Wild pedigrees inform mutation rates and historic abundance in baleen whales

Phylogeny-based estimates suggesting a low germline mutation rate (μ) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated μ directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of μ reduces previous genetic-based estimates of preexploitation whale abundance by 86% and suggests that μ cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate μ directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.

Social modulation of oogenesis and egg laying in Drosophila melanogaster

Being part of a group facilitates cooperation between group members but also creates competition for resources. This is a conundrum for gravid females, whose future offspring benefit from being in a group only if there are enough resources relative to group size. Females may therefore be expected to modulate reproductive output depending on social context. In the fruit fly Drosophila melanogaster, females actively attract conspecifics to lay eggs on the same resources, generating groups in which individuals may cooperate or compete. The genetic tractability of this species allows dissecting the mechanisms underlying physiological adaptation to social context. Here, we show that females produce eggs increasingly faster as group size increases. By laying eggs faster when grouped than when isolated, females reduce competition between offspring and increase offspring survival. In addition, grouped females lay eggs during the day, while isolated females lay them at night. We show that responses to the presence of others requires visual input and that flies from any sex, mating status, or species can trigger these responses. The mechanisms of this modulation of egg laying by group is connected to a lifting of the inhibition of light on oogenesis and egg laying, possibly mediated in part by an increase in juvenile hormone activity. Because modulation of reproduction by social context is a hallmark of animals with higher levels of sociality, our findings in a species considered solitary question the validity of this nomenclature and suggest a widespread and profound influence of social context on reproduction.

Can we ignore trait-dependent colonization and diversification in island biogeography?

The application of state-dependent speciation and extinction models to phylogenetic trees has shown an important role for traits in diversification. However, this role remains comparatively unexplored on islands, which can include multiple independent clades resulting from different colonization events. To explore whether assuming no dependence on traits leads to bias in inference on island dynamics, we extend an island biodiversity model, DAISIE (Dynamic Assembly of Islands through Speciation, Immigration, and Extinction) to include trait-dependent diversification simulations, and evaluate the robustness of the inference model which ignores this trait-dependence. Our results indicate that when the differences between colonization, extinction, and speciation rates between trait states are moderate, the model shows negligible error for a variety of island diversity metrics, suggesting that island diversity dynamics can be accurately estimated without the need to explicitly model trait dependence. We conclude that for many biologically realistic scenarios with trait-dependent diversification and colonization, this simple trait-less inference model is informative and robust to trait effects on colonization, speciation, and extinction. Nonetheless, our new simulation model may provide a useful tool for studying patterns of trait variation.

Evolutionary radiation in canids following continental colonizations

Colonization of a new environment may trigger an evolutionary radiation, defined as an accelerated accumulation of species in a short period of time. However, how often colonization events trigger such radiations is still an open question. We studied the worldwide dispersal of Caninae to investigate whether the invasion of new continents resulted in elevated species diversification. We used a combination of ancestral range estimation and phylogenetic analyses to estimate the ancestral ranges of 56 extant and extinct species of Caninae, as well as variation in speciation and extinction rates through time and across clades. Our findings indicate that canids experienced an evolutionary radiation event when lineages were able to reach Eurasia and South America around 11 million years ago. A large number of species arising in a short period of time suggests that canids experienced ecological opportunity events within the new areas, implying that the differences in the ecological settings between continents, and size variation among Canidae and other carnivores may be responsible for the variation in clade dynamics. We suggest that the increase of grasslands and the new herbivorous fauna that came with it were the major forces responsible for the diversification of wolves in North America, while empty niches and the absence of competitors can explain the success of canids in Africa and South America. Interaction with other carnivores probably also affected the diversification dynamics of canids.

