Diversity begets stability: Sublinear growth and competitive coexistence across ecosystems

The worldwide loss of species diversity brings urgency to understanding how diverse ecosystems maintain stability. Whereas early ecological ideas and classic observations suggested that stability increases with diversity, ecological theory makes the opposite prediction, leading to the long-standing "diversity-stability debate." Here, we show that this puzzle can be resolved if growth scales as a sublinear power law with biomass (exponent <1), exhibiting a form of population self-regulation analogous to models of individual ontogeny. We show that competitive interactions among populations with sublinear growth do not lead to exclusion, as occurs with logistic growth, but instead promote stability at higher diversity. Our model realigns theory with classic observations and predicts large-scale macroecological patterns. However, it makes an unsettling prediction: Biodiversity loss may accelerate the destabilization of ecosystems.

Sexual and natural selection interplay in sexual head shape dimorphism of two sympatric racerunners (Squamata: Lacertidae)

Both natural and sexual selection can shape sexual dimorphism. However, determination of the contribution of these selection pressures is challenging. In lizards, sexual selection can contribute to the larger head size of males than that of females. However, males and females can also diverge in their head size to prey on different food resources under conditions of limited resources (and/or high competitors). Here, 109 individuals from two sympatric desert racerunners (Eremias grammica: 28 males and 30 females; Eremias velox: 25 males and 26 females) were studied to determine their sexual head shape (head length, width, and depth). Additionally, 191 and 169 feces samples of E. grammica and E. velox, respectively, were collected to assess the niche divergence hypothesis (a proxy for natural selection). We found that both species had dimorphic head shapes; male heads (i.e., length, width, and depth) were significantly larger than female heads (P &lt; 0.05, in all cases) in E. grammica, and male heads of E. velox were significantly longer than those of females (P &lt; 0.05). Chi-square test revealed that there were significant differences in the proportion (Hymenopteran and Orthopteran) and sizes of prey type between the two sexes of E. grammica; conspecific males and females of E. velox differed in the proportion of Coleopteran and Hymenopteran prey. Both males and females of these two species had a high niche overlap index (range from ∼ 0.78 to 0.99) with each other. There were also significant differences in the sizes of the heads and prey between the two species (P &lt; 0.05). However, the interspecific differences were mainly caused by interspecific male–male differences in morphological and prey traits. In summary, we believe that both natural (pressures from resource competition) and sexual selection drive sexual head shape dimorphism in these two sympatric lizards, owing to high food resource competition in arid regions. Therefore, head trait divergence can reduce competition by resulting in a preference for different prey types.

Machine learning approaches identify male body size as the most accurate predictor of species richness

BACKGROUND

A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness -the number of different species in a community or region - among comparable taxonomic lineages. Multiple biotic and abiotic factors have been hypothesized to have an effect on species richness and have been used as its predictors, but identifying accurate predictors is not straightforward. Spiders are a highly diverse group, with some 48,000 species in 120 families; yet nearly 75% of all species are found within just the ten most speciose families. Here we use a Random Forest machine learning algorithm to test the predictive power of different variables hypothesized to affect species richness of spider genera.

RESULTS

We test the predictive power of 22 variables from spiders' morphological, genetic, geographic, ecological and behavioral landscapes on species richness of 45 genera selected to represent the phylogenetic and biological breath of Araneae. Among the variables, Random Forest analyses find body size (specifically, minimum male body size) to best predict species richness. Multiple Correspondence analysis confirms this outcome through a negative relationship between male body size and species richness. Multiple Correspondence analyses furthermore establish that geographic distribution of congeneric species is positively associated with genus diversity, and that genera from phylogenetically older lineages are species poorer. Of the spider-specific traits, neither the presence of ballooning behavior, nor sexual size dimorphism, can predict species richness.

CONCLUSIONS

We show that machine learning analyses can be used in deciphering the factors associated with diversity patterns. Since no spider-specific biology could predict species richness, but the biologically universal body size did, we believe these conclusions are worthy of broader biological testing. Future work on other groups of organisms will establish whether the detected associations of species richness with small body size and wide geographic ranges hold more broadly.

