NICHE DIMENSIONALITY AND THE GENETICS OF ECOLOGICAL SPECIATION

Phenotypic covariation predicts diversification in an adaptive radiation of pupfishes

Phenotypic covariation among suites of traits may constrain or promote diversification both within and between species, yet few studies have empirically tested this relationship. In this study, we investigate whether phenotypic covariation of craniofacial traits is associated with diversification in an adaptive radiation of pupfishes found only on San Salvador Island, Bahamas (SSI). The radiation includes generalist, durophagous, and lepidophagous species. We compared phenotypic variation and covariation (i.e., the P matrix) between (1) allopatric populations of generalist pupfish from neighboring islands and estuaries in the Caribbean, (2) SSI pupfish allopatric lake populations with only generalist pupfish, and (3) SSI lake populations containing the full radiation in sympatry. Additionally, we examine patterns observed in the P matrices of two independent lab-reared F2 hybrid crosses of the two most morphologically distinct members of the radiation to make inferences about the underlying mechanisms contributing to the variation in craniofacial traits in SSI pupfishes. We found that the P matrix of SSI allopatric generalist populations exhibited higher levels of mean trait correlation, constraints, and integration with simultaneously lower levels of flexibility compared to allopatric generalist populations on other Caribbean islands and sympatric populations of all three species on SSI. We also document that while many craniofacial traits appear to result from additive genetic effects, variation in key traits such as head depth, maxilla length, and lower jaw length may be produced via non-additive genetic mechanisms. Ultimately, this study suggests that differences in phenotypic covariation significantly contribute to producing and maintaining organismal diversity.

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.

Genetically Encoded Lizard Color Divergence for Camouflage and Thermoregulation

Local adaptation is critical in speciation and evolution, yet comprehensive studies on proximate and ultimate causes of local adaptation are generally scarce. Here, we integrated field ecological experiments, genome sequencing, and genetic verification to demonstrate both driving forces and molecular mechanisms governing local adaptation of body coloration in a lizard from the Qinghai-Tibet Plateau. We found dark lizards from the cold meadow population had lower spectrum reflectance but higher melanin contents than light counterparts from the warm dune population. Additionally, the colorations of both dark and light lizards facilitated the camouflage and thermoregulation in their respective microhabitat simultaneously. More importantly, by genome resequencing analysis, we detected a novel mutation in Tyrp1 that underpinned this color adaptation. The allele frequencies at the site of SNP 459# in the gene of Tyrp1 are 22.22% G/C and 77.78% C/C in dark lizards and 100% G/G in light lizards. Model-predicted structure and catalytic activity showed that this mutation increased structure flexibility and catalytic activity in enzyme TYRP1, and thereby facilitated the generation of eumelanin in dark lizards. The function of the mutation in Tyrp1 was further verified by more melanin contents and darker coloration detected in the zebrafish injected with the genotype of Tyrp1 from dark lizards. Therefore, our study demonstrates that a novel mutation of a major melanin-generating gene underpins skin color variation co-selected by camouflage and thermoregulation in a lizard. The resulting strong selection may reinforce adaptive genetic divergence and enable the persistence of adjacent populations with distinct body coloration.

Ecology and the origin of non-ephemeral species

AbstractResearch over the past three decades has shown that ecology-based extrinsic reproductive barriers can rapidly arise to generate incipient species-but such barriers can also rapidly dissolve when environments change, resulting in incipient species collapse. Understanding the evolution of unconditional, "intrinsic" reproductive barriers is therefore important for understanding the longer-term buildup of biodiversity. In this article, we consider ecology's role in the evolution of intrinsic reproductive isolation. We suggest that this topic has fallen into a gap between disciplines: while evolutionary ecologists have traditionally focused on the rapid evolution of extrinsic isolation between co-occurring ecotypes, speciation geneticists studying intrinsic isolation in other taxa have devoted little attention to the ecological context in which it evolves. We argue that for evolutionary ecology to close this gap, the field will have to expand its focus beyond rapid adaptation and its traditional model systems. Synthesizing data from several subfields, we present circumstantial evidence for and against different forms of ecological adaptation as promoters of intrinsic isolation and discuss alternative forces that may be significant. We conclude by outlining complementary approaches that can better address the role of ecology in the evolution of nonephemeral reproductive barriers and, by extension, less ephemeral species.

Rate of environmental variation impacts the predictability in evolution

In the two last decades, we have improved our understanding of the adaptive evolution of natural populations under constant and stable environments. For instance, experimental methods from evolutionary biology have allowed us to explore the structure of fitness landscapes and survey how the landscape properties can constrain the adaptation process. However, understanding how environmental changes can affect adaptation remains challenging. Very little progress has been made with respect to time-varying fitness landscapes. Using the adaptive-walk approximation, we survey the evolutionary process of populations under a scenario of environmental variation. In particular, we investigate how the rate of environmental variation influences the predictability in evolution. We observe that the rate of environmental variation not only changes the duration of adaptive walks towards fitness peaks of the fitness landscape, but also affects the degree of repeatability of both outcomes and evolutionary paths. In general, slower environmental variation increases the predictability in evolution. The accessibility of endpoints is greatly influenced by the ecological dynamics. The dependence of these quantities on the genome size and number of traits is also addressed. To our knowledge, this contribution is the first to use the predictive approach to quantify and understand the impact of the speed of environmental variation on the degree of parallelism of the evolutionary process.

