Strong Reproductive Isolation Research Articles

Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes

Abstract Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to the completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the 2 ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for > 1,000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, 2 of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species.

Despite genetic isolation in sympatry, post-copulatory reproductive barriers have not evolved between bat- and human-associated common bedbugs (Cimex lectularius L.)

BackgroundThe common bedbug Cimex lectularius is a widespread ectoparasite on humans and bats. Two genetically isolated lineages, parasitizing either human (HL) or bat (BL) hosts, have been suggested to differentiate because of their distinct ecology. The distribution range of BL is within that of HL and bedbugs live mostly on synanthropic bat hosts. This sympatric co-occurrence predicts strong reproductive isolation at the post-copulatory level.ResultsWe tested the post-copulatory barrier in three BL and three HL populations in reciprocal crosses, using a common-garden blood diet that was novel to both lineages. We excluded pre-copulation isolation mechanisms and studied egg-laying rates after a single mating until the depletion of sperm, and the fitness of the resulting offspring. We found a higher sperm storage capability in BL, likely reflecting the different seasonal availability of HL and BL hosts. We also observed a notable variation in sperm function at the population level within lineages and significant differences in fecundity and offspring fitness between lineages. However, no difference in egg numbers or offspring fitness was observed between within- and between-lineage crosses.ConclusionsDifferences in sperm storage or egg-laying rates between HL and BL that we found did not affect reproductive isolation. Neither did the population-specific variation in sperm function. Overall, our results show no post-copulatory reproductive isolation between the lineages. How genetic differentiation in sympatry is maintained in the absence of a post-copulatory barrier between BL and HL remains to be investigated.

Population genetic structure and hybrid zone analyses for species delimitation in the Japanese toad (Bufo japonicus).

Hybridization following secondary contact may produce different outcomes depending on the extent to which genetic diversity and reproductive barriers have accumulated during isolation. The Japanese toad, Bufo japonicus, is distributed on the main islands of Japan. In the present study, we applied multiplexed inter-simple sequence repeat genotyping by sequencing to achieve the fine-scale resolution of the genetic cluster in B. j. japonicus and B. j. formosus. We also elucidated hybridization patterns and gene flow degrees across contact zones between the clusters identified. Using SNP data, we found four genetic clusters in B. j. japonicus and B. j. formosus and three contact zones of the cluster pairs among these four clusters. The two oldest diverged lineages, B. j. japonicus and B. j. formosus, formed a narrow contact zone consistent with species distinctiveness. Therefore, we recommend that these two subspecies be elevated to the species level. In contrast, the less diverged pairs of two clusters in B. j. japonicus and B. j. formosus, respectively, admixed over a hundred kilometers, suggesting that they have not yet developed strong reproductive isolation and need to be treated as conspecifics. These results will contribute to resolving taxonomic confusion in Japanese toads.

Differences in mating system and predicted parental conflict affect post-pollination reproductive isolation in a flowering plant.

Mating system shifts from outcrossing to selfing are frequent in plant evolution. Relative to outcrossing, selfing is associated with reduced parental conflict over seed provisioning, which may result in postzygotic, asymmetric, reproductive isolation in crosses between populations of different mating systems. To test the hypothesis that post-pollination reproductive isolation between populations increases with increasing differences in mating system and predicted parental conflict, we performed a crossing experiment involving all combinations of three self-compatible populations (with low outcrossing rates), and three self-incompatible populations (with high outcrossing rates) of the arctic-alpine herb Arabis alpina, assessing fitness-related seed and plant traits of the progeny. Predicted levels of parental conflict ("genome strength") were quantified based on strength of self-incompatibility and estimates of outcrossing rates. Crosses between self-compatible and self-incompatible populations yielded very small seeds of low viability, resulting in strong reproductive isolation. In 14 of 15 reciprocal between-population crosses, seeds were heavier when the paternal plant had the stronger genome, and seed mass differences between cross directions increased with an increased difference in parental conflict. Overall, our results suggest that, when sufficiently large, differences in mating system and hence in expected parental conflict may result in strong post-pollination reproductive barriers contributing to speciation.

Flexible drought deciduousness in a neotropical understory herb.

