Hybrid speciation and independent evolution in lineages of alpine butterflies

Non-random sorting of parental chemical compounds during hybrid speciation

The role of hybridization during speciation remains partially understood, yet introgression among lineages may trigger reproductive isolation (RI). Hybrid speciation may reveal how specific traits drive RI and how characters are sorted following admixture. Here, we study hybrid speciation in a complex of butterfly species (Coenonympha spp.) in which 2 hybrid lineages (C. darwiniana and C. cephalidarwiniana) received about 75% of their genomes from C. arcania, and 25% from C. gardetta. By contrast with their genomic ancestry compositions, hybrid lineages mate readily with their minor parent in contact zones, while the major parent shows nearly complete isolation from all lineages. To test whether hybrid speciation operated via the non-random sorting of traits acting as pre-zygotic barriers, we assessed chemical profile similarity between species using gas chromatography-mass spectrometry and contrasted it to genomic composition and natural patterns of hybridization. Both hybrid species exhibited profiles strikingly similar to their minor parent despite the genomic contribution of the major parent, matching predictions for isolating traits. This suggests that chemical traits were sorted non-randomly during hybrid speciation and that they contributed to RI from the major parent. Our results reveal how hybridization may trigger rapid speciation and underscore the significance of chemical signalling in shaping barriers among emerging species.

Fluctuating reproductive isolation and stable ancestry structure in a fine-scaled mosaic of hybridizing Mimulus monkeyflowers

Hybridization among taxa impacts a variety of evolutionary processes from adaptation to extinction. We seek to understand both patterns of hybridization across taxa and the evolutionary and ecological forces driving those patterns. To this end, we use whole-genome low-coverage sequencing of 458 wild-grown and 1565 offspring individuals to characterize the structure, stability, and mating dynamics of admixed populations of Mimulus guttatus and Mimulus nasutus across a decade of sampling. In three streams, admixed genomes are common and a M. nasutus organellar haplotype is fixed in M. guttatus, but new hybridization events are rare. Admixture is strongly unidirectional, but each stream has a unique distribution of ancestry proportions. In one stream, three distinct cohorts of admixed ancestry are spatially structured at ~20-50m resolution and stable across years. Mating system provides almost complete isolation of M. nasutus from both M. guttatus and admixed cohorts, and is a partial barrier between admixed and M. guttatus cohorts. Isolation due to phenology is near-complete between M. guttatus and M. nasutus. Phenological isolation is a strong barrier in some years between admixed and M. guttatus cohorts, but a much weaker barrier in other years, providing a potential bridge for gene flow. These fluctuations are associated with differences in water availability across years, supporting a role for climate in mediating the strength of reproductive isolation. Together, mating system and phenology accurately predict fluctuations in assortative mating across years, which we estimate directly using paired maternal and offspring genotypes. Climate-driven fluctuations in reproductive isolation may promote the longer-term stability of a complex mosaic of hybrid ancestry, preventing either complete isolation or complete collapse of species barriers.

A Next Generation of Hierarchical Bayesian Analyses of Hybrid Zones Enables Model-Based Quantification of Variation in Introgression in R

Hybrid zones, where genetically distinct groups of organisms meet and interbreed, offer valuable insights into the nature of species and speciation. Here, we present a new R package, bgchm, for population genomic analyses of hybrid zones. This R package extends and updates the existing bgc software and combines Bayesian analyses of hierarchical genomic clines with Bayesian methods for estimating hybrid indexes, interpopulation ancestry proportions, and geographic clines. Compared to existing software, bgchm offers enhanced efficiency through Hamiltonian Monte Carlo sampling and the ability to work with genotype likelihoods combined with a hierarchical Bayesian approach, enabling inference for diverse types of genetic data sets. The package also facilitates the quantification of introgression patterns across genomes, which is crucial for understanding reproductive isolation and speciation genetics. We first describe the models underlying bgchm and then provide an overview of the R package and illustrate its use through the analysis of simulated and empirical data sets. We show that bgchm generates accurate estimates of model parameters under a variety of conditions, especially when the genetic loci analyzed are highly ancestry informative. This includes relatively robust estimates of genome-wide variability in clines, which has not been the focus of previous models and methods. We also illustrate how both selection and genetic drift contribute to variability in introgression among loci and how additional information can be used to help distinguish these contributions. We conclude by describing the promises and limitations of bgchm, comparing bgchm to other software for genomic cline analyses, and identifying areas for fruitful future development.

