Genetic variation in a population of the wild quail Coturnix coturnix japonica

To investigate genetic variation and to compare it with those of domestic quail populations, enzymatic and non-enzymatic proteins in a wild quail population were examined electrophoretically.
The wild quail population had a genetic variability considerably lower than those of domestic populations. The average heterozygosity estimated for 22 loci was 0.090 in the wild quail population.     

Protein polymorphism in two populations of the wild quail Coturnix coturnix japonica

To evaluate genetic variability in two populations of the wild quail Cofurnix coturnix japonica , proteins and enzymes were examined by starch gel electrophoresis.
Rare variants so far not observed in domestic quail were found in the following five enzymes; aspartate aminotransferase, acid phosphatase, pancreatic esterase, isocitrate dehydrogenase and lactate dehydrogenase. The proportion of polymorphic loci ( P _poly) and the expected average heterozygosity ( H ) in one of the two populations were estimated to be 0.484 (15/31) and 0.085, respectively. Those in another population were 0.433 (13/30) and 0.086, respectively. The genetic distance (Nei, 1975) between the two wild quail populations was D = 0.0074. D values of 0.0321 and 0.0189 were estimated between the laboratory quail population previously examined (Kimura et al., 1982) and each of these two wild populations.     

Lack of introgression of Japanese quail in a captive population of common quail

Farm-reared quails are released to the wild in Europe in vast numbers every year to increase hunting bag quotas. Experimental studies indicate that rather than the native common quail (Coturnix coturnix), the restocking is often done with domestic Japanese quail (Coturnix japonica) or with hybrids of domestic Japanese quail and common quail. Such practices are thought to be a severe threat for the native species as it could lead to introgression of domestic Japanese quail alleles into the wild common quail genome and potentially alter the migratory and reproductive behaviour in wild populations. In this study, we assessed the genetic purity of a captive population of common quail that was established from wild-caught founders caught on the Southern Italian coast in Sicily (Italy). We evaluated the proportion of ancestry to common and Japanese quail in this captive population via genetic screening using nuclear microsatellite markers and mitochondrial DNA analyses. We showed that the captive farm quail in our study had no sign of admixture with domestic Japanese quail and had similar genotype frequencies relative to wild common quail, confirming the success of the breeding programme for the native species. We propose that raising common quails in captivity for restocking purposes rather than domestic Japanese quails or hybrids would be a feasible alternative that could minimise the risk of genetic pollution of wild common quail populations.     

Study on genetic coadaptability of wild quail populations in China

Genetic coadaptability, developed from the process of evolution, is one of the properties of gene pool as well as gene frequency of each locus. It was explained in detail by Nei[1] in 1973. He proposed that during evolutionary process, non-allelic genes o…     

Study on genetic coadaptability of wild quail populations in China

Genetic coadaptability of wild Japanese quail, wild Common quail and Domestic quail populations in China was studied using 7 microsatellite DNA markers and Monte Carlo method to test genetic disequilibrium. The molecular effects of genetic coadaptability were analyzed through a new statistical model of neutral site. The results showed that genetic coadaptability dominated the genetic disequilibrium of the three quail populations, and totally 16.67%, 9.66% and 10.05% of non-allelic combinations were in the genetic disequilibrium in wild Japanese quail, wild Common quail and Domestic quail populations, respectively. Genetic coadaptability existed at almost all the tested sites. In the molecular point of view, genetic coadaptability plays an important role of keeping lots of polymorphisms in natural populations. Therefore, it is another key factor to the genetic disequilibrium in the population except for linkage. The results enrich the conceptions and connotations of genetic disequilibrium, and help us know more about genetic coadaptability and its effects, and lay a foundation of evaluation and protection of wild quail genetic resources in China.     

Genetic variability and population differentiation in captive baird's Tapirs (Tapirus bairdii)

The objectives of this study were to assess the level of genetic variability and population differentiation within captive populations of an endangered large mammal, Baird's tapir (Tapirus bairdii). We genotyped 37 captive animals from North American (NA) and Central American (CA) zoos and conservation ranches using six polymorphic microsatellite loci. Standard indices of genetic variability (allelic richness and diversity, and heterozygosity) were estimated and compared between captive populations, and between captive and wild population samples. In addition, we evaluated levels of population differentiation using Weir and Cockerham's version of Wright's F-statistics. The results indicate that the NA and CA captive populations of Baird's tapirs have retained levels of genetic variability similar to that measured in a wild population. However, inbreeding coefficients estimated from the molecular data indicate that the CA captive population is at increased risk of losing genetic variability due to inbreeding. Despite this, estimated levels of population differentiation indicate limited divergence of the CA captive population from the wild population. Careful management appears to have kept inbreeding coefficients low in the NA captive population; however, population differentiation levels indicate that the NA population has experienced increased divergence from wild populations due to a founder effect and isolation. Based on these results, we conclude that intermittent exchanges of Baird's tapirs between the NA and CA captive populations will benefit both populations by increasing genetic variability and effective population size, while reducing inbreeding and divergence from wild populations. Zoo Biol 23:521–531, 2004. © 2004 Wiley-Liss, Inc.     

