Jacek M. Szymura

Genetic analysis of a hybrid zone between the fire-bellied toads, Bombina bombina and B. variegata, near Cracow in Southern Poland

The fire‐bellied toads Bombina bombina and B. variegata differ extensively in biochemistry, morphology, and behavior. We use a survey of five diagnostic enzyme loci across the hybrid zone near Cracow in Southern Poland to estimate the dispersal rate, selection pressures, and numbers of loci which maintain this zone. The enzyme clines coincide closely with each other and with morphological and mitochondrial DNA clines. Although the zone lies on a broad transition between environments suitable for bombina and variegata, the close concordance of diverse characters, together with increased aberrations and mortality in hybrids, suggest that the zone is maintained largely by selection against hybrids. There are strong “linkage disequilibria” between each pair of (unlinked) enzyme loci (R̄ = 0.129 [2‐unit support limits: 0.119–0.139]). These are probably caused by gene flow into the zone, and they give an estimate of dispersal (σ = 890 [790–940] m gen−½). The clines are sharply stepped, with most of the change occurring within 6.15 (5.45–6.45) km, but with long tails of introgression on either side. This implies that the effective selection pressure on each enzyme marker (due largely to disequilibrium with other loci) is s* = 0.17 (0.159–0.181) at the center but that the selection acting directly on the enzyme loci is weak or zero (se < 0.0038). The stepped pattern implies a barrier to gene flow of 220 (48–415) km. This would substantially delay neutral introgression but would have little effect on advantageous alleles; the two taxa need not evolve independently. Strong selection is needed to maintain such a barrier: hybrid populations must have their mean fitness reduced by a factor of 0.65 (0.60–0.77). This selection must be spread over a large number of loci to account for the concordant patterns and the observed cline widths (N = 300 [80–2,000]).

THE GENETIC STRUCTURE OF THE HYBRID ZONE BETWEEN THE FIRE-BELLIED TOADS BOMBINA BOMBINA AND B. VARIEGATA : COMPARISONS BETWEEN TRANSECTS AND BETWEEN LOCI

We compare the pattern of morphological and electrophoretic variation in the hybrid zone between Bombina bombina and B. variegata across two transects: one near Cracow and one 200 km away, near Przemyśl in southeastern Poland. Morphological variation across the Przemyśl transect had been surveyed more than 50 years ago; though we found a significant shift at one site, there is no evidence for gross movement over this period. Morphological and electrophoretic changes coincide, and the average shape of the clines is the same across both transects. At the center, most of the change in frequency of six diagnostic allozymes occurs within w = 6.05 km (2‐unit support limits 5.56–6.54 km). These steep gradients are generated not by selection on the allozymes themselves, but by associations with other loci: though these markers are unlinked, they are in strong linkage disequilibrium with each other [R = D/√pquv = 0.22 (0.15–0.29) at the center]. Disequilibria are broken up as alleles diffuse away from the zone and flow into the new genetic background. The net barrier to the flow of genes from bombina into variegata, which is generated by these disequilibria, is B = 51 (22–81) km. The fitness of hybrids must be substantially reduced to produce such a barrier [W̄H/W̄P = 0.58 (0.54–0.68)], and this selection must be spread over many loci [N = 55 (26–88)]. Alleles introgress significantly less far than would be expected from the age of the zone and the estimated dispersal rate [σ = 0.99 (0.82–1.14) km gen.1/2]: this implies selection of se = 0.37 (0.15–0.58)% on the enzymes themselves. There is weak but significant linkage disequilibrium well away from the center of the zone; this, together with the presence of parental and F1 genotypes, suggests some long‐range migration. However, such migration is not likely to cause significant introgression.

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 Pešćenica, 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 (FIS) 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 FIS 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.

Nuclear markers, mitochondrial DNA and male secondary sexual traits variation in a newt hybrid zone (Triturus vulgaris x T. montandoni).

The smooth and the Montandons newts (Triturus vulgaris and T. montandoni) are genetically similar sister species with highly divergent male secondary sexual traits involved in complex courtship behaviour. Their parapatric ranges overlap at moderate elevations in the Carpathian Mountains where they hybridize readily. Here we present a detailed study of genetic and morphological variation in populations from the area of sympatry. Analysis of variation at seven nuclear markers, mtDNA and male sexual secondary traits was complemented with an ecological survey of breeding sites characteristics. Extensive hybridization was revealed with back‐cross individuals similar to either parental species predominating among hybrids. The hybrid zone exhibited a mosaic pattern: the genetic composition of the populations was correlated only weakly with their geographical position. No association with habitat type was found. Departures from Hardy–Weinberg proportions, significant linkage disequilibria and bimodal distribution of genotypes suggest strongly that assortative mating is an important factor shaping the genetic composition of hybrid populations. The pattern of cytonuclear disequilibria did not indicate much asymmetry in interspecific matings. Changes in the frequency of nuclear markers were highly concordant, whereas mtDNA showed much wider bidirectional introgression with 14% excess of T. montandoni haplotype. We argue that the mosaic structure of the newt hybrid zone results mainly from stochastic processes related to extinction and recolonization. Microgeographical differences in mtDNA introgression are explained by historical range shifts. Since morphologically intermediate males were underrepresented when compared to hybrid males identified by genetic markers, sexual selection acting against the morphological intermediates is implied. We discuss the implications of these findings in the context of reinforcement of prezygotic isolation in newts.