The phylogenetic limits to diversity-dependent diversification

While the theory of micro-evolution by natural selection assigns a crucial role to competition, its role in macroevolution is less clear. Phylogenetic evidence for a decelerating accumulation of lineages suggests a feedback of lineage diversity on diversification. However, does this feedback only occur between close relatives, or do distant relatives also influence their diversification? In other words: are there phylogenetic limits to this diversity-dependence? Islands form ideal systems to answer these questions, because their boundedness facilitates an overview of all potential competitors. The DAISIE (Dynamic Assembly of Island biota through Speciation Immigration and Extinction) framework allows for testing the presence of diversity-dependence on islands given phylogenetic data on colonization and branching times. The current inference models in DAISIE assume that this diversity-dependence only applies within a colonizing clade, i.e. all mainland species can colonize and diversify independently from one another. We term this clade-specific (CS) diversity-dependence. Here we introduce a new DAISIE model that assumes that diversity-dependence applies to all island species of a taxonomic group regardless of their mainland ancestry, i.e. diversity-dependence applies both to species within the same clade and between different clades established by different mainland species. We call this island-wide (IW) diversity-dependence. We present a method to compute a likelihood for this model given phylogenetic data on colonization and branching events and use likelihood ratio bootstrapping to compare it to the likelihood of the CS model in order to overcome biases known for standard model selection. We apply it to the diversification of Eleutherodactylus frogs on Hispaniola. Across the Greater Antilles archipelago, this radiation shows repeated patterns of diversification in ecotypes which are similar across clades. This could be suggestive of overlapping niche space and hence between-clade interactions, i.e. IW diversity-dependence. But it could also be suggestive of only within-clade interactions, because between-clade interactions would have blocked the same ecotype re-appearing. We find that the CS model fits the data much better than the IW model, indicating that different colonizations, while resulting in similar ecotypes, are sufficiently distinct to avoid interacting strongly. We argue that non-overlapping distributions between clades (both spatially and in terms of ecotypes) cannot be used as evidence of CS diversity-dependence, because this pattern may be a consequence of IW diversity-dependence. By contrast, by using phylogenetic data rather than distributional data our method does allow for inferring the phylogenetic limits to diversity-dependent diversification. We discuss possibilities for future extensions and applications of our modelling approach.

Contribution of opsins and chromophores to cone pigment variation across populations of Lake Victoria cichlids

Adaptation to heterogeneous sensory environments has been implicated as a key parameter in speciation. Cichlid fish are a textbook example of divergent visual adaptation, mediated by variation in the sequences and expression levels of cone opsin genes (encoding the protein component of visual pigments). In some vertebrates including fish, visual sensitivity is also tuned by the ratio of vitamin A₁ /A₂ -derived chromophores (i.e., the light-sensitive component of the visual pigment bound to the opsin protein), where higher proportions of A₂ cause a more red-shifted wavelength absorbance. This study explores the variation in chromophore ratios across multiple cichlid populations in Lake Victoria, using as a proxy the expression of the gene Cyp27c1, which has been shown to regulate the conversion of vitamin A₁ into vitamin A₂ in several vertebrates. This study focuses on sympatric Pundamilia cichlids, where species with blue or red male coloration co-occur at multiple islands but occupy different depths and consequently different visual habitats. In the red species, we found higher cyp27c1 expression in populations from turbid waters than from clear waters, but there was no such pattern in the blue species. Across populations, differences between the sympatric species in cyp27c1 expression had a consistent relationship with species differences in opsin expression patterns, but the red/blue identity reversed between clear and turbid waters. To assess the contribution of heritable vs. environmental causes of variation, we tested whether light manipulations induce a change in cyp27c1 expression in the laboratory. We found that cyp27c1 expression was not influenced by experimental light conditions, suggesting that the observed variation in the wild is due to genetic differences. Nonetheless, compared to other cichlid species, cyp27c1 is expressed at very low levels in Pundamilia, suggesting that it may not be relevant for visual adaptation in this species. Conclusively, establishing the biological importance of this variation requires testing of actual A₁ /A₂ ratios in the eye, as well as its consequences for visual performance.

Microbiome Heritability and Its Role in Adaptation of Hosts to Novel Resources

Microbiomes are involved in most vital processes, such as immune response, detoxification, and digestion and are thereby elementary to organismal functioning and ultimately the host’s fitness. In turn, the microbiome may be influenced by the host and by the host’s environment. To understand microbiome dynamics during the process of adaptation to new resources, we performed an evolutionary experiment with the two-spotted spider mite, Tetranychus urticae. We generated genetically depleted strains of the two-spotted spider mite and reared them on their ancestral host plant and two novel host plants for approximately 12 generations. The use of genetically depleted strains reduced the magnitude of genetic adaptation of the spider mite host to the new resource and, hence, allowed for better detection of signals of adaptation via the microbiome. During the course of adaptation, we tested spider mite performance (number of eggs laid and longevity) and characterized the bacterial component of its microbiome (16S rRNA gene sequencing) to determine: (1) whether the bacterial communities were shaped by mite ancestry or plant environment and (2) whether the spider mites’ performance and microbiome composition were related. We found that spider mite performance on the novel host plants was clearly correlated with microbiome composition. Because our results show that only little of the total variation in the microbiome can be explained by the properties of the host (spider mite) and the environment (plant species) we studied, we argue that the bacterial community within hosts could be valuable for understanding a species’ performance on multiple resources.

Nucleotide substitutions during speciation may explain substitution rate variation

Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life. [Molecular clock; phylogenetic reconstruction; speciation; substitution rate variation.]

