SYMPATRIC SEA SHELLS ALONG THE SEA'S SHORE: THE GEOGRAPHY OF SPECIATION IN THE MARINE GASTROPOD TEGULA

Uncertainty and controversy surround the geographical and ecological circumstances that create genetic differences between populations that eventually lead to reproductive isolation. Two aspects of marine organisms further complicate this situation: (1) many species possess planktonic larvae capable of great dispersal; and (2) obvious barriers to movement between populations are rare. Past studies of speciation in the sea have focussed on identifying the effects of past land barriers and on biogeographical breakpoints. However, assessing the role such undeniable barriers actually play in the initial divergence leading to reproductive isolation requires phylogenetic studies of recent radiations living in varying degrees of sympatry and allopatry to see which barriers (if any) tend to separate sister species. Here I infer phylogenetic relationship between 23 species of the marine snail Tegula using DNA sequences from two regions of the mitochondrial genome: cytochrome c oxidase I (COI) and the small ribosomal subunit (12S) These snails possess planktonic larvae with moderate dispersal capabilities and have speciated rapidly with over 40 extant species arising since the genus first appeared in the mid-Miocene (about 15 M.Y.B.P.). Trees constructed from the COI and 12S regions (which yielded 205 and 137 phylogenetically informative sites, respectively) were robust with respect to tree-building method, bootstrapping, and the relative weightings of transitions, transversions, and gaps Within clades where all extant species have been sampled, five of six identified sister species pairs broadly coexist on the same side of biogeographical boundaries. These data suggest strong geographical barriers to gene flow may not always be required for speciation in the sea; transient allopatry or even ecological barriers may suffice. A survey of the geographic distributions of marine radiations suggests that coastal distributions may favor the sympatry of sister taxa more than island distributions do.     

Gene flow,divergent selection and resistance to introgression in two species of morning glories (Ipomoea)

Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggest that sufficiently strong divergent selection can overpower gene flow, leading to loci that are highly differentiated compared to others. However, there are also alternative explanations for this pattern. Independent evidence that loci in highly differentiated regions are under divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here, we present multiple lines of evidence that many of the highly divergent SNPs in a pair of sister morning glory species, Ipomoea cordatotriloba and I. lacunosa, are the result of divergent selection in the face of gene flow. We analysed a SNP data set across the genome to assess the amount of gene flow, resistance to introgression and patterns of selection on loci resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with interspecific gene flow in sympatry. Gene flow appears to be substantially greater from I. lacunosa to I. cordatotriloba than in the reverse direction, resulting in sympatric and allopatric I. cordatotriloba being substantially more different than sympatric and allopatric I. lacunosa. Many SNPs highly differentiated in allopatry have experienced divergent selection, and, despite gene flow in sympatry, resist homogenization in sympatry. Finally, five out of eight floral and inflorescence characteristics measured exhibit asymmetric convergence in sympatry. Consistent with the pattern of gene flow, I. cordatotriloba traits become much more like those of I. lacunosa than the reverse. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.     

THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION‐WITH‐GENE‐FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING

During speciation‐with‐gene‐flow, effective migration varies across the genome as a function of several factors, including proximity of selected loci, recombination rate, strength of selection, and number of selected loci. Genome scans may provide better empirical understanding of the genome‐wide patterns of genetic differentiation, especially if the variance due to the previously mentioned factors is partitioned. In North American lake whitefish (Coregonus clupeaformis), glacial lineages that diverged in allopatry about 60,000 years ago and came into contact 12,000 years ago have independently evolved in several lakes into two sympatric species pairs (a normal benthic and a dwarf limnetic). Variable degrees of reproductive isolation between species pairs across lakes offer a continuum of genetic and phenotypic divergence associated with adaptation to distinct ecological niches. To disentangle the complex array of genetically based barriers that locally reduce the effective migration rate between whitefish species pairs, we compared genome‐wide patterns of divergence across five lakes distributed along this divergence continuum. Using restriction site associated DNA (RAD) sequencing, we combined genetic mapping and population genetics approaches to identify genomic regions resistant to introgression and derive empirical measures of the barrier strength as a function of recombination distance. We found that the size of the genomic islands of differentiation was influenced by the joint effects of linkage disequilibrium maintained by selection on many loci, the strength of ecological niche divergence, as well as demographic characteristics unique to each lake. Partial parallelism in divergent genomic regions likely reflected the combined effects of polygenic adaptation from standing variation and independent changes in the genetic architecture of postzygotic isolation. This study illustrates how integrating genetic mapping and population genomics of multiple sympatric species pairs provide a window on the speciation‐with‐gene‐flow mechanism.     