The diverse effects of phenotypic dominance on hybrid fitness

When divergent populations interbreed, their alleles are brought together in hybrids. In the initial F1 cross, most divergent loci are heterozygous. Therefore, F1 fitness can be influenced by dominance effects that could not have been selected to function well together. We present a systematic study of these F1 dominance effects by introducing variable phenotypic dominance into Fisher's geometric model. We show that dominance often reduces hybrid fitness, which can generate optimal outbreeding followed by a steady decline in F1 fitness, as is often observed. We also show that "lucky" beneficial effects sometimes arise by chance, which might be important when hybrids can access novel environments. We then show that dominance can lead to violations of Haldane's Rule (reduced fitness of the heterogametic F1) but strengthens Darwin's Corollary (F1 fitness differences between cross directions). Taken together, results show that the effects of dominance on hybrid fitness can be surprisingly difficult to isolate, because they often resemble the effects of uniparental inheritance or expression. Nevertheless, we identify a pattern of environment-dependent heterosis that only dominance can explain, and for which there is some suggestive evidence. Our results also show how existing data set upper bounds on the size of dominance effects. These bounds could explain why additive models often provide good predictions for later-generation recombinant hybrids, even when dominance qualitatively changes outcomes for the F1.

The phoenix hypothesis of speciation

Genetic divergence among allopatric populations builds reproductive isolation over time. This process is accelerated when populations face a changing environment that allows large-effect mutational differences to accumulate, but abrupt change also places populations at risk of extinction. Here we use simulations of Fisher's geometric model with explicit population dynamics to explore the genetic changes that occur in the face of environmental changes. Because evolutionary rescue leads to the fixation of mutations whose phenotypic effects are larger on average compared with populations not at risk of extinction, these mutations are thus more likely to lead to reproductive isolation. We refer to the formation of new species from the ashes of populations in decline as the phoenix hypothesis of speciation. The phoenix hypothesis predicts more substantial hybrid fitness breakdown among populations surviving a higher extinction risk. The hypothesis was supported when many loci underlie adaptation. With only a small number of potential rescue mutations, however, mutations that fixed in different populations were more likely to be identical, with such parallel changes reducing isolation. Consequently, reproductive isolation builds fastest in populations subject to an intermediate extinction risk, given a limited number of mutations available for adaptation.

Whether intelligentization promotes regional industrial competitiveness: Evidence from China

Intelligentization-oriented development is a fast-developing trend of technological revolution. It promotes the reconstruction of the industrial system of a region and affects its overall industrial competitiveness. This paper sets up a variety of models featuring intelligentization level and multi-dimensional industrial competitiveness, and collects data of 28 provinces and cities in China from 2003 to 2017 to test the influence of industrial intelligentization level on the industrial competitiveness of a region. The result reveals that: 1) In China’s provincial jurisdictions, the higher the level of intelligentization is, the lower the overall level of industrial competitiveness and the lower the proportion of industry in the economic system will be. In regions where the facilities are highly intelligentialized, the production sectors tend to move to the less developed regions, and the growth effect of technological dividends is the focus. 2) Compared with the middle region and the Western region of China, the Eastern region, which is more developed with higher intelligentization level, has stronger ability in the research and development (R&D) of technologies, and the economic structure of the industry there tends to be stable, manifesting a strong growth potential.

Heterosis counteracts hybrid breakdown to forestall speciation by parallel natural selection

In contrast to ecological speciation, where reproductive isolation evolves as a consequence of divergent natural selection, speciation by parallel natural selection has been less thoroughly studied. To test whether parallel evolution drives speciation, we leveraged the repeated evolution of benthic and limnetic ecotypes of threespine stickleback fish and estimated fitness for pure crosses and within-ecotype hybrids in semi-natural ponds and in laboratory aquaria. In ponds, we detected hybrid breakdown in both ecotypes but this was counterbalanced by heterosis and the strength of post-zygotic isolation was nil. In aquaria, we detected heterosis in limnetic crosses and breakdown in benthic crosses, which is suggestive of process- and ecotype-specific environment-dependence. In ponds, heterosis and breakdown were three times greater in limnetic crosses than in benthic crosses, contrasting the prediction that the fitness consequences of hybridization should be greater in crosses among more derived ecotypes. Consistent with a primary role for stochastic processes, patterns differed among crosses between populations from different lakes. Yet, the observation of qualitatively similar patterns of heterosis and hybrid breakdown for both ecotypes when averaging the lake pairs indicates that the outcome of hybridization is repeatable in a general sense.

Evolution: How important is the dimensionality of natural selection in local adaptation?

Organisms adapt to their local environments, which may vary in one aspect, or many. A new study shows that such dimensionality matters, as it impacts the magnitude and dynamics of local adaptation, with broader ecological consequences, such as the evolution of generalists.

