Fisher's Geometric Model as a Tool to Study Speciation

Interactions between alleles and across environments play an important role in the fitness of hybrids and are at the heart of the speciation process. Fitness landscapes capture these interactions and can be used to model hybrid fitness, helping us to interpret empirical observations and clarify verbal models. Here, we review recent progress in understanding hybridization outcomes through Fisher's geometric model, an intuitive and analytically tractable fitness landscape that captures many fitness patterns observed across taxa. We use case studies to show how the model parameters can be estimated from different types of data and discuss how these estimates can be used to make inferences about the divergence history and genetic architecture. We also highlight some areas where the model's predictions differ from alternative incompatibility-based models, such as the snowball effect and outlier patterns in genome scans.

The effect of divergent and parallel selection on the genomic landscape of divergence

While the role of selection in divergence along the speciation continuum is theoretically well understood, defining specific signatures of selection in the genomic landscape of divergence is empirically challenging. Modelling approaches can provide insight into the potential role of selection on the emergence of a heterogenous genomic landscape of divergence. Here, we extend and apply an individual-based approach that simulates the phenotypic and genotypic distributions of two populations under a variety of selection regimes, genotype-phenotype maps, modes of migration, and genotype-environment interactions. We show that genomic islands of high differentiation and genomic valleys of similarity may respectively form under divergent and parallel selection between populations. For both types of between-population selection, negative and positive frequency-dependent selection within populations generated genomic islands of higher magnitude and genomic valleys of similarity, respectively. Divergence rates decreased under strong dominance with divergent selection, as well as in models including genotype-environment interactions under parallel selection. For both divergent and parallel selection models, divergence rate was higher under an intermittent migration regime between populations, in contrast to a constant level of migration across generations, despite an equal number of total migrants. We highlight that interpreting a particular evolutionary history from an observed genomic pattern must be done cautiously, as similar patterns may be obtained from different combinations of evolutionary processes. Modelling approaches such as ours provide an opportunity to narrow the potential routes that generate the genomic patterns of specific evolutionary histories.

Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss)

BACKGROUND AND AIMS

New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae.

METHODS

We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally.

KEY RESULTS

Using sliding-window population genetic analyses we find that differentiation is concentrated within 'islands' of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap.

CONCLUSIONS

We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth's climate rapidly changes.

How subcultures emerge

Sympatric speciation is typically presented as a rare phenomenon, but urban subcultures frequently emerge even in the absence of geographic isolation. Is there perhaps something that culture has but biological inheritance does not that would account for this difference? We present a novel model that combines assortative interaction and multidimensional inheritance. Our computer simulations show that assortment alone can lead to the formation of cohesive clusters of individuals with low within-group and large between-group variability even in the absence of a spatial separation or disruptive natural selection. All it takes is a proportionality between the variance of inputs (cultural 'parents') and outputs (cultural 'offspring'). We argue that variability-dependent inheritance cannot be easily accomplished by genes alone, but it may be the norm, not the exception, in the transmission of culture between humans. This model explains the frequent emergence of subcultures and behavioural clustering in our species and possibly also other cultural animals.

Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex

The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspecies (Anas crecca crecca, A. c. nimia, and A. c. carolinensis) with a close relative, the yellow-billed teal (Anas flavirostris) from South America. A. c. crecca and A. c. carolinensis are seasonal migrants, while the other taxa are sedentary. We examined divergence and speciation patterns in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and genome-wide nuclear DNA obtained from 1,393 ultraconserved element (UCE) loci. Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca, A. c. nimia, and A. c. carolinensis clustering together to form one polytomous clade, with A. flavirostris sister to this clade. This relationship can be summarized as (crecca, nimia, carolinensis)(flavirostris). However, whole mitogenomes revealed a different phylogeny: (crecca, nimia)(carolinensis, flavirostris). The best demographic model for key pairwise comparisons supported divergence with gene flow as the probable speciation mechanism in all three contrasts (crecca-nimia, crecca-carolinensis, and carolinensis-flavirostris). Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris (M ∼0.1-0.4 individuals/generation), albeit low, was not expected. Three geographically oriented modes of divergence are likely involved in the diversification of this complex: heteropatric (crecca-nimia), parapatric (crecca-carolinensis), and (mostly) allopatric (carolinensis-flavirostris). Our study shows that ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems with historically uncertain relationships and species limits.

In the land of the blind: Exceptional subterranean speciation of cryptic troglobitic spiders of the genus Tegenaria (Araneae: Agelenidae) in Israel

Caves have long been recognized as a window into the mechanisms of diversification and convergent evolution, due to the unique conditions of isolation and life in the dark. These lead to adaptations and reduce dispersal and gene flow, resulting in high levels of speciation and endemism. The Israeli cave arachnofauna remains poorly known, but likely represents a rich assemblage. In a recent survey, we found troglophilic funnel-web spiders of the genus Tegenaria in 26 caves, present mostly at the cave entrance ecological zone. In addition, we identified at least 14 caves inhabited by troglobitic Tegenaria, which are present mostly in the twilight and dark ecological zones. Ten of the caves, located in the north and center of Israel, are inhabited by both troglophilic and troglobitic Tegenaria. These spiders bear superficial phenotypic similarities but differ in the levels of eye reduction and pigmentation. To test whether these taxa constitute separate species, as well as understand their relationships to epigean counterparts, we conducted a broad geographic sampling of cave-dwelling Tegenaria in Israel and Palestine, using morphological and molecular evidence. Counterintuitively, our results show that the troglobitic Tegenaria we studied are distantly related to the troglophilic Tegenaria found at each of the cave entrances we sampled. Moreover, seven new troglobitic species can be identified based on genetic differences, eye reduction level, and features of the female and male genitalia. Our COI analysis suggest that the Israeli troglobitic Tegenaria species are more closely related to eastern-Mediterranean congeners than to the local sympatric troglophile Tegenaria species, suggesting a complex biogeographic history.

