Extreme genetic differentiation among the remnant populations of marble trout (Salmo marmoratus) in Slovenia

Populations of the marble trout (Salmo marmoratus) have declined critically due to introgression by brown trout (Salmo trutta) strains. In order to define strategies for long-term conservation, we examined the genetic structure of the 8 known pure populations using 15 microsatellite loci. The analyses reveal extraordinarily strong genetic differentiation among populations separated by < 15 km, and extremely low levels of intrapopulation genetic variability. As natural recolonization seems highly unlikely, appropriate management and conservation strategies should comprise the reintroduction of pure populations from mixed stocks (translocation) to avoid further loss of genetic diversity.     

Genetic introgression between wild and stocked brown trout in the Douro River basin, Spain

The genetic diversity of Spanish brown trout is currently threatened by stocking with exogenous brown trout from Central and Northern Europe. In the Douro River basin 25% of the analysed populations in the present study showed introgression by genes of hatchery origin. The mean introgression estimated by the single locus approach ( S ) varied from 0 to 22% among populations, with a mean value of 3%. The hatchery allele markers were absent in populations where stocking ceased in 1993. However, the introgression effect was observed in all populations stocked until 1998. It seems that cessation of stocking is a good measure for restoring native populations. A thorough review of published and present data of genetic interactions between wild and stocked brown trout in Spanish rivers indicates different levels of introgression between basins. The absence of a clear geographical pattern in the introgression level suggests that ecological interactions and local stocking programmes may play an important role in stocking success. Finally, several guidelines are provided for conservation and management of native brown trout populations in Spanish rivers.     

Geometric morphometrics reveals body shape differences between sympatric redfish Sebastes mentella, Sebastes fasdatus and their hybrids in the Gulf of St Lawrence

Significant body shape differences were observed between two commercially important redfish species Sebastes fasdatus and Sebastes mentella , in the Gulf of St Lawrence, first classified according to the variability at the MDH-A* locus, a diagnostic criterion for the two species in allopatry. The observed sexual dimorphism was probably related to the presence of gravid females in the sample. Sebastes mentella appeared to be more fusiform than S. fasdatus , a characteristic that may reflect the more pelagic behaviour of S. mentella . The body shape of their hybrids was closer to that of S. mentella . Similarities between hybrids and S. mentella were also observed for meristic characteristics and depth distribution. The implications of these similarities for introgression are discussed. Body shape variability of specimens of hybrid origin was greater than that of either parental species, with features ranging from S. mentella-like to S. fasciatus -like. The role of introgression in generating morphological variability is emphasized.     

Asymmetric introgression between fishes in the Red River basin of Texas is associated with variation in water quality

When ecologically divergent taxa encounter one another, hybrid zones can form when reproductive isolation is incomplete. The location of such hybrid zones can be influenced by environmental variables, and an ecological context can provide unique insights into the mechanisms by which species diverge and are maintained. Two ecologically differentiated species of small benthic fishes, the endemic and imperiled prairie chub, Macrhybopsis australis, and the shoal chub, Macrhybopsis hyostoma, are locally sympatric within the upper Red River Basin of Texas. We integrated population genomic data and environmental data to investigate species divergence and the maintenance of species boundaries in these two species. We found evidence of advanced‐generation asymmetric hybridization and introgression, with shoal chub alleles introgressing more frequently into prairie chubs than the reciprocal. Using a Bayesian Genomic Cline framework, patterns of genomic introgression were revealed to be quite heterogeneous, yet shoal chub alleles were found to have likely selectively introgressed across species boundaries significantly more often than prairie chub alleles, potentially explaining some of the observed asymmetry in hybridization. These patterns were remarkably consistent across two sampled geographic regions of hybridization. Several environmental variables were found to significantly predict individual admixture, suggesting ecological isolation might maintain species boundaries.     

