DISCORDANT DIVERGENCE TIMES AMONG Z-CHROMOSOME REGIONS BETWEEN TWO ECOLOGICALLY DISTINCT SWALLOWTAIL BUTTERFLY SPECIES

The Impact of Fast Radiation on the Phylogeny of Bactrocera Fruit Flies as Revealed by Multiple Evolutionary Models and Mutation Rate-Calibrated Clock

Several true fruit flies (Tephritidae) cause major damage to agriculture worldwide. Among them, species of the genus Bactrocera are extensively studied to understand the traits associated with their invasiveness and ecology. Comparative approaches based on a reliable phylogenetic framework are particularly effective, but several nodes of the Bactrocera phylogeny are still controversial, especially concerning the reciprocal affinities of the two major pests B. dorsalis and B. tryoni. Here, we analyzed a newly assembled genomic-scaled dataset using different models of evolution to infer a phylogenomic backbone of ten representative Bactrocera species and two outgroups. We further provide the first genome-scaled inference of their divergence by calibrating the clock using fossil records and the spontaneous mutation rate. The results reveal a closer relationship of B. dorsalis with B. latifrons than to B. tryoni, contrary to what was previously supported by mitochondrial-based phylogenies. By employing coalescent-aware and heterogeneous evolutionary models, we show that this incongruence likely derives from a hitherto undetected systematic error, exacerbated by incomplete lineage sorting and possibly hybridization. This agrees with our clock analysis, which supports a rapid and recent radiation of the clade to which B. dorsalis, B. latifrons and B. tryoni belong. These results provide a new picture of Bactrocera phylogeny that can serve as the basis for future comparative analyses.

An Evolutionary Approach to the History of Barley (Hordeum vulgare) Cultivation in the Canary Islands

The Canary Islands are an archipelago that lies about 100 km west of North Africa. Barley (Hordeum vulgare) has been continuously cultivated since the colonization of the islands. To investigate the agricultural history of the islands, the DNA from multiple individuals of six extant landraces of barley was sequenced, and the resulting data were analyzed with ABC modeling. Estimates of separation times of barley populations on the different islands and the mainland were congruent with archaeological dating of the earliest settlements on the islands. The results of the genetic analyses were consistent with the continuous cultivation of barley on Lanzarote island since it was first colonized, but suggested cultivation was carried out at a smaller scale than on Gran Canaria and Tenerife. Contrary to archaeological evidence and early written historical sources, the genetic analyses suggest that barley was cultivated on a larger scale on Tenerife than on Gran Canaria. The genetic analysis of contemporary barley added support to the dating of the colonization of the islands and pointed to the need for more archaeological data concerning barley cultivation on Tenerife.

Assessing ecological and physiological costs of melanism in North American Papilio glaucus females: two decades of dark morph frequency declines

Polymorphisms for melanic form of insects may provide various selective advantages. However, melanic alleles may have significant/subtle pleiotrophic "costs." Several potential pleiotrophic effects of the W (=Y)-linked melanism gene in Papilio glaucus L. (Lepidoptera) showed no costs for melanic versus yellow in adult size, oviposition preferences, fecundity, egg viability, larval survival/growth rates, cold stress tolerance, or postdiapause emergence times. Sexual selection (males choosing yellow rather than mimetic dark females) had been suggested to provide a balanced polymorphism in P. glaucus, but spermatophore counts in wild females and direct field tethering studies of size-matched pairs of virgin females (dark and yellow), show that male preferences are random or frequency-dependent from Florida to Michigan, providing no yellow counter-advantages. Recent frequency declines of dark (melanic/mimetic) females in P. glaucus populations are shown in several major populations from Florida (27.3°N latitude) to Ohio (38.5° N). Summer temperatures have increased significantly at all these locations during this time (1999-2018), but whether dark morphs may be more vulnerable (in any stage) to such climate warming remains to be determined. Additional potential reasons for the frequency declines in mimetic females are discussed: (i) genetic introgression of Z-linked melanism suppressor genes from P. canadensis (R & J) and the hybrid species, P. appalachiensis (Pavulaan & Wright), (ii) differential developmental incompatibilities, or Haldane effects, known to occur in hybrids, (iii) selection against intermediately melanic ("dusty") females (with the W-linked melanic gene, b+) which higher temperatures can cause.

