Bidirectional mitochondrial introgression between Korean cobitid fish mediated by hybridogenetic hybrids

Genomic introgression through interspecific hybridization has been observed in some species of the freshwater fish family Cobitidae. Within this family, a Cobitis hankugensis–Iksookimia longicorpa diploid–triploid hybrid species complex on the Korean peninsula is unique in displaying hybridogenesis, a unisexual reproduction mode that allows hybrids to mediate the transfer of mitochondrial DNA (but not nuclear DNA) between the two parent species. However, populations of the parental species in the wild have never been examined for the potential effect of introgression on their genomes. To address the genetic consequences of unisexual hybridization on the parental species, we examined genetic structure of the two parental species, C. hankugensis and I. longicorpa, in three independent natural habitats where they coexist with their hybrid complex using DNA sequence data of one mitochondrial gene and three nuclear genes. We found that mitochondrial introgression between the two species was extensive in all the examined localities, while there was no evidence of nuclear introgression across the species boundary. This result indicates that the hybridogenetic individuals mediate mitochondrial introgression from one species to the other, producing mito‐nuclear mosaic genomes such as C. hankugensis nuclear genomes associated with I. longicorpa mitochondrial DNA and the reverse. The direction and degree of introgression varied among the three localities, but the underlying mechanisms for this observation proved elusive. Introgression might depend on which species serves as the predominant sperm or ovum donor or the environmental conditions of the localities. The present study suggests that introgressive hybridization between pure C. hankugensis and I. longicorpa species is highly likely where the two species co‐occur with hybridogenetic individuals, but the consequence of introgression could be variable due to the history and environmental characteristics of particular populations across the parental species’ ranges.     

Biased introgression of mitochondrial and nuclear genes: a comparison of diploid and haplodiploid systems

Hybridization between recently diverged species, even if infrequent, can lead to the introgression of genes from one species into another. The rates of mitochondrial and nuclear introgression often differ, with some taxa showing biases for mitochondrial introgression and others for nuclear introgression. Several hypotheses exist to explain such biases, including adaptive introgression, sex differences in dispersal rates, sex‐specific prezygotic isolation and sex‐specific fitness of hybrids (e.g. Haldane's rule). We derive a simple population genetic model that permits an analysis of sex‐specific demographic and fitness parameters and measures the relative rates of mitochondrial and nuclear introgression between hybridizing pairs. We do this separately for diploid and haplodiploid species. For diploid taxa, we recover results consistent with previous hypotheses: an excess of one sex among the hybridizing migrants or sex‐specific prezygotic isolation causes a bias for one type of marker or the other; when Haldane's rule is obeyed, we find a mitochondrial bias in XY systems and a nuclear bias in ZW systems. For haplodiploid taxa, the model reveals that owing to their unique transmission genetics, they are seemingly assured of strong mitochondrial biases in introgression rates, unlike diploid taxa, where the relative fitness of male and female hybrids can tip the bias in either direction. This heretofore overlooked aspect of hybridization in haplodiploids provides what is perhaps the most likely explanation for differential introgression of mitochondrial and nuclear markers and raises concerns about the use of mitochondrial DNA barcodes for species delimitation in these taxa.     

Repeated unidirectional introgression of nuclear and mitochondrial DNA between four congeneric Tanganyikan cichlids

With an increasing number of reported cases of hybridization and introgression, interspecific gene flow between animals has recently become a widely accepted and broadly studied phenomenon. In this study, we examine patterns of hybridization and introgression in Ophthalmotilapia spp., a genus of cichlid fish from Lake Tanganyika, using mitochondrial and nuclear DNA from all four species in the genus and including specimens from over 800 km of shoreline. These four species have very different, partially overlapping distribution ranges, thus allowing us to study in detail patterns of gene flow between sympatric and allopatric populations of the different species. We show that a significant proportion of individuals of the lake-wide distributed O. nasuta carry mitochondrial and/or nuclear DNA typical of other Ophthalmotilapia species. Strikingly, all such individuals were found in populations living in sympatry with each of the other Ophthalmotilapia species, strongly suggesting that this pattern originated by repeated and independent episodes of genetic exchange in different parts of the lake, with unidirectional introgression occurring into O. nasuta. Our analysis rejects the hypotheses that unidirectional introgression is caused by natural selection favoring heterospecific DNA, by skewed abundances of Ophthalmotilapia species or by hybridization events occurring during a putative spatial expansion in O. nasuta. Instead, cytonuclear incompatibilities or asymmetric behavioral reproductive isolation seem to have driven repeated, unidirectional introgression of nuclear and mitochondrial DNA into O. nasuta in different parts of the lake.     

