Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus

Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles

Most tree species underwent cycles of contraction and expansion during the Quaternary. These cycles led to an ancient and complex genetic structure that has since been affected by extensive gene flow and by strong local adaptation. The extent to which hybridization played a role in this multi-layered genetic structure is important to be investigated. To study the effect of hybridization on the joint population genetic structure of two dominant species of the Eurasian boreal forest, Picea abies and P. obovata, we used targeted resequencing and obtained around 480 K nuclear SNPs and 87 chloroplast SNPs in 542 individuals sampled across most of their distribution ranges. Despite extensive gene flow and a clear pattern of Isolation-by-Distance, distinct genetic clusters emerged, indicating the presence of barriers and corridors to migration. Two cryptic refugia located in the large hybrid zone between the two species played a critical role in shaping their current distributions. The two species repeatedly hybridized during the Pleistocene and the direction of introgression depended on latitude. Our study suggests that hybridization helped both species to overcome main shifts in their distribution ranges during glacial cycles and highlights the importance of considering whole species complex instead of separate entities to retrieve complex demographic histories.

A unified framework to investigate and interpret hybrid and allopolyploid biodiversity across biological scales

Premise

Hybridization and polyploidization are common in vascular plants and important drivers of biodiversity by facilitating speciation and ecological diversification. A primary limitation to making broad synthetic discoveries in hybrid and allopolyploid biodiversity research is the absence of a standardized framework to compare data across studies and biological scales.

Methods

Here, I present a new quantitative framework to investigate and interpret patterns in hybrid and allopolyploid biology called the divergence index (DI). The DI framework produces standardized data that are comparable across studies and variables. To show how the DI framework can be used to synthesize data, I analyzed published biochemical, physiological, and ecological trait data of hybrids and allopolyploids. I also apply key ecological and evolutionary concepts in hybrid and polyploid biology to translate nominal outcomes, including transgression, intermediacy, expansion, and contraction, in continuous DI space.

Results

Biochemical, physiological, ecological, and evolutionary data can all be analyzed, visualized, and interpreted in the DI framework. The DI framework is particularly suited to standardize and compare variables with very different scales. When using the DI framework to understand niche divergence, a metric of niche overlap can be used to complement insights to centroid and breadth changes.

Discussion

The DI framework is an accessible framework for hybrid and allopolyploid biology and represents a flexible and intuitive tool that can be used to reconcile outstanding problems in plant biodiversity research.

Fluctuating selection in a Monkeyflower hybrid zone

While hybridization was viewed as a hindrance to adaptation and speciation by early evolutionary biologists, recent studies have demonstrated the importance of hybridization in facilitating evolutionary processes. However, it is still not well-known what role spatial and temporal variation in natural selection play in the maintenance of naturally occurring hybrid zones. To identify whether hybridization is adaptive between two closely related monkeyflower species, Mimulus guttatus and Mimulus laciniatus, we performed repeated reciprocal transplants between natural hybrid and pure species' populations. We planted parental genotypes along with multiple experimental hybrid generations in a dry (2021) and extremely wet (2023) year in the Sierra Nevada, CA. By taking fine scale environmental measurements, we found that the environment of the hybrid zone is more similar to M. laciniatus's seasonally dry rocky outcrop habitat than M. guttatus's moist meadows. In our transplants hybridization does not appear to be maintained by a consistent fitness advantage of hybrids over parental species in hybrid zones, but rather a lack of strong selection against hybrids. We also found higher fitness of the drought adapted species, M. laciniatus, than M. guttatus in both species' habitats, as well as phenotypic selection for M. laciniatus-like traits in the hybrid habitat in the dry year of our experiment. These findings suggest that in this system hybridization might function to introduce drought-adapted traits and genes from M. laciniatus into M. guttatus, specifically in years with limited soil moisture. However, we also find evidence of genetic incompatibilities in second generation hybrids in the wetter year, which may balance a selective advantage of M. laciniatus introgression. Therefore, we find that hybridization in this system is both potentially adaptive and costly, and that the interaction of positive and negative selection likely determines patterns of gene flow between these Mimulus species.

Major patterns in the introgression history of Heliconius butterflies

Gene flow between species, although usually deleterious, is an important evolutionary process that can facilitate adaptation and lead to species diversification. It also makes estimation of species relationships difficult. Here, we use the full-likelihood multispecies coalescent (MSC) approach to estimate species phylogeny and major introgression events in Heliconius butterflies from whole-genome sequence data. We obtain a robust estimate of species branching order among major clades in the genus, including the 'melpomene-silvaniform' group, which shows extensive historical and ongoing gene flow. We obtain chromosome-level estimates of key parameters in the species phylogeny, including species divergence times, present-day and ancestral population sizes, as well as the direction, timing, and intensity of gene flow. Our analysis leads to a phylogeny with introgression events that differ from those obtained in previous studies. We find that Heliconius aoede most likely represents the earliest-branching lineage of the genus and that 'silvaniform' species are paraphyletic within the melpomene-silvaniform group. Our phylogeny provides new, parsimonious histories for the origins of key traits in Heliconius, including pollen feeding and an inversion involved in wing pattern mimicry. Our results demonstrate the power and feasibility of the full-likelihood MSC approach for estimating species phylogeny and key population parameters despite extensive gene flow. The methods used here should be useful for analysis of other difficult species groups with high rates of introgression.

Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus

Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.

Agricultural weeds: the contribution of domesticated species to the origin and evolution of feral weeds

Agricultural weeds descended from domesticated ancestors, directly from crops (endoferality) and/or from crop-wild hybridization (exoferality), may have evolutionary advantages by rapidly acquiring traits pre-adapted to agricultural habitats. Understanding the role of crops on the origin and evolution of agricultural weeds is essential to develop more effective weed management programs, minimize crop losses due to weeds, and accurately assess the risks of cultivated genes escaping. In this review, we first describe relevant traits of weediness: shattering, seed dormancy, branching, early flowering and rapid growth, and their role in the feralization process. Furthermore, we discuss how the design of "super-crops" can affect weed evolution. We then searched for literature documenting cases of agricultural weeds descended from well-domesticated crops, and describe six case studies of feral weeds evolved from major crops: maize, radish, rapeseed, rice, sorghum, and sunflower. Further studies on the origin and evolution of feral weeds can improve our understanding of the physiological and genetic mechanisms underpinning the adaptation to agricultural habitats and may help to develop more effective weed-control practices and breeding better crops. © 2022 Society of Chemical Industry.