A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities

Biodiversity accumulates hierarchically by means of ecological and evolutionary processes and feedbacks. Within ecological communities drift, dispersal, speciation, and selection operate simultaneously to shape patterns of biodiversity. Reconciling the relative importance of these is hindered by current models and inference methods, which tend to focus on a subset of processes and their resulting predictions. Here we introduce massive ecoevolutionary synthesis simulations (MESS), a unified mechanistic model of community assembly, rooted in classic island biogeography theory, which makes temporally explicit joint predictions across three biodiversity data axes: (i) species richness and abundances, (ii) population genetic diversities, and (iii) trait variation in a phylogenetic context. Using simulations we demonstrate that each data axis captures information at different timescales, and that integrating these axes enables discriminating among previously unidentifiable community assembly models. MESS is unique in generating predictions of community‐scale genetic diversity, and in characterizing joint patterns of genetic diversity, abundance, and trait values. MESS unlocks the full potential for investigation of biodiversity processes using multidimensional community data including a genetic component, such as might be produced by contemporary eDNA or metabarcoding studies. We combine MESS with supervised machine learning to fit the parameters of the model to real data and infer processes underlying how biodiversity accumulates, using communities of tropical trees, arthropods, and gastropods as case studies that span a range of data availability scenarios, and spatial and taxonomic scales.

Evolutionary dynamics of the elevational diversity gradient in passerine birds

Low-elevation regions harbour the majority of the world's species diversity compared to high-elevation areas. This global gradient suggests that lowland species have had more time to diversify, or that net diversification rates have been higher in the lowlands. However, highlands seem to be cradles of diversity as they contain many young endemics, suggesting that their rates of speciation are exceptionally fast. Here we use a phylogenetic diversification model that accounts for the dispersal of species between different elevations to examine the evolutionary dynamics of the elevational diversity gradient in passerine birds, a group that has radiated globally to occupy almost all elevations and latitudes. We find strong support for a model in which passerines diversify at the same rate in the highlands and the lowlands but in which the per-capita rate of dispersal from high to low elevations is more than twice as fast as that in the reverse direction. This suggests that while there is no consistent trend in diversification across elevations, part of the diversity generated by highland regions migrates into the lowlands, thus setting up the observed gradient in passerine diversity. We find that this process drives tropical regions but for temperate areas, the analysis could be hampered by their lower richness. Despite their lower diversity, highland regions are disproportionally important for maintaining diversity in the adjacent lowlands.

Miocene Climate and Habitat Change Drove Diversification in Bicyclus, Africa's Largest Radiation of Satyrine Butterflies

Compared to other regions, the drivers of diversification in Africa are poorly understood. We studied a radiation of insects with over 100 species occurring in a wide range of habitats across the Afrotropics to investigate the fundamental evolutionary processes and geological events that generate and maintain patterns of species richness on the continent. By investigating the evolutionary history of Bicyclus butterflies within a phylogenetic framework, we inferred the group's origin at the Oligo-Miocene boundary from ancestors in the Congolian rainforests of central Africa. Abrupt climatic fluctuations during the Miocene (ca. 19-17 Ma) likely fragmented ancestral populations, resulting in at least eight early-divergent lineages. Only one of these lineages appears to have diversified during the drastic climate and biome changes of the early Miocene, radiating into the largest group of extant species. The other seven lineages diversified in forest ecosystems during the late Miocene and Pleistocene when climatic conditions were more favourable-warmer and wetter. Our results suggest changing Neogene climate, uplift of eastern African orogens, and biotic interactions might have had different effects on the various subclades of Bicyclus, producing one of the most spectacular butterfly radiations in Africa.

Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach

The branching patterns of molecular phylogenies are generally assumed to contain information on rates of the underlying speciation and extinction processes. Simple birth-death models with constant, time-varying, or diversity-dependent rates have been invoked to explain these patterns. They have one assumption in common: all lineages have the same set of diversification rates at a given point in time. It seems likely, however, that there is variability in diversification rates across subclades in a phylogenetic tree. This has inspired the construction of models that allow multiple rate regimes across the phylogeny, with instantaneous shifts between these regimes. Several methods exist for calculating the likelihood of a phylogeny under a specified mapping of diversification regimes and for performing inference on the most likely diversification history that gave rise to a particular phylogenetic tree. Here, we show that the likelihood computation of these methods is not correct. We provide a new framework to compute the likelihood correctly and show, with simulations of a single shift, that the correct likelihood indeed leads to parameter estimates that are on average in much better agreement with the generating parameters than the incorrect likelihood. Moreover, we show that our corrected likelihood can be extended to multiple rate shifts in time-dependent and diversity-dependent models. We argue that identifying shifts in diversification rates is a nontrivial model selection exercise where one has to choose whether shifts in now-extinct lineages are taken into account or not. Hence, our framework also resolves the recent debate on such unobserved shifts. [Diversification; macroevolution; phylogeny; speciation].