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.

Adaptive divergence and the evolution of hybrid trait mismatch in threespine stickleback

Selection against mismatched traits in hybrids is the phenotypic analogue of intrinsic hybrid incompatibilities. Mismatch occurs when hybrids resemble one parent population for some phenotypic traits and the other parent population for other traits, and is caused by dominance in opposing directions or from segregation of alleles in recombinant hybrids. In this study, we used threespine stickleback fish (Gasterosteus aculeatus L.) to test the theoretical prediction that trait mismatch in hybrids should increase with the magnitude of phenotypic divergence between parent populations. We measured morphological traits in parents and hybrids in crosses between a marine population representing the ancestral form and twelve freshwater populations that have diverged from this ancestral state to varying degrees according to their environments. We found that trait mismatch was greater in more divergent crosses for both F₁ and F₂ hybrids. In the F₁, the divergence–mismatch relationship was caused by traits having dominance in different directions, whereas it was caused by increasing segregating phenotypic variation in the F₂. Our results imply that extrinsic hybrid incompatibilities accumulate as phenotypic divergence proceeds.

Allen Orr and the genetics of adaptation

Over most of the 20th century, evolutionary biologists predominantly subscribed to a strong form of "micro-mutationism," in which adaptive phenotypic divergence arises from allele frequency changes at many loci, each with a small effect on the phenotype. To be sure, there were well-known examples of large-effect alleles contributing to adaptation, yet such cases were generally regarded as atypical and unrepresentative of evolutionary change in general. In 1998, Allen Orr published a landmark theoretical paper in Evolution, which showed that both small- and large-effect mutations are likely to contribute to "adaptive walks" of a population to an optimum. Coupled with a growing set of empirical examples of large-effect alleles contributing to divergence (e.g., from QTL studies), Orr's paper provided a mathematical formalism that converted many evolutionary biologists from micro-mutationism to a more pluralistic perspective on the genetic basis of evolutionary change. We revisit the theoretical insights emerging from Orr's paper within the historical context leading up to 1998, and track the influence of this paper on the field of evolutionary biology through an examination of its citations over the last two decades and an analysis of the extensive body of theoretical and empirical research that Orr's pioneering paper inspired.

Multidimensional divergent selection, local adaptation, and speciation

Divergent selection applied to one or more traits drives local adaptation and may lead to ecological speciation. Divergent selection on many traits might be termed "multidimensional" divergent selection. There is a commonly held view that multidimensional divergent selection is likely to promote local adaptation and speciation to a greater extent than unidimensional divergent selection. We disentangle the core concepts underlying dimensionality as a property of the environment, phenotypes, and genome. In particular, we identify a need to separate the overall strength of selection and the number of loci affected from dimensionality per se, and to distinguish divergence dimensionality from dimensionality of stabilizing selection. We then critically scrutinize this commonly held view that multidimensional selection promotes speciation, re-examining the evidence base from theory, experiments, and nature. We conclude that the evidence base is currently weak and generally suffers from confounding of possible causal effects. Finally, we propose several mechanisms by which multidimensional divergent selection and related processes might influence divergence, both as a driver and as a barrier.

The geometry and genetics of hybridization

When divergent populations form hybrids, hybrid fitness can vary with genome composition, current environmental conditions, and the divergence history of the populations. We develop analytical predictions for hybrid fitness, which incorporate all three factors. The predictions are based on Fisher's geometric model, and apply to a wide range of population genetic parameter regimes and divergence conditions, including allopatry and parapatry, local adaptation, and drift. Results show that hybrid fitness can be decomposed into intrinsic effects of admixture and heterozygosity, and extrinsic effects of the (local) adaptedness of the parental lines. Effect sizes are determined by a handful of geometric distances, which have a simple biological interpretation. These distances also reflect the mode and amount of divergence, such that there is convergence toward a characteristic pattern of intrinsic isolation. We next connect our results to the quantitative genetics of line crosses in variable or patchy environments. This means that the geometrical distances can be estimated from cross data, and provides a simple interpretation of the "composite effects." Finally, we develop extensions to the model, involving selectively induced disequilibria, and variable phenotypic dominance. The geometry of fitness landscapes provides a unifying framework for understanding speciation, and wider patterns of hybrid fitness.

Phylogeny, taxonomic reassessment and ‘ecomorph’ relationship of the Orientallactaga sibirica complex (Rodentia: Dipodidae: Allactaginae)

The ecological gradient–morphological variation (‘ecomorph’) relationship has long interested ecologists and evolutionary biologists, but it is applied far less frequently than genetic differentiation in cryptic species detection and species identification. With integrative methods, we revise taxonomic uncertainties in the Orientallactaga sibirica complex (OSC), with 298 sequence specimens and 469 voucher specimens from 138 localities covering nearly the entire distribution of the OSC. Phylogenetic relationships are assessed by Bayesian inference and maximum likelihood using two mitochondrial and nine nuclear genes. We use species-delimitation approaches to divide and validate the ‘candidate species’. We evaluate correlations between ecological divergence and phylogenetic splits, and visualize geographical patterns of morphological variation. The OSC is divided into four phylogenetic groups, the Ognevi, Altay, Bogda and Sibirica groups, and the OSC exhibits a significant ecomorph relationship and ecological divergence pattern. Morphological variations not only follow the general regularity under a large gradient of ecological factors, but are also closely related to the local environment/habitat. We suggest considering the comprehensive ecomorph relationship to identify species. Molecular analyses reveal that the OSC more easily forms deeply divergent lineages in the foothills and this differentiation depth may be related to mountain system size.