Contrasting patterns of gene diversity between microsatellites and mitochondrial SNPs in farm and wild Atlantic salmon

Levels of genetic variability at 12 microsatellite loci and 19 single nucleotide polymorphisms in mitochondrial DNA were studied in four farm strains and four wild populations of Atlantic salmon. Within populations, the farm strains showed significantly lower allelic richness and expected heterozygosity than wild populations at the 12 microsatellite loci, but a significantly higher genetic variability with respect to observed number of haplotypes and haplotype diversity in mtDNA. Significant differences in allele- and haplotype-frequencies were observed between farm strains and wild populations, as well as between different farm strains and between different wild populations. The large genetic differentiation at mitochondrial DNA between wild populations (F_ST = 0.24), suggests that the farm strains attained a high mitochondrial genetic variability when created from different wild populations seven generations ago. A large proportion of this variability remains despite an expected lower effective population size for mitochondrial than nuclear DNA. This is best explained by the particular mating schemes in the breeding programmes, with 2–4 females per male. Our observations suggest that for some genetic polymorphisms farm populations might currently hold equal or higher genetic variability than wild populations, but lower overall genetic variability. In the short-term, genetic interactions between escaped farm salmon and wild salmon might increase genetic variability in wild populations, for some, but not most, genetic polymorphisms. In the long term, further losses of genetic variability in farm populations are expected for all genetic polymorphisms, and genetic variability in wild populations will be reduced if escapes of farm salmon continue.     

The role of nest‐site selection and cereal production in differential nest predation in Common Quail Coturnix coturnix and hybrid quail C. coturnix × C. japonica

In Europe, farm‐reared quail used for restocking purposes are often hybrids between the Common Quail Coturnix coturnix and the Japanese Quail Coturnix japonica. These hybrids interbreed with wild Common Quail populations and suffer higher rates of nest predation, which would suggest that the two quail types have different nest‐site selection patterns. We monitored 103 radiotagged nesting females (77 wild Common Quail over 18 breeding seasons and 26 hybrid quail over six breeding seasons) and analysed their nest placement behaviour. Our results did not provide any evidence that the quail types showed different nest‐site selection trends, as they all preferred to nest near cereal field margins. The higher nest predation rate experienced by hybrids might therefore be explained by less effective anti‐predator behaviour among hybrid females during incubation. As no edge effect on nest predation was observed, the preference for nesting close to cereal margins could be due to the greater food resources of field margins. Moreover, Common Quail nest predation decreased with a rise in barley straw production, supporting evidence that nest cover plays an important role in the prevention of nest predation in this species. No such relationship was found for hybrid quail, but this result is not conclusive, as the data on barley straw production for hybrid quail covered a much smaller range of interannual variability. Barley straw production in Catalonia decreased significantly between 1992 and 2012, possibly as a result of a change in the barley varieties used. This practice could entail a conservation threat for ground‐nesting bird species.     

Microsatellite loci in Japanese quail and cross-species amplification in chicken and guinea fowl

In line with the Gifu University''s initiative to map the Japanese quail genome, a total of 100 Japanese quail microsatellite markers isolated in our laboratory were evaluated in a population of 20 unrelated quails randomly sampled from a colony of wild quail origin. Ninety-eight markers were polymorphic with an average of 3.7 alleles per locus and a mean heterozygosity of 0.423. To determine the utility of these markers for comparative genome mapping in Phasianidae, cross-species amplification of all the markers was tested with chicken and guinea fowl DNA. Amplification products similar in size to the orthologous loci in quail were observed in 42 loci in chicken and 20 loci in guinea fowl. Of the cross-reactive markers, 57.1% in chicken and 55.0% in guinea fowl were polymorphic when tested in 20 birds from their respective populations. Five of 15 markers that could cross-amplify Japanese quail, chicken, and guinea fowl DNA were polymorphic in all three species. Amplification of orthologous loci was confirmed by sequencing 10 loci each from chicken and guinea fowl and comparing with them the corresponding quail sequence. The microsatellite markers reported would serve as a useful resource base for genetic mapping in quail and comparative mapping in Phasianidae.     

