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Native plant communities are commonly invaded by invasive plants to different degrees. However, the relative contribution of the invasive plant abundance vs. phylogenetic evenness to the responses of wetland communities to different degrees of invasion is still unclear. In addition, whether such contribution varies with environmental conditions such as flooding is also unclear. To address these questions, we chose Alternanthera philoxeroides as the invasive plant, and set up four invasive degrees by changing the community species composition under both flooding and non-flooding conditions. The relative abundance of A. philoxeroides and phylogenetic evenness changed simultaneously with the change in the community invasion degree. The invasion degree significantly affected the individual biomass of A. philoxeroides and some native species. Variation partitioning showed that the relative abundance of A. philoxeroides contributed more to variation in community indicators than phylogenetic evenness, regardless of flooding. Spearman rank correlation test showed that the relative abundance of A. philoxeroides was negatively correlated with the individual biomass of A. philoxeroides and some native species, while the phylogenetic evenness was positively correlated with only a few native species. And their correlation strength and significance were all affected by specific species and flooded environment. In conclusion, our results suggest that the relative abundance of A. philoxeroides can more effectively explain the wetland community response to different invasion degrees than phylogenetic evenness, regardless of flooding.

The impact of climate change on global biodiversity is firmly established, but the differential effect of climate change on populations within the same species is rarely considered. In ectotherms, melanism (i.e. darker integument due to heavier deposition of melanin) can significantly influence thermoregulation, as dark individuals generally heat more and faster than bright ones. Therefore, darker ectotherms might be more susceptible to climate change. Using the colour-polyphenic lizard Karusasaurus polyzonus (Squamata: Cordylidae), we hypothesized that, under future climatic projections, darker populations will decrease their activity time more than brighter ones due to their greater potential for overheating. To test this, we mechanistically modelled the body temperatures of 56 individuals from five differently coloured populations under present and future climate conditions. We first measured morphological traits and integumentary reflectance from live animals, and then collected physiological data from the literature. We used a biophysical model to compute activity time of individual lizards as proxy for their viability, and thereby predict how different populations will cope with future climate conditions. Contrary to our expectations, we found that all populations will increase activity time and, specifically, that darker populations will become relatively more active than bright ones. This suggests that darker populations of K. polyzonus may benefit from global warming. Our study emphasizes the importance of accounting for variation between populations when studying responses to climate change, as we must consider these variations to develop efficient and specific conservation strategies. A free Plain Language Summary can be found within the Supporting Information of this article.

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.

Background and Aims The Canary Islands have strong floristic affinities with the Mediterranean Basin. One of the most characteristic and diverse vegetation belts of the archipelago is the thermophilous woodland (between 200 and 900 m.a.s.l.). This thermophilous plant community consists of many non-endemic species shared with the Mediterranean Floristic Region together with Canarian endemic species. Consequently, phytogeographic studies have historically proposed the hypothesis of an origin of the Canarian thermophilous species following the establishment of the summer-dry mediterranean climate in the Mediterranean Basin around 2.8 million years ago. Methods Time-calibrated phylogenies for 39 plant groups including Canarian thermophilous species were primarily analysed to infer colonization times. In particular, we used 26 previously published phylogenies together with 13 new time-calibrated phylogenies (including newly generated plastid and nuclear DNA sequence data) to assess whether the time interval between stem and crown ages of Canarian thermophilous lineages postdates 2.8 Ma. For lineages postdating this time threshold, we additionally conducted ancestral area reconstructions to infer the potential source area for colonization. Key Results A total of 43 Canarian thermophilous lineages were identified from 39 plant groups. Both mediterranean (16) and pre-mediterranean (9) plant lineages were found. However, we failed to determine the temporal origin for 18 lineages because a stem–crown time interval overlaps with the 2.8-Ma threshold. The spatial origin of thermophilous lineages was also heterogeneous, including ancestral areas from the Mediterranean Basin (nine) and other regions (six). Conclusions Our findings reveal an unexpectedly heterogeneous origin of the Canarian thermophilous species in terms of colonization times and mainland source areas. A substantial proportion of the lineages arrived in the Canaries before the summer-dry climate was established in the Mediterranean Basin. The complex temporal and geographic origin of Canarian thermophilous species challenges the view of the Canary Islands (and Madeira) as a subregion within the Mediterranean Floristic Region.

Adaptive radiation is proposed to play a key role in generating differences in species richness among lineages and geographical regions. Due to the importance of ecological divergence in adaptive radiation, species richness is predicted to be influenced by equilibrium diversity dynamics, although the concept continues to generate much debate. An additional important question is whether radiating clades have intrinsic biological characteristics that make them particularly prone to diversify. We tackle these questions by analysing (i) the temporal patterns of diversification of Caribbean Eleutherodactylus frogs, and (ii) assembly of the complete native anuran community of the Caribbean archipelago (197 species), testing for the presence of equilibrium dynamics and whether diversification patterns of Eleutherodactylus differ from those of the rest of the Caribbean anurans. Diversification rates follow the predicted pattern of rapid diversification early in the radiation which gradually decreases towards the present. Eleutherodactylus diversification is significantly faster than that of the Caribbean anuran community, and although equilibrium dynamics influence richness of all Caribbean anurans, Eleutherodactylus shows higher carrying capacity. Our results indicate that ecological opportunity per se is not sufficient for adaptive radiation and that diverse lineages present intrinsic characteristics that enable them to make the most of available opportunity.

