Phylogenetically nested comparisons for testing correlates of species richness: a simulation study of continuous variables

On the Selection and Analysis of Clades in Comparative Evolutionary Studies

Researchers commonly present results of comparative studies of taxonomic groups. In this review, we criticize the focus on named clades, usually, comparably ranked groups such as families or orders, for comparative evolutionary analyses and question the general practice of using clades as units of analysis. The practice of analyzing sets of named groups persists despite widespread appreciation that the groups we have chosen to name are based on subjective human concerns rather than objective properties of nature. We demonstrate an effect of clade selection on results in one study and present some potential alternatives to selecting named clades for analysis that are relatively objective in clade choice. However, we note that these alternatives are only partial solutions for clade-based studies. The practice of analyzing named clades obviously is biased and problematic, but its issues portend broader problems with the general approach of employing clades as units of analysis. Most clade-based studies do not account for the nonindependence of clades, and the biological insight gained from demonstrating some pattern among a particular arbitrary sample of groups is arguable. [Clades; comparative biology; taxonomic groups.].

Uncovering Higher-Taxon Diversification Dynamics from Clade Age and Species-Richness Data

The relationship between clade age and species richness has been increasingly used in macroevolutionary studies as evidence for ecologically versus time-dependent diversification processes. However, theory suggests that phylogenetic structure, age type (crown or stem age), and taxonomic delimitation can affect estimates of the age-richness correlation (ARC) considerably. We currently lack an integrative understanding of how these different factors affect ARCs, which in turn, obscures further interpretations. To assess its informative breadth, we characterize ARC behavior with simulated and empirical phylogenies, considering phylogenetic structure and both crown and stem ages. First, we develop a two-state birth-death model to simulate phylogenies including the origin of higher taxa and a hierarchical taxonomy to determine ARC expectations under ecologically and time-dependent diversification processes. Then, we estimate ARCs across various taxonomic ranks of extant amphibians, squamate reptiles, mammals, birds, and flowering plants. We find that our model reproduces the general ARC trends of a wide range of biological systems despite the particularities of taxonomic practice within each, suggesting that the model is adequate to establish a framework of ARC null expectations for different diversification processes when taxa are defined with a hierarchical taxonomy. ARCs estimated with crown ages were positive in all the scenarios we studied, including ecologically dependent processes. Negative ARCs were only found at less inclusive taxonomic ranks, when considering stem age, and when rates varied among clades. This was the case both in ecologically and time-dependent processes. Together, our results warn against direct interpretations of single ARC estimates and advocate for a more integrative use of ARCs across age types and taxonomic ranks in diversification studies. [Birth-Death models; crown age; diversity dependence; extinction; phylogenetic structure; speciation; stem age; taxonomy; time dependence; tree simulations.].

Phylogenetic analyses suggest that diversification and body size evolution are independent in insects

BACKGROUND

Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda (insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate the link between size and diversity within this ancient and highly diverse lineage.

RESULTS

The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes including significant phylogenetic conservatism.

CONCLUSIONS

Based on our findings we suggest that the use of models derived from well-studied but atypical clades, such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may collectively enhance our understanding of this key component of terrestrial ecosystems.

Dispersal capacity predicts both population genetic structure and species richness in reef fishes

Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of diversity across a diverse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae; in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological diversification and underscore the importance of dispersal-related traits in influencing the mode and tempo of evolution.

Standard sister clade comparison fails when testing derived character States

Comparing species richness in sister clades that differ in a character state is one of the ways to study factors influencing diversification. While most of its applications have focussed on traits that increase diversification, some have been used to study the association of a trait with lower species richness, e.g., the occurrence of dioecy in flowering plants. We show here, using simulations and an analytical model, that the null expectation of equal species richness that is generally used in sister clade comparisons is wrong in the case of a derived trait occurring independently from speciation: one should expect fewer species in the clade with the derived character state when there is no difference in diversification rates. This is due to the waiting time for the derived state to appear, which causes it to occur more often on longer branches. This has the important implication that the probability for a clade to possess the derived state depends on the tree geometry, and thus on species richness: species-poorer clades are more likely to possess the derived state. We develop a statistical test for sister clade comparisons to study the effect of a derived character state. Applying it to a data set of dioecious clades, we find that we cannot confirm earlier work that concluded that dioecy decreases diversification; on the contrary, it seems to be associated to higher species richness than expected. [angiosperms; dioecy; diversification; sister clades; species richness.].