厚壳贻贝养殖群体与野生群体线粒体DNA的遗传分析(英文）

采用线粒体DNA COI基因序列对厚壳贻贝2个养殖群体与2个野生群体的遗传多样性进行了研究。4个群体共获得30个单倍型。结果显示：在养殖群体中单倍型的数量和遗传多样性要比野生群体的低,可能是由于只有少量的有效父母本对养殖群体的遗传变异有贡献所致。养殖群体与当地野生群体之间也未发生显著的遗传分化,可能是因为它们之间存在基因流。在今后厚壳贻贝养殖过程中,本研究可以用在对养殖群体进行遗传监测,从而保证养殖群体的遗传多样性水平。     

Genetic variability in captive populations of Crocodylus moreletii (Crocodylia: Crocodylidae) using microsatellites markers

Crocodylus moreletii, an extinction threatened species, represents an emblem for tropical ecosystems in Mexico. Surprisingly, there is a lack of information about their genetic constitution, which should be evaluated for a proper management ex situ and for making decisions on the release of crocodiles into natural habitats. The aim of this study was to characterize and compare the genetic variability of four populations of C. moreletii (two wild versus two born ex situ). Through PCR were amplified seven microsatellite polymorphic loci, however a heterozygote deficit, diminished by the presence of null alleles, was found in the populations (average Ho=0.02). The AMOVA indicated that the highest proportion of genetic variability is within populations, and a limited genetic differentiation among populations (average F(ST)=0.03), probably due to high inbreeding index (average F(IS)=0.97). When comparing the genetic variability between and within other crocodilian species, we found that in C. moreletii is well below those reported. We concluded that the limited genetic variability in ex situ born populations is probably due to a founder effect derived from the social structure of their progenitors, and by the bottleneck effect, inferred by the limited effective population size, that historically characterizes their natural distribution in wild populations.     

Population genetic structure in wild and hatchery populations of white cloud mountain minnow (Tanichthys albonubes): Recommendations for conservation

We used mitochondrial (mt) cytochrome b gene (cyt b) to compare the genetic variability in three hatchery broodstocks of white cloud mountain minnow with the variability in six wild populations sampled in two river drainages. A total of 43 haplotypes in 102 specimens were observed, with no haplotype shared between wild and hatchery populations. The nucleotide diversity of the wild samples (0.048) was significantly higher than that of the hatchery ones (0.007), but the haplotype diversity was almost similar between them. Two major phylogenetic haplotype groups were revealed and estimated to diverge about 6.531 myr (million years) ago. Significant genetic differentiation was revealed between wild and hatchery populations as well as among nine sampled populations, suggesting at chance effect during the founding process for the hatchery population and a subsequent genetic drift. According to the network, the connection between wild and hatchery populations indicates that present hatchery populations originated from single wild population. We suggested that two regions (Pearl River system and Lu River) identified by reciprocal mtDNA monophyly and SAMOVA should be regarded as three different ESUs and two different MUs in South China, respectively.     

Rodrigues fruit bats (<Emphasis Type="Italic">Pteropus rodricensis</Emphasis>, Megachiroptera: Pteropodidae) retain genetic diversity despite population declines and founder events

Fruit bats of the genus Pteropus are important contributors to ecosystem maintenance on islands through their roles as pollinators and seed dispersers. However, island faunas are the most prone to extinction and there is a real need to assess the possible genetic implications of population reductions in terms of extinction risk. An effective method of ameliorating extinction risk in endangered species is the establishment of captive populations ex situ. The effectiveness of captive breeding programmes may be assessed by comparing the genetic variability of captive colonies to that of wild counterparts. Here, we use polymorphic microsatellite loci to assess genetic variability in wild, critically endangered Rodrigues fruit bats (Pteropus rodricensis, Dobson 1878) and we compare this variability to that in a captive colony. We document remarkable conservation of genetic variability in both the wild and captive populations, despite population declines and founder events. Our results demonstrate that the wild population has withstood the negative effects of population reductions and that captive breeding programmes can fulfil the goals of retaining genetic diversity and limiting inbreeding.     