Host-plant adaptation as a driver of incipient speciation in the fall armyworm (Spodoptera frugiperda)

Background

Divergent selection on host-plants is one of the main evolutionary forces driving ecological speciation in phytophagous insects. The ecological speciation might be challenging in the presence of gene flow and assortative mating because the direction of divergence is not necessarily the same between ecological selection (through host-plant adaptation) and assortative mating. The fall armyworm (FAW), a major lepidopteran pest species, is composed of two sympatric strains, corn and rice strains, named after two of their preferred host-plants. These two strains have been hypothesized to undergo incipient speciation, based on (i) several lines of evidence encompassing both pre- and post-zygotic reproductive isolation, and (ii) the presence of a substantial level of genetic differentiation. Even though the status of these two strains has been established a long time ago, it is still yet to be found whether these two strains indeed exhibit a marked level of genetic differentiation from a large number of genomic loci. Here, we analyzed whole genome sequences from 56 FAW individuals either collected from pasture grasses (a part of the favored host range of the rice strain) or corn to assess the role of host-plant adaptation in incipient speciation.

Results

Principal component analysis of whole genome data shows that the pattern of divergence in the fall armyworm is predominantly explained by the genetic differentiation associated with host-plants. The level of genetic differentiation between corn and rice strains is particularly marked in the Z chromosome. We identified one autosomal locus and two Z chromosome loci targeted by selective sweeps specific to rice strain and corn strain, respectively. The autosomal locus has both increased DXY and FST while the Z chromosome loci had decreased DXY and increased FST.

Conclusion

These results show that the FAW population structure is dominated by the genetic differentiation between corn and rice strains. This differentiation involves divergent selection targeting at least three loci, which include a locus potentially causing reproductive isolation. Taken together, these results suggest the evolutionary scenario that host-plant speciation is a driver of incipient speciation in the fall armyworm.

Global abundance of short tandem repeats is non-random in rodents and primates

Background

While of predominant abundance across vertebrate genomes and significant biological implications, the relevance of short tandem repeats (STRs) (also known as microsatellites) to speciation remains largely elusive and attributed to random coincidence for the most part. Here we collected data on the whole-genome abundance of mono-, di-, and trinucleotide STRs in nine species, encompassing rodents and primates, including rat, mouse, olive baboon, gelada, macaque, gorilla, chimpanzee, bonobo, and human. The collected data were used to analyze hierarchical clustering of the STR abundances in the selected species.

Results

We found massive differential STR abundances between the rodent and primate orders. In addition, while numerous STRs had random abundance across the nine selected species, the global abundance conformed to three consistent < clusters>, as follows: <rat, mouse>, <gelada, macaque, olive baboon>, and <gorilla, chimpanzee, bonobo, human>, which coincided with the phylogenetic distances of the selected species (p < 4E-05). Exceptionally, in the trinucleotide STR compartment, human was significantly distant from all other species.

Conclusion

Based on hierarchical clustering, we propose that the global abundance of STRs is non-random in rodents and primates, and probably had a determining impact on the speciation of the two orders. We also propose the STRs and STR lengths, which predominantly conformed to the phylogeny of the selected species, exemplified by (t)10, (ct)6, and (taa4). Phylogenetic and experimental platforms are warranted to further examine the observed patterns and the biological mechanisms associated with those STRs.

Sexual imprinting leads to speciation in locally adapted populations

Sexual imprinting is widespread in birds and other species but its existence requires explanation. Our results suggest that sexual imprinting leads to speciation in locally-adapted populations if a neutral mating cue-e.g., novel plumage coloration-arises through mutation. Importantly, the mating cue locus is not linked to adaptation loci. Local adaptation is a necessary precursor to speciation and occurs when evolution results in stable genetic polymorphisms with one allele predominating in some areas while others predominate elsewhere. Here we use a deterministic two-niche population genetic model to map the set of migration and selection rates for which polymorphic evolutionary outcomes, i.e., local adaptations, can occur. Approximate equations for the boundaries of the set of polymorphic evolutionary outcomes were derived by Bulmer (American Naturalist, 106, 254, 1972), but our results, obtained by deterministic simulation of the evolutionary process, show that one of Bulmer's equations is inaccurate except when the level of dominance is 0.5, and fails if one of the alleles is dominant. Having an accurate map of the set of migration and selection rates for which polymorphic evolutionary outcomes can occur, we then show using the model of Sibly et al. (Ecology and Evolution, 9, 13506, 2019) that local adaptation in all analyzed cases leads to speciation if a new neutral mating cue arises by mutation. We finish by considering how genome sequencing makes possible testing our model and its predictions.

Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico

Secondary contact of recently diverged species may have several outcomes, ranging from rampant hybridization to reinforced reproductive isolation. In plants, selfing tolerance and disjunct reproductive phenology may lead to reproductive isolation at contact zones. However, they may also evolve under both allopatric or parapatric frameworks and originate from adaptive and/or neutral forces. Inferring the historical demography of diverging taxa is thus a crucial step to identify factors that may have led to putative reproductive isolation. We explored various competing demographypotheses to account for the rapid divergence of a fir species complex (Abies flinckii-A. religiosa) distributed in "sky-islands" across central Mexico (i.e., along the Trans-Mexican Volcanic Belt; TMVB). Despite co-occurring in two independent sympatric regions (west and centre), these taxa rarely interbreed because of disjunct reproductive phenologies. We genotyped 1147 single nucleotide polymorphisms, generated by GBS (genotyping by sequencing), across 23 populations, and compared multiple scenarios based on the geological history of the TMVB. The best-fitting model revealed one of the most rapid and complete speciation cases for a conifer species-pair, dating back to ~1.2 million years ago. Coupled with the lack of support for stepwise colonization, our coalescent inferences point to an early cessation of interspecific gene flow under parapatric speciation; ancestral gene flow during divergence was asymmetrical (mostly from western firs into A. religiosa) and exclusive to the most ancient (i.e., central) contact zone. Factors promoting rapid reproductive isolation should be explored in other slowly evolving species complexes as they may account for the large tropical and subtropical diversity.

Protracted speciation under the state-dependent speciation and extinction approach

How long does speciation take? The answer to this important question in evolutionary biology lies in the genetic difference not only among species, but also among lineages within each species. With the advance of genome sequencing in non-model organisms and the statistical tools to improve accuracy in inferring evolutionary histories among recently diverged lineages, we now have the lineage-level trees to answer these questions. However, we do not yet have an analytical tool for inferring speciation processes from these trees. What is needed is a model of speciation processes that generates both the trees and species identities of extant lineages. The model should allow calculation of the probability that certain lineages belong to certain species and have an evolutionary history consistent with the tree. Here, we propose such a model and test the model performance on both simulated data and real data. We show that maximum-likelihood estimates of the model are highly accurate and give estimates from real data that generate patterns consistent with observations. We discuss how to extend the model to account for different rates and types of speciation processes across lineages in a species group. By linking evolutionary processes on lineage level to species level, the model provides a new phylogenetic approach to study not just when speciation happened, but how speciation happened. [Micro–macro evolution; Protracted birth–death process; speciation completion rate; SSE approach.]

Dispersal ability and its consequences for population genetic differentiation and diversification

Dispersal ability is known to influence geographical structuring of genetic variation within species, with a direct relationship between low vagility and population genetic structure, which can potentially give rise to allopatric speciation. However, our general understanding of the relationship between dispersal ability, population differentiation and lineage diversification is limited. To address this issue, we sampled mitochondrial DNA variation within lineages of beetles and spiders across the Canary Islands to explore the relationships between dispersal ability, differentiation within lineages and diversification. We found positive relationships between population genetic structure and diversification for both beetles and spiders. Comparisons between dispersive and non-dispersive lineages revealed significant differences for both lineage differentiation and diversification. For both taxa, non-dispersive lineages had stronger population genetic structure. Genus-level endemic species richness and proxies for diversification rate within genera were higher in non-dispersive taxa for both beetles and spiders. Comparisons of average and maximum node divergences within genera suggest that species turnover may be higher in non-dispersive genera. Our results reveal a model where dispersal limitation may shape the diversity of lineages across evolutionary timescales by positively influencing intraspecific and species diversity, moderated by higher extinction rates compared to more dispersive lineages.

We get by with a little help from our friends: shared adaptive variation provides a bridge to novel ecological specialists during adaptive radiation

Adaptive radiations involve astounding bursts of phenotypic, ecological and species diversity. However, the microevolutionary processes that underlie the origins of these bursts are still poorly understood. We report the discovery of an intermediate C. sp. 'wide-mouth' scale-eating ecomorph in a sympatric radiation of Cyprinodon pupfishes, illuminating the transition from a widespread algae-eating generalist to a novel microendemic scale-eating specialist. We first show that this ecomorph occurs in sympatry with generalist C. variegatus and scale-eating specialist C. desquamator on San Salvador Island, Bahamas, but is genetically differentiated, morphologically distinct and often consumes scales. We then compared the timing of selective sweeps on shared and unique adaptive variants in trophic specialists to characterize their adaptive walk. Shared adaptive regions swept first in both the specialist desquamator and the intermediate 'wide-mouth' ecomorph, followed by unique sweeps of introgressed variation in 'wide-mouth' and de novo variation in desquamator. The two scale-eating populations additionally shared 9% of their hard selective sweeps with the molluscivore C. brontotheroides, despite no single common ancestor among specialists. Our work provides a new microevolutionary framework for investigating how major ecological transitions occur and illustrates how both shared and unique genetic variation can provide a bridge for multiple species to access novel ecological niches.