Many of Madagascar’s unique species are threatened with extinction. However, the severity of recent and potential extinctions in a global evolutionary context is unquantified. Here, we compile a phylogenetic dataset for the complete non-marine mammalian biota of Madagascar and estimate natural rates of extinction, colonization, and speciation. We measure how long it would take to restore Madagascar’s mammalian biodiversity under these rates, the “evolutionary return time” (ERT). At the time of human arrival there were approximately 250 species of mammals on Madagascar, resulting from 33 colonisation events (28 by bats), but at least 30 of these species have gone extinct since then. We show that the loss of currently threatened species would have a much deeper long-term impact than all the extinctions since human arrival. A return from current to pre-human diversity would take 1.6 million years (Myr) for bats, and 2.9 Myr for non-volant mammals. However, if species currently classified as threatened go extinct, the ERT rises to 2.9 Myr for bats and 23 Myr for non-volant mammals. Our results suggest that an extinction wave with deep evolutionary impact is imminent on Madagascar unless immediate conservation actions are taken.

Evolution has traditionally been a historical and descriptive science and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ, for example we could try to predict which genotype will dominate, the fitness of the population, or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data that are used to make these predictions in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability, and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by creating a common language for evolutionary predictions.

Through the scope of this dissertation, I discuss the implications of diversity-dependent diversification, both as a phenomenological and a mechanistic model. Each of the following research chapters address an aspect of diversity-dependent diversification, in turn tackling its detectability in molecular phylogenies (Chapter 2), modelling the ecological processes that are hypothesized to lead to it (Chapter 3), and challenging a central assumption of the model and exploring how it impacts inference (Chapter 4). Finally, I summarise the findings of these three chapters and discuss their implications for the field of macroevolution (Chapter 5), particularly in regard to recent developments that arose during the course of the PhD.In Chapter 2, I focus on characterizing differences between diversity-dependence and time-dependence and develop a method to reliably infer which better explains the distribution of branches in molecular phylogenies.In Chapter 3, I depart from the phenomenological view and study an individual-based model, where trait-mediated interactions between organisms and their environment drive an adaptive radiation in a finite ecological niche space. As the radiation proceeds, niche space fills up and speciation becomes much less frequent, a process that is in line with the ecological interpretation of diversity-dependence. In Chapter 4, I extend the individual-based model used through Chapter 2 to consider the case of multiple clades evolving in a common niche space. The ecological scenario then approximates diversification on islands. Through these approaches, I hope to bring a better understanding of this major diversification process and more generally, how ecological dynamics influence macroevolution.

Elevated CO2 concentrations (eCO2) have been widely observed to stimulate microbial growth. However, the effect of eCO2 on soil microbial biomass may depend on several factors and their interactions, such as the increase in atmospheric CO2 levels, experimental duration and mean annual precipitation (MAP). We conducted a global meta-analysis from 62 studies that included the responses of soil microbial biomass to eCO2. We found a significant positive eCO2 effect on the bacterial biomass (+9.1 %), fungi (+11 %), arbuscular mycorrhizal fungi (AMF) (+10.2 %) and actinomycetes (ACT) (+16.4 %). The positive effects were mainly observed in studies with low eCO2 levels (≤200 ppm) rather than high levels of eCO2 (>200 ppm), which could be attributable to soil N limitation. It was also found that eCO2 had a significant positive effect on soil microbial biomass in the short term (≤3 y) and under a high MAP (>800 mm). Importantly, we revealed interactive effects between the eCO2 levels, experimental duration on soil microbial biomass. With an increase in eCO2, the total microbial biomass (TMB), bacterial biomass and fungal biomass decreased over the long term (>3 y). These findings indicate the need to incorporate interactions between eCO2 and environmental factors into ecosystem models, to predict future global climate change effects more accurately and their impact on ecosystem functions.

AimBiodiversity on islands is influenced by geophysical processes and sea-level fluctuations. Oceanic islands (never connected to a landmass) are initially vacant with diversity accumulating via colonisation and speciation, and then declining as islands shrink. Continental islands have species upon disconnection from the mainland and may have transient land-bridge connections. Theoretical predictions for the effects of these geophysical processes on rates of colonisation, speciation, and extinction have been proposed. However, paleogeographic reconstructions are currently unavailable for most islands, and phylogenetic models overlook island ontogeny, sea-level changes, or past landmass connections. We analyse to what extent ignoring geodynamics in the inference model affects model predictions when confronted with data simulated with geodynamics.LocationSimulations of oceanic and continental islands.TaxaSimulated lineages.MethodsWe extend the island biogeography simulation model DAISIE to include: (i) area-dependent rates of colonisation and diversification associated with island ontogeny and sea-level fluctuations, (ii) continental islands with biota present upon separation from the mainland, and (iii) shifts in colonisation to mimic temporary land-bridges. We quantify the error of ignoring geodynamic processes by applying DAISIE's inference method to geodynamic simulations.ResultsRobustness of the model to dynamic island area is generally high for oceanic islands and for continental islands that have been separated for a long time, suggesting that it is possible to obtain reliable results when ignoring geodynamics. However, for continental islands that have been recently or frequently connected, robustness of the model is low.Main conclusionsUnder many island biogeographic geodynamic scenarios (oceanic islands and ancient continental fragments) a simple phylogenetic model ignoring geodynamics is empirically applicable and informative. However, recent connection to the continent cannot be ignored, requiring new model development. Our results show that for oceanic islands, reliable insights can be obtained from phylogenetic data in the absence of paleogeographic reconstructions of island area.