Gene flow-dependent genomic divergence between Anopheles gambiae M and S forms

Anopheles gambiae sensu stricto exists as two often-sympatric races termed the M and S molecular forms, characterized by fixed differences at an X-linked marker. Extreme divergence between M and S forms at pericentromeric "genomic islands" suggested that selection on variants therein could be driving interform divergence in the presence of ongoing gene flow, but recent work has detected much more widespread genomic differentiation. Whether such genomic islands are important in reproductive isolation or represent ancestral differentiation preserved by low recombination is currently unclear. A critical test of these competing hypotheses could be provided by comparing genomic divergence when rates of recent introgression vary. We genotyped 871 single nucleotide polymorphisms (SNPs) in A. gambiae sensu stricto from locations of M and S sympatry and allopatry, encompassing the full range of observed hybridization rates (0-25%). M and S forms were readily partitioned based on genomewide SNP variation in spite of evidence for ongoing introgression that qualitatively reflects hybridization rates. Yet both the level and the heterogeneity of genomic divergence varied markedly in line with levels of introgression. A few genomic regions of differentiation between M and S were common to each sampling location, the most pronounced being two centromere-proximal speciation islands identified previously but with at least one additional region outside of areas expected to exhibit reduced recombination. Our results demonstrate that extreme divergence at genomic islands does not simply represent segregating ancestral polymorphism in regions of low recombination and can be resilient to substantial gene flow. This highlights the potential for islands comprising a relatively small fraction of the genome to play an important role in early-stage speciation when reproductive isolation is limited.     

Recombination and Speciation: Loci Near Centromeres Are More Differentiated Than Loci Near Telomeres Between Subspecies of the European Rabbit (Oryctolagus cuniculus)

Recent empirical and theoretical studies suggest that regions of restricted recombination play an important role in the formation of new species. To test this idea, we studied nucleotide variation in two parapatric subspecies of the European rabbit (Oryctolagus cuniculus). We surveyed five loci near centromeres, where recombination is expected to be suppressed, and five loci near telomeres, where recombination is expected to be higher. We analyzed this multilocus data set using a divergence-with-gene flow framework and we report three main findings. First, we estimated that these subspecies diverged ~1.8 MYA and maintained large effective population sizes (O. c. algirus N_e ≈ 1,600,000 and O. c. cuniculus N_e ≈ 780,000). Second, we rejected a strict allopatric model of divergence without gene flow; instead, high rates of gene flow were inferred in both directions. Third, we found different patterns between loci near centromeres and loci near telomeres. Loci near centromeres exhibited higher levels of linkage disequilibrium than loci near telomeres. In addition, while all loci near telomeres showed little differentiation between subspecies, three of five loci near centromeres showed strong differentiation. These results support a view of speciation in which regions of low recombination can facilitate species divergence in the presence of gene flow.     