System drift and speciation

Even if a species' phenotype does not change over evolutionary time, the underlying mechanism may change, as distinct molecular pathways can realize identical phenotypes. Here we use linear system theory to explore the consequences of this idea, describing how a gene network underlying a conserved phenotype evolves, as the genetic drift of small changes to these molecular pathways causes a population to explore the set of mechanisms with identical phenotypes. To do this, we model an organism's internal state as a linear system of differential equations for which the environment provides input and the phenotype is the output, in which context there exists an exact characterization of the set of all mechanisms that give the same input-output relationship. This characterization implies that selectively neutral directions in genotype space should be common and that the evolutionary exploration of these distinct but equivalent mechanisms can lead to the reproductive incompatibility of independently evolving populations. This evolutionary exploration, or system drift, is expected to proceed at a rate proportional to the amount of intrapopulation genetic variation divided by the effective population size ( Ne$N_e$ ). At biologically reasonable parameter values this could lead to substantial interpopulation incompatibility, and thus speciation, on a time scale of Ne$N_e$ generations. This model also naturally predicts Haldane's rule, thus providing a concrete explanation of why heterogametic hybrids tend to be disrupted more often than homogametes during the early stages of speciation.

Estimation of the strength of mate preference from mated pairs observed in the wild

A number of key processes in evolution are driven by individuals preferring mates with particular phenotypes. However, despite long‐standing interest, it is difficult to quantify the strength of mate preference from phenotypic observations in nature in a way that connects directly to key parameters in theoretical models. To bridge the gap between mathematical models and empirical data, we develop a novel maximum likelihood‐based method to estimate the strength and form of mate preference, where preference depends on traits expressed in both males and females. Using simulated data, we demonstrate that our method accurately infers model parameters, including the strength of mate preference and the optimal offset match between trait values in mated pairs when model assumptions are satisfied. Applying our method to two previous studies of assortative mating in marine gastropods and the European common frog, we support previous findings, but also give additional insight into the role of mate preference in each system. Our method can be generalized to a variety of plant and animal taxa that exhibit mating preferences to facilitate the testing of evolutionary hypotheses and link empirical data to theoretical models of assortative mating, sexual selection, and speciation.

Flightlessness in insects enhances diversification and determines assemblage structure across whole communities

Dispersal limitation has been recurrently suggested to shape both macroecological patterns and microevolutionary processes within invertebrates. However, because of potential interactions among biological, environmental, temporal, and spatial variables, causal links among flight-related traits, diversification and spatial patterns of community assembly remain elusive. Integrating genetic variation within species across whole insect assemblages, within a simplified spatial and environmental framework, can be used to reduce the impact of these potentially confounding variables. Here, we used standardized sampling and mitochondrial DNA sequencing for a whole-community characterization of the beetle fauna inhabiting a singular forested habitat (laurel forest) within an oceanic archipelago setting (Canary Islands). The spatial structure of species assemblages together with species-level genetic diversity was compared at the archipelago and island scales for 104 winged and 110 wingless beetle lineages. We found that wingless beetle lineages have: (i) smaller range sizes at the archipelago scale, (ii) lower representation in younger island communities, (iii) stronger population genetic structure, and (iv) greater spatial structuring of species assemblages between and within islands. Our results reveal that dispersal limitation is a fundamental trait driving diversity patterns at multiple hierarchical levels by promoting spatial diversification and affecting the spatial configuration of entire assemblages at both island and archipelago scales.

Using mathematical modelling to investigate the adaptive divergence of whitefish in Fennoscandia

Modern speciation theory has greatly benefited from a variety of simple mathematical models focusing on the conditions and patterns of speciation and diversification in the presence of gene flow. Unfortunately the application of general theoretical concepts and tools to specific ecological systems remains a challenge. Here we apply modeling tools to better understand adaptive divergence of whitefish during the postglacial period in lakes of northern Fennoscandia. These lakes harbor up to three different morphs associated with the three major lake habitats: littoral, pelagic, and profundal. Using large-scale individual-based simulations, we aim to identify factors required for in situ emergence of the pelagic and profundal morphs in lakes initially colonized by the littoral morph. The importance of some of the factors we identify and study - sufficiently large levels of initial genetic variation, size- and habitat-specific mating, sufficiently large carrying capacity of the new niche - is already well recognized. In addition, our model also points to two other factors that have been largely disregarded in theoretical studies: fitness-dependent dispersal and strong predation in the ancestral niche coupled with the lack of it in the new niche(s). We use our theoretical results to speculate about the process of diversification of whitefish in Fennoscandia and to identify potentially profitable directions for future empirical research.

Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage

Recently diverged taxa showing marked phenotypic and ecological diversity provide optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white-eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographical forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on single nucleotide polymorphism data from genotyping-by-sequencing and pooled RAD-seq approaches show that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified TYRP1, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system holds promise for investigating how adaptation and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.