From hybridization to introgression between two closely related sympatric ant species

Interspecific hybridization is becoming more frequent worldwide due to increasing global changes and translocations of organisms. For individual organisms, the most significant negative consequences are sterility or inviability of hybrid offspring. However, hybridization sometimes leads to fertile offspring, promoting introgression from one species into another. In such situations, hybridization can play a key role in evolution and speciation. Combining hypervariable DNA (microsatellites) and mitochondrial DNA markers with the use of several modeling methods allow an efficient detection of hybridization processes. The present study therefore investigates hybridization between two ant species, Tetramorium immigrans and T. caespitum, using multiple methods, and systematically comparing results with simulated data to ensure accurate identification of hybrids. Introgression was revealed both by backcross detection based on 14 nuclear microsatellite loci and by mitochondrial‐nuclear discordance based on comparison with mitochondrial DNA (cytochrome c oxidase subunit I). Results were spatially consistent, with hybrids located at latitudes where parental species are sympatric. The causes and consequences of hybridization and introgression between T. caespitum and T. immigrans remain to be further investigated, especially because T. immigrans could be an invasive species in France.     

Evidence for bimodal hybrid zones between two species of char (Pisces: Salvelinus) in northwestern North America

Dolly Varden (Salvelinus malma, Pisces: Salmonidae) and bull trout (Salvelinus confluentus) have widely overlapping, but largely parapatric ranges in watersheds in northwestern North America from Washington State to northern British Columbia. Genetic analysis of natural populations using diagnostic molecular markers revealed widespread local sympatry and hybridization with hybrids comprising 0-25% of the local samples. In a detailed analysis of hybridization using four nuclear DNA markers and mitochondrial DNA within the Thutade Lake watershed, northcentral British Columbia, hybrid genotypes constituted up to 9% of the population of juvenile char. There were significant deviations from Hardy-Weinberg, gametic, and cytonuclear equilibria, and local samples showed bimodal frequency distributions of genotypes. Pure parental and inferred backcross genotypes were most common, and F1 and F(n) hybrids were comparatively rare. Interspecific hybridization was asymmetrical, with most F1 hybrids (five of six) bearing S. confluentus mtDNA. The introgression of nuclear and mitochondrial alleles was asymmetrical, with S. confluentus mtDNA and Growth Hormone 2 introgressing into S. malma significantly more than either introgression of the three other nuclear loci, or introgression of S. malma alleles into S. confluentus. Substantial prezygotic isolation between the species likely depends on the large body size difference between them in sympatry: S. malma have small bodies and a stream resident life history (12-21 cm adult fork length at maturity), while S. confluentus are larger and adfluvial, i.e., they migrate to Thutade Lake where they grow to maturity before returning to tributary streams to spawn (40-90 cm at maturity). These traits may limit interspecific pairings because of size assortative pairing and size-dependent reproductive habitat use.     

Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species

Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular characterization of hybrids consisted of cloning and sequencing two nuclear genes (ITS and ASF), sequencing of two further nuclear loci (BT and HSP) and of two mitochondrial loci (COI and NADH). Additionally, phenotypic traits including morphology of sporangia and optima and maxima temperatures for growth were also determined. In most cases the nuclear genes were biparentally and in all cases the mtDNA were uniparentally inherited, indicating hybrid formation through sexual crosses. Some isolates bear the molecular signature of three parents suggesting additional hybrid events, although it cannot be determined from the data if these were sequential or simultaneous. These species and their hybrids co-exist in riparian ecosystems and waterways where their ability for rapid asexual proliferation would enable them to rapidly colonize green plant litter. The apparent ease of hybridization could eventually lead to the merging of species through introgression. However, at this point in time, species integrity has been maintained and a more likely scenario is that the hybrids are not stable evolutionary lineages, but rather transient hybrid clones.     

