Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time

Abstract Bombina bombina and B. variegata are two anciently diverged toad taxa that have adapted to different breeding habitats yet hybridize freely in zones of overlap where their parapatric distributions meet. Here, we report on a joint genetic and ecological analysis of a hybrid zone in the vicinity of Stryi in western Ukraine. We used five unlinked allozyme loci, two nuclear single nucleotide polymorphisms and a mitochondrial DNA haplotype as genetic markers. Parallel allele frequency clines with a sharp central step occur across a sharp ecotone, where transitions in aquatic habitat, elevation, and terrestrial vegetation coincide. The width of the hybrid zone, estimated as the inverse of the maximum gradient in allele frequency, is 2.3 km. This is the smallest of four estimates derived from different clinal transects across Europe. We argue that the narrow cline near Stryi is mainly due to a combination of habitat distribution and habitat preference. Adult toads show a preference for either ponds ( B. bombina ) or puddles ( B. variegata ), which is known to affect the distribution of genotypes within the hybrid zones. At Stryi, it should cause a reduction of the dispersal rate across the ecotone and thus narrow the cline. A detailed comparison of all five intensively studied Bombina transects lends support to the hypothesis that habitat distribution plus habitat preference can jointly affect the structure of hybrid zones and, ultimately, the resulting barriers to gene flow between differentiated gene pools. This study also represents a resampling of an area that was last studied more than 70 years ago. Our allele-frequency clines largely coincide with those that were described then on the basis of morphological variation. However, we found asymmetrical introgression of B. variegata genes into B. bombina territory along the bank of a river.     

A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae)

Stable hybrid zones in which ecologically divergent taxa give rise to a range of recombinants are natural laboratories in which the genetic basis of adaptation and reproductive isolation can be unraveled. One such hybrid zone is formed by the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae). Adaptations to permanent and ephemeral breeding habitats, respectively, have shaped numerous phenotypic differences between the taxa. All of these are, in principle, candidates for a genetic dissection via QTL mapping. We present here a linkage map of 28 codominant and 10 dominant markers in the Bombina genome. In an F2 cross, markers that were mainly microsatellites, SSCPs or allozymes were mapped to 20 linkage groups. Among the 40 isolated CA microsatellites, we noted a preponderance of compound and frequently interleaved CA-TA repeats as well as a striking polarity at the 5' end of the repeats.     

HABITAT PREFERENCE IN THE BOMBINA HYBRID ZONE IN CROATIA

This paper demonstrates the effect of habitat heterogeneity and a habitat preference on the genetic structure of a hybrid zone between the toads Bombina bombina and B. variegata (Anura: Discoglossidae); 1613 toads from 85 sites across a transect near Pe??enica, Croatia, were scored for five unlinked diagnostic allozyme markers. These were found to be largely concordant. Aside from minor systematic deviations, there was little variance in allele frequency among loci within sites. Yet the allele frequencies did not follow a smooth cline, but formed a mosaic in the center, such that neighboring sites could differ markedly in their enzyme score. A detailed ecological survey revealed a correlation between this pattern and habitat. In keeping with the typical breeding sites of the parental taxa, B. bombina-like hybrids were found more often in ponds, whereas B. variegata-like hybrids were more common in puddles. In addition, there was significant heterozygote deficit (F_IS) and strong linkage disequilibrium (R), both of which were stronger on the B. bombina side of the transect, and stronger in puddles than ponds. Mark-recapture data showed: (1) that the animals disperse beyond the scale of the habitat pattern; (2) frequent turn-over of individuals within sites; and (3) nonrandom movement between two sites of different habitat type. We conclude that an active habitat preference must contribute to the observed association between marker alleles and habitat. As a consequence, there is incomplete mixing of the two gene pools, which could explain the high level of F_IS and R. The asymmetry in these parameters may reflect asymmetry in the preference or in the distribution of habitats across the zone. We discuss the implications of habitat preference for the dynamics of hybrid zones.     

