Diversity patterns in terrestrial tetrapod clades are governed by equilibrium dynamics.

Explaining the disparity of species richness across the tree of life is one of the great challenges in evolutionary biology. Some lineages are exceptionally species rich, while others are relatively species poor. One explanation for heterogeneity among clade richness is that older clades are more species rich because they have had more time to accrue diversity than younger clades. Alternatively, disparity in species richness may be due to among-lineage diversification rate variation. Here we investigate diversification in water scavenger beetles (Hydrophilidae), which vary in species richness among major lineages by as much as 20 fold. Using a time-calibrated phylogeny and comparative methods, we test for a relationship between clade age and species richness and for shifts in diversification rate in hydrophilids. We detected a single diversification rate increase in Megasternini, a relatively young and species rich clade whose diversity might be explained by the stunning diversity of ecological niches occupied by this clade. We find that Amphiopini, an old clade, is significantly more species poor than expected, possibly due to its restricted geographic range. The remaining lineages show a correlation between species richness and clade age, suggesting that both clade age and variation in diversification rates explain the disparity in species richness in hydrophilids. We find little evidence that transitions between aquatic, semiaquatic, and terrestrial habitats are linked to shifts in diversification rates.

The topic of this thesis is the latitudinal diversity gradient: the general increase in numbers of species from high latitudes towards the equator. Although it is a well-documented and very general pattern, there is little consensus among biologists as to the causes of high tropical species richness. In Chapter 1 I give an overview of the latitudinal diversity gradient and hypotheses proposed to explain it, and outline a framework for developing and testing hypotheses. The emphasis in this thesis is on non-equilibrium hypotheses, and in particular on the idea that rates of species diversification are higher at low latitudes. In Chapter 2 I directly test the hypothesis that rates of species diversification increase towards the equator, using the phylogenetic method of sister-group comparisons. For birds and butterflies, 1 show that there does indeed appear to be an increase in rates of diversification towards lower latitudes. One possible explanation for this pattern links climatic conditions at low latitudes to faster speciation, via a causal chain which includes a higher rate of molecular evolution. In Chapter 3 I test the prediction that rates of molecular evolution are faster at low latitudes, using phylogenies reconstructed from DNA sequence data for birds. Although the results provide no evidence for a latitudinal effect on rates of cytb and ND2 evolution in birds, this chapter demonstrates a way in which further tests on a wider range of genes and taxa can be carried out as more sequence data becomes available. If rates of diversification are higher in the tropics, this may result from latitudinal gradients in life history traits which could influence rates of speciation or extinction. However, previous attempts to test for such patterns have rarely controlled for phylogenetic relationships among species, and have never controlled for geographic range overlap. In Chapter 4 I present a method for analyzing latitudinal variation in life history traits which takes both of these problems into account. For birds, this method indicates strong latitudinal variation in geographic range size and clutch size, less strong variation in body size and niche width, and no variation in the strength of sexual selection. While this does not prove that life history plays a part in generating the latitudinal diversity gradient, a robust demonstration of latitudinal variation in life history traits is an important prerequisite for any hypotheses which link life history with high tropical species richness. Speciation and extinction rates are believed to vary with species' life history and ecology. If speciation or extinction rates also vary with latitude, we should expect species with certain traits to show stronger latitudinal diversity gradients than others. We should also expect to see latitudinal variation in the macroecological structure of species assemblages. Chapters 5 and 6 confirm these expectations. In Chapter 5 I show that smaller-bodied bird species have steeper latitudinal diversity gradients than larger species. This is reflected in systematic latitudinal variation in the shape of body size frequency distributions, usually thought to be relatively consistent across regions. In Chapter 6 I show that body size - abundance relationships in the Australian marsupial fauna differ considerably between temperate and tropical subsets of the fauna. Whereas the temperate species display the typical negative relationship, the tropical species show no significant relationship. This pattern is consistent with the explanation that extinction rates vary with respect to body size, abundance and the latitude in which a species occurs. Together, the results of the analyses presented in this thesis provide evidence in favour of the non-equilibrium view that there are more species in the tropics because rates of species diversification are higher. It seems likely that this is due to latitudinal variation in environmental conditions, leading to latitudinal variation in species' life histories and the structure of species assemblages, and to latitudinal variation in rates of speciation or extinction. However, it is still difficult to judge whether it is variation in speciation rate (cradle model) or extinction rate (museum model) which is of primary importance, or if both are equally important. Further work on this question, applying the large-scale comparative methodology used here, will be necessary to progress towards a full understanding of the high species richness of the tropics.