Pollen competition in hybridizing Cakile species: How does a latecomer win the race?

PREMISE

Hybridization between cross-compatible species depends on the extent of competition between alternative mates. Even if stigmatic compatibility allows for hybridization, hybridization requires the heterospecific pollen to be competitive. Here, we determined whether conspecific pollen has an advantage in the race to fertilize ovules and the potential handicap to be overcome by heterospecific pollen in invasive Cakile species.

METHODS

We used fluorescence microscopy to measure pollen tube growth after conspecific and heterospecific hand-pollination treatments. We then determined siring success in the progeny relative to the timing of heterospecific pollen arrival on the stigma using CAPS markers.

RESULTS

In the absence of pollen competition, pollination time and pollen recipient species had a significant effect on the ratio of pollen tube growth. In long-styled C. maritima (outcrosser), pollen tubes grew similarly in both directions. In short-styled C. edentula (selfer), conspecific and heterospecific pollen tubes grew differently. Cakile edentula pollen produced more pollen tubes, revealing the potential for a mating asymmetry whereby C. edentula pollen had an advantage relative to C. maritima. In the presence of pollen competition, siring success was equivalent when pollen deposition was synchronous. However, a moderate 1-h advantage in the timing of conspecific pollination resulted in almost complete assortative mating, while an equivalent delay in conspecific pollination resulted in substantial hybrid formation.

CONCLUSIONS

Hybridization can aid the establishment of invasive species through the transfer of adaptive alleles from cross-compatible species, but also lead to extinction through demographic or genetic swamping. Time of pollen arrival on the stigma substantially affected hybridization rate, pointing to the importance of pollination timing in driving introgression and genetic swamping.

Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus)

To what extent is evolution repeatable? Little is known about whether the evolution of hybrids is more (or less) repeatable than that of nonhybrids. We used field experimental evolution in annual sunflowers (Helianthus) in Texas to ask the extent to which hybrid evolution is repeatable across environments compared to nonhybrid controls. We created hybrids between Helianthus annuus (L.) and H. debilis (Nutt.) and grew plots of both hybrids and nonhybrid controls through eight generations at three sites in Texas. We collected seeds from each generation and grew each generation × treatment × home site combination at two final common gardens. We estimated the strength and direction of evolution in terms of fitness and 24 traits, tested for repeated versus nonrepeated evolution, and assessed overall phenotypic evolution across lineages and in relation to a locally adapted phenotype. Hybrids consistently evolved higher fitness over time, while controls did not, although trait evolution varied in strength across home sites. Repeated evolution was more evident in hybrids versus nonhybrid controls, and hybrid evolution was often in the direction of the locally adapted phenotype. Our findings have implications for both the nature of repeatability in evolution and the contribution of hybridization to evolution across environmental contexts.

Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges

The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid‐origin lineages to occupy unique environmental space relative to one (or both) parent(s). We document such a case of hybridization between two sedge species, Carex nova and Carex nelsonii (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (C. nelsonii) is at the edge of its environmental tolerance. Hybrid‐origin individuals display mixed ancestry between the parental taxa—of nearly 7000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage—approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid‐origin lineage, we conducted genotype–environment association analyses on different combinations of loci—with and without excess ancestry—and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (C. nelsonii), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent.

Morphological, cytological, and molecular evidences for natural hybridization between Roegneria stricta and Roegneria turczaninovii (Triticeae: Poaceae)

Some plants with low fertility are morphologically intermediate between Roegneria stricta and Roegneria turczaninovii, and were suspected to be natural hybrids between these species. In this study, karyotype analysis showed that natural hybrids and their putative parents were tetraploids (2n = 4x = 28). Meiotic pairing in natural hybrids is more irregular than its putative parents. Results of genomic in situ hybridization and fluorescence in situ hybridization indicate that natural hybrids contain the same genome as their putative parents. The nuclear gene DNA meiotic recombinase 1 (DMC1) and the chloroplast gene rps16 of natural hybrids and their putative parents were analyzed for evidence of hybridization. The results from molecular data supported by morphology and cytology demonstrated that the plants represent natural hybrids between R. stricta and R. turczaninovii. The study is important for understanding species evolution in the genus since it demonstrates for the first time the existence of populations of natural homoploid hybrids in Roegneria. The study also reports for the first time that the composition of the genomic formula of R. turczaninovii is StY, confirming that the current taxonomic status is correct.

Admixture may be extensive among hyperdominant Amazon rainforest tree species

Admixture is a mechanism by which species of long-lived plants may acquire novel alleles. However, the potential role of admixture in the origin and maintenance of tropical plant diversity is unclear. We ask whether admixture occurs in an ecologically important clade of Eschweilera (Parvifolia clade, Lecythidaceae), which includes some of the most widespread and abundant tree species in Amazonian forests. Using target capture sequencing, we conducted a detailed phylogenomic investigation of 33 species in the Parvifolia clade and investigated specific hypotheses of admixture within a robust phylogenetic framework. We found strong evidence of admixture among three ecologically dominant species, E. coriacea, E. wachenheimii and E. parviflora, but a lack of evidence for admixture among other lineages. Accepted species were largely distinguishable from one another, as was geographic structure within species. We show that hybridization may play a role in the evolution of the most widespread and ecologically variable Amazonian tree species. While admixture occurs among some species of Eschweilera, it has not led to widespread erosion of most species' genetic or morphological identities. Therefore, current morphological based species circumscriptions appear to provide a useful characterization of the clade's lineage diversity.