Localizing FST outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation‐with‐gene‐flow

Populations that maintain phenotypic divergence in sympatry typically show a mosaic pattern of genomic divergence, requiring a corresponding mosaic of genomic isolation (reduced gene flow). However, mechanisms that could produce the genomic isolation required for divergence‐with‐gene‐flow have barely been explored, apart from the traditional localized effects of selection and reduced recombination near centromeres or inversions. By localizing F_ST outliers from a genome scan of wild pea aphid host races on a Quantitative Trait Locus (QTL) map of key traits, we test the hypothesis that between‐population recombination and gene exchange are reduced over large ‘divergence hitchhiking’ (DH) regions. As expected under divergence hitchhiking, our map confirms that QTL and divergent markers cluster together in multiple large genomic regions. Under divergence hitchhiking, the nonoutlier markers within these regions should show signs of reduced gene exchange relative to nonoutlier markers in genomic regions where ongoing gene flow is expected. We use this predicted difference among nonoutliers to perform a critical test of divergence hitchhiking. Results show that nonoutlier markers within clusters of F_ST outliers and QTL resolve the genetic population structure of the two host races nearly as well as the outliers themselves, while nonoutliers outside DH regions reveal no population structure, as expected if they experience more gene flow. These results provide clear evidence for divergence hitchhiking, a mechanism that may dramatically facilitate the process of speciation‐with‐gene‐flow. They also show the power of integrating genome scans with genetic analyses of the phenotypic traits involved in local adaptation and population divergence.     

Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae

Previous efforts to uncover the genetic underpinnings of ongoing ecological speciation of the M and S forms of the African malaria vector Anopheles gambiae revealed two centromere‐proximal islands of genetic divergence on X and chromosome 2. Under the assumption of considerable ongoing gene flow between M and S, these persistently divergent genomic islands were widely considered to be ‘speciation islands’. In the course of microarray‐based divergence mapping, we discovered a third centromere‐associated island of divergence on chromosome 3, which was validated by targeted re‐sequencing. To test for genetic association between the divergence islands on all three chromosomes, SNP‐based assays were applied in four natural populations of M and S spanning West, Central and East Africa. Genotyping of 517 female M and S mosquitoes revealed nearly complete linkage disequilibrium between the centromeres of the three independently assorting chromosomes. These results suggest that despite the potential for inter‐form gene flow through hybridization, actual (realized) gene flow between M and S may be substantially less than commonly assumed and may not explain most shared variation. Moreover, the possibility of very low gene flow calls into question whether diverged pericentromeric regions—characterized by reduced levels of variation and recombination—are in fact instrumental rather than merely incidental to the speciation process.     

Genomic Evidence for Speciation with Gene Flow in Broadcast Spawning Marine Invertebrates

How early stages of speciation in free-spawning marine invertebrates proceed is poorly understood. The Western Pacific abalones, Haliotis discus, H. madaka, and H. gigantea, occur in sympatry with shared breeding season and are capable of producing viable F₁ hybrids in spite of being ecologically differentiated. Population genomic analyses revealed that although the three species are genetically distinct, there is evidence for historical and ongoing gene flow among these species. Evidence from demographic modeling suggests that reproductive isolation among the three species started to build in allopatry and has proceeded with gene flow, possibly driven by ecological selection. We identified 27 differentiation islands between the closely related H. discus and H. madaka characterized by high F_ST and d_A, but not high d_XY values, as well as high genetic diversity in one H. madaka population. These genomic signatures suggest differentiation driven by recent ecological divergent selection in presence of gene flow outside of the genomic islands of differentiation. The differentiation islands showed low polymorphism in H. gigantea, and both high F_ST, d_XY, and d_A values between H. discus and H. gigantea, as well as between H. madaka and H. gigantea. Collectively, the Western Pacific abalones appear to occupy the early stages speciation continuum, and the differentiation islands associated with ecological divergence among the abalones do not appear to have acted as barrier loci to gene flow in the younger divergences but appear to do so in older divergences.     