Mating patterns in a hybrid zone of fire-bellied toads (Bombina): inferences from adult and full-sib genotypes

We present two novel methods to infer mating patterns from genetic data. They differ from existing statistical methods of parentage inference in that they apply to populations that deviate from Hardy-Weinberg and linkage equilibrium, and so are suited for the study of assortative mating in hybrid zones. The core data set consists of genotypes at several loci for a number of full-sib clutches of unknown parentage. Our inference is based throughout on estimates of allelic associations within and across loci, such as heterozygote deficit and pairwise linkage disequilibrium. In the first method, the most likely parents of a given clutch are determined from the genotypic distribution of the associated adult population, given an explicit model of nonrandom mating. This leads to estimates of the strength of assortment. The second approach is based solely on the offspring genotypes and relies on the fact that a linear relation exists between associations among the offspring and those in the population of breeding pairs. We apply both methods to a sample from the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Disco glossidae) in Croatia. Consistently, both approaches provide no evidence for a departure from random mating, despite adequate statistical power. Instead, B. variegata-like individuals among the adults contributed disproportionately to the offspring cohort, consistent with their preference for the type of breeding habitat in which this study was conducted.     

Limited mitochondrial DNA introgression in a Bombina hybrid zone

We analysed the variation at mitochondrial DNA (mtDNA) and six allozyme loci in two transects across a hybrid zone between the fire-bellied toads Bombina bombina and Bombina variegata in southern Poland. The mtDNA cline was narrower than allozyme clines in one transect (Przemyśl, β = 0.435, w  = 3.42 km) and shifted to the B .  bombina side in both (near Kraków by 1.32 km, α = 0.437, and near Przemyśl by 0.97 km, α = 0.319). Cytonuclear associations were weak. Narrowed mtDNA clines could be a by-product of female demography and lowered effective population size of mtDNA. Alternatively, restricted mtDNA introgression is a likely result of negative epistasis in recombinants augmented by environment-dependent selection because divergence of Bombina mitochondrial and nuclear genomes is large. The shift of the mtDNA cline, contrary to expectations from initial mating preferences and fecundity differences between the species, suggests that on the B .  bombina side of the zone hybrid females with B .  variegata mtDNA have a higher chance of leaving progeny.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 295–306.     

Incipient habitat race formation in an amphibian

Theory defines conditions under which sympatric speciation may occur, and several possible examples of the process in action have been identified. In most cases, organisms specialize onto habitats that fall into discrete categories, such as host species used by herbivores and parasites. Ecological specialization within a continuous habitat gradient is theoretically possible, but becomes less likely with increasing gene flow among clinal habitat types. Here, I show that habitat race formation is underway in a frog, Rana temporaria, along a continuous and spatially mosaic habitat gradient. Tadpoles from 23 populations raised in an outdoor mesocosm experiment showed adaptive phenotypic variation correlated with the predator density in their pond of origin. A survey of microsatellite markers in 48 populations found that neutral genetic divergence was enhanced between ponds with very different densities of predators. This represents a new example of habitat specialization along a continuous habitat gradient with no spatial autocorrelation in habitat.     

Morphological and genetic divergence of intralacustrine stickleback morphs in Iceland: a case for selective differentiation?

The evolutionary processes involved in population divergence and local adaptation are poorly understood. Theory predicts that divergence of adjacent populations is possible but depends on several factors including gene flow, divergent selection, population size and the number of genes involved in divergence and their distribution on the genome. We analyse variation in neutral markers, markers linked to putative quantitative trait loci and morphological traits in a recent (<10000 years) zone of primary divergence between stickleback morphs in Lake Thingvallavatn, Iceland. Environmental factors, especially predation, are clearly implicated in reducing gene flow between morphs. There is continuous morphological and genetic variation between habitats with a zone centre similar to secondary contact zones. Individual microsatellite loci are implicated as being linked to adaptive variation by direct tests as well as by differences in cline shape. Patterns of linkage disequilibria indicate that the morphs have diverged at several loci. This divergence shows parallels and differences with the well-studied limnetic-benthic stickleback morphs, both in phenotypic divergence and at the genomic level.     

