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.     

Mating system and the hybridization between self-compatible Phlox cuspidata and self-incompatible Phlox drummondii

Mating system can impact the frequency of hybridization and therefore the maintenance of species diversity. I evaluate the effects of weak self-incompatibility (SI) in Phlox cuspidata and SI in Phlox drummondii on mating success within species and on hybridization dynamics between species under controlled conditions. The effects of SI on hybridization frequency were assessed by manipulating the relatedness of conspecific pollen and the relative timing of pollen deposition in mixed-donor interspecific pollinations. Selfing as opposed to outcrossing increased hybridization by 16% in P. cuspidata maternal plants and by 48% in P. drummondii maternal plants because self pollen did not compete as well against heterospecific pollen. The relative timing of conspecific versus heterospecific pollen deposition also impacted hybridization. In self-compatible P. cuspidata, the deposition of self pollen 5 h earlier than heterospecific pollen decreased hybridization by 28%. In self-incompatible P. drummondii, a 5 h delay in the deposition of compatible conspecific pollen increased hybridization by 32%. In this hybrid system, early self-pollination can decrease hybridization (but increase inbreeding) by P. cuspidata maternal plants, and SI may increase hybridization by P. drummondii maternal plants.     

Restricted gene flow within and between rapidly diverging Neotropical plant species

Speciation involves the evolution of traits and genetic differences that contribute to reproductive isolation and the cessation of gene flow, and studying closely related species and divergent populations gives insight into how these phenomena proceed. Here, we document patterns of gene flow within and between two members of a rapid Neotropical species radiation, Costus pulverulentus and Costus scaber (Costaceae). These species co‐occur in the tropical rainforest and share pollinators, but are reproductively isolated by a series of prezygotic barriers, some of which show evidence of reinforcement at sympatric sites. Here, we genotype microsatellite markers in plants from eight sites that span the geographical range of both species, including four sympatric sites. We also genotype putative hybrids found at two sympatric sites. We find high levels of genetic isolation among populations within each species and low but detectable levels of introgression between species at sympatric sites. Putative hybrids identified by morphology are consistent with F1 or more advanced hybrids. Our results highlight the effectiveness of prezygotic isolating mechanisms at maintaining species boundaries in young radiations and provide empirical data on levels of gene flow consistent with reinforcement.     

Natural hybridization between an outcrossing and a selfingPhlox (Polemoniaceae): The maternal species of F1 hybrids

Natural F₁ hybrids between the outcrossingPhlox drummondii and the predominantly selfingP. cuspidata were examined to ascertain the proportion of hybrid individuals mothered by each species. Species-specific restriction fragment patterns (both nrDNA and cpDNA) were established as markers, and synthetic hybrids of known parentage were utilized to determine that the chloroplast genome is maternally inherited. Of 89 mature natural hybrids examined, approximately two thirds were mothered byP. drummondii, the outcrosser. That the outcrosser should mother most hybrids is expected since it is dependent upon incoming pollen for fertilization, and hybrids may result when heterospecific pollen is received. The fact that the highly selfingP. cuspidata mothered nearly one third of the hybrids is surprising, and may be related to both pre-zygotic and post-zygotic factors. Which species mothers hybrids has important implications for the potential for introgression as well as its direction.     

Maintaining their genetic distance: Little evidence for introgression between widely hybridizing species of Geum with contrasting mating systems

Within the plant kingdom, many genera contain sister lineages with contrasting outcrossing and inbreeding mating systems that are known to hybridize. The evolutionary fate of these sister lineages is likely to be influenced by the extent to which they exchange genes. We measured gene flow between outcrossing Geum rivale and selfing Geum urbanum, sister species that hybridize in contemporary populations. We generated and used a draft genome of G. urbanum to develop dd‐RAD data scorable in both species. Coalescent analysis of RAD data from allopatric populations indicated that the species diverged 2–3 Mya, and that historical gene flow between them was extremely low (1 migrant every 25 generations). Comparison of genetic divergence between species in sympatry and allopatry, together with an analysis of allele frequencies in potential parental and hybrid populations, provided no evidence of contemporary introgression in sympatric populations. Cluster‐ and species‐specific marker analyses revealed that, apart from four early‐generation hybrids, individuals in sympatric populations fell into two genetically distinct groups that corresponded exactly to their morphological species classification with maximum individual admixture estimates of only 1–3%. However, we did observe joint segregation of four putatively introgressed SNPs across two scaffolds in the G. urbanum population that was associated with significant morphological variation, interpreted as tentative evidence for rare, recent interspecific gene flow. Overall, our results indicate that despite the presence of hybrids in contemporary populations, genetic exchange between G. rivale and G. urbanum has been extremely limited throughout their evolutionary history.     

Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the overlap of ancestral populations. In this study, we performed population genetic analyses, species delimitation, simulations and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito‐nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation–migration analyses, however, revealed near‐zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.     

Fine‐scale geographic patterns of gene flow and reproductive character displacement in Drosophila subquinaria and Drosophila recens

When two species are incompletely isolated, strengthening premating isolation barriers in response to the production of low fitness hybrids may complete the speciation process. Here, we use the sister species Drosophila subquinaria and Drosophila recens to study the conditions under which this reinforcement of species boundaries occurs in natural populations. We first extend the region of known sympatry between these species, and then we conduct a fine‐scale geographic survey of mate discrimination coupled with estimates of gene flow within and admixture between species. Within D. subquinaria, reinforcement is extremely effective: we find variation in mate discrimination both against D. recens males and against conspecific allopatric males on the scale of a few kilometres and in the face of gene flow both from conspecific populations and introgression from D. recens. In D. recens, we do not find evidence for increased mate discrimination in sympatry, even where D. recens is rare, consistent with substantial gene flow throughout the species’ range. Finally, we find that introgression between species is asymmetric, with more from D. recens into D. subquinaria than vice versa. Within each species, admixture is highest in the geographic region where it is rare relative to the other species, suggesting that when hybrids are produced they are of low fitness. In sum, reinforcement within D. subquinaria is effective at maintaining species boundaries, but even when reinforcing selection is strong it may not always result in a pattern of strong reproductive character displacement due to variation in the frequency of hybridization and gene flow from neighbouring populations.     

ON THE COYNE AND ORR‐IGIN OF SPECIES: EFFECTS OF INTRINSIC POSTZYGOTIC ISOLATION,ECOLOGICAL DIFFERENTIATION,X CHROMOSOME SIZE,AND SYMPATRY ON DROSOPHILA SPECIATION

Coyne and Orr found that mating discrimination (premating isolation) evolves much faster between sympatric than allopatric Drosophila species pairs. Their meta‐analyses established that this pattern, expected under reinforcement, is common and that Haldane's rule is ubiquitous in Drosophila species divergence. We examine three possible contributors to the reinforcement pattern: intrinsic postzygotic isolation, dichotomized as to whether hybrid males show complete inviability/sterility; host‐plant divergence, as a surrogate for extrinsic postzygotic isolation; and X chromosome size, whether roughly 20% or 40% of the genome is X‐linked. We focus on “young” species pairs with overlapping ranges, contrasted with allopatric pairs. Using alternative criteria for “sympatry” and tests that compare either level of prezygotic isolation in sympatry or frequency of sympatry, we find no statistically significant effects associated with X chromosome size or our coarse quantifications of intrinsic postzygotic isolation or ecological differentiation. Although sympatric speciation seems very rare in animals, the pervasiveness of the reinforcement pattern and the commonness of range overlap for close relatives indicate that speciation in Drosophila is often not purely allopatric. It remains to determine whether increased premating isolation with sympatry results from secondary contact versus parapatric speciation and what drives this pattern.     