Microbiome and environment explain the absence of correlations between consumers and their diet in Bornean microsnails

Classical ecological theory posits that species partition resources such that each species occupies a unique resource niche. In general, the availability of more resources allows more species to co-occur. Thus, a strong relationship between communities of consumers and their resources is expected. However, correlations may be influenced by other layers in the food web, or by the environment. Here we show, by studying the relationship between communities of consumers (land snails) and individual diets (from seed plants), that there is in fact no direct, or at most a weak but negative, relationship. However, we found that the diversity of the individual microbiome positively correlates with both consumer community diversity and individual diet diversity in three target species. Moreover, these correlations were affected by various environmental variables, such as anthropogenic activity, habitat island size, and a possibly important nutrient source, guano runoff from nearby caves. Our results suggest that the microbiome and the environment explain the absence of correlations between diet and consumer community diversity. Hence, we advocate that microbiome inventories are routinely added to any community dietary analysis, which our study shows can be done with relatively little extra effort. Our approach presents the tools to quickly obtain an overview of the relationships between consumers and their resources. We anticipate our approach to be useful for ecologists and environmentalists studying different communities in a local food web.

Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification

One of the primary goals of macroevolutionary biology has been to explain general trends in long‐term diversity patterns, including whether such patterns correspond to an upscaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity‐dependent (DD) diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time dependence without diversity dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time‐dependent, but diversity‐independent model that matches the expected diversity through time of a DD model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity dependence. We advocate that tests encompassing additional data, for example, traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.

Inferring the Effect of Species Interactions on Trait Evolution

Models of trait evolution form an important part of macroevolutionary biology. The Brownian motion model and Ornstein–Uhlenbeck models have become classic (null) models of character evolution, in which species evolve independently. Recently, models incorporating species interactions have been developed, particularly involving competition where abiotic factors pull species toward an optimal trait value and competitive interactions drive the trait values apart. However, these models assume a fitness function rather than derive it from population dynamics and they do not consider dynamics of the trait variance. Here, we develop a general coherent trait evolution framework where the fitness function is based on a model of population dynamics, and therefore it can, in principle, accommodate any type of species interaction. We illustrate our framework with a model of abundance-dependent competitive interactions against a macroevolutionary background encoded in a phylogenetic tree. We develop an inference tool based on Approximate Bayesian Computation and test it on simulated data (of traits at the tips). We find that inference performs well when the diversity predicted by the parameters equals the number of species in the phylogeny. We then fit the model to empirical data of baleen whale body lengths, using three different summary statistics, and compare it to a model without population dynamics and a model where competition depends on the total metabolic rate of the competitors. We show that the unweighted model performs best for the least informative summary statistic, while the model with competition weighted by the total metabolic rate fits the data slightly better than the other two models for the two more informative summary statistics. Regardless of the summary statistic used, the three models substantially differ in their predictions of the abundance distribution. Therefore, data on abundance distributions will allow us to better distinguish the models from one another, and infer the nature of species interactions. Thus, our framework provides a conceptual approach to reveal species interactions underlying trait evolution and identifies the data needed to do so in practice. [Approximate Bayesian computation; competition; phylogeny; population dynamics; simulations; species interaction; trait evolution.]

Deep Macroevolutionary Impact of Humans on New Zealand's Unique Avifauna

Islands are at the frontline of the anthropogenic extinction crisis [1]. A vast number of island birds have gone extinct since human colonization [2], and an important proportion is currently threatened with extinction [3]. While the number of lost or threatened avian species has often been quantified [4], the macroevolutionary consequences of human impact on island biodiversity have rarely been measured [5]. Here, we estimate the amount of evolutionary time that has been lost or is under threat due to anthropogenic activity in a classic example, New Zealand. Half of its bird taxa have gone extinct since humans arrived [6, 7] and many are threatened [8], including lineages forming highly distinct branches in the avian tree of life [9-11]. Using paleontological and ancient DNA information, we compiled a dated phylogenetic dataset for New Zealand's terrestrial avifauna. We extend the method DAISIE developed for island biogeography [12] to allow for the fact that many of New Zealand's birds are evolutionarily isolated and use it to estimate natural rates of speciation, extinction, and colonization. Simulating under a range of human-induced extinction scenarios, we find that it would take approximately 50 million years (Ma) to recover the number of species lost since human colonization of New Zealand and up to 10 Ma to return to today's species numbers if currently threatened species go extinct. This study puts into macroevolutionary perspective the impact of humans in an isolated fauna and reveals how conservation decisions we take today will have repercussions for millions of years.

Performance in a novel environment subject to ghost competition

Background

A central tenet of the evolutionary theory of communities is that competition impacts evolutionary processes such as local adaptation. Species in a community exert a selection pressure on other species and may drive them to extinction. We know, however, very little about the influence of unsuccessful or ghost species on the evolutionary dynamics within the community.

Methods

Here we report the long-term influence of a ghost competitor on the performance of a more successful species using experimental evolution. We transferred the spider mite Tetranychus urticae onto a novel host plant under initial presence or absence of a competing species, the congeneric mite T. ludeni.

