Regionally high rates of hybridization and introgression in German wildcat populations (Felis silvestris, Carnivora, Felidae)

While the western populations of the wildcat ( Felis silvestris silvestris ) in Germany come into contact with wildcats in France and Switzerland, the eastern distribution area is geographically completely isolated and consists of scattered subpopulations. To investigate population structure, evolutionary relationships and degree of hybridization with domestic cats we analysed the mitochondrial control region of 86 cats in combination with 11 microsatellite loci of 149 cats. According to our microsatellite data, German wildcats are divided into two separate populations corresponding to the western and eastern distribution areas. We found no indication of a further subdivision of the eastern population. German wildcat populations are genetically distinct from domestic cats in the main, but we identified 18.4% of the whole wildcat sample as being of hybrid origin, corresponding to 4.2% of the eastern and 42.9% of the western wildcat population, and 2.7% of the domestic cat sample. The mitochondrial haplotypes form a network of three connected clusters and reveal a high level of genetic diversity, especially within the eastern population. Our findings are explained at best in terms of continuous introgression between domestic cats and wildcat populations and differing degrees of recent hybridization in the various populations. Future conservation efforts should focus on preserving the existing gene flow between the isolated distribution areas, but also on preventing the spread of hybrids and limiting the habitat alterations that lead to increased contact with domestic cats. In conclusion we discuss possible evolutionary reasons for the still traceable genetic integrity of the wildcat despite its long history of interbreeding.     

Landscape genetic connectivity in European wildcat (Felis silvestris silvestris): a matter of food,shelters and demographic status of populations

Understanding landscape impacts on gene flow is necessary to plan comprehensive management and conservation strategies of both the species of interest and its habitat. Nevertheless, only a few studies have focused on the landscape genetic connectivity of the European wildcat, an umbrella species whose conservation allows the preservation of numerous other species and habitat types. We applied population and landscape genetics approaches, using genotypes at 30 microsatellites from 232 genetically-identified wildcats to determine if, and how, landscape impacted gene flow throughout France. Analyses were performed independently within two population patches: the historical north-eastern patch and the central patch considered as the colonization front. Our results showed that gene flow occurred at large spatial scales but also revealed significant spatial genetic structures within population patches. In both population patches, arable areas, pastures and permanent grasslands and lowly fragmented forested areas were permeable to gene flow, suggesting that shelters and dietary resources are among the most important parameters for French wildcat landscape connectivity, while distance to forest had no detectable effect. Anthropized areas appeared highly resistant in the north-eastern patch but highly permeable in the central patch, suggesting that different behaviours can be observed according to the demographic context in which populations are found. In line with this hypothesis, spatial distribution of genetic variability seemed uneven in the north-eastern patch and more clinal in the central patch. Overall, our results highlighted that European wildcat might be a habitat generalist species and also the importance of performing spatial replication in landscape genetics studies.

     

Gene diversity analysis of mitochondrial DNA, microsatellites and allozymes in landlocked Atlantic salmon

This study investigates the patterns of genetic diversity detected in allozymes, mtDNA, and microsatellites, in order to assess their relative efficacy to differentiate sympatric landlocked salmon populations and to estimate changes in genetic diversity between wild and first-generation hatchery fish. Overall, the three genetic markers indicated a genetic differentiation between two sympatric populations of Lake Saint-Jean, Québec. MtDNA and microsatellites also showed significant differences between wild and first-generation hatchery fish originating from the same river. Allozyme analysis was the most limited approach due to the low genetic diversity detected and the necessity to kill specimens. Although low polymorphism was found in mtDNA, it was the most discriminant marker between wild populations. Microsatellite analysis appears to be a promising approach due to its high sensitivity in differentiating wild populations, in detecting changes in allele composition between wild and first-generation hatchery fish and its potential for increased resolution by augmenting the number of polymorphic loci. Given the benefits and disadvantages of the three methods, the combination of mtDNA and microsatellite analyses will best address our research objectives.     

A suite of genetic markers useful in assessing wildcat (Felis silvestris ssp.)-domestic cat (Felis silvestris catus) admixture

The wildcat (Felis silvestris ssp.) is a conservation concern largely due to introgressive hybridization with its congener F. s. catus, the common domestic cat. Because of a recent divergence and entirely overlapping ranges, hybridization is common and pervasive between these taxa threatening the genetic integrity of remaining wildcat populations. Identifying pure wildcats for inclusion in conservation programs using current morphological discriminants is difficult because of gross similarity between them and the domestic, critically hampering conservation efforts. Here, we present a vetted panel of microsatellite loci and mitochondrial polymorphisms informative for each of the 5 naturally evolved wildcat subspecies and the derived domestic cat. We also present reference genotypes for each assignment class. Together, these marker sets and corresponding reference genotypes allow for the development of a genetic rational for defining "units of conservation" within a phylogenetically based taxonomy of the entire F. silvestris species complex. We anticipate this marker panel will allow conservators to assess genetic integrity and quantify admixture in managed wildcat populations and to be a starting point for more in-depth analysis of hybridization.     

