model the size, shape, and location of species' geographical ranges in a multivariate heterogeneous environmental landscape by simulating an evolutionary process in which environmental fluctuations create geographic range fragmentation, which, in turn, regulates speciation and extinction. We applied the model to the South American domain, adjusting parameters to maximize the correspondence between observed and predicted patterns in richness of about 3,000 bird species. Predicted spatial patterns, which closely resemble observed ones (r2=0.795), proved sensitive to niche dynamics processes. Our simulations allow evaluation of the roles of both evolutionary and ecological processes in explaining spatial patterns in species richness, revealing the enormous potential of the link between ecology and historical biogeography under integrated theoretical and methodological frameworks.     

Habitat diversity associated to island size and environmental filtering control the species richness of rock‐savanna plants in neotropical inselbergs

Disentangling the multiple factors controlling species diversity is a major challenge in ecology. Island biogeography and environmental filtering are two influential theories emphasizing respectively island size and isolation, and the abiotic environment, as key drivers of species richness. However, few attempts have been made to quantify their relative importance and investigate their mechanistic basis. Here, we applied structural equation modelling, a powerful method allowing test of complex hypotheses involving multiple and indirect effects, on an island‐like system of 22 French Guianan neotropical inselbergs covered with rock‐savanna. We separated the effects of size (rock‐savanna area), isolation (density of surrounding inselbergs), environmental filtering (rainfall, altitude) and dispersal filtering (forest‐matrix openness) on the species richness of all plants and of various ecological groups (terrestrial versus epiphytic, small‐scale versus large‐scale dispersal species). We showed that the species richness of all plants and terrestrial species was mainly explained by the size of rock‐savanna vegetation patches, with increasing richness associated with higher rock‐savanna area, while inselberg isolation and forest‐matrix openness had no measurable effect. This size effect was mediated by an increase in terrestrial‐habitat diversity, even after accounting for increased sampling effort. The richness of epiphytic species was mainly explained by environmental filtering, with a positive effect of rainfall and altitude, but also by a positive size effect mediated by enhanced woody‐plant species richness. Inselberg size and environmental filtering both explained the richness of small‐scale and large‐scale dispersal species, but these ecological groups responded in opposite directions to altitude and rainfall, that is positively for large‐scale and negatively for small‐scale dispersal species. Our study revealed both habitat diversity associated with island size and environmental filtering as major drivers of neotropical inselberg plant diversity and showed the importance of plant species growth form and dispersal ability to explain the relative importance of each driver.