Cryptic ecological and geographic diversification in coral-associated nudibranchs

Coral reefs are among the most biologically diverse ecosystems of the world, yet little is known about the processes creating and maintaining their diversity. Ecologically, corallivory in nudibranchs resembles phytophagy in insects- a process that for decades has served as a model for ecological speciation via host shifting. This study uses extensive field collections, DNA sequencing, and phylogenetic analyses to reconstruct the evolutionary history of coral-associated nudibranchs and assess the relative roles that host shifting and geography may have played in their diversification. We find that the number of species is three times higher than the number previously known to science, with evidence for both allopatric and ecological divergence through host shifting and host specialization. Results contribute to growing support for the importance of ecological diversification in marine environments and provide evidence for new species in the genus Tenellia.

How phenotypic matching based on neutral mating cues enables speciation in locally adapted populations

Maynard Smith's (American Naturalist, 1966, 100, 637) suggestion that in some cases a prerequisite for speciation is the existence of local ecological adaptations has not received much attention to date. Here, we test the hypothesis using a model like that of Maynard Smith but differing in the way animals disperse between niches. In previous studies, males disperse randomly between niches but females stay put in their natal niche. As a first step toward generalizing the model, we here analyze the case that equal proportions of the two sexes disperse between niches before breeding. Supporting Maynard Smith's (1966) hypothesis, we find that once local adaptations are established, a neutral mating cue at an independent locus can rapidly enable speciation in populations with a suitable mechanism for phenotype matching. We find that stable ecological polymorphisms are relatively insensitive to the strength of selection, but depend crucially on the extent of dispersal between niches, with a threshold of ~5% if population sizes in two niches are equal. At higher levels of dispersal, ecological differentiation is lost. These results contrast with those of earlier studies and shed light on why parapatric speciation is limited by the extent of gene flow. Our testable model provides a candidate explanation for the rapid speciation rates, diversity of appearance and occurrence of "species flocks" observed among some African cichlids and neotropical birds and may also have implications for the occurrence of punctuational change on phylogenies.

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.

The paradox behind the pattern of rapid adaptive radiation: how can the speciation process sustain itself through an early burst?

Rapid adaptive radiation poses a distinct question apart from speciation and adaptation: what happens after one speciation event? That is, how are some lineages able to continue speciating through a rapid burst? This question connects global macroevolutionary patterns to microevolutionary processes. Here we review major features of rapid radiations in nature and their mismatch with theoretical models and what is currently known about speciation mechanisms. Rapid radiations occur on three major diversification axes - species richness, phenotypic disparity, and ecological diversity - with exceptional outliers on each axis. The paradox is that the hallmark early stage of adaptive radiation, a rapid burst of speciation and niche diversification, is contradicted by most existing speciation models which instead predict continuously decelerating speciation rates and niche subdivision through time. Furthermore, while speciation mechanisms such as magic traits, phenotype matching, and physical linkage of co-adapted alleles promote speciation, it is often not discussed how these mechanisms could promote multiple speciation events in rapid succession. Additional mechanisms beyond ecological opportunity are needed to understand how rapid radiations occur. We review the evidence for five emerging theories: 1) the 'transporter' hypothesis: introgression and the ancient origins of adaptive alleles, 2) the 'signal complexity' hypothesis: the dimensionality of sexual traits, 3) the connectivity of fitness landscapes, 4) 'diversity begets diversity', and 5) flexible stem/'plasticity first'. We propose new questions and predictions to guide future work on the mechanisms underlying the rare origins of rapid radiation.

Assortative Mating in Animals and Its Role for Speciation

Evolutionary theory predicts that positive assortative mating-the tendency of similar individuals to mate with each other-plays a key role for speciation by generating reproductive isolation between diverging populations. However, comprehensive tests for an effect of assortative mating on species richness at the macroevolutionary scale are lacking. We used a meta-analytic approach to test the hypothesis that the strength of assortative mating within populations is positively related to species richness across a broad range of animal taxa. Specifically, we ran a phylogenetically independent meta-analysis using an extensive database of 1,447 effect sizes for the strength of assortative mating, encompassing 307 species from 130 families and 14 classes. Our results suggest that there is no relationship between the strength of assortative mating and species richness across and within major taxonomic groups and trait categories. Moreover, our analysis confirms an earlier finding that animals typically mate assortatively (global Pearson correlation coefficient: r=0.36; 95% confidence interval: 0.19-0.52) when accounting for phylogenetic nonindependence. We argue that future advances will rely on a better understanding of the evolutionary causes and consequences of the observed intra- and interspecific variation in the strength of assortative mating.

John ME. How to Investigate the Origins of Novelty: Insights Gained from Genetic, Behavioral, and Fitness Perspectives

Biologists are drawn to the most extraordinary adaptations in the natural world, often referred to as evolutionary novelties, yet rarely do we understand the microevolutionary context underlying the origins of novel traits, behaviors, or ecological niches. Here we discuss insights gained into the origins of novelty from a research program spanning biological levels of organization from genotype to fitness in Caribbean pupfishes. We focus on a case study of the origins of novel trophic specialists on San Salvador Island, Bahamas and place this radiation in the context of other rapid radiations. We highlight questions that can be addressed about the origins of novelty at different biological levels, such as measuring the isolation of novel phenotypes on the fitness landscape, locating the spatial and temporal origins of adaptive variation contributing to novelty, detecting dysfunctional gene regulation due to adaptive divergence, and connecting behaviors with novel traits. Evolutionary novelties are rare, almost by definition, and we conclude that integrative case studies can provide insights into this rarity relative to the dynamics of adaptation to more common ecological niches and repeated parallel speciation, such as the relative isolation of novel phenotypes on fitness landscapes and the transient availability of ecological, genetic, and behavioral opportunities.