Phenotypic plasticity allows organisms to rapidly adjust to environmental changes. Cichlid fish inhabit a wide range of light environments and show a large diversity in visual system properties, which makes them a good model system to address the role of phenotypic plasticity in visual adaptation. Cichlid retinal cone pigments consist of opsin proteins bound to Vitamin A1or A2-derived chromophores. Plasticity in expression has been shown for cichlidopsingenes, but less is known about the contribution ofcyp27c1,the enzyme that converts Vitamin A1into A2,. Here, we studied bothopsinandcyp27c1expression patterns for three closely related cichlid species from different visual habitats in Lake Victoria, across different light treatments. We found differences incyp27c1as well as inopsinexpression patterns between the three species. Experimental light treatments affected the developmental trajectory ofcyp27c1expression in one species andopsinexpression in all three species. Within each species, we found large individual variation incyp27c1expression levels and no consistent association withopsinexpression levels. These results indicate that visual system plasticity of even closely related species can be differentially mediated byopsinandcyp27c1expression, possibly associated with species differences in visual niche.

Anthus correndera has a wide distribution in southern South America with several subspecies assigned to the taxon. We take an integrative approach, analysing genome-wide single-nucleotide polymorphism (SNP) data collected using ddRAD sequencing, songs and linear morphological data, to evaluate the evolutionary history of A. correndera and divergence of each subspecies. The final genomic data set of 11,467 SNPs for 40 individuals supports a primary divergence of two main lineages: one in the Andean highlands and another in the lowlands. Estimated divergence times suggest the Andean and lowland groups diverged around 135.5 to 99 thousand years ago (Ka), whereas divergence among populations within each group was much more recent, ranging from 54.7 Ka among the Andean populations to as recent as 20.6 Ka among the lowland populations. Analyses of territorial songs showed slight differences between all operational taxonomic units; however, morphological differences were apparent only between geographically distant populations (i.e. Puna vs. South Georgia). Based on multiple lines of evidence, we propose to reduce the number of subspecies within the correndera complex to three: A. c. calcaratus on the Andean Altiplano (treating A. c. catamarcae as a junior synonym), A. c. correndera in the lowlands (treating A. c. chilensis and A. c. grayi as junior synonyms), and A. c. antarcticus on South Georgia.

Aim Neotropical savanna birds occur north and south of, but mostly not in the Amazon Basin, except for a few isolated savanna patches. Here, we investigate the phylogeography of 23 taxa of Neotropical savanna birds co-distributed across multiple isolated savanna patches to assess to what extent these species have a shared history of spatial diversification. We explore the role of the forested Amazon Basin as a vicariant barrier separating northern and southern populations, particularly focusing on the role of the coastal savannas of Amapa as a potential corridor of gene flow between northern and southern populations. Location Neotropical savannas. Taxon Aves. Method We employ 775 mtDNA samples of 24 co-distributed savanna bird taxa from all major savanna patches in South America to infer phylogeographic patterns. For this purpose, we use 24 genomic samples (UCEs) of a subset of 12 taxa in addition to the mtDNA samples to estimate timing of divergence across the Amazon Basin. We use phylogeographic concordance factors (PCF) to assess the level of phylogeographic congruence across co-distributed taxa. Finally, we assess to which level physical distance drives genetic structuring by estimating isolation-by-distance (IBD) effects. Results We find that although the study taxa generally do not share similar diversification patterns geographically, many have at least two distinct genetic groups, one north and one south of the Amazon Basin, that have only recently diverged. The timing of divergence between both areas is generally centered in the late Pleistocene, but somewhat variable, indicating there is no single vicariant event responsible for driving diversification. Main conclusions Variability in divergence times indicates that landscape processes have not led to shared phylogeographic responses, which indicates a relatively minor role for vicariance. Shallow divergences suggest that Neotropical grassland habitats may have recently been more connected or that gene flow has played an important role. We did not find evidence of a single dominant corridor of dispersal between savannas north and south of the forested Amazon Basin.

Sociability – an individual’s propensity to engage in group activities – is a conserved trait throughout most of life. Sociability can be considered as a personality type in humans when showing correlated sociability measures across different assays. Our knowledge of the mechanisms that drive sociability and explain its inter-individual variation is still limited. To enhance our mechanistic understanding, the genetically tractable Drosophila melanogaster is increasingly being used as a model for research on social behaviour. High and low sociability phenotypes, indicative of a variation of sociability levels among the population have been documented in this species. However, sociability traits have been measured through unidimensional assays, which do not allow us to assess whether sociability is a personality type in fruit flies. Here, we present a multidimensional approach to assess sociability, using a combination of three behavioural assays that each captures a different functional feature of social interactions in D.melanogaster. We applied our approach to the Drosophila melanogaster Genetic Reference Panel (DGRP) lines and revealed continuous variation in the strength of response to others. We found that sociability levels varied between genetically distinct lines, indicative of a genetic component of sociability.The three sociability traits were, however, not correlated, making it questionable whether sociability can be considered a personality type in D. melanogaster.

Phenotypic plasticity allows individuals to cope with different environmental conditions without the need for genetic adaptation. Consequently, plasticity affects the nature and strength of selection on traits. Plasticity enables individuals to experience novel selection pressures, for example through migration, possibly leading to genetic adaptation. At the same time, plasticity may shield the genotype from selection, impeding genetic adaptation. Plasticity, therefore, can have opposing effects on evolutionary change and population divergence.The visual system of cichlid fish is a suitable model trait to study the relationship between plasticity and evolutionary change, because of the high species richness and the variation among species in visual habitat. Furthermore, plasticity in the expression of genes involved in the cichlid’ visual system is well established. Here, we test whether visual plasticity is correlated to the degree of ecological specialisation and clade species richness. We quantify plasticity in the expression of these genes in species from species-poor and species-rich clades, inhabiting different visual habitats in nature, by exposing individuals to different light conditions and determining light-induced variation in gene expression. Preliminary results indicate that expression indeed differs among light treatments, in multiple species. We expect our study to provide a better understanding of the impact of phenotypic plasticity on divergent evolution.