Genetic Diversity on the Sex Chromosomes

Levels and patterns of genetic diversity can provide insights into a population’s history. In species with sex chromosomes, differences between genomic regions with unique inheritance patterns can be used to distinguish between different sets of possible demographic and selective events. This review introduces the differences in population history for sex chromosomes and autosomes, provides the expectations for genetic diversity across the genome under different evolutionary scenarios, and gives an introductory description for how deviations in these expectations are calculated and can be interpreted. Predominantly, diversity on the sex chromosomes has been used to explore and address three research areas: 1) Mating patterns and sex-biased variance in reproductive success, 2) signatures of selection, and 3) evidence for modes of speciation and introgression. After introducing the theory, this review catalogs recent studies of genetic diversity on the sex chromosomes across species within the major research areas that sex chromosomes are typically applied to, arguing that there are broad similarities not only between male-heterogametic (XX/XY) and female-heterogametic (ZZ/ZW) sex determination systems but also any mating system with reduced recombination in a sex-determining region. Further, general patterns of reduced diversity in nonrecombining regions are shared across plants and animals. There are unique patterns across populations with vastly different patterns of mating and speciation, but these do not tend to cluster by taxa or sex determination system.

Sex Chromosomes of the Iconic Moth Abraxas grossulariata (Lepidoptera, Geometridae) and Its Congener A. sylvata

The magpie moth, Abraxas grossulariata, is an iconic species in which female heterogamety was discovered at the beginning of the 20th century. However, the sex chromosomes of this species have not yet been cytologically identified. We describe the sex chromosomes of A. grossulariata and its congener, A. sylvata. Although these species split only around 9.5 million years ago, and both species have the expected WZ/ZZ chromosomal system of sex determination and their sex chromosomes share the major ribosomal DNA (rDNA) representing the nucleolar organizer region (NOR), we found major differences between their karyotypes, including between their sex chromosomes. The species differ in chromosome number, which is 2n = 56 in A. grossularita and 2n = 58 in A. sylvata. In addition, A. grossularita autosomes exhibit massive autosomal blocks of heterochromatin, which is a very rare phenomenon in Lepidoptera, whereas the autosomes of A. sylvata are completely devoid of distinct heterochromatin. Their W chromosomes differ greatly. Although they are largely composed of female-specific DNA sequences, as shown by comparative genomic hybridization, cross-species W-chromosome painting revealed considerable sequence differences between them. The results suggest a relatively rapid molecular divergence of Abraxas W chromosomes by the independent spreading of female-specific repetitive sequences.

The role of latitudinal, genetic and temperature variation in the induction of diapause of Papilio glaucus (Lepidoptera: Papilionidae)

A key adaptation in insects for dealing with variable environmental conditions is the ability to diapause. The tiger swallowtail butterflies, Papilio glaucus and P. canadensis are ideal species to explore the genetic causes and population genetic consequences of diapause because divergence in this trait is believed to be a salient factor in maintaining a hybrid zone between these species. Yet little is known about the factors that influence diapause induction in this system. Here we explored how spatial (latitudinal), environmental (temperature) and genetic (hybridization) factors affect diapause induction in this system. Specifically, a series of growth chamber experiments using wild caught individuals from across the eastern United States were performed to: (1) evaluate how critical photoperiod varies with latitude, (2) isolate the stage in which induction occurs, (3) test whether changes in temperature affected rates of diapause induction, and (4) explore how the incidence of diapause is affected in hybrid offspring. We find that induction occurs in the larval stage, is not sensitive to a relatively broad range of temperatures, appears to have a complex genetic basis (i.e., is not simply a dominant trait following a Mendelian inheritance pattern) and that the critical photoperiod increases by 0.4 h with each increasing degree in latitude. This work deepens our understanding of how spatial, environmental and genetic variation influences a key seasonal adaptation (diapause induction) in a well-developed ecological model system and will make possible future studies that explore how climatic variation affects the population dynamics and genetics of this system.

Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling

Climate-mediated changes in hybridization will dramatically alter the genetic diversity, adaptive capacity, and evolutionary trajectory of interbreeding species. Our ability to predict the consequences of such changes will be key to future conservation and management decisions. Here we tested through simulations how recent warming (over the course of a 32-y period) is affecting the geographic extent of a climate-mediated developmental threshold implicated in maintaining a butterfly hybrid zone (Papilio glaucus and Papilio canadensis; Lepidoptera: Papilionidae). These simulations predict a 68-km shift of this hybrid zone. To empirically test this prediction, we assessed genetic and phenotypic changes using contemporary and museum collections and document a 40-km northward shift of this hybrid zone. Interactions between the two species appear relatively unchanged during hybrid zone movement. We found no change in the frequency of hybridization, and regions of the genome that experience little to no introgression moved largely in concert with the shifting hybrid zone. Model predictions based on climate scenarios predict this hybrid zone will continue to move northward, but with substantial spatial heterogeneity in the velocity (55-144 km/1 °C), shape, and contiguity of movement. Our findings suggest that the presence of nonclimatic barriers (e.g., genetic incompatibilities) and/or nonlinear responses to climatic gradients may preserve species boundaries as the species shift. Further, we show that variation in the geography of hybrid zone movement could result in evolutionary responses that differ for geographically distinct populations spanning hybrid zones, and thus have implications for the conservation and management of genetic diversity.

Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase: A potential case of cytonuclear cointrogression

Introgression is the effective exchange of genetic information between species through natural hybridization. Previous genetic analyses of the Drosophila yakuba—D. santomea hybrid zone showed that the mitochondrial genome of D. yakuba had introgressed into D. santomea and completely replaced its native form. Since mitochondrial proteins work intimately with nuclear‐encoded proteins in the oxidative phosphorylation (OXPHOS) pathway, we hypothesized that some nuclear genes in OXPHOS cointrogressed along with the mitochondrial genome. We analyzed nucleotide variation in the 12 nuclear genes that form cytochrome c oxidase (COX) in 33 Drosophila lines. COX is an OXPHOS enzyme composed of both nuclear‐ and mitochondrial‐encoded proteins and shows evidence of cytonuclear coadaptation in some species. Using maximum‐likelihood methods, we detected significant gene flow from D. yakuba to D. santomea for the entire COX complex. Interestingly, the signal of introgression is concentrated in the three nuclear genes composing subunit V, which shows population migration rates significantly greater than the background level of introgression in these species. The detection of introgression in three proteins that work together, interact directly with the mitochondrial‐encoded core, and are critical for early COX assembly suggests this could be a case of cytonuclear cointrogression.

Differential introgression among loci across a hybrid zone of the intermediate horseshoe bat (Rhinolophus affinis)

Background

Hybrid zones formed by the secondary contact of divergent lineages represent natural laboratories for studying the genetic basis of speciation. Here we tested for patterns of differential introgression among three X-linked and 11 autosomal regions to identify candidate loci related to either reproductive isolation or adaptive introgression across a hybrid zone between two Chinese mainland subspecies of the intermediate horseshoe bat Rhinolophus affinis: R. a. himalayanus and R. a. macrurus.

Results

Our results support the previous suggestion that macrurus formed when a third subspecies (R. a. hainanus) recolonized the mainland from Hainan Island, and that himalayanus is the ancestral taxon. However, this overall evolutionary history was not reflected in all loci examined, with considerable locus-wise heterogeneity seen in gene tree topologies, levels of polymorphism, genetic differentiation and rates of introgression. Coalescent simulations suggested levels of lineage mixing seen at some nuclear loci might result from incomplete lineage sorting. Isolation with migration models supported evidence of gene flow across the hybrid zone at one intronic marker of the hearing gene Prestin.

Conclusions

We suggest that phylogenetic discordance with respect to the species tree seen here is likely to arise via a combination of incomplete lineage sorting and a low incidence of introgression although we cannot rule out other explanations such as selection and recombination. Two X-linked loci and one autosomal locus were identified as candidate regions related to reproductive isolation across the hybrid zone. Our work highlights the importance of including multiple genomic regions in characterizing patterns of divergence and gene flow across a hybrid zone.