REINFORCING SELECTION IS EFFECTIVE UNDER A RELATIVELY BROAD SET OF CONDITIONS IN A MOSAIC HYBRID ZONE

Many hybrid zones have a mosaic structure, yet we know of no theoretical work that examines the impact of mosaicism on the outcome of evolution. We developed a computer simulation model designed to test whether the outcome of reinforcing selection differs in a mosaic and a clinal hybrid zone. Our model was a one-dimensional stepping-stone model. The mosaic and clinal hybrid zones that we modeled were, respectively, a mosaic maintained by differential fitness of the interacting taxa in patchy habitats and a tension zone. We modeled changes in gene frequency at two biallelic loci, A and B. Hybrids at the A locus were selected against. An allele at the B locus caused assortative mating at the A locus, which promoted reinforcement; there was a selective cost to this allele. In a mosaic hybrid zone, spatial variation in the fitness of A-locus homozygotes in different patches caused gene and genotype frequencies at the A and B loci to differ greatly from those in a tension zone. Compared to a tension zone, a mosaic hybrid zone had a broader region in which hybrids could be formed and, thus, a broader region in which the assortative-mating allele provided a net selective advantage (via decreased production of the less fit A-locus hybrids). This caused the assortative-mating allele to be favored under a broader set of conditions in a mosaic hybrid zone than in a tension zone. In mosaic and tension hybrid zones, both low and high levels of migration could prevent the establishment of the allele that promoted reinforcement, but the allele could establish under a wider range of migration rates in a mosaic than in a tension zone. In a tension zone, both low and high levels of selection against A-locus hybrids could prevent the establishment of the assortative-mating allele. In a mosaic hybrid zone, the assortative-mating allele established under lower levels of selection against hybrids than in a tension zone, and high levels of selection did not impede the establishment of this allele. Overall, our work illustrates how the structure of a hybrid zone can alter the outcome of an important evolutionary process, in this case, reinforcement.     

ECOLOGICAL GENETICS OF A MOSAIC HYBRID ZONE: MITOCHONDRIAL,NUCLEAR, AND REPRODUCTIVE DIFFERENTIATION OF CRICKETS BY SOIL TYPE

We investigated the effects that habitat variation has on the structure and dynamics of a hybrid zone between two closely related crickets in Connecticut. A collecting protocol was developed in which crickets were sampled from characteristic habitats on either side of the hybrid zone and from two distinct habitat types within the zone. Presumptive pure Gryllus pennsylvanicus were sampled from fields in northwestern Connecticut and represent “inland” populations. “Pure” Gryllus firmus were sampled from beaches along the coast and represent the “coastal” populations. Crickets from within the hybrid zone were sampled from two different soil types: the “loam” populations from loamy soils and the “sand” populations from sandy soils. Moreover, an attempt was made to identify closely adjacent sand and loam localities to determine the scale of habitat variation and its possible effects on hybrid-zone structure. In general, there was little variation in morphological traits or in allozyme and mtDNA genotype frequencies among localities from within each of the four habitat types. Between each of the closely situated sand and loam localities within the hybrid zone, however, there were very significant differences in each of these sets of markers. In addition, crickets from hybrid-zone populations were tested for reproductive isolation. The asymmetric outcome of hybrid crosses that exists across the zone (Harrison, 1983) also exists on a finer ecological scale within the zone. Thus, this hybrid zone is a mosaic of strikingly differentiated populations. The dynamics of hybrid zones with mosaic structures are discussed in contrast to the traditional clinal models. The data are also discussed in light of the semipermeable nature of species boundaries. The extent to which a species boundary is permeable varies not only from one genetic marker to the next, but also with the ecological and geographic context of species interaction.     

