The Biogeography of Adaptive Radiations and the Geographic Overlap of Sister Species

Cryptic species conservation: a review

Cryptic species are groups of two or more taxa that were previously classified as single nominal species. Being almost morphologically indistinguishable, cryptic species have historically been hard to detect. Only through modern morphometric, genetic, and molecular analyses has the hidden biodiversity of cryptic species complexes been revealed. Cryptic diversity is now widely acknowledged, but unlike more recognisable, charismatic species, scientists face additional challenges when studying cryptic taxa and protecting their wild populations. Demographical and ecological data are vital to facilitate and inform successful conservation actions, particularly at the individual species level, yet this information is lacking for many cryptic species due to their recent taxonomic description and lack of research attention. The first part of this article summarises cryptic speciation and diversity, and explores the numerous barriers and considerations that conservation biologists must navigate to detect, study and manage cryptic species populations effectively. The second part of the article seeks to address how we can overcome the challenges associated with efficiently and non-invasively detecting cryptic species in-situ, and filling vital knowledge gaps that are currently inhibiting applied conservation. The final section discusses future directions, and suggests that large-scale, holistic, and collaborative approaches that build upon successful existing applications will be vital for cryptic species conservation. This article also acknowledges that sufficient data to implement effective species-specific conservation will be difficult to attain for many cryptic animals, and protected area networks will be vital for their conservation in the short term.

Evolutionary plant-pollinator responses to anthropogenic land-use change: impacts on ecosystem services

Agricultural intensification at field and landscape scales, including increased use of agrochemicals and loss of semi-natural habitats, is a major driver of insect declines and other community changes. Efforts to understand and mitigate these effects have traditionally focused on ecological responses. At the same time, adaptations to pesticide use and habitat fragmentation in both insects and flowering plants show the potential for rapid evolution. Yet we lack an understanding of how such evolutionary responses may propagate within and between trophic levels with ensuing consequences for conservation of species and ecological functions in agroecosystems. Here, we review the literature on the consequences of agricultural intensification on plant and animal evolutionary responses and interactions. We present a novel conceptualization of evolutionary change induced by agricultural intensification at field and landscape scales and emphasize direct and indirect effects of rapid evolution on ecosystem services. We exemplify by focusing on economically and ecologically important interactions between plants and pollinators. We showcase available eco-evolutionary theory and plant-pollinator modelling that can improve predictions of how agricultural intensification affects interaction networks, and highlight available genetic and trait-focused methodological approaches. Specifically, we focus on how spatial genetic structure affects the probability of propagated responses, and how the structure of interaction networks modulates effects of evolutionary change in individual species. Thereby, we highlight how combined trait-based eco-evolutionary modelling, functionally explicit quantitative genetics, and genomic analyses may shed light on conditions where evolutionary responses impact important ecosystem services.

Widespread sympatry in a species-rich clade of marine fishes (Carangoidei)

A universal paradigm describing patterns of speciation across the tree of life has been debated for decades. In marine organisms, inferring patterns of speciation using contemporary and historical patterns of biogeography is challenging due to the deficiency of species-level phylogenies and information on species' distributions, as well as conflicting relationships between species' dispersal, range size and co-occurrence. Most research on global patterns of marine fish speciation and biogeography has focused on coral reef or pelagic species. Carangoidei is an ecologically important clade of marine fishes that use coral reef and pelagic environments. We used sequence capture of 1314 ultraconserved elements (UCEs) from 154 taxa to generate a time-calibrated phylogeny of Carangoidei and its parent clade, Carangiformes. Age-range correlation analyses of the geographical distributions and divergence times of sister species pairs reveal widespread sympatry, with 73% of sister species pairs exhibiting sympatric geographical distributions, regardless of node age. Most species pairs coexist across large portions of their ranges. We also observe greater disparity in body length and maximum depth between sympatric relative to allopatric sister species. These and other ecological or behavioural attributes probably facilitate sympatry among the most closely related carangoids.

The interactive effects of environmental gradient and dispersal shape spatial phylogenetic patterns

Introduction

The emergence and maintenance of biodiversity include interacting environmental conditions, organismal adaptation to such conditions, and dispersal. To understand and quantify such ecological, evolutionary, and spatial processes, observation and interpretation of phylogenetic relatedness across space (e.g., phylogenetic beta diversity) is arguably a way forward as such patterns contain signals from all the processes listed above. However, it remains challenging to extract information about complex eco-evolutionary and spatial processes from phylogenetic patterns.

