Insights into the genetic history of Green‐legged Partridgelike fowl: mtDNA and genome‐wide SNP analysis

The Green‐legged Partridgelike (GP) fowl, an old native Polish breed, is characterised by reseda green‐coloured shanks rather than yellow, white, slate or black commonly observed across most domestic breeds of chicken. Here, we investigate the origin, genetic relationships and structure of the GP fowl using mtDNA D‐loop sequencing and genome‐wide SNP analysis. Genome‐wide association analysis between breeds enables us to verify the genetic control of the reseda green shank phenotype, a defining trait for the breed. Two mtDNA D‐loop haplogroups and three autosomal genetic backgrounds are revealed. Significant associations of SNPs on chromosomes GGA24 and GGAZ indicate that the reseda green leg phenotype is associated with recessive alleles linked to the W and Id loci. Our results provide new insights into the genetic history of European chicken, indicating an admixd origin of East European traditional breeds of chicken on the continent, as supported by the presence of the reseda green phenotype and the knowledge that the GP fowl as a breed was developed before the advent of commercial stocks.     

Microsatellite loci reveal highly significant genetic differentiation among Atlantic salmon (Salmo salar L.) stocks from the east coast of Canada

Allele frequency data from eight microsatellite loci provide evidence of highly significant genetic differentiation among stocks of Atlantic salmon Salmo salar L. from the Bay of Fundy, eastern and north-western Nova Scotia and Newfoundland. Estimates of genetic structure ( R _ST and θ) were significant both among all samples taken from the different geographical locations and among samples from geographical regions for which more than one stock was sampled. Samples from the Bay of Fundy taken from stocks which are phenotypically and behaviourally diverse showed particularly high levels of genetic structure. Rogers', allele sharing and (δμ)² distances also revealed significant differences among stock samples and were significantly correlated [Rogers' and (δμ)²] with sea distance between rivers. Results suggest that stocks of Atlantic salmon in eastern Canada are highly diverse genetically and that this should be an important consideration in any management programme for stocks in the area.     

Assessing Genetic Differentiation in Geographic Populations of Labeo calbasu Using Allozyme Markers

The population structure of Labeo calbasu from 11 rivers belonging to the Indus, Ganges, Bhima, Mahanadi, and Godavari basins was investigated using allozyme marker systems. Seven out of 20 allozyme loci (35%) were polymorphic (P < 0.99). Both probability and score tests indicated significant deviation of genotype proportions from Hardy–Weinberg expectations at two loci, XDH* (Mahanadi, Bhima, and Godavari) and G6PDH* (Mahanadi). A pairwise genetic homogeneity test and F _ST values indicated a low-to-moderate level (0.0515) of genetic structuring in the wild population of L. calbasu. AMOVA analysis also indicated moderate differentiation among the samples from different river basins. Analysis for genetic bottleneck was performed under the infinite allele model. The study revealed nine genetic stocks of L. calbasu from the natural population across Indian rivers. Evidence of genetic bottlenecks in some rivers was also revealed.     

Microsatellite genetic variation reveals extensive introgression between wild and introduced stocks, and a new evolutionary unit in French pike Esox lucius L.

The genetic variability of 11 French pike Esox lucius populations from rivers or extensive aquaculture ponds was analysed using seven microsatellite markers. The fish stocking of eastern European pike in French rivers is widespread, so five supplementary populations from this region were also analysed. Genetic variability within the French population was small, and similar to that previously found in Europe for this species. French populations from stocked rivers and extensive farms formed a genetically homogeneous group, and did not diverge from most eastern European samples, which may reflect either ancestral polymorphism or a complete introgression of French populations by introduced stocks. Bayesian analysis of the admixture between populations enabled identification of the French populations that were likely to be affected by introduced stocks (of local or foreign origin). Three genetically distinct evolutionary branches were identified: continental Europe, Danube basin, and south‐western France. The last is a new finding in the species which needs to be further explored by comparisons with wild populations at other sites.     