Parallel evolution and ecological selection: replicated character displacement in spadefoot toads

Ecological character displacement—trait evolution stemming from selection to lessen resource competition between species—is most often inferred from a pattern in which species differ in resource-use traits in sympatry but not in allopatry, and in which sympatric populations within each species differ from conspecific allopatric populations. Yet, without information on population history, the presence of a divergent phenotype in multiple sympatric populations does not necessarily imply that there has been repeated evolution of character displacement. Instead, such a pattern may arise if there has been character displacement in a single ancestral population, followed by gene flow carrying the divergent phenotype into multiple, derived, sympatric populations. Here, we evaluate the likelihood of such historical events versus ongoing ecological selection in generating divergence in trophic morphology between multiple populations of spadefoot toad (Spea multiplicata) tadpoles that are in sympatry with a heterospecific and those that are in allopatry. We present both phylogenetic and population genetic evidence indicating that the same divergent trait, which minimizes resource competition with the heterospecific, has arisen independently in multiple sympatric populations. These data, therefore, provide strong indirect support for competition''s role in divergent trait evolution.     

Reanalysis suggests that genomic islands of speciation are due to reduced diversity,not reduced gene flow

The metaphor of ‘genomic islands of speciation’ was first used to describe heterogeneous differentiation among loci between the genomes of closely related species. The biological model proposed to explain these differences was that the regions showing high levels of differentiation were resistant to gene flow between species, while the remainder of the genome was being homogenized by gene flow and consequently showed lower levels of differentiation. However, the conditions under which such differentiation can occur at multiple unlinked loci are restrictive; additionally, essentially, all previous analyses have been carried out using relative measures of divergence, which can be misleading when regions with different levels of recombination are compared. Here, we test the model of differential gene flow by asking whether absolute divergence is also higher in the previously identified ‘islands’. Using five species pairs for which full sequence data are available, we find that absolute measures of divergence are not higher in genomic islands. Instead, in all cases examined, we find reduced diversity in these regions, a consequence of which is that relative measures of divergence are abnormally high. These data therefore do not support a model of differential gene flow among loci, although islands of relative divergence may represent loci involved in local adaptation. Simulations using the program IMa2 further suggest that inferences of any gene flow may be incorrect in many comparisons. We instead present an alternative explanation for heterogeneous patterns of differentiation, one in which postspeciation selection generates patterns consistent with multiple aspects of the data.     

Divergence and isolation of cryptic sympatric taxa within the annual legume Amphicarpaea bracteata

The amphicarpic annual legume Amphicarpaea bracteata is unusual in producing aerial and subterranean cleistogamous flowers that always self‐fertilize and, less commonly, aerial chasmogamous flowers that outcross. Although both morphologic and genetic variants are known in this highly selfing species, debate continues over whether this variation is continuous, reflecting the segregation of standing genetic variation, or discontinuous, reflecting distinct taxa that rarely intercross. We characterized SNP variation in 128 individuals in southern Wisconsin to assess within‐ and among‐population variation at 3928 SNPs. We also assessed genotype and leaf morphology in an additional 76 individuals to connect phenotypic variation with genetic variation. Genetic variation maps onto three strongly divergent and highly inbred genetic groups showing little relation to site location. Each group has a distinct phenotype, but the divergence of these groups differs from the varietal divisions previously identified based on morphological characters. Like previous authors, we argue that the taxonomy of this species should be revised. Despite extensive sympatry, estimates of among‐group migration rates are low, and hybrid individuals were at low frequency (<2%) in our dataset. Restricted gene flow likely results from high selfing rates and partial reproductive incompatibility as evidenced by the U‐shaped distribution of pairwise F_ST values reflecting “islands” of genomic divergence. These islands may be associated with hybrid incompatibility loci that arose in allopatry. The coexistence of lineages within sites may reflect density‐dependent attack by species‐specific strains of pathogenic fungi and/or root‐nodulating bacteria specializing on distinct genotypes.     