Weak coupling among barrier loci and waves of neutral and adaptive introgression across an expanding hybrid zone

Hybridization can serve as an evolutionary stimulus, but we have little understanding of introgression at early stages of hybrid zone formation. We analyze reproductive isolation and introgression between a range‐limited and a widespread species. Reproductive barriers are estimated based on differences in flowering time, ecogeographic distributions, and seed set from crosses. We find an asymmetrical mating barrier due to cytonuclear incompatibility that is consistent with observed clusters of coincident and concordant tension zone clines (barrier loci) for mtDNA haplotypes and nuclear SNPs. These groups of concordant clines are spread across the hybrid zone, resulting in weak coupling among barrier loci and extensive introgression. Neutral clines had nearly equal introgression into both species’ ranges, whereas putative cases of adaptive introgression had exceptionally wide clines with centers shifted toward one species. Analyses of cline shape indicate that secondary contact was initiated within the last 800 generations with the per‐generation dispersal between 200 and 400 m, and provide some of the first estimates of the strength of selection required to account for observed levels of adaptive introgression. The weak species boundary between these species appears to be in early stages of dissolution, and ultimately will precipitate genetic swamping of the range‐limited species.

Genomic analysis of distinct bleaching tolerances among cryptic coral species

Reef-building coral species are experiencing an unprecedented decline owing to increasing frequency and intensity of marine heatwaves and associated bleaching-induced mortality. Closely related species from the Acropora hyacinthus species complex differ in heat tolerance and in their association with heat-tolerant symbionts. We used low-coverage full genome sequencing of 114 colonies monitored across the 2015 bleaching event in American Samoa to determine the genetic differences among four cryptic species (termed HA, HC, HD and HE) that have diverged in these species traits. Cryptic species differed strongly at thousands of single nucleotide polymorphisms across the genome which are enriched for amino acid changes in the bleaching-resistant species HE. In addition, HE also showed two particularly divergent regions with strong signals of differentiation. One approximately 220 kb locus, HES1, contained the majority of fixed differences in HE. A second locus, HES2, was fixed in HE but polymorphic in the other cryptic species. Surprisingly, non-HE individuals with HE-like haplotypes at HES2 were more likely to bleach. At both loci, HE showed particular sequence similarity to a congener, Acropora millepora. Overall, resilience to bleaching during the third global bleaching event was strongly structured by host cryptic species, buoyed by differences in symbiont associations between these species.

Rampant Genome-Wide Admixture across the Heliconius Radiation

How frequent is gene flow between species? The pattern of evolution is typically portrayed as a phylogenetic tree, yet gene flow between good species may be an important mechanism in diversification, spreading adaptive traits and leading to a complex pattern of phylogenetic incongruence. This process has thus far been studied mainly among a few closely related species, or in geographically restricted areas such as islands, but not on the scale of a continental radiation. Using a genomic representation of 40 out of 47 species in the genus, we demonstrate that admixture has played a role throughout the evolution of the charismatic Neotropical butterflies Heliconius. Modeling of phylogenetic networks based on the exome uncovers up to 13 instances of interspecific gene flow. Admixture is detected among the relatives of Heliconius erato, as well as between the ancient lineages leading to modern clades. Interspecific gene flow played a role throughout the evolution of the genus, although the process has been most frequent in the clade of Heliconius melpomene and relatives. We identify Heliconius hecalesia and relatives as putative hybrids, including new evidence for introgression at the loci controlling the mimetic wing patterns. Models accounting for interspecific gene flow yield a more complete picture of the radiation as a network, which will improve our ability to study trait evolution in a realistic comparative framework.

Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad

Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Skåne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation.

Standing variation rather than recent adaptive introgression probably underlies differentiation of the texanus subspecies of Helianthus annuus

The origins of geographic races in wide-ranging species are poorly understood. In Texas, the texanus subspecies of Helianthus annuus has long been thought to have acquired its defining phenotypic traits via introgression from a local congener, H. debilis, but previous tests of this hypothesis were inconclusive. Here, we explore the origins of H. a. texanus using whole genome sequencing data from across the entire range of H. annuus and possible donor species, as well as phenotypic data from a common garden study. We found that although it is morphologically convergent with H. debilis, H. a. texanus has conflicting signals of introgression. Genome wide tests (Patterson's D and TreeMix) only found evidence of introgression from H. argophyllus (sister species to H. annuus and also sympatric), but not H. debilis, with the exception of one individual of 109 analysed. We further scanned the genome for localized signals of introgression using PCAdmix and found minimal but nonzero introgression from H. debilis and significant introgression from H. argophyllus in some populations. Given the paucity of introgression from H. debilis, we argue that the morphological convergence observed in Texas is probably from standing genetic variation. We also found that genomic differentiation in H. a. texanus is mostly driven by large segregating inversions, several of which have signatures of natural selection based on haplotype frequencies.

Hybrid watermilfoil (Myriophyllum spicatum × Myriophyllum sibiricum) exhibits traits associated with greater invasiveness than its introduced and native parental taxa

Hybridization has been associated with increased invasiveness in plants. In North America, the hybrid aquatic plant Myriophyllum spicatum × Myriophyllum sibiricum (hybrid watermilfoil, hereafter HWM) is a cross between non-native invasive Eurasian watermilfoil (M. spicatum, EWM) and native northern watermilfoil (M. sibiricum, NWM). Lab-based trials have demonstrated higher growth rates in HWM compared to EWM and NWM, but these patterns have not been systematically examined in the field. In this study, we compared the invasiveness of HWM to its parental taxa, EWM and NWM, by examining the amount and timing of: (1) flowering, (2) surface cover, and (3) biomass (using stem counts as a proxy). We conducted repeat surveys of Myriophyllum beds at eight lakes (2–3 lakes/taxon) in the Minneapolis–St. Paul Metropolitan area (Minnesota, USA) between June 2017 and November 2018. HWM produced more flower spikes earlier and overall, and maintained consistently more flower spikes throughout the growing season than EWM and NWM. In addition, surface cover reached greater annual peaks and was higher for longer throughout the growing season for HWM than for both parental taxa. We did not observe a significant difference in stem counts among the three taxa, but HWM did reach a higher maximum number of stems than either parental taxon. This study provides field-based evidence of increased invasiveness associated with hybridization between EWM and NWM; specifically, greater reproductive potential via flowering and greater surface cover may increase HWM spread, have greater impacts on native species, and pose more of a nuisance to lake users.

Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts

Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here, we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (Populus angustifolia) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate change impacts. We found that (1) P. angustifolia is differentiated into six genetic groups across its range from México to Canada and (2) different populations occupy distinct climate niches representing unique ecotypes. Comparing model discriminatory power, (3) all genetically informed ecological niche models (gENMs) outperformed the standard species-level ENM (3-14% increase in AUC; 1-23% increase in pROC). Furthermore, (4) gENMs predicted large differences among ecotypes in both the direction and magnitude of responses to climate change and (5) revealed evidence of niche divergence, particularly for the Eastern Rocky Mountain ecotype. (6) Models also predicted progressively increasing fragmentation and decreasing overlap between ecotypes. Contact zones are often hotspots of diversity that are critical for supporting species' capacity to respond to present and future climate change, thus predicted reductions in connectivity among ecotypes is of conservation concern. We further examined the generality of our findings by comparing our model developed for a higher elevation Rocky Mountain species with a related desert riparian cottonwood, P. fremontii. Together our results suggest that incorporating intraspecific genetic information can improve model performance by addressing this important source of variance. gENMs bring an evolutionary perspective to niche modeling and provide a truly "adaptive management" approach to support conservation genetic management of species facing global change.

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.

Hybridization and introgression of native and foreign Sorbus tree species in unique environments of protected mountainous areas

Hybridization and introgression are important processes influencing the genetic diversity and evolution of species. These processes are of particular importance in protected areas, where they can lead to the formation of hybrids between native and foreign species and may ultimately result in the loss of parental species from their natural range. Despite their importance, the contribution of hybridization and introgression to genetic diversity in Sorbus genus remains not fully recognized. We analysed the genetic and morphological variability of several Sorbus species including native (Sorbus aria), foreign (S. intermedia) and potentially hybrid (S. carpatica) individuals from the Polish Carpathian range. Patterns of variation at 13 nuclear microsatellite loci show hybridization between the tested species and confirm the existence of the hybrid form S. carpatica. Biometric analysis on leaves, based of 10 metric features and three parameters, identified several characters for preliminary taxonomic classification; however, none of them could be used as a fully diagnostic marker for faultless annotation of S. intermedia and S. carpatica. The genetic structure analysis indicated complex patterns of population differentiation and its diverse origin. The results allow assessment of genetic variation and identification of parental species participating in hybridization. This knowledge will advance the management of genetic diversity and development of conservation strategies for efficient maintenance of the unique protected ecosystem.

Patterns, Predictors, and Consequences of Dominance in Hybrids

AbstractCompared to those of their parents, are the traits of first-generation (F₁) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? To address this empirical gap, we compiled data from 233 crosses in which traits were measured in a common environment for two parent taxa and their F₁ hybrids. We find that individual traits in F₁s are halfway between the parental midpoint and one parental value. Considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (parent bias) about 50% more than the other, while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that parent bias improves fitness, whereas mismatch reduces fitness. Our study has three major conclusions. First, hybrids are not phenotypically intermediate but rather exhibit substantial mismatch. Second, dominance is likely determined by the idiosyncratic evolutionary trajectories of individual traits and populations. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.

Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity

Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing interspecific gene flow. However, hybridization in Amazonia's megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, using targeted sequence capture our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by reticulation, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ~19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species that co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and persistent hybridization. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization's rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.

Large-scale mutation in the evolution of a gene complex for cryptic coloration

The types of mutations affecting adaptation in the wild are only beginning to be understood. In particular, whether structural changes shape adaptation by suppressing recombination or by creating new mutations is unresolved. Here, we show that multiple linked but recombining loci underlie cryptic color morphs of Timema chumash stick insects. In a related species, these loci are found in a region of suppressed recombination, forming a supergene. However, in seven species of Timema, we found that a megabase-size "supermutation" has deleted color loci in green morphs. Moreover, we found that balancing selection likely contributes more to maintaining this mutation than does introgression. Our results show how suppressed recombination and large-scale mutation can help to package gene complexes into discrete units of diversity such as morphs, ecotypes, or species.

Genomics of Evolutionary Novelty in Hybrids and Polyploids

It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.

Massive haplotypes underlie ecotypic differentiation in sunflowers

Species often include multiple ecotypes that are adapted to different environments¹. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations^2-4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1-100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H. argophyllus (probably through deletion of a homologue of FLOWERING LOCUS T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other-possibly now-extinct-congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation.

Ambiguous species boundaries: Hybridization and morphological variation in two closely related Rubus species along altitudinal gradients

Although hybridization frequently occurs among plant species, hybrid zones of divergent lineages formed at species boundaries are less common and may not be apparent in later generations of hybrids with more parental-like phenotypes, as a consequence of backcrossing. To determine the effects of dispersal and selection on species boundaries, we compared clines in leaf traits and molecular hybrid index along two hybrid zones on Yakushima Island, Japan, in which a temperate (Rubus palmatus) and subtropical (Rubus grayanus) species of wild raspberry are found. Leaf sinus depth in the two hybrid zones had narrower clines at 600 m a.s.l. than the molecular hybrid index and common garden tests confirmed that some leaf traits, including leaf sinus depth that is a major trait used in species identification, are genetically divergent between these closely related species. The sharp transition in leaf phenotypic traits compared to molecular markers indicated divergent selection pressure on the hybrid zone structure. We suggest that species boundaries based on neutral molecular data may differ from those based on observed morphological traits.

VolcanoFinder: Genomic scans for adaptive introgression

Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method—VolcanoFinder—to detect recent events of adaptive introgression using polymorphism data from the recipient species only. VolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity. Using coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH-RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder.

