Widespread mito‐nuclear discordance with evidence for introgressive hybridization and selective sweeps in Lycaeides

We investigated the extent and potential cause(s) of mitochondrial introgression within the polytypic North American Lycaeides species complex (Lepidoptera). By comparing population genetic structure based on mitochondrial DNA (COI and COII) and nuclear DNA (251 polymorphic amplified fragment length polymorphism markers), we detected substantial mito‐nuclear discordance, primarily involving a single mitochondrial haplotype (h01), which is likely due to mitochondrial introgression between differentiated Lycaeides populations and/or species. We detected reduced mitochondrial genetic diversity relative to nuclear genetic diversity in populations where mitochondrial haplotype h01 occurs, suggesting that the spread of this haplotype was facilitated by selection. We found no evidence that haplotype h01 is associated with increased fitness (in terms of survival to eclosion, fresh adult weight, and adult longevity) in a polymorphic Lycaeides melissa population. However, we did find a positive association between mitochondrial haplotype h01 and infection by the endoparasitic bacterium Wolbachia in one out of three lineages tested. Linkage disequilibrium between mitochondrial haplotype h01 and Wolbachia infection status may have resulted in indirect selection favouring the spread of haplotype h01 in at least one lineage of North American Lycaeides. These results illustrate the potential for introgressive hybridization to produce substantial mito‐nuclear discordance and demonstrate that an individual's mitochondrial and nuclear genome may have strikingly different evolutionary histories resulting from non‐neutral processes and intrinsic differences in the inheritance and biology of these genomes.     

Introgressive hybridization and evolution of a novel protein phenotype: Glue protein profiles in thenasuta-albomicans complex ofDrosophila

Glue proteins are tissue-specific proteins synthesized by larval salivary gland cells ofDrosophila. InDrosophila nasuta nasuta andD. n. albomicans of thenasuta subgroup, the genes that encode the major glue protein fractions are X-linked. In the present study, these X-linked markers have been employed to trace the pattern of introgression ofD. n. nasuta andD. n. albomicans genomes with respect to the major glue protein fractions in their interracial hybrids, called cytoraces. These cytoraces have inherited the chromosomes of both parents and have been maintained in the laboratory for over 400–550 generations. The analysis has revealed that cytoraces withD. n. albomicans X chromosome show eitherD. n. nasuta pattern or a completely novel pattern of glue protein fractions. Further, quantitative analysis also shows lack of correlation between the chromosomal pattern of inheritance and overall quantity of the major glue protein fractions in the cytoraces. Thus, in cytoraces the parental chromosomes are not just differentially represented but there is evidence for introgression even at the gene level.     

Extensive hybridization in hawksbill turtles (Eretmochelys imbricata) nesting in Brazil revealed by mtDNA analyses

Bahia state hosts over 90% of hawksbill (Eretmochelys imbricata) nests registered in the main nesting sites monitored by Projeto Tamar-IBAMA in Brazil. The genetic diversity of this hawksbill population (n=119) was assayed through the analyses of 752 bp of the mitochondrial DNA control region in nesting females. Seven distinct haplotypes, defined by 125 polymorphic sites, were found. Most of the individuals (n=67) display four typical hawksbill haplotypes, 50 individuals display two haplotypes characteristic of the loggerhead turtle (Caretta caretta) and two individuals had a haplotype affiliated with the olive ridley (Lepidochelys olivacea). These results demonstrate hybridization between the hawksbills and two species that nest along the Bahia coast. Of special interest is the high occurrence of loggerhead × hawksbill hybrids (42%), which display loggerhead mtDNA haplotypes but are characterized morphologically as hawksbills. The true hawksbill haplotypes present only three variable sites and low genetic diversity values (h=0.358±0.069; π=0.0005±0.0001). The occurrence of several nesting individuals with identical mtDNA from another species may also suggest a long history of introgression between species producing likely F2 or further generation hybrids. Marine turtle hybrids have been previously reported, but the high frequency observed in Bahia is unprecedented. Such introgression may influence evolutionary pathways for all three species, or may introduce novel morphotypes that develop apart from the parental species. The presence of a unique hybrid swarm has profound conservation implications and will significantly influence the development and implementation of appropriate management strategies for these species.     