Results

The competitor species, T. ludeni, unintentionally went extinct soon after the start of the experiment, but we nevertheless completed the experiment and found that the early competitive pressure of this ghost competitor positively affected the performance (i.e., fecundity) of the surviving species, T. urticae. This effect on T. urticae lasted for at least 25 generations.

Discussion

Our study suggests that early experienced selection pressures can exert a persistent evolutionary signal on species’ performance in novel environments.

A simple dynamic model explains the diversity of island birds worldwide

Colonization, speciation and extinction are dynamic processes that influence global patterns of species richness^1-6. Island biogeography theory predicts that the contribution of these processes to the accumulation of species diversity depends on the area and isolation of the island^7,8. Notably, there has been no robust global test of this prediction for islands where speciation cannot be ignored⁹, because neither the appropriate data nor the analytical tools have been available. Here we address both deficiencies to reveal, for island birds, the empirical shape of the general relationships that determine how colonization, extinction and speciation rates co-vary with the area and isolation of islands. We compiled a global molecular phylogenetic dataset of birds on islands, based on the terrestrial avifaunas of 41 oceanic archipelagos worldwide (including 596 avian taxa), and applied a new analysis method to estimate the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation). Our model predicts-with high explanatory power-several global relationships. We found a decline in colonization with isolation, a decline in extinction with area and an increase in speciation with area and isolation. Combining the theoretical foundations of island biogeography^7,8 with the temporal information contained in molecular phylogenies¹⁰ proves a powerful approach to reveal the fundamental relationships that govern variation in biodiversity across the planet.

Additional Analytical Support for a New Method to Compute the Likelihood of Diversification Models

Molecular phylogenies have been increasingly recognized as an important source of information on species diversification. For many models of macroevolution, analytical likelihood formulas have been derived to infer macroevolutionary parameters from phylogenies. A few years ago, a general framework to numerically compute such likelihood formulas was proposed, which accommodates models that allow speciation and/or extinction rates to depend on diversity. This framework calculates the likelihood as the probability of the diversification process being consistent with the phylogeny from the root to the tips. However, while some readers found the framework presented in Etienne et al. (Proc R Soc Lond B Biol Sci 279(1732):1300-1309, 2012) convincing, others still questioned it (personal communication), despite numerical evidence that for special cases the framework yields the same (i.e., within double precision) numerical value for the likelihood as analytical formulas do that were independently derived for these special cases. Here we prove analytically that the likelihoods calculated in the new framework are correct for all special cases with known analytical likelihood formula. Our results thus add substantial mathematical support for the overall coherence of the general framework.

Transient local adaptation and source-sink dynamics in experimental populations experiencing spatially heterogeneous environments

Local adaptation is determined by the strength of selection and the level of gene flow within heterogeneous landscapes. The presence of benign habitat can act as an evolutionary stepping stone for local adaptation to challenging environments by providing the necessary genetic variation. At the same time, migration load from benign habitats will hinder adaptation. In a community context, interspecific competition is expected to select against maladapted migrants, hence reducing migration load and facilitating adaptation. As the interplay between competition and spatial heterogeneity on the joint ecological and evolutionary dynamics of populations is poorly understood, we performed an evolutionary experiment using the herbivore spider mite Tetranychus urticae as a model. We studied the species's demography and local adaptation in a challenging environment that consisted of an initial sink (pepper plants) and/or a more benign environment (cucumber plants). Half of the experimental populations were exposed to a competitor, the congeneric T. ludeni. We show that while spider mites only adapted to the challenging pepper environment when it was spatially interspersed with benign cucumber habitat, this adaptation was only temporary and disappeared when the populations in the benign cucumber environment were expanding and spilling-over to the challenging pepper environment. Although the focal species outcompeted the competitor after about two months, a negative effect of competition on the focal species's performance persisted in the benign environment. Adaptation to challenging habitat in heterogeneous landscapes thus highly depends on demography and source-sink dynamics, but also on competitive interactions with other species, even if they are only present for a short time span.

Incomplete datasets obscure associations between traits affecting dispersal ability and geographic range size of reef fishes in the Tropical Eastern Pacific

