First passage time to allopatric speciation

CO1 barcodes resolve an asymmetric biphyletic clade for Diabrotica undecimpunctata subspecies and provide nucleotide variants for differentiation from related lineages using real-time PCR

Diabrotica undecimpunctata is a multivoltine polyphagous beetle species that has long been documented as a significant agricultural pest throughout its native range in North America. This beetle can vector bacterial and viral plant pathogens that result in major losses to crops such as cucumber and soybean. Many countries outside the Americas treat D. undecimpunctata as a species of quarantine importance, while in the USA only the subspecies D. u. duodecimnotata is subject to quarantine, to prevent introduction from Mexico. Identification of D. undecimpunctata on the basis of morphology alone can be complicated given the use of conflicting characters in the description of some subspecific taxa. To better understand relationships among D. undecimpunctata subspecies and other related species, we sequenced mitochondrial cytochrome oxidase 1 (CO1) and nuclear internal transcribed spacer 2 (ITS2) DNA from individuals in different subspecific taxa and across different parts of the species range using museum samples and interceptions. When our data were combined with publicly available Diabrotica data, no pattern of divergence consistent with the currently recognized subspecific designations was found. In addition, we compared phylogenetic patterns in CO1 data from the congener D. virgifera to demonstrate the utility of mitochondrial data in resolving subspecies. From the CO1 data, a diagnostic real-time PCR assay was developed that could successfully identify all haplotypes within the large D. undecimpunctata clade for use in surveys and identification at ports of entry. These findings underscore the need to resolve molecular and morphological datasets into cogent, lineage-based groupings. Such efforts will provide an evolutionary context for the study of agriculturally important attributes of Diabrotica such as host preferences, xenobiotic metabolism, and natural and anthropogenic patterns of dispersal.

Diversity patterns and speciation processes in a two-island system with continuous migration

Geographic isolation is a central mechanism of speciation, but perfect isolation of populations is rare. Although speciation can be hindered if gene flow is large, intermediate levels of migration can enhance speciation by introducing genetic novelty in the semi-isolated populations or founding small communities of migrants. Here, we consider a two-island neutral model of speciation with continuous migration and study diversity patterns as a function of the migration probability, population size, and number of genes involved in reproductive isolation (dubbed as genome size). For small genomes, low levels of migration induce speciation on the islands that otherwise would not occur. Diversity, however, drops sharply to a single species inhabiting both islands as the migration probability increases. For large genomes, sympatric speciation occurs even when the islands are strictly isolated. Then species richness per island increases with the probability of migration, but the total number of species decreases as they become cosmopolitan. For each genome size, there is an optimal migration intensity for each population size that maximizes the number of species. We discuss the observed modes of speciation induced by migration and how they increase species richness in the insular system while promoting asymmetry between the islands and hindering endemism.

Evolution of an Amazonian Fish Is Driven by Allopatric Divergence Rather Than Ecological Divergence

Lowland central Amazonia is characterized by heterogeneous riverscapes dominated by two chemically divergent water types: black (ion-poor, rich in dissolved organic carbonate and acidic) and white (rich in nutrient and turbid) waters. Recent phylogeographic and genomic studies have associated the ecotone formed by these environments to an ecologically driven genetic divergence between fish present in both water types. With the objective of better understanding the evolutionary forces behind the central Amazonian teleostean diversification, we sampled 240 Mesonauta festivus from 12 sites on a wide area of the Amazonian basin. These sites included three confluences of black and white water environments to seek for repeated evidences of ecological divergence at the junction of these ecotones. Results obtained through our genetic assessment based on 41,268 single nucleotide polymorphism (SNPs) contrast with previous findings and support a low influence of diverging water physicochemical characteristics on the genetic structuration of M. festivus populations. Conversely, we detected patterns of isolation by downstream water current and evidence of past events of vicariance potentially linked to the Amazon River formation. Using a combination of population genetics, phylogeographic analysis and environmental association models, we decomposed the spatial and environmental genetic variances to assess which evolutionary forces shaped inter-population differences in M. festivus’ genome. Our sampling design, comprising three confluences of black and white water rivers, supports the main role of evolution by allopatry. While an ecologically driven evolution admittedly played a role in Amazonian fish diversification, we argue that neutral evolutionary processes explain most of the divergence between M. festivus populations.

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.