Methods

We link environmental gradients and organismal dispersal with phylogenetic beta diversity using a trait-based and eco-evolutionary model of diversification along environmental gradients. The combined effect of the environment and dispersal leads to distinct phylogenetic patterns between subsets of species and across geographical distances.

Results and discussion

Steep environmental gradients combined with low dispersal lead to asymmetric phylogenies, a high phylogenetic beta diversity, and the phylogenetic diversity between communities increases linearly along the environmental gradient. High dispersal combined with a less steep environmental gradient leads to symmetric phylogenies, low phylogenetic beta diversity, and the phylogenetic diversity between communities along the gradient increases in a sigmoidal form. By disentangling the eco-evolutionary mechanisms that link such interacting environment and dispersal effects and community phylogenetic patterns, our results improve understanding of biodiversity in general and help interpretation of observed phylogenetic beta diversity.

Importance of interindividual interactions in eco-evolutionary population dynamics: The rise of demo-genetic agent-based models

The study of eco-evolutionary dynamics, that is of the intertwinning between ecological and evolutionary processes when they occur at comparable time scales, is of growing interest in the current context of global change. However, many eco-evolutionary studies overlook the role of interindividual interactions, which are hard to predict and yet central to selective values. Here, we aimed at putting forward models that simulate interindividual interactions in an eco-evolutionary framework: the demo-genetic agent-based models (DG-ABMs). Being demo-genetic, DG-ABMs consider the feedback loop between ecological and evolutionary processes. Being agent-based, DG-ABMs follow populations of interacting individuals with sets of traits that vary among the individuals. We argue that the ability of DG-ABMs to take into account the genetic heterogeneity-that affects individual decisions/traits related to local and instantaneous conditions-differentiates them from analytical models, another type of model largely used by evolutionary biologists to investigate eco-evolutionary feedback loops. Based on the review of studies employing DG-ABMs and explicitly or implicitly accounting for competitive, cooperative or reproductive interactions, we illustrate that DG-ABMs are particularly relevant for the exploration of fundamental, yet pressing, questions in evolutionary ecology across various levels of organization. By jointly modelling the effects of management practices and other eco-evolutionary processes on interindividual interactions and population dynamics, DG-ABMs are also effective prospective and decision support tools to evaluate the short- and long-term evolutionary costs and benefits of management strategies and to assess potential trade-offs. Finally, we provide a list of the recent practical advances of the ABM community that should facilitate the development of DG-ABMs.

Ecological opportunity and adaptive radiations reveal eco-evolutionary perspectives on community structure in competitive communities

It is well known that ecological and evolutionary processes act in concert while shaping biological communities. Diversification can, for example, arise through ecological opportunity and adaptive radiations and competition play an essential role in such diversification. Eco-evolutionary components of competition are thus important for our understanding of community assembly. Such understanding in turn facilitates interpretation of trait- and phylogenetic community patterns in the light of the processes that shape them. Here, I investigate the link between competition, diversification, and trait- and phylogenetic- community patterns using a trait-based model of adaptive radiations. I evaluate the paradigm that competition is an ecological process that drives large trait- and phylogenetic community distances through limiting similarity. Contrary to the common view, I identify low or in some cases counterintuitive relationships between competition and mean phylogenetic distances due to diversification late in evolutionary time and peripheral parts of niche space when competition is weak. Community patterns as a function of competition also change as diversification progresses as the relationship between competition and trait similarity among species can flip from positive to negative with time. The results thus provide novel perspectives on community assembly and emphasize the importance of acknowledging eco-evolutionary processes when interpreting community data.

Modelling the tempo and mode of lineage dispersal

Lineage dispersal is a basic macroevolutionary process shaping the distribution of biodiversity. Probabilistic approaches in biogeography, epidemiology, and macroecology often model dispersal as a background process to explain extant or infer past distributions. We propose framing questions around the mode, timing, rate, and direction of lineage dispersal itself, from a lineage- or geography-centric perspective. We review available methods for modelling lineage dispersal. Likelihood- and simulation-based approaches to modelling dispersal have made progress in accounting for the variation of lineage dispersal over space, time, and branches of a phylogeny and its interaction with diversification. Methodological improvements, guided by a focus on model adequacy, will lead to more realistic models that can answer fundamental questions about the tempo and mode of lineage dispersal.