Fine-scale genetic structure of Atlantic salmon (Salmo salar) using microsatellite markers: effects of restocking and natural recolonization

1. An important goal of conservation biology is to preserve the evolutionary potential of a species by maintaining natural levels of genetic diversity. Here, we assess the population differentiation in the Atlantic salmon, Salmo salar, listed in Annex II of the European Habitats Directive, to provide valuable information for its conservation in Normandy (France).
2. Samples collected from 10 natural sites revealed that 13 of 14 microsatellite loci were polymorphic. Significant differentiation among populations was detected ( F _ST = 0.054, P  <   0.001), and all F _ST pairwise comparisons except one were significant. A genetic split was observed between populations inhabiting streams with limestone geology compared to those inhabiting streams with siliceous geology, which could reflect adaptative differences.
3. Hatchery stocks used for the restocking of two rivers were genetically distinct from native stocks.
4. Analysis of three stream habitats restored in 1995 showed that all were recolonized naturally by wild salmon from geographically close populations and no founder effects were detected. Allelic richness was similar between recolonized and wild populations.
5. From a management perspective, our study revealed that restoration of habitat is very effective to recreate new populations in rivers from which salmon have disappeared and that natural recolonization can be fast and effective in terms of genetic diversity.     

Incongruent estimates of population differentiation among brook charr, Salvelinus fontinalis, from Cape Race, Newfoundland, Canada, based upon allozyme and mitochondrial DNA variation

We determined the amount and temporal stability of genetic differentiation among brook cham sampled from five rivers on Cape Race, Newfoundland, with an electrophoretic analysis of 42 protein coding loci. Fish from four of these rivers were analysed for restriction fragment length polymorphisms in mitochondrial DNA (mtDNA). A single mtDNA clone was observed in all rivers sampled, except one, where 47% offish were from a different and relatively divergent clone (0.31 % sequence divergence). In contrast, Cape Race brook charr show large amounts of genetic differentiation at six enzyme coding loci; Nei's genetic distance ranged between 0,020 and 0.048. This differentiation is relatively stable as no significant differences in allele frequencies were detected between fish sampled from two rivers over two consecutive years. The most divergent population based on protein polymorphism is not that with two mtDNA clonal lineages. In contrast to the commonly held view, mtDNA analyses do not necessarily provide greater resolution of population structure than allozyme analyses.     

Phylogeographical relationships of Sicilian brown trout and the effects of genetic introgression on morphospace occupation

Genetic introgression of aquaculture stocks in local forms is well documented in many fish species but their evolutionary consequences for the local populations have not been thoroughly explored. Due to its wide geographical range, the existence of many locally adapted forms and the frequent occurrence of introgression of aquaculture stocks in local forms, brown trout represents the ideal system to study the effects of such introgressions. Here, we focus on a group of rivers and streams in Sicily (Italy), and, by using molecular tools, we show that autochthonous populations are probably derived from the Southern Atlantic clade, which is present in the Iberian peninsula and North Africa. Three out of the four studied rivers reveal signs of genetic introgression of domestic stocks. Finally, by using advanced geometric morphometric analyses, we show that genetic introgression produces a higher degree of morphological variability relative to that observed in non‐introgressed populations. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 387–398.     

Genetic Variation of the Siberian Sturgeon (<Emphasis Type="Italic">Acipenser baerii</Emphasis> Brandt, 1869) in Aquaculture

Genetic variation of aquaculture broodstocks of the Siberian sturgeon of different origin from 13 farms across the Russian Federation was assessed at five tetraploid microsatellite loci and the mitochondrial DNA control region. At present, in aquaculture stocks of Siberian sturgeon originating from the Lena and Ob rivers, a sharp decline of haplotype diversity is observed. The most part of aquaculture individuals carry two major haplotypes characteristic of the European part of Russia (the Lena aquaculture) and two haplotypes characteristic of the western part of Siberia (the Ob aquaculture). According to the results of the microsatellite analysis, in sturgeon aquaculture stock originating from the Lena River, two genetic clusters can be distinguished. One of these clusters is represented by the stocks composed of inbred individuals and, because of this, is characterized by depleted allelic variation and the loss of rare alleles.     