Introgression from extinct species facilitates adaptation to its vacated niche

Anthropogenic disturbances of ecosystems are causing a loss of biodiversity at an unprecedented rate. Species extinctions often leave ecological niches underutilized, and their colonization by other species may require new adaptation. In Lake Constance, on the borders of Germany, Austria and Switzerland, an endemic profundal whitefish species went extinct during a period of anthropogenic eutrophication. In the process of extinction, the deep-water species hybridized with three surviving whitefish species of Lake Constance, resulting in introgression of genetic variation that is potentially adaptive in deep-water habitats. Here, we sampled a water depth gradient across a known spawning ground of one of these surviving species, Coregonus macrophthalmus, and caught spawning individuals at greater depths (down to 90 m) than historically recorded. We sequenced a total of 96 whole genomes, 11-17 for each of six different spawning depth populations (4, 12, 20, 40, 60 and 90 m), to document genomic intraspecific differentiation along a water depth gradient. We identified 52 genomic regions that are potentially under divergent selection between the deepest (90 m) and all shallower (4-60 m) spawning habitats. At 12 (23.1%) of these 52 loci, the allele frequency pattern across historical and contemporary populations suggests that introgression from the extinct species potentially facilitates ongoing adaptation to deep water. Our results are consistent with the syngameon hypothesis, proposing that hybridization between members of an adaptive radiation can promote further niche expansion and diversification. Furthermore, our findings demonstrate that introgression from extinct into extant species can be a source of evolvability, enabling rapid adaptation to environmental change, and may contribute to the ecological recovery of ecosystem functions after extinctions.

Genomic evidence of speciation by fusion in a recent radiation of grasshoppers

Postdivergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). Although neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (about 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate their long-term persistence through geographic isolation from parental forms in topographically complex landscapes.

A continental-scale survey of Wolbachia infections in blue butterflies reveals evidence of interspecific transfer and invasion dynamics

Infections by maternally inherited bacterial endosymbionts, especially Wolbachia, are common in insects and other invertebrates but infection dynamics across species ranges are largely under studied. Specifically, we lack a broad understanding of the origin of Wolbachia infections in novel hosts, and the historical and geographical dynamics of infections that are critical for identifying the factors governing their spread. We used Genotype-by-Sequencing data from previous population genomics studies for range-wide surveys of Wolbachia presence and genetic diversity in North American butterflies of the genus Lycaeides. As few as one sequence read identified by assembly to a Wolbachia reference genome provided high accuracy in detecting infections in host butterflies as determined by confirmatory PCR tests, and maximum accuracy was achieved with a threshold of only 5 sequence reads per host individual. Using this threshold, we detected Wolbachia in all but 2 of the 107 sampling localities spanning the continent, with infection frequencies within populations ranging from 0% to 100% of individuals, but with most localities having high infection frequencies (mean = 91% infection rate). Three major lineages of Wolbachia were identified as separate strains that appear to represent 3 separate invasions of Lycaeides butterflies by Wolbachia. Overall, we found extensive evidence for acquisition of Wolbachia through interspecific transfer between host lineages. Strain wLycC was confined to a single butterfly taxon, hybrid lineages derived from it, and closely adjacent populations in other taxa. While the other 2 strains were detected throughout the rest of the continent, strain wLycB almost always co-occurred with wLycA. Our demographic modeling suggests wLycB is a recent invasion. Within strain wLycA, the 2 most frequent haplotypes are confined almost exclusively to separate butterfly taxa with haplotype A1 observed largely in Lycaeides melissa and haplotype A2 observed most often in Lycaeides idas localities, consistent with either cladogenic mode of infection acquisition from a common ancestor or by hybridization and accompanying mutation. More than 1 major Wolbachia strain was observed in 15 localities. These results demonstrate the utility of using resequencing data from hosts to quantify Wolbachia genetic variation and infection frequency and provide evidence of multiple colonizations of novel hosts through hybridization between butterfly lineages and complex dynamics between Wolbachia strains.

Hybridization fuelled diversification in Spialia butterflies

The importance of hybridization and introgression is well documented in the evolution of plants but, in insects, their role is not fully understood. Given the fact that insects are the most diverse group of organisms, assessing the impact of reticulation events on their evolution may be key to comprehend the emergence of such remarkable diversity. Here, we used an insect model, the Spialia butterflies, to gather genomic evidence of hybridization as a promoter of novel diversity. By using double‐digest RADseq (ddRADseq), we explored the phylogenetic relationships between Spialia orbifer, S. rosae and S. sertorius, and documented two independent events of interspecific gene flow. Our data support that the Iberian endemism S. rosae probably received genetic material from S. orbifer in both mitochondrial and nuclear DNA, which could have contributed to a shift in the ecological preferences of S. rosae. We also show that admixture between S. sertorius and S. orbifer probably occurred in Italy. As a result, the admixed Sicilian populations of S. orbifer are differentiated from the rest of populations both genetically and morphologically, and display signatures of reproductive character displacement in the male genitalia. Additionally, our analyses indicated that genetic material from S. orbifer is present in S. sertorius along the Italian Peninsula. Our findings add to the view that hybridization is a pervasive phenomenon in nature and in butterflies in particular, with important consequences for evolution due to the emergence of novel phenotypes.