The modality of nine Triturus newt hybrid zones assessed with nuclear,mitochondrial and morphological data

The shape of hybrid zones provides insight into genetic isolation between the evolutionary lineages involved: the greater the limitation to gene flow, the farther along the unimodal to bimodal continuum. We study hybrid zone modality in a group of closely related species at a variety of levels of genetic divergence. We explore the degree and the geography of hybridization in 12 transects of Triturus newts, for nine of the ten secondary contact zones in Europe, using nuclear and mitochondrial encoded genetic data and morphological characteristics. Species status is verified by examining the correlation between the three marker systems in a geographical context. At 40 allozyme loci, two transects classify as unimodal, three as bimodal and two as intermediate, while the signal for hybridization is weak or absent in five transects. One zone studied in duplicate was classified as intermediate in one region and as bimodal in another region. mtDNA introgression is frequent and extends beyond nuclear introgression in two transects. Morphology provides additional evidence for hybridity, including one transect for which the signal of nuclear gene flow is weak. Compared to simulations allowing panmixia, the observed allozyme transitions at contact zones show a deficit of backcrossing to various degrees. Over all transects, there is a weak negative relationship between the level of hybridization and allozyme genetic distance for species pairs, consistent with Bateson–Dobzhansky–Muller effects. This observation, based upon highly comparable data for a single genus, supports conclusions derived from analyses over a wide variety of other taxa. © 2014 The Authors. Biological Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 604–622.     

Morphological variation in intergrade pupfish populations from the Pecos River, Texas, U.S.A.

In the early 1980s, sheepshead minnow Cyprinodon variegates was introduced into the Pecos River, Texas, U.S.A. where it hybridized with the endemic Pecos pupfish C. pecosensis . By 1985, pupfish populations throughout approximately 300 km of the river consisted exclusively of individuals of hybrid origin (intergrades). There was significant ( P <0·05) geographic variation in most morphological characters; the general pattern of variation was of a bidirectional cline centred near Pecos, Texas. At that site, morphology of intergrade populations resembled mostly that of the introduced species. Upstream and downstream from Pecos, morphology shifted progressively toward that typical of the native form. Intergrade populations were morphologically intermediate to the parental forms, showed a rapid approach to random assortment of characters, and generally exhibited greater morphological variability than occurred in either parent species. These observations and the consistent lack of bimodality in frequency distributions of a morphological hybrid index support the contention that intergrade populations comprise panmictic admixtures of C. variegates and C. pecosensis .     

Genetic analysis of natural hybrids between endemic and alien Rubus (Rosaceae) species in Hawai`i

A population of putative hybrids between theendemic Rubus hawaiensis and naturalizedR. rosifolius was discovered inKpahulu Valley, on the island of Maui inthe Hawaiian archipelago. The goal of thisstudy was to molecularly characterize thisnatural hybridization event, investigate themode of hybridization, and determine the malefertility of the hybrid individuals. Bothmorphological and RAPD marker data indicatethat the putative hybrid individuals are theprogeny of R. rosifolius and R.hawaiensis. All 39 hybrid individuals sampledhad the chloroplast DNA haplotype of R.rosifolius. Thus hybridization appears to beasymmetric, with R. rosifolius acting asthe maternal parent. All hybrid individualsassessed for pollen stainability were sterile,and there was no evidence of backcrossing toeither parent. This result suggests thathybrids are of the first filial generation andthat variation among hybrids reflectsdifferences within the parental populations.Sympatric populations of R. hawaiensisand R. rosifolius occur on four islandsand six additional alien species of Rubusare naturalized and sympatric with R. hawaiensisin Hawai`i. Further investigationis merited to assess whether hybridization maypose a threat to the long term viability ofR. hawaiensis. This study highlights theincreasing frequency and negative consequencesof native-alien hybridization and theimportance of maintaining active alien speciescontrol programs in the Hawaiian Islands.     