Lacustrine spatial distribution of landlocked Atlantic salmon populations assessed across generations by multilocus individual assignment and mixed-stock analyses

The objective of this study was to assess the spatiotemporal distribution of four landlocked Atlantic salmon (Salmo salar) populations during their sympatric feeding phase in lake St-Jean (Québec, Canada). A total of 1100 fish captured over a period of 25 years was genotyped at six microsatellite loci in order to assess the temporal stability of the relative proportion of each population in different lake sectors using both individual-based assignment and mixed-stock analysis. Estimates of relative proportions obtained from both methods were highly correlated. A nonrandom spatial distribution of populations was observed for each period and, despite the fact that the overall proportion of each population varied over time, the pattern of differential distribution remained generally stable over time. Furthermore, there were indications that the extent of horizontal spatial overlap among populations was negatively correlated with that of their genetic differentiation at both microsatellites and a major histocompatibility complex locus, and independent of the geographical distance between the rivers of origin. We discuss the hypothesis that the temporal stability of spatial distribution, the lack of an association between spatial partitioning and geographical distance between rivers of origin, and the apparent negative correlation between spatial overlap and genetic differentiation, reflect the outcome of selective pressures driving behavioural differences for spatial niche partitioning among populations.     

AFLP to assess genetic variation in laboratory gerbils (Meriones unguiculatus)

The amplified fragment length polymorphism (AFLP) technique has been increasingly employed for characterizing inbred breeds of animals and detecting strain-specific polymorphisms. The majority of animals studies conducted in biomedical research are performed on rodent species, among which laboratory-reared Mongolian gerbils can be included. Despite the wide use of gerbils in scientific studies, their genetics has rarely been studied. Therefore we investigated the genetic differentiation of laboratory bred gerbils by means of AFLP markers. Six EcoRI/TaqI primer combinations were selected among 13 different combinations to assess the genetic polymorphisms in four stocks of animals: Charles River (CR), Harlan (Ha), Parma (Pr), and Crossbred (Cb). CR and Ha gerbils were purchased from commercial vendors, while Pr and Cb were derived from animals bred in our animal colony. A total of 228 fragments ranging between 70 and 650 bp were obtained. The mean percentage of polymorphic loci across primer combinations was 7.5%. Calculation of genetic distances through application of different algorithms (Nei's, BSI, and Jaccard's indexes) confirmed the poor genetic diversity between stocks. Nevertheless, a differentiation of the Pr and Cb stocks from the more homogeneous CR and Ha was revealed, in agreement with the different breeding derivation and management of the stocks.     

Differentiation of chum salmon Oncorhynchus keta Walbaum populations as revealed with microsatellite and allozyme markers: a comparison

The character and extent of population differentiation in chum salmon Oncorhynchus keta from Sakhalin and Iturup were comparatively studied with 10 microsatellite and 12 allozyme markers. It was demonstrated with the example of allozyme polymorphism at the EstD locus that the effect of an individual locus with one major allele is capable of distorting the total picture of population differentiation. Multiallelic microsatellites were more efficient in revealing the genetic structure of chum salmon populations at the levels of differences between regional populations and between the stocks of individual rivers of the same region.     