Predictors of genomic differentiation within a hybrid taxon

Hybridization is increasingly recognized as an important evolutionary force. Novel genetic methods now enable us to address how the genomes of parental species are combined in hybrid lineages. However, we still do not know the relative importance of admixed proportions, genome architecture and local selection in shaping hybrid genomes. Here, we take advantage of the genetically divergent island populations of Italian sparrow on Crete, Corsica and Sicily to investigate the predictors of genomic variation within a hybrid taxon. We test if differentiation is affected by recombination rate, selection, or variation in ancestry proportions. We find that the relationship between recombination rate and differentiation is less pronounced within hybrid lineages than between the parent species, as expected if purging of minor parent ancestry in low recombination regions reduces the variation available for differentiation. In addition, we find that differentiation between islands is correlated with differences in signatures of selection in two out of three comparisons. Signatures of selection within islands are correlated across all islands, suggesting that shared selection may mould genomic differentiation. The best predictor of strong differentiation within islands is the degree of differentiation from house sparrow, and hence loci with Spanish sparrow ancestry may vary more freely. Jointly, this suggests that constraints and selection interact in shaping the genomic landscape of differentiation in this hybrid species.

Hybridization Outcomes Have Strong Genomic and Environmental Contingencies

AbstractExtreme F₂ phenotypes known as transgressive segregants can cause increased or decreased fitness in hybrids beyond the ranges seen in parental populations. Despite the usefulness of transgression for plant and animal breeding and its potential role in hybrid speciation, the genetic mechanisms and predictors of transgressive segregation remain largely untested. We generated seven hybrid crosses between five widely divergent Saccharomyces yeast species and measured the fitness of the parents and their viable F₁ and F₂ hybrids in seven stressful environments. We found that on average 16.6% of all replicate F₂ hybrids had higher fitness than both parents. Against our predictions, transgression frequency was not a function of parental genetic and phenotypic distances across test environments. Within environments, some relationships were significant, but not in the predicted direction; for example, genetic distance was negatively related to transgression in ethanol and hydrogen peroxide. Significant effects of hybrid cross, test environment, and cross × environment interactions suggest that the amount of transgression produced in a hybrid cross is highly context specific and that outcomes of hybridization differ even among crosses made from the same two parents. If the goal is to reliably predict hybrid fitness and forecast the evolutionary potential of admixed populations, we need more efforts to identify patterns beyond the idiosyncrasies caused by specific genomic or environmental contexts.

Genetic, morphological and ecological variation across a sharp hybrid zone between two alpine butterfly species

Identifying the mechanisms involved in the formation and maintenance of species is a central question in evolutionary biology, and distinguishing the selective drivers of populations' divergence from demographic processes is of particular interest to better understand the speciation process. Hybrid zones are recognized to provide ideal places to investigate the genetic architecture of speciation and to identify the mechanisms allowing diverging species to maintain their integrity in the face of gene flow. Here, we studied two alpine butterfly species, Coenonympha macromma and C. gardetta, which can be found flying together and hybridizing in narrow contact zones in the southern French Alps. We characterized the genomic composition of individuals, their morphology and their local habitat requirements, within and around a hybrid zone. Genetic diversity analysis at 794 SNPs revealed that all individuals within the hybrid zone were highly admixed, which was not the case outside the hybrid zone. Cline analysis showed that, despite ongoing hybridization, 56 out of 122 loci differentially fixed or nearly so between the two species were impermeable to introgression across the sharp hybrid zone (9 km wide). We also found concordance in cline position and width among genetic, morphological and environmental variation, suggesting a coupling of different reproductive barriers. Habitat characteristics such as the presence of trees and shrubs and the start of the growing season were strongly associated with the genetic variation, and we found evidence of divergence at genetic markers associated with morphology and physiology, putatively involved in visual or environmental reproductive isolation. We discuss the various behavioural and ecological factors that might interplay to maintain current levels of divergence and gene flow between this species pair.

Salticidae (Arachnida, Araneae) of Thailand: new species and records of Epeus Peckham & Peckham, 1886 and Ptocasius Simon, 1885

The study is based on new material from the collections of the Naturalis Biodiversity Centre in Leiden (RNHM) and the Hungarian Natural History Museum (HNHM) and addresses issues in two genera: Epeus Peckham & Peckham, 1886 and Ptocasius Simon, 1885 from Thailand. Both genera are of Asian/Indomalayan origin, the latter with a diversity hotspot in the subtropical valleys of the Himalayas. Based on morphological data, we propose three new species of Epeus (Epeus daiqini sp. nov. (♂♀), Epeus pallidus sp. nov. (♀), Epeus szirakii sp. nov. (♀)) and two new species of Ptacasius (Ptocasius metzneri sp. nov. (♂♀) and Ptocasius sakaerat sp. nov. (♀)). Additionally, we redescribed E. tener (Simon, 1877) and added photographs of morphological characters. The genus Ptocasius is redefined due to the inclusion of 37 species, previously included in Yaginumaella Prószyński, 1979. Relationships and distribution of both genera are discussed in reference to molecular, morphological and distributional data, published by other authors in recent years.