Genetic diversity of Tunisian figs (Ficus carica L.) as revealed by nuclear microsatellites

The present study portrays the achievement of the genetic polymorphism surveying and the establishment of an ecotypes identification key on the basis of simple sequence repeats data. Seventy-two Tunisian fig ecotypes in situ and ex situ conserved were analyzed using six microsatellite loci. A total of 58 alleles and 124 genotypes were revealed and permitted to evidence high degree of genetic diversity mainly explained at the intra group level. Cluster analysis based on genetic distances proved that a typical continuous genetic diversity characterizes the local germplasm. In addition, the microsatellite multilocus genotyping has permitted to unambiguously distinguish 70 well-defined ecotypes (resolving power of 97.22%). Data are discussed in relation with the reliability of the used markers to check the conformity of the plant material and to rationally manage the conservation of this crop.     

The Genetic Integrity of the Ex Situ Population of the European Wildcat (Felis silvestris silvestris) Is Seriously Threatened by Introgression from Domestic Cats (Felis silvestris catus)

Studies on the genetic diversity and relatedness of zoo populations are crucial for implementing successful breeding programmes. The European wildcat, Felis s. silvestris, is subject to intensive conservation measures, including captive breeding and reintroduction. We here present the first systematic genetic analysis of the captive population of Felis s. silvestris in comparison with a natural wild population. We used microsatellites and mtDNA sequencing to assess genetic diversity, structure and integrity of the ex situ population. Our results show that the ex situ population of the European wildcat is highly structured and that it has a higher genetic diversity than the studied wild population. Some genetic clusters matched the breeding lines of certain zoos or groups of zoos that often exchanged individuals. Two mitochondrial haplotype groups were detected in the in situ populations, one of which was closely related to the most common haplotype found in domestic cats, suggesting past introgression in the wild. Although native haplotypes were also found in the captive population, the majority (68%) of captive individuals shared a common mtDNA haplotype with the domestic cat (Felis s. catus). Only six captive individuals (7.7%) were assigned as wildcats in the STRUCTURE analysis (at K = 2), two of which had domestic cat mtDNA haplotypes and only two captive individuals were assigned as purebred wildcats by NewHybrids. These results suggest that the high genetic diversity of the captive population has been caused by admixture with domestic cats. Therefore, the captive population cannot be recommended for further breeding and reintroduction.     

The occurrence of an Australian leech species (genus Helobdella) in German freshwater habitats as revealed by mitochondrial DNA sequences

The freshwater leech Helobdella europaea Kutschera 1987 was discovered twenty years ago in Germany and described as a new species. Here, we show that this leech is genetically identical with the Australian species Helobdella papillornata (CO-I-mt-DNA sequence identity of alignment positions: 98%). We conclude that H. europaea (syn. H. papillornata) represents an introduced annelid that occupies the same ecological niche as the common European leech H. stagnalis L.     

Genetic variation and evolutionary demography of Fenneropenaeus chinensis populations, as revealed by the analysis of mitochondrial control region sequences

Genetic variation and evolutionary demography of the shrimp Fenneropenaeus chinensis were investigated using sequence data of the complete mitochondrial control region (CR). Fragments of 993 bp of the CR were sequenced for 93 individuals from five localities over most of the species' range in the Yellow Sea and the Bohai Sea. There were 84 variable sites defining 68 haplotypes. Haplotype diversity levels were very high (0.95 ± 0.03-0.99 ± 0.02) in F. chinensis populations, whereas those of nucleotide diversity were moderate to low (0.66 ± 0.36%-0.84 ± 0.46%). Analysis of molecular variance and conventional population statistics (F(ST) ) revealed no significant genetic structure throughout the range of F. chinensis. Mismatch distribution, estimates of population parameters and neutrality tests revealed that the significant fluctuations and shallow coalescence of mtDNA genealogies observed were coincident with estimated demographic parameters and neutrality tests, in implying important past-population size fluctuations or range expansion. Isolation with Migration (IM) coalescence results suggest that F. chinensis, distributed along the coasts of northern China and the Korean Peninsula (about 1000 km apart), diverged recently, the estimated time-split being 12,800 (7,400-18,600) years ago.     