Self-sterility in flowering plants: preventing self-fertilization increases family diversification rates

BACKGROUND AND SCOPE

New data are presented on the distribution and frequency of self-sterility (SS) - predominantly pre-zygotic self-incompatibility (SI) systems - in flowering plants and the hypothesis is tested that families with self-sterile taxa have higher net diversification rates (DRs) than those with exclusively self-compatible taxa using both absolute and relative rate tests.

KEY RESULTS

Three major forms of SI systems (where pollen is rejected at the stigmatic, stylar or ovarian interface) are found to occur in the oldest families of flowering plants, with times of divergence >100 million years before the present (mybp), while post-fertilization SS and heterostyly appear in families with crown ages of 81 and 87 mybp, respectively. It is also founnd that many (22) angiosperm families exhibit >1 SI phenotype and that the distribution of different types of SS does not show strong phylogenetic clustering, collectively suggesting that SS and SI systems have evolved repeatedly de novo in angiosperm history. Families bearing self-sterile taxa have higher absolute DRs using all available calibrations of the angiosperm tree, and this affect is caused mostly by the high DR of families with homomorphic SI systems (in particular stigmatic SI) or those in which multiple SS/SI phenotypes have been observed (polymorphic). Lastly, using sister comparisons, it is further demonstrated that in 29 of 38 sister pairs (including 95 families), the self-sterile sister group had higher species richness and DR than its self-compatible sister based on either the total number of taxa in the clade with SS or only the estimated fraction to harbour SS based on literature surveys.

CONCLUSIONS

Collectively, these analyses point to the importance of SS, particularly pre-zygotic SI in the evolution of flowering plants.

Correlates of species richness in the largest Neotropical amphibian radiation

Although tropical environments are often considered biodiversity hotspots, it is precisely in such environments where least is known about the factors that drive species richness. Here, we use phylogenetic comparative analyses to study correlates of species richness for the largest Neotropical amphibian radiation: New World direct-developing frogs. Clade-age and species richness were nonsignificantly, negatively correlated, suggesting that clade age alone does not explain among-clade variation in species richness. A combination of ecological and morphological traits explained 65% of the variance in species richness. A more vascularized ventral skin, the ability to colonize high-altitude ranges, encompassing a large variety of vegetation types, correlated significantly with species richness, whereas larger body size was marginally correlated with species richness. Hence, whereas high-altitude ranges play a role in shaping clade diversity in the Neotropics, intrinsic factors, such as skin structures and possibly body size, might ultimately determine which clades are more speciose than others.

Contrasted patterns of hyperdiversification in Mediterranean hotspots

Dating the Tree of Life has now become central to relating patterns of biodiversity to key processes in Earth history such as plate tectonics and climate change. Regions with a Mediterranean climate have long been noted for their exceptional species richness and high endemism. How and when these biota assembled can only be answered with a good understanding of the sequence of divergence times for each of their components. A critical aspect of dating by using molecular sequence divergence is the incorporation of multiple suitable age constraints. Here, we show that only rigorous phylogenetic analysis of fossil taxa can lead to solid calibration and, in turn, stable age estimates, regardless of which of 3 relaxed clock-dating methods is used. We find that Proteaceae, a model plant group for the Mediterranean hotspots of the Southern Hemisphere with a very rich pollen fossil record, diversified under higher rates in the Cape Floristic Region and Southwest Australia than in any other area of their total distribution. Our results highlight key differences between Mediterranean hotspots and indicate that Southwest Australian biota are the most phylogenetically diverse but include numerous lineages with low diversification rates.

Relating traits to diversification: a simple test

We describe a simple comparative method for determining whether rates of diversification are correlated with continuous traits in species-level phylogenies. This involves comparing traits of species with net speciation rate (number of nodes linking extant species with the root divided by the root to tip evolutionary distance), using a phylogenetically corrected correlation. We use simulations to examine the power of this test. We find that the approach has acceptable power to uncover relationships between speciation and a continuous trait and is robust to background random extinction; however, the power of the approach is reduced when the rate of trait evolution is decreased. The test has low power to relate diversification to traits when extinction rate is correlated with the trait. Clearly, there are inherent limitations in using only data on extant species to infer correlates of extinction; however, this approach is potentially a powerful tool in analyzing correlates of speciation.

