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1.
Tejedor MT Monteagudo LV Mautner S Hadjisterkotis E Arruga MV 《The Journal of heredity》2007,98(2):179-182
In order to detect introgression of other Alectoris genus species into wild populations of Spanish Alectoris rufa, we studied a sample of 93 red-legged partridges (supposed to be A. rufa) captured in the island of Majorca. A set of 31 chukar partridges (Alectoris chukar) from Cyprus and 33 red-legged partridges (A. rufa) from one Spanish farm were also studied to provide suitable populations for comparison. Factorial correspondence analysis on microsatellite genotypes supported a clear distinction of birds from Cyprus, whereas partridges from Majorca and the Spanish farm overlapped in a wide area. The existence of A. chukar mitochondrial DNA in 16 individuals from Majorca indicated introgression into their maternal lineage even if their phenotypes were not different from A. rufa. Bayesian inference based on microsatellite analysis indicated a noticeable degree of genetic proximity to A. chukar only for one of these hybrids. 相似文献
2.
M. T. Tejedor L. V. Monteagudo E. Hadjisterkotis M. V. Arruga 《European Journal of Wildlife Research》2005,51(4):232-236
For the first time, microsatellite loci were used to study the genetic structure in Alectoris chukar cypriotes. Four of the ten tested microsatellite loci were found to be polymorphic in 33 individuals from four regions of Cyprus. The differentiation test between all the pairs of samples gave non-differentiation exact P values in every case (P>0.05). The posterior probability distribution on the number of source populations indicated only one population (P=0.977); also, a high Bayes factor value (130.020) was obtained. Posterior co-assignment probabilities (measures of similarity) for all pairs of individuals ranged from 0.984 to 1. The global FIS value was not found to be significant. A recent bottleneck of the Cypriot total partridge population is suggested and this is supported by a significant Wilcoxon test (P=0.031) under the Infinite Alleles Model (IAM) and shifted mode in the alleles frequencies distribution. The results suggest that all the individuals studied belong to only one randomly mating (panmictic) population, with low genetic variation and evidence of recent effective population size reduction (genetic bottleneck). A big hunting pressure exists on the island and about 200,000 captive-bred birds are released every year; these individuals are descendant from a small number of eggs collected in a small area of Cyprus in 1986 and this founder effect could explain the existence of a bottleneck and the low genetic variability. 相似文献
3.
The analysis of 135 mitochondrial D-loop sequences of the Iberian autochthonous red-legged partridge (Alectoris rufa) from wild population hunting bags from various locations and fowl runs in Spain yielded 37 different haplotypes. Among these,
three haplotypes correspond to chukar partridges (Alectoris chukar), indicating genetic introgression from birds illegally introduced for restocking: three individuals carrying such haplotypes
where found in natural populations, one appeared among those sampled on a mass reproduction farm and the remaining 10 in another
fowl-run. The geographical origin of the contaminating chukar haplotypes could be assigned to the most easterly area of the
chukar partridge geographical distribution in China. Molecular diversity parameters in the A. rufa samples indicate a considerable amount of genetic variation. ΦST showed significant differences among populations that are not explained by geographical distance alone. Particularly, one
northern population (Palencia) shows a certain degree of genetic differentiation that could reflect a previously suggested
subspecies division.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
4.
Paulo Corti Aaron B. A. Shafer David W. Coltman Marco Festa-Bianchet 《Conservation Genetics》2011,12(1):119-128
Small populations in fragmented habitats can lose genetic variation through drift and inbreeding. The huemul (Hippocamelus bisulcus) is an endangered deer endemic to the southern Andes of Chile and Argentina. Huemul numbers have declined by 99% and its
distribution by 50% since European settlement. The total population is estimated at less than 2,000 individuals and is highly
fragmented. At one isolated population in Chilean Patagonia we sampled 56 individuals between 2005 and 2007 and genotyped
them at 14 microsatellite loci. Despite low genetic variability (average 2.071 alleles/locus and average H
O of 0.341), a low inbreeding coefficient (F
IS) of 0.009 suggests nearly random mating. Population genetic bottleneck tests suggest both historical and contemporary reductions
in population size. Simulations indicated that the population must be maintained at 75% of the current size of 120 individuals
to maintain 90% of its current genetic diversity over the next 100 years. Potential management strategies to maintain genetic
variability and limit future inbreeding include the conservation and establishment of habitat corridors to facilitate gene
flow and the enlargement of protected areas to increase effective population size. 相似文献
5.