REPRODUCTIVE CHARACTER DISPLACEMENT IN PHLOX

Plants of the red- and pink-flowered P. drummondii were introduced into a natural population of P. cuspidata. Their seeds were progeny-tested, and the percentage hybrid seed determined for each variant. Thirty-eight percent of the seed from the pink variant were hybrid compared to 13% of the red. The difference in hybrid production is best explained by corolla color. The self- and cross-compatibility of nine sympatric and nine allopatric populations were studied in the greenhouse. On the average, sympatric populations are more self-compatible than allopatric populations. Pollen germination is 13.7% vs. 7.3%, the difference being statistically significant. The self-compatibility differential was accompanied by a self seedset differential. On the average, sympatric populations are more cross-compatible with P. cuspidata than are allopatric populations. The germination of P. cuspidata pollen on sympatric P. drummondii stigmas was 13.3% vs. 9.8% on allopatric stigmas. However, the difference is not statistically significant. The presence of P. cuspidata has promoted reproductive character divergence in P. drummondii. The shift in corolla color and the increase in self-compatibility reduce the potential for gametic wastage and interspecific hybridization.     

Pollen competition and environmental effects on hybridization dynamics between Phlox drummondii and Phlox cuspidata

Pollen competition between species strongly influences hybridization dynamics in plants. By performing single- and mixed-donor pollinations, we show that soil Ca alters the outcome of interspecific pollen competition in the annual Phlox hybrid system of Phlox cuspidata and P. drummondii. In the absence of interspecific pollen competition, heterospecific pollen siring success of both species was influenced most strongly by the maternal growth environment, such that hybridization was facilitated when heterospecific pollen was deposited on stigmas of maternal plants growing in high Ca soils. When heterospecific pollen was forced to compete against conspecific pollen, however, the maternal growth environment did not influence hybridization, but the environmental origin of heterospecific pollen did, and this effect depended on the maternal species. Pollen of P. drummondii was more effective at outcompeting P. cuspidata pollen and preventing hybridization in P. drummondii dams when P. cuspidata pollen was derived from low Ca. Pollen competition within pistils of P. cuspidata was unaffected by pollen Ca environment. In situations in which P. cuspidata grows in lower soil Ca than P. drummondii, as has been documented in one population, these results suggest that the competitive ability of heterospecific pollen will be diminished by environmental effects of soil Ca. Thus, the environment in which pollen develops can influence interspecific pollen competition and hybridization frequency.     

Maintenance of species boundaries in a Neotropical radiation of Begonia

A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by‐product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in Begonia by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between B. heracleifolia and B. nelumbiifolia are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between B. heracleifolia and B. sericoneura contains a higher proportion of F1s, but little evidence of introgression. The lack of later‐generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that Begonia demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.     

Molecular signatures of selection on reproductive character displacement of flower color in Phlox drummondii

Character displacement, which arises when species diverge in sympatry to decrease competition for resources or reproductive interference, has been observed in a wide variety of plants and animals. A classic example of reproductive character displacement, presumed to be caused by reinforcing selection, is flower‐color variation in the native Texas wildflower Phlox drummondii. Here, we use population genetic analyses to investigate molecular signatures of selection on flower‐color variation in this species. First, we quantify patterns of neutral genetic variation across the range of P. drummondii to demonstrate that restricted gene flow and genetic drift cannot explain the pattern of flower‐color divergence in this species. There is evidence of extensive gene flow across populations with different flower colors, suggesting selection caused flower‐color divergence. Second, analysis of sequence variation in the genes underlying this divergence reveals a signature of a selective sweep in one of the two genes, further indicating selection is responsible for divergence in sympatry. The lack of a signature of selection at the second locus does not necessarily indicate a lack of selection on this locus but instead brings attention to the uncertainty in depending on molecular signatures to identify selection.     

INBREEDING DEPRESSION IN PARTIALLY SELF-FERTILIZING PHLOX

Inbreeding depression was measured in terms of the relative survivorship of self versus cross seed in 14 Phlox drummondii cultivars and 10 populations of P. cuspidata. The cultivars are predominantly outcrossing; P. cuspidata is predominantly self-fertilizing. The relative survivorship of self versus cross seed averages 0.84 in the cultivars and 0.99 in P. cuspidata. In wild P. drummondii, the average is 0.83. The mean number of lethal equivalents per zygote averages 0.69 in the cultivars and 0.05 in P. cuspidata, versus 0.79 in the wild P. drummondii. There is a significant negative correlation between the amount of automatic self-seed produced by a cultivar and the number of lethal equivalents it carries (r = ?0.60). Phlox cuspidata has a lower level of cross-seed abortion than P. drummondii, which probably is not due to a difference in the incidence of lethal genes in their populations.     