The predictability of evolution is expected to depend on the relative contribution of deterministic and stochastic processes. This ratio is modulated by effective population size. Smaller effective populations harbor less genetic diversity and stochastic processes are generally expected to play a larger role, leading to less repeatable evolutionary trajectories. Empirical insight into the relationship between effective population size and repeatability is limited and focused mostly on asexual organisms. Here, we tested whether fitness evolution was less repeatable after a population bottleneck in obligately outcrossing populations of Caenorhabditis elegans. Replicated populations founded by 500, 50, or five individuals (no/moderate/strong bottleneck) were exposed to a novel environment with a different bacterial prey. As a proxy for fitness, population size was measured after one week of growth before and after 15 weeks of evolution. Surprisingly, we found no significant differences among treatments in their fitness evolution. Even though the strong bottleneck reduced the relative contribution of selection to fitness variation, this did not translate to a significant reduction in the repeatability of fitness evolution. Thus, although a bottleneck reduced the contribution of deterministic processes, we conclude that the predictability of evolution may not universally depend on effective population size, especially in sexual organisms. ispartof: EVOLUTION vol:76 issue:8 pages:1896-1904 ispartof: location:United States status: published

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 favorable—warmer and wetter. Our results suggest changing Neogene climate, uplift of eastern African orogens, and biotic interactions have had different effects on the various subclades of Bicyclus, producing one of the most spectacular butterfly radiations in Africa. [Afrotropics; biodiversity; biome; biotic interactions; Court Jester; extinction; grasslands; paleoclimates; Red Queen; refugia forests; dependent-diversification; speciation.]

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.

SummaryPhylogenetic trees are currently routinely reconstructed from an alignment of character sequences (usually nucleotide sequences). Bayesian tools, such as MrBayes, RevBayes and BEAST2, have gained much popularity over the last decade, as they allow joint estimation of the posterior distribution of the phylogenetic trees and the parameters of the underlying inference model. An important ingredient of these Bayesian approaches is the species tree prior. In principle, the Bayesian framework allows for comparing different tree priors, which may elucidate the macroevolutionary processes underlying the species tree. In practice, however, only macroevolutionary models that allow for fast computation of the prior probability are used. The question is how accurate the tree estimation is when the real macroevolutionary processes are substantially different from those assumed in the tree prior.Here we presentpirouette, a free and open-source R package that assesses the inference error made by Bayesian phylogenetics for a given macroevolutionary diversification model.pirouettemakes use of BEAST2, but its philosophy applies to any Bayesian phylogenetic inference tool.We describepirouette’s usage providing full examples in which we interrogate a model for its power to describe another.Last, we discuss the results obtained by the examples and their interpretation.

Aim Rates of colonization, speciation and extinction determine species richness and endemism in insular systems. The general dynamic model of island biogeography (GDM) predicts that speciation and extinction rates depend on island area and elevation via their control on ecological limits to diversification and therefore covary with an island's geological history. Additionally, the colonization rate may increase with area and elevation through the 'target effect', which can be mediated by reduced 'environmental filtering'. Here we test whether the area and depth expansion of an island-like ecosystem, a lake, caused a shift in diversity dynamics. Location Lake Biwa, Japan, whose geological history and biota are well documented. Taxon Fishes. Methods We extended the phylogenetic island biogeography framework DAISIE (Dynamic Assembly of Island biota through Speciation, Immigration and Extinction) to accommodate time-shifts in macroevolutionary rates and in carrying capacity. Using phylogenetic information on colonization and speciation times for the complete Lake Biwa fish community (70 taxa), we tested for a shift in macroevolutionary assembly rates and reconstructed the temporal diversity trajectory in the lake. We assessed the power to identify a shift through a wide range of scenarios and benchmarked against simulated fossil records. Results We detected an increase in colonization rate of fishes at 0.2 million years ago (Ma), with limited support for the existence of ecological limits. The reconstructed diversity trajectory was close to a source-sink equilibrium diversity prior to the shift and remained well below a new shift-driven elevated equilibrium thereafter. We found sufficient power to identify an increase in colonization rate up to 1.5 Ma, whereas extinction concealed the signal of earlier shifts. Main conclusions The fish diversity dynamics of Lake Biwa show a response to changes in area and depth and phylogenies carry a signature of these changes. The detected increase in colonization rate following Lake Biwa's expansion, elevating the fish diversity, is unlikely due to a predicted increase in ecological limits feeding back on colonization rate. We therefore call for (additional) explanations: the target effect, whereby larger islands attract more species, and reduced environmental filtering due to higher habitat diversity associated with increased lake area/depth.

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]

To successfully colonize new habitats, organisms not only need to gain access to it, but also need to cope with the selective pressures imposed by the local biotic and abiotic conditions. The number of immigrants, the preadaptation to the local habitat and the presence of competitors are important factors determining the success of colonization. Here, using an experimental set-up, we test the combined effect of propagule pressure, preadaptation and interspecific competition on the colonization success of new habitats using the two-spotted spider mite (Tetranychus urticae) as our model system and the red spider mite (Tetranychus evansi) as a competitor. Our results show that propagule pressure and preadaptation positively affect colonization success. More successful populations reach larger final population sizes either by having higher per capita growth rate (due to preadaptation effect) or by starting a population with a larger number of individuals. Although populations are more successful colonizing non-competitive environments than competitive ones, propagule pressure and preadaptation counteract the negative effects of competition, promoting colonization success. Our results show the importance of propagule pressure and preadaptation to cope both with the exigencies of the new environment and the community context for successful colonization of new habitats.