Limonium narbonense Miller is a fertile tetraploid species with a sporophytic self-incompatibility system. This sea lavender is found in coastal
salt marshes which have been under intense human pressure during the past decades resulting in significant habitat fragmentation.
Eleven microsatellite loci specifically designed for this species were amplified in 135 individuals from five populations.
These markers were used to investigate the polyploid nature, the levels of genetic diversity and population structure in this
species. L. narbonense showed high levels of genetic diversity (A = 7.82, P = 100% H
T = 0.446), consistent with its likely autotetraploid origin revealed in this study and obligate outcrossing breeding system.
Inbreeding (F
IS) values were low in the three southern populations (mean F
IS = 0.062), and higher in the northern populations (mean F
IS = 0.184). Bayesian analysis of population structure revealed that populations could be grouped into two genetic clusters,
one including three southern populations and the other the two northernmost ones. Individuals from the two northernmost populations
showed higher admixture of the two genetic clusters than individuals from the three southern ones. A thorough analysis of
microsatellite electrophoretic patterns suggests an autotetraploid origin for L. narbonense. The genetic structure revealed in this study is attributed to a recent migration from the southern area. This result suggests
a net gene flow from the south to the north, likely facilitated by migratory movements of birds visiting the temporary flooded
ponds occupied by L. narbonense. 相似文献
6.
Marina Barilani Athanassios Sfougaris Alexis Giannakopoulos Nadia Mucci Cristiano Tabarroni Ettore Randi 《Conservation Genetics》2007,8(2):343-354
The nominal subspecies of rock partridge (Alectoris graeca graeca) is widely distributed in Greece, where populations are declining due to over-hunting and habitat changes. Captive-reared
chukars (A. chukar) have been massively released throughout the country, raising fear that introgressive hybridisation might have disrupted
local adaptations leading to further population declines. In this study we used mtDNA control-region sequences and Bayesian
admixture analyses of multilocus genotypes determined at eight microsatellite loci, to assess the extent of introgressive
hybridisation in 319 wild rock partridges collected in Greece. A neighbour-joining tree split the mtDNA haplotypes into three
strongly supported clades, corresponding to rock, red-legged (A.␣rufa) and chukar partridges. We did not detect any case of maternal introgression. In contrast, admixture analyses of microsatellite
genotypes identified from four to 28 putative hybrids (according to different assignment criteria), corresponding to 1.2–8.8%
of the samples, which were widespread throughout all the country. Power and limits of admixture analyses were assessed using
simulated hybrid genotypes, which revealed that a small number of markers can detect all first and second generation hybrids
(F
1 and F
2), and up to 90% of the first generation backrossess. Thus, the true proportion of recently introgressed rock partridges in
Greece might be ca. 20%. These findings indicate that introgressive hybridisation is widespread, suggesting that released
captive-bred partridges have reproduced and hybridised in nature polluting the gene pool of wild rock partridge populations
in Greece. 相似文献
7.
Labeo rohita, popularly known as rohu is a widely cultured species in the whole Indian subcontinent. Knowledge of the genetic diversity of this species is important to support management and conservation programs which will subsequently help in sustainable production of this species. DNA markers, mostly microsatellite markers are excellent tool to evaluate genetic variation of populations. Genetic variation of three wild and one farm population was assessed using eleven microsatellite loci. In analyzing 192 samples, the number of alleles ranged from 4 to 23; observed heterozygosity 0.500 to 0.870 and expected heterozygosity from 0.389 to 0.878. Exact test for Hardy Weinberg disequilibrium revealed that each riverine sample had at least one locus not in equilibrium except one river. Negative inbreeding coefficients (FIS) were observed across populations indicating very high level of genetic diversity but little genetic differentiation among populations. 相似文献
8.