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.

Transcriptome analysis of female reproductive tissues of Anastrepha obliqua and molecular evolution of eggshell proteins in the fraterculus group

The investigation of cDNA libraries has been an important tool for the identification of new genes in nonmodel species such as the fruit flies from the Anastrepha fraterculus group. In the present study, we constructed a cDNA library from the female reproductive tissues of Anastrepha obliqua aiming to identify genes with high evolutionary rates. We sequenced 2304 clones obtained from the female reproductive tissues of A. obliqua flies. The expressed sequence tags generated a total of 816 unigenes which were classified into different protein classes. Among these,we identified chorionic and vitelline protein genes as being among the most highly expressed. We used unigene sequences to amplify a set of chorionic and vitelline genes, involved in the formation of the eggshell,in species of the fraterculus group. Four chorionic genes and two vitelline genes showed evidence of positive selection along the Anastrepha and/or Tephritidae lineage. The signal of selection detected for Vm26Aa was possibly generated by a gene duplication event. The rapid evolutionary rates indicate that these genes could serve as important markers in population and evolutionary studies, not only for species of this group, but possibly also for other Diptera.

Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit

Maintenance of genetic distinction in the face of gene flow is an important aspect of the speciation process. Here, we provide a detailed spatial and genetic characterization of a hybrid zone between two subspecies of the European rabbit. We examined patterns of allele frequency change for 22 markers located on the autosomes, X-chromosome, Y-chromosome and mtDNA in 1078 individuals sampled across the hybrid zone. While some loci revealed extremely wide clines (w ≥ 300 km) relative to an estimated dispersal of 1.95-4.22 km/generation, others showed abrupt transitions (w ≈ 10 km), indicating localized genomic regions of strong selection against introgression. The subset of loci showing steep clines had largely coincident centers and stepped changes in allele frequency that did not co-localize with any physical barrier or ecotone, suggesting that the rabbit hybrid zone is a tension zone. The steepest clines were for X- and Y-chromosome markers. Our results are consistent with previous inference based on DNA sequence variation of individuals sampled in allopatry in suggesting that a large proportion of each genome has escaped the overall barrier to gene flow in the middle of the hybrid zone. These results imply an old history of hybridization and high effective gene flow and anticipate that isolation factors should often localize to small genomic regions.

Linkage map of the peppered moth, Biston betularia (Lepidoptera, Geometridae): a model of industrial melanism

We have constructed a linkage map for the peppered moth (Biston betularia), the classical ecological genetics model of industrial melanism, aimed both at localizing the network of loci controlling melanism and making inferences about chromosome dynamics. The linkage map, which is based primarily on amplified fragment length polymorphisms (AFLPs) and genes, consists of 31 linkage groups (LGs; consistent with the karyotype). Comparison with the evolutionarily distant Bombyx mori suggests that the gene content of chromosomes is highly conserved. Gene order is conserved on the autosomes, but noticeably less so on the Z chromosome, as confirmed by physical mapping using bacterial artificial chromosome fluorescence in situ hybridization (BAC-FISH). Synteny mapping identified three pairs of B. betularia LGs (11/29, 23/30 and 24/31) as being orthologous to three B. mori chromosomes (11, 23 and 24, respectively). A similar finding in an outgroup moth (Plutella xylostella) indicates that the B. mori karyotype (n=28) is a phylogenetically derived state resulting from three chromosome fusions. As with other Lepidoptera, the B. betularia W chromosome consists largely of repetitive sequence, but exceptionally we found a W homolog of a Z-linked gene (laminin A), possibly resulting from ectopic recombination between the sex chromosomes. The B. betularia linkage map, featuring the network of known melanization genes, serves as a resource for melanism research in Lepidoptera. Moreover, its close resemblance to the ancestral lepidopteran karyotype (n=31) makes it a useful reference point for reconstructing chromosome dynamic events and ancestral genome architectures. Our study highlights the unusual evolutionary stability of lepidopteran autosomes; in contrast, higher rates of intrachromosomal rearrangements support a special role of the Z chromosome in adaptive evolution and speciation.