Euphilotes ancilla purpura and cryptica (Lycaenidae), butterflies endemic to the Spring Mountains (Clark Co., Nevada), have been described as two univoltine, temporally isolated, sympatric taxa that utilize different early- and late-flowering larval host plant varieties (Eriogonum umbellatum). However, our results from field and laboratory indicate that this is not the case. The subspecies overlap in timing of adult reproductive flight (compilation of field records 1977 to 2018) and laboratory emergence of adults from early-season, non-diapause pupae indicate butterflies are not univoltine. Genetic samples collected from putative E. a. purpura (Early cohort) and cryptica (Late cohort) subpopulations show no evidence of genetic structure indicative of allochronic isolation in phylogenies of 26 mitochondrial DNA COI haplotypes and 18 nuclear ITS1 alleles. Analysis of molecular variance revealed 89% of mitochondrial DNA variation structured within and among subpopulations, with only 11% between the purportedly isolated subspecies. Analysis of isolation and migration indicated gene flow from the Early to Late cohort was 3 × greater than in the opposite direction. We conclude that, rather than two separate subspecies, Euphilotes ancilla exists in a network of partially interconnected subpopulations extending from 1750 to 3000 m across much of the Spring Mountains. Gene flow is related to the timing of adult flight and host plant flowering, contributing to the genetic variation in phenology necessary for evolutionary tracking of shifting flowering periods of larval host plants. Maintenance of connectivity and gene flow across the Spring Mountains is therefore essential for population persistence of both cohorts in the face of environmental change.

International audience; Phylogenetic trees are types of networks that describe the temporal relationship between individuals, species, or other units that are subject to evolutionary diversification. Many phylogenetic trees are constructed from molecular data that is often only available for extant species, and hence they lack all or some of the branches that did not make it into the present. This feature makes inference on the diversification process challenging. For relatively simple diversification models, analytical or numerical methods to compute the likelihood exist, but these do not work for more realistic models in which the likelihood depends on properties of the missing lineages. In this article, we study a general class of species diversification models, and we provide an expectation-maximization framework in combination with a uniform sampling scheme to perform maximum likelihood estimation of the parameters of the diversification process.

In plant communities, genotypic diversity can impact the plant community structure and ecosystem functions, but related research has focused on native plants. Therefore, whether genotypic diversity affects the growth of invasive plants and then changes the wetland microecosystem remains unresolved. In this study, six different genotypes of Hydrocotyle vulgaris, a common invasive plant in China, were selected to construct populations with three different genotypic diversity levels (one, three, and six genotype combinations, respectively) to explore the effects of different genotypic diversity levels on the growth and physiological traits of H. vulgaris, and soil nutrients and greenhouse gas emissions of the wetland microecosystem under flooding conditions. We found that genotypic diversity improved the leaf area, root to shoot ratio and photosynthetic physiological traits of H. vulgaris, especially under flooding. Moreover, genotypic diversity increased soil organic matter (SOM) contents in the wetland microecosystem, while it reduced the cumulative nitrous oxide emissions under flooding conditions. Overall, genotype diversity improved photosynthetic traits of H. vulgaris, further increased SOM, and reduced the N2O emissions of the wetland microecosystem. The results of this study can provide a theoretical basis for exploring how genotypic diversity levels affect the invasiveness of invasive plants and ecosystems in wetland microecosystems.

The Black-tailed Godwit Limosa limosa is a globally Near Threatened species but a common winter visitor to Bangladesh. Although the total wintering population size and trend are unknown, we suspect it is declining due to habitat degradation. Nijhum Dweep National Park is one of the most important sites for Black-tailed Godwits in Bangladesh. Here we report on the site use of Black-tailed Godwits in this national park and adjacent Char Birbira. From October to March 2016–2017 to 2019–2020, we performed 17 winter counts. High-tide roosts were counted from vantage points in these tidal areas, whereas foraging activities were observed from boats during low tide. Black-tailed Godwits were always present, with counts ranging from 735 in January 2020 to 8,269 in December 2017 with a mean of 3,304. The uncertainty of these counts and population estimates for this area in general suggest that better assessment methods, such as simultaneous high-tide counts undertaken at the same time each year, are needed. Our study area met the Ramsar 1% threshold population criterion for the species for 13 of the 17 counts, demonstrating the international importance of this area for Black-tailed Godwits. A local decline of >80% from 9,000 to 1,707 birds over the last decade was apparent on Damar Char West. Over the decades, the landscape of Damar Char has changed, with increased numbers of households, more land converted to agricultural fields, and increased fishing effort. These changes call for better assessments of bird movements and disturbance and more effective conservation actions to help birds and people coexist. We suggest that there should be a monitoring and protection scheme in the Nijhum Dweep management plan that focuses on waterbirds, and restricts and regulates access to Damar Char West, East and Char Birbira. An urgent attempt to create awareness among the main stakeholders, fishers and crab hunters, to provide context and engage them in conservation action, should be a priority.