Outlier loci highlight the direction of introgression in oaks

Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Quercus petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and nonoutlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q. petraea (a late‐successional species) than in Q. robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with nonoutlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q. petraea caused by the species' contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized.     

HYBRIDIZATION BETWEEN ANNUAL SPECIES OF PHLOX: POPULATION STRUCTURE

Phlox cuspidata (n = 7) and P. drummondii subsp. drummondii (n = 7) are closely related annuals which are indigenous to eastern and central Texas. The species typically occupy different ecological niches but may form contiguous or confluent populations in disturbed habitats and hybridize therein. On the basis of correlative interpretations of exomorphic, chromatographic and fertility information, hybridizing populations can be segregated into three distinct classes: (1) highly fertile plants with the morphological and phenolic attributes of P. drummondii; (2) highly fertile plants with the morphological and chemical attributes of P. cuspidata; (3) sterile plants with manifestly intermediate morphology and complementary chromatographic patterns. These data strongly suggest that hybridizing populations of P. drummondii and P. cuspidata are tritypic, being composed of “pure” or essentially “pure” parental species and a group of plants which has all of the attributes characteristic of an F₁ hybrid.     

Phylogeography and lineage‐specific patterns of genetic diversity and molecular evolution in a group of North American skinks

Geography influences the evolutionary trajectory of species by mediating opportunities for hybridization, gene flow, demographic shifts and adaptation. We sought to understand how geography and introgression can generate species‐specific patterns of genetic diversity by examining phylogeographical relationships in the North American skink species Plestiodon multivirgatus and P. tetragrammus (Squamata: Scincidae). Using a multilocus dataset (three mitochondrial genes, four nuclear genes; a total of 3455 bp) we discovered mito‐nuclear discordance, consistent with mtDNA introgression. We further tested for evidence of species‐wide mtDNA introgression by using comparisons of genetic diversity, selection tests and extended Bayesian skyline analyses. Our findings suggest that P. multivirgatus acquired its mitochondrial genome from P. tetragrammus after their initial divergence. This putative species‐wide mitochondrial capture was further evidenced by statistically indistinguishable substitution rates between mtDNA and nDNA in P. multivirgatus. This rate discrepancy was observed in P. multivirgatus but not P. tetragrammus, which has important implications for studies that combine mtDNA and nDNA sequences when inferring time since divergence between taxa. Our findings suggest that by facilitating opportunities for interspecific introgression, geography can alter the course of molecular evolution between recently diverged lineages.     

Evidence for divergence and adaptive isolation in post‐glacially derived bimodal allopatric and sympatric rainbow smelt populations

The roles of ecological speciation and reinforcement in the formation of contemporary diversity remain contentious. In the present study, we contrast phenotypic and molecular divergence within morphologically diverged bimodal sympatric and allopatric pairs of rainbow smelt, Osmerus mordax. We hypothesize that, in sympatry, evidence of selection associated with resource partitioning will be visible through strong divergence, reinforcement, and greater character displacement. Parallel morphological divergence was observed between the two trophic forms (macrophagous and microphagous), with several examples of greater trait divergence in sympatry than allopatry. Mitochondrial DNA sequence analysis indicated no association between historical clades and morphology; however, Bayesian clustering using microsatellites supported the isolation of these morphs under both allopatry and sympatry. Estimates of genetic isolation were one order of magnitude lower than measures of morphological divergence, consistent with a hypothesis of strong contemporary selection. Using experimental crosses, we obtained similar rates of fertilization success among the allopatric hybrid and pure crosses; whereas, in the sympatric hybrid crosses, fertilization rates dropped by 30–50%, suggesting a clear role for reinforcement through prezygotic incompatibilities. The present study supports the hypothesis that processes of post‐glacial radiation and diversification differ between sympatry and allopatry, and indicates a role for reinforcement and ecological processes in recent sympatric diversification. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 583–594.     