Whatever criteria are used to measure evolutionary success – species numbers, geographic range, ecological abundance, ecological and life history diversity, background diversification rates, or the presence of rapidly evolving clades – the legume family is one of the most successful lineages of flowering plants. Despite this, we still know rather little about the dynamics of lineage and species diversification across the family through the Cenozoic, or about the underlying drivers of diversification. There have been few attempts to estimate net species diversification rates or underlying speciation and extinction rates for legume clades, to test whether among-lineage variation in diversification rates deviates from null expectations, or to locate species diversification rate shifts on specific branches of the legume phylogenetic tree. In this study, time-calibrated phylogenetic trees for a set of species-rich legume clades – Calliandra, Indigofereae, Lupinus, Mimosa and Robinieae – and for the legume family as a whole, are used to explore how we might approach these questions. These clades are analysed using recently developed maximum likelihood and Bayesian methods to detect species diversification rate shifts and test for among-lineage variation in speciation, extinction and net diversification rates. Possible explanations for rate shifts in terms of extrinsic factors and/or intrinsic trait evolution are discussed. In addition, several methodological issues and limitations associated with these analyses are highlighted emphasizing the potential to improve our understanding of the evolutionary dynamics of legume diversification by using much more densely sampled phylogenetic trees that integrate information across broad taxonomic, geographical and temporal levels.

Genetic diversity is critical for species evolution and their adaptability to global changes, while speciation rate is critical for explaining large-scale patterns of species richness. Exploring correlates of variation in genetic diversity and speciation rates across species is a major interest of evolutionary biologists, but these two questions have mostly been investigated independently. Here, we assess the relationship between intra-specific genetic diversity and speciation rate for 1897 mammal species (~one third of the total diversity) covering all mammalian orders. We find a negative association between mitochondrial genetic diversity and speciation rate across mammalian clades globally. This association is not accounted for by differences in the ecological attributes of species. Our findings suggest a systematic link between micro- and macroevolutionary processes that need to be better understood and considered when investigating determinants of either genetic diversity or speciation rates.

Biodiversity results from origination and extinction, justifying interest in identifying traits that influence this balance. Traits implicated in the success or failure of lineages include dispersal, colonization ability, and geographic range size. We investigated the impact of dispersal and range size on contemporary diversity in the Rosales. We used the multiple-state speciation and extinction (MuSSE) method to explore the effects on genus-level diversification of two genus-level traits (geographic range size and within-genus proclivity to speciate) and two species traits (seed dispersal and growth habit) and the multiple hidden-state speciation and extinction (MuHiSSE) method for species-level associations. Finally, we conducted a PGLS (phylogenetic least-squares) analysis to distinguish between speciation within genera versus origination of new genera. At the species level, animal dispersal enhances diversification rate in both woody and herbaceous lineages, while woody lineages without animal dispersal have higher extinction rates than speciation rates. At the genus level, herbaceous taxa have positive diversification rates regardless of other character states. Diversification rate variation is also explained by two interactions: (1) a three-way interaction between large geographic range, animal-mediated dispersal, and high within-genus species richness, whereby genera possessing all three traits have high diversification rates, and (2) a four-way interaction by which the three-way interaction is stronger in woody genera than in herbaceous genera. Colonization ability may underlie the relationship between dispersal type and range size and may influence past diversification rates by decreasing extinction rates during late Cenozoic climate volatility. Thus, colonization ability could be used to predict future extinction risk to aid conservation.