Rates of nucleotide substitution in Cornaceae (Cornales)-Pattern of variation and underlying causal factors

Identifying causes of genetic divergence is a central goal in evolutionary biology. Although rates of nucleotide substitution vary among taxa and among genes, the causes of this variation tend to be poorly understood. In the present study, we examined the rate and pattern of molecular evolution for five DNA regions over a phylogeny of Cornus, the single genus of Cornaceae. To identify evolutionary mechanisms underlying the molecular variation, we employed Bayesian methods to estimate divergence times and to infer how absolute rates of synonymous and nonsynonymous substitutions and their ratios change over time. We found that the rates vary among genes, lineages, and through time, and differences in mutation rates, selection type and intensity, and possibly genetic drift all contributed to the variation of substitution rates observed among the major lineages of Cornus. We applied independent contrast analysis to explore whether speciation rates are linked to rates of molecular evolution. The results showed no relationships for individual genes, but suggested a possible localized link between species richness and rate of nonsynonymous nucleotide substitution for the combined cpDNA regions. Furthermore, we detected a positive correlation between rates of molecular evolution and morphological change in Cornus. This was particularly pronounced in the dwarf dogwood lineage, in which genome-wide acceleration in both molecular and morphological evolution has likely occurred.

Increasing morphological complexity in multiple parallel lineages of the Crustacea

The prospect of finding macroevolutionary trends and rules in the history of life is tremendously appealing, but very few pervasive trends have been found. Here, we demonstrate a parallel increase in the morphological complexity of most of the deep lineages within a major clade. We focus on the Crustacea, measuring the morphological differentiation of limbs. First, we show a clear trend of increasing complexity among 66 free-living, ordinal-level taxa from the Phanerozoic fossil record. We next demonstrate that this trend is pervasive, occurring in 10 or 11 of 12 matched-pair comparisons (across five morphological diversity indices) between extinct Paleozoic and related Recent taxa. This clearly differentiates the pattern from the effects of lineage sorting. Furthermore, newly appearing taxa tend to have had more types of limbs and a higher degree of limb differentiation than the contemporaneous average, whereas those going extinct showed higher-than-average limb redundancy. Patterns of contemporary species diversity partially reflect the paleontological trend. These results provide a rare demonstration of a large-scale and probably driven trend occurring across multiple independent lineages and influencing both the form and number of species through deep time and in the present day.

Engines of speciation: a comparative study in birds of prey

Sexual selection as a promoter of speciation has received much attention in recent years, but has produced highly equivocal evidence. Here, I test whether sexual conflict is related to species richness among genera in accipitrid birds of prey using phylogenetically controlled comparative analyses. Increased species richness was associated with both 'male-win' as well as 'female-win' situations, i.e. males being able to promote gene flow through mating or females being able to restrict gene flow through female choice. Species richness was higher when plumage differed between males and females and in polygynous breeding systems compared with monogamous ones. To assess the relative importance of sexual conflict and natural selection as correlates of species richness simultaneously, I also performed a multivariate analysis of correlates of species richness. Population density, plumage polymorphism, geographic range size and breeding latitude were predictors of species richness for birds of prey. These results stress the importance of both sexual and natural selection in determining species richness but with a clear overall emphasis on natural selection in birds of prey.

Estimating diversification rates from phylogenetic information

Patterns of species richness reflect the balance between speciation and extinction over the evolutionary history of life. These processes are influenced by the size and geographical complexity of regions, conditions of the environment, and attributes of individuals and species. Diversity within clades also depends on age and thus the time available for accumulating species. Estimating rates of diversification is key to understanding how these factors have shaped patterns of species richness. Several approaches to calculating both relative and absolute rates of speciation and extinction within clades are based on phylogenetic reconstructions of evolutionary relationships. As the size and quality of phylogenies increases, these approaches will find broader application. However, phylogeny reconstruction fosters a perceptual bias of continual increase in species richness, and the analysis of primarily large clades produces a data selection bias. Recognizing these biases will encourage the development of more realistic models of diversification and the regulation of species richness.