Experimental Hybridization Studies Suggest That Pleiotropic Alleles Commonly Underlie Adaptive Divergence between Natural Populations

The alleles used for adaptation can pleiotropically affect traits under stabilizing selection. The fixation of alleles with deleterious pleiotropic side effects causes compensatory alleles to be favored by selection. Such compensatory alleles might segregate in interpopulation hybrids, resulting in segregation variance for traits where parents have indistinguishable phenotypes. If adaptation typically involves pleiotropy and compensation, then the segregation variance for traits under stabilizing selection is expected to increase with the magnitude of adaptive phenotypic divergence between parents. This prediction has not been tested empirically, and I gathered data from experimental hybridization studies to evaluate it. I found that pairs of parents that are more phenotypically divergent beget hybrids with more segregation variance in traits for which the parents are statistically indistinguishable. This result suggests that adaptive divergence between pairs of natural populations proceeds via pleiotropy and compensation and that deleterious transgressive segregation variance accumulates systematically as populations diverge.

The Impact of Neutral Mutations on Genome Evolvability

Beneficial mutations are rare and deleterious mutations are purged by natural selection. As a result, the vast majority of mutations that accumulate in genomes belong to the class of neutral mutations. Over the last two decades, neutral mutations, despite their null effect on fitness, have been shown to affect evolvability by providing access to new phenotypes through subsequent mutations that would not have been available otherwise. Here we propose that in addition, many mutations - independent of their selective effects - can affect the mutability of neighboring DNA sequences and modulate the efficacy of homologous recombination. Such mutations do not change the spectrum of accessible phenotypes, but rather the rate at which new phenotypes will be produced. Therefore, neutral mutations that accumulate in genomes have an important long-term impact on the evolutionary fate of genomes.

A Few Stickleback Suffice for the Transport of Alleles to New Lakes

Threespine stickleback populations provide a striking example of local adaptation to divergent habitats in populations that are connected by recurrent gene flow. These small fish occur in marine and freshwater habitats throughout the Northern Hemisphere, and in numerous cases the smaller freshwater populations have been established “de novo” from marine colonists. Independently evolved freshwater populations exhibit similar phenotypes that have been shown to derive largely from the same standing genetic variants. Geographic isolation prevents direct migration between the freshwater populations, strongly suggesting that these shared locally adaptive alleles are transported through the marine population. However it is still largely unknown how gene flow, recombination, and selection jointly impact the standing variation that might fuel this adaptation. Here we use individual-based, spatially explicit simulations to determine the levels of gene flow that best match observed patterns of allele sharing among habitats in stickleback. We aim to better understand how gene flow and local adaptation in large metapopulations determine the speed of adaptation and re-use of standing genetic variation. In our simulations we find that repeated adaptation uses a shared set of alleles that are maintained at low frequency by migration-selection balance in oceanic populations. This process occurs over a realistic range of intermediate levels of gene flow that match previous empirical population genomic studies in stickleback. Examining these simulations more deeply reveals how lower levels of gene flow leads to slow, independent adaptation to different habitats, whereas higher levels of gene flow leads to significant mutation load – but an increased probability of successful population genomic scans for locally adapted alleles. Surprisingly, we find that the genealogical origins of most freshwater adapted alleles can be traced back to the original generation of marine individuals that colonized the lakes, as opposed to subsequent migrants. These simulations provide deeper context for existing studies of stickleback evolutionary genomics, and guidance for future empirical studies in this model. More broadly, our results support existing theory of local adaptation but extend it by more completely documenting the genealogical history of adaptive alleles in a metapopulation.

Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana)

Patterns of genomic divergence between hybridizing taxa can be heterogeneous along the genome. Both differential introgression and local adaptation may contribute to this pattern. Here, we analysed two teosinte subspecies, Zea mays ssp. parviglumis and ssp. mexicana, to test whether their divergence has occurred in the face of gene flow and to infer which environmental variables have been important drivers of their ecological differentiation. We generated 9,780 DArTseqTM SNPs for 47 populations, and used an additional data set containing 33,454 MaizeSNP50 SNPs for 49 populations. With these data, we inferred features of demographic history and performed genome wide scans to determine the number of outlier SNPs associated with climate and soil variables. The two data sets indicate that divergence has occurred or been maintained despite continuous gene flow and/or secondary contact. Most of the significant SNP associations were to temperature and to phosphorus concentration in the soil. A large proportion of these candidate SNPs were located in regions of high differentiation that had been identified previously as putative inversions. We therefore propose that genomic differentiation in teosintes has occurred by a process of adaptive divergence, with putative inversions contributing to reduced gene flow between locally adapted populations.

Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)

Allopolyploidy has played a major role in plant evolution but its impact on genome diversity and expression patterns remains to be understood. Some studies found important genomic and transcriptomic changes in allopolyploids, whereas others detected a strong parental legacy and more subtle changes. The allotetraploid C. bursa-pastoris originated around 100,000 years ago and one could expect the genetic polymorphism of the two subgenomes to follow similar trajectories and their transcriptomes to start functioning together. To test this hypothesis, we sequenced the genomes and the transcriptomes (three tissues) of allotetraploid C. bursa-pastoris and its parental species, the outcrossing C. grandiflora and the self-fertilizing C. orientalis. Comparison of the divergence in expression between subgenomes, on the one hand, and divergence in expression between the parental species, on the other hand, indicated a strong parental legacy with a majority of genes exhibiting a conserved pattern and cis-regulation. However, a large proportion of the genes that were differentially expressed between the two subgenomes, were also under trans-regulation reflecting the establishment of a new regulatory pattern. Parental dominance varied among tissues: expression in flowers was closer to that of C. orientalis and expression in root and leaf to that of C. grandiflora. Since deleterious mutations accumulated preferentially on the C. orientalis subgenome, the bias in expression towards C. orientalis observed in flowers indicates that expression changes could be adaptive and related to the selfing syndrome, while biases in the roots and leaves towards the C. grandiflora subgenome may be reflective of the differential genetic load.

Most plant species have a polyploid at some stage of their ancestry. Polyploidy, genome doubling through either multiple copies of a single species or through genomes of different species coming into the same nucleus, is therefore a crucial step in plant evolution. Understanding its impact on basic biological functions is thus a matter of interest. Shepherd’s purse (Capsella bursa-pastoris) is a major weed that appeared about 100,000 years ago through hybridization of two diploid species of the same genus. In the present project, we measured genetic diversity and analyzed gene expression patterns in flowers, roots, and leaves of C. bursa-pastoris individuals as well as in its two parental species, the outcrossing C. grandiflora and the self-fertilizing C. orientalis. Our data shows that, after 100,000 generations of evolution, the origin of the two subgenomes can still be seen: the genome inherited from C. grandiflora still differs from the one inherited from self-fertilizing C. orientalis. However, there are also signs that the two genomes have started to work together and are jointly regulated, and the way expression pattern varied across the three tissues indicates that the evolution of gene expression was adaptive.

Parallel genetic evolution and speciation from standing variation

Adaptation often proceeds from standing variation, and natural selection acting on pairs of populations is a quantitative continuum ranging from parallel to divergent. Yet, it is unclear how the extent of parallel genetic evolution during adaptation from standing variation is affected by the difference in the direction of selection between populations. Nor is it clear whether the availability of standing variation for adaptation affects progress toward speciation in a manner that depends on the difference in the direction of selection. We conducted a theoretical study investigating these questions and have two primary findings. First, the extent of parallel genetic evolution between two populations rapidly declines as selection changes from fully parallel toward divergent, and this decline is steeper in organisms with more traits (i.e., greater dimensionality). This rapid decline happens because small differences in the direction of selection greatly reduce the fraction of alleles that are beneficial in both populations. For example, populations adapting to optima separated by an angle of 33° might have only 50% of potentially beneficial alleles in common. Second, relative to when adaptation is from only new mutation, adaptation from standing variation improves hybrid fitness under parallel selection and reduces hybrid fitness under divergent selection. Under parallel selection, genetic parallelism from standing variation reduces the phenotypic segregation variance in hybrids, thereby increasing mean fitness in the parental environment. Under divergent selection, larger pleiotropic effects of alleles fixed from standing variation cause maladaptive transgressive phenotypes when combined in hybrids. Adaptation from standing genetic variation therefore slows progress toward speciation under parallel selection and facilitates progress toward speciation under divergent selection.

Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns

Natural selection plays a variety of roles in hybridization, speciation, and admixture. Most research has focused on two extreme cases: crosses between closely related inbred lines, where hybrids are fitter than their parents, or crosses between effectively isolated species, where hybrids suffer severe breakdown. But many natural populations must fall into intermediate regimes, with multiple types of gene interaction, and these are more difficult to study. Here, we develop a simple fitness landscape model, and show that it naturally interpolates between previous modeling approaches, which were designed for the extreme cases, and invoke either mildly deleterious recessives, or discrete hybrid incompatibilities. Our model yields several new predictions, which we test with genomic data from Mytilus mussels, and published data from plants (Zea, Populus, and Senecio) and animals (Mus, Teleogryllus, and Drosophila). The predictions are generally supported, and the model explains a number of surprising empirical patterns. Our approach enables novel and complementary uses of genome-wide datasets, which do not depend on identifying outlier loci, or "speciation genes" with anomalous effects. Given its simplicity and flexibility, and its predictive successes with a wide range of data, the approach should be readily extendable to other outstanding questions in the study of hybridization.