PremiseAdaptive divergence across environmental gradients is a key driver of speciation. Precipitation seasonality gradients are common in the tropics, yet drought adaptation is nearly unexplored in neotropical understory herbs. Here, we examined two recently diverged neotropical spiral gingers, one adapted to seasonal drought and one reliant on perennial water, to uncover the basis of drought adaptation.MethodsWe combined ecophysiological trait measurements in the field and greenhouse with experimental and observational assessments of real‐time drought response to determine how Costus villosissimus (Costaceae) differs from C. allenii to achieve drought adaptation.ResultsWe found that drought‐adapted C. villosissimus has several characteristics indicating flexible dehydration avoidance via semi‐drought‐deciduousness and a fast economic strategy. Although the two species do not differ in water‐use efficiency, C. villosissimus has a more rapid growth rate, lower leaf mass per area, lower stem density, higher leaf nitrogen, and a strong trend of greater light‐saturated photosynthetic rates. These fast economic strategy traits align with both field‐based observations and experimental dry‐down results. During drought, C. villosissimus displays facultative drought‐deciduousness, losing lower leaves during the dry season and rapidly growing new leaves in the wet season.ConclusionsWe revealed a drought adaptation strategy that has not, to our knowledge, previously been documented in tropical herbs. This divergent drought adaptation evolved recently and is an important component of reproductive isolation between C. villosissimus and C. allenii, indicating that adaptive shifts to survive seasonal drought may be an underappreciated axis of neotropical understory plant diversification.

Admixture of evolutionary rates across a butterfly hybrid zone.

Hybridization is a major evolutionary force that can erode genetic differentiation between species, whereas reproductive isolation maintains such differentiation. In studying a hybrid zone between the swallowtail butterflies Papilio syfanius and Papilio maackii (Lepidoptera: Papilionidae), we made the unexpected discovery that genomic substitution rates are unequal between the parental species. This phenomenon creates a novel process in hybridization, where genomic regions most affected by gene flow evolve at similar rates between species, while genomic regions with strong reproductive isolation evolve at species-specific rates. Thus, hybridization mixes evolutionary rates in a way similar to its effect on genetic ancestry. Using coalescent theory, we show that the rate-mixing process provides distinct information about levels of gene flow across different parts of genomes, and the degree of rate-mixing can be predicted quantitatively from relative sequence divergence ([Formula: see text]) between the hybridizing species at equilibrium. Overall, we demonstrate that reproductive isolation maintains not only genomic differentiation, but also the rate at which differentiation accumulates. Thus, asymmetric rates of evolution provide an additional signature of loci involved in reproductive isolation.

Reproductive isolation among lineages of Silene nutans (Caryophyllaceae): A potential involvement of plastid-nuclear incompatibilities

Early stages of speciation in plants might involve genetic incompatibilities between plastid and nuclear genomes, leading to inter-lineage hybrid breakdown due to the disruption between co-adapted plastid and nuclear genes encoding subunits of the same plastid protein complexes. We tested this hypothesis in Silene nutans, a gynodioecious Caryophyllaceae, where four distinct genetic lineages exhibited strong reproductive isolation among each other, resulting in chlorotic or variegated hybrids. By sequencing the whole gene content of the four plastomes through gene capture, and a large part of the nuclear genes encoding plastid subunits from RNAseq data, we searched for non-synonymous substitutions fixed in each lineage on both genomes. Lineages of S. nutans exhibited a high level of dN/dS ratios for plastid and nuclear genes encoding most plastid complexes, with a strong pattern of coevolution for genes encoding the subunits of ribosome and cytochrome b6/f that could explain the chlorosis of hybrids. Overall, relaxation of selection due to past bottlenecks and positive selection have driven the diversity pattern observed in S. nutans plastid complexes, leading to plastid-nuclear incompatibilities. We discuss the possible role of gynodioecy in the evolutionary dynamics of the plastomes through linked selection.

Parapatric speciation with recurrent gene flow of two sexual dichromatic pheasants