Stable individual profiles of daily timing of migratory restlessness in European quail

Temporal characteristics of migratory behavior in birds are usually studied at the species and population levels, and rarely at the individual level. Variations among species and populations of the seasonal onset of migratory behavior have been widely investigated, but very little is known about its daily organization or whether birds are conservative in their behavior. The determination of intra- and inter-individual variability is important for the study of genetic variations and can reveal the existence of different adaptation capacities within populations. This laboratory study analyzed intra- and inter-individual variability of daily initiation and time course of nocturnal restlessness in partial-migrant European quail (Coturnix coturnix coturnix). Thirty-five quail were selected randomly from a captive stock, and their spring activity was recorded under natural daylenghs. Eighteen of the thirty-five quail presented behavioral profiles of migrant birds. Migrant birds initiated their nocturnal activity punctually, and the time courses of the nocturnal activity of 88% of them revealed intra-individual stability over six consecutive nights. All birds initiated their nocturnal activity after sunset and civil twilight, and they were more active at the beginning than the middle or end of the night, suggesting that their drive to migrate could be synchronized with particular skylight conditions. For the first time, stable individual profiles in the daily time course of migratory restlessness are shown. These results support previous findings concerning biological rhythms of quail and raise questions concerning the timing of migratory behavior.     

Microsatellite variability reveals the necessity for genetic input from wild giant pandas (Ailuropoda melanoleuca) into the captive population

Recent success in breeding giant pandas in captivity has encouraged panda conservationists to believe that the ex situ population is ready to serve as a source for supporting the wild population. In this study, we used 11 microsatellite DNA markers to assess the amount and distribution of genetic variability present in the two largest captive populations (Chengdu Research Base of Giant Panda Breeding, Sichuan Province and the China Research and Conservation Center for the Giant Panda at Wolong, Sichuan Province). The data were compared with those samples from wild pandas living in two key giant panda nature reserves (Baoxing Nature Reserve and Wanglang Nature Reserve). The results show that the captive populations have retained lower levels of allelic diversity and heterozygosity compared to isolated wild populations. However, low inbreeding coefficients indicate that captive populations are under careful genetic management. Excessive heterozygosity suggests that the two captive populations have experienced a genetic bottleneck, presumably caused by founder effects. Moreover, evidence of increased genetic divergence demonstrates restricted breeding options within facilities. Based on these results, we conclude that the genetic diversity in the captive populations is not optimal. Introduction of genetic materials from wild pandas and improved exchange of genetic materials among institutions will be necessary for the captive pandas to be representative of the wild populations.     

Genetic Structure of Different Populations of Walking Catfish (Clarias batrachus L.) in Bangladesh

Information on genetic variation is essential for conservation and stock improvement programs. Seven dinucleotide microsatellite loci were analyzed to reveal genetic variability in three wild populations (Kella beel, Hakaluki haor, and Shobornokhali beel) and one hatchery population of the freshwater walking catfish, Clarias batrachus, in Bangladesh. Upon PCR amplification, the alleles were separated on polyacrylamide gel using a sequencing gel electrophoresis system and visualized by the silver-staining method. The loci were polymorphic (P95) in all the populations. Differences were observed in number and frequency of alleles as well as heterozygosity in the studied populations. Current gene diversity (He) was higher than expected under mutation-drift equilibrium, significantly in the Hakaluki haor and Shobornokhali beel populations, indicating a recent genetic bottleneck. Population differentiation (FST) values were significant (P<0.05) in all the population pairs. A relatively high level of gene flow and a low level of FST values were found between wild population pairs compared to hatchery-wild pairs. The unweighted pair group method with averages dendrogram based on genetic distance resulted in two major clusters: the hatchery population was alone in one cluster whereas the three wild populations made another cluster. The results reflect some degree of genetic variability in C. batrachus populations indicating potentialities for improving this species through a selective breeding program. The results revealed a recent bottleneck in some wild populations of C. batrachus. Protection of habitat may help increase the population size and lower the risk of vulnerability of the species in the future.     

Wild sunflower diversity in Argentina revealed by ISSR and SSR markers: an approach for conservation and breeding programmes

