Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers

Evolutionary history of Muscicapidae flycatchers is inferred from nuclear and mitochondrial DNA (mtDNA) sequence comparisons and population genetic analysis of nuclear and mtDNA markers. Phylogenetic reconstruction based on sequences from the two genomes yielded similar trees with respect to the order at which the species split off. However, the genetic distances fitted a nonlinear, polynomial model reflecting diminishing divergence rate of the mtDNA sequences compared to the nuclear DNA sequences. This could be explained by Haldane's rule because genetic isolation might evolve more rapidly on the mitochondrial rather than the nuclear genome in birds. This is because hybrid sterility of the heterogametic sex (females) would predate that of the homogametic sex (males), leading to sex biased introgression of nuclear genes. Analyses of present hybrid zones of pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) may indicate a slight sexual bias in rate of introgression, but the introgression rates were too low to allow proper statistical analyses. It is suggested, however, that the observed deviation from linearity can be explained by a more rapid mutational saturation of the mtDNA sequences than of the nuclear DNA sequences, as supported by analyses of third codon position transversions at two protein coding mtDNA genes. A phylogeographic scenario for the black and white flycatcher species is suggested based on interpretation of the genetic data obtained. Four species appear to have diverged from a common ancestor relatively simultaneously during the Pleistocene. After the last glaciation period, pied and collared flycatchers expanded their breeding ranges and eventually came into secondary contact in Central and Eastern Europe and on the Baltic Isles.     

Genetic differentiation and hybridization between greater and lesser spotted eagles (Accipitriformes:Aquila clanga, A. pomarina)

Greater and lesser spotted eagles (Aquila clanga, A. pomarina) are two closely related forest eagles overlapping in breeding range in east-central Europe. In recent years a number of mixed pairs have been observed, some of which fledged hybrid young. Here we use mitochondrial (control region) DNA sequences and AFLP markers to estimate genetic differentiation and possible gene flow between these species. In a sample of 83 individuals (61 pomarina, 20 clanga, 2 F1-hybrids) we found 30 mitochondrial haplotypes which, in a phylogenetic network, formed two distinct clusters differing on average by 3.0% sequence divergence. The two species were significantly differentiated both at the mitochondrial and nuclear (AFLP) genetic level. However, five individuals with pomarina phenotype possessed clanga-type mtDNA, suggesting occasional gene flow. Surprisingly, AFLP markers indicated that these mismatched birds (originating from Germany, E Poland and Latvia) were genetically intermediate between the samples of individuals in which mtDNA haplotype and phenotype agreed. This indicates that mismatched birds were either F1 or recent back-cross hybrids. Mitochondrial introgression was asymmetrical (no pomarina haplotype found in clanga so far), which may be due to assortative mating by size. Gene flow of nuclear markers was estimated to be about ten times stronger than for mtDNA, indicating a sex-bias in hybrid fertility in accordance with Haldanes rule. Hybridization between the two species may be more frequent and may occur much further west than hitherto assumed. This is supported by the recent discovery of a mixed pair producing at least one fledgling in NE Germany.     

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.     

Nesting habitat overlap between the Common Buzzard Buteo buteo and the Lesser Spotted Eagle Clanga pomarina for conservation planning in Natura 2000 sites

Capsule: The nesting habitat of the Common Buzzard Buteo buteo and Lesser Spotted Eagle Clanga pomarina extensively overlap, indicating that they exploit similar resources.

Aim: We aimed to determine the overlap in the nest platforms, nest trees and nest stands used by these raptors, find any evidence for the avoidance of the larger Lesser Spotted Eagle by the smaller Common Buzzard, and provide conservation implications for habitat protection of the former species in habitats that overlap extensively.

Methods: Nest sites were mapped during 2012–2014 in the Bir?ai Forest Spatial Protection Area, northern Lithuania. Fifty-three nest sites occupied by Common Buzzards and 26 by Lesser Spotted Eagles were compared.

Results: The nest platforms of both raptors were similarly placed in the tree canopies. Most Lesser Spotted Eagle nests were built in spruce, while the Common Buzzard usually nested in birch. The nest stands of the eagles were on wetter soil and located closer to the forest edge than those of the buzzards, otherwise, the nest stands did not differ significantly. There was no evidence for spatial avoidance of the larger raptor by the Common Buzzard.