Genetic population structure in flatfishes and potential impact of aquaculture and stock enhancement on wild populations in Europe

Marine fish wild stocks are known to be heavily depleted by overfishing and flatfish species are no exception. Wild catches being soon insufficient for responding to consumer demand, the cultivation of marine species appeared as a logical response to the need of seafood. Nevertheless, fish aquaculture also entails major impacts on wild populations from which genetic ones are now better known. The hybridization between domestic and native strains potentially have a genetic impact on recipient populations as long as 1) domestic populations are distinct from native wild ones (through domestication process, genetic improvement of captive stocks) and/or 2) the native wild populations are structured (metapopulation structure, local adaptation). Some of the flatfish species exhibit population differentiation and even local adaptation and the release of domestic genetically modified fishes (selected, transgenic) could threaten their survival in case of introgression. The impact of aquaculture on flatfishes is probably still low as land-based farms and low production levels guaranty low rates of escapes and therefore limited contacts between wild and farmed strains. However, flatfish aquaculture is regarded by experts as a rapidly growing domain that will greatly develop soon. In our opinion, this perspective, added to the quite good performances of farmed flatfishes when released into the wild, fully justifies a stronger interest from the scientific community to the conservation of their wild stocks.     

Persistence of vigilance and flight response behaviour in wild reindeer with varying domestic ancestry

Knowledge about changes in behavioural traits related to wildness and tameness is for most mammals lacking, despite the increased trend of using domestic stock to re‐establish wild populations into historical ranges. To test for persistence of behavioural traits of wild reindeer (Rangifer tarandus L.) exposed to hunting, we sampled DNA, vigilance and flight responses in wild reindeer herds with varying domestic ancestry. Analyses of 14 DNA microsatellite loci revealed a dichotomous main genetic structure reflecting their native origin, with the Rondane reindeer genetically different from the others and with least differentiation towards the Hardangervidda reindeer. The genetic clustering of the reindeer in Norefjell‐Reinsjøfjell, Ottadalen and Forollhogna, together with domestic reindeer, supports a predominant domestic origin of these herds. Despite extensive hunting in all herds, the behavioural measures indicate increasing vigilance, alert and flight responses with increasing genetic dissimilarity with domestic herds. Vigilance frequency and time spent vigilant were higher in Rondane compared to Hardangervidda, which again were higher than herds with a domestic origin. We conclude that previous domestication has preserved a hard wired behavioural trait in some reindeer herds exhibiting less fright responses towards humans that extensive hunting has, but only slightly, altered. This brings novel and relevant knowledge to discussions about genetic diversity of wildlife in general and wild reindeer herds in Norway in specific.     

Differentiation of chum salmon Oncorhynchus keta Wallbaum populations as revealed with microsatellite and allozyme markers: A comparative study

The features and extent of population differentiation in chum salmon Oncorhynchus keta from Sakhalin and Iturup Islands were studied with 10 microsatellite and 12 allozyme markers. It was demonstrated with the example of allozyme polymorphism at the EstD locus that the effect of an individual locus with one major allele is capable of distorting the total picture of population differentiation. Multiallelic microsatellites were more efficient in revealing the genetic structure of chum salmon populations at the levels of differences between regional populations and between the stocks of individual rivers of the same region.     

Genetic diversity and differentiation of the Korean starry flounder (Platichthys stellatus) between and within cultured stocks and wild populations inferred from microsatellite DNA analysis

The Korean starry flounder, Platichthys stellatus, is economically valuable coastal resident fish species. However, the annual catch of this fish has fluctuated and suffered major declines in Korea. We examined the genetic diversity and population structure for four wild populations and three hatchery stocks of Korean starry flounder to protect its genetic integrity using nine microsatellites. A group of 339 genotypes belonging to seven populations were screened. High degrees of polymorphism at the microsatellite loci were observed within both the wild and hatchery populations. Compared to the wild populations, genetic changes, including reduced genetic diversity and highly significant differentiation, have occurred in cultured stocks. Significant population differentiation was also observed in wild starry flounder populations. Similar degrees of inbreeding and significant Hardy–Weinberg equilibrium deviations were detected in both the wild and the hatchery populations. The genetic connectivity pattern identified four distinct metapopulations of starry flounder in Korea by clustering in the phylogenetic tree, Bayesian analyses, molecular variance analysis, PCA and multidimensional scaling analysis. A pattern of isolation-by-distance was not significant. This genetic differentiation may be the result of the co-effects of various factors, such as historic dispersal, local environment or anthropogenic activities. These results provide useful information for the genetic monitoring of P. stellatus hatchery stocks, for the genetic improvement of this species by selective breeding and for designing suitable management guidelines for the conservation of this species.     

Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls

Genetic diversity and phylogenetic relationships among 568 individuals of two red jungle fowl subspe- cies (Gallus gallus spadiceus in China and Gallus gallus gallus in Thailand) and 14 Chinese domestic chicken breeds were evaluated with 29 microstaellite loci, the genetic variability within population and genetic differentiation among population were estimated, and then genetic diversity and phylogenetic relationships were analyzed among red jungle fowls and Chinese domestic fowls. A total of 286 alleles were detected in 16 population with 29 microsatellite markers and the average number of the alleles observed in 29 microsatellite loci was 9.86±6.36. The overall expected heterozygosity of all population was 0.6708±0.0251, and the number of population deviated from Hardy-Weinberg equilibrium per locus ranged from 0 to 7. In the whole population, the average of genetic differentiation among population, measured as FST value, was 16.7% (P<0.001), and all loci contributed significantly (P<0.001) to this differentiation. It can also be seen that the deficit of heterozygotes was very high (0.015) (P<0.01). Reynolds' distance values varied between 0.036 (Xiaoshan chicken-Luyuan chicken pair) and 0.330 (G. gallus gallus-Gushi chicken pair). The Nm value ranged from 0.533 (between G. gallus gallus and Gushi chicken) to 5.833 (between Xiaoshan chicken and Luyuan chicken). An unrooted consensus tree was constructed using the neighbour-joining method and the Reynolds' genetic distance. The heavy-body sized chicken breeds, Luyuan chicken, Xiaoshan chicken, Beijing Fatty chicken, Henan Game chicken, Huainan Partridge and Langshan chicken formed one branch, and it had a close genetic relationship between Xiaoshan chicken-Luyuan chicken pair and Chahua chicken-Tibetan chicken pair. Chahua chicken and Tibetan chicken had closer genetic relationship with these two subspecies of red jungle fowl than other domestic chicken breeds. G. gallus spadiceus showed closer phylogenetic relationship with Chinese domestic chicken breeds than G. gallus gallus. All 29 microstaellite loci in this study showed high levels of polymorphism and significant genetic differentiation was observed among two subspecies of red jungle fowl and 14 Chinese domestic chicken breeds. The evolutional dendrogram is as follows: evolutional breeds→primitive breeds (Chahua chicken and Tibetan)→red jungle fowl in China (G. gallus spadiceus)→red jungle fowl in Thailand (G. gallus gallus). The results supported the theory that the domestic fowls might originate from different subspecies of red jungle fowl and Chinese domestic fowls had independent origin.     

Morphological and molecular divergence of Indian hill trout,Barilius bendelisis (Hamilton, 1822) stocks from different Rivers in Indo‐Burma biodiversity hotspot: Does river altitude and Dam play a role?

The present study explains the intraspecific variation in Indian Hill trout (Barilius bendelisis) on the basis of image based truss network system and D‐loop region of mtDNA. A total of 210 samples were collected from three different rivers (Teesta, Kameng and Myntudu River) of North East India in Indo‐Burma Biodiversity Hotspot. By using the software applications (tpsDig version 2.1 and PAST), a total of 25 morphometric measurements were generated from 10 landmarks. The Analysis of Variance (ANOVA), Factor Analysis (FA) and Discriminate Function Analysis (DFA) showed, out of the total variations, factor 1 explained 46.74% while factor 2 and factor 3 explained 27.14% and 11.92%, respectively. Using these variables 83.33% of the cross‐validated specimens were classified into distinct groups. Analysis of Molecular Variance (AMOVA) and pairwise Fst value for D‐loop region of mtDNA also showed high to medium level of genetic variation among the stocks and within the stocks. We conclude that the observed discrete stocks might be the result of changing environmental conditions in different rivers of the hotspot as the rivers are present at different altitudinal labels. It is also believed that the variation might be due to the construction of barrages across the river which hinder the mixing among the stocks.     