Sodhi M Mukesh M Ahlawat SP Sobti RC Gahlot GC Mehta SC Prakash B Mishra BP 《Biochemical genetics》2008,46(3-4):124-136
This study aims to assess the genetic diversity and population structure of two major zebu dairy breeds (Tharparkar and Rathi)
adapted to the arid region of Rajasthan state of India. Various variability estimates indicate the existence of sufficient
within-breed genetic diversity. Mean estimates of F-statistics are significantly different from zero: F
IS = 0.112 ± 0.029, F
IT = 0.169 ± 0.033, F
ST = 0.065 ± 0.017. The overall positive value of F
IS (0.112) and an F
IT value (0.169) that is more than the F
ST (0.065) indicate departure from random mating. The drift-based estimates reflect a moderate yet significant level of breed
differentiation between the Tharparkar and Rathi breeds. The evaluation of an exact test, showing that allele frequencies
across all the loci differed significantly, supports the population differentiation. This is paralleled by the outcome of
neighbor-joining clustering based on allele-sharing distance measures. The allocation of a high percentage of individuals
(95.7%) to their population of origin and correspondence analysis further substantiates the existence of a cohesive genetic
structure in both the breeds. 相似文献
9.
Alessandro Negri Irene Pellegrino Nadia Mucci Ettore Randi Paolo Tizzani Pier Giuseppe Meneguz Giorgio Malacarne 《European Journal of Wildlife Research》2013,59(3):407-419
Genetic introgression with exotic genomes represents a major conservation concern for the red-legged partridge (Alectoris rufa, Phasianidae). In particular, massive releases of chukar partridges (Alectoris chukar) and/or red-legged × chukar partridge hybrids for hunting purposes have cast serious doubts on the Italian present-day occurrence of wild A. rufa populations not affected by introgressive hybridization. This study investigates the genetic structure of red-legged partridges populations in two ecologically different areas in Northern Italy. Analysis of maternal mitochondrial DNA and biparental microsatellite markers excluded the presence of hybridization in a typical agricultural habitat where hunting and release of reared birds are strictly banned. By contrast, signs of chukar introgression were detected in a perifluvial habitat unusual for the red-legged partridge in Italy. The present study documents the first red-legged partridge population with no genetic evidences of recent chukar introgression presently living in Italy. We recommend that urgent conservation actions are taken to preserve the genetic integrity of this population from the risk of hybridization with farm-reared birds and to support its long-term conservation. 相似文献
10.
J. P. Holzman A. J. Bohonak L. R. Kirkendall D. Gottlieb A. R. Harari S. T. Kelley 《Journal of evolutionary biology》2009,22(5):1076-1087
We investigated the mating system and population genetic structure of the invasive haplodiploid palm‐seed borer Coccotrypes dactyliperda in California. We focused on whether these primarily inbreeding beetles have a ‘mixed‐breeding’ system that includes occasional outbreeding, and whether local inbreeding coefficients (FIS) varied with dominant environmental factors. We also analysed the genetic structure of C. dactyliperda populations across local and regional scales. Based on the analysis of genetic variation at seven microsatellite loci in 1034 individual beetles from 59 populations, we found both high rates of inbreeding and plentiful evidence of mixed‐breeding. FIS ranged from ?0.56 to 0.90, the highest variability reported within any animal species. There was a negative correlation between FIS and latitude, suggesting that some latitude‐associated factor affecting mating decisions influenced inbreeding rates. Multiple regressions suggested that precipitation, but not temperature, may be an important correlate. Finally, we found highly significant genetic differentiation among sites, even over short geographic distances (< 1000 m). 相似文献
11.
Genetic characterization and breed assignment in five Italian sheep breeds using microsatellite markers 总被引:1,自引:0,他引:1
R. Bozzi P. DeglInnocenti P. Rivera Diaz L. Nardi A. Crovetti C. Sargentini A. Giorgetti 《Small Ruminant Research》2009,85(1):50-57
The knowledge of the genetic relationship and admixture among neighbouring populations is crucial for conservation efforts. The aim of this study was to analyse the genetic diversity of five Italian sheep breeds (Appenninica, Garfagnina Bianca, Massese, Pomarancina and Zerasca) using a panel of 24 microsatellite markers. Blood samples from 226 individuals belonging to the aforementioned populations were obtained and genotyped. All the investigated breeds showed a significant heterozygote deficiency caused by the high level of inbreeding indicated also by the high level of FIS (0.146). Genetic differentiation between breeds was moderate (FST = 0.05) but significant and the individuals could be assigned to their breeds with an high success rate even if the inter-individual distances showed that few animals clustered separately from the other individuals of the same breed, especially for Pomarancina breed. The genetic distances reflect the historical knowledge of these breeds and some patterns of ancestral and recent gene flow between neighbour populations arise. The clustering analysis detects the presence of six clusters. Massese and Zerasca breeds were grouped together as well as Appenninica and Pomarancina with the latter forming two distinct clusters equally represented. The formation of this last breed is occurred with the absorption of individuals of the Appenninica breed and the gene flow probably continued in these recent years allowing the presence of a population substructure for Pomarancina breed. Such substructure supports the high level of heterozygote deficiency found for this breed despite the relatively high population size. The five populations analysed presented some genetic similarities but a clear uniqueness of the populations has been showed for almost all of them. Special attention to monitor genetic variability and to organize mating plans should be given especially for the three endangered breeds. 相似文献
12.