Introgressive hybridization of human and rodent schistosome parasites in western Kenya

Hybridization and introgression can have important consequences for the evolution, ecology and epidemiology of pathogenic organisms. We examined the dynamics of hybridization between a trematode parasite of humans, Schistosoma mansoni, and its sister species, S. rodhaini, a rodent parasite, in a natural hybrid zone in western Kenya. Using microsatellite markers, rDNA and mtDNA, we showed that hybrids between the two species occur in nature, are fertile and produce viable offspring through backcrosses with S. mansoni. Averaged across collection sites, individuals of hybrid ancestry comprised 7.2% of all schistosomes collected, which is a large proportion given that one of the parental species, S. rodhaini, comprised only 9.1% of the specimens. No F1 individuals were collected and all hybrids represented backcrosses with S. mansoni that were of the first or successive generations. The direction of introgression appears highly asymmetric, causing unidirectional gene flow from the rodent parasite, S. rodhaini, to the human parasite, S. mansoni. Hybrid occurrence was seasonal and most hybrids were collected during the month of September over a 2-year period, a time when S. rodhaini was also abundant. We also examined the sex ratios and phenotypic differences between the hybrids and parental species, including the number of infective stages produced in the snail host and the time of day the infective stages emerge. No statistical differences were found in any of these characteristics, and most of the hybrids showed an emergence pattern similar to that of S. mansoni. One individual, however, showed a bimodal emergence pattern that was characteristic of both parental species. In conclusion, these species maintain their identity despite hybridization, although introgression may cause important alterations of the biology and epidemiology of schistosomiasis in this region.     

Cytonuclear genetic signatures of hybridization phenomena: Rationale,utility, and empirical examples from fishes and other aquatic animals

By definition, organisms of hybrid ancestry carry amalgamations of divergent genomes. Thus, exaggerated effects of genomic interactions might be anticipated in hybrid populations, thereby magnifying the impact of natural selection and making this and other evolutionary forces easier to document. Mating biases and other gender-based asymmetries also frequently characterize hybrid populations. Thus, maternally inherited cytoplasmic polymorphisms assayed jointly with those at biparentally inherited nuclear loci provide powerful genetic markers to dissect ethological, ecological, and evolutionary processes in hybrid settings. Population-level topics that can be addressed using cytonuclear markers include the frequency of hybridization and introgression in nature, behavioral and ecological factors (such as mating preferences and hybrid fitnesses) influencing the genetic architectures of hybrid zones, the degree of consistency in genetic outcomes across multiple hybrid contact regions, and environmental impacts (including the introduction of alien species) on hybridization processes. Several empirical studies on fish populations in hybrid settings illustrate the application of cytonuclear appraisals in such contexts.     

Introgressive hybridization between Galaxias depressiceps and Galaxias sp D (Teleostei: Galaxiidae) in Otago, New Zealand: Secondary contact mediated by water races

Central Otago (New Zealand) was the focus of an intense period ofgold mining in the late 19th century. Mining relied on high waterpressure for sluicing, often requiring extensive systems of water raceslinking headwaters over large distances. On Rough Ridge, races connectedheadwaters of Otago's two major river systems, the Taieri and theClutha. We employed genetic analysis of freshwater fish(Galaxias) populations to assess the biological implications ofrace-development. The two galaxiid taxa found on Rough Ridge (G. spD and G. depressiceps) are reciprocally monophyletic formtDNA and have three fixed allozyme differences. Rough Ridge aside,G. sp D is apparently absent from the Taieri system and G.depressiceps from the Clutha system. Distributions of mitochondrialDNA, allozyme and microsatellite alleles imply that artificialconnections have facilitated bidirectional introgression: movementof G. sp D alleles into the Taieri system and G.depressiceps alleles into the Clutha. The finding of some identicalcontrol region haplotypes (of both lineages) on either side of thecatchment boundary confirms the recency of genetic exchange. Near theinferred region of contact, samples from Linn Burn (Taieri) are pureG. depressiceps for three diagnostic allozymes and mtDNA.Samples from upper Pool Burn (Clutha) are pure G. sp D forthese same four markers. However, other collections from around thecontact zone represent genetic mixtures forming a cline. We fear thatsimilar human-induced mixing may have happened elsewhere in uplandOtago.     