The process by which beneficial alleles are introduced into a species from a closely-related species is termed adaptive introgression. We present an analytically-tractable model for the effects of adaptive introgression on non-adaptive genetic variation in the genomic region surrounding the beneficial allele. The result we describe is a characteristic volcano-shaped pattern of increased variability that arises around the positively-selected site, and we introduce an open-source method VolcanoFinder to detect this signal in genomic data. Importantly, VolcanoFinder is a population-genetic likelihood-based approach, rather than a comparative-genomic approach, and can therefore probe genomic variation data from a single population for footprints of adaptive introgression, even from a priori unknown and possibly extinct donor species.

Environment-dependent introgression from Quercus dentata to a coastal ecotype of Quercus mongolica var. crispula in northern Japan

Introgression from one species in a specific environment to another may facilitate colonization of the environment by the recipient species. However, such environment-dependent introgression has been clarified in limited plant taxa. In northern Japan, there are two interfertile oak species: Quercus dentata (Qd) in coastal areas and Q. mongolica var. crispula (Qc) in inland areas. However, at higher latitudes where Qd is rare, a coastal Qc ecotype with Qd-like traits is distributed in the coastal areas. We distinguished inland Qc, coastal Qc, and coastal Qd populations based on genome-wide genotypes and multitrait phenotypes and verified introgression from coastal Qd to coastal Qc using reduced library sequencing. Genotypes and phenotypes differed among the populations, and coastal Qc was intermediate between inland Qc and coastal Qd. The ABBA-BABA test showed introgression from coastal Qd to coastal Qc. In coastal Qc, we found various stages of introgression after the first generation of backcross but detected no genomic regions where introgression was enhanced. Overall, we show evidence for introgression from a coastal species to an ecotype of an inland species, which has colonized the coastal environment. It remains unclear whether introgressed alleles are selected in the coastal environment.

Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum

BACKGROUND AND AIMS

The mosses Homalothecium lutescens and H. sericeum are genetically, morphologically and ecologically differentiated; mixed populations sometimes occur. In sympatric populations, intermediate character states among gametophytes and sporophytes have been observed, suggesting hybridization and introgression in such populations.

METHODS

We determined genotypes using bi-allelic co-dominant single nucleotide polymorphism (SNP) markers, specific to either H. lutescens or H. sericeum, to estimate the degree of genetic mixing in 449 moss samples collected from seven sympatric and five allopatric populations on the island of Öland, south Sweden. The samples represented three generations: haploid maternal gametophytes; diploid sporophytes; and haploid sporelings.

KEY RESULTS

Admixture analyses of SNP genotypes identified a majority as pure H. lutescens or H. sericeum, but 76 samples were identified as mildly admixed (17 %) and 17 samples (3.8 %) as strongly admixed. Admixed samples were represented in all three generations in several populations. Hybridization and introgression were bidirectional.

CONCLUSIONS

Our results demonstrate that admixed genomes are transferred between the generations, so that the populations behave as true hybrid zones. Earlier studies of sympatric bryophyte populations with admixed individuals have not been able to show that admixed alleles are transferred beyond the first generation. The presence of true hybrid zones has strong evolutionary implications because genetic material transferred across species boundaries can be directly exposed to selection in the long-lived haploid generation of the bryophyte life cycle, and contribute to local adaptation, long-term survival and speciation.

Rapid genomic DNA variation in newly hybridized carp lineages derived from Cyprinus carpio (♀) × Megalobrama amblycephala (♂)

Background

Distant hybridization can generate changes in phenotypes and genotypes that lead to the formation of new hybrid lineages with genetic variation. In this study, the establishment of two bisexual fertile carp lineages, including the improved diploid common carp (IDC) lineage and the improved diploid scattered mirror carp (IDMC) lineage, from the interspecific hybridization of common carp (Cyprinus carpio, 2n = 100) (♀) × blunt snout bream (Megalobrama amblycephala, 2n = 48) (♂), provided a good platform to investigate the genetic relationship between the parents and their hybrid progenies.

Result

In this study, we investigated the genetic variation of 12 Hox genes in the two types of improved carp lineages derived from common carp (♀) × blunt snout bream (♂). Hox gene clusters were abundant in the first generation of IDC, but most were not stably inherited in the second generation. In contrast, we did not find obvious mutations in Hox genes in the first generation of IDMC, and almost all the Hox gene clusters were stably inherited from the first generation to the second generation of IDMC. Interestingly, we found obvious recombinant clusters of Hox genes in both improved carp lineages, and partially recombinant clusters of Hox genes were stably inherited from the first generation to the second generation in both types of improved carp lineages. On the other hand, some Hox genes were gradually becoming pseudogenes, and some genes were completely pseudogenised in IDC or IDMC.

Conclusions

Our results provided important evidence that distant hybridization produces rapid genomic DNA changes that may or may not be stably inherited, providing novel insights into the function of hybridization in the establishment of improved lineages used as new fish resources for aquaculture.

Importance of Pollinator-Mediated Interspecific Pollen Transfer for Angiosperm Evolution

Understanding how pollen moves between species is critical to understanding speciation, diversification, and evolution of flowering plants. For co-flowering species that share pollinators, competition through interspecific pollen transfer (IPT) can profoundly impact floral evolution, decreasing female fitness via heterospecific pollen deposition on stigmas and male fitness via pollen misplacement during visits to heterospecific flowers. The pollination literature demonstrates that such reproductive interference frequently selects for reproductive character displacement in floral traits linked to pollinator attraction, pollen placement, and mating systems and has also revealed that IPT between given pairs of species is typically asymmetric. More recent work is starting to elucidate its importance to the speciation process, clarifying the link between IPT and current and historical patterns of hybridization, the evolution of phenotypic novelty through adaptive introgression, and the rise of reproductive isolation. Our review aims to stimulate further research on IPT as a ubiquitous mechanism that plays a central role in angiosperm diversification.