Hawthorn-infesting populations of Rhagoletis pomonella in Mexico and speciation mode plurality

Categorizing speciation into dichotomous allopatric versus nonallopatric modes may not always adequately describe the geographic context of divergence for taxa. If some of the genetic changes generating inherent barriers to gene flow between populations evolved in geographic isolation, whereas others arose in sympatry, then the mode of divergence would be mixed. The apple maggot fly, Rhagoletis pomonella, has contributed to this emerging concept of a mixed speciation mode "plurality." Genetic studies have implied that a source of diapause life-history variation associated with inversions and contributing to sympatric host race formation and speciation for R. pomonella in the United States may have introgressed from the Eje Volcanico Trans Mexicano (EVTM; a.k.a. the Altiplano) in the past. A critical unresolved issue concerning the introgression hypothesis is how past gene flow occurred given the current 1200-km disjunction in the ranges of hawthorn-infesting flies in the EVTM region of Mexico and the southern extreme of the U.S. population in Texas. Here, we report the discovery of a hawthorn-infesting population of R. pomonella in the Sierra Madre Oriental Mountains (SMO) of Mexico. Sequence data from 15 nuclear loci and mitochondrial DNA imply that the SMO flies are related to, but still different from, U.S. and EVTM flies. The host affiliations, diapause characteristics, and phylogeography of the SMO population are consistent with it having served as a conduit for gene flow between Mexico and the United States. We also present evidence suggesting greater permeability of collinear versus rearranged regions of the genome to introgression, in accord with recent models of chromosomal speciation. We discuss the implications of the results in the context of speciation mode plurality. We do not argue for abandoning the terms sympatry or allopatry, but caution that categorizing divergence into either/or geographic modes may not describe the genetic origins of all species. For R. pomonella in the United States, the proximate selection pressures triggering race formation and speciation stem from sympatric host shifts. However, some of the phenological variation contributing to host-related ecological adaptation and reproductive isolation in sympatry at the present time appears to have an older history, having originated and become packaged into inversion polymorphism in allopatry.     

Space Use Variation in Co-Occurring Sister Species: Response to Environmental Variation or Competition?

Coexistence often involves niche differentiation either as the result of environmental divergence, or in response to competition. Disentangling the causes of such divergence requires that environmental variation across space is taken into account, which is rarely done in empirical studies. We address the role of environmental variation versus competition in coexistence between two rodent species: Rhabdomys bechuanae (bechuanae) and Rhabdomys dilectus dilectus (dilectus) comparing their habitat preference and home range (HR) size in areas with similar climates, where their distributions abut (allopatry) or overlap (sympatry). Using Outlying Mean Index analyses, we test whether habitat characteristics of the species deviate significantly from a random sample of available habitats. In allopatry, results suggest habitat selection: dilectus preferring grasslands with little bare soil while bechuanae occurring in open shrublands. In sympatry, shrubland type habitats dominate and differences are less marked, yet dilectus selects habitats with more cover than bechuanae. Interestingly, bechuanae shows larger HRs than dilectus, and both species display larger HRs in sympatry. Further, HR overlaps between species are lower than expected. We discuss our results in light of data on the phylogeography of the genus and propose that evolution in allopatry resulted in adaptation leading to different habitat preferences, even at their distribution margins, a divergence expected to facilitate coexistence. However, since sympatry occurs in sites where environmental characteristics do not allow complete species separation, competition may explain reduced inter-species overlap and character displacement in HR size. This study reveals that both environmental variation and competition may shape species coexistence.     