Enriched genomic libraries were used to isolate and characterize dinucleotide microsatellite loci in Erica coccinea, a South African Cape fynbos heath species with distinct resprouter and seeder populations. Microsatellites were required
to investigate the effect of the contrasting demographic pattern driven by these two post-fire responses in the population
genetic structure of seeder and resprouter forms within this species. Eight microsatellite loci were characterised and amplified
a total of 106 alleles in 2 samples each of 30 individuals from 1 resprouter and 1 seeder population. Mean allele numbers
were 7.88 and 11.0 for the resprouter and seeder population, respectively. Both populations showed similar average observed
and expected heterozygosity levels, H
O(resprouter) = 0.683, H
O(seeder) = 0.696; H
E(resprouter) = 0.726, H
E(seeder) = 0.756, and average positive inbreeding coefficients F
IS(resprouter) = 0.058, F
IS(seeder) = 0.080. This set of microsatellite loci will be used to conduct a population genetic survey of seeder and resprouter
populations throughout the range of the species. Cross-species transferability was also assayed in four other South African
and four European species of the genus Erica, supporting their potential use for population genetic analyses. 相似文献
13.
Y. Djè D. Forcioli M. Ater C. Lefèbvre X. Vekemans 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(1-2):157-163
The level of genetic diversity and the population genetic structure of sorghum landraces from North-western Morocco have
been investigated based on direct field-sampling using both allozyme and microsatellite markers. As expected, microsatellite
markers showed a much higher degree of polymorphism than allozymes, but relative measures of genetic structure such as Wright’s
inbreeding coefficient F
IS and Nei’s coefficient of genetic differentiation G
ST were similar for the two sets of markers. Substantial inbreeding was found to occur within fields, which confirms that sorghum
is predominantly selfing under cultivation. Most of the genetic diversity in Moroccan landraces occurs within fields (more
than 85%), as opposed to among fields or among regions, a result which contrasts to those of studies based on accessions from
germplasm collections. It is suggested that individual fields of sorghum constitute valuable units of conservation in the
context of in situ conservation practices.
Received: 8 December 1998 / Accepted: 28 December 1998 相似文献
14.
Reproductive systems like partial asexuality participate to shape the evolution of genetic diversity within populations, which is often quantified by the inbreeding coefficient F
IS. Understanding how those mating systems impact the possible distributions of F
IS values in theoretical populations helps to unravel forces shaping the evolution of real populations. We proposed a population genetics model based on genotypic states in a finite population with mutation. For populations with less than 400 individuals, we assessed the impact of the rates of asexuality on the full exact distributions of F
IS, the probabilities of positive and negative F
IS, the probabilities of fixation and the probabilities to observe changes in the sign of F
IS over one generation. After an infinite number of generations, we distinguished three main patterns of effects of the rates of asexuality on genetic diversity that also varied according to the interactions of mutation and genetic drift. Even rare asexual events in mainly sexual populations impacted the balance between negative and positive F
IS and the occurrence of extreme values. It also drastically modified the probability to change the sign of F
IS value at one locus over one generation. When mutation prevailed over genetic drift, increasing rates of asexuality continuously increased the variance of F
IS that reached its highest value in fully asexual populations. In consequence, even ancient asexual populations showed the entire F
IS spectrum, including strong positive F
IS. The prevalence of heterozygous loci only occurred in full asexual populations when genetic drift dominated. 相似文献
15.