Dispersal is thought to be an important process determining range size, especially for species in highly spatially structured habitats, such as tropical reef fishes. Despite intensive research efforts, there is conflicting evidence about the role of dispersal in determining range size. We hypothesize that traits related to dispersal drive range sizes, but that complete and comprehensive datasets are essential for detecting relationships between species' dispersal ability and range size. We investigate the roles of six traits affecting several stages of dispersal (adult mobility, spawning mode, pelagic larval duration (PLD), body size, aggregation behavior, and circadian activity), in explaining range size variation of reef fishes in the Tropical Eastern Pacific (TEP). All traits, except for PLD (148 species), had data for all 497 species in the region. Using a series of statistical models, we investigated which traits were associated with large range sizes, when analyzing all TEP species or only species with PLD data. Furthermore, using null models, we analyzed whether the PLD-subset is representative of the regional species pool. Several traits affecting dispersal ability were strongly associated with range size, although these relationships could not be detected when using the PLD-subset. Pelagic spawners (allowing for passive egg dispersal) had on average 56% larger range sizes than nonpelagic spawners. Species with medium or high adult mobility had on average a 25% or 33% larger range, respectively, than species with low mobility. Null models showed that the PLD-subset was nonrepresentative of the regional species pool, explaining why model outcomes using the PLD-subset differed from the ones based on the complete dataset. Our results show that in the TEP, traits affecting dispersal ability are important in explaining range size variation. Using a regionally complete dataset was crucial for detecting the theoretically expected, but so far empirically unresolved, relationship between dispersal and range size.

The Latitudinal Diversity Gradient: Novel Understanding through Mechanistic Eco-evolutionary Models

The latitudinal diversity gradient (LDG) is one of the most widely studied patterns in ecology, yet no consensus has been reached about its underlying causes. We argue that the reasons for this are the verbal nature of existing hypotheses, the failure to mechanistically link interacting ecological and evolutionary processes to the LDG, and the fact that empirical patterns are often consistent with multiple explanations. To address this issue, we synthesize current LDG hypotheses, uncovering their eco-evolutionary mechanisms, hidden assumptions, and commonalities. Furthermore, we propose mechanistic eco-evolutionary modeling and an inferential approach that makes use of geographic, phylogenetic, and trait-based patterns to assess the relative importance of different processes for generating the LDG.

Inferring Diversification Rate Variation From Phylogenies With Fossils

Time-calibrated phylogenies of living species have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification-extinction rates in particular-can be unreliable in the absence of paleontological data. We introduce a general framework based on the fossilized birth-death process for studying speciation-extinction dynamics on phylogenies of extant and extinct species. The model assumes that phylogenies can be modeled as a mixture of distinct evolutionary rate regimes and that a hierarchical Poisson process governs the number of such rate regimes across a tree. We implemented the model in BAMM, a computational framework that uses reversible jump Markov chain Monte Carlo to simulate a posterior distribution of macroevolutionary rate regimes conditional on the branching times and topology of a phylogeny. The implementation, we describe can be applied to paleontological phylogenies, neontological phylogenies, and to phylogenies that include both extant and extinct taxa. We evaluate performance of the model on data sets simulated under a range of diversification scenarios. We find that speciation rates are reliably inferred in the absence of paleontological data. However, the inclusion of fossil observations substantially increases the accuracy of extinction rate estimates. We demonstrate that inferences are relatively robust to at least some violations of model assumptions, including heterogeneity in preservation rates and misspecification of the number of occurrences in paleontological data sets.

The influence of ecological and geographic limits on the evolution of species distributions and diversity

The role of ecological limits in regulating the distribution and diversification of species remains controversial. Although such limits must ultimately arise from constraints on local species coexistence, this spatial context is missing from most macroevolutionary models. Here, we develop a stochastic, spatially explicit model of species diversification to explore the phylogenetic and biogeographic patterns expected when local diversity is bounded. We show how local ecological limits, by regulating opportunities for range expansion and thus rates of speciation and extinction, lead to temporal slowdowns in diversification and predictable differences in equilibrium diversity between regions. However, our models also show that even when regions have identical diversity limits, the dynamics of diversification and total number of species supported at equilibrium can vary dramatically depending on the relative size of geographic and local ecological niche space. Our model predicts that small regions with higher local ecological limits support a higher standing diversity and more balanced phylogenetic trees than large geographic areas with more stringent constraints on local coexistence. Our findings highlight how considering the spatial context of diversification can provide new insights into the role of ecological limits in driving variation in biodiversity across space, time, and clades.

Detecting local diversity-dependence in diversification

Whether there are ecological limits to species diversification is a hotly debated topic. Molecular phylogenies show slowdowns in lineage accumulation, suggesting that speciation rates decline with increasing diversity. A maximum-likelihood (ML) method to detect diversity-dependent (DD) diversification from phylogenetic branching times exists, but it assumes that diversity-dependence is a global phenomenon and therefore ignores that the underlying species interactions are mostly local, and not all species in the phylogeny co-occur locally. Here, we explore whether this ML method based on the nonspatial diversity-dependence model can detect local diversity-dependence, by applying it to phylogenies, simulated with a spatial stochastic model of local DD speciation, extinction, and dispersal between two local communities. We find that type I errors (falsely detecting diversity-dependence) are low, and the power to detect diversity-dependence is high when dispersal rates are not too low. Interestingly, when dispersal is high the power to detect diversity-dependence is even higher than in the nonspatial model. Moreover, estimates of intrinsic speciation rate, extinction rate, and ecological limit strongly depend on dispersal rate. We conclude that the nonspatial DD approach can be used to detect diversity-dependence in clades of species that live in not too disconnected areas, but parameter estimates must be interpreted cautiously.