Divergence in drought-response traits between sympatric species of Mimulus

Differential adaptation to local environmental conditions is thought to be an important driver of speciation. Plants, whose sedentary lifestyle necessitates fine-tuned adaptation to edaphic conditions such as water availability, are often distributed based on these conditions. Populations occupying water-limited habitats may employ a variety of strategies, involving numerous phenotypes, to prevent and withstand desiccation. In sympatry, two closely related Mimulus species-M. guttatus and M. nasutus-occupy distinct microhabitats that differ in seasonal water availability. In a common garden experiment, we characterized natural variation within and between sympatric M. guttatus and M. nasutus in the ability to successfully set seed under well-watered and drought conditions. We also measured key phenotypes for drought adaptation, including developmental timing, plant size, flower size, and stomatal density. Consistent with their microhabitat associations in nature, M. nasutus set seed much more successfully than M. guttatus under water-limited conditions. This divergence in reproductive output under drought was due to differences in mortality after the onset of flowering, with M. nasutus surviving at a much higher rate than M. guttatus. Higher seed set in M. nasutus was mediated, at least in part, by a plastic increase in the rate of late-stage development (i.e., fruit maturation), consistent with the ability of this species to inhabit more ephemeral habitats in the field. Our results suggest adaptation to water availability may be an important factor in species maintenance of these Mimulus taxa in sympatry.

Population structure of Betula albosinensis and Betula platyphylla: evidence for hybridization and a cryptic lineage

BACKGROUND AND AIMS

Differences in local abundance and ploidy level are predicted to impact the direction of introgression between species. Here, we tested these hypotheses on populations of Betula albosinensis (red birch) and Betula platyphylla (white birch) which were thought to differ in ploidy level, the former being tetraploid and the latter diploid.

METHODS

We sampled 391 birch individuals from nine localities in China, and classified them into species based on leaf morphology. Twelve nuclear microsatellite markers were genotyped in each sample, and analysed using principal coordinates analysis and STRUCTURE software. We compared the effects of two different methods of scoring polyploid genotypes on population genetic analyses. We analysed the effect of ploidy, local species abundance and latitude on levels of introgression between the species.

KEY RESULTS

Leaf morphology divided our samples into red and white birch, but genetic analyses unexpectedly revealed two groups within red birch, one of which was tetraploid, as expected, but the other of which appeared to have diploid microsatellite genotypes. Five individuals were identified as early-generation hybrids or backcrosses between white birch and red birch and five were identified between red birch and 'diploid' red birch. Cline analysis showed that levels of admixture were not significantly correlated with latitude. Estimated genetic differentiation among species was not significantly different between determined tetraploid and undetermined tetraploid genotypes.

CONCLUSIONS

Limited hybridization and gene flow have occurred between red birch and white birch. Relative species abundance and ploidy level do not impact the direction of introgression between them, as genetic admixture is roughly symmetrical. We unexpectedly found populations of apparently diploid red birch and this taxon may be a progenitor of allotetraploid red birch populations. Incomplete lineage sorting may explain patterns of genetic admixture between apparently diploid and allotetraploid red birch.

Hybridization speeds adaptive evolution in an eight-year field experiment

Hybridization is a common phenomenon, yet its evolutionary outcomes remain debated. Here, we ask whether hybridization can speed adaptive evolution using resynthesized hybrids between two species of Texas sunflowers (Helianthus annuus and H. debilis) that form a natural hybrid in the wild (H. annuus ssp. texanus). We established separate control and hybrid populations and allowed them to evolve naturally in a field evolutionary experiment. In a final common-garden, we measured fitness and a suite of key traits for these lineages. We show that hybrid fitness evolved in just seven generations, with fitness of the hybrid lines exceeding that of the controls by 14% and 51% by the end of the experiment, though only the latter represents a significant increase. More traits evolved significantly in hybrids relative to controls, and hybrid evolution was faster for most traits. Some traits in both hybrid and control lineages evolved in an adaptive manner consistent with the direction of phenotypic selection. These findings show a causal pathway from hybridization to rapid adaptation and suggest an explanation for the frequently noted association between hybridization and adaptive radiation, range expansion, and invasion.

Adaptive introgression: a plant perspective

Introgression is emerging as an important source of novel genetic variation, alongside standing variation and mutation. It is adaptive when such introgressed alleles are maintained by natural selection. Recently, there has been an explosion in the number of studies on adaptive introgression. In this review, we take a plant perspective centred on four lines of evidence: (i) introgression, (ii) selection, (iii) phenotype and (iv) fitness. While advances in genomics have contributed to our understanding of introgression and porous species boundaries (task 1), and the detection of signatures of selection in introgression (task 2), the investigation of adaptive introgression critically requires links to phenotypic variation and fitness (tasks 3 and 4). We also discuss the conservation implications of adaptive introgression in the face of climate change. Adaptive introgression is particularly important in rapidly changing environments, when standing genetic variation and mutation alone may only offer limited potential for adaptation. We conclude that clarifying the magnitude and fitness effects of introgression with improved statistical techniques, coupled with phenotypic evidence, has great potential for conservation and management efforts.

Chloroplast DNA variation in a hyperdiverse tropical tree community

We investigate chloroplast DNA variation in a hyperdiverse community of tropical rainforest trees in French Guiana, focusing on patterns of intraspecific and interspecific variation. We test whether a species genetic diversity is higher when it has congeners in the community with which it can exchange genes and if shared haplotypes are more frequent in genetically diverse species, as expected in the presence of introgression.We sampled a total of 1,681 individual trees from 472 species corresponding to 198 genera and sequenced them at a noncoding chloroplast DNA fragment.Polymorphism was more frequent in species that have congeneric species in the study site than in those without congeners (30% vs. 12%). Moreover, more chloroplast haplotypes were shared with congeners in polymorphic species than in monomorphic ones (44% vs. 28%).Despite large heterogeneities caused by genus-specific behaviors in patterns of hybridization, these results suggest that the higher polymorphism in the presence of congeners is caused by local introgression rather than by incomplete lineage sorting. Our findings suggest that introgression has the potential to drive intraspecific genetic diversity in species-rich tropical forests.

Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation

Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as "adaptive introgression". Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers' knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.