HALDANE'S RULE AND SEX BIASSED GENE FLOW BETWEEN TWO HYBRIDIZING FLYCATCHER SPECIES (FICEDULA ALBICOLLIS AND F. HYPOLEUCA,AVES: MUSCICAPIDAE)

The collared flycatcher (Ficedula albicollis) and the pied flycatcher (F. hypoleuca) hybridize where their geographic ranges overlap. Restriction fragment comparison of 5% of the mitochondrial genome showed a sequence divergence of 10% between these flycatcher species. This degree of sequence divergence between a closely related pair of bird species is unusually high and contrasts with the low level of divergence between F. albicollis and F. hypoleuca in nuclear genes (Nei's D = 0.0006) revealed by enzyme electrophoresis. The low nuclear differentiation is explained by sex biassed gene flow and introgression in nuclear genes (via fertile male hybrids), while the high mitochondrial DNA sequence divergence is preserved by sterility of female hybrids, which prevents mitochondrial introgression. This pattern is in accordance with Haldane's rule and is supported by field data on hybrid fertility. The high mtDNA differentiation could be explained by transfer of mitochondrial DNA from a third species during a past period of hybridization.     

Conservation genomics: disequilibrium mapping of domestic cattle chromosomal segments in North American bison populations

Introgressive hybridization is one of the major threats to species conservation, and is often induced by human influence on the natural habitat of wildlife species. The ability to accurately identify introgression is critical to understanding its importance in evolution and effective conservation management of species. Hybridization between North American bison (Bison bison) and domestic cattle (Bos taurus) as a result of human activities has been recorded for over 100 years, and domestic cattle mitochondrial DNA was previously detected in bison populations. In this study, linked microsatellite markers were used to identify domestic cattle chromosomal segments in 14 genomic regions from 14 bison populations. Cattle nuclear introgression was identified in five populations, with an average frequency per population ranging from 0.56% to 1.80%. This study represents the first use of linked molecular markers to examine introgression between mammalian species and the first demonstration of domestic cattle nuclear introgression in bison. To date, six public bison populations have been identified with no evidence of mitochondrial or nuclear domestic cattle introgression, providing information critical to the future management of bison genetic resources. The ability to identify even low levels of introgression resulting from historic hybridization events suggests that the use of linked molecular markers to identify introgression is a significant development in the study of introgressive hybridization across a broad range of taxa.     

Analysis of multilocus DNA reveals hybridization in a contact zone between Empidonax flycatchers

Contact zones between recently diverged taxa offer unique opportunities to test whether the forms are reproductively isolated and therefore distinct species. The Pacific‐slope flycatcher Empidonax difficilis and Cordilleran flycatcher Empidonax occidentalis are closely related taxa that were officially separated into two species in 1989, a treatment that has been controversial due to reports of phenotypically intermediate birds across the southern interior of British Columbia and Alberta. We present the first analysis of molecular variation across this region, in order to determine whether there is genetic introgression between the taxa. Allopatric populations of Pacific‐slope and Cordilleran flycatchers belong to distinct mitochondrial clades, and all of the individuals sampled in interior southwestern Canada have the Pacific‐slope haplotype. In contrast, variation in nuclear DNA (AFLPs) indicates hybridization between Pacific‐slope and Cordilleran flycatchers in this region. We suggest that the discordance between the mitochondrial and nuclear markers most likely results from stochastic loss of Cordilleran mitochondrial haplotype lineages facilitated by asymmetries in mating due to earlier arrival and greater abundance of Pacific‐slope flycatchers in the contact zone. The discovery of hybridization between Pacific‐slope and Cordilleran flycatchers in southwestern Canada may call into question the decision to split them into two species. On the other hand, allopatric populations are genetically distinct in both mitochondrial and nuclear DNA, and the hybridization might not affect populations outside of the contact zone. This study highlights the importance of employing multiple genetic markers in studies of contact zones between closely related species.     