Understanding speciation has long been a fundamental goal of evolutionary biology. It is widely accepted that speciation requires an interruption of gene flow to generate strong reproductive isolation between species. The mechanism of how speciation in sexually dichromatic species operates in the face of gene flow remains an open question. Two species in the genus Chrysolophus, the Golden Pheasant (C. pictus) and Lady Amherst's Pheasant (C. amherstiae), both of which exhibit significant plumage dichromatism, are currently parapatric in southwestern China with several hybrid recordings in field. In this study, we estimated the pattern of gene flow during the speciation of the two pheasants using the Approximate Bayesian Computation (ABC) method based on data from multiple genes. Using a newly assembled de novo genome of Lady Amherst's Pheasant and resequencing of widely distributed individuals, we reconstructed the demographic history of the two pheasants by the PSMC (pairwise sequentially Markovian coalescent) method. The results provide clear evidence that the gene flow between the two pheasants was consistent with the predictions of the isolation with migration model during divergence, indicating that there was long-term gene flow after the initial divergence (ca. 2.2 million years ago). The data further support the occurrence of secondary contact between the parapatric populations since around 30 kya with recurrent gene flow to the present, a pattern that may have been induced by the population expansion of the Golden Pheasant in the late Pleistocene. The results of the study support the scenario of speciation between the Golden Pheasant and Lady Amherst's Pheasant with cycles of mixing-isolation-mixing, possibly due to the dynamics of geographical context in the late Pleistocene. The two species provide a good research system as an evolutionary model for testing reinforcement selection in speciation.

Application of multivariate morphometrics to delimit three Japanese species of Arisaema sect. Pistillata (Araceae)

The Arisaema serratum group sensu stricto (Araceae) is a Japanese species assemblage characterized by a well‐developed leaf rachis and a long pseudostem. It has been regarded as a complex including many species with few decisive traits. They were previously considered as a single species due to their wide intraspecific variation, but recent monographs have recognized about 13 species. In this group, A. maekawae and A. pseudoangustatum var. pseudoangustatum were recently divided from A. angustatum from the type localities. An earlier study found sympatric populations of the three species in the Chugoku region, far from the type localities, and distinguished them by qualitative observations, but there are no quantitative data to delimit the species boundaries objectively. Since high phenotypic plasticity hinders species delimitation in the A. serratum group s.s. using just a few quantitative traits, I investigated the morphological discontinuity among them using principal component analysis with eleven quantitative characters. In an ordination space including the three species, the morphological variation was roughly divided into A. maekawae and the others, and largely overlapped between A. angustatum and A. pseudoangustatum var. pseudoangustatum. However, the morphological variation clearly distinguished the two latter species when A. maekawae was excluded from the PCA. To conclude, the three Arisaema species appeared to be morphologically distinct. The strong reproductive isolation reported previously also ensures the species distinction according to the biological species concept. The discriminating traits between A. angustatum and the other two species partly differed from those in the type localities, suggesting that examination of intraspecific variation is needed between geographically isolated populations. This study showed that a combination of quantitative traits effectively supports tentative species identifications using qualitative traits and reinforces the usefulness of multivariate morphometrics for future systematic studies.

Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish

How ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback fish population pair adapted to contiguous, ecologically different lake and stream habitats. Clinal whole-genome sequence data reveal numerous genome regions (nearly) fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow because a steep cline in allele frequencies is observed across the entire genome, and because the cline center closely matches the habitat transition. Simulations confirm that such strong divergence can be maintained by polygenic selection despite high dispersal and small per-locus selection coefficients. Finally, comparing samples from near the habitat transition before and after an unusual ecological perturbation demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale.

Nuclear phylogenies and genomics of a contact zone establish the species rank of Podarcis lusitanicus (Squamata, Lacertidae)

Unravelling when divergent lineages constitute distinct species can be challenging, particularly in complex scenarios combining cryptic diversity and phylogenetic discordances between different types of molecular markers. Combining a phylogenetic approach with the study of contact zones can help to overcome such difficulties. The Podarcis hispanicus species complex has proven to be prosperous in independent evolutionary units, sometimes associated with cryptic diversity. Previous studies have revealed that one of the species of this complex, P. guadarramae, comprises two deeply divergent yet morphologically indistinguishable evolutionary units, currently regarded as subspecies (P. g. guadarramae and P. g. lusitanicus). In this study we used molecular data to address the systematics of the two lineages of Podarcis guadarramae and the closely related P. bocagei. Firstly, we reconstructed the species tree of these three and two additional taxa based on 30 nuclear loci using the multispecies coalescent with and without gene flow. Secondly, we used SNPs obtained from RADseq data to analyze the population structure across the distribution limits P. g. lusitanicus and P. g. guadarramae, and for comparison, a contact zone between P. bocagei and P. g. lusitanicus. Nuclear phylogenetic relationships between these three taxa are clearly difficult to determine due to the influence of gene flow, but our results give little support to the monophyly of P. guadarramae, potentially due to a nearly simultaneous divergence between them. Genetic structure and geographic cline analysis revealed that the two lineages of P. guadarramae replace each other abruptly across the sampled region and that gene flow is geographically restricted, implying the existence of strong reproductive isolation. Podarcis bocagei and P. g. lusitanicus show a similar degree of genetic differentiation and reproductive isolation, with very low levels of admixture in syntopy. These results support that all three forms are equally differentiated and reproductively isolated. In consequence, we conclude that the two former subspecies of Podarcis guadarramae constitute valid, yet cryptic species, that should be referred to as P. lusitanicus and P. guadarramae.