Searching for Sympatric Speciation in the Genomic Era

Sympatric speciation illustrates how natural and sexual selection may create new species in isolation without geographic barriers. However, recent genomic reanalyses of classic examples of sympatric speciation reveal complex histories of secondary gene flow from outgroups into the radiation. In contrast, the rich theoretical literature on this process distinguishes among a diverse range of models based on simple genetic histories and different types of reproductive isolating barriers. Thus, there is a need to revisit how to connect theoretical models of sympatric speciation and their predictions to empirical case studies in the face of widespread gene flow. Here, theoretical differences among different types of sympatric speciation and speciation-with-gene-flow models are reviewed and summarized, and genomic analyses are proposed for distinguishing which models apply to case studies based on the timing and function of adaptive introgression. Investigating whether secondary gene flow contributed to reproductive isolation is necessary to test whether predictions of theory are ultimately borne out in nature.

Sympatric speciation in the Simulium arcticum s. l. complex (Diptera: Simuliidae): The Rothfels model updated

ABSTRACT

We tested the Rothfels sympatric speciation model for black flies by comparing all available data for sex-chromosome diversity with the geographic locations of larval collection sites within the Simulium arcticum complex of black flies (Diptera: Simuliidae). Five separate data sets equaling about 20,000 larvae were included from throughout the geographic range of this complex. We record a total of 31 taxa having unique sex chromosomes, all of which demonstrate linkage disequilibrium with most taxa sharing autosomal polymorphisms. All siblings share portions of their distributions with S. negativum, the presumed oldest member of the complex. Twenty-one of 22 cytotypes have distributions within the ranges of siblings thus supporting the sympatric speciation model of Rothfels. Chromosomally diverse sites may require analysis of as many as 200 larvae to be properly described. There is no effect of any inversions influencing the occurrence of other inversions. Finally, we report a new cytotype, Simulium arcticum IIL-6, which we originally discovered in Alaska. Aspects of future genomic research are discussed as they relate to the main chromosomal structural/functional tenants of the model.

OPEN RESEARCH BADGE

This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data are available at https://doi.org/10.6084/m9.figshare.7719398.

Current geography masks dynamic history of gene flow during speciation in northern Australian birds

Genome divergence is greatly influenced by gene flow during early stages of speciation. As populations differentiate, geographic barriers can constrain gene flow and so affect the dynamics of divergence and speciation. Current geography, specifically disjunction and continuity of ranges, is often used to predict the historical gene flow during the divergence process. We test this prediction in eight meliphagoid bird species complexes codistributed in four regions. These regions are separated by known biogeographical barriers across northern Australia and Papua New Guinea. We find that bird populations currently separated by terrestrial habitat barriers within Australia and marine barriers between Australia and Papua New Guinea have a range of divergence levels and probability of gene flow not associated with current range connectivity. Instead, geographic distance and historical range connectivity better predict divergence and probability of gene flow. In this dynamic environmental context, we also find support for a nonlinear decrease of the probability of gene flow during the divergence process. The probability of gene flow initially decreases gradually after a certain level of divergence is reached. Its decrease then accelerates until the probability is close to zero. This implies that although geographic connectivity may have more of an effect early in speciation, other factors associated with higher divergence may play a more important role in influencing gene flow midway through and later in speciation. Current geographic connectivity may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation.

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.

Molecular Fitness Landscapes from High-Coverage Sequence Profiling

The function of fitness (or molecular activity) in the space of all possible sequences is known as the fitness landscape. Evolution is a random walk on the fitness landscape, with a bias toward climbing hills. Mapping the topography of real fitness landscapes is fundamental to understanding evolution, but previous efforts were hampered by the difficulty of obtaining large, quantitative data sets. The accessibility of high-throughput sequencing (HTS) has transformed this study, enabling large-scale enumeration of fitness for many mutants and even complete sequence spaces in some cases. We review the progress of high-throughput studies in mapping molecular fitness landscapes, both in vitro and in vivo, as well as opportunities for future research. Such studies are rapidly growing in number. HTS is expected to have a profound effect on the understanding of real molecular fitness landscapes.

Signatures of Microevolutionary Processes in Phylogenetic Patterns

Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem, we analyzed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.

A Stochastic Model for Reproductive Isolation Under Asymmetrical Mating Preferences

More and more evidence shows that mating preference is a mechanism that may lead to a reproductive isolation event. In this paper, a haploid population living on two patches linked by migration is considered. Individuals are ecologically and demographically neutral on the space and differ only on a trait, a or A, affecting both mating success and migration rate. The special feature of this paper is to assume that the strengths of the mating preference and the migration depend on the trait carried. Indeed, patterns of mating preferences are generally asymmetrical between the subspecies of a population. I prove that mating preference interacting with frequency-dependent migration behavior can lead to a reproductive isolation. Then, I describe the time before reproductive isolation occurs. To reach this result, I use an original method to study the limiting dynamical system, analyzing first the system without migration and adding migration with a perturbation method. Finally, I study how the time before reproductive isolation is influenced by the parameters of migration and of mating preferences, highlighting that large migration rates tend to favor types with weak mating preferences.