QUANTITATIVE VARIATION IN PHLOX: COMPARISON OF SELFING AND OUTCROSSING SPECIES

Variation of 20 quantitative characters was examined within and among 10 populations of the predominantly outcrossing Phlox drummondii and 4 populations of the predominantly selfing P. cuspidata grown in a greenhouse. Multivariate analysis of variance, considering all characters simultaneously, indicated that there were significant differences among populations in both species while analysis of individual characters demonstrated that there were significant population differences for 19 characters in P. drummondii and 13 characters in P. cuspidata. On average, 16% of the total phenotypic variation in P. drummondii occurred among populations compared to less than 4% of the total variation in P. cuspidata. In addition, P. drummondii exhibited significant differences among families within populations more frequently than P. cuspidata. Most observed variation in both species occurred within families where environmental and genetic sources of variation could not be partitioned. There was a trend for P. drummondii to have higher heritabilities than P. cuspidata for most characters even when assumptions about breeding systems were relaxed. Thus, the outbreeding species exhibited larger genetic differences among populations and among families within populations than the selfing species in the greenhouse environment. These data suggest that P. drummondii has the greater evolutionary potential of the two species and are consistent with the hypothesis that differences in population structure result from differences in the breeding systems of the two species.     

Deep mitochondrial introgression and hybridization among ecologically divergent vole species

The completion of speciation is typically difficult to ascertain in rapidly diverging taxa but the amount of hybridization and gene flow in sympatry or parapatry contains important information about the level of reproductive isolation achieved. Here, we examined the progress in speciation between the Mediterranean (Microtus duodecimcostatus) and the Lusitanian pine vole (M. lusitanicus), which are part of the most rapid radiation of species known in mammals. These two Iberian pine voles are classified as separate species because of differences in morphology and ecology, but relatively many ambiguous individuals can be found in sympatric conditions. Our phylogenetic analyses of rangewide data from the mitochondrial cytochrome b gene (mtDNA) demonstrated high levels of diversity and a basal separation in two parapatric lineages. However, mtDNA affiliation was at odds with morphological classification or geographical distribution of the taxa. In contrast, statistical analyses of microsatellites (nucDNA) showed two clear genetic clusters in allopatry and sympatry generally matching morphological classification. This cytonuclear discordance over a large geographic area suggests historical introgression of mtDNA from M. duodecimcostatus to M. lusitanicus. There was statistical evidence for at least two recent hybrids in the sympatry zone but gene flow is apparently low given clear‐cut differences in nucDNA. Our results indicate a relatively advanced speciation process in these Iberian pine voles without fully established reproductive isolation. This situation enables use of combined population genomic and experimental approaches for the separation of patterns and mechanisms in the ongoing explosive diversification of these and other Arvicoline rodents in the future.     

Strength of sexual and postmating prezygotic barriers varies between sympatric populations with different histories and species abundances

The impact of different reproductive barriers on species or population isolation may vary in different stages of speciation depending on evolutionary forces acting within species and through species’ interactions. Genetic incompatibilities between interacting species are expected to reinforce prezygotic barriers in sympatric populations and lead to cascade reinforcement between conspecific populations living within and outside the areas of sympatry. We tested these predictions and studied whether and how the strength and target of reinforcement between Drosophila montana and Drosophila flavomontana vary between sympatric populations with different histories and species abundances. All barriers between D. montana females and D. flavomontana males were nearly complete, while in the reciprocal cross strong postzygotic isolation was accompanied by prezygotic barriers whose strength varied according to population composition. Sexual isolation between D. flavomontana females and D. montana males was increased in long‐established sympatric populations, where D. flavomontana is abundant, while postmating prezygotic (PMPZ) barriers were stronger in populations where this species is a new invader and still rare and where female discrimination against heterospecific males was lower. Strengthening of sexual and PMPZ barriers in this cross also induced cascade reinforcement of respective barriers between D. flavomontana populations, which is a classic signature of reinforcement process.