Wild sunflower Helianthus annuus originates from North America and has naturalised in Argentina where it is considered invasive. The present study attempts to assess the genetic diversity using two different molecular marker systems to study the wild genetic patterns and to provide data applicable to conservation and breeding uses. Ten natural populations sampled throughout the wild range and six inbred lines were studied using inter‐simple sequence repeat (ISSR) and simple sequence repeats (SSR) markers. A total of 64 ISSR bands and 29 SSR alleles were produced from 106 wild and cultivated plants. We found 9 ISSR private bands and 21 SSR private alleles in wild accessions, but no private bands/alleles were found in cultivated sunflowers. Molecular variability in wild populations was approximately 60% higher than in inbred lines. Local wild sunflowers kept considerable diversity levels in comparison with populations in the centre of origin (approximately 70%) and therefore they might possess a potential for adaptive evolutionary change. Analysis of molecular variance (AMOVA) indicated population structure with nearly 20% of genetic variability attributable to between‐population differentiation. Principal coordinate analyses (PCO) grouped wild populations from different geographic locations, and a Mantel test showed low congruence between genetic distance (GD) and geographic distances (GGD); hence, molecular data could not rule out multiple wild introduction events. Low correlations were found between ISSR and SSR GD at individual and population levels; thus, divergent evolutionary groups were not evident in local wild sunflowers. Several genetic diversity criteria were utilised to assign conservation value and certain wild populations emerged as interesting sites for more extensive sampling.     

Stable Individual Profiles of Daily Timing of Migratory Restlessness in European Quail

Temporal characteristics of migratory behavior in birds are usually studied at the species and population levels, and rarely at the individual level. Variations among species and populations of the seasonal onset of migratory behavior have been widely investigated, but very little is known about its daily organization or whether birds are conservative in their behavior. The determination of intra‐ and inter‐individual variability is important for the study of genetic variations and can reveal the existence of different adaptation capacities within populations. This laboratory study analyzed intra‐ and inter‐individual variability of daily initiation and time course of nocturnal restlessness in partial‐migrant European quail (Coturnix coturnix coturnix). Thirty‐five quail were selected randomly from a captive stock, and their spring activity was recorded under natural daylenghs. Eighteen of the thirty‐five quail presented behavioral profiles of migrant birds. Migrant birds initiated their nocturnal activity punctually, and the time courses of the nocturnal activity of 88% of them revealed intra‐individual stability over six consecutive nights. All birds initiated their nocturnal activity after sunset and civil twilight, and they were more active at the beginning than the middle or end of the night, suggesting that their drive to migrate could be synchronized with particular skylight conditions. For the first time, stable individual profiles in the daily time course of migratory restlessness are shown. These results support previous findings concerning biological rhythms of quail and raise questions concerning the timing of migratory behavior.     

New polymorphic microsatellite markers in Pacific abalone Haliotis discus hannai and their application to genetic characterization of wild and aquaculture populations

Seven new microsatellite markers were developed for the Pacific abalone (Haliotis discus hannai, Haliotidae), and allelic variability was compared between a wild population and a hatchery population in Yeosu, Korea. All loci amplified readily and demonstrated allelic variability, with the number of alleles ranging from 6 to 15 in the wild population and from 3 to 12 in farmed populations. Average observed and expected heterozygosities were estimated at 0.65 and 0.77 in the hatchery samples, and 0.79 and 0.87 in the wild samples. These results indicated lower genetic variability in the hatchery population, as compared with the wild population and significant genetic differentiation between the wild population and the hatchery samples (F _ST=0.055, p<0.001). These microsatellite loci may be valuable for future population genetic studies and for tracking hatchery samples used in stock enhancement programs.     

Evidence of parasite-mediated disruptive selection on genetic diversity in a wild fish population

Identifying the processes maintaining genetic variability in wild populations is a major concern in conservation and evolutionary biology. Parasite-mediated selection may strongly affect genetic variability in wild populations. The inbreeding depression theory predicts that directional selection imposed by parasites should act against the most inbred hosts, thus favouring genetic diversity in wild populations. We have tested this prediction by evaluating the strength and shape of the relationship between the load of a harmful fin-feeder ectoparasite ( Tracheliastes polycolpus ) and the genome-wide genetic diversity (i.e. heterozygosity measured at a set of 15 microsatellites) of its fish host, the rostrum dace ( Leuciscus leuciscus ). Contrary to expectation, we found a nonlinear relationship between host genetic diversity and ectoparasite load, with hosts that were either homozygous or heterozygous harbouring significantly fewer parasites than hosts with an intermediate level of heterozygosity. This relationship suggests that parasites could increase the variance of global heterozygosity in this host population through disruptive selection on genetic diversity. Moreover, when genetic diversity was measured at each locus separately, we found two very strong positive associations between host genetic diversity and the ectoparasite load. This latter result has three main implications: (i) genome-wide effect cannot alone explain the nonlinear relationship between global heterozygosity and ectoparasite load, (ii) negative non-additive allelic interactions (i.e. underdominance) may be a mechanism for resisting ectoparasite infection, and (iii) ectoparasites may favour homozygosity at some loci in this host population.