Why are there so many insect species? Perspectives from fossils and phylogenies

Over half of all described species are insects, but until recently our understanding of the reasons for this diversity was based on very little macroevolutionary evidence. Here I summarize the hypotheses that have been posed, tests of these hypotheses and their results, and hence identify gaps in knowledge for future researchers to pursue. I focus on inferences from the following sources: (i) the fossil record, normally at family level, and (ii) insect phylogenies, sometimes combined with: (iii) the species richness of insect higher taxa, and (iv) current extinction risks. There is evidence that the species richness of insects has been enhanced by: (i) their relative age, giving time for diversification to take place; (ii) low extinction rates. There is little evidence that rates of origination have generally been high or that there are limits on numbers of species. However, the evidence on macroevolutionary rates is not yet so extensive or coherent as to present unequivocal messages. As regards morphological, ecological, or behavioural hypotheses, there is evidence that diversity has been enhanced by (iii) flight or properties resulting from it like enhanced dispersal, (iv) wing folding, and (v) complete metamorphosis. However, in all these cases the evidence is somewhat equivocal, either because of statistical issues or because evidence from different sources is conflicting. There is extensive evidence that diversity is affected by (vi) the ecological niche. Comparative studies indicate that phytophagy generally increases net diversification rates, and reduces extinction risk. However, niche specialization is also associated with an increase in extinction risk. Small body size (vii) is often associated with low extinction risk in comparative studies, but as yet there is no solid evidence that it consistently enhances net rates of diversification. Mouthpart diversity (viii) has generally increased over time in the insects, but cannot explain the apparent great increase in diversity seen in the Cretaceous and Tertiary. Sexual selection and sexual conflict (ix) are two processes that are widespread in insects, and there is comparative evidence linking both to increased diversification. Although some comparative evidence links tropical distributions (x) to increased rates of diversification, the extent to which latitudinal richness gradients are unusual in insects is equivocal. There is little to no direct evidence from fossils and phylogenies that insect diversity has generally been affected by (i) sensory- or neuro-sophistication, (ii) population size or density, (iii) generation time or fecundity, (iv) the presence of an exoskeleton or cuticle, (v) segmentation or appendage diversity, (vi) adaptability or genetic versatility, though all of these remain plausible hypotheses awaiting further tests. The data suggest that the insect body ground plan itself had no direct effect on insect diversity. Thus, whilst studies to date have given substantial understanding, substantial gaps still remain. Future challenges include: (i) interpreting conflicting messages from different sources of data; (ii) rating the importance of different hypotheses that are statistically supported; (iii) linking specific proximate to specific ultimate explanations and vice versa; and (iv) understanding how different ultimate hypotheses might be dependent on each other.

History and Diversity: Explorations at the Intersection of Ecology and Evolution

Phylogenetic analysis provides an important tool for assessing the influence of historical and evolutionary processes on the structure of contemporary ecological systems. Patterns of diversity, for example, represent the regional buildup of species through immigration and diversification, their loss through extinction, and the sorting of species ecologically within the region. Colonization-extinction dynamics on islands can be inferred from lineage accumulation through time. Lineage branching within clades can be used to estimate rates of speciation and extinction. However, simulations of these processes show potential ambiguities in the interpretation of data. Clade size is unrelated to age in many studies, suggesting that speciation and extinction might be in long-term equilibrium and raising questions about unobserved past diversity. Among passerine birds and other groups, the size of similar-aged clades is positively related to the size of the region within which they have diversified, and it is greater in tropical than in temperate regions. There is no consensus on the causes of these patterns. Finally, the ecological interactions between populations within regions brings the timescale of species sorting and species production close to each other and emphasizes the important interaction of ecological and evolutionary processes in shaping ecological systems.

Parasites and the evolutionary diversification of primate clades

Coevolutionary interactions such as those between hosts and parasites have been regarded as an underlying cause of evolutionary diversification, but evidence from natural populations is limited. Among primates and other mammalian groups, measures of host diversification rates vary widely among lineages, but comparative studies have not yet identified a reliable explanation for this variation. In this study, we used a comprehensive data set of disease-causing organisms from free-living primates to illustrate how phylogenetic comparative methods can be used to examine mammalian lineage diversity in relation to parasite species richness. Our results provide evidence that the phylogenetic diversity of primate clades is correlated positively with the number of parasite species harbored by each host and that this pattern is largely independent of other host traits that have been shown to influence diversification rates and parasite species richness in primates. We investigated two possible mechanisms that could explain this association, namely that parasites themselves drive host evolutionary diversification through processes linked with sexual selection and that host shifts or host sharing increases parasite species richness among diverse primate clades. Neither parasite species richness nor host diversification is related to measures of sexual selection in primates. Further, we found only partial evidence that more rapidly diversifying host lineages produced increased opportunities for host sharing or host shifting by parasites through mechanisms involving species' geographic range overlap. Thus, our analyses provide evidence for an important link between the evolutionary diversification of primates and the richness of their parasite communities, but other mechanisms, particularly those related to reciprocal selection or coextinction of hosts and parasites, require further investigation.

Ecology predicts large-scale patterns of phylogenetic diversification in birds

One of the most striking patterns in evolutionary biology is that clades may differ greatly in the number of species they contain. Numerous hypotheses have been put forward to explain this phenomenon, and several have been tested using phylogenetic methods. Remarkably, however, all such tests performed to date have been characterized by modest explanatory power, which has generated an interest in explanations stressing the importance of random processes. Here we make use of phylogenetic methods to test whether ecological variables, typically ignored in previous models, may explain phylogenetic tree imbalance in birds. We show that diversification rate possesses an intermediate phylogenetic signal across families. Using phylogenetic comparative methods, we then build a multipredictor model that explains more than 50% of the variation in diversification rate among clades. High annual dispersal is identified as the strongest predictor of high rates of diversification. In addition, high diversification rate is strongly associated with feeding generalization. In all but one instance, these key findings remain qualitatively unchanged when we use an alternative phylogeny and methodology and when small clades, containing five species or less, are excluded. Taken together, these results suggest that large-scale patterns in avian diversification can be explained by variation in intrinsic biology.