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 ∼ 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.

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.

Nuclear and mitochondrial phylogeography of the European fire-bellied toads Bombina bombina and Bombina variegata supports their independent histories

Exact location and number of glacial refugia still remain unclear for many European cold‐blooded terrestrial vertebrates. We performed a fine‐scaled multilocus phylogeographic analysis of two Bombina species combining mitochondrial variation of 950 toads from 385 sites and nuclear genes (Rag‐1, Ncx‐1) from a subset of samples to reconstruct their colonization and contemporary variation patterns. We identified the lowlands northwest of the Black Sea and the Carpathians to be important refugial areas for B. bombina and B. variegata, respectively. This result emphasizes the importance of Central European refugia for ectothermic terrestrial species, far north of the Mediterranean areas regarded as exclusive glacial refugia for the animals. Additional refugia for B. variegata have been located in the southern Apennines and Balkans. In contrast, no evidence for the importance of other east European plains as refugial regions has been found. The distribution of mtDNA and Ncx‐1 variation suggests the presence of local refugia near the Black Sea for B. bombina; however, coalescent simulations did not allow to distinguish whether one or two refugia were present in the region. Strong genetic drift apparently accompanied postglacial expansions reducing diversity in the colonization areas. Extended sampling, coupled with the multilocus isolation with migration analysis, revealed a limited and geographically restricted gene flow from the Balkan to Carpathian populations of B. variegata. However, despite proximity of inferred B. bombina and B. variegata refugia, gene exchange between them was not detected.

Variation in mating call across the hybrid zone between the fire-bellied toads bombina bombina and B. variegata

Three components of mating call (pulse duration, cycle length, and fundamental frequency) were measured and six diagnostic enzyme loci scored across the hybrid zone between the toads Bombina bombina and B. variegata. All three call components differ significantly, but only cycle length is diagnostic. The clines in call coincide with those for enzymes, and have similar widths. This suggests that there is no strong selection on any of these characters. There are significant correlations between electrophoretic markers and call components, but these are no stronger than would be expected if the electrophoretic loci and the genes causing mating call were neutral. The selection differential on the call is no greater than 6% of the difference in mean cycle length between the two taxa. There is a substantial increase in the variance of cycle length in the center of the zone, suggesting that a small number of loci are involved (≈ three). Recombination between these loci will hinder the evolution of reinforcement and may partly be responsible for the lack of premating isolation between B. bombina and B. variegata.

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.

Complete mitochondrial genomes resolve phylogenetic relationships within Bombina (Anura: Bombinatoridae).

A highly resolved and time-calibrated phylogeny based on nucleotide variation in 18 complete mitochondrial genomes is presented for all extant species and major lineages of fire-bellied toads of the genus Bombina (Bombinatoridae). Two sets of divergence time estimates are inferred by applying alternative fossil constraints as minima. Divergence time estimates from both analyses differed for the two oldest nodes. The earliest phylogenetic split occurred between small- and large-bodied Bombina (subgenera Bombina and Grobina, respectively) either in the Middle Oligocene or the Early Miocene. East Asian B. orientalis and European B. bombina+B. variegata diverged in the early or Middle Miocene. Divergence times inferred using the alternative fossil calibration strategies converged for the younger nodes, with broadly overlapping HPD intervals. The split between Bombina bombina and B. variegata occurred in the Late Miocene of Europe and somewhat preceded another deep mtDNA division between the Balkan B. v. scabra and B. v. variegata inhabiting the Carpathian Mts. Concurrently, the genetically distinct B. maxima diverged from other Grobina in southeast Asia in the Late Miocene or Pliocene. Our mtDNA phylogeny and a new species-tree analysis of published data (nuclear and mtDNA) suggest that B. fortinuptialis, B. lichuanensis and B. microdeladigitora may be conspecific geographic forms that separated due to Pleistocene climatic fluctuations in southeastern Asia. In the western Palearctic, the Late Pliocene to Pleistocene climatic vagaries most probably induced vicariant events in the evolutionary history of B. variegata that led to the formation of the two Balkan B. v. scabra lineages and the allopatric B. v. pachypus in the Apennine Peninsula. Divergence among B. bombina mtDNA lineages is low, with an Anatolian Turkey lineage as the sister group to the European mtDNA clades. In sum, Miocene diversification in the genus Bombina established six allopatrically distributed major mtDNA lineages that diversified during the Pliocene and Pleistocene and have survived until the present. The narrow habitat requirements of fire-bellied toads and extensive environmental changes throughout the Palearctic in the Neogene may have contributed to a putatively high extinction rate in these anurans resulting in the current east/west disjunction of their ranges.