Genetic introgression between native and introduced brown trout Salmo trutta L. populations in the Rhone River Basin

In the Doubs River (Rhône drainage) two distinct brown trout ( S. trutta ) phenotypes are observed. One phenotype is locally called Doubs trout and is characterized by four black stripes on the sides, similar to perch ( Perca fluviatilis L.) and the other is the common phenotype of the fluviatile ecotype of brown trout, Salmo trutta f. fario . Protein data for three samples from the Doubs show that the Doubs trout belongs to the Mediterranean population group of brown trout, whereas the fario phenotype originates from stocking with hatchery strains of Atlantic basin origin. The two forms, however, do not hybridize freely. This is indicated by considerable gametic phase disequilibrium between alleles of hatchery and Doubs trout at one sampling site, and by lack of intermediate genotypes and phenotypes at another sampling site. The introgression patterns observed at the two sites suggest that differences in local habitat conditions can affect the degree of hybridization and introgression.     

The impact of hybrids between genetically modified crop plants and their related species: introgression and weediness

Assessing the impact of hybrids between transgenic plants and nontarget wild species involves answering several questions such as: (i) what are the hybridization and introgression rates; (ii) what is the behaviour of a transgene in a wild population; and (iii) what will be the consequences of the expression of a transgene in a wild population? These issues are discussed using results from experiments on oilseed rape and wild related Brassiceae. Evidence is given of large variations in the estimates of cross-fertilization probabilities. The first stage of introgression into wild populations is demonstrated to occur spontaneously through back-crossing. Population analysis may also be valuable to detect traces of past introgression. Data from the literature on weed biology, and especially herbicide resistance, are used to illustrate the behaviour of a new gene in weed populations. The need for computer models simulating the introgression process is stressed.     

Genetic,morphological, and niche variation in the widely hybridizing Rhus integrifolia-Rhus ovata species complex

Hybridization and introgression are common processes among numerous plant species that present both challenges and opportunities for studies of species delimitation, phylogenetics, taxonomy and adaptation. Rhus integrifolia and R. ovata are two ecologically important shrubs native to the southwestern USA and Mexico, and are known to hybridize frequently, but the morphological, genetic and ecological implications of hybridization in these species are poorly studied on a broad geographic scale. Analyses were conducted using leaf morphology, genetic variation of plastid and nuclear loci, and species distribution models for both species and their putative hybrid introgressants across 19 localities in California and Arizona, USA. These analyses revealed evidence for morphological and genetic distinction among localities comprising putative parental species, but a high degree of morpho-genetic intermediacy among localities with putative hybrids. Comparison of morphological and genetic population structure among localities revealed evidence for putative local adaptation or widespread phenotypic plasticity. Multiple regression models identified a weak but statistically significant negative association between leaf area and precipitation. Finally, species distribution modeling inferred northward range shifts over time, with both species predicted to occupy more coastal regions in the future, possibly increasing the frequency of hybridization among them. These findings underscore the importance of integrative assessment of multiple data sources in the study of hybridizing species and highlight the R. integrifolia-ovata complex as a powerful model for investigating the adaptive implications of hybridization.     

Phylogenetic relationships and introgression patterns between incipient parapatric species of Italian brown trout (Salmo trutta L. complex)

Genetic variation at 47 protein loci was investigated in 16 wild brown trout populations from the Pô basin and three major domesticated stocks used for stocking this area. Twenty-four loci were polymorphic and large frequency differences were found at 15 of them. The most significant allozyme variations were congruent with the mtDNA sequence polymorphism previously observed in the same samples. We confirmed the occurrence of two parapatric incipient species, Salmo marmoratus and S. trutta fario , previously identified by morphological traits. These two species were fixed or nearly fixed for alternate alleles at eight loci (Nei's standard genetic distance = 0.16–0.18), but introgression was detected between adjacent samples of the two forms. Divergence levels at both mtDNA and nuclear loci suggested that the differentiation between S. marmoratus and S. trutta fario started between 3 and 1 million years before present. Variation at protein loci and mtDNA supported the hypothesis that the third species found in this area, S. carpio (an endemic population of the lake Garda) was issued from a recent hybridization of the two first species. Finally, we showed that three of the major Italian fish-farm strains originated from the Atlantic side and displayed substantial genetic differences with the natural populations of the Pô basin. Most of these populations were contaminated by stocking with introgression rate ranging from 0 to 70% and measures of protection and restoration of the rich genetic diversity present in this area should be urgently applied.     