Chaos and the (un)predictability of evolution in a changing environment

Among the factors that may reduce the predictability of evolution, chaos, characterized by a strong dependence on initial conditions, has received much less attention than randomness due to genetic drift or environmental stochasticity. It was recently shown that chaos in phenotypic evolution arises commonly under frequency-dependent selection caused by competitive interactions mediated by many traits. This result has been used to argue that chaos should often make evolutionary dynamics unpredictable. However, populations also evolve largely in response to external changing environments, and such environmental forcing is likely to influence the outcome of evolution in systems prone to chaos. We investigate how a changing environment causing oscillations of an optimal phenotype interacts with the internal dynamics of an eco-evolutionary system that would be chaotic in a constant environment. We show that strong environmental forcing can improve the predictability of evolution by reducing the probability of chaos arising, and by dampening the magnitude of chaotic oscillations. In contrast, weak forcing can increase the probability of chaos, but it also causes evolutionary trajectories to track the environment more closely. Overall, our results indicate that, although chaos may occur in evolution, it does not necessarily undermine its predictability.

Plant size: a key determinant of diversification?

Explaining the variation in diversification rate across groups of plants has long been an important goal of botanists. In plants, complex scenarios involving a combination of extrinsic opportunities and intrinsic traits have been used to explain rapid diversification in certain groups. However, we feel that a very simple trait has been neglected from theories of plant diversification, namely plant height. Here, we argue that decreasing plant size should generally lead to an increase in speciation rate and a decrease in extinction rate. Theory suggests that all population genetic processes involved in speciation are influenced by plant size and its correlates, including seed dispersal distance, population size, generation time and the spatial scale at which plants perceive environmental heterogeneity. In addition, several of these variables, notably population size, also influence rates of extinction. We support our arguments with an empirical analysis showing that plant height is indeed negatively correlated with net diversification rate across families of angiosperms. Finally, we outline how the finer aspects of our hypothesis could be tested, at both micro- and macroevolutionary scales. In addition to strengthening our understanding of the effect of plant size on evolutionary processes, such a research agenda should contribute novel insights to speciation theory in general.

Intrinsic incompatibilities evolving as a by-product of divergent ecological selection: Considering them in empirical studies on divergence with gene flow

The possibility of intrinsic barriers to gene flow is often neglected in empirical research on local adaptation and speciation with gene flow, for example when interpreting patterns observed in genome scans. However, we draw attention to the fact that, even with gene flow, divergent ecological selection may generate intrinsic barriers involving both ecologically selected and other interacting loci. Mechanistically, the link between the two types of barriers may be generated by genes that have multiple functions (i.e., pleiotropy), and/or by gene interaction networks. Because most genes function in complex networks, and their evolution is not independent of other genes, changes evolving in response to ecological selection can generate intrinsic barriers as a by-product. A crucial question is to what extent such by-product barriers contribute to divergence and speciation-that is whether they stably reduce gene flow. We discuss under which conditions by-product barriers may increase isolation. However, we also highlight that, depending on the conditions (e.g., the amount of gene flow and the strength of selection acting on the intrinsic vs. the ecological barrier component), the intrinsic incompatibility may actually destabilize barriers to gene flow. In practice, intrinsic barriers generated as a by-product of divergent ecological selection may generate peaks in genome scans that cannot easily be interpreted. We argue that empirical studies on divergence with gene flow should consider the possibility of both ecological and intrinsic barriers. Future progress will likely come from work combining population genomic studies, experiments quantifying fitness and molecular studies on protein function and interactions.

Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): Inference from transcriptome-wide coalescence analyses

Ancient origins, profound ecological divergence, and extensive hybridization make the fire‐bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae) an intriguing test case of ecological speciation. Previous modeling has proposed that the narrow Bombina hybrid zones represent strong barriers to neutral introgression. We test this prediction by inferring the rate of gene exchange between pure populations on either side of the intensively studied Kraków transect. We developed a method to extract high confidence sets of orthologous genes from de novo transcriptome assemblies, fitted a range of divergence models to these data and assessed their relative support with analytic likelihood calculations. There was clear evidence for postdivergence gene flow, but, as expected, no perceptible signal of recent introgression via the nearby hybrid zone. The analysis of two additional Bombina taxa (B. v. scabra and B. orientalis) validated our parameter estimates against a larger set of prior expectations. Despite substantial cumulative introgression over millions of years, adaptive divergence of the hybridizing taxa is essentially unaffected by their lack of reproductive isolation. Extended distribution ranges also buffer them against small‐scale environmental perturbations that have been shown to reverse the speciation process in other, more recent ecotypes.

The genetics of speciation: Insights from Fisher's geometric model

Research in speciation genetics has uncovered many robust patterns in intrinsic reproductive isolation, and fitness landscape models have been useful in interpreting these patterns. Here, we examine fitness landscapes based on Fisher's geometric model. Such landscapes are analogous to models of optimizing selection acting on quantitative traits, and have been widely used to study adaptation and the distribution of mutational effects. We show that, with a few modifications, Fisher's model can generate all of the major findings of introgression studies (including "speciation genes" with strong deleterious effects, complex epistasis and asymmetry), and the major patterns in overall hybrid fitnesses (including Haldane's Rule, the speciation clock, heterosis, hybrid breakdown, and male-female asymmetry in the F1). We compare our approach to alternative modeling frameworks that assign fitnesses to genotypes by identifying combinations of incompatible alleles. In some cases, the predictions are importantly different. For example, Fisher's model can explain conflicting empirical results about the rate at which incompatibilities accumulate with genetic divergence. In other cases, the predictions are identical. For example, the quality of reproductive isolation is little affected by the manner in which populations diverge.