Genetic introgression between an introduced babbler, the Chinese hwamei Leucodioptron c. canorum, and the endemic Taiwan hwamei L. taewanus: a multiple marker systems analysis

Identification of interspecific hybrids is often a subject of primary concern in the development of conservation strategies. Here we performed a genetic analysis combining mitochondrial DNA (mtDNA), microsatellites and single nucleotide polymorphic sites (SNPs) to assay the level of hybridization and introgression between an introduced babbler, Chinese hwamei Leucodioptron canorus, and its close relative, the endemic Taiwan hwamei L. taewanus in Taiwan. Fifty‐five Chinese hwameis from the Asian mainland and 69 Taiwan hwameis, including nine morphological hybrids, were sampled and analyzed. Evidences of mitochondrial introgression were found in three hybrids and one Taiwan hwamei. Five unlinked interspecific SNPs were identified at nine anonymous nuclear loci with interspecific differentiation (total Fst=0.77) that was much higher than that at seven highly polymorphic microsatellite loci combined (total Fst=0.1). Bayesian cluster analysis based on five interspecific SNP loci and two highly differentiated microsatellite loci (Fst>0.08) suggested that twelve individuals sampled in Taiwan were likely F2 or backcross hybrids, among which eight were morphological intermediates. A total of 20.3% (14/69) individuals sampled in Taiwan were suggested to be hybrids, suggesting that fitness reduction in hybrids might be negligible. These results imply that without an effective management strategy, the entire Taiwan hwamei population could easily become an admixed with Chinese hwamei and loose its evolutionary integrity. To reduce introgressive hybridization, illegal trade of Chinese hwamei should be strictly regulated and only the expensive male Chinese hwameis should be legally imported to minimize the chance for Chinese hwameis being released into the field. In our study we also found interspecific SNP markers to outperform microsatellite loci in detecting hybridization and introgression between two closely related species, which may be ascribed to the lower level of homoplasy of SNP loci.     

Introgression at differentially aged hybrid zones in red-tailed chipmunks

Hybrid zones allow us to investigate the maintenance and the break down of reproductive isolation; they are a window into the speciation process. Tamias ruficaudus (red-tailed chipmunk) has a roughly ring-like distribution in the Inland Northwest and includes two morphologically well-differentiated subspecies, T. r. ruficaudus (in the eastern portion of its range) and T. r. simulans (in the western portion). These taxa meet at two contact zones: the Lochsa River in Idaho and 200 km to the north, near Whitefish, Montana. The Lochsa Zone is encompassed within the Clearwater River Drainage, which has been proposed as a glacial refugium for many taxa throughout the Pleistocene, whereas the Whitefish Zone was under the Cordilleran ice sheet during the most recent glacial maxima approximately 10,000 years ago. Mitochondrial DNA introgression has been documented at both contact zones, yet the subspecies remain significantly distinct with respect to bacular morphology and no intermediate morphologies have ever been reported. Here, we elucidate differentiation and introgression of the nuclear genome using ten microsatellite loci and compare findings to previously described mitochondrial DNA haplotype distribution and introgression. We found significant substructure in the nuclear data; each subspecies is divided into at least two genetically distinct demes. At the Lochsa contact zone, individuals restricted to the mtDNA zone of introgression form a distinct deme at microsatellite loci whereas in the younger, Whitefish contact zone, there is no hybrid-zone specific group. The genetic distances of the demes within these two subspecies indicate recent northward expansion.     

Bayesian analysis of hybridization and introgression between the endangered european mink (Mustela lutreola) and the polecat (Mustela putorius)

Human-mediated global change will probably increase the rates of natural hybridization and genetic introgression between closely related species, and this will have major implications for conservation of the taxa involved. In this study, we analyse both mitochondrial and nuclear data to characterize ongoing hybridization and genetic introgression between two sympatric sister species of mustelids, the endangered European mink (Mustela lutreola) and the more abundant polecat (M. putorius). A total of 317 European mink, 114 polecats and 15 putative hybrid individuals were collected from different localities in Europe and genotyped with 13 microsatellite nuclear markers. Recently developed Bayesian methods for assigning individuals to populations and identifying admixture proportions were applied to the genetic data. To identify the direction of hybridization, we additionally sequenced mtDNA and Y chromosomes from 78 individuals and 29 males respectively. We found that both hybridization and genetic introgression occurred at low levels (3% and 0.9% respectively) and indicated that hybridization is asymmetric, as only pure polecat males mate with pure European mink females. Furthermore, backcrossing and genetic introgression was detected only from female first-generation (F1) hybrids of European mink to polecats. This latter result implies that Haldane's rule may apply. Our results suggest that hybridization and genetic introgression between the two species should be considered a rather uncommon event. However, the current low densities of European mink might be changing this trend.     