Patterns of transcriptome divergence in the male accessory gland of two closely related species of field crickets

One of the central questions in evolutionary genetics is how much of the genome is involved in the early stages of divergence between populations, causing them to be reproductively isolated. In this article, we investigate genomic differentiation in a pair of closely related field crickets (Gryllus firmus and G. pennsylvanicus). These two species are the result of allopatric divergence and now interact along an extensive hybrid zone in eastern North America. Genes encoding seminal fluid proteins (SFPs) are often divergent between species, and it has been hypothesized that these proteins may play a key role in the origin and maintenance of reproductive isolation between diverging lineages. Hence, we chose to scan the accessory gland transcriptome to enable direct comparisons of differentiation for genes known to encode SFPs with differentiation in a much larger set of genes expressed in the same tissue. We have characterized differences in allele frequency between two populations for >6000 SNPs and >26,000 contigs. About 10% of all SNPs showed nearly fixed differences between the two species. Genes encoding SFPs did not have significantly elevated numbers of fixed SNPs per contig, nor did they seem to show larger differences than expected in their average allele frequencies. The distribution of allele frequency differences across the transcriptome is distinctly bimodal, but the relatively high proportion of fixed SNPs does not necessarily imply "ancient" divergence between these two lineages. Further studies of linkage disequilibrium and introgression across the hybrid zone are needed to direct our attention to those genome regions that are important for reproductive isolation.

The language of speciation

The literature on speciation has expanded dramatically in recent years, catalyzed by the emergence of new conceptual frameworks, new theoretical approaches, and new methods for characterizing pattern and inferring process. As a consequence, the language used to describe the speciation process has become more complex. Increasing complexity may be an accurate reflection of current thinking with respect to how phenotypic differences limit gene flow, how selection results in the evolution of reproductive isolation, and genetic changes that contribute to speciation. However, increased language complexity has come at a cost; old definitions have been reconfigured and new terms have been introduced. In some instances, the introduction of new terminology has failed to recognize historical usage, leading to unnecessary ambiguity and redundancy. Although the writings of Mayr and Dobzhansky remain a reference point in the language of speciation, the last decades of the 20th century saw substantial changes in our thinking about the speciation process. During that period, the language of speciation remained relatively stable. In contrast, the first decade of the 21st century has witnessed a remarkable expansion of the language of speciation. Here, the origin and evolution of ideas about speciation are viewed through the lens of changing language use.

Candidate targets of balancing selection in the genome of Staphylococcus aureus

Signatures of balancing selection can highlight polymorphisms and functions that are important to the long-term fitness of a species. We performed a first genome-wide scan for balancing selection in a bacterial species, Staphylococcus aureus, which is a common cause of serious antimicrobial-resistant infections of humans. Using a sliding window approach, the genomes of 16 strains of S. aureus, including 5 new genome sequences presented here, and 1 outgroup strain of S. epidermidis were scanned for signatures of balancing selection. A total of 195 short windows were investigated based on their extreme values of both Tajima's D (>2.03) and π/K ratios (>0.12) relative to the rest of the genome. To test the unusualness of these windows, an Approximate Bayesian Computation framework was used to select a null demographic model that better accounted for the observed data than did the standard neutral model. A total of 186 windows were demonstrated to be unusual under the null model and, thus, represented candidate loci under balancing selection. These 186 candidate windows were located within 99 candidate genes that were spread across 62 different loci. Nearly all the signal (97.2%) was located within coding sequences; balancing selection on gene regulation apparently occurs through the targeting of global regulators such as agr and gra/aps. The agr locus had some of the strongest signatures of balancing selection, which provides new insight into the causes of diversity at this locus. The list of candidate genes included multiple virulence-associated genes and was significantly enriched for functions in amino acid and inorganic ion transport and metabolism and in defense mechanisms against innate immunity and antimicrobials, highlighting these particular functions as important to the fitness of this pathogen.