Strong yet incomplete reproductive isolation in Vermivora is not contradicted by other lines of evidence: A reply to Toews et al.

Toews et al. assert that strong reproductive isolation in Vermivora is inconsistent with other lines of evidence. Here, we discuss how strong yet incomplete reproductive isolation is consistent with other results from this system.

Natural hybridization between two butterfly bushes in Tibet: dominance of F1 hybrids promotes strong reproductive isolation

BackgroundIt has been recognized that a certain amount of habitat disturbance is a facilitating factor for the occurrence of natural hybridization, yet to date we are unaware of any studies exploring hybridization and reproductive barriers in those plants preferentially occupying disturbed habitats. Buddleja plants (also called butterfly bush) generally do grow in disturbed habitats, and several species with hybrid origin have been proposed, based solely on morphological evidence.ResultsIn the present study, we test the hypothesis that B. × wardii is of natural hybridization origin in two sympatric populations of three taxa including B. × wardii and its parents (B. alternifolia and B. crispa) plus 4 referenced parental populations, using four nuclear genes and three chloroplast intergenic spacers, as well as with 10 morphological characters. Our results suggest that at both sites B. × wardii is likely to be a hybrid between B. alternifolia and B. crispa, and moreover, we confirm that most of the hybrids examined are F1s. That these plants are F1s is further supported by morphology, as no transgressive characters were detected. B. crispa was found to be the maternal parent in the Bahe (BH) population, from cpDNA evidence. However, in the Taji (TJ) population, the direction of hybridization was difficult to establish due to the shared cpDNA haplotypes between B. alternifolia and B. crispa, however we still predicted a similar unidirectional hybridization pattern due to results from cross-specific pollination treatments which supported the “SI × SC rule”.ConclusionsThe presence of mainly F1 hybrids can successfully impede gene flow and thus maintain species boundaries in parental species in a typical distribution of Buddleja, i.e. in disturbed habitats.

Genomic landscape of geographically structured colour polymorphism in a temperate marine fish

The study of phenotypic variation patterns among populations is fundamental to elucidate the drivers of evolutionary processes. Empirical evidence that supports ongoing genetic divergence associated with phenotypic variation remains very limited for marine species where larval dispersal is a common homogenizing force. We present a genome‐wide analysis of a marine fish, Labrus bergylta, comprising 144 samples distributed from Norway to Spain, a large geographical area that harbours a gradient of phenotypic differentiation. We analysed 39,602 biallelic single nucleotide polymorphisms and found a clear latitudinal gradient of genomic differentiation strongly correlated with the variation in phenotypic morph frequencies observed across the North Atlantic. We also detected a strong association between the latitude and the number of loci that appear to be under divergent selection, which increased with differences in coloration but not with overall genetic differentiation. Our results demonstrate that strong reproductive isolation is occurring between sympatric colour morphs of L. bergylta found at the southern areas and provide important new insights into the genomic changes shaping early stages of differentiation that might precede speciation with gene flow.

Variable levels of introgression between the endangered Podarcis carbonelli and highly divergent congeneric species.

Recent empirical studies have demonstrated that speciation with gene flow is more common than previously thought. From a conservation perspective, the potential negative effects of hybridization raise concerns on the genetic integrity of endangered species. However, introgressive hybridization has also been growingly recognized as a source of diversity and new advantageous alleles. Carbonell's wall lizard (Podarcis carbonelli) is an endangered species whose distribution overlaps with four other congeneric species. Our goal here was to determine whether P. carbonelli is completely reproductively isolated from its congeners and to evaluate the relevance of hybridization and interspecific gene flow for developing a conservation plan. We used restriction site associated DNA (RAD) sequencing to discover SNPs in samples from four contact zones between P. carbonelli and four other species. Principal component analysis, multilocus genotype assignment and interspecific heterozygosity suggest incomplete reproductive isolation and ongoing gene flow between species. However, hybridization dynamics vary across all pairs, suggesting complex interactions between multiple intrinsic and extrinsic barriers. Despite seemingly ubiquitous interspecific gene flow, we found evidence of strong reproductive isolation across most contact zones. Instead, indirect effects of hybridization like waste of reproductive effort in small isolated populations may be more problematic. Our results highlight the need to further evaluate the consequences of introgression for P. carbonelli, both on a geographic and genomic level and included in a comprehensive and urgently needed conservation plan. Besides, those findings will add important insights on the potential effects of hybridization and introgression for endangered species.