Genetic structuring of European anchovy (Engraulis encrasicolus) populations through mitochondrial DNA sequences

Mitochondrial DNA sequence variation in 655?bpfragments of the cytochrome oxidase c subunit I gene, known as the DNA barcode, of European anchovy (Engraulis encrasicolus) was evaluated by analyzing 1529 individuals representing 16 populations from the Black Sea, through the Marmara Sea and the Aegean Sea to the Mediterranean Sea. A total of 19 (2.9%) variable sites were found among individuals, and these defined 10 genetically diverged populations with an overall mean distance of 1.2%. The highest nucleotide divergence was found between samples of eastern Mediterranean and northern Aegean (2.2%). Evolutionary history analysis among 16 populations clustered the Mediterranean Sea clades in one main branch and the other clades in another branch. Diverging pattern of the European anchovy populations correlated with geographic dispersion supports the genetic structuring through the Black Sea-Marmara Sea-Aegean Sea-Mediterranean Sea quad.     

Genetic diversity of Setipinna taty (Engraulidae) populations from the China Sea based on mitochondrial DNA control region sequences

The genetic diversity of Setipinna taty, which is commercially fished in the China Sea, was studied based on mitochondrial DNA control region sequences. PCR was used to amplify the control region fragment in 100 individuals of S. taty collected from Weihai (WH), Yantai (YT), Zhoushan (ZS), Xiangshan (XS), and Ninghai (NH) in China. A control region fragment of 656 bp was successfully sequenced in these 100 individuals. The A+T content of this S. taty control region was 71.7%; 172 variable sites and 62 haplotypes were found. Nucleotide diversity in the WH, YT, ZS, XS, and NH groups was 0.0228, 0.0247, 0.0441, 0.0126, and 0.0238, respectively. The haplotype diversity was 0.984, 0.911, 0.989, 0.926, and 0.979, respectively. Analysis of molecular variance showed that 97.95% of genetic variation was within populations, and only 2.05% among populations. The neighbor-joining phylogenetic tree obtained based on genetic distance showed that no significant genealogical structure exists throughout this range of S. taty. These results indicate no apparent geographical differentiation in the comparison of Yellow Sea and East China Sea populations of S. taty. Within the control region, we identified an extended termination-associated sequence domain, a central conserved sequence block domain and a conserved sequence block domain; insertions of short tandem repeat sequence segments were found at the 5' end of the control region.     

Differentiation and levels of genetic variation in northern European lynx (Lynx lynx) populations revealed by microsatellites and mitochondrial DNA analysis

The European lynx (Lynx lynx) hasexperienced significant decline in populationnumbers over large parts of its formerdistribution area in central and northernEurope. In Scandinavia (Sweden and Norway), thespecies has been subject to intense hunting and inthe early 20th century the population size mayhave been as low as about 100 animals. Duringthe rest of the century there have beenalternating periods of restricted hunting andtotal protection. Future management of theScandinavian lynx population will requireinsight into what effects demographicbottlenecks may have had on genetic variabilityand structure. For this purpose, 276 lynxesfrom Sweden, Norway, Finland, Estonia andLatvia were analysed for polymorphism at 11feline microsatellite loci and at themitochondrial DNA (mtDNA) control region.Scandinavian lynxes were found to be fixed fora single mtDNA haplotype, while this and threeadditional haplotypes were seen in Finland andthe Baltic States (Estonia and Latvia); thehaplotypes were all very similar, onlydiffering at 1–4 sites within a 700 bp regionsequenced. Microsatellite variability wasmoderate (H_e = 0.51–0.62) with lowerheterozygosity and fewer alleles in Scandinaviathan in Finland and the Baltic States together,though significant so only for the latter.Heterozygosity data in Scandinavia wereconsistent with a recent population bottleneck.Various analyses (e.g. F_st, individual-basedtree, assignment test) revealed distinctgenetic differentiation between Scandinavianlynxes and animals from Finland and the BalticStates. Some structure was evident withinScandinavia as well, suggesting an isolation bydistance. The observed partition of geneticvariability between Scandinavia and the easterncountries thereof indicates that lynxpopulations from the two regions may need to beseparately managed. We discuss what factors canhave contributed to the population geneticstructure seen in northern European lynxpopulations of today.     