Relative contribution of neutral and deterministic processes in shaping fruit-feeding butterfly assemblages in Afrotropical forests

The unified neutral theory of biodiversity and biogeography has gained the status of a quantitative null model for explaining patterns in ecological (meta)communities. The theory assumes that individuals of trophically similar species are functionally equivalent. We empirically evaluate the relative contribution of neutral and deterministic processes in shaping fruit-feeding butterfly assemblages in three tropical forests in Africa, using both direct (confronting the neutral model with species abundance data) and indirect approaches (testing the predictions of neutral theory using data other than species abundance distributions). Abundance data were obtained by sampling butterflies using banana baited traps set at the forest canopy and understorey strata. Our results indicate a clear consistency in the kind of species or species groups observed at either the canopy or understorey in the three studied communities. Furthermore, we found significant correlation between some flight-related morphological traits and species abundance at the forest canopy, but not at the understorey. Neutral theory's contribution to explaining our data lies largely in identifying dispersal limitation as a key process regulating fruit-feeding butterfly community structure. Our study illustrates that using species abundance data alone in evaluating neutral theory can be informative, but is insufficient. Species-level information such as habitat preference, host plants, geographical distribution, and phylogeny is essential in elucidating the processes that regulate biodiversity community structures and patterns.

Robustness of the approximate likelihood of the protracted speciation model

The protracted speciation model presents a realistic and parsimonious explanation for the observed slowdown in lineage accumulation through time, by accounting for the fact that speciation takes time. A method to compute the likelihood for this model given a phylogeny is available and allows estimation of its parameters (rate of initiation of speciation, rate of completion of speciation and extinction rate) and statistical comparison of this model to other proposed models of diversification. However, this likelihood computation method makes an approximation of the protracted speciation model to be mathematically tractable: it sometimes counts fewer species than one would do from a biological perspective. This approximation may have large consequences for likelihood-based inferences: it may render any conclusions based on this method completely irrelevant. Here, we study to what extent this approximation affects parameter estimations. We simulated phylogenies from which we reconstructed the tree of extant species according to the original, biologically meaningful protracted speciation model and according to the approximation. We then compared the resulting parameter estimates. We found that the differences were larger for high values of extinction rates and small values of speciation-completion rates. Indeed, a long speciation-completion time and a high extinction rate promote the appearance of cases to which the approximation applies. However, surprisingly, the deviation introduced is largely negligible over the parameter space explored, suggesting that this approximate likelihood can be applied reliably in practice to estimate biologically relevant parameters under the original protracted speciation model.

Quantifying species contributions to ecosystem processes: a global assessment of functional trait and phylogenetic metrics across avian seed-dispersal networks

Quantifying the role of biodiversity in ecosystems not only requires understanding the links between species and the ecological functions and services they provide, but also how these factors relate to measurable indices, such as functional traits and phylogenetic diversity. However, these relationships remain poorly understood, especially for heterotrophic organisms within complex ecological networks. Here, we assemble data on avian traits across a global sample of mutualistic plant-frugivore networks to critically assess how the functional roles of frugivores are associated with their intrinsic traits, as well as their evolutionary and functional distinctiveness. We find strong evidence for niche complementarity, with phenotypically and phylogenetically distinct birds interacting with more unique sets of plants. However, interaction strengths-the number of plant species dependent on a frugivore-were unrelated to evolutionary or functional distinctiveness, largely because distinct frugivores tend to be locally rare, and thus have fewer connections across the network. Instead, interaction strengths were better predicted by intrinsic traits, including body size, gape width and dietary specialization. Our analysis provides general support for the use of traits in quantifying species ecological functions, but also highlights the need to go beyond simple metrics of functional or phylogenetic diversity to consider the multiple pathways through which traits may determine ecological processes.