Recent hybrids recapitulate ancient hybrid outcomes

Genomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone in Lycaeides butterflies predict patterns of ancestry in geographically adjacent, older hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa, Lycaeides melissa, on the Z chromosome in both the old and contemporary hybrids. The same pattern of reduced L. melissa ancestry on the Z chromosome is seen in two other ancient hybrid lineages. More generally, we find that patterns of ancestry in old or ancient hybrids are remarkably predictable from contemporary hybrids, which suggests selection and recombination affect hybrid genomes in a similar way across disparate time scales and during distinct stages of speciation and species breakdown.

Evidence for adaptive introgression of exons across a hybrid swarm in deer

Background

Secondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, we examined genetic population structure, extent of introgression, and selection pressures in freely interbreeding populations of mule deer and black-tailed deer using mitochondrial DNA sequences, 9 microsatellite loci, and 95 SNPs from protein-coding genes.

Results

We observed bi-directional hybridization and classified approximately one third of the 172 individuals as hybrids, almost all of which were beyond the F1 generation. High genetic differentiation between black-tailed deer and mule deer at protein-coding genes suggests that there is positive divergent selection, though selection on these loci is relatively weak. Contrary to predictions, there was not greater selection on protein-coding genes thought to be associated with immune function and mate choice. Geographic cline analyses were consistent across genetic markers, suggesting long-term stability (over hundreds of generations), and indicated that the center of the hybrid swarm is 20-30 km to the east of the Cascades ridgeline, where there is a steep ecological transition from wet, forested habitat to dry, scrub habitat.

Conclusions

Our data are consistent with a genetic boundary between mule deer and black-tailed deer that is porous but maintained by many loci under weak selection having a substantial cumulative effect. The absence of clear reproductive barriers and the consistent centering of geographic clines at a sharp ecotone suggests that ecology is a driver of hybrid swarm dynamics. Adaptive introgression in this study (and others) promotes gene flow and provides valuable insight into selection strength on specific genes and the evolutionary trajectory of hybridizing taxa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1497-x) contains supplementary material, which is available to authorized users.

Hybridization is a recurrent evolutionary stimulus in wild yeast speciation

Hybridization can result in reproductively isolated and phenotypically distinct lineages that evolve as independent hybrid species. How frequently hybridization leads to speciation remains largely unknown. Here we examine the potential recurrence of hybrid speciation in the wild yeast Saccharomyces paradoxus in North America, which comprises two endemic lineages SpB and SpC, and an incipient hybrid species, SpC*. Using whole-genome sequences from more than 300 strains, we uncover the hybrid origin of another group, SpD, that emerged from hybridization between SpC* and one of its parental species, the widespread SpB. We show that SpD has the potential to evolve as a novel hybrid species, because it displays phenotypic novelties that include an intermediate transcriptome profile, and partial reproductive isolation with its most abundant sympatric parental species, SpB. Our findings show that repetitive cycles of divergence and hybridization quickly generate diversity and reproductive isolation, providing the raw material for speciation by hybridization.

Hybridization can contribute to diversity from the genomic to the species level. Here, Eberlein, Hénault et al. investigate genomic, transcriptomic and phenotypic variation among wild lineages of the yeast Saccharomyces paradoxus and suggest that an incipient species has formed by recurrent hybridization.

Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process

An increasing number of species are thought to have originated by homoploid hybrid speciation (HHS), but in only a handful of cases are details of the process known. A previous study indicated that Picea purpurea, a conifer in the Qinghai-Tibet Plateau (QTP), originated through HHS from P. likiangensis and P. wilsonii. To investigate this origin in more detail, we analysed transcriptome data for 114 individuals collected from 34 populations of the three Picea species from their core distributions in the QTP. Phylogenetic, principal component and admixture analyses of nuclear SNPs showed the species to be delimited genetically and that P. purpurea was admixed with approximately 60% of its ancestry derived from P. wilsonii and 40% from P. likiangensis. Coalescent simulations revealed the best-fitting model of origin involved formation of an intermediate hybrid lineage between P. likiangensis and P. wilsonii approximately 6 million years ago (mya), which backcrossed to P. wilsonii to form P. purpurea approximately one mya. The intermediate hybrid lineage no longer exists and is referred to as a "ghost" lineage. Our study emphasizes the power of population genomic analysis combined with coalescent analysis for reconstructing the stages involved in the origin of a homoploid hybrid species over an extended period. In contrast to other studies, we show that these stages can in some instances span a relatively long period of evolutionary time.