Food habits of the wildcat (Felis silvestris) in a peculiar habitat: the Mediterranean high mountain

The feeding spectrum of the wildcat Felis silvestris Schreber, 1777 was studied in two sites with different ecological characteristics, both situated in the same Mediterranean environment in the high mountain of the Sierra Nevada National Park, south-east Spain, where the rabbit Oryctolagus cuniculus is absent. Scat analysis ( n =101 faeces; n =402 prey items) showed that the diet is based on rodents, fundamentally wood mouse Apodemus sylvaticus , Mediterranean pine vole Microtus duodecimcostatus and south-western water vole Arvicola sapidus . Results showed strong differences between the two sites (χ²=74.04, d.f.=5, P <0.001), that is a predominance of voles in the mesic Chico river, whereas mice are predominant in the xeric Tejos ravine. Red-legged partridge Alectoris rufa and carrion also played an important role, especially in biomass terms. The overall diet differed essentially from that of the Mediterranean region, which surrounds the study area, since in these areas rabbits constitute the primary prey. However, the diet of the mountain wildcats is similar to that in the Eurosiberian floral region, despite its distance from the Sierra Nevada. In conclusion, the Iberian wildcat seems to behave as a facultative specialist, since it prefers rabbits whenever they are available, but rodents constitute most of its diet if rabbits are scarce or absent.     

Genetic diversity in domestic cats Felis catus of the Tsushima Islands, based on mitochondrial DNA cytochrome b and control region nucleotide sequences

Nucleotide sequences of mitochondrial DNA (mtDNA) of 50 domestic cats (Felis catus) obtained from the Tsushima Islands were determined and the genetic diversity was analyzed. In the cats, six haplotypes of the complete cytochrome b sequences (1,140 base-pairs, bp) and ten haplotypes of the partial control region sequences (350 bp) were identified. Haplotypes obtained from both genes showed existence of at least 11 maternal lineages of domestic cats in Tsushima. Mean values of polymorphic site numbers and sequences differences in the control region were 2.4 times and 1.8 times higher than those in the cytochrome b gene, respectively. Our results support the idea that the evolutionary rate of the control region was faster than that of the cytochrome b as reported in other mammals. Molecular phylogenetic trees showed the similar clustering of haplotypes for both genes. Meanwhile, no individual variations within the Tsushima leopard cat (Felis bengalensis euptilura), which is native to Tsushima, were observed, possibly as a result of genetic drift in the small ancestral population by geographical isolation. In contrast, the diversity of the domestic cat population was higher than that of the leopard cats, because the genetic variability of the former's founders, which were repeatedly brought to Tsushima in the past, still remains. In addition, no sequences of the leopard cat mtDNA were detected in any domestic cats. However, because the possibility that the domestic cat would crossbreed with the leopard cat cannot be denied, genetic monitoring of two species is necessary to biological conservation in Tsushima.     

Molecular diversity and phylogeography of the Asian leopard cat, Felis bengalensis, inferred from mitochondrial and Y-chromosomal DNA sequences

To investigate genetic diversity and phylogeography of the Asian leopard cat (Felis bengalensis), mitochondrial DNA (mtDNA) sequences were determined for 39 individuals from various areas. Sequences combining the complete cytochrome b gene (1,140 bp) with the partial control region (646-810 bp) were classified into 24 haplotypes: 21 types from 21 animals, one from eight animals from Tsushima Islands, one from eight animals from Iriomote Island, and one from two animals from Southeast Asia. Phylogenetic trees of the 24 haplotypes clearly showed three clades: a Northern Lineage and Southern Lineages 1 and 2. The Northern Lineage consisted of animals from Tsushima Islands, the Korean Peninsula, the continental Far East, Taiwan, and Iriomote Island. Within the Northern Lineage, genetic contacts could have occurred between geographically neighboring populations before isolation by straits. Southern Lineage 1, comprising Southeast Asian animals, showed higher genetic diversity. Southern Lineage 2 had large genetic distances from other lineages. Within the control region, the Asian leopard cats shared two to four repetitive motifs, and the number of motifs and their constitution were highly variable among individuals. The motifs were polymorphic even within individuals and could be classified into 31 types. Finally, males of mtDNA Southern Lineage 1 had either of two types of the Y-chromosomal gene ZFY, whereas all males of Northern Lineage shared only one type. Our results indicate that the diversity of southern populations is higher and that genetic differentiation among northern local populations reflects past geographical isolation.     

Genetic diversity and population structure of miiuy croaker populations in East China Sea revealed by the mitochondrial DNA control region sequence

The genetic diversity and population structure of the miiuy croaker (Miichthys miiuy) were investigated. Seventy-six individuals were sampled from six localities of the East China Sea. Genetic variation in DNA sequences was examined from the 5′-end of the mitochondrial DNA control region. High levels of haplotype diversity (h = 0.99333) in the control region were detected, indicating a high level of genetic diversity. A total of 81 polymorphic sites were found, and 65 haplotypes were defined. The results of AMOVA analysis indicated that 97.9% of the genetic variation contained within populations and 2.14% occurred among populations. No significant genealogical branches or clusters were recognized on the NJ tree. Tests of neutral evolution and analysis of mismatch distribution suggested that miiuy croaker might have undergone a population expansion. The knowledge on genetic diversity and genetic structure will be crucial to establish appropriate fishery management stocks for the species.