A tiny ornithodiran archosaur from the Triassic of Madagascar and the role of miniaturization in dinosaur and pterosaur ancestry

Early members of the dinosaur-pterosaur clade Ornithodira are very rare in the fossil record, obscuring our understanding of the origins of this important group. Here, we describe an early ornithodiran (Kongonaphon kely gen. et sp. nov.) from the Mid-to-Upper Triassic of Madagascar that represents one of the smallest nonavian ornithodirans. Although dinosaurs and gigantism are practically synonymous, an analysis of body size evolution in dinosaurs and other archosaurs in the context of this taxon and related forms demonstrates that the earliest-diverging members of the group may have been smaller than previously thought, and that a profound miniaturization event occurred near the base of the avian stem lineage. In phylogenetic analysis, Kongonaphon is recovered as a member of the Triassic ornithodiran clade Lagerpetidae, expanding the range of this group into Africa and providing data on the craniodental morphology of lagerpetids. The conical teeth of Kongonaphon exhibit pitted microwear consistent with a diet of hard-shelled insects, indicating a shift in trophic ecology to insectivory associated with diminutive body size. Small ancestral body size suggests that the extreme rarity of early ornithodirans in the fossil record owes more to taphonomic artifact than true reflection of the group's evolutionary history.

What Explains Patterns of Diversification and Richness among Animal Phyla?

Animal phyla vary dramatically in species richness (from one species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g., sponges), parasitic worms (e.g., nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ∼74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, nonmarine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (∼67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g., head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species.

Darwinism for the Genomic Age: Connecting Mutation to Diversification

A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness. Here we draw together empirical studies and theoretical concepts that may help to build links in the explanatory chain that connects mutation to diversification. First we consider the way that mutation rates vary between species. We then explore how differences in mutation rates have flow-through effects to the rate at which populations acquire substitutions, which in turn influences the speed at which populations become reproductively isolated from each other due to the acquisition of genomic incompatibilities. Since diversification rate is commonly measured from phylogenetic analyses, we propose a conceptual approach for relating events of reproductive isolation to bifurcations on molecular phylogenies. As we examine each of these relationships, we consider theoretical models that might shine a light on the observed association between rate of molecular evolution and diversification rate, and critically evaluate the empirical evidence for these links, focusing on phylogenetic comparative studies. Finally, we ask whether we are getting closer to a real understanding of the way that the processes of molecular evolution connect to the observable patterns of diversification.

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.

Immune and stress responses in oysters with insights on adaptation

Oysters are representative bivalve molluscs that are widely distributed in world oceans. As successful colonizers of estuaries and intertidal zones, oysters are remarkably resilient against harsh environmental conditions including wide fluctuations in temperature and salinity as well as prolonged air exposure. Oysters have no adaptive immunity but can thrive in microbe-rich estuaries as filter-feeders. These unique adaptations make oysters interesting models to study the evolution of host-defense systems. Recent advances in genomic studies including sequencing of the oyster genome have provided insights into oyster's immune and stress responses underlying their amazing resilience. Studies show that the oyster genomes are highly polymorphic and complex, which may be key to their resilience. The oyster genome has a large gene repertoire that is enriched for immune and stress response genes. Thousands of genes are involved in oyster's immune and stress responses, through complex interactions, with many gene families expanded showing high sequence, structural and functional diversity. The high diversity of immune receptors and effectors may provide oysters with enhanced specificity in immune recognition and response to cope with diverse pathogens in the absence of adaptive immunity. Some members of expanded immune gene families have diverged to function at different temperatures and salinities or assumed new roles in abiotic stress response. Most canonical innate immunity pathways are conserved in oysters and supported by a large number of diverse and often novel genes. The great diversity in immune and stress response genes exhibited by expanded gene families as well as high sequence and structural polymorphisms may be central to oyster's adaptation to highly stressful and widely changing environments.

Body size distribution of free-living marine nematodes from a Caribbean coral reef

Body size is a fundamental property of organisms but its distribution is almost unknown for marine nematodes. We measured the length and width of 7446 nematodes of 186 species to describe their morphological landscape and the relationship between abundance and body size. The body shape has a bimodal distribution with two morphotypes, suggesting adaptations to lifestyle. In fine sediments (seagrass bed), slender nematodes dominated, whereas sandy sediments had mostly stout nematodes but also slender forms. Seaweed turf from hard bottom substrates may favour mostly slender nematodes, whereas dead coral harbours both morphotypes, probably as a result of high heterogeneity of the substrate. The size spectra of abundance vs mass class shows a negative exponential relationship, suggesting that the energetic equivalence hypothesis holds for nematodes. The shape and position of the size spectra depended on the type of habitat. Body size is an important organismal trait that offers valuable information for disentangling ecological patterns in Nematoda.