Genetic variation among trout in the River Neretva basin, Bosnia and Herzegovina

Mitochondrial DNA haplotypes, characteristic of the Adriatic, Danubian and Atlantic lineages of brown trout Salmo trutta and of Salmo obtusirostris were found in trout inhabiting the River Neretva basin. With the exception of the one associated with softmouth trout, haplotypes were not correlated with operational taxonomic units based on phenotype. Nuclear DNA analysis identified four genetic assemblages corresponding to S. obtusirostris , different geographically confined autochthonous S. trutta populations, introduced S. trutta and a genetically heterogeneous group located between S. obtusirostris and S. trutta in the dendrogram of individuals, indicating the existence of hybrid swarms in the Neretva basin. Genetic assemblages corresponding to Salmo marmoratus and the recently proposed Salmo cf. montenigrinus were not detected. The presence of genetic intermediates indicates that the studied taxa are not completely reproductively isolated and that genetic stability has been either anthropogenically interrupted or not yet achieved among Neretva trout. This finding should be considered in management decisions since such an unstable community must be particularly susceptible to breakdown in genetic population structure as a result of hybridization between native and non-native introduced trout stocks.     

Hybridization between tetraploid species of Alopecurus L. (Poaceae): morphological studies of natural and artificial hybrids

The morphology of individuals of mixed natural populations of three species of Alopecurus, A. pratensis, A. geniculars and A. arundinaceus , is described. It is suggested that plants morphologically intermediate between the parental species are hybrids or of hybrid origin. Hybridization occurs more readily between A. pratensis and A. arundinaceus than between A. pratensis and A. geniculate , since intermediate forms were recovered from all mixed populations of A. pratensis and A. arundinaceus. The intermediate forms occur only in a few populations of A. pratensis and A. geniculars where an appropriate habitat is available. Evidence of backcrossing and therefore introgression comes from the continuum of intermediate forms that exists between the species. Scatter diagrams for individual populations show distinct differences in the degree of introgression. Observations on artificially produced hybrids are similar to those on naturally occurring hybrids.     

Breakdown of the brown trout evolutionary history due to hybridization between native and cultivated fish

Genetic changes in the population structure of brown trout Salmo trutta in the eastern Pyrenees were monitored during the 1990s. Stocking with cultivated exogenous fish has resulted in introgressed populations where those with higher introgression coefficients also have the highest values of heterozygosity. Nevertheless, this increase of local diversity reflects a decrease of genetic differentiation between populations and loss of native alleles. These changes obscure native gene pools and modify evolutionary distinctions among native brown trout populations.     

Stocking impact and allozyme diversity in brown trout from Mediterranean southern France

Analysis of trout from 13 stations on the Mediterranean slopes of the French Pyrenees by 31 presumptive enzyme loci demonstrated the major impact of restocking programmes. Although the annual introgression resulting from these introductions was small, the accumulation of genes of Atlantic origin has resulted in a change in allele frequencies. Genetic disequilibria within and between loci exist. Introgression by genes of domestic (hatchery) origin varied from 0 to 77% among stations. Natural Mediterranean populations show no detectable geographical structure. There was a direct relation between the degree of introgression and heterozygosity. However, restocking could not explain all of the observed genetic disequilibria.     