Conclusions: The different components of the nesting habitats extensively overlapped, and the distribution of the interspecific pairs lacked spatial avoidance. We suggest that the nest sites of both raptors were a largely shared resource, especially if located close to the forest edges. We propose, as a rule of thumb, applying protection by way of buffer zones around buzzard nest sites if they are located close to eagle nest sites and the forest edge.     

No suggestion of hybridization between the vulnerable black-faced impala (Aepyceros melampus petersi) and the common impala (A. m. melampus) in Etosha National Park, Namibia

There are two recognized subspecies of impala in sub-Saharan Africa: the common impala (Aepyceros melampus melampus) -- widespread in southern and east Africa -- and the vulnerable black-faced impala (A. m. petersi) -- found naturally in only a small enclave in southwest Africa. The Etosha National Park (NP) in Namibia harbours the largest and only protected-area population of black-faced impala, numbering some 1500 individuals. Due to translocations of the exotic common impala to commercial farms in Namibia during the past decades, the black-faced impala in Etosha is faced with the potentially serious threat of hybridization posed by secondary contact with the common impala inhabiting bordering farms. Using eight microsatellite DNA markers, we analysed 127 black-faced impala individuals from the five subpopulations in Etosha NP, to determine the degree, if any, of hybridization within the park. We found that (a) the black-faced impala were highly genetically differentiated from the common impala (pairwise theta-values ranged from 0.18 to 0.39 between subspecies; overall value = 0.27) and (b) black-faced samples showed high levels of genetic variability [average expected heterozygosity (H(E)) = 0.61 +/- 0.01 SE], although not as high as that observed in the common impala (average H(E) = 0.69 +/- 0.02 SE). (c) No hybridization between the subspecies in Etosha was suggested. A Bayesian Markov Chain Monte Carlo approach revealed clear distinction of individuals into groups according to their subspecies of origin, with a zero level of 'genetic admixture' among subspecies.     

Ecology and genetics of interspecific hybridization in the swallowtails, Papilio hospiton Gene and P. machaon L., in Corsica (Lepidoptera: Papiliomdae)

The Corsican swallowtail butterfly, Papilio hospiton , is endemic to Corsica and Sardinia (France and Italy) and included in the list of endangered species by the Washington Convention, It is spread all over Corsica in scattered populations linked to diverse habitats. A study by enzyme electrophoresis showed that the genetic diversity of the species is of the same order of magnitude as that of Papilio machaon from continental France and Corsica. The differentiation between populations is rather low, which is consistent with the high vagility of the adults. Natural hybridization between P. hospiton and P. machaon is frequent, and laboratory crosses show that the hybrids are not sterile. However, developmental perturbations impair the viability of further hybrid progenies. Although limited introgression between the two species is likely to take place, enzyme electrophoresis and PCR-RFLP analysis of mitochondrial DNA show that their gene pools remain distincfTtienetic assimilation by P. machaon therefore does not seem to be a threat for P. hospiton.     

Sequenced RAPD markers to detect hybridization in the barbary partridge (Alectoris barbara, Phasianidae)

In the Alectoris partridges (Phasianidae), hybridization occurs occasionally as a result of the natural breakdown of isolating mechanisms but more frequently as a result of human activity. No genetic record of hybridization is known for the barbary partridge (A. barbara). This species is distributed mostly in North Africa and, in Europe, on the island of Sardinia (Italy) and on Gibraltar. The risk of hybridization between barbary and red-legged partridge (A. rufa: Iberian Peninsula, France, Italy) is high in Sardinia and in Spain. We developed two random amplified polymorphic DNA (RAPD) markers to detect A. barbara × A. rufa hybrid partridges. We tested them on 125 experimental hybrids, sequenced the relative species-specific bands and found that the bands and their corresponding sequences were reliably transmitted through a number of generations (F1, F2, F3, BC1, BC2). Our markers represent a highly valuable tool for the preservation of the A. barbara genome from the pressing threat of A. rufa pollution.     