Stifled sex in sympatry: patterns of sexual incompatibility among desmognathine salamanders

Sexual incompatibility due to differences in mate-recognition systems can be an important factor in preventing hybridization and gene flow between animal populations in sympatry. We tested in the laboratory for sexual incompatibility between populations of two species of desmognathine salamanders that occur in sympatry in south-eastern Kentucky, North America, Desmognathus monticola and D. welteri (Caudata: Plethodontidae: Desmognathinae). Spermatophore deposition and insemination (two related measures of sexual success) were frequent in intraspecific encounters, but interspecific encounters never resulted in the deposition of spermatophores by males (Experiment 1). The sexual behaviour patterns of these two species are similar qualitatively, but all encounters staged between them failed to progress beyond the most preliminary of courtship interactions (Experiment 2), perhaps due to species differences in chemosensory communication. Our data on sexual incompatibility between D. monticola and D. welteri are similar to those available for other desmognathine taxa that occur in sympatry. Review of a broader data-set on patterns of sexual incompatibility both within and between species, and in allopatry and in sympatry, provides evidence for both divergence of mate-recognition systems in allopatry and enhancement of sexual incompatibility in sympatry for desmognathine salamanders. We hypothesize that diversification in allopatry may be a consequence of natural and/or sexual selection acting to promote sexual success within populations. Enhancement in sympatry may be a consequence of subsequent selection for accurate species recognition under the threat of hybridization or gene flow between species.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 367–375.     

Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry

Hybrid zones are geographic regions where isolating barriers between divergent populations are challenged by admixture. Identifying factors that facilitate or inhibit hybridization in sympatry can illuminate the processes that maintain those reproductive barriers. We analysed patterns of hybridization and phenotypic variation across two newly discovered hybrid zones between three subspecies of barn swallow (Hirundo rustica). These subspecies differ in ventral coloration and wing length, traits that are targets of sexual and natural selection, respectively, and are associated with genome‐wide differentiation in allopatry. We tested the hypothesis that the degree of divergence in these traits is associated with the extent of hybridization in secondary contact. We applied measures of population structure based on >23,000 SNPs to confirm that named subspecies correspond to distinct genomic clusters, and assessed coincidence between geographic clines for ancestry and phenotype. Although gene flow was ongoing across both hybrid zones and pairwise F_ST between subspecies was extremely low, we found striking differences in the extent of hybridization. In the more phenotypically differentiated subspecies pair, clines for ancestry, wing length and ventral coloration were steep and coincident, suggestive of strong isolation and, potentially, selection associated with phenotype. In the less phenotypically differentiated pair, gene flow and phenotypic variation occurred over a wide geographic span, indicative of weaker isolation. Traits associated with genome‐wide differentiation in allopatry may thus also contribute to isolation in sympatry. We discuss potentially important additional roles for evolutionary history and ecology in shaping variation in the extent hybridization between closely related pairs of subspecies.     

Evidence for large-scale effects of competition: niche displacement in Canada lynx and bobcat

Determining the patterns, causes and consequences of character displacement is central to our understanding of competition in ecological communities. However, the majority of competition research has occurred over small spatial extents or focused on fine-scale differences in morphology or behaviour. The effects of competition on broad-scale distribution and niche characteristics of species remain poorly understood but critically important. Using range-wide species distribution models, we evaluated whether Canada lynx (Lynx canadensis) or bobcat (Lynx rufus) were displaced in regions of sympatry. Consistent with our prediction, we found that lynx niches were less similar to those of bobcat in areas of sympatry versus allopatry, with a stronger reliance on snow cover driving lynx niche divergence in the sympatric zone. By contrast, bobcat increased niche breadth in zones of sympatry, and bobcat niches were equally similar to those of lynx in zones of sympatry and allopatry. These findings suggest that competitively disadvantaged species avoid competition at large scales by restricting their niche to highly suitable conditions, while superior competitors expand the diversity of environments used. Our results indicate that competition can manifest within climatic niche space across species’ ranges, highlighting the importance of biotic interactions occurring at large spatial scales on niche dynamics.     