Mitochondrial DNA variation in the hybridizing fire-bellied toads, Bombina bombina and B. variegata

Using five restriction enzymes, geographical variation of mitochondrial DNA (mtDNA) in Bombina bombina and B. variegata was studied in samples from 20 locations. Each restriction enzyme produced a species-specific fragment pattern. B. bombina haplotypes A and B were closely related to each other. In contrast, haplotypes A and B of B. variegata formed two distinct lineages. A very distinctive haplotype (C) was found in the Carpathian Mountains, whereas two other haplotypes, D and E (differing by a single AvaI site), were present in western Europe and the Balkans, respectively. Populations polymorphic for haplotypes D and E occurred in the central Balkans where the haplotypes could replace each other clinally. mtDNA sequence divergence between B. bombina and B. variegata was estimated as 6.0-8.1% and 4.7-5.2% between type C and types D/E of B. variegata. The latter divergence is contrary to allozyme and morphological data that place the western and Carpathian B. v. variegata together (Nei's D = 0.07) and separate them from the Balkan subspecies B. v. scabra (Nei's D = 0.18). Broad interspecific correlation among morphology, allozymes and mtDNA types in European fire-bellied toads argues that, despite continuous hybridization (interrupted perhaps during Pleistocene glacial maxima), little or no mtDNA introgression between the species has occurred outside the narrow hybrid zones that separate these parapatric species.     

Evidence for morphological and adaptive genetic divergence between lake and stream habitats in European minnows (Phoxinus phoxinus, Cyprinidae)

Natural selection drives local adaptation, potentially even at small temporal and spatial scales. As a result, adaptive genetic and phenotypic divergence can occur among populations living in different habitats. We investigated patterns of differentiation between contrasting lake and stream habitats in the cyprinid fish European minnow (Phoxinus phoxinus) at both the morphological and genomic levels using geometric morphometrics and AFLP markers, respectively. We also used a spatial correlative approach to identify AFLP loci associated with environmental variables representing potential selective forces responsible for adaptation to divergent habitats. Our results identified different morphologies between lakes and streams, with lake fish presenting a deeper body and caudal peduncle compared to stream fish. Body shape variation conformed to a priori predictions concerning biomechanics and swimming performance in lakes vs. streams. Moreover, morphological differentiation was found to be associated with several environmental variables, which could impose selection on body and caudal peduncle shape. We found adaptive genetic divergence between these contrasting habitats in the form of 'outlier' loci (2.9%) whose genetic divergence exceeded neutral expectations. We also detected additional loci (6.6%) not associated with habitat type (lake vs. stream), but contributing to genetic divergence between populations. Specific environmental variables related to trophic dynamics, landscape topography and geography were associated with several neutral and outlier loci. These results provide new insights into the morphological divergence and genetic basis of adaptation to differentiated habitats.     

Adaptation to a steep environmental gradient and an associated barrier to gene exchange in Littorina saxatilis

Steep environmental gradients offer important opportunities to study the interaction between natural selection and gene flow. Allele frequency clines are expected to form at loci under selection, but unlinked neutral alleles may pass easily across these clines unless a generalized barrier evolves. Here we consider the distribution of forms of the intertidal gastropod Littorina saxatilis, analyzing shell shape and amplified fragment length polymorphism (AFLP) loci on two rocky shores in Britain. On the basis of previous work, the AFLP loci were divided into differentiated and undifferentiated groups. On both shores, we have shown a sharp cline in allele frequencies between the two morphs for differentiated AFLP loci. This is coincident with a habitat transition on the shore where the two habitats (cliff and boulder field) are immediately contiguous. The allele frequency clines coincide with a cline in shell morphology. In the middle of the cline, linkage disequilibrium for the differentiated loci rises in accordance with expectation. The clines are extremely narrow relative to dispersal, probably as a result of both strong selection and habitat choice. An increase in F(ST) for undifferentiated AFLPs between morphs, relative to within-morph comparisons, is consistent with there being a general barrier to gene flow across the contact zone. These features are consistent either with an episode of allopatric divergence followed by secondary contact or with primary, nonallopatric divergence. Further data will be needed to distinguish between these alternatives.     