Epistasis and the Structure of Fitness Landscapes: Are Experimental Fitness Landscapes Compatible with Fisher's Geometric Model?

The fitness landscape defines the relationship between genotypes and fitness in a given environment and underlies fundamental quantities such as the distribution of selection coefficient and the magnitude and type of epistasis. A better understanding of variation in landscape structure across species and environments is thus necessary to understand and predict how populations will adapt. An increasing number of experiments investigate the properties of fitness landscapes by identifying mutations, constructing genotypes with combinations of these mutations, and measuring the fitness of these genotypes. Yet these empirical landscapes represent a very small sample of the vast space of all possible genotypes, and this sample is often biased by the protocol used to identify mutations. Here we develop a rigorous statistical framework based on Approximate Bayesian Computation to address these concerns and use this flexible framework to fit a broad class of phenotypic fitness models (including Fisher's model) to 26 empirical landscapes representing nine diverse biological systems. Despite uncertainty owing to the small size of most published empirical landscapes, the inferred landscapes have similar structure in similar biological systems. Surprisingly, goodness-of-fit tests reveal that this class of phenotypic models, which has been successful so far in interpreting experimental data, is a plausible in only three of nine biological systems. More precisely, although Fisher's model was able to explain several statistical properties of the landscapes-including the mean and SD of selection and epistasis coefficients-it was often unable to explain the full structure of fitness landscapes.

Ecological divergence and conservatism: spatiotemporal patterns of niche evolution in a genus of livebearing fishes (Poeciliidae: Xiphophorus)

Background

Ecological factors often have a strong impact on spatiotemporal patterns of biodiversity. The integration of spatial ecology and phylogenetics allows for rigorous tests of whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence. We address this question in a genus of livebearing fishes for which the role of sexual selection in speciation has long been studied, but in which the potential role of ecological divergence during speciation has not been tested.

Results

By combining reconstruction of ancestral climate tolerances and disparity indices, we show that the earliest evolutionary split in Xiphophorus was associated with significant divergence for temperature variables. Niche evolution and present day niches were most closely associated with each species’ geographic distribution relative to a biogeographic barrier, the Trans-Mexican Volcanic Belt. Tests for similarity of the environmental backgrounds of closely related species suggested that the relative importance of niche conservatism and divergence during speciation varied among the primary clades of Xiphophorus. Closely related species in the two swordtail clades exhibited higher levels of niche overlap than expected given environmental background similarity indicative of niche conservatism. In contrast, almost all species of platyfish had significantly divergent niches compared to environmental backgrounds, which is indicative of niche divergence.

Conclusion

The results suggest that the relative importance of niche conservatism and divergence differed among the clades of Xiphophorus and that traits associated with niche evolution may be more evolutionarily labile in the platyfishes. Our results ultimately suggest that the taxonomic scale of tests for conservatism and divergence could greatly influence inferences of their relative importance in the speciation process.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0593-4) contains supplementary material, which is available to authorized users.

Maintenance of Quantitative Genetic Variance Under Partial Self-Fertilization, with Implications for Evolution of Selfing

We analyze two models of the maintenance of quantitative genetic variance in a mixed-mating system of self-fertilization and outcrossing. In both models purely additive genetic variance is maintained by mutation and recombination under stabilizing selection on the phenotype of one or more quantitative characters. The Gaussian allele model (GAM) involves a finite number of unlinked loci in an infinitely large population, with a normal distribution of allelic effects at each locus within lineages selfed for τ consecutive generations since their last outcross. The infinitesimal model for partial selfing (IMS) involves an infinite number of loci in a large but finite population, with a normal distribution of breeding values in lineages of selfing age τ. In both models a stable equilibrium genetic variance exists, the outcrossed equilibrium, nearly equal to that under random mating, for all selfing rates, r, up to critical value, [Formula: see text], the purging threshold, which approximately equals the mean fitness under random mating relative to that under complete selfing. In the GAM a second stable equilibrium, the purged equilibrium, exists for any positive selfing rate, with genetic variance less than or equal to that under pure selfing; as r increases above [Formula: see text] the outcrossed equilibrium collapses sharply to the purged equilibrium genetic variance. In the IMS a single stable equilibrium genetic variance exists at each selfing rate; as r increases above [Formula: see text] the equilibrium genetic variance drops sharply and then declines gradually to that maintained under complete selfing. The implications for evolution of selfing rates, and for adaptive evolution and persistence of predominantly selfing species, provide a theoretical basis for the classical view of Stebbins that predominant selfing constitutes an "evolutionary dead end."