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.

Ecological opportunity and upward prey-predator radiation cascades

A general goal in community ecology and evolutionary biology is to understand how diversity has arisen. In our attempts to reach such goals we become increasingly aware of interacting ecological and evolutionary processes shaping biodiversity. Ecological opportunity and adaptive radiations can, for example, drive diversification in competitive communities but little is known about how such processes propagate through trophic levels in adaptive radiation cascades. I use an eco-evolutionary model of trait-based ecological interactions and micro-evolutionary processes to investigate the macro-evolutionary aspects of predator diversification in such cascades. Prey diversification facilitates predator radiation through predator feeding opportunity and disruptive selection. Predator radiation, however, often disconnects from the prey radiation as the diversification progresses. Only when predators have an intermediate niche width, high predatory efficiency, and high evolutionary potential can radiation cascades be maintained over macro-evolutionary time scales. These results provide expectations for predator response to prey divergence and insight into eco-evolutionary feedbacks between trophic levels. Such expectations are crucial for future studies that aim for a better understanding of how diversity is generated and maintained in complex communities.

Time spent together and time spent apart affect song, feather colour and range overlap in tinkerbirds

Most studies on the processes driving evolutionary diversification highlight the importance of genetic drift in geographical isolation and natural selection across ecological gradients. Direct interactions among related species have received much less attention, but they can lead to character displacement, with recent research identifying patterns of displacement attributed to either ecological or reproductive processes. Together, these processes could explain complex, trait-specific patterns of diversification. Few studies, however, have examined the possible effects of these processes together or compared the divergence in multiple traits between interacting species among contact zones. Here, we show how traits of two Pogoniulus tinkerbird species vary among regions across sub-Saharan Africa. However, in addition to variation between regions consistent with divergence in refugial isolation, both song and morphology diverge between the species where they coexist. In West Africa, where the species are more similar in plumage, there is possible competitive or reproductive exclusion. In Central and East Africa, patterns of variation are consistent with agonistic character displacement. Molecular analyses support the hypothesis that differences in the age of interaction among regions can explain why species have evolved phenotypic differences and coexist in some regions but not others. Our findings suggest that competitive interactions between species and the time spent interacting, in addition to the time spent in refugial isolation, play important roles in explaining patterns of species diversification.

Evolution of resource specialisation in competitive metacommunities

Spatial environmental heterogeneity coupled with dispersal can promote ecological persistence of diverse metacommunities. Does this premise hold when metacommunities evolve? Using a two-resource competition model, we studied the evolution of resource-uptake specialisation as a function of resource type (substitutable to essential) and shape of the trade-off between resource uptake affinities (generalist- to specialist-favouring). In spatially homogeneous environments, evolutionarily stable coexistence of consumers is only possible for sufficiently substitutable resources and specialist-favouring trade-offs. Remarkably, these same conditions yield comparatively low diversity in heterogeneous environments, because they promote sympatric evolution of two opposite resource specialists that, together, monopolise the two resources everywhere. Consumer diversity is instead maximised for intermediate trade-offs and clearly substitutable or clearly essential resources, where evolved metacommunities are characterised by contrasting selection regimes. Taken together, our results present new insights into resource-competition-mediated evolutionarily stable diversity in homogeneous and heterogeneous environments, which should be applicable to a wide range of systems.