RAD-seq reveals genetic structure of the F2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression

BACKGROUND

Hybridization of species with porous genomes can eventually lead to introgression via repeated backcrossing. The potential for introgression between species is reflected by the extent of segregation distortion in later generation hybrids. Here we studied a population of hybrids between Salix purpurea and S. helvetica that has emerged within the last 30 years on a glacier forefield in the European Alps due to secondary contact of the parental species. We used 5758 biallelic SNPs produced by RAD sequencing with the aim to ascertain the predominance of backcrosses (F1 hybrid x parent) or F2 hybrids (F1 hybrid x F1 hybrid) among hybrid offspring. Further, the SNPs were used to study segregation distortion in the second hybrid generation.

RESULTS

The analyses in STRUCTURE and NewHybrids revealed that the population consisted of parents and F1 hybrids, whereas hybrid offspring consisted mainly of backcrosses to either parental species, but also some F2 hybrids. Although there was a clear genetic differentiation between S. purpurea and S. helvetica (FST = 0.24), there was no significant segregation distortion in the backcrosses or the F2 hybrids. Plant height of the backcrosses resembled the respective parental species, whereas F2 hybrids were more similar to the subalpine S. helvetica.

CONCLUSIONS

The co-occurrence of the parental species and the hybrids on the glacier forefield, the high frequency of backcrossing, and the low resistance to gene flow via backcrossing make a scenario of introgression in this young hybrid population highly likely, potentially leading to the transfer of adaptive traits. We further suggest that this willow hybrid population may serve as a model for the evolutionary processes initiated by recent global warming.

A comparison of genomic islands of differentiation across three young avian species pairs

Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., "islands of differentiation" in F_ST ), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray's/mourning warblers; Townsend's/black-throated green warblers; and Audubon's/myrtle warblers) consists of forms that were likely separated in western and eastern North American refugia during cycles of Pleistocene glaciations and have now come into contact in western Canada, where each forms a narrow hybrid zone. We show strong differences between pairs in their patterns of genomic heterogeneity in F_ST , suggesting differing selective forces and/or differing genomic responses to similar selective forces among the three pairs. Across most of the genome, levels of within-group nucleotide diversity (π_Within ) are almost as large as levels of between-group nucleotide distance (π_Between ) within each pair, suggesting recent common ancestry and/or gene flow. In two pairs, a pattern of the F_ST peaks having low π_Between suggests that selective sweeps spread between geographically differentiated groups, followed by local differentiation. This "sweep-before-differentiation" model is consistent with signatures of gene flow within the yellow-rumped warbler species complex. These findings add to our growing understanding of speciation as a complex process that can involve phases of adaptive introgression among partially differentiated populations.

Genetic basis and evolution of rapid cycling in railway populations of tetraploid Arabidopsis arenosa

Spatially structured plant populations with diverse adaptations provide powerful models to investigate evolution. Human-generated ruderal habitats are abundant and low-competition, but are challenging for plants not adapted to them. Ruderal habitats also sometimes form networked corridors (e.g. roadsides and railways) that allow rapid long-distance spread of successfully adapted variants. Here we use transcriptomic and genomic analyses, coupled with genetic mapping and transgenic follow-up, to understand the evolution of rapid cycling during adaptation to railway sites in autotetraploid Arabidopsis arenosa. We focus mostly on a hybrid population that is likely a secondary colonist of a railway site. These mountain railway plants are phenotypically similar to their cosmopolitan cousins. We thus hypothesized that colonization primarily involved the flow of adaptive alleles from the cosmopolitan railway variant. But our data shows that it is not that simple: while there is evidence of selection having acted on introgressed alleles, selection also acted on rare standing variation, and new mutations may also contribute. Among the genes we show have allelic divergence with functional relevance to flowering time are known regulators of flowering, including FLC and CONSTANS. Prior implications of these genes in weediness and rapid cycling supports the idea that these are “evolutionary hotspots” for these traits. We also find that one of two alleles of CONSTANS under selection in the secondary colonist was selected from rare standing variation in mountain populations, while the other was introgressed from the cosmopolitan railway populations. The latter allele likely arose in diploid populations over 700km away, highlighting how ruderal populations could act as allele conduits and thus influence local adaptation.

The Response of Photosynthetic Functions of F1 Cutting Seedlings From Physocarpus amurensis Maxim (♀) × Physocarpus opulifolius "Diabolo" (♂) and the Parental Seedlings to Salt Stress

This paper selected clonal cutting seedlings from the F1 hybrid varieties of Physocarpus amurensis Maxim (♀) × P. opulifolius "Diabolo" (♂) as research material to study the response of the photosynthetic gas exchange parameters and chlorophyll fluorescence parameters of P. amurensis hybrids and their parental leaves to NaCl stress (with concentrations of 0, 50, 100, and 200 mmol⋅L-1). The results showed that under salt stress, the stomatal conductance (Gs), transpiration rate (Tr), and net photosynthetic rate (Pn) of the three kinds of P. amurensis all significantly decreased. When the NaCl concentration was below 100 mmol⋅L-1, the intercellular CO2 concentration (Ci) of leaves of the three samples declined with the increase of salt concentration; however, when the concentration increased to 200 mmol⋅L-1, Ci did not decrease significantly, especially when the Ci of P. opulifolius "Diabolo" presented a slight increase. This indicated that the decline of photosynthetic carbon assimilation capacity induced by salt stress was the consequence of interaction between stomatal factors and non-stomatal factors, and the stomatal factors played an important role when the salt concentration was below 200 mmol⋅L-1. Compared with P. amurensis, the photosynthetic gas exchange capability of P. opulifolius "Diabolo" leaves was more sensitive to salt stress, and the limitation of non-stomatal factors was relatively evident. However, the photosynthetic capacity of hybrid P. amurensis leaves with the desired purple color was improved compared with P. amurensis. Under salt stress, the PSII activity of the three kinds of P. amurensis leaves declined, the electron transfer was inhibited, and obvious signs of photoinhibition were present. The PSII activity of P. opulifolius "Diabolo" leaves was more sensitive to salt stress than that in P. amurensis. Under salt stress, the NPQ of P. opulifolius "Diabolo" leaves decreased greatly, while under high salt concentrations the degree of photoinhibition in P. amurensis and hybrid P. amurensis were reduced due to a relatively high NPQ. With the increase of salt concentration, the Vk of P. amurensis and hybrid P. amurensis leaves presented a decreasing trend. However, the Vk of P. opulifolius "Diabolo" leaves increased slightly. This suggested that the effects of salt stress on the oxygen-evolving complex (OEC) of the three P. amurensis sample types were relatively limited and only the OEC of P.s opulifolius "Diabolo" leaves were slightly sensitive to salt stress. The VJ of all leaves from the three P. amurensis types increased under salt stress, and the VJ increased significantly when the salt concentration increased to 200 mmol⋅L-1, indicating that salt stress obviously impeded the electron transfer chain from QA to QB on the PSII receptor side. Moreover, high salt concentrations caused thylakoid membrane dissociation. The electron transfer and degree of damage to the thylakoid membrane of P. opulifolius "Diabolo" leaves were obviously higher than that of P. amurensis. However, the electron transfer capacity on the PSII receptor side as well as the degree of damage of the thylakoid membrane of hybrid P. amurensis leaves was obviously lower than those of P. opulifolius "Diabolo." The salt tolerance of photosynthetic functions of hybrid P. amurensis (♀) × P. opulifolius "Diabolo" (♂) leaves was improved compared with that of parental P. opulifolius "Diabolo," and the hybrid shows obvious hybrid vigor for photosynthesis.