Phylogeography of the fire-bellied toads Bombina: independent Pleistocene histories inferred from mitochondrial genomes

The fire-bellied toads Bombina bombina and Bombina variegata, interbreed in a long, narrow zone maintained by a balance between selection and dispersal. Hybridization takes place between local, genetically differentiated groups. To quantify divergence between these groups and reconstruct their history and demography, we analysed nucleotide variation at the mitochondrial cytochrome b gene (1096 bp) in 364 individuals from 156 sites representing the entire range of both species. Three distinct clades with high sequence divergence (K2P = 8-11%) were distinguished. One clade grouped B. bombina haplotypes; the two other clades grouped B. variegata haplotypes. One B. variegata clade included only Carpathian individuals; the other represented B. variegata from the southwestern parts of its distribution: Southern and Western Europe (Balkano-Western lineage), Apennines, and the Rhodope Mountains. Differentiation between the Carpathian and Balkano-Western lineages, K2P approximately 8%, approached interspecific divergence. Deep divergence among European Bombina lineages suggests their preglacial origin, and implies long and largely independent evolutionary histories of the species. Multiple glacial refugia were identified in the lowlands adjoining the Black Sea, in the Carpathians, in the Balkans, and in the Apennines. The results of the nested clade and demographic analyses suggest drastic reductions of population sizes during the last glacial period, and significant demographic growth related to postglacial colonization. Inferred history, supported by fossil evidence, demonstrates that Bombina ranges underwent repeated contractions and expansions. Geographical concordance between morphology, allozymes, and mtDNA shows that previous episodes of interspecific hybridization have left no detectable mtDNA introgression. Either the admixed populations went extinct, or selection against hybrids hindered mtDNA gene flow in ancient hybrid zones.     

Mating signal variation and bimodality in a mosaic hybrid zone between Chorthippus grasshopper species

The grasshoppers Chorthippus brunneus and Chorthippus jacobsi are easily distinguished by male calling song and the number of stridulatory pegs on the hind femur, and form a mosaic hybrid zone in northern Spain. In this paper, we fit a two-dimensional cline to variation in male calling song characters, which are of particular interest as they are likely to be involved in mate choice by females. As with variation in peg number, local habitat makes only a small contribution in explaining deviations in mean song score from clinal expectations. However, the fitted width of the cline for song characters is significantly narrower than for peg number, suggesting that mating signals may be associated with reduced hybrid fitness in the field and that recombination rates are sufficient to allow clines for different characters to diverge in width. Despite this, estimates for the overall elevation in linkage disequilibrium at the zone center, based on covariance between peg and song characters, reveal a substantial overrepresentation of parental genotypes at the cline center relative to the expectations of a tension zone of similar width. Examination of covariance at individual sites reveals that this inflated estimate of linkage disequilibrium is caused by several sites where the distribution of phenotypes is effectively bimodal. This substantial variation in linkage disequilibrium at the cline center could result from local variation in the strength of assortative mating or selection against hybrids, or may reflect the long-distance colonization of empty habitat from outside the hybrid zone, which would continually create new contacts between parental genotypes at the cline center. Hybrid zones like this, in which strong linkage disequilibrium occurs in some situations but not in others, are of particular relevance to speciation research and allow investigation of the spread of combinations of alleles through different genetic and ecological backgrounds.     

Testing an hypothesis of hybrid zone movement for toads in France

Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequilibrium is predicted to exist ahead of the centre of the moving hybrid zone. We test these predictions of the movement hypothesis in a hybrid zone between common (Bufo bufo) and spined toads (B. spinosus), using 31 nuclear and one mtDNA SNPs along a transect in the northwest of France. Average effective selection in Bufo hybrids is low and clines vary in shape and centre. A weak pattern of asymmetric introgression is inferred from cline discordance of seven nuclear markers. The dominant direction of gene flow is from B. spinosus to B. bufo and is in support of southward movement of the hybrid zone. Conversely, a peak of admixture linkage disequilibrium north of the hybrid zone suggests northward movement. These contrasting results can be explained by reproductive isolation of the B. spinosus and B. bufo gene pools at the southern (B. spinosus) side of the hybrid zone. The joint occurrence of asymmetric introgression and admixture linkage disequilibrium can also be explained by the combination of low dispersal and random genetic drift due to low effective population sizes.     