Formal properties of the probability of fixation: identities, inequalities and approximations

The formula for the probability of fixation of a new mutation is widely used in theoretical population genetics and molecular evolution. Here we derive a series of identities, inequalities and approximations for the exact probability of fixation of a new mutation under the Moran process (equivalent results hold for the approximate probability of fixation under the Wright-Fisher process, after an appropriate change of variables). We show that the logarithm of the fixation probability has particularly simple behavior when the selection coefficient is measured as a difference of Malthusian fitnesses, and we exploit this simplicity to derive inequalities and approximations. We also present a comprehensive comparison of both existing and new approximations for the fixation probability, highlighting those approximations that induce a reversible Markov chain when used to describe the dynamics of evolution under weak mutation. To demonstrate the power of these results, we consider the classical problem of determining the total substitution rate across an ensemble of biallelic loci and prove that, at equilibrium, a strict majority of substitutions are due to drift rather than selection.

Properties of selected mutations and genotypic landscapes under Fisher's geometric model

The fitness landscape-the mapping between genotypes and fitness-determines properties of the process of adaptation. Several small genotypic fitness landscapes have recently been built by selecting a handful of beneficial mutations and measuring fitness of all combinations of these mutations. Here, we generate several testable predictions for the properties of these small genotypic landscapes under Fisher's geometric model of adaptation. When the ancestral strain is far from the fitness optimum, we analytically compute the fitness effect of selected mutations and their epistatic interactions. Epistasis may be negative or positive on average depending on the distance of the ancestral genotype to the optimum and whether mutations were independently selected, or coselected in an adaptive walk. Simulations show that genotypic landscapes built from Fisher's model are very close to an additive landscape when the ancestral strain is far from the optimum. However, when it is close to the optimum, a large diversity of landscape with substantial roughness and sign epistasis emerged. Strikingly, small genotypic landscapes built from several replicate adaptive walks on the same underlying landscape were highly variable, suggesting that several realizations of small genotypic landscapes are needed to gain information about the underlying architecture of the fitness landscape.

The Utility of Fisher's Geometric Model in Evolutionary Genetics

The accumulation of data on the genomic bases of adaptation has triggered renewed interest in theoretical models of adaptation. Among these models, Fisher Geometric Model (FGM) has received a lot of attention over the last two decades. FGM is based on a continuous multidimensional phenotypic landscape, but it is for the emerging properties of individual mutation effects that it is mostly used. Despite an apparent simplicity and a limited number of parameters, FGM integrates a full model of mutation and epistatic interactions that allows the study of both beneficial and deleterious mutations, and subsequently the fate of evolving populations. In this review, I present the different properties of FGM and the qualitative and quantitative support they have received from experimental evolution data. I later discuss how to estimate the different parameters of the model and outline some future directions to connect FGM and the molecular determinants of adaptation.

Patterns of Macroinvertebrate and Fish Diversity in Freshwater Sulphide Springs

Extreme environments are characterised by the presence of physicochemical stressors and provide unique study systems to address problems in evolutionary ecology research. Sulphide springs provide an example of extreme freshwater environments; because hydrogen sulphide’s adverse physiological effects induce mortality in metazoans even at micromolar concentrations. Sulphide springs occur worldwide, but while microbial communities in sulphide springs have received broad attention, little is known about macroinvertebrates and fish inhabiting these toxic environments. We reviewed qualitative occurrence records of sulphide spring faunas on a global scale and present a quantitative case study comparing diversity patterns in sulphidic and adjacent non-sulphidic habitats across replicated river drainages in Southern Mexico. While detailed studies in most regions of the world remain scarce, available data suggests that sulphide spring faunas are characterised by low species richness. Dipterans (among macroinvertebrates) and cyprinodontiforms (among fishes) appear to dominate the communities in these habitats. At least in fish, there is evidence for the presence of highly endemic species and populations exclusively inhabiting sulphide springs. We provide a detailed discussion of traits that might predispose certain taxonomic groups to colonize sulphide springs, how colonizers subsequently adapt to cope with sulphide toxicity, and how adaptation may be linked to speciation processes.

Estimating the duration of speciation from phylogenies

Speciation is not instantaneous but takes time. The protracted birth–death diversification model incorporates this fact and predicts the often observed slowdown of lineage accumulation toward the present. The mathematical complexity of the protracted speciation model has barred estimation of its parameters until recently a method to compute the likelihood of phylogenetic branching times under this model was outlined (Lambert et al. 2014). Here, we implement this method and study using simulated phylogenies of extant species how well we can estimate the model parameters (rate of initiation of speciation, rate of extinction of incipient and good species, and rate of completion of speciation) as well as the duration of speciation, which is a combination of the aforementioned parameters. We illustrate our approach by applying it to a primate phylogeny. The simulations show that phylogenies often do not contain enough information to provide unbiased estimates of the speciation-initiation rate and the extinction rate, but the duration of speciation can be estimated without much bias. The estimate of the duration of speciation for the primate clade is consistent with literature estimates. We conclude that phylogenies combined with the protracted speciation model provide a promising way to estimate the duration of speciation.