New prospects in the detection and comparative analysis of hybridization in the tree of life

Assessing the relative importance of the various pathways to diversification is a central goal of biodiversity researchers. For plant biologists, and increasingly across the spectrum of biological sciences, among these pathways of interest is hybridization. New methodological developments are moving the field away from questions of whether natural hybridization occurs or hybrids can persist and toward more direct assessments of the long-term impact of hybridization on diversification and genome organization. Advances in theory and new data, especially phylogenomic data, have changed the face of this field, revealing extensive occurrences of hybridization at both shallow and deep levels, but lacking is a synthesis of these advancements. Here we provide an overview of methods that have been proposed for detecting hybridization with molecular data and advocate a time-extended, comparative view of reticulate evolution. In particular, we pose three overarching questions, newly placed within reach, that are critical for advancing our understanding of hybridization pattern and process: (1) How often is introgression biased toward certain genomes and loci, and is this bias selectively neutral? (2) What are the relative rates of formation of hybrid species and introgressants, and how does this compare to their subsequent fates? (3) Has the frequency of hybridization increased under historical periods of greater dynamism in climate and geographic range, such as the Pleistocene?

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.

Conflict between heterozygote advantage and hybrid incompatibility in haplodiploids (and sex chromosomes)

In many diploid species, the sex chromosomes play a special role in mediating reproductive isolation. In haplodiploids, where females are diploid and males haploid, the whole genome behaves similarly to the X/Z chromosomes of diploids. Therefore, haplodiploid systems can serve as a model for the role of sex chromosomes in speciation and hybridization. A previously described population of Finnish Formica wood ants displays genome-wide signs of ploidally and sexually antagonistic selection resulting from hybridization. Here, hybrid females have increased survivorship but hybrid males are inviable. To understand how the unusual hybrid population may be maintained, we developed a mathematical model with hybrid incompatibility, female heterozygote advantage, recombination and assortative mating. The rugged fitness landscape resulting from the co-occurrence of heterozygote advantage and hybrid incompatibility results in a sexual conflict in haplodiploids, which is caused by the ploidy difference. Thus, whereas heterozygote advantage always promotes long-term polymorphism in diploids, we find various outcomes in haplodiploids in which the population stabilizes either in favour of males, females or via maximizing the number of introgressed individuals. We discuss these outcomes with respect to the potential long-term fate of the Finnish wood ant population and provide approximations for the extension of the model to multiple incompatibilities. Moreover, we highlight the general implications of our results for speciation and hybridization in haplodiploids versus diploids and how the described fitness relationships could contribute to the outstanding role of sex chromosomes as hotspots of sexual antagonism and genes involved in speciation.

Introgression between ecologically distinct species following increased salinity in the Colorado Delta- Worldwide implications for impacted estuary diversity

We investigate hybridization and introgression between ecologically distinct sister species of silverside fish in the Gulf of California through combined analysis of morphological, sequence, and genotypic data. Water diversions in the past century turned the Colorado River Delta from a normal estuary to a hypersaline inverse estuary, raising concerns for the local fauna, much of which is endangered. Salinity differences are known to generate ecological species pairs and we anticipated that loss of the fresher-water historic salinity regime could alter the adaptive factors maintaining distinction between the broadly distributed Gulf-endemic Colpichthys regis and the narrowly restricted Delta-endemic Colpichthys hubbsi, the species that experienced dramatic environmental change. In this altered environmental context, these long-isolated species (as revealed by Cytochrome b sequences) show genotypic (RAG1, microsatellites) evidence of active hybridization where the species ranges abut, as well as directional introgression from C. regis into the range center of C. hubbsi. Bayesian group assignment (STRUCTURE) on six microsatellite loci and multivariate analyses (DAPC) on both microsatellites and phenotypic data further support substantial recent admixture between the sister species. Although we find no evidence for recent population decline in C. hubbsi based on mitochondrial sequence, introgression may be placing an ancient ecological species at risk of extinction. Such introgressive extinction risk should also pertain to other ecological species historically sustained by the now changing Delta environment. More broadly, salinity gradient associated ecological speciation is evident in silverside species pairs in many estuarine systems around the world. Ecological species pairs among other taxa in such systems are likely poorly understood or cryptic. As water extraction accelerates in river systems worldwide, salinity gradients will necessarily be altered, impacting many more estuary and delta systems. Such alteration of habitats will place biodiversity at risk not only from direct effects of habitat destruction, but also from the potential for the breakdown of ecological species. Thus, evolutionary response to the anthropogenic alteration of salinity gradients in estuaries merits investigation as the number of impacted systems increases around the globe, permitting parallel study of multiple systems, while also permitting a conservation management response to help preserve this little championed component of biodiversity.

Hybrids and horizontal transfer: introgression allows adaptive allele discovery

Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.