Understanding the mechanisms that generate the outstanding biological diversity on our planet has been extensively studied. However, to this date many questions remain unresolved. A fundamental process that produces biodiversity is divergent adaptation: here populations diversify by adapting to different environmental conditions. In this project, I investigated the role of the sensory system in this process, as sensory perception is critical for survival and reproduction: How do sensory systems adapt to local environments and (how) does individual flexibility contribute to this process? The fish visual system provides an excellent opportunity to study these questions as it shows extensive variation among species/populations. Fish inhabit different visual environments, as a result of wavelength-dependent light attenuation in water. There are strong indications that adaptation of the visual pigments in fish eyes plays a role in the origin and persistence of species. In this thesis I focused on cichlid fish, one of the most species-rich vertebrate families. At the level of visual pigment molecular composition, I showed that closely related species deal in different ways with variation in light conditions and differ in their plastic response to experimental light treatments. Despite these differences, fish did not go where they saw best in a behavioural choice experiment. Instead, they had a general preference for blue light. Finally, in a comparative analysis I found no evidence that diversification rates depend on the visual environment of a lineage. Together, my findings highlight that vision rapidly diverges between species/populations, impacts behaviour and is also influenced by individual flexibility.

Few biological groups have a well-documented fossil history, detailed trait datasets, reliable distribution maps, and are distributed on a global scale. The Canidae family is one of them, which allows us to tackle several topics related to evolutionary processes and species’ relationship with their environment. Here, I bring a broader view on distinct spatial patterns of Canidae, elucidating many points that are not yet very well understood about this group. By assembling distinct datasets (e.g., phylogenetic trees, paleontological data, species distribution maps, and environmental variables) together with several methods to extract information from these data, I demonstrate which were the main continental dispersal events over the last 13 million years in Canidae, and how these events shaped the diversification patterns of this clade leading to explosive diversification right after the colonization of new areas. I also show that environmental factors are more important than species interactions to explain how Canidae assemblages are structured spatially at the present. Moreover, I demonstrate the drastic climatic scenario for the majority of canids around the world during the next 54 years. In this thesis, I also test if diversification rates of canids are associated with distinct areas around the planet. The results show that when fossils species are incorporated in the analyses distinct diversification patterns are not related to geographic areas.

Group-living facilitates cooperation between individuals, but also creates competition for limited resources. Individuals should thus modulate their reproductive output in response to the presence of others. However, mechanisms that lead to such social context-dependent modulation of reproduction are poorly understood. 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 gave me an opportunity to dissect the mechanisms by which females adjust their behaviour and physiology to their social environment. I discovered social facilitation of oogenesis and egg-laying in Drosophila melanogaster and described the neuro-hormonal mechanisms underlying this modulation. I demonstrated that social environment affects ovarian activity of females in a density-dependent manner. I showed that these responses to the presence of others are mediated by vision through the motion detection pathway and are the result of the stimulation of the juvenile hormone pathway. While social modulation of reproduction is considered a sign of sociality and is mostly expressed in social hymenopterans, my findings thus demonstrate that such phenomenon can already be found in rather solitary species such as D. melanogaster, making the concept of solitary vs social species a bit artificial. I moreover proposed a new approach to explore the variation in sociability among D. melanogaster through the quantification of multiple sociability traits. I found significant variation between the flies in the strength of responses to others, demonstrating the existence of a sociability spectrum in this species.

Herbivore diets are often generalistic, and communities of herbivores tend to share much of their diets. In the tropical lowlands of Malaysian Borneo, tens of different noncarnivorous land snail species are able to coexist in communities on limestone outcrops. We tried to answer the question whether diet differentiation plays a role in their coexistence. We show, with a large metabarcoding study of the plant diet from gut contents of 658 individual snails (from 26 species, with a focus on three of the most common species in the region), that the different snail species indeed share much of their plant diet, but that mean diet richness varies strongly among species (up to 15.3×). These differences are mostly explained by snail size, with larger snails having wider diets. Furthermore, phylogenetic analyses of the plant diet by individual snails showed signs of clustering in c. 28% of the individuals, possibly suggesting phylogenetic specialization, although such clustering was weak when diets were considered by species. We discuss how observed trends in diet richness and diet clustering could also be explained by random feeding, with larger species simply eating more or less specifically, and by other, noncompetitive interactions, such as snails avoiding desiccation. Our study shows how to efficiently put the power of metabarcoding to work in unravelling the complex community processes commonly encountered in tropical ecosystems and is thus of substantial relevance to both community ecologists and conservationists.

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.

Interspecific competition and plant-soil feedbacks are powerful drivers of plant community structure. However, across a range of edaphic conditions the interactive effects of these drivers on complex plant communities remain unclear. For example, plant-soil feedback studies focus on soil trained by a single plant species. We developed a method to assess effects of plant-microbial interactions (PMI) on a complex plant community. We established mesocosms with 13 grassland species, grown individually or together, in overgrazed or restored soil, with or without soil microbial inoculum collected from a productive and diverse native grassland. We assessed biomass production as influenced by edaphic conditions, interspecific competition and PMI. Furthermore, we assessed potential influences of interspecific competition and edaphic conditions on strength and direction of PMI. Our results indicate PMI drives negative growth responses for graminoids while forbs experience positive growth responses. Generally, interspecific competition did not alter the magnitude or direction of PMI-mediated growth responses. Edaphic conditions altered the influence of soil microbial communities on individual plant growth while PMI facilitated plant evenness. In plant community mesocosms, PMI-associated benefits were observed in overgrazed soil. However, interspecific competition overwhelmed plant growth benefits associated with soil microbial communities when plant communities were grown in restored soil. In mesocosms containing dominant grass species, interspecific competition had negative effects on species coexistence, but both positive and negative PMI partially counterbalanced this influence on plant species evenness. Understanding these mechanisms may improve our capacity to manage diverse and productive grasslands by enabling prediction of plant community composition following disturbance and subsequent restoration.