Water limitation prevails over energy in European diversity gradients of sheetweb spiders (Araneae: Linyphiidae)

AimBiodiversity is not uniformly distributed across the Earth’s surface, even among physiographically comparable biomes in different biogeographic regions. For lizards, the world’s large desert regions are characterized by extreme heterogeneity in species richness, spanning some of the most species‐rich (arid Australia) and species‐poor (central Asia) biomes overall. Regional differences in species diversity may arise as a consequence of the interplay of several factors (e.g., evolutionary time, diversification rate, environment), but their relative importance for biogeographic patterns remains poorly known. Here we use distributional and phylogenetic data to assess the evolutionary and ecological drivers of large‐scale variation in desert lizard diversity.LocationDeserts worldwide.Major taxa studiedLizards (non‐snake squamates).MethodsWe specifically test whether diversity patterns are best explained by differences in the ages of arid‐adapted lineages (evolutionary time hypothesis), by regional variation in speciation rate, by geographic area of the arid systems, and by spatial variation related to environment (climate, topography, and productivity).ResultsWe found no effect of recent speciation rate and geographic area on differences in desert lizard diversity. We demonstrate that the extreme species richness of the Australian deserts cannot be explained by greater evolutionary time, because species began accumulating more recently there than in more species‐poor arid regions. We found limited support for relationships between regional lizard richness and environmental variables, but these effects were inconsistent across deserts, showing a differential role of the environment in shaping the lizard diversity in different arid regions.Main conclusionsOur results provide evidence against several classic hypotheses for interregional variation in species richness, but also highlight the complexity of processes underlying vertebrate community richness in the world’s great arid systems.

AimsLong‐term climate stability, contemporary climate and environmental heterogeneity have been linked to bird diversity patterns through their direct impacts on diversification rate, as well as through their indirect effects on plant species richness, which could also directly and indirectly affect bird diversity. This study aimed to quantitatively assess whether these potential drivers could indirectly affect bird species richness through their direct effects on the diversification rate in birds in eastern Asia.LocationMainland China.TaxonBirds.MethodsUsing the distribution data of 1127 bird species across 320 prefecture cities in China and a phylogenetic tree of these bird species, we analysed the distribution patterns of bird species richness and diversification rate of all birds, passerine birds and non‐passerine birds, respectively. We also investigated their relationships with long‐term climate stability, contemporary climate, elevation range and plant diversity using ordinary least squares regression model and simultaneous autoregressive model. In addition, structural equation model was used to analyse whether these drivers could indirectly affect bird species richness through their direct effects on bird diversification rate.ResultsThe results showed that bird species richness and diversification rate were highest in southwestern China. Additionally, diversification rate for passerine birds was higher than non‐passerine birds and all birds. Regression analyses revealed that plant species richness was the variable most associated with bird species richness and diversification rate across the three groups. Notably, results from structural equation model indicated that plant species richness, elevation range and glacial–interglacial climate change can indirectly influence bird species richness by directly affecting diversification rates.Main ConclusionsThese findings emphasize the importance of considering diversification rate when understanding the geographic distribution patterns of bird diversity. The direct and indirect effects of plant species richness, elevation range and glacial–interglacial climate change on bird diversity highlight the crucial role of mountain regions with higher plant diversity and stable paleoclimate in forming and maintaining biodiversity.