Aspects, Including Pitfalls, of Temporal Sampling of Flying Insects, with Special Reference to Aphids

Since the advent and widespread use of high-resolution molecular markers in the late 1970s, it is now well established that natural populations of insects are not necessarily homogeneous genetically and show variations at different spatial scales due to a variety of reasons, including hybridization/introgression events. In a similar vein, populations of insects are not necessarily homogenous in time, either over the course of seasons or even within a single season. This of course has profound consequences for surveys examining, for whatever reason/s, the temporal population patterns of insects, especially flying insects as mostly discussed here. In the present article, the topics covered include climate and climate change; changes in ecological niches due to changes in available hosts, i.e., essentially, adaptation events; hybridization influencing behaviour⁻host shifts; infection by pathogens and parasites/parasitoids; habituation to light, sound and pheromone lures; chromosomal/genetic changes affecting physiology and behaviour; and insecticide resistance. If such phenomena-i.e., aspects and pitfalls-are not considered during spatio-temporal study programmes, which is even more true in the light of the recent discovery of morphologically similar/identical cryptic species, then the conclusions drawn in terms of the efforts to combat pest insects or conserve rare and endangered species may be in error and hence end in failure.

The genomic and ecological context of hybridization affects the probability that symmetrical incompatibilities drive hybrid speciation

Despite examples of homoploid hybrid species, theoretical work describing when, where, and how we expect homoploid hybrid speciation to occur remains relatively rare. Here, I explore the probability of homoploid hybrid speciation due to "symmetrical incompatibilities" under different selective and genetic scenarios. Through simulation, I test how genetic architecture and selection acting on traits that do not themselves generate incompatibilities interact to affect the probability that hybrids evolve symmetrical incompatibilities with their parent species. Unsurprisingly, selection against admixture at "adaptive" loci that are linked to loci that generate incompatibilities tends to reduce the probability of evolving symmetrical incompatibilities. By contrast, selection that favors admixed genotypes at adaptive loci can promote the evolution of symmetrical incompatibilities. The magnitude of these outcomes is affected by the strength of selection, aspects of genetic architecture such as linkage relationships and the linear arrangement of loci along a chromosome, and the amount of hybridization following the formation of a hybrid zone. These results highlight how understanding the nature of selection, aspects of the genetics of traits affecting fitness, and the strength of reproductive isolation between hybridizing taxa can all be used to inform when we expect to observe homoploid hybrid speciation due to symmetrical incompatibilities.

Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird

Hybrid speciation is rare in vertebrates, and reproductive isolation arising from hybridization is infrequently demonstrated. Here, we present evidence supporting a hybrid-speciation event involving the genetic admixture of the snow-capped (Lepidothrix nattereri) and opal-crowned (Lepidothrix iris) manakins of the Amazon basin, leading to the formation of the hybrid species, the golden-crowned manakin (Lepidothrix vilasboasi). We used a genome-wide SNP dataset together with analysis of admixture, population structure, and coalescent modeling to demonstrate that the golden-crowned manakin is genetically an admixture of these species and does not represent a hybrid zone but instead formed through ancient genetic admixture. We used spectrophotometry to quantify the coloration of the species-specific male crown patches. Crown patches are highly reflective white (snow-capped manakin) or iridescent whitish-blue to pink (opal-crowned manakin) in parental species but are a much less reflective yellow in the hybrid species. The brilliant coloration of the parental species results from nanostructural organization of the keratin matrix feather barbs of the crown. However, using electron microscopy, we demonstrate that the structural organization of this matrix is different in the two parental species and that the hybrid species is intermediate. The intermediate nature of the crown barbs, resulting from past admixture appears to have rendered a duller structural coloration. To compensate for reduced brightness, selection apparently resulted in extensive thickening of the carotenoid-laden barb cortex, producing the yellow crown coloration. The evolution of this unique crown-color signal likely culminated in premating isolation of the hybrid species from both parental species.

What, if anything, are hybrids: enduring truths and challenges associated with population structure and gene flow

Hybridization is a potent evolutionary process that can affect the origin, maintenance, and loss of biodiversity. Because of its ecological and evolutionary consequences, an understanding of hybridization is important for basic and applied sciences, including conservation biology and agriculture. Herein, we review and discuss ideas that are relevant to the recognition of hybrids and hybridization. We supplement this discussion with simulations. The ideas we present have a long history, particularly in botany, and clarifying them should have practical consequences for managing hybridization and gene flow in plants. One of our primary goals is to illustrate what we can and cannot infer about hybrids and hybridization from molecular data; in other words, we ask when genetic analyses commonly used to study hybridization might mislead us about the history or nature of gene flow and selection. We focus on patterns of variation when hybridization is recent and populations are polymorphic, which are particularly informative for applied issues, such as contemporary hybridization following recent ecological change. We show that hybridization is not a singular process, but instead a collection of related processes with variable outcomes and consequences. Thus, it will often be inappropriate to generalize about the threats or benefits of hybridization from individual studies, and at minimum, it will be important to avoid categorical thinking about what hybridization and hybrids are. We recommend potential sampling and analytical approaches that should help us confront these complexities of hybridization.