The latitudinal diversity gradient (LDG) is one of Earth’s most iconic biodiversity patterns and still one of the most debated. Explanations for the LDG are often categorized into three broad pathways in which the diversity gradient is created by (1) differential diversification rates, (2) differential carrying capacities (ecological limits), or (3) differential time to accumulate species across latitude. Support for these pathways has, however, been mostly verbally expressed. Here, we present a minimal model to clarify the essential assumptions of the three pathways and explore the sensitivity of diversity dynamics to these pathways. We find that an LDG arises most easily from a gradient in ecological limits compared with a gradient in the time for species accumulation or diversification rate in most modeled scenarios. Differential diversification rates create a stronger LDG than ecological limits only when speciation and dispersal rates are low, but then the predicted LDG seems weaker than the observed LDG. Moreover, range dynamics may reduce an LDG created by a gradient in diversification rates or time for species accumulation, but they cannot reduce an LDG induced by differential ecological limits. We conclude that our simple model provides a null prediction for the effectiveness of the three LDG pathways and can thus aid discussions about the causal mechanisms underlying the LDG or motivate more complex models to confirm or falsify our findings., The American Naturalist, 194 (5), ISSN:0003-0147, ISSN:1537-5323

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of a widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or sibling) lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.

The evolution of Neotropical birds of open landscapes remains largely unstudied. We investigate the diversification and biogeography of a group of Neotropical obligate grassland birds (Anthus: Motacillidae). We use a multilocus phylogeny of 22 taxa of Anthus to test the hypothesis that these birds radiated contemporaneously with the development of grasslands in South America. We employ the R package DDD to analyze the dynamics of Anthus diversification across time in Neotropical grasslands, explicitly testing for shifts in dynamics associated with the Miocene development of grasslands, the putative Pleistocene expansion of arid lowland biomes, and Pleistocene sundering of Andean highland grasslands. A lineage-through-time plot revealed increases in the number of lineages, and DDD detected shifts to a higher clade-level carrying capacity during the late Miocene, indicating an early burst of diversification associated with grassland colonization. However, we could not corroborate the shift using power analysis, probably reflecting the small number of tips in our tree. We found evidence of a divergence at similar to 1 Mya between northern and southern Amazonian populations of Anthus lutescens, countering Haffer's idea of Pleistocene expansion of open biomes in the Amazon Basin. We used BioGeoBears to investigate ancestral areas and directionality of colonization of Neotropical grasslands. Members of the genus diversified into, out of, and within the Andes, within-Andean diversification being mostly Pleistocene in origin.

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.

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. Here, we explore variation in chromophore ratios across multiple cichlid populations in Lake Victoria, using as a proxy the enzyme CYP27C1 that catalyses the conversion of Vitamin A1-into A2. We focus 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-water than from clear-water locations, 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-water locations. To assess the contribution of heritable versus 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. Establishing the biological importance of this variation requires testing the link between cyp27c1 expression and A1/A2 ratios in the eye, as well as its consequences for visual performance.

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. ispartof: FRONTIERS IN MICROBIOLOGY vol:13 ispartof: location:Switzerland status: published

Neotropical grassland birds are intimately tied to their habitat and form a phylogenetically diverse group that has been poorly studied from an evolutionary point of view. Here we present a brief review of the biogeographical history of Neotropical grasslands of relevance to grassland birds. Based on this review, we have formulated the most relevant hypotheses related to the diversification and evolution of Neotropical grassland birds. Several of the hypotheses tested are complementary to those that can be tested for forest birds and may offer the researcher fruitful foci of study for assessing the role of South American geological evolution in shaping the diversification of the world’s most diverse avifauna.

The thermal environment can affect the evolution of morpho-behavioral adaptations of ectotherms. Heat is transferred from substrates to organisms by conduction and reflected radiation. Because brightness influences the degree of heat absorption, substrates could affect the evolution of integumentary optical properties. Here, we show that vipers (Squamata:Viperidae) inhabiting hot, highly radiative and superficially conductive substrates have evolved bright ventra for efficient heat transfer. We analyzed the brightness of 4161 publicly available images from 126 species, and we found that substrate type, alongside latitude and body mass, strongly influences ventral brightness. Substrate type also significantly affects dorsal brightness, but this is associated with different selective forces: activity-pattern and altitude. Ancestral estimation analysis suggests that the ancestral ventral condition was likely moderately bright and, following divergence events, some species convergently increased their brightness. Vipers diversified during the Miocene and the enhancement of ventral brightness may have facilitated the exploitation of arid grounds. We provide evidence that integument brightness can impact the behavioral ecology of ectotherms., Jonathan Goldenberg et al. use photographic data and ancestral state reconstruction of 126 viper species to show that substrate type influences the evolution of ventral brightness for efficient heat transfer. Their results suggest that these patterns may have been involved in the diversification of vipers during the Miocene, and highlight the importance of ventral body regions when considering behavioral ecology and evolution.

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 Eco-evolutionary 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 multi-dimensional community data including a genetic component, such as might be produced by contemporary eDNA or metabarcoding studies. We combine 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., Funding was provided by grants from FAPESP (BIOTA, 2013/50297-0 to MJH and AC Carnaval), the Synthesis Centre of iDiv (DFG FZT 118), NASA through the Dimensions of Biodiversity Program (DOB 1343578) and the National Science Foundation (DEB-1253710 to MJH; DEB 1745562 to AC Carnaval; DBI 1927319 to AJR). IO was supported by the Mina Rees Dissertation Fellowship in the Sciences provided by the Graduate Center of the City University of New York. MR was supported by the Bioinformatics and Computational Biology Fellowship through the Institute for Bioinformatics and Evolutionary Studies at the University of Idaho. AJR was supported by the Santa Fe Institute Omidyar Fellowship. JR was supported by fellowships from the Natural Environment Research Council (NERC) (NE/I021179, NE/L011611/1). RSE was supported by an NWO-VICI grant. This work is a contribution to Imperial College’s Grand Challenges in Ecosystems and the Environment initiative, through JR.