Sex chromosome mosaicism and hybrid speciation among tiger swallowtail butterflies

Hybrid speciation, or the formation of a daughter species due to interbreeding between two parental species, is a potentially important means of diversification, because it generates new forms from existing variation. However, factors responsible for the origin and maintenance of hybrid species are largely unknown. Here we show that the North American butterfly Papilio appalachiensis is a hybrid species, with genomic admixture from Papilio glaucus and Papilio canadensis. Papilio appalachiensis has a mosaic phenotype, which is hypothesized to be the result of combining sex-linked traits from P. glaucus and P. canadensis. We show that P. appalachiensis' Z-linked genes associated with a cooler thermal habitat were inherited from P. canadensis, whereas its W-linked mimicry and mitochondrial DNA were inherited from P. glaucus. Furthermore, genome-wide AFLP markers showed nearly equal contributions from each parental species in the origin of P. appalachiensis, indicating that it formed from a burst of hybridization between the parental species, with little subsequent backcrossing. However, analyses of genetic differentiation, clustering, and polymorphism based on molecular data also showed that P. appalachiensis is genetically distinct from both parental species. Population genetic simulations revealed P. appalachiensis to be much younger than the parental species, with unidirectional gene flow from P. glaucus and P. canadensis into P. appalachiensis. Finally, phylogenetic analyses, combined with ancestral state reconstruction, showed that the two traits that define P. appalachiensis' mosaic phenotype, obligatory pupal diapause and mimicry, evolved uniquely in P. canadensis and P. glaucus, respectively, and were then recombined through hybridization to form P. appalachiensis. These results suggest that natural selection and sex-linked traits may have played an important role in the origin and maintenance of P. appalachiensis as a hybrid species. In particular, ecological barriers associated with a steep thermal cline appear to maintain the distinct, mosaic genome of P. appalachiensis despite contact and occasional hybridization with both parental species.

Speciation in the European rabbit (Oryctolagus cuniculus): islands of differentiation on the X chromosome and autosomes

Studies of gene flow between closely related taxa can provide insight into the genetic basis of speciation. To evaluate the importance of the X chromosome in reproductive isolation between subspecies of the European rabbit and to study the genomic scale over which islands of differentiation extend, we resequenced a total of 34 loci distributed along the X chromosome and chromosome 14. Previous studies based on few markers suggested that loci in centromeric regions were highly differentiated between rabbit subspecies, whereas loci in telomeric regions were less differentiated. Here, we confirmed this finding but also discovered remarkable variation in levels of differentiation among loci, with F(ST) values from nearly 0 to 1. Analyses using isolation-with-migration models suggest that this range appears to be largely explained by differential levels of gene flow among loci. The X chromosome was significantly more differentiated than the autosomes. On chromosome 14, differentiation decayed very rapidly at increasing distances from the centromere, but on the X chromosome distinct islands of differentiation encompassing several megabases were observed both at the centromeric region and along the chromosome arms. These findings support the idea that the X chromosome plays an important role in reproductive isolation between rabbit subspecies. These results also demonstrate the mosaic nature of the genome at species boundaries.

Darwin and the origin of interspecific genetic incompatibilities

Darwin's Origin of Species is often criticized for having little to say about speciation. The complaint focuses in particular on Darwin's supposed failure to explain the evolution of the sterility and inviability of interspecific hybrids. But in his chapter on hybridism, Darwin, working without genetics, got as close to the modern understanding of the evolution of hybrid sterility and inviability as might reasonably be expected. In particular, after surveying what was then known about interspecific crosses and the resulting hybrids, he established two facts that, while now taken for granted, were at the time radical. First, the sterility barriers between species are neither specially endowed by a creator nor directly favored by natural selection but rather evolve as incidental by-products of interspecific divergence. Second, the sterility of species hybrids results when their development is "disturbed by two organizations having been compounded into one." Bateson, Dobzhansky, and Muller later put Mendelian detail to Darwin's inference that the species-specific factors controlling development (i.e., genes) are sometimes incompatible. In this article, I highlight the major developments in our understanding of these interspecific genetic incompatibilities--from Darwin to Muller to modern theory--and review comparative, genetic, and molecular rules that characterize the evolution of hybrid sterility and inviability.