Natural hybridization in eastern-Mediterranean firs: The case of Abies borisii-regis

The genus Abies is represented in southern Balkans by A. alba, A. cephalonica, and A. borisii-regis. To infer the status of southern-Balkans firs, as well as the extent and patterns of introgression within this taxonomical complex, we analyzed genetic variation patterns of 29 indigenous fir populations in Bulgaria, Macedonia, Greece, and Calabria using a combination of maternally and biparentally inherited markers. Three mitochondrial lineages were observed, one comprising Calabrian populations and two distributed in the Balkans, coinciding with A. alba and A. cephalonica. The boundary between lineages is sharp; only two populations containing a mixture of haplotypes were found. Bayesian analysis of population structure based on seven nuclear microsatellite (nSSR) loci revealed the existence of two clusters whose proportions exhibited a latitudinal cline with a width of 2.3° ( ≈ 255 km). Populations in the center of the latitudinal cline exhibit the most symmetrical, the flattest, and the broadest distributions of cluster proportions within individual tree genomes. A neighbor-net network reflects the cline resulting from the Bayesian analysis. The observed variation patterns are not consistent with the hypothesis of A. borisii-regis as a monophyletic taxon or a stabilized hybridogenous species resulted from ancient hybridization; the taxon rather is a product of recent introgression.     

Introgression of Luxilus cornutus mtDNA into allopatric populations of Luxilus chrysocephalus (Teleostei: Cyprinidae) in Missouri and Arkansas

The cyprinid fishes Luxilus cornutus and Luxilus chrysocephalus hybridize extensively in a zone extending through the Great Lakes region with extensive introgression of L. cornutus mtDNA occurring in populations of L. chrysocephalus south of the present hybrid zone in Ohio. Western populations of these two species occur adjacent to one another in Missouri but hybridization has never been observed. In order to determine if hybridization has occurred historically in Missouri, allopatric populations of L. chrysocephalus were analysed for mtDNA introgression. Extensive introgression of L. ***cornutus mtDNA was observed in most populations of L. chrysocephalus in Missouri resulting in the elimination of L. chrysocephalus mtDNA in many populations. Luxilus cornutus mtDNA in L. chrysocephalus is found approximately 300 km south of extant L. cornutus populations in Missouri. Luxilus chrysocephalus mtDNA was replaced by four unique L. cornutus mtDNA haplotypes, with one particular haplotype becoming fixed in several L. chrysocephalus populations. The pattern of introgression suggests that historically L. cornutus occupied a more southern distribution in Missouri bringing it into contact with western populations of L. chrysocephalus and resulting in a hybrid zone.     

The rise and fall of the mountain hare (Lepus timidus) during Pleistocene glaciations: expansion and retreat with hybridization in the Iberian Peninsula

The climatic fluctuations during glaciations have affected differently arctic and temperate species. In the northern hemisphere, cooling periods induced the expansion of many arctic species to the south, while temperate species were forced to retract in southern refugia. Consequently, in some areas the alternation of these species set the conditions for competition and eventually hybridization. Hares in the Iberian Peninsula appear to illustrate this phenomenon. Populations of Iberian hare (Lepus granatensis), brown hare (Lepus europaeus) and broom hare (Lepus castroviejoi) in Northern Iberia harbour mitochondrial haplotypes from the mountain hare (Lepus timidus), a mainly boreal and arctic species presently absent from the peninsula. To understand the history of this past introgression we analysed sequence variation and geographical distribution of mitochondrial control region and cytochrome b haplotypes of L. timidus origin found in 378 specimens of these four species. Among 124 L. timidus from the Northern Palaearctic and the Alps we found substantial nucleotide diversity (2.3%) but little differentiation between populations. Based on the mismatch distribution of the L. timidus sequences, this could result from an expansion at a time of temperature decrease favourable to this arctic species. The nucleotide diversity of L. timidus mtDNA found in Iberian L. granatensis, L. europaeus and L. castroviejoi (183, 70 and 1 specimens, respectively) was of the same order as that in L. timidus over its range (1.9%), suggesting repeated introgression of multiple lineages. The structure of the coalescent of L. granatensis sequences indicates that hybridization with L. timidus was followed by expansion of the introgressed haplotypes, as expected during a replacement with competition, and occurred when temperatures started to rise, favouring the temperate species. Whether a similar scenario explains the introgression into Iberian L. europaeus remains unclear but it is possible that it hybridized with already introgressed L. granatensis.     

Introgressive hybridization as the breakdown of postzygotic isolation: a theoretical perspective

In this paper, both the empirical and theoretical genetic aspects of human-mediated introgressive hybridization are reviewed in terms of their association with the breakdown of postzygotic isolating mechanisms. I also compare several simulation models with an ecological or genetic focus that are relevant to the prediction and risk assessment of genetic extinction due to hybridization. One barrier to devising comprehensive risk assessment frameworks is a lack of sufficient population genetic studies that associate introgressive hybridization with specific isolating mechanisms. A gametic model based on multilocus underdominant fitness is one of the best genetic models for introgressive hybridization because it explicitly incorporates the postzygotic isolating mechanism known as Dobzhansky–Muller genetic incompatibility.     