Patterns of Genetic and Reproductive Traits Differentiation in Mainland vs. Corsican Populations of Bumblebees

Populations on islands often exhibit lower levels of genetic variation and ecomorphological divergence compared to their mainland relatives. While phenotypic differentiation in characters, such as size or shape among insular organisms, has been well studied, insular differentiation in quantitative reproductive traits involved in chemical communication has received very little attention to date. Here, we investigated the impact of insularity on two syntopic bumblebee species pairs: one including species that are phylogenetically related (Bombus terrestris and B. lucorum), and the other including species that interact ecologically (B. terrestris and its specific nest inquiline B. vestalis). For each bumblebee species, we characterized the patterns of variation and differentiation of insular (Corsican) vs. mainland (European) populations (i) with four genes (nuclear and mitochondrial, 3781 bp) and (ii) in the chemical composition of male marking secretions (MMS), a key trait for mate attraction in bumblebees, by gas chromatography-mass spectrometry (GC-MS). Our results provide evidence for genetic differentiation in Corsican bumblebees and show that, contrary to theoretical expectations, island populations of bumblebees exhibit levels of genetic variation similar to the mainland populations. Likewise, our comparative chemical analyses of MMS indicate that Corsican populations of bumblebees are significantly differentiated from the mainland yet they hold comparative levels of within-population MMS variability compared to the mainland. Therefore, insularity has led Corsican populations to diverge both genetically and chemically from their mainland relatives, presumably through genetic drift, but without a decrease of genetic diversity in island populations. We hypothesize that MMS divergence in Corsican bumblebees was driven by a persistent lack of gene flow with mainland populations and reinforced by the preference of Corsican females for sympatric (Corsican) MMS. The impoverished Corsican bumblebee fauna has not led to relaxation of stabilizing selection on MMS but to consistent differentiation chemical reproductive traits on the island.     

Breaking down barriers in morning glories

One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One problem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the study is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates.     

Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species: size,relative age and chromosomal localization

We analysed the size, relative age and chromosomal localization of nuclear sequences of plastid and mitochondrial origin (NUPTs-nuclear plastid DNA and NUMTs-nuclear mitochondrial DNA) in six completely sequenced plant species. We found that the largest insertions showed lower divergence from organelle DNA than shorter insertions in all species, indicating their recent origin. The largest NUPT and NUMT insertions were localized in the vicinity of the centromeres in the small genomes of Arabidopsis and rice. They were also present in other chromosomal regions in the large genomes of soybean and maize. Localization of NUPTs and NUMTs correlated positively with distribution of transposable elements (TEs) in Arabidopsis and sorghum, negatively in grapevine and soybean, and did not correlate in rice or maize. We propose a model where new plastid and mitochondrial DNA sequences are inserted close to centromeres and are later fragmented by TE insertions and reshuffled away from the centromere or removed by ectopic recombination. The mode and tempo of TE dynamism determines the turnover of NUPTs and NUMTs resulting in their species-specific chromosomal distributions.     

Effects of species invasion on population dynamics,vital rates and life histories of the native species

Invasions occurring in natural environments provide the opportunity to study how vital rates change and life histories evolve in the presence of a competing species. In this work, we estimate differences in reproductive traits, individual growth trajectories, survival, life histories and population dynamics between a native species living in allopatry and in sympatry with an invasive species of the same taxonomic Family. We used as a model system marble trout Salmo marmoratus (native species) and rainbow trout Oncorhynchus mykiss (non-native) living in the Idrijca River (Slovenia). An impassable waterfall separates the stream into two sectors only a few 100 meters apart: a downstream sector in which marble trout live in sympatry with rainbow trout and an upstream sector in which marble trout live in allopatry. We used an overarching modelling approach that uses tag-recapture and genetic data (>2,500 unique marble and rainbow trout were sampled and genotyped) to reconstruct pedigrees, test for synchrony of population dynamics and model survival and growth, while accounting for individual heterogeneity. The population dynamics of the two marble trout populations and of rainbow trout were synchronous. We found higher prevalence of younger parents, higher mortality and lower population density in marble trout living in sympatry with rainbow trout than in marble trout living in allopatry. There were no differences in the average individual growth trajectories between the two marble trout populations. Faster life histories of marble trout living in sympatry with rainbow trout are consistent with predictions of life history theory.