Hybridization promotes speciation in Coenonympha butterflies

Hybridization has become a central element in theories of animal evolution during the last decade. New methods in population genomics and statistical model testing now allow the disentangling of the complexity that hybridization brings into key evolutionary processes such as local adaptation, colonization of new environments, species diversification and extinction. We evaluated the consequences of hybridization in a complex of three alpine butterflies in the genus Coenonympha, by combining morphological, genetic and ecological analyses. A series of approximate Bayesian computation procedures based on a large SNP data set strongly suggest that the Darwin's Heath (Coenonympha darwiniana) originated through hybridization between the Pearly Heath (Coenonympha arcania) and the Alpine Heath (Coenonympha gardetta) with different parental contributions. As a result of hybridization, the Darwin's Heath presents an intermediate morphology between the parental species, while its climatic niche seems more similar to the Alpine Heath. Our results also reveal a substantial genetic and morphologic differentiation between the two geographically disjoint Darwin's Heath lineages leading us to propose the splitting of this taxon into two different species.

Homoploid hybrid speciation and genome evolution via chromosome sorting

Genomes of numerous diploid plant and animal species possess traces of interspecific crosses, and many researches consider them as support for homoploid hybrid speciation (HHS), a process by which a new reproductively isolated species arises through hybridization and combination of parts of the parental genomes, but without an increase in ploidy. However, convincing evidence for a creative role of hybridization in the origin of reproductive isolation between hybrid and parental forms is extremely limited. Here, through studying Agrodiaetus butterflies, we provide proof of a previously unknown mode of HHS based on the formation of post-zygotic reproductive isolation via hybridization of chromosomally divergent parental species and subsequent fixation of a novel combination of chromosome fusions/fissions in hybrid descendants. We show that meiotic segregation, operating in the hybrid lineage, resulted in the formation of a new diploid genome, drastically rearranged in terms of chromosome number. We also demonstrate that during the heterozygous stage of the hybrid species formation, recombination was limited between rearranged chromosomes of different parental origin, representing evidence that the reproductive isolation was a direct consequence of hybridization.

A Continuous Correlated Beta Process Model for Genetic Ancestry in Admixed Populations

Admixture and recombination create populations and genomes with genetic ancestry from multiple source populations. Analyses of genetic ancestry in admixed populations are relevant for trait and disease mapping, studies of speciation, and conservation efforts. Consequently, many methods have been developed to infer genome-average ancestry and to deconvolute ancestry into continuous local ancestry blocks or tracts within individuals. Current methods for local ancestry inference perform well when admixture occurred recently or hybridization is ongoing, or when admixture occurred in the distant past such that local ancestry blocks have fixed in the admixed population. However, methods to infer local ancestry frequencies in isolated admixed populations still segregating for ancestry do not exist. In the current paper, I develop and test a continuous correlated beta process model to fill this analytical gap. The method explicitly models autocorrelations in ancestry frequencies at the population-level and uses discriminant analysis of SNP windows to take advantage of ancestry blocks within individuals. Analyses of simulated data sets show that the method is generally accurate such that ancestry frequency estimates exhibited low root-mean-square error and were highly correlated with the true values, particularly when large (±10 or ±20) SNP windows were used. Along these lines, the proposed method outperformed post hoc inference of ancestry frequencies from a traditional hidden Markov model (i.e., the linkage model in structure), particularly when admixture occurred more distantly in the past with little on-going gene flow or was followed by natural selection. The reliability and utility of the method was further assessed by analyzing genetic ancestry in an admixed human population (Uyghur) and three populations from a hybrid zone between Mus domesticus and M. musculus. Considerable variation in ancestry frequencies was detected within and among chromosomes in the Uyghur, with a large region of excess French ancestry harboring a gene with a known disease association. Similar variation was detected in the mouse hybrid zone, with notable constancy in regions of excess ancestry among admixed populations. By filling what has been an analytical gap, the proposed method should be a useful tool for many biologists. A computer program (popanc), written in C++, has been developed based on the proposed method and is available on-line at http://sourceforge.net/projects/popanc/.

Taxonomist's Nightmare … Evolutionist's Delight : An Integrative Approach Resolves Species Limits in Jumping Bristletails Despite Widespread Hybridization and Parthenogenesis