Neutral and Adaptive Drivers of Microgeographic Genetic Divergence within Continuous Populations: The Case of the Neotropical Tree Eperua falcata (Aubl.)

BackgroundIn wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation among subpopulations, microgeographical variations in environmental conditions can drive adaptive divergence through natural selection at some targeted loci. Such phenomena have recurrently been observed in plant populations occurring across sharp environmental boundaries, but the interplay between selective processes and neutral genetic divergence has seldom been studied.MethodsWe assessed the extent of within-stand neutral and environmentally-driven divergence in the Neotropical tree Eperua falcate Aubl. (Fabaceae) through a genome-scan approach. Populations of this species grow in dense stands that cross the boundaries between starkly contrasting habitats. Within-stand phenotypic and candidate-gene divergence have already been proven, making this species a suitable model for the study of genome-wide microgeographic divergence. Thirty trees from each of two habitats (seasonally flooded swamps and well-drained plateaus) in two separate populations were genotyped using thousands of AFLPs markers. To avoid genotyping errors and increase marker reliability, each sample was genotyped twice and submitted to a rigorous procedure for data cleaning, which resulted in 1196 reliable and reproducible markers.ResultsDespite the short spatial distances, we detected within-populations genetic divergence, probably caused by neutral processes, such as restrictions in gene flow. Moreover, habitat-structured subpopulations belonging to otherwise continuous stands also diverge in relation to environmental variability and habitat patchiness: we detected convincing evidence of divergent selection at the genome-wide level and for a fraction of the analyzed loci (comprised between 0.25% and 1.6%). Simulations showed that the levels of differentiation for these outliers are compatible with scenarios of strong divergent selection.     

Divergence in coloration and ecological speciation in the Anolis marmoratus species complex

Adaptive divergence in coloration is expected to produce reproductive isolation in species that use colourful signals in mate choice and species recognition. Indeed, many adaptive radiations are characterized by differentiation in colourful signals, suggesting that divergent selection acting on coloration may be an important component of speciation. Populations in the Anolis marmoratus species complex from the Caribbean island of Guadeloupe display striking divergence in the colour and pattern of adult males that occurs over small geographic distances, suggesting strong divergent selection. Here we test the hypothesis that divergence in coloration results in reduced gene flow among populations. We quantify variation in adult male coloration across a habitat gradient between mesic and xeric habitats, use a multilocus coalescent approach to infer historical demographic parameters of divergence, and examine gene flow and population structure using microsatellite variation. We find that colour variation evolved without geographic isolation and in the face of gene flow, consistent with strong divergent selection and that both ecological and sexual selection are implicated. However, we find no significant differentiation at microsatellite loci across populations, suggesting little reproductive isolation and high levels of contemporary gene exchange. Strong divergent selection on loci affecting coloration probably maintains clinal phenotypic variation despite high gene flow at neutral loci, supporting the notion of a porous genome in which adaptive portions of the genome remain fixed whereas neutral portions are homogenized by gene flow and recombination. We discuss the impact of these findings for studies of colour evolution and ecological speciation.     