A Probable Case of Incipient Speciation in Schizocosa Wolf Spiders Driven by Allochrony, Habitat Use, and Female Mate Choice

There is growing evidence that speciation can occur between populations that are not geographically isolated. The emergence of assortative mating is believed to be critical to this process, but how assortative mating arises in diverging populations is poorly understood. The wolf spider genus Schizocosa has become a model system for studying mechanisms of assortative mating. We conducted a series of experiments to identify the factors that control mate pair formation in a Schizocosa population that includes both ornamented and nonornamented males. We show that the population also includes two previously unrecognized female phenotypes. One female phenotype mates mostly or exclusively with ornamented males, and the other mates mostly or exclusively with unornamented males. Assortative mating within these groups is maintained by differences in maturation time, microhabitat use, and female mate preference. We conclude that the population is not a single species, as previously believed, but rather an incipient species pair with multiple overlapping mechanisms of reproductive isolation. The identification of a new incipient species pair in the well-studied and rapidly speciating Schizocosa clade presents new opportunities for the study of speciation without geographic isolation.

Looking for the right mate in diploid species: How does genetic dominance affect the spatial differentiation of a sexual trait?

Divergence between populations for a given trait can be driven by sexual selection, interacting with migration behaviour. Mating preference for different phenotypes may lead to specific migration behaviour, with departures from populations where the preferred trait is rare. Such preferences can then trigger the emergence and persistence of differentiated populations, even without any local adaptation. However the genetic architecture underlying the trait targeted by mating preference may have a profound impact on population divergence. In particular, dominance between alleles encoding for divergent phenotypes can interfere with the differentiation process. Using a diploid model of a trait determining both mating success and migration rate, we explored differentiation between two connected populations, assuming either co-dominance or strict dominance between alleles. The model assumes that individuals prefer mating with partners displaying the same phenotype and therefore tend to move to the other population when their own phenotype is rare. We show that the emergence of differentiated populations in this diploid moded is limited as compared to results obtained with the same model assuming haploidy. When assuming co-dominance, differentiation arises only when migration is limited compared to the strength of the preference. Such differentiation is less dependent on migration when assuming strict dominance between haplotypes. Dominant alleles frequently invade populations because their phenotype is more frequently expressed, resulting in higher local mating success and a rapid decrease in migration. However, depending on the initial distribution of alleles, this advantage associated with dominance (i.e. Haldane's sieve) may lead to fixation of the dominant allele throughout both populations. Depending on the initial distribution of heterozygotes in the two populations, persistence of polymorphisms within populations can also occur because heterozygotes displaying the predominant phenotype benefit from high mating success. Altogether, our results highlight that heterozygotes' behaviour has a strong impact on population differentiation and highlight the need for diploid models of differentiation and speciation driven by sexual selection.

Diversification rates indicate an early role of adaptive radiations at the origin of modern echinoid fauna

Evolutionary radiations are fascinating phenomena corresponding to a dramatic diversification of taxa and a burst of cladogenesis over short periods of time. Most evolutionary radiations have long been regarded as adaptive but this has seldom been demonstrated with large-scale comparative datasets including fossil data. Originating in the Early Jurassic, irregular echinoids are emblematic of the spectacular diversification of mobile marine faunas during the Mesozoic Marine Revolution. They diversified as they colonized various habitats, and now constitute the main component of echinoid fauna in modern seas. The evolutionary radiation of irregular echinoids has long been considered as adaptive but this hypothesis has never been tested. In the present work we analyze the evolution of echinoid species richness and morphological disparity over 37 million years based on an extensive fossil dataset. Our results demonstrate that morphological and functional diversifications in certain clades of irregular echinoids were exceptionally high compared to other clades and that they were associated with the evolution of new modes of life and so can be defined as adaptive radiations. The role played by ecological opportunities in the diversification of these clades was critical, with the evolution of the infaunal mode of life promoting the adaptive radiation of irregular echinoids.

Comparing the consequences of natural selection, adaptive phenotypic plasticity, and matching habitat choice for phenotype-environment matching, population genetic structure, and reproductive isolation in meta-populations

Organisms commonly experience significant spatiotemporal variation in their environments. In response to such heterogeneity, different mechanisms may act that enhance ecological performance locally. However, depending on the nature of the mechanism involved, the consequences for populations may differ greatly. Building on a previous model that investigated the conditions under which different adaptive mechanisms (co)evolve, this study compares the ecological and evolutionary population consequences of three very different responses to environmental heterogeneity: matching habitat choice (directed gene flow), adaptive plasticity (associated with random gene flow), and divergent natural selection. Using individual‐based simulations, we show that matching habitat choice can have a greater adaptive potential than plasticity or natural selection: it allows for local adaptation while protecting genetic polymorphism despite global mating or strong environmental changes. Our simulations further reveal that increasing environmental fluctuations and unpredictability generally favor the emergence of specialist genotypes but that matching habitat choice is better at preventing local maladaptation by individuals. This confirms that matching habitat choice can speed up the genetic divergence among populations, cause indirect assortative mating via spatial clustering, and hence even facilitate sympatric speciation. This study highlights the potential importance of directed dispersal in local adaptation and speciation, stresses the difficulty of deriving its operation from nonexperimental observational data alone, and helps define a set of ecological conditions which should favor its emergence and subsequent detection in nature.