The occurrence of mountain hare mitochondrial DNA in wild brown hares

If interspecific hybrids are fertile and backcross to either parental species, transmission of mitochondrial DNA over the species barrier can occur. To investigate if such transmission has occurred between the brown hare Lepus europeus Pall and the mountain hare L. timidus L. in Scandinavia, an analysis of genetic variation in mitochondrial DNA from 36 hares, collected from 15 localities, was performed. Sequence divergence of mtDNA between species was estimated at 8 ± 1% (SD). Intraspecific mtDNA sequence divergence varied between 0.09 and 0.38% in brown hares and 0.10 and 1.44% in mountain hares. In six out of 18 brown hares examined, two different haplotypes of mountain hare origin were detected, demonstrating a transmission of mtDNA haplotypes from mountain hares to brown hares. The results indicate that interspecific hybridization between the two species occurs in wild populations.     

Genetic evidence for natural hybridization and apparent introgression between freshwater snail species (Viviparus ater and V. contectus)

We examined six allozyme markers and shell morphology to study gene flow between the naturally sympatric freshwater snail species Viviparus ater and V. contectus in Lake Garda, Italy, using offspring from experimental crosses and snails collected from natural populations. Hybrid offspring obtained from experimental crosses and hybrids collected from natural populations were heterozygous at four or five out of five diagnostic loci. Shell morphology was a poor predictor of the hybrid status of individual snails. Backcrossed offspring from experimentally bred hybrids and either of the parental species morphologically resembled the parental species. There was no evidence of segregation distortion at the six loci. Linkage analysis revealed one pair of linked loci (GPI and PNP). These cross experiments indicated a Mendelian type hybrid system in which gene introgression may occur. F₁ hybrids were found at four out of six sampling sites of Lake Garda, Italy. Local frequencies of F₁ hybrids ranged from 0% to 1.6% (estimated average = 0.74%) of the total population including both species. Alleles typical of V. ater were found at low frequencies in V. contectus at all six sampling sites. Alleles typical of V. contectus were found at low frequencies in V. ater at three out of six sampling sites. This is consistent with the hypothesis of introgression in both directions.     

Introgressive hybridization between two species of waterstriders (Hemiptera: Gerridae: Limnoporus): geographical structure and temporal change of a hybrid zone

Where the distribution ranges of the waterstriders Limnoporus notabilis and L. dissortis meet in western Canada, extensive hybridization and introgression occurs. Multivariate ordination analyses of genetic and morphometric data by principal component analysis revealed that a single axis separating the two parent species could account for nearly all the variation in both data sets. Maps of principal component scores for both data sets revealed geographical patterns of variation reflecting specific topographic features in the region. Comparisons of morphometric data from some of the samples collected in the 1980s and from the same sites revisited in the 1990s revealed substantial changes. An ‘island’ of dissortis‐like populations inside the range of L. notabilis in interior British Columbia expanded, and a marked local protrusion of notabilis‐like phenotypes into the range of L. dissortis on the east slope of the Rocky Mountains diminished during the decade between collections. We conclude that introgressive hybridization between these two species of waterstriders is a spatially complex and highly dynamic process.     

Phylogenetic relationships based on two mitochondrial genes and hybridization patterns in Anatidae

We produced DNA sequence data from two mitochondrial genes (cytochrome b and the NADH dehydrogenase subunit 2) to reconstruct the phylogenetic relationships among 121 species of the Anseriformes (waterfowls including ducks, geese, swans, the magpie goose and screamers). Phylogenetic analyses converged into a congruent topology and defined several well-supported clades. We calibrated a molecular clock and reconstructed ancestral biogeographical areas using Bayesian inference supporting an austral continental (Gondwanaland) origin of the waterfowls. Ducks, swans and geese might have diversified during the Miocene (23–5 Myr ago) reaching northern distributions in Holarctic and Afrotropical regions. The evolution of hybridization patterns in Anseriformes has been investigated using a cladistic analysis (morphology), which may underestimate or overestimate the phylogenetic divergence among species, or restricted only to ducks. Using a phylogenetic framework, genetic-based distances and a Bayesian time calibration, our data support the hypothesis based on immunological distances of slow rate of appearance of reproductive incompatibilities in waterfowls compared with other vertebrates and the view that these birds may be like frogs in having lost their interspecific hybridization potential more slowly than mammals.