Equilibrium Bird Species Diversity in Atlantic Islands

Half a century ago, MacArthur and Wilson proposed that the number of species on islands tends toward a dynamic equilibrium diversity around which species richness fluctuates [1]. The current prevailing view in island biogeography accepts the fundamentals of MacArthur and Wilson's theory [2] but questions whether their prediction of equilibrium can be fulfilled over evolutionary timescales, given the unpredictable and ever-changing nature of island geological and biotic features [3-7]. Here we conduct a complete molecular phylogenetic survey of the terrestrial bird species from four oceanic archipelagos that make up the diverse Macaronesian bioregion-the Azores, the Canary Islands, Cape Verde, and Madeira [8, 9]. We estimate the times at which birds colonized and speciated in the four archipelagos, including many previously unsampled endemic and non-endemic taxa and their closest continental relatives. We develop and fit a new multi-archipelago dynamic stochastic model to these data, explicitly incorporating information from 91 taxa, both extant and extinct. Remarkably, we find that all four archipelagos have independently achieved and maintained a dynamic equilibrium over millions of years. Biogeographical rates are homogeneous across archipelagos, except for the Canary Islands, which exhibit higher speciation and colonization. Our finding that the avian communities of the four Macaronesian archipelagos display an equilibrium diversity pattern indicates that a diversity plateau may be rapidly achieved on islands where rates of in situ radiation are low and extinction is high. This study reveals that equilibrium processes may be more prevalent than recently proposed, supporting MacArthur and Wilson's 50-year-old theory.

Community assembly in Lake Tanganyika cichlid fish: quantifying the contributions of both niche-based and neutral processes

The cichlid family features some of the most spectacular examples of adaptive radiation. Evolutionary studies have highlighted the importance of both trophic adaptation and sexual selection in cichlid speciation. However, it is poorly understood what processes drive the composition and diversity of local cichlid species assemblages on relatively short, ecological timescales. Here, we investigate the relative importance of niche-based and neutral processes in determining the composition and diversity of cichlid communities inhabiting various environmental conditions in the littoral zone of Lake Tanganyika, Zambia. We collected data on cichlid abundance, morphometrics, and local environments. We analyzed relationships between mean trait values, community composition, and environmental variation, and used a recently developed modeling technique (STEPCAM) to estimate the contributions of niche-based and neutral processes to community assembly. Contrary to our expectations, our results show that stochastic processes, and not niche-based processes, were responsible for the majority of cichlid community assembly. We also found that the relative importance of niche-based and neutral processes was constant across environments. However, we found significant relationships between environmental variation, community trait means, and community composition. These relationships were caused by niche-based processes, as they disappeared in simulated, purely neutrally assembled communities. Importantly, these results can potentially reconcile seemingly contrasting findings in the literature about the importance of either niche-based or neutral-based processes in community assembly, as we show that significant trait relationships can already be found in nearly (but not completely) neutrally assembled communities; that is, even a small deviation from neutrality can have major effects on community patterns.

Phylogenetic congruence between subtropical trees and their associated fungi

Recent studies have detected phylogenetic signals in pathogen–host networks for both soil‐borne and leaf‐infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next‐generation high‐throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK, rbcL, atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host–fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant–fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant–fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.

The Role of Within-Host Competition for Coexistence in Multiparasitoid-Host Systems

Multiparasitism (females of multiple species parasitizing the same host) is a ubiquitous phenomenon in parasitoids, yet the role of within-host competition has been mostly ignored in multiparasitoid-host models. Here we study the effect of varying the degree of competition at different life stages: competition over oviposition sites (between-adult competition) and larval competition over resources within the host (within-host competition). We adapt a Nicholson-Bailey model to allow for varying levels of between-adult competition (varying the overlap in species distributions) and within-host competition (varying the number of offspring that can successfully emerge from a host). Surprisingly, while stronger between-adult competition reduces coexistence, stronger within-host competition promotes it. Asymmetric between-adult competition (a fecundity difference between the two species) reduces coexistence when compared to symmetric competition; this can be counteracted by asymmetric within-host competition (within-host competitive advantage of the lower-fecundity species), but only when within-host competition is strong and the correlation between the parasitoids' distributions is intermediate. We discuss our results in the context of the interaction between two parasitoid species, Nasonia vitripennis and Nasonia giraulti, which have strongly correlated distributions and high levels of multiparasitism in the field. We conclude that either low or asymmetric within-host competition is unlikely to explain their coexistence.

Arbuscular mycorrhizal fungi counteract the Janzen-Connell effect of soil pathogens

Soilborne pathogens can contribute to diversity maintenance in tree communities through the Janzen-Connell effect, whereby the pathogenic reduction of seedling performance attenuates with distance from conspecifics. By contrast, arbuscular mycorrhizal fungi (AMF) have been reported to promote seedling performance; however, it is unknown whether this is also distance dependent. Here, we investigate the distance dependence of seedling performance in the presence of both pathogens and AMF. In a subtropical forest in south China, we conducted a four-year field census of four species with relatively large phylogenetic distances and found no distance-dependent mortality for newly germinated seedlings. By experimentally separating the effects of AMF and pathogens on seedling performance of six subtropical tree species in a shade house, we found that soil pathogens significantly inhibited seedling survival and growth while AMF largely promoted seedling growth, and these effects were host specific and declined with increasing conspecific distance. Together, our field and experimental results suggest that AMF can neutralize the negative effect of pathogens and that the Janzen-Connell effect may play a less prominent role in explaining diversity of nondominant tree species than previously thought.