Ancient hybridization and mitochondrial capture between two species of chipmunks

Models that posit speciation in the face of gene flow are replacing classical views that hybridization is rare between animal species. We use a multilocus approach to examine the history of hybridization and gene flow between two species of chipmunks ( Tamias ruficaudus and T. amoenus ). Previous studies have shown that these species occupy different ecological niches and have distinct genital bone morphologies, yet appear to be incompletely isolated reproductively in multiple areas of sympatry. We compared data from four sequenced nuclear loci and from seven microsatellite loci to published cytochrome b sequences. Interspecific gene flow was primarily restricted to introgression of the T. ruficaudus mitochondrial genome into a sympatric subspecies of T. amoenus , T. a. canicaudus , with the four sequenced nuclear loci showing little to no interspecific allele sharing. Microsatellite data were consistent with high levels of differentiation between the species and also showed no current gene flow between broadly sympatric populations of T. a. canicaudus and T. ruficaudus . Coalescent analyses date the mtDNA introgression event from the mid-Pleistocene to late Pliocene. Overall, these data indicate that introgression has had a minimal impact on the nuclear genomes of T. amoenus and T. ruficaudus despite multiple independent hybridization events. Our findings challenge long-standing assumptions on patterns of reproductive isolation in chipmunks and suggest that there may be other examples of hybridization among the 23 species of Tamias that occur in western North America.     

Natural selection influences AFLP intraspecific genetic variability and introgression patterns in Atlantic eels

Investigating patterns of genetic variation in hybridizing species provides an opportunity to understand the impact of natural selection on intraspecific genetic variability and interspecific gene exchange. The Atlantic eels Anguilla rostrata and A. anguilla each occupy a large heterogeneous habitat upon which natural selection could differentially shape genetic variation. They also produce viable hybrids only found in Iceland. However, the possible footprint of natural selection on patterns of genetic variation within species and introgressive hybridization in Icelandic eels has never been assessed. We revisited amplified fragment length polymorphism data collected previously using population genomics and admixture analyses to test if (i) genetic variation could be influenced by non-neutral mechanisms at both the intra- and interspecific levels, and if (ii) selection could shape the spatio-temporal distribution of Icelandic hybrids. We first found candidate loci for directional selection within both species. Spatial distributions of allelic frequencies displayed by some of these loci were possibly related with the geographical patterns of life-history traits in A. rostrata , and could have been shaped by natural selection associated with an environmental gradient along European coasts in A. anguilla . Second, we identified outlier loci at the interspecific level. Non-neutral introgression was strongly suggested for some of these loci. We detected a locus at which typical A. rostrata allele hardly crossed the species genetic barrier, whereas three other loci showed accelerated patterns of introgression into A. anguilla in Iceland. Moreover, the level of introgression at these three loci increased from the glass eel to the yellow eel stage, supporting the hypothesis that differential survival of admixed genotypes partly explains the spatio-temporal pattern of hybrid abundance previously documented in Iceland.     

Variable extent of hybridization between invasive sika (Cervus nippon) and native red deer (C. elaphus) in a small geographical area

Instances of hybridization between endemic and alien species pose a threat to species integrity but also provide us with an opportunity to study the dynamics of gene flow between two species as they first meet. Here, we used variation at 22 highly differentiated microsatellite loci and one mitochondrial DNA (mtDNA) marker in a sample of 735 individuals, to investigate the genetic consequences of an introduction of Japanese sika deer ( Cervus nippon ) for native red deer ( C. elaphus ) on the Kintyre Peninsula in Scotland. We investigated population structure, estimated null-allele frequency and assigned individual hybrid scores using a Bayesian clustering algorithm implemented in structure 2.2. The dataset clearly divided into two clusters and generally, introgression into red and sika was low. However at one site, West Loch Awe, 43% of individuals were hybrids. MtDNA introgression indicated that hybridization was occurring between red-deer hinds and sika-deer stags. We argue that the pattern of differential introgression across the study area is primarily due to the rarity of hybridization events between the two species and the limited time the two species have been in contact (< 120 years). This contrasts with the causes of classic mosaic hybrid zones (selection induced by habitat variability). Currently, it seems possible that, in time, the level of hybridization found at West Loch Awe could also be found across the whole of the peninsula.     