Accurate species delimitation is fundamental to biology. Traditionally, species were delimited based on morphological characters, sometimes leading to taxonomic uncertainty in morphologically conserved taxa. Recently, multiple taxonomically challenging cases have benefited from integrative taxonomy-an approach that highlights congruence among different disciplines and invokes evolutionary explanations for incongruence, acknowledging that different methods can mirror different stages of the speciation continuum. Here, we used a cohesive protocol for integrative taxonomy to revise species limits in 20 nominal species and 4 morphospecies of an ancestrally wingless insect group, the jumping bristletail genus Machilis from the European Eastern Alps. Even though morphologically conserved, several small-scale endemic species have been described from the Eastern Alps based on variation in hypodermal pigmentation patterns-a highly questionable character. As valuable as these endemics are for conservation, they have never been verified by alternative methods. Using traditional morphometrics, mitochondrial DNA, ribosomal DNA, and amplified fragment-length polymorphism markers, we identify six nominal species as taxonomic junior synonyms (Machilis alpicola Janetschek, 1953 syn. n. under M. vagans Wygodzinsky, 1941; M. ladensis Janetschek, 1950 syn. n., M. robusta Wygodzinsky, 1941 syn. n., and M. vicina Wygodzinsky, 1941 syn. n. under M. inermis Wygodzinsky, 1941; M. aleamaculata Wygodzinsky, 1941 syn. n. under M. montana Wygodzinsky, 1941; M. pulchra Janetschek, 1950 syn. n. under M. helleri Verhoeff, 1910) and describe two new species (Machilis cryptoglacialis sp. n. and Machilis albida sp. n.), one uncovered from morphological crypsis and one never sampled before. Building on numerous cases of incongruence among data sources, we further shed light on complex evolutionary histories including hybrid speciation, historical and recent hybridization, and ongoing speciation. We hypothesize that an inherent affinity to hybridization, combined with parallel switches to parthenogenesis and repeated postglacial colonization events may have boosted endemicity in Eastern Alpine Machilis We thus emphasize the importance of integrative taxonomy for rigorous species delimitation and its implication for evolutionary research and conservation in taxonomically challenging taxa.

Adaptive introgression as a resource for management and genetic conservation in a changing climate

Current rates of climate change require organisms to respond through migration, phenotypic plasticity, or genetic changes via adaptation. We focused on questions regarding species' and populations' ability to respond to climate change through adaptation. Specifically, the role adaptive introgression, movement of genetic material from the genome of 1 species into the genome of another through repeated interbreeding, may play in increasing species' ability to respond to a changing climate. Such interspecific gene flow may mediate extinction risk or consequences of limited adaptive potential that result from standing genetic variation and mutation alone, enabling a quicker demographic recovery in response to changing environments. Despite the near dismissal of the potential benefits of hybridization by conservation practitioners, we examined a number of case studies across different taxa that suggest gene flow between sympatric or parapatric sister species or within species that exhibit strong ecotypic differentiation may represent an underutilized management option to conserve evolutionary potential in a changing environment. This will be particularly true where advanced-generation hybrids exhibit adaptive traits outside the parental phenotypic range, a phenomenon known as transgressive segregation. The ideas presented in this essay are meant to provoke discussion regarding how we maintain evolutionary potential, the conservation value of natural hybrid zones, and consideration of their important role in adaptation to climate.

Morphological outcomes of gynandromorphism in Lycaeides butterflies (Lepidoptera: Lycaenidae)

The genitalia of male insects have been widely used in taxonomic identification and systematics and are potentially involved in maintaining reproductive isolation between species. Although sexual selection has been invoked to explain patterns of morphological variation in genitalia among populations and species, developmental plasticity in genitalia likely contributes to observed variation but has been rarely examined, particularly in wild populations. Bilateral gynandromorphs are individuals that are genetically male on one side of the midline and genetically female on the other, while mosaic gynandromorphs have only a portion of their body developing as the opposite sex. Gynandromorphs might offer unique insights into developmental plasticity because individuals experience abnormal cellular interactions at the genitalic midline. In this study, we compare the genitalia and wing patterns of gynandromorphic Anna and Melissa blue butterflies, Lycaeides anna (Edwards) (formerly L. idas anna) and L. melissa (Edwards) (Lepidoptera: Lycaenidae), to the morphology of normal individuals from the same populations. Gynandromorph wing markings all fell within the range of variation of normal butterflies; however, a number of genitalic measurements were outliers when compared with normal individuals. From these results, we conclude that the gynandromorphs' genitalia, but not wing patterns, can be abnormal when compared with normal individuals and that the gynandromorphic genitalia do not deviate developmentally in a consistent pattern across individuals. Finally, genetic mechanisms are considered for the development of gynandromorphism in Lycaeides butterflies.

The effect of hybrid transgression on environmental tolerance in experimental yeast crosses

Evidence is rapidly accumulating that hybridization generates adaptive variation. Transgressive segregation in hybrids could promote the colonization of new environments. Here, we use an assay to select hybrid genotypes that can proliferate in environmental conditions beyond the conditions tolerated by their parents, and we directly compete them against parental genotypes in habitats across environmental clines. We made 45 different hybrid swarms by crossing yeast strains (both Saccharomyces cerevisiae and S. paradoxus) with different genetic and phenotypic divergence. We compared the ability of hybrids and parents to colonize seven types of increasingly extreme environmental clines, representing both natural and novel challenges (mimicking pollution events). We found that a significant majority of hybrids had greater environmental ranges compared to the average of both their parents' ranges (mid-parent transgression), but only a minority of hybrids had ranges exceeding their best parent (best-parent transgression). Transgression was affected by the specific strains involved in the cross and by the test environment. Genetic and phenotypic crossing distance predicted the extent of transgression in only two of the seven environments. We isolated a set of potentially transgressive hybrids selected at the extreme ends of the clines and found that many could directly outcompete their parents across whole clines and were between 1.5- and 3-fold fitter on average. Saccharomyces yeast is a good model for quantitative and replicable experimental speciation studies, which may be useful in a world where hybridization is becoming increasingly common due to the relocation of plants and animals by humans.