Understanding the processes that drive diversification of species is essential and urgent. Although detailed data collection and modern genetics have helped enormously in being able to map existing species back to their common ancestor, extinct species are blatantly missing in these analyses, leaving us with only a very partial and biased picture of the extinction process. Nevertheless, extinct species can leave behind a signal in the phylogeny the currently extant species. Over the past decades simple macro-evolutionary models have been proposed for this signal. Unfortunately, these models lack biological plausibility and more complex versions of such models, which incorporate species interactions, are computationally almost intractable, because a coherent description of these interactions results in an extremely large set of coupled differential equations. Moreover, fitting this complex model to the molecular phylogeny of extant species requires integration over a high-dimensional space of partially extinct tree topologies, which is computationally unfeasible with current methods.In this thesis we present a novel quantitative framework, combining statistical methodologies with data augmentation techniques, that allows the integration, combination and incorporation of biological realism into a general class of models making it possible to consider the complexity of ecological interactions. We illustrate our framework by studying novel species diversification models that include dependence of diversification on phylogenetic diversity. We conclude that our methodology has great potential to overcome and quantify a broad variety of hypotheses in theoretical and evolutionary community ecology.

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.]

This thesis provides new tools for extracting information on the process of diversification from a phylogenetic tree. To do so the standard approach is to employ likelihood functions in order to estimate the best parameters for the diversification models via likelihood maximization. The parameters for this kind of models usually represent the diversification rates at which the various evolutionary events (e.g., speciations or extinctions) can take place in the process.

Most ecological communities are facing changing environments, particularly due to global climate change. When migration is impossible, adaptation to these altered environments is necessary to survive. Yet, we have little theoretical understanding how ecological communities respond both ecologically and evolutionarily to such environmental change. Here we introduce a simple eco-evolutionary model, the Community-Wide Rescue (CWR) model, in which a community faces environmental deterioration and each species within the community is forced to undergo adaptation or become extinct. We assume that all species in the community are equivalent except for their initial abundance. This individual based simulation model thus combines community ecology and evolutionary rescue theory. We show that under Community-Wide Rescue a rapid loss of rare species occurs. This loss occurs due to competition and a limited supply of beneficial mutations. The rapid loss of rare species provides a testable prediction regarding the impact of Community-Wide Rescue on species abundance distributions in ecological communities.

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.

An evolutionary tree (also known as a phylogeny), is a tree-like diagram that shows the evolutionary relationship among species (e.g. humans are closer related to chimps than to crocodiles). Creating and interpreting these are important to understand speciation. A biologist makes quite some assumptions when creating an evolutionary species tree from DNA. When are these assumptions too simple or needlessly complicated? This research proposes a novel method to answer this question. This Bayesian method, named 'pirouette', does so for standard speciation models, but also for new, less explored ones.When applying 'pirouette' to a new speciation model, we conclude that, would nature allow multiple speciations to occur simultaneously, standard speciation models still give satisfactory evolutionary trees.

Vascular epiphytes form a diverse group of almost 30 000 species, yet theory concerning their community structure is still largely lacking. We therefore employed the simplest models of biodiversity, (near-)neutral models, to generate hypotheses concerning their community structure. With recently developed tools for (near-)neutral models we analyzed species abundance data from many samples in Central and South America which we divided into four metacommunities (Mesoamerica, Central America, Amazonia and Paraná), where for each metacommunity we considered two subsets differing in dispersal syndrome: an animal-dispersed guild and a wind-dispersed guild. We considered three models differing in the underlying speciation mode. Across all metacommunities, we found observed patterns to be indistinguishable from patterns generated by neutral or near-neutral processes. Furthermore, we found that subdivision in different dispersal guilds was often supported, with recruitment limitation being stronger for animal-dispersed species than for wind-dispersed species. This is the first time that (near-)neutral theory has been applied to epiphyte communities. Future efforts with additional data sets and more refined models are expected to further improve our understanding of community structure in epiphytes and will have to test the generality of our findings.

Body mass has been considered one of the most critical organismal traits, and its role in many ecological processes has been widely studied. In hummingbirds, body mass has been linked to ecological features such as foraging performance, metabolic rates, and cost of flying, among others. We used an evolutionary approach to test whether body mass is a good predictor of two of the main ecological features of hummingbirds: their abundances and behavioral dominance. To determine whether a species was abundant and/or behaviorally dominant, we used information from the literature on 249 hummingbird species. For abundance, we classified a species as “plentiful” if it was described as the most abundant species in at least part of its geographic distribution, while we deemed a species to be “behaviorally dominant” when it was described as pugnacious (notably aggressive). We found that plentiful hummingbird species had intermediate body masses and were more phylogenetically related to each other than expected by chance. Conversely, behaviorally dominant species tended to have larger body masses and showed a random pattern of distribution in the phylogeny. Additionally, small‐bodied hummingbird species were not considered plentiful by our definition and did not exhibit behavioral dominance. These results suggest a link between body mass, abundance, and behavioral dominance in hummingbirds. Our findings indicate the existence of a body mass range associated with the capacity of hummingbird species to be plentiful, behaviorally dominant, or to show both traits. The mechanisms behind these relationships are still unclear; however, our results provide support for the hypothesis that body mass is a supertrait that explains abundance and behavioral dominance in hummingbirds.