Ecological opportunity and predator-prey interactions: linking eco-evolutionary processes and diversification in adaptive radiations

Much of life's diversity has arisen through ecological opportunity and adaptive radiations, but the mechanistic underpinning of such diversification is not fully understood. Competition and predation can affect adaptive radiations, but contrasting theoretical and empirical results show that they can both promote and interrupt diversification. A mechanistic understanding of the link between microevolutionary processes and macroevolutionary patterns is thus needed, especially in trophic communities. Here, we use a trait-based eco-evolutionary model to investigate the mechanisms linking competition, predation and adaptive radiations. By combining available micro-evolutionary theory and simulations of adaptive radiations we show that intraspecific competition is crucial for diversification as it induces disruptive selection, in particular in early phases of radiation. The diversification rate is however decreased in later phases owing to interspecific competition as niche availability, and population sizes are decreased. We provide new insight into how predation tends to have a negative effect on prey diversification through decreased population sizes, decreased disruptive selection and through the exclusion of prey from parts of niche space. The seemingly disparate effects of competition and predation on adaptive radiations, listed in the literature, may thus be acting and interacting in the same adaptive radiation at different relative strength as the radiation progresses.

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.

Clade diversification dynamics and the biotic and abiotic controls of speciation and extinction rates

How ecological interactions, genetic processes, and environmental variability jointly shape the evolution of species diversity remains a challenging problem in biology. We developed an individual-based model of clade diversification to predict macroevolutionary dynamics when resource competition, genetic differentiation, and landscape fluctuations interact. Diversification begins with a phase of geographic adaptive radiation. Extinction rates rise sharply at the onset of the next phase. In this phase of niche self-structuring, speciation and extinction processes, albeit driven by biotic mechanisms (competition and hybridization), have essentially constant rates, determined primarily by the abiotic pace of landscape dynamics. The final phase of diversification begins when intense competition prevents dispersing individuals from establishing new populations. Species’ ranges shrink, causing negative diversity-dependence of speciation rates. These results show how ecological and microevolutionary processes shape macroevolutionary dynamics and rates; they caution against the notion of ecological limits to diversity, and suggest new directions for the phylogenetic analysis of diversification.

The history and patterns of species diversity are shaped by a variety of ecological and evolutionary factors. Here, the authors develop a computational model to predict clade diversification dynamics and rates of speciation and extinction under the influences of resource competition, genetic differentiation, and random landscape fluctuation.

Pollinator-mediated assemblage processes in California wildflowers

Community assembly is the result of multiple ecological and evolutionary forces that influence species coexistence. For flowering plants, pollinators are often essential for plant reproduction and establishment, and pollinator-mediated interactions may influence plant community composition. Here, we use null models and community phylogenetic analyses of co-occurrence patterns to determine the role of pollinator-mediated processes in structuring plant communities dominated by congeners. We surveyed three species-rich genera (Limnanthes, Mimulus and Clarkia) with centres of diversity in the Sierra Nevada of California. Each genus contains species that co-flower and share pollinators, and each has a robust phylogeny. Within each genus, we surveyed 44-48 communities at three spatial scales, measured floral and vegetative traits and tested for segregation or aggregation of: (i) species, (ii) floral traits (which are likely to be influenced by pollinators), and (iii) vegetative traits (which are likely affected by other environmental factors). We detected both aggregation and segregation of floral traits that were uncorrelated with vegetative trait patterns; we infer that pollinators have shaped the community assembly although the mechanisms may be varied (competition, facilitation, or filtering). We also found that mating system differences may play an important role in allowing species co-occurrence. Together, it appears that pollinators influence community assemblage in these three clades.

The Species versus Subspecies Conundrum: Quantitative Delimitation from Integrating Multiple Data Types within a Single Bayesian Approach in Hercules Beetles

With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species, irrespective of whether they were given species or subspecies designations. By considering multiple data types, as opposed to relying exclusively on genetic data alone, we also show that both previously recognized species and subspecies represent a variety of points along the speciation spectrum (i.e., previously recognized species are not systematically further along the continuum than subspecies). For example, based on evolutionary models of divergence, some taxa are statistically distinguishable on more than one axis of differentiation (e.g., along both phenotypic and genetic dimensions), whereas other taxa can only be delimited statistically from a single data type. Because both phenotypic and genetic data are analyzed in a common Bayesian framework, our study provides a framework for investigating whether disagreements in species boundaries among data types reflect (i) actual discordance with the actual history of lineage splitting, or instead (ii) differences among data types in the amount of time required for differentiation to become apparent among the delimited taxa. We discuss what the answers to these questions imply about what characters are used to delimit species, as well as the diverse processes involved in the origin and maintenance of species boundaries. With this in mind, we then reflect more generally on how quantitative methods for species delimitation are used to assign taxonomic status.