Correlates of Species Richness in Mammals: Body Size, Life History, and Ecology

We present the most extensive examination to date of proposed correlates of species richness. We use rigorous phylogenetic comparative techniques, data for 1,692 mammal species in four clades, and multivariate statistics to test four hypotheses about species richness and compare the evidence for each. Overall, we find strong support for the life-history model of diversification. Species richness is significantly correlated with shorter gestation period in the carnivores and large litter size in marsupials. These traits and short interbirth intervals are also associated with species richness in a pooled analysis of all four clades. Additionally, we find some support for the abundance hypotheses in different clades of mammals: abundance correlates positively with species richness in primates but negatively in microchiropterans. Our analyses provide no evidence that mammalian species richness is associated with body size or degree of sexual dimorphism.

Range expansions in the flightless longhorn cactus beetles, Moneilema gigas and Moneilema armatum, in response to Pleistocene climate changes

Pollen cores and plant and animal fossils suggest that global climate changes at the end of the last glacial period caused range expansions in organisms indigenous to the North American desert regions, but this suggestion has rarely been investigated from a population genetic perspective. In order to investigate the impact of Pleistocene climate changes and glacial/interglacial cycling on the distribution and population structure of animals in North American desert communities, biogeographical patterns in the flightless, warm-desert cactus beetles, Moneilema gigas and Moneilema armatum, were examined using mitochondrial DNA (mtDNA) sequence data from the cytochrome oxidase I (COI) gene. Gene tree relationships between haplotypes were inferred using parsimony, maximum-likelihood, and Bayesian analysis. Nested clade analysis and coalescent modelling using the programs mdiv and fluctuate were used to identify demographically independent populations, and to test the hypothesis that Pleistocene climate changes caused recent range expansions in these species. A sign test was used to evaluate the probability of observing concerted population growth across multiple, independent populations. The phylogeographical and nested clade analyses reveal a history of northward expansion in both of these species, as well as a history of past range fragmentation, followed by expansion from refugia. The coalescent analyses provide highly significant evidence for independent range expansions from multiple refugia, but also identify biogeographical patterns that predate the most recent glacial period. The results indicate that widespread desert environments are more ancient than has been suggested in the past.

Environmental energy and evolutionary rates in flowering plants

The latitudinal gradient in species richness is a pervasive feature of the living world, but its underlying causes remain unclear. We evaluated the hypothesis that environmental energy drives evolutionary rates and thereby diversification in flowering plants. We estimated energy levels across angiosperm family distributions in terms of evapotranspiration, temperature and UV radiation taken from satellite and climate databases. Using the most comprehensive DNA-based phylogenetic tree for angiosperms to date, analysis of 86 sister-family comparisons shows that molecular evolutionary rates have indeed been faster in high-energy regions, but that this is not an intermediate step between energy and diversity. Energy has strong, but independent effects on both species richness and molecular evolutionary rates.

The inverse relationship between species diversity and body mass: do primates play by the "rules"?

Evolutionary biologists have long commented on a seemingly universal "rule" of nature-that in large taxonomic assemblages from groups as diverse as bacteria, plants, insects, marine invertebrates, fish, reptiles, amphibians, birds, and mammals, there exists a frequency distribution of body sizes among species that is highly skewed to the right (positive skewness). This distribution reflects the strong inverse, or negative, relationship often noted between mean body size of taxa and the number of species they contain--i.e., the observation that small body size is often associated with high species diversity (speciosity). This is sometimes "explained" by recourse to the idea that smaller-bodied taxa are able to subdivide their environments more finely than larger-bodied taxa. With but few exceptions, the applicability of this "rule" to the Order Primates has not been studied in any detail. In this study I address the following questions of (paleo)anthropological interest: (1) How speciose is the Order Primates? (2) Does this biological "rule" characterize the Order Primates (at any taxonomic level) in any meaningful way? (3) Does the association between speciosity and body mass within the Order Primates provide any useful models for interpreting and/or predicting speciosity in the fossil primate record? Using phylogenetically independent contrasts methods, I conclude that the answers to those three questions are: (1) not very; (2) no; and (3) not particularly (with the possible exception of larger-bodied taxa).