Ecology and evolution of mammalian biodiversity

Mammals have incredible biological diversity, showing extreme flexibility in eco-morphology, physiology, life history and behaviour across their evolutionary history. Undoubtedly, mammals play an important role in ecosystems by providing essential services such as regulating insect populations, seed dispersal and pollination and act as indicators of general ecosystem health. However, the macroecological and macroevolutionary processes underpinning past and present biodiversity patterns are only beginning to be explored on a global scale. It is also particularly important, in the face of the global extinction crisis, to understand these processes in order to be able to use this knowledge to prevent future biodiversity loss and loss of ecosystem services. Unfortunately, efforts to understand mammalian biodiversity have been hampered by a lack of data. New data compilations on current species' distributions, ecologies and evolutionary histories now allow an integrated approach to understand this biodiversity. We review and synthesize these new studies, exploring the past and present ecology and evolution of mammalian biodiversity, and use these findings to speculate about the mammals of our future.

The Humpbacked Species Richness-Curve: A Contingent Rule for Community Ecology

Functional relationships involving species richness may be unimodal, monotonically increasing, monotonically decreasing, bimodal, multimodal, U-shaped, or with no discernable pattern. The unimodal relationships are the most interesting because they suggest dynamic, nonequilibrium community processes. For that reason, they are also contentious. In this paper, we provide a wide-ranging review of the literature on unimodal (humpbacked) species richness-relationships. Though not as widespread as previously thought, unimodal patterns of species richness are often associated with disturbance, predation and herbivory, productivity, spatial heterogeneity, environmental gradients, time, and latitude. These unimodal patterns are contingent on organism and environment; we examine unimodal species richness-curves involving plants, invertebrates, vertebrates, plankton, and microbes in marine, lacustrine, and terrestrial habitats. A goal of future research is to understand the contingent patterns and the complex, interacting processes that generate them.

Biodiversity and body size are linked across metazoans

Body size variation across the Metazoa is immense, encompassing 17 orders of magnitude in biovolume. Factors driving this extreme diversification in size and the consequences of size variation for biological processes remain poorly resolved. Species diversity is invoked as both a predictor and a result of size variation, and theory predicts a strong correlation between the two. However, evidence has been presented both supporting and contradicting such a relationship. Here, we use a new comprehensive dataset for maximum and minimum body sizes across all metazoan phyla to show that species diversity is strongly correlated with minimum size, maximum size and consequently intra-phylum variation. Similar patterns are also observed within birds and mammals. The observations point to several fundamental linkages between species diversification and body size variation through the evolution of animal life.

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.

EVOLUTIONARY DYNAMICS OF VERTEBRATE BODY MASS RANGE

Change in body mass with time has been considered for many clades, often with reference to Cope's rule, which predicts a tendency to increase in body size. A more general rule, namely increase in the range of body mass with time, is analyzed here for vertebrates. The log range of log vertebrate body mass is shown to increase linearly and highly significantly with the log of duration of clade existence. The resulting regression equations are used to predict the origin age, initial body mass, and subsequent dynamics of body mass range for primate clades such as the New World monkeys (Platyrrhini, 32 million years ago, initial mass of 1.7 kg) and the Anthropoidea (57 million years ago, initial mass of 0.12 kg), tested against the primate fossil record. Using these methods, other major primate clades such as Lemuriformes and Adapoidea are also estimated to have originated in the Tertiary (63 and 64 million years ago, respectively), with only the Plesiadapiformes originating in the Cretaceous (83 million years ago). Similarities of body mass range between primate and other vertebrate sister groups are discussed. Linear relationships of log range and log duration are considered with respect to Brownian processes, with the expected regression coefficients from the latter explored through simulations. The observed data produce regression coefficients that overlap with or are higher than those under Brownian processes. Overall, the analyses suggest the dynamics of vertebrate body mass range in morphologically disparate clades are highly predictable over many tens of million years and that the dynamics of phenotypic characteristics can assist molecular clock and fossil models in dating evolutionary events.