Understanding evolutionary and ecological dynamics using a continuum limit

Continuum limits in the form of stochastic differential equations are typically used in theoretical population genetics to account for genetic drift or more generally, inherent randomness of the model. In evolutionary game theory and theoretical ecology, however, this method is used less frequently to study demographic stochasticity. Here, we review the use of continuum limits in ecology and evolution. Starting with an individual-based model, we derive a large population size limit, a (stochastic) differential equation which is called continuum limit. By example of the Wright-Fisher diffusion, we outline how to compute the stationary distribution, the fixation probability of a certain type, and the mean extinction time using the continuum limit. In the context of the logistic growth equation, we approximate the quasi-stationary distribution in a finite population.

Recurrent speciation rates on islands decline with species number

In an archipelagic system, species diversity is maintained and determined by the balance among speciation, extinction and migration. As the number of species increases, the average population size of each species decreases, and the extinction likelihood of any given species grows. By contrast, the role of reduced population size in geographic speciation has received comparatively less research attention. Here, to study the rate of recurrent speciation, we adopted a simple multi-species two-island model and considered symmetric interspecific competition on each island. As the number of species increases on an island, the competition intensifies, and the size of the resident population decreases. By contrast, the number of migrants is likely to exhibit a weaker than proportional relationship with the size of the source population due to rare oceanic dispersal. If this is the case, as the number of species on the recipient island increases, the impact of migration strengthens and decelerates the occurrence of further speciation events. According to our analyses, the number of species can be stabilized at a finite level, even in the absence of extinction.

A tipping point in parapatric speciation

More than two loci are involved in reproductive isolation in most cases of putative recent speciation. We study the speciation between two geographically isolated populations connected by infrequent migration, in which incompatibility is controlled by quantitative loci. Incompatibility genetic distance is defined as the fraction of compatibility controlling loci that are different between individuals. Speciation is established when genetic distance reaches a threshold level in spite of occasional migration and subsequent hybridization that reduce genetic distance. With stochastic analysis, we investigate how the time to speciation depends on the manner in which the magnitude of incompatibility increases with genetic distance. Results are: (1) The time to speciation is short if the migration rate is smaller than the mutation rate, or if intermediate levels of genetic distance cause mild incompatibility, making migrants less effective in reducing genetic distance. (2) Genetic distance may fluctuate around a positive quasi-equilibrium level for a long time, and suddenly show a quick passage to speciation when it goes beyond a "tipping point." Notably a gradual increase in incompatibility can result in a sudden and rapid formation of a new species. (3) Speciation becomes very slow if incompatibility is effective for individuals differing at only one locus. These findings provide testable predictions on reproductive traits controlled by specific incompatibility accumulation forms that facilitate the speciation process.

Parapatric speciation in three islands: dynamics of geographical configuration of allele sharing

We studied the time to speciation by geographical isolation for a species living on three islands connected by rare migration. We assumed that incompatibility was controlled by a number of quantitative loci and that individuals differing in loci by more than a threshold did not mix genetically with each other. For each locus, we defined the geographical configuration (GC), which specifies islands with common alleles, and traced the stochastic transitions between different GCs. From these results, we calculated the changes in genetic distances. As a single migration event provides an opportunity for transitions in multiple loci, the GCs of different loci are correlated, which can be evaluated by constructing the stochastic differential equations of the number of loci with different GCs. Our model showed that the low number of incompatibility loci facilitates parapatric speciation and that migrants arriving as a group shorten the waiting time to speciation compared with the same number of migrants arriving individually. We also discuss how speciation rate changes with geographical structure.

A forecast for extinction debt in the presence of speciation

Predicting biodiversity relaxation following a disturbance is of great importance to conservation biology. Recently-developed models of stochastic community assembly allow us to predict the evolution of communities on the basis of mechanistic processes at the level of individuals. The neutral model of biodiversity, in particular, has provided closed-form solutions for the relaxation of biodiversity in isolated communities (no immigration or speciation). Here, we extend these results by deriving a relaxation curve for a neutral community in which new species are introduced through the mechanism of random fission speciation (RFS). The solution provides simple closed-form expressions for the equilibrium species richness, the relaxation time and the species-individual curve, which are good approximation to the more complicated formulas existing for the same model. The derivation of the relaxation curve is based on the assumption of a broken-stick species-abundance distribution (SAD) as an initial community configuration; yet for commonly observed SADs, the maximum deviation from the curve does not exceed 10%. Importantly, the solution confirms theoretical results and observations showing that the relaxation time increases with community size and thus habitat area. Such simple and analytically tractable models can help crystallize our ideas on the leading factors affecting biodiversity loss.