ABC as a flexible framework to estimate demography over space and time: some cons, many pros

The analysis of genetic variation to estimate demographic and historical parameters and to quantitatively compare alternative scenarios recently gained a powerful and flexible approach: the Approximate Bayesian Computation (ABC). The likelihood functions does not need to be theoretically specified, but posterior distributions can be approximated by simulation even assuming very complex population models including both natural and human-induced processes. Prior information can be easily incorporated and the quality of the results can be analysed with rather limited additional effort. ABC is not a statistical analysis per se, but rather a statistical framework and any specific application is a sort of hybrid between a simulation and a data-analysis study. Complete software packages performing the necessary steps under a set of models and for specific genetic markers are already available, but the flexibility of the method is better exploited combining different programs. Many questions relevant in ecology can be addressed using ABC, but adequate amount of time should be dedicated to decide among alternative options and to evaluate the results. In this paper we will describe and critically comment on the different steps of an ABC analysis, analyse some of the published applications of ABC and provide user guidelines.

Approximate Bayesian Computation (ABC) in practice

Understanding the forces that influence natural variation within and among populations has been a major objective of evolutionary biologists for decades. Motivated by the growth in computational power and data complexity, modern approaches to this question make intensive use of simulation methods. Approximate Bayesian Computation (ABC) is one of these methods. Here we review the foundations of ABC, its recent algorithmic developments, and its applications in evolutionary biology and ecology. We argue that the use of ABC should incorporate all aspects of Bayesian data analysis: formulation, fitting, and improvement of a model. ABC can be a powerful tool to make inferences with complex models if these principles are carefully applied.

Doubts about complex speciation between humans and chimpanzees

Two patterns from large-scale DNA sequence data have been put forward as evidence that speciation between humans and chimpanzees was complex, involving hybridization and strong selection. First, divergence between humans and chimpanzees varies considerably across the autosomes. Second, divergence between humans and chimpanzees (but not gorillas) is markedly lower on the X chromosome. Here, we describe how simple speciation and neutral molecular evolution explain both patterns. In particular, the wide range in autosomal divergence is consistent with stochastic variation in coalescence times in the ancestral population; and the lower human-chimpanzee divergence on the X chromosome is consistent with species differences in the strength of male-biased mutation caused by differences in mating system. We also highlight two further patterns of divergence that are problematic for the complex speciation model. Our conclusions raise doubts about complex speciation between humans and chimpanzees.

Genealogical discordance and patterns of introgression and selection across a cricket hybrid zone

In recently diverged species, ancestral polymorphism and introgression can cause incongruence between gene and species trees. In the face of hybridization, few genomic regions may exhibit reciprocal monophyly, and these regions, usually evolving rapidly under selection, may be important for the maintenance of species boundaries. In animals with internal fertilization, genes encoding seminal protein are candidate barrier genes. Recently diverged hybridizing species such as the field crickets Gryllus firmus and G. pennsylvanicus, offer excellent opportunities to investigate the origins of barriers to gene exchange. These recently diverged species form a well-characterized hybrid zone, and share ancestral polymorphisms across the genome. We analyzed DNA sequence divergence for seminal protein loci, housekeeping loci, and mtDNA, using a combination of analytical approaches and extensive sampling across both species and the hybrid zone. We report discordant genealogical patterns and differential introgression rates across the genome. The most dramatic outliers, showing near-zero introgression and more structured species trees, are also the only two seminal protein loci under selection. These are candidate barrier genes with possible reproductive functions. We also use genealogical data to examine the demographic history of the field crickets and the current structure of the hybrid zone.

An approximate likelihood for genetic data under a model with recombination and population splitting

We describe a new approximate likelihood for population genetic data under a model in which a single ancestral population has split into two daughter populations. The approximate likelihood is based on the 'Product of Approximate Conditionals' likelihood and 'copying model' of Li and Stephens [Li, N., Stephens, M., 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165 (4), 2213-2233]. The approach developed here may be used for efficient approximate likelihood-based analyses of unlinked data. However our copying model also considers the effects of recombination. Hence, a more important application is to loosely-linked haplotype data, for which efficient statistical models explicitly featuring non-equilibrium population structure have so far been unavailable. Thus, in addition to the information in allele frequency differences about the timing of the population split, the method can also extract information from the lengths of haplotypes shared between the populations. There are a number of challenges posed by extracting such information, which makes parameter estimation difficult. We discuss how the approach could be extended to identify haplotypes introduced by migrants.