AimGeographical gradients of vertebrate species richness are determined jointly by evolutionary and environmental factors. Support for these factors comes mostly from tetrapods and, recently, marine fishes, but their validity and relative importance in freshwater fishes is not well understood. Here, we describe the species richness gradient for the major component of the viviparous freshwater fishes of the Americas, the poeciliids, and test the effects of evolutionary and environmental factors on this pattern.LocationThe Americas.Time periodApproximatley 56–0 Ma.Major taxa studiedPoeciliidae (Teleostei: Cyprinodontiformes).MethodsWe constructed geographical ranges for 93% (256) of poeciliids to describe and evaluate their species richness gradient. Evolutionary factors (evolutionary time and speciation rate) were derived from a recent phylogeny. Environmental factors were represented as basin area, topographical heterogeneity, energy, climate seasonality and past climatic stability. We tested the influence of these factors with a piecewise structural equation model (pSEM).ResultsThe distribution of Poeciliidae is biased to the Atlantic coast, with species richness showing a bimodal latitudinal gradient, peaking in middle latitudes near the Tropics of Cancer and Capricorn, and exhibiting the highest richness in Middle America. The pSEM showed that this species richness pattern was influenced positively by evolutionary time and past climatic stability and negatively by climate seasonality.Main conclusionThe species richness gradient of Poeciliidae has been shaped by the interplay of evolutionary time in addition to current and historical climate. Indeed, regions with high poeciliid richness were those containing by ancient lineages, supporting the time‐for‐speciation effect, and that have experienced low historical stability in temperature and currently show low temperature seasonality. Conversely, species‐poor regions contained younger lineages and experienced greater temperature seasonality. Our study highlights the need to assess jointly the evolutionary, historical and climatic drivers of species richness in order to unravel the causes of diversity gradients.

A major goal of ecology and evolutionary biology is to explain geographic patterns of species richness. Richness is often correlated with climatic variables. However, the processes underlying these climate‐diversity relationships remain poorly understood. Two potential hypotheses to explain these relationships involve: (i) faster diversification rates (speciation minus extinction) in high‐richness climates and (ii) earlier colonization of high‐richness climates, allowing more time for speciation to build up richness. Few studies have tested these hypotheses directly, and most focused on animal clades with limited richness. In this study, we test these hypotheses in Chinese angiosperms, encompassing ~10% of Earth's plant species, using large‐scale phylogenetic, climatic, and distributional data including 26,977 species. We find that climatic zones that were colonized earlier have higher species richness. By contrast, relationships between diversification rates and richness of climatic zones are often nonsignificant or negative. Our study reveals that even when richness is strongly correlated with climate, the underlying explanation may still be rooted in phylogenetic history. Thus, climate may not be a competing explanation for richness patterns relative to colonization times and diversification rates. We also show that the timing of colonization can be crucial for explaining richness patterns. Yet, many recent studies have ignored this explanation and instead have focused solely on rates of speciation and diversification as drivers of diversity gradients.

Summary1. Rates of evolutionary diversification play a fundamental role in the assembly of regional communities, but the relative balance of diversity‐dependent and diversity‐independent rate control remains controversial. Recent studies have reported a significant relationship between the amount of time a geographic region has been occupied and species richness, implying that feedbacks between species interactions and diversification rates may be less important than diversity‐independent mechanisms in generating regional species pools.2. Previous analyses of the regional age‐diversity relationship have used a range of metrics to quantify the amount of ‘evolutionary time’ that a region has been occupied, but the relative performance of these metrics has not been quantified.3. Here, I evaluate the performance of the most commonly used methods and data transformations for assessing the regional age‐diversity relationship.4. I find that process‐based models of diversification are more appropriate than process‐independent models for evaluating the influence of time on species richness. I also demonstrate that time should not be log‐transformed when testing the regional time‐for‐speciation hypothesis, as in some recent studies.5. Application of this framework to patterns of elevational richness in several recent studies provides support for a logistic model of diversity accumulation within elevational bands and implies that evolutionary age alone cannot fully account for current species richness.6. These results indicate that process‐based models, in concert with appropriate data transformation, provide a robust foundation for inference on the causes of regional diversity gradients.

Most empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking pre-existing niches, whereas constant rates have been attributed to non-adaptive processes such as sexual selection and mutation. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the temporal trend in the speciation rate can also be explained by frequency-dependent selection. We construct a frequency-dependent and DNA sequence-based model of speciation. We compare our model to empirical diversity patterns observed for cichlid fish and Darwin's finches, two classic systems for which speciation rates and richness data exist. Negative frequency-dependent selection predicts well both the declining speciation rate found in cichlid fish and explains their species richness. For groups like the Darwin's finches, in which speciation rates are constant and diversity is lower, speciation rate is better explained by a model without frequency-dependent selection. Our analysis shows that differences in diversity may be driven by incipient species abundance with frequency-dependent selection. Our results demonstrate that genetic-distance-based speciation and frequency-dependent selection are sufficient to explain the high diversity observed in natural systems and, importantly, predict decay through time in speciation rate in the absence of pre-existing niches.