Genetic analysis of the hybridization zone between two subspecies Mus musculus domesticus and Mus musculus musculus in Bulgaria

The hybrid zone between the two subspecies of mice Mus musculus domesticus and Mus musculus musculus, which has been studied extensively in Denmark, crosses Europe to the Black Sea through the Alps and the Balkans. Two hundred and seventy-nine animals were captured in 22 localities along a transect across the Balkans. The animals were characterized for seven diagnostic nuclear loci by protein electrophoresis and by restriction pattern analysis of their mitochondrial DNA. The nuclear data show a sharp transition between the two subspecies, most of the variations in allele frequencies (from 0.9 to 0.1) occurring within a 36-km section of the transect. The introgression varies from one locus to the other and is more pronounced, in terms of distance, in M. m. musculus territory. Mitochondrial DNA introgression is important but occurs in one direction only, i.e. from M. m. musculus to M. m. domesticus, while a cytoplasmic transfer from M. m. domesticus to M. m. musculus has been reported. A previous study showed that no Y chromosome introgression occurs. The different behaviour of these three types of markers could be due to the interaction between selection against hybrid genomes and meiotic recombination. Objectively, it would appear that the genes that can introgress are neutral or nearly so and have been separated from deleterious genes they were linked to by recombination. This could explain the differential introgression between autosomal loci. The mitochondrial and Y chromosomes undergo no or very little recombination and each is transmitted as a whole. Their degree of introgression is thus indicative of the intensity of selection resulting from the amount of functional differentiation between the two taxa, which seems to be strong for the Y chromosome and weak for mitochondrial DNA. We propose that the asymmetry of nuclear introgression is due to different population structures. As M. m. musculus is relatively less structured, the rapid spreading of introgressed genes would be favoured. Such a scheme, however, can hardly account for the unidirectionality of the mitochondrial flow, which could be due to sex-dependent behaviour.     

Hybridization and population genetics of two macaque species in Sulawesi, Indonesia

This study investigates hybridization and population genetics of two species of macaque monkey in Sulawesi, Indonesia, using molecular markers from mitochondrial, autosomal, and Y-chromosome DNA. Hybridization is the interbreeding of individuals from different parental taxa that are distinguishable by one or more heritable characteristics. Because hybridization can affect population structure of the parental taxa, it is an important consideration for conservation management. On the Indonesian island of Sulawesi an explosive diversification of macaques has occurred; seven of 19 species in the genus Macaca live on this island. The contact zone of the subjects of this study, M. maura and M. tonkeana, is located at the base of the southwestern peninsula of Sulawesi. Land conversion in Sulawesi is occurring at an alarming pace; currently two species of Sulawesi macaque, one of which is M. maura, are classified as endangered species. Results of this study indicate that hybridization among M. maura and M. tonkeana has led to different distributions of molecular variation in mitochondrial DNA and nuclear DNA in the contact zone; mitochondrial DNA shows a sharp transition from M. maura to M. tonkeana haplotypes, but nuclear DNA from the parental taxa is homogenized in a narrow hybrid zone. Similarly, within M. maura divergent mitochondrial DNA haplotypes are geographically structured but population subdivision in the nuclear genome is low or absent. In M. tonkeana, mitochondrial DNA haplotypes are geographically structured and a high level of nuclear DNA population subdivision is present in this species. These results are largely consistent with a macaque behavioral paradigm of female philopatry and obligate male dispersal, suggest that introgression between M. maura and M. tonkeana is restricted to the hybrid zone, and delineate one conservation management unit in M. maura and at least two in M. tonkeana.     