Compensatory releases reduce genetic differentiation among Atlantic salmon populations in the Baltic Sea: evidence from the River Ume‐Vindelälven

About 90% of salmon smolts in the Baltic Sea derive from hatchery enhancement programmes designed to compensate for loss of catches and genetic resources due to the damming of salmon rivers. The potential threat of genetic homogenization from extensive hatchery releases, however, has not been thoroughly investigated. We provide evidence that straying from deliberate releases poses a threat to indigenous populations by identifying the origin of 127 fin‐clipped (hatchery) salmon caught in the River Ume‐Vindelälven during 1997 to 2000, using mtDNA and six microsatellite loci. The analysis of eight potential donor stocks revealed that compensatory releases from the R. Ångerman and R. Luleälven hatcheries have resulted in a significant amount of straying to the river Ume‐Vindelälven (at least 10 and 12 migrants per year). As predicted to due to increased migration, the analysis of temporal samples from the wild population of R. Vindelälven showed a decreasing trend in genetic differentiation estimates (measured as Fst) relative to hatchery the hatchery strains of R. Ångermanälven and R. Luleälven. Our results suggest that gene flow from compensatory releases poses a serious threat to the genetic makeup of the existing wild populations in the Baltic.     

Stocking‐related patterns of genetic variation at enzymatic loci in south European Atlantic salmon populations

Genetic variation at 24 enzymatic loci was investigated in eight south European Atlantic salmon populations from the rivers Nivelle, Cares, Sella, Narcea, Esva, Navia, Porcia and Eo. In these rivers, management based on supplementation of native populations with foreign stocks was carried out for more than one decade. Population genetic patterns expressed in terms of allele frequencies, mean heterozygosity and conformity to Hardy‐Weinberg equilibrium, were significantly different between populations. Relevant temporal changes of genetic variability were reported. Evidence that foreign stocking has disturbed the genetic patterns of some of the studied populations is presented.     

ILLEGAL TRANSLOCATION AND GENETIC STRUCTURE OF FERAL PIGS IN WESTERN AUSTRALIA

Abstract: Unlike many regions in the world where wild pigs (Sus scrofa) are threatened, in Australia they are a significant invasive species. As such, the molecular ecology of feral pigs was investigated to understand their social and population genetic structure. Samples from 269 adult animals were collected over their distribution in southwestern Australia. Using 14 highly polymorphic microsatellite markers, we identified 7 inferred feral pig populations that had moderate heterozygosity (mean = 0.580) and displayed a high level of differentiation (mean R_ST = 0.180). In revealing the genetic structure of feral pigs, we detected anomalies in the putative origin of some individuals. Samples from these animals were collected from 2 main areas: recently colonized regions that were previously uninfested, and established feral pig populations, where animals from geographically isolated areas had been introduced. In the latter, these corresponded to areas that were in close proximity to public road access and towns. Given the large distances immigrants were found from their population of origin (from 50 to >400 km), the generally low levels of dispersal of southwest feral pigs, and the grouping and sex of these pigs, we suggest that these individuals have been deliberately and illegally translocated to supplement recreational hunting stocks. Additionally, we could not detect any genetic contribution in these feral pigs from domestic pig herds, suggesting that the deliberate release of domestic pigs to restock feral populations is relatively uncommon. Our molecular data allowed some inferences regarding the success or lack thereof of current management practices, and offered considerable insights into the dynamics of the feral pig populations and identification of “new” approaches that may allow for better control of this highly destructive species.