Study of the latitudinal diversity gradient to date has focused largely on pattern description, with relatively little work on the possible mechanisms underlying the pattern. One proximate mechanism is a latitudinal bias in the discrepancy between speciation and extinction rates, leading to higher rates of species diversification toward lower latitudes. Despite being central to many explanations for high tropical diversity, this mechanism is tested very rarely. We discuss some of the problems involved in testing for latitudinal bias in diversification rates and present an example phylogenetic analysis for endemic bird genera of the New World. The results provide evidence for higher diversification rates in clades inhabiting lower latitudes, both when genera are considered independent and when phylogeny is controlled for using independent contrasts. High rates of diversification are also associated with larger geographic area and higher net primary productivity, although these do not fully account for the latitudinal effect. The latitudinal pattern is stronger in younger clades, supporting the prediction of a simple model in which the signal of latitudinal bias in diversification rates diminishes as clades age and become saturated with species. Our study demonstrates that a clade-based approach can help answer important questions that a geographic approach cannot, but large phylogenies and geographic databases are needed to cope with the large amount of noise inherent in this type of analysis.

BackgroundUnderstanding the patterns and processes of species distributions has long remained a central focus of biogeographical and ecological research. While the evidence for elevational patterns in species richness is widespread, our understanding of underlying causes and mechanisms remains limited. Therefore, this study aimed to entangle the influence of environmental variables on plant species richness along elevational gradients in the Western Himalayas.MethodsWe compiled elevational distribution for about 1150 vascular plants using the published literature and available database. The species richness was estimated in 100-m elevational bands using the range interpolation method. We used the generalised linear model and structural equation modelling (SEM) framework to identify the direct and indirect effects of climatic factors on species richness.ResultsOur results indicated that primary environmental correlates of species richness varied with elevational gradients. Climatic variables combined with energy and water availability were more important than the topographic heterogeneity. Further, the direct and interaction effects of climatic variables were more substantial than their indirect effects. The indirect effects of climate are more strongly mediated by water–energy dynamics than the energy alone.ConclusionsOverall, our findings emphasise the importance of considering direct effects and interactions among environmental variables while studying the underlying mechanisms governing elevational biodiversity gradients. Species richness appeared to be shaped by climatic tolerances rather than habitat heterogeneity at regional scales. This information can have implications for biodiversity dynamics under environmental change.

The taxonomic evolution of Jurassic and Cretaceous calcareous nannofossil species is described using the following indices: species diversity, rate of speciation, rate of extinction, rate of diversification, rate of turnover, survivorship, and species accretion. The Jurassic prior to the late Oxfordian is characterized by positive diversification rates, that is, rates of speciation exceeded rates of extinction. Highest rates of diversification occurred in the late Lias and early Oxfordian. During the generally regressive latest Jurassic, diversification rates remained low and rates of extinctions exceed rates of speciation. In the early Cretaceous, rates of diversification are positive and peak in the early Valanginian, early Aptian, and middle Albian, after which time rates of extinction generally exceed rates of speciation. Such peaks in rate of evolution coincide with times of increased accumulation of organic carbon in the ocean (“anoxic events”). Peaks in rates of extinction result in very high rates of turnover during times of major regressions, in particular, in the Tithonian and Maastrichtian. Survivorship analyses for three datum planes (74.5, 144, and 160 Ma) show relatively constant extinction rates with some stepping in the older part; they are best explained by a temporally fluctuating abiotic environment causing changes in the probability of extinction. Species accretion curves are also relatively linear with some indication of changing rates of speciation. The coincidences of major changes in evolutionary rates with major paleoceanographic events are indicative of a predominantly abiotic control of nannoplankton evolution. Relationships of evolutionary rates of calcareous nannoplankton with deep ocean ventilation, sea level, and ocean fertility indicates that global tectonic processes are the ultimate causes of evolutionary change.