Smallness of the number of incompatibility loci can facilitate parapatric speciation

We studied the time to speciation by geographic isolation for a species living on two islands connected by infrequent migration. Assumptions were that incompatibility was controlled by a finite number of quantitative loci, and individuals differing in loci of more than some threshold fraction do not mix genetically with each other. We also assumed sexual haploid species, each population being nearly monomorphic, and free recombination between loci for within-population processes. The genetic distance (defined as the fraction of loci differing between populations) followed stochastic processes, which were analyzed by means of stochastic differential equations, diffusion equations, and individual-based simulations. The distance increases by the accumulation of novel mutations but decreases by migration and hybridization. It may converge to a quasi-equilibrium around which it fluctuates thereafter. If the threshold fraction of speciation is controlled, the smallness of the number of incompatibility loci enhanced the magnitude of fluctuation around the quasi-equilibrium and shortened the time to speciation considerably. Novel species were created by mutation accumulation and repeated infrequent migration, and the rate of species creation was the fastest for an intermediate rate of migration. A smaller number of loci increased the optimal migration rate and the species creation rate.

Repeated landmass reformation limits diversification in the widespread littoral zone mosquito Anopheles sundaicus sensu lato in the Indo-Oriental Region

Southeast Asia harbours abundant biodiversity, hypothesized to have been generated by Pliocene and Pleistocene climatic and environmental change. Vicariance between the island of Borneo, the remaining Indonesian archipelago and mainland Southeast Asia caused by elevated sea levels during interglacial periods has been proposed to lead to diversification in the littoral zone mosquito Anopheles (Cellia) sundaicus (Rodenwaldt) sensu lato. To test this biogeographical hypothesis, we inferred the population history and assessed gene flow of A. sundaicus s.l. sampled from 18 populations across its pan-Asian species range, using sequences from mitochondrial cytochrome c oxidase subunit 1 (CO1), the internal transcribed spacer 2 (ITS2) and the mannose phosphate isomerase (Mpi) gene. A hypothesis of ecological speciation for A. sundaicus involving divergent adaptation to brackish and freshwater larval habitats was also previously proposed, based on a deficiency of heterozygotes for Mpi allozyme alleles in sympatry. This hypothesis was not supported by Mpi sequence data, which exhibited no fixed differences between brackish and freshwater larval habitats. Mpi and CO1 supported the presence of up to eight genetically distinct population groupings. Counter to the hypothesis of three allopatric species, divergence was often no greater between Borneo, Sumatra/Java and the Southeast Asian mainland than it was between genetic groupings within these landmasses. An isolation-with-migration (IM) model indicates recurrent gene flow between the current major landmasses. Such gene flow would have been possible during glacial periods when the current landmasses merged, presenting opportunities for dispersal along expanding and contracting coastlines. Consequently, Pleistocene climatic variation has proved a homogenizing, rather than diversifying, force for A. sundaicus diversity.

Modelling biological evolution: recent progress, current challenges and future direction

Mathematical modelling is widely recognized as a powerful and convenient theoretical tool for investigating various aspects of biological evolution and explaining the existing genetic complexity of the real world. It is increasingly apparent that understanding the key mechanisms involved in the processes of species biodiversity, natural selection and inheritance, patterns of animal behaviour and coevolution of species in complex ecological systems is simply impossible by means of laboratory experiments and field observations alone. Mathematical models are so important because they provide wide-ranging exploration of the problem without a need for experiments with biological systems—which are usually expensive, often require long time and can be potentially dangerous. However, as the number of theoretical works on modelling biological evolution is constantly accelerating each year as different mathematical frameworks and various aspects of evolutionary problems are considered, it is often hard to avoid getting lost in such an immense flux of publications. The aim of this issue of Interface Focus is to provide a useful guide to important recent findings in some key areas in modelling biological evolution, to refine the existing challenges and to outline possible future directions. In particular, the following topics are addressed here by world-leading experts in the modelling of evolution: (i) the origins of biodiversity observed in ecosystems and communities; (ii) evolution of decision-making by animals and the optimal strategy of populations; (iii) links between evolutionary and ecological processes across different time scales; (iv) quantification of biological information in evolutionary models; and (v) linking theoretical models with empirical data. Most of the works presented here are in fact contributed papers from the international conference ‘Modelling Biological Evolution’ (MBE 2013), which took place in Leicester, UK, in May 2013 and brought together theoreticians and empirical evolutionary biologists with the main aim of creating debates and productive discussions between them. Finally, we should emphasize that the individual papers in this issue are not limited to only one of the topics mentioned above, but often lie at the interface of them.