Flexible mate choice may contribute to ecotype assortative mating in pumpkinseed sunfish (Lepomis gibbosus)

Gene flow is expected to limit adaptive divergence, but the ecological and behavioural factors that govern gene flow are still poorly understood, particularly at the earliest stages of population divergence. Reduced gene flow through mate choice (sexual isolation) can evolve even under conditions of subtle population divergence if intermediate phenotypes have reduced fitness. We indirectly tested the hypothesis that mate choice has evolved between coexisting littoral and pelagic ecotypes of polyphenic pumpkinseed sunfish (Lepomis gibbosus) that have diverged in morphology and resource use and where intermediate phenotypes have reduced performance. We assessed the ecotype of nesting males and females using stable isotope estimates of diet and a divergent male morphological trait, oral jaw width. We found positive assortative mating between ecotypes in a common spawning habitat along exposed lake shorelines, but contrary to expectations, assortative mating was variably expressed between two sampling years. Although the factors that influence variable assortative mating remain unclear, our results are consistent with mate choice being expressed by ecotypes. Despite being variably expressed, mate choice will reduce gene flow between ecotypes and could contribute to further adaptive divergence depending on its frequency and strength in the population. Our findings add to a growing body of evidence indicating mate choice behaviour can be a plastic trait, an idea that should be more explicitly considered in empirical studies of mate choice as well as conceptual frameworks of mate choice evolution and adaptive divergence.

A novel method for estimating the strength of positive mating preference by similarity in the wild

Mating preference can be a driver of sexual selection and assortative mating and is, therefore, a key element in evolutionary dynamics. Positive mating preference by similarity is the tendency for the choosy individual to select a mate which possesses a similar variant of a trait. Such preference can be modelled using Gaussian‐like mathematical functions that describe the strength of preference, but such functions cannot be applied to empirical data collected from the field. As a result, traditionally, mating preference is indirectly estimated by the degree of assortative mating (using Pearson's correlation coefficient, r) in wild captured mating pairs. Unfortunately, r and similar coefficients are often biased due to the fact that different variants of a given trait are nonrandomly distributed in the wild, and pooling of mating pairs from such heterogeneous samples may lead to “false–positive” results, termed “the scale‐of‐choice effect” (SCE). Here we provide two new estimators of mating preference (C_rough and C_scaled) derived from Gaussian‐like functions which can be applied to empirical data. Computer simulations demonstrated that r coefficient showed robust estimations properties of mating preference but it was severely affected by SCE, C_rough showed reasonable estimation properties and it was little affected by SCE, while C_scaled showed the best properties at infinite sample sizes and it was not affected by SCE but failed at biological sample sizes. We recommend using C_rough combined with the r coefficient to infer mating preference in future empirical studies.

Managing cryptic biodiversity: Fine-scale intralacustrine speciation along a benthic gradient in Alpine whitefish (Coregonus spp.)

Whitefish (Coregonus spp.) are an important catch for many freshwater fisheries, particularly in Switzerland. In support of this, supplemental stocking of whitefish species is carried out, despite lacking complete knowledge of the extent, distribution and origin of whitefish diversity in these lakes, potentially threatening local endemics via artificial gene flow. Here, we investigate phenotypic and genetic differentiation among coexisting whitefish species spawning along a depth gradient in a subalpine Swiss lake to better delineate intralacustrine whitefish biodiversity. We find depth‐related clines in adaptive morphology and in neutral genetic markers. This individual variation is structured in three distinct clusters with spatial overlap. Individual genetic distances correlate strongly with differences in growth rate and gill‐raker number, consistent with predictions of isolation‐by‐adaptation and ecological speciation. Genetic differentiation between species suggests reproductive isolation, despite demographic admixture on spawning grounds. Our results are consistent with clinal speciation resulting in three species coexisting in close ecological parapatry, one (C. sp. “benthic intermediate”) being previously unknown. A second unknown species spawning in close proximity was found to be of potential allochthonous origin. This study highlights the importance of taxonomically unbiased sampling strategies to both understand evolutionary mechanisms structuring biodiversity and to better inform conservation and fisheries management.

Ecological speciation of bacteriophage lambda in allopatry and sympatry

Understanding the conditions that allow speciation to occur is difficult because most research has focused on either long-lived organisms or asexual microorganisms. We propagated bacteriophage λ, a virus with rapid generations and frequent recombination, on two Escherichia coli host genotypes that expressed either the LamB or OmpF receptor. When supplied with either single host (allopatry), phage λ improved its binding to the available receptor while losing its ability to use the alternative. When evolving on both hosts together (sympatry), the viruses split into two lineages with divergent receptor preferences. Although the level of divergence varied among replicates, some lineages evolved reproductive isolation via genetic incompatibilities. This outcome indicates that, under suitable conditions, allopatric and sympatric speciation can occur with similar ease.