Recombination and speciation: loci near centromeres are more differentiated than loci near telomeres between subspecies of the European rabbit (Oryctolagus cuniculus)

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

Hybridization leads to host-use divergence in a polyphagous butterfly sibling species pair

Climate warming has lead to increased genetic introgression across a narrow hybrid zone separating the eastern and Canadian tiger swallowtails (Papilio glaucus and Papilio canadensis). This situation has led to the formation of an allochronically separated hybrid population with a delayed emerging phenotype or "late flight". Here, we assess how the recombination of the parental genomes that lead to this phenotype may have facilitated another major ecological shift, host-use divergence. We first contrast the ovipositional profiles of the late flight population to that of the parental species P. glaucus and P. canadensis. Subsequently we contrast the larval survival and growth of the late flight, a P. canadensis and a P. glaucus population, and a population from the northern edge of the hybrid zone on five hosts. Our results indicate that the ovipositional preference of this hybrid swarm is identical to that of the introgressing parental species, P. glaucus. Due to the absence of the preferred hosts of P. glaucus (Liriodendron tulipifera L. and Ptelea trifoliata L.) where the late flight occurs, this ovipositional pattern implies a functional specialization onto a secondary host of both parental species, Fraxinus americana L. In contrast, the larval host-use abilities represent a mixture of P. glaucus and P. canadensis, indicating divergence in larval host-use abilities has not taken place. However, high genetic variability (genetic coefficient of variation) is present for growth on F. americana in the late flight hybrid swarm and tradeoffs for larval performance on the preferred hosts of the parental species are evident; indicating a strong potential for future specialization in larval host-use abilities. This current scenario represents an instance where a shift in a major ecological trait, host use, is likely occurring as a byproduct of a shift in an unrelated trait (delayed emergence) leading to partial reproductive isolation.

Searching for candidate speciation genes using a proteomic approach: seminal proteins in field crickets

In many animals, male seminal proteins influence gamete interactions and fertilization ability and are probably involved in barriers to gene flow between diverging lineages. Here we use a proteomic approach to identify seminal proteins that are transferred to females during copulation and that may be involved in fertilization barriers between two hybridizing field crickets (Gryllus firmus and Gryllus pennsylvanicus). Analyses of patterns of divergence suggest that much of the field cricket genome has remained undifferentiated following the evolution of reproductive isolation. By contrast, seminal protein genes are highly differentiated. Tests of selection reveal that positive selection is likely to be responsible for patterns of differentiation. Together, our observations suggest that some of the loci encoding seminal proteins may indeed play a role in fertilization barriers in field crickets.

Ecological niche dimensionality and the evolutionary diversification of stick insects

The degree of phenotypic divergence and reproductive isolation between taxon pairs can vary quantitatively, and often increases as evolutionary divergence proceeds through various stages, from polymorphism to population differentiation, ecotype and race formation, speciation, and post-speciational divergence. Although divergent natural selection promotes divergence, it does not always result in strong differentiation. For example, divergent selection can fail to complete speciation, and distinct species pairs sometimes collapse (‘speciation in reverse’). Widely-discussed explanations for this variability concern genetic architecture, and the geographic arrangement of populations. A less-explored possibility is that the degree of phenotypic and reproductive divergence between taxon pairs is positively related to the number of ecological niche dimensions (i.e., traits) subject to divergent selection. Some data supporting this idea stem from laboratory experimental evolution studies using Drosophila, but tests from nature are lacking. Here we report results from manipulative field experiments in natural populations of herbivorous Timema stick insects that are consistent with this ‘niche dimensionality’ hypothesis. In such insects, divergent selection between host plants might occur for cryptic colouration (camouflage to evade visual predation), physiology (to detoxify plant chemicals), or both of these niche dimensions. We show that divergent selection on the single niche dimension of cryptic colouration can result in ecotype formation and intermediate levels of phenotypic and reproductive divergence between populations feeding on different hosts. However, greater divergence between a species pair involved divergent selection on both niche dimensions. Although further replication of the trends reported here is required, the results suggest that dimensionality of selection may complement genetic and geographic explanations for the degree of diversification in nature.