Adaptations to "Thermal Time" Constraints in Papilio: Latitudinal and Local Size Clines Differ in Response to Regional Climate Change

Adaptations to "thermal time" (=Degree-day) constraints on developmental rates and voltinism for North American tiger swallowtail butterflies involve most life stages, and at higher latitudes include: smaller pupae/adults; larger eggs; oviposition on most nutritious larval host plants; earlier spring adult emergences; faster larval growth and shorter molting durations at lower temperatures. Here we report on forewing sizes through 30 years for both the northern univoltine P. canadensis (with obligate diapause) from the Great Lakes historical hybrid zone northward to central Alaska (65° N latitude), and the multivoltine, P. glaucus from this hybrid zone southward to central Florida (27° N latitude). Despite recent climate warming, no increases in mean forewing lengths of P. glaucus were observed at any major collection location (FL to MI) from the 1980s to 2013 across this long latitudinal transect (which reflects the "converse of Bergmann's size Rule", with smaller females at higher latitudes). Unlike lower latitudes, the Alaska, Ontonogon, and Chippewa/Mackinac locations (for P. canadensis) showed no significant increases in D-day accumulations, which could explain lack of size change in these northernmost locations. As a result of 3-4 decades of empirical data from major collection sites across these latitudinal clines of North America, a general "voltinism/size/D-day" model is presented, which more closely predicts female size based on D-day accumulations, than does latitude. However, local "climatic cold pockets" in northern Michigan and Wisconsin historically appeared to exert especially strong size constraints on female forewing lengths, but forewing lengths quickly increased with local summer warming during the recent decade, especially near the warming edges of the cold pockets. Results of fine-scale analyses of these "cold pockets" are in contrast to non-significant changes for other Papilio populations seen across the latitudinal transect for P. glaucus and P. canadensis in general, highlighting the importance of scale in adaptations to climate change. Furthermore, we also show that rapid size increases in cold pocket P. canadensis females with recent summer warming are more likely to result from phenotypic plasticity than genotypic introgression from P. glaucus, which does increase size in late-flight hybrids and P. appalachiensis.

Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes

Comprising 50%-75% of the world's fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including "invasive species" in various ecosystems as they may become disrupted in different ways by rapid climate change. "Invasive genes" (into new species and populations) need to be recognized for their positive creative potential and addressed in conservation programs. "Genetic rescue" via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae) with their long-term historical data base (phylogeographical diversity changes) and recent (3-decade) climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced "reshuffling" (recombinations) of species composition, genotypes, and genomes may become increasingly ecologically and evolutionarily predictable, but future conservation management programs are more likely to remain constrained by human behavior than by lack of academic knowledge.

Stacks: an analysis tool set for population genomics

Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.

Understanding the origin of species with genome-scale data: modelling gene flow

As it becomes easier to sequence multiple genomes from closely related species, evolutionary biologists working on speciation are struggling to get the most out of very large population genomic data sets. Such data hold the potential to resolve long-standing questions in evolutionary biology about the role of gene exchange in species formation. In principle, the new population genomic data can be used to disentangle the conflicting roles of natural selection and gene flow during the divergence process. However, there are great challenges in taking full advantage of such data, especially with regard to including recombination in genetic models of the divergence process. Current data, models, methods and the potential pitfalls in using them will be considered here.

The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing

Next-generation sequencing (NGS) techniques are now key tools in the detection of population genomic and gene expression differences in a large array of organisms. However, so far few studies have utilized such data for phylogenetic estimations. Here, we use NGS data obtained from genome-wide restriction site-associated DNA (RAD) (∼66000 SNPs) to estimate the phylogenetic relationships among all 26 species of swordtail and platyfish (genus Xiphophorus) from Central America. Past studies, both sequence and morphology-based, have differed in their inferences of the evolutionary relationships within this genus, particularly at the species-level and among monophyletic groupings. We show that using a large number of markers throughout the genome, we are able to infer the phylogenetic relationships with unparalleled resolution for this genus. The relationships among all three major clades and species within each of them are highly resolved and consistent under maximum likelihood, Bayesian inference and maximum parsimony. However, we also highlight the current cautions with this data type and analyses. This genus exhibits a particularly interesting evolutionary history where at least two species may have arisen through hybridization events. Here, we are able to infer the paternal lineages of these putative hybrid species. Using the RAD-marker-based tree we reconstruct the evolutionary history of the sexually selected sword trait and show that it may have been present in the common ancestor of the genus. Together our results highlight the outstanding capacity that RAD sequencing data has for resolving previously problematic phylogenetic relationships, particularly among relatively closely related species.