No evidence for hybridization betweenCalanus finmarchicusandCalanus glacialisin a subarctic area of sympatry

AbstractIn the North Atlantic and the Arctic Ocean, four species of the copepod genus Calanus dominate the zooplankton biomass. Because of their morphological resemblance, knowledge of their respective distribution range has long been biased by misidentification, until the recent use of molecular tools uncovered numerous areas of sympatry. As hybridization between Calanus finmarchicus and Calanus glacialis has been claimed in the East‐Canadian Arctic based on microsatellites, we investigated further the potential for interbreeding in newly uncovered areas of sympatry. Calanus species and stage composition were analyzed during winter in two Norwegian subarctic fjords, using molecular markers developed specifically for species identification and hybrid detection between C. finmarchicus and C. glacialis. Overall, C. glacialis were the most abundant throughout the winter, followed by C. finmarchicus and Calanus hyperboreus with only a few records of Calanus helgolandicus. The presence of C. glacialis, C. hyperboreus, and C. finmarchicus' nauplii was recorded, indicating that these species reproduce locally. In January and February, the simultaneous occurrence of males and females of both C. finmarchicus and C. glacialis suggested a potential for interspecies mating. However, genetic admixture tests performed on all 1126 individuals revealed no signal of hybridization, implying a strong reproductive isolation mechanism. We conclude that no evidence supports a potential for hybridization between C. finmarchicus and C. glacialis.

Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers.

Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Evolutionary dynamics of pre- and postzygotic reproductive isolation in cichlid fishes.

Cichlid fishes are exceptionally species-rich, speciated at explosive rates and, hence, are a model system in speciation research. Yet, their reproductive isolating barriers have, so far, not been comprehensively studied. Here, we review current knowledge on pre- and postzygotic mechanisms in cichlids. While premating isolation is the norm in cichlids, its strength varies across lineages and with the geographical setting. Moreover, manipulations of ambient conditions tended to reduce assortative mating among closely related species, suggesting that premating isolation in cichlids is often fragile and context dependent. The observed lack of complete reproductive isolation is supported by past and present hybridization events that have contributed to diversity by creating novel allelic combinations. On the other hand, our meta-analysis highlights that intrinsic postzygotic isolation might accumulate faster than assumed. Mild forms of genetic incompatibilities, such as sex ratio distortion, can already be observed among closely related species. Therefore, cessation of gene flow by strong reproductive isolation in cichlids requires a combination of premating prezygotic isolation supplemented with intrinsic and extrinsic postzygotic barriers. Further, we suggest crucial next steps to improve our knowledge about reproductive barriers in cichlids to understand the evolutionary dynamics of pre- and postzygotic isolation mechanisms during adaptive radiations. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Adaptive zones shape the magnitude of premating reproductive isolation in Timema stick insects.

Simpson's fossil-record inspired model of 'adaptive zones' proposes that evolution is dominated by small fluctuations within adaptive zones, occasionally punctuated by larger shifts between zones. This model can help explain why the process of population divergence often results in weak or moderate reproductive isolation (RI), rather than strong RI and distinct species. Applied to the speciation process, the adaptive zones hypothesis makes two inter-related predictions: (i) large shifts between zones are relatively rare, (ii) when large shifts do occur they generate stronger RI than shifts within zones. Here, we use ecological, phylogenetic and behavioural data to test these predictions in Timema stick insects. We show that host use in Timema is dominated by moderate shifts within the systematic divisions of flowering plants and conifers, with only a few extreme shifts between these divisions. However, when extreme shifts occur, they generate greater RI than do more moderate shifts. Our results support the adaptive zones model, and suggest that the net contribution of ecological shifts to diversification is dependent on both their magnitude and frequency. We discuss the generality of our findings in the light of emerging evidence from diverse taxa that the evolution of RI is not always the only factor determining the origin of species diversity. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Evolution of strong reproductive isolation in plants: broad-scale patterns and lessons from a perennial model group.

Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the 'escape' of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.