Hybrid populations selectively filter gene introgression between species

Hybrids have long been recognized as a potential pathway for gene flow between species that can have important consequences for evolution and conservation biology. However, few studies have demonstrated that genes from one species can introgress or invade another species over a broad geographic area. Using 35 genetically mapped restriction fragment length polymorphism (RFLP) markers of two species of cottonwoods (Populus fremontii x P. angustifolia) and their hybrids (n = 550 trees), we showed that the majority of the genome is prohibited from introgressing from one species into the other. However, this barrier was not absolute; Fremont cpDNA and mtDNA were found throughout the geographic range of narrowleaf cottonwood, and 20% of the nuclear markers of Fremont cottonwood introgressed varying distances (some over 100 km) into the recipient species' range. Rates of nuclear introgression were variable, but two nuclear markers introgressed as fast as the haploid, cytoplasmically inherited chloroplast and mitochondrial markers. Our genome-wide analysis provides evidence for positive, negative, and neutral effects of introgression. For example, we predict that DNA fragments that introgress through several generations of backcrossing will be small, because small fragments are less likely to contain deleterious genes. These results argue that recombination will be important, that introgression can be very selective, and that evolutionary forces within the hybrid population to effectively "filter" gene flow between species. A strong filter may make introgression adaptive, prevent genetic assimilation, lead to relaxed isolating mechanisms, and contribute to the stability of hybrid zones. Thus, rather than hybridization being a negative factor as is commonly argued, natural hybridization between native species may provide important genetic variation that impacts both ecological and evolutionary processes. Finally, we propose two hypotheses that contrast the likelihood of contemporary versus ancient introgression in this system.     

Investigating hybridization in the parthenogenetic New Zealand stick insect Acanthoxyla (Phasmatodea) using single-copy nuclear loci

The New Zealand stick insect genus Acanthoxyla Uvarov is extremely unusual among higher taxa of animals in that all known species are obligate parthenogens. We have used a combination of the mitochondrial DNA genes cytochrome oxidase subunits I and II, 28S nuclear ribosomal RNA, and the two single-copy nuclear genes elongation factor 1alpha and phosphoglucose isomerase to test hypotheses on the role of hybridization in the evolution of this genus. Alleles at the single-copy nuclear loci in three sampled species of Acanthoxyla were resolved by cloning the PCR products. Analysis of multilocus genotypes shows that most sampled individuals of Acanthoxyla possess three alleles at the single-copy nuclear loci, which we have interpreted to indicate triploidy. Because most of the alleles from Acanthoxyla form a monophyletic group, including sets of alleles possessed by the putative triploids, we have inferred that the extant parthenogenetic lineages formed via hybridization between species of Acanthoxyla, at least one of which must have been sexual. More recently, there have been multiple introgression events from the related species Clitarchus hookeri White, although C. hookeri does not appear to be involved with the origin of parthenogenesis in Acanthoxyla. Our study demonstrates the utility of cloning alleles from multiple single-copy nuclear genes for resolving the origins of parthenogenetic lineages.     

Limited gene exchange between two sister species of leaf beetles within a hybrid zone in the Alps

Analysing genomic variation within and between sister species is a first step towards understanding species boundaries. We focused on two sister species of cold‐resistant leaf beetles, Gonioctena quinquepunctata and G. intermedia, whose ranges overlap in the Alps. A previous study of DNA sequence variation had revealed multiple instances of mitochondrial genome introgression in this region, suggesting recent hybridization between the two species. To evaluate the extent of gene exchange resulting from these hybridization events, we sampled individuals of both species inside and outside the hybrid zone and analysed genomic variation among them using RAD‐seq markers. Individual levels of introgression in the nuclear genome were estimated first by defining species‐specific SNPs (displaying a fixed difference between species) a priori and second by using model‐based methods. Both types of analyses indicated little gene exchange, if any, between species at the level of the nuclear genome. Whereas the first method suggested slightly more gene flow, we argue that it has likely overestimated introgression in the phylogeographic context of this study. We conclude that strong intrinsic barriers prevent genetic exchange at the level of the nuclear genome between the two species. The apparent discrepancy observed between introgression occurring in the nuclear and mitochondrial genomes could be explained by selection acting in favour of the latter. Also, these results have consequences for the phylogeographic study of each species, since we can assume that genetic diversity in the overlapping portion of their ranges is not the product of introgression.