Interspecific hybridization in Rorippa (Brassicaceae): Patterns and processes

The current knowledge on natural hybridization between European lowland Rorippa species is reviewed. Morphological, cytological and molecular markers provide substantial evidence that four Rorippa species (R. amphibia, R. austriaca, R. palustris and R. sylvestris) are involved in hybridization processes. The main factors promoting initial hybridization events between Rorippa species in Europe are (1) natural and anthropogenic habitat disturbance, (2) the invasion of non‐native R. austriaca into western central Europe and (3) the self‐incompatibility system of R. amphibia, R. austriaca and R. sylvestris coupled with clonal growth. Outcomes of hybridization between European Rorippa species show a broad range from incidental hybrids through the formation of hybrid swarms to the evolution of new hybrid taxa. Rorippa × armoracioides is certainly the most successful Rorippa hybrid. It results from hybridization between R. austriaca and R. sylvestris and is known from many localities in the native range of R. austriaca and in regions invaded by R. austriaca. Within this system hybrid zones of different age provide the rare opportunity to analyse different stages of hybrid formation and hybrid speciation in natural populations.     

Status and ecology of the Bonelli's Eagle,Aquila fasciatus,in the Pentadaktylos Mountain Range,Cyprus (Aves: Falconiformes)

The Bonelli's Eagle is endangered in Europe, and the Cyprus population is estimated to be the 4^th largest in Europe. During 2011 and 2012, ten active nests were confirmed in Pentadactylos Mountains with 8 additional sites meriting further investigation. Observations suggest a varied opportunistic diet largely based on Black Rat (Rattus rattus). Lowland wetland sites are confirmed as important foraging grounds. Bonelli's Eagle is under a variety of anthropogenic threats in Pentadactylos Mountains most significantly hunting and poisoning, evidence for which are discussed.     

Characterization and the broad cross‐species applicability of 20 anonymous nuclear loci isolated from the Taiwan Hwamei (Garrulax taewanus)

We isolated 20 anonymous nuclear loci (8556 bp in total) from the Taiwan Hwamei (Garrulax taewanus), an endemic songbird of Taiwan. A panel of nine to 15 individuals with unknown relationship was used to characterize polymorphism of these loci. We identified 46 single nucleotide polymorphic sites (SNPs) in 15 polymorphic loci. Frequency of SNPs was one per every 186 bp in average. Nucleotide diversity, θ, ranged from 0.00054 to 0.00371 per locus. We also tested cross‐species applicability of these loci on 17 species from eight different passerine families. All 20 loci could be successfully amplified (ranged from one to 16 species, mean = 7.9 species).     

Molecular and morphological evidence of hybridization between newts Triturus vulgaris and T. montandoni (Caudata: Salamandridae) in Slovakia

Natural hybridization and introgression is recorded between the newt species Triturus vulgaris and T. montandoni in Slovakia. To confirm a hybrid status of two putative hybrids, morphological and Randomly Amplified Polymorphic DNA (RAPD) markers specific for T. vulgaris and T. montandoni were used. The individuals found in Zbojská (Veporské vrchy Mts, Slovakia; analyzed morphologically and genetically) and Zubrohlava (Oravská kotlina basin, Slovakia; analyzed only morphologically) possessed markers of both species. Segregation of RAPD markers together with a model-based Bayesian analysis revealed that the specimen from Zbojská belonged to later generation hybrids.     

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.     

Introgressive hybridization of Senecio hercynicus and S. ovatus (Compositae,Senecioneae) along an altitudinal gradient in Harz National Park (Germany)

Introgressive hybridization of Senecio hercynicus and S. ovatus (Compositae, Senecioneae) was studied in a hybrid zone on the southern slopes of Mt Brocken (Harz Mountains, Germany). A total of 415 plants representing 10 stands along an altitudinal gradient were investigated using multivariate statistical analyses of morphological characters and molecular markers (random amplified polymorphic DNA[RAPD]). Both types of traits detected pure S. hercynicus stands on the summit plateau, pure S. ovatus stands at the lowest elevations, and hybrid swarms at intermediate elevations. While morphological and molecular patterns coincided, some individuals in hybrid stands combined morphological patterns typical of S. ovatus with RAPD patterns typical of S. hercynicus, and vice versa. In general, introgression was symmetrical within stands, though one stand combined S. ovatus characters with the glandular hair typical for S. hercynicus, and two stands combined a S. hercynicus typical RAPD genotype with morphological characters shifted towards S. ovatus. Because pure stands of S. hercynicus occurred only on the summit plateau of Mt Brocken, and markers typical for S. ovatus were detectable in stands up to 1040 m a.s.l., future fusion or assimilation of the rare form, S. hercynicus, by the more widespread S. ovatus appears possible at Mt Brocken.     