Clade age and not diversification rate explains species richness among animal taxa

Animal taxa show remarkable variability in species richness across phylogenetic groups. Most explanations for this disparity postulate that taxa with more species have phenotypes or ecologies that cause higher diversification rates (i.e., higher speciation rates or lower extinction rates). Here we show that clade longevity, and not diversification rate, has primarily shaped patterns of species richness across major animal clades: more diverse taxa are older and thus have had more time to accumulate species. Diversification rates calculated from 163 species-level molecular phylogenies were highly consistent within and among three major animal phyla (Arthropoda, Chordata, Mollusca) and did not correlate with species richness. Clades with higher estimated diversification rates were younger, but species numbers increased with increasing clade age. A fossil-based data set also revealed a strong, positive relationship between total extant species richness and crown group age across the orders of insects and vertebrates. These findings do not negate the importance of ecology or phenotype in influencing diversification rates, but they do show that clade longevity is the dominant signal in major animal biodiversity patterns. Thus, some key innovations may have acted through fostering clade longevity and not by heightening diversification rate.

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.

How Dispersal Limitation Shapes Species–Body Size Distributions in Local Communities

A critical but poorly understood pattern in macroecology is the often unimodal species-body size distribution (also known as body size-diversity relationship) in a local community (embedded in a much larger regional species pool). Purely neutral community models that assume functional equivalence among species are incapable of explaining this pattern because body size is the key determinant of functional differences between species. Several niche-based explanations have been offered, but none of them is completely satisfactory. Here we develop a simple model that unites a neutral community model with niche-based theory to explain the relationship. In the model, species of similar size are assumed to belong to the same size guild. Within a size guild, all individuals are equivalent in their competition for resources, sensu Hubbell's neutral community model; they have the same speciation rate and dispersal capacities. Between size guilds, however, the total number of individuals, the speciation rate, and the dispersal capacities differ, but using known allometric scaling laws for these properties, we can describe the differences between size guilds. Our model predicts that species richness reaches an optimum at an intermediate body size, in agreement with observations. The optimum at intermediate body size is basically the result of a trade-off between, on the one hand, allometric scaling laws for the number of individuals and the speciation rate that decrease with body size and, on the other hand, the scaling law for active dispersal that increases with body size.

Geographic range size, life history and rates of diversification in Australian mammals

What causes species richness to vary among different groups of organisms? Two hypotheses are that large geographical ranges and fast life history either reduce extinction rates or raise speciation rates, elevating a clade's rate of diversification. Here we present a comparative analysis of these hypotheses using data on the phylogenetic relationships, geographical ranges and life history of the terrestrial mammal fauna of Australia. By comparing species richness patterns to null models, we show that species are distributed nonrandomly among genera. Using sister-clade comparisons to control for clade age, we then find that faster diversification is significantly associated with larger geographical ranges and larger litters, but there is no evidence for an effect of body size or age at first breeding on diversification rates. We believe the most likely explanation for these patterns is that larger litters and geographical ranges increase diversification rates because they buffer species from extinction. We also discuss the possibility that positive effects of litter size and range size on diversification rates result from elevated speciation rates.

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

Explaining the uneven distribution of species among lineages is one of the oldest questions in evolution. Proposed correlations between biological traits and species diversity are routinely tested by making comparisons between phylogenetic sister clades. Several recent studies have used nested sister-clade comparisons to test hypotheses linking continuously varying traits, such as body size, with diversity. Evaluating the findings of these studies is complicated because they differ in the index of species richness difference used, the way in which trait differences were treated, and the statistical tests employed. In this paper, we use simulations to compare the performance of four species richness indices, two choices about the branch lengths used to estimate trait values for internal nodes and two statistical tests under a range of models of clade growth and character evolution. All four indices returned appropriate Type I error rates when the assumptions of the method were met and when branch lengths were set proportional to time. Only two of the indices were robust to the different evolutionary models and to different choices of branch lengths and statistical tests. These robust indices had comparable power under one nonnull scenario. Regression through the origin was consistently more powerful than the t-test, and the choice of branch lengths exerts a strong effect on both the validity and power. In the light of our simulations, we re-evaluate the findings of those who have previously used nested comparisons in the context of species richness. We provide a set of simple guidelines to maximize the performance of phylogenetically nested comparisons in tests of putative correlates of species richness.

Are most species small? Not within species-level phylogenies

The robust macro-ecological observation that there are more small-bodied species implies that small-bodied organisms have experienced elevated net rates of diversification. We investigate the role of body size in creating non-random differences in rates of cladogenesis using a set of 38 species-level phylogenies drawn from a range of animal groups. We use independent contrasts to explore the relationship between body size and species richness within individual phylogenies and across related sets of phylogenies. We also carry out a meta-analysis looking for associations between body size and species richness across the taxa. We find little evidence for increased cladogenesis among small-bodied organisms within taxa, and no evidence for any consistent differences between taxa. We explore possible explanations for the inconsistency of our findings with macro-ecological patterns.