Comparative Analysis of Mitochondrial Genomes in <Emphasis Type="Italic">Bombina</Emphasis> (Anura; Bombinatoridae)

The complete mitochondrial genomes of two basal anurans, Bombina bombina and B. variegata (Anura; Bombinatoridae), were sequenced. The gene order of their mitochondrial DNA (mtDNA) is identical to that of canonical vertebrate mtDNA. In contrast, we show that there are structural differences in regulatory regions and protein coding genes between the mtDNA of these two closely related species. Corrected sequence divergence between the mtDNA of B. bombina and B. variegata amounts to 8.7% (2.3% divergence in amino acids). Comparisons with two East Asian congeners show that the control region contains two repeat regions, LV1 and LV2, present in all species except for B. bombina, in which LV2 has been secondarily lost. The rRNAs and tRNAs are characterized by low nucleotide divergence. The protein coding genes are considerably more disparate, although functional constraint is high but variable among genes, as evidenced by dN/dS ratios. A mtDNA phylogeny established the distribution of autapomorphic nonsynonomous substitutions in the mitogenomes of B. bombina and B. variegata. Nine of 98 nonsynonomous substitutions led to radical amino acid replacements that may alter mitochondrial protein function. Most radical substitutions were found in ND2, ND4, or ND5, encoding mitochondrial subunits of complex I of the electron transport system. The extensive divergence between the mitogenomes of B. bombina and B. variegata is discussed in terms of its possible role in impeding gene flow in natural hybrid zones between these two species.     

Long Distance Linkage Disequilibrium and Limited Hybridization Suggest Cryptic Speciation in Atlantic Cod

Hybrid zones provide unprecedented opportunity for the study of the evolution of reproductive isolation, and the extent of hybridization across individuals and genomes can illuminate the degree of isolation. We examine patterns of interchromosomal linkage disequilibrium (ILD) and the presence of hybridization in Atlantic cod, Gadus morhua, in previously identified hybrid zones in the North Atlantic. Here, previously identified clinal loci were mapped to the cod genome with most (∼70%) occurring in or associated with (<5 kb) coding regions representing a diverse array of possible functions and pathways. Despite the observation that clinal loci were distributed across three linkage groups, elevated ILD was observed among all groups of clinal loci and strongest in comparisons involving a region of low recombination along linkage group 7. Evidence of ILD supports a hypothesis of divergence hitchhiking transitioning to genome hitchhiking consistent with reproductive isolation. This hypothesis is supported by Bayesian characterization of hybrid classes present and we find evidence of common F1 hybrids in several regions consistent with frequent interbreeding, yet little evidence of F2 or backcrossed individuals. This work suggests that significant barriers to hybridization and introgression exist among these co-occurring groups of cod either through strong selection against hybrid individuals, or genetic incompatibility and intrinsic barriers to hybridization. In either case, the presence of strong clinal trends, and little gene flow despite extensive hybridization supports a hypothesis of reproductive isolation and cryptic speciation in Atlantic cod. Further work is required to test the degree and nature of reproductive isolation in this species.     

Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages

Diverging semi‐isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the latter, although both reduce gene flow between groups. Rarely are these two patterns of spatial distribution reported in the same study system. Here, we report that the long‐snouted seahorse Hippocampus guttulatus is subdivided into discrete panmictic entities by both types of hybrid zones. Along the European Atlantic coasts, a northern and a southern lineage meet in the southwest of France where they coexist in sympatry—i.e., in the same geographical zone—with little hybridization. In the Mediterranean Sea, two lineages have a mosaic distribution, associated with lagoon‐like and marine habitats. A fifth lineage was identified in the Black Sea. Genetic homogeneity over large spatial scales contrasts with isolation maintained in sympatry or close parapatry at a fine scale. A high variation in locus‐specific introgression rates provides additional evidence that partial reproductive isolation must be maintaining the divergence. We find that fixed differences between lagoon and marine populations in the Mediterranean Sea belong to the most differentiated SNPs between the two Atlantic lineages, against the genome‐wide pattern of structure that mostly follow geography. These parallel outlier SNPs cluster on a single chromosome‐wide island of differentiation. Since Atlantic lineages do not map to lagoon‐sea habitat variation, genetic parallelism at the genomic island suggests a shared genetic barrier contributes to reproductive isolation in contrasting contexts–i.e., spatial versus ecological. We discuss how a genomic hotspot of parallel differentiation could have evolved and become associated both with space and with a patchy environment in a single study system.