Genetic characterization of hybridization between the New Zealand everlastings Helichrysum lanceolatum and Anaphalioides bellidioides (Asteraceae: Gnaphalieae)

Intergeneric hybridization between the endemic New Zealand species Helichrysum lanceolatum and Anaphalioides bellidioides (Asteraceae: Gnaphalieae) at two Banks Peninsula populations was investigated by DNA sequencing and amplified fragment length polymorphism fingerprinting. Crosses in both directions have contributed to the generation of the F1 hybrids, but in the study season hybridization was far more common with H. lanceolatum as the maternal parent. F1 hybrids have reduced, but considerable, fertility and seed collected from them includes back-crosses. Two hybrid plants sampled from the wild appear to be back-crosses to H. lanceolatum. Despite back-crossing, introgression was not demonstrated and is at most limited in scope. These results also corroborate important roles for small population size and rarity in the formation of hybrid lineages in New Zealand's everlastings.  © 2007 Landcare Research New Zealand Ltd. Journal compilation © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 154 , 89–98.     

Investigation of X- and Y-specific single nucleotide polymorphisms in taurine (Bos taurus) and indicine (Bos indicus) cattle

Initially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossbreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle breeds (four Sanga breeds, including Raya Azebu, Danakil, Caprivi, Nguni; and two Zebu breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X-chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX ) and ZFX genes, and five previously identified Y-chromosomal markers in the DDX3Y (previously DBY ) and ZFY genes. In total, 90 (57 bulls and 33 cows) samples from the African breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies; in addition to pure taurine, indicine and hybrid X-chromosome individuals, recombinant X-chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle breeds.     

Phylogeography and introgressive hybridization: chipmunks (genus Tamias) in the northern Rocky Mountains

Abstract. If phylogeographic studies are to be broadly used for assessing population-level processes relevant to speciation and systematics, the ability to identify and incorporate instances of hybridization into the analytical framework is essential. Here, we examine the evolutionary history of two chipmunk species, Tamias ruficaudus and Tamias amoenus , in the northern Rocky Mountains by integrating multivariate morphometrics of bacular (os penis) variation, phylogenetic estimation, and nested clade analysis with regional biogeography. Our results indicate multiple examples of mitochondrial DNA introgression layered within the evolutionary history of these nonsister species. Three of these events are most consistent with recent and/or ongoing asymmetric introgression of mitochondrial DNA across morphologically defined secondary contact zones. In addition, we find preliminary evidence where a fourth instance of nonconcordant characters may represent complete fixation of introgressed mitochondrial DNA via a more ancient hybridization event, although alternative explanations of convergence or incomplete sorting of ancestral polymorphisms cannot be dismissed with these data. The demonstration of hybridization among chipmunks with strongly differentiated bacular morphology contradicts long-standing assumptions that variation within this character is diagnostic of complete reproductive isolation within Tamias . Our results illustrate the utility of phylogeographic analyses for detecting instances of reticulate evolution and for incorporating this and other information in the inference of the evolutionary history of species.     

Differential patterns of morphological and molecular hybridization between Fraxinus excelsior L. and Fraxinus angustifolia Vahl (Oleaceae) in eastern and western France

We examined large‐scale patterns of morphology, genetic structure and ecological correlates of Fraxinus excelsior and the closely related species Fraxinus angustifolia in France, in order to determine the degree of hybridization between them. We sampled 24 populations in two putative hybrid zones (Loire and Saône), and five control populations of each species. We measured foliar characteristics of adult trees and used five nuclear microsatellites as molecular markers. Canonical discriminant analysis indicated that the two species differ in morphology, but that intermediate types are common in the Loire region but less frequent in the Saône region. Bayesian population assignment identified one F. angustifolia and two F. excelsior gene pools. Most Loire individuals clustered genetically with the F. angustifolia gene pool. In contrast, the Saône region presented individuals belonging mostly to F. excelsior pools, although the F. angustifolia type was frequent in certain populations. The lowest F_ST values were found between the Loire and F. angustifolia controls that also exhibited no significant isolation by distance. The proportion of the F. angustifolia gene pool in each locality was negatively correlated with winter temperatures, suggesting that a cold climate may be limiting. Hybridization is probably favoured by the intermediate climatic conditions in the Loire region that allow both species to occur, but is somewhat hampered by the harsher winters in the Saône area where morphological introgression has apparently not yet occurred.