Phylogeographic analysis of mitochondrial gene flow and introgression in the salamander, Plethodon shermani

Plethodon shermani comprises a series of geographically disjunct populations occupying high-elevation mountain isolates. These populations hybridize at their borders with salamanders of the Plethodon glutinosus species complex, and past range expansions inferred from Pleistocene climatic cycles may have increased the possible genetic interactions between P. shermani and species of the P. glutinosus complex. Because mitochondrial DNA haplotypes often show introgression across species borders, we survey mtDNA variation for evidence of past and ongoing genetic interactions between P. shermani, its close relative Plethodon cheoah, and species of the P. glutinosus complex. Ongoing hybridization with the P. glutinosus-complex species Plethodon teyahalee is accompanied by extensive mitochondrial introgression in some Unicoi populations of P. shermani, but it has little genetic impact on P. shermani populations outside hybrid zones at three other isolates (Tusquitee, Wayah Bald, Standing Indian). Some Unicoi populations of P. shermani exhibit mtDNA evidence of past hybridization with diverse lineages from P. aureolus and P. glutinosus. The Tusquitee isolate of P. shermani is also characterized by mtDNA haplotypes most closely related to Plethodon aureolus and P. glutinosus, presumably introduced by past genetic contact with these species or with introgressed populations of Unicoi P. shermani. The mtDNA variation in sampled populations of the Wayah Bald and Standing Indian isolates of P. shermani appears largely unaffected by ongoing hybridization. Principal components analyses of allozymic data indicate that P. shermani isolates collectively form a genetically homogeneous unit clearly demarcated from species with which they have had current or past genetic interactions. Rapid mtDNA introgression associated with transient contacts between P. shermani and other species permits a fine-level resolution of evolutionary lineages not evident from allozymic data.     

The impact of hybrids between genetically modified crop plants and their related species: general considerations

Factors influencing the fate and impact of hybrids between crop plants and their related species operate from the early zygote, through to plant establishment in different habitats, to their ability to form self-sustaining populations. Many of the classes of genes being introduced by modern methods of genetic modification are similar to those manipulated by conventional plant breeding. In assessing the impact of transgenes in hybrids between crops and related species, therefore, it is important to be informed about the consequences of hybridization between conventionally bred varieties and their relatives. Some transgenes will have novel effects (e.g. production of pharmaceutical substances or certain fatty acids) on plants, and are likely to need specific assessment studies to determine their impact on hybrids. This will be particularly important if there is the possibility of these transgenes becoming established in wild populations. Some recommendations for further research are outlined.     

Interspecific differentiation and intraspecific substructure in two closely related clupeids with extensive hybridization, Alosa alosa and Alosa fallax

In this study, the evolutionary relationships within and among populations of European shads, Alosa alosa and Alosa fallax , was investigated. Screening of allelic variation across eight allozyme loci and sequencing 448 bp of the mtDNA cytochrome b gene in 14 rivers throughout the range of the species supported that the two taxa were independent lineages (1·3% net nucleotide divergence) despite extensive hybridization. Genetic diversity and structure was considerably higher in A. fallax than A. alosa and the former species revealed evidence of distinct lineages in the Mediterranean and Atlantic basins. A Bayesian clustering approach combined with gill raker counts verified that individuals of the two species could be assigned to their parent group with relatively high confidence. Evaluation of hybridization in the Lima and Mondego Rivers in Portugal provided evidence that introgression is extensive but is not currently obscuring (through hybrid swarming) the diagnosability of the two species.     

The impact of hybrids between genetically modified crop plants and their related species: biological models and theoretical perspectives

Forces affecting the rate of spread and increase of hybrids between genetically modified crop plants and their related species remain qualitatively similar, irrespective of whether genetic modification was achieved using traditional methods, those of biotechnology or as a result of the natural evolutionary process. However, the precise magnitude of the forces and, consequently, the likely environmental impact of such hybrids, may depend strongly on the nature of the gene or genes introduced into the native species. While many classes of transgenes are similar to those manipulated by conventional breeding techniques or evolution, biotechnology offers the potential to introduce genes into crops which are novel both from the point of view of function and origin. The qualitative similarity between transgenes and the products of conventional or evolutionary modification suggests that a historical view of the environmental impact of hybrids between traditionally produced crops or exotic species and their relatives would be of use in estimating the probable fate of hybrids containing transgenes in the environment. However, with certain classes of transgenes for which there are no existing analogues, there will need to be greater care in assessing the possible risks associated with release into the environment.