Nonamplified (null) alleles are a common feature of microsatellite genotyping and can bias estimates of allele and genotype frequencies, thereby hindering population genetic analyses. The frequency of microsatellite null alleles in diploid populations can be estimated for populations that are in Hardy–Weinberg equilibrium. However, many microsatellite data sets are from nonequilibrium populations, often with known inbreeding coefficients (F) or fixation indices (FIS or FST). Here, we propose a novel null allele estimator that can be used to estimate the null allele frequency and adjust visible allele frequencies in populations for which independent estimates of F, FIS or FST are available. The algorithm is currently available as an Excel macro that can be downloaded at no cost from http://www.microchecker.hull.ac.uk/ and will be incorporated into the software micro ‐checker . 相似文献
16.
J.H. Calvo J. Alvarez-RodriguezA. Marcos-Carcavilla M. SerranoA. Sanz 《Small Ruminant Research》2011,95(1):34-39
The aim of the present study was to estimate the genetic intra-breed variability of Churra tensina and Churra lebrijana endangered breeds and to establish genetic relationships with Churra, Latxa and Merino breeds, as well as Spanish mouflon, by using 28 microsatellite markers, to provide useful information for their conservation. Allele frequencies and heterozygosity revealed high genetic variation in the two endangered breeds despite their small population size. Estimates of inbreeding coefficient (FIS) were significant for all breeds studied, except for Churra lebrijana breed. The highest inbreeding coefficient (FIS = 0.143) was found in the Spanish mouflon. Genetic differentiation tests (FST = 0.121) and assignment of individuals to populations indicated the existence of defined breed populations, and low genetic flow between these breeds. The highest pairwise Reynolds distance (DR) values were observed between Mouflon and the domestic sheep breeds. Considering only domestic sheep breeds, the Churra lebrijana breed showed the highest pairwise DR values. The lowest values were found between Latxa and the other domestic sheep, except for Churra lebrijana. Results of pairwise DR values, as well as phylogenetic tree and bottleneck analysis showed an important genetic isolation of the Churra lebrijana breed from the other Churra types, and genetic signatures of a demographic bottleneck. Finally, structure analysis of populations detected a population subdivision in the Latxa sheep breed. In conclusion, this study presents valuable insight into the existing genetic variability of two Spanish endangered breeds, as well as the first study in Spanish mouflon based on microsatellite analysis. The high degree of variability demonstrated in Churra tensina and Churra lebrijana implies that these populations are rich reservoirs of genetic diversity. 相似文献
17.
Conserving endangered wild rice species requires a thorough understanding of their population genetic structure and appropriate approaches. We applied six and seven microsatellite loci to study the genetic structure of six populations throughout the range of Chinese Oryza rufipogon and Oryza officinalis, respectively. The results showed that O. rufipogon possesses higher levels of genetic diversity but lower differentiation (RS = 3.2713, P = 100.0%, HO = 0.1401, HS = 0.5800, FST = 0.271) than O. officinalis (RS = 2.0545, P = 57.14%, HO = 0.0470, HS = 0.2830, FST = 0.554). Mean population FIS was slightly larger for O. officinalis (FIS = 0.844) than that for O. rufipogon (FIS = 0.755), indicating that O. officinalis has slightly higher departures from Hardy–Weinberg expectations and heterozygosity deficits than O. rufipogon. In addition to different origins and evolutionary histories, O. officinalis has restricted gene flow, high inbreeding, isolated small populations and fewer opportunities of hybridization with other taxa, which may determine major differences in population genetic structure from O. rufipogon. Our results suggest the adoption of a plan of involving fewer populations but more individuals within populations for O. rufipogon, while both the number of populations and the individuals for a sampled population should be almost equally considered for O. officinalis. The known high degree of inbreeding in the populations of both species implies that conservation and restoration genetics should particularly focus on the maintenance of historically significant processes such as high levels of outbreeding, gene flow and large effective population sizes. We finally proposed to further estimate the role of rice gene flow in the conservation of O. rufipogon, and to perform detailed analysis of mating systems in both species for better conservation perspectives of their ecological and evolutionary processes. 相似文献
18.
The purpose of this study was to assess the genetic characteristics of six breeds of Chinese local sheep using 19 microsatellite loci and to effectively validate statistical methods for individual assignment based on informative microsatellites. All the six breeds deviated from Hardy–Weinberg equilibrium expectations, while the majority of markers complied. The polymorphism information content (PIC) of overall loci for the six populations ranged from 0.283 (SRCRSP5) to 0.852 (OarVH72). Tibetan sheep were the most diverse population with the highest mean allelic richness (6.895), while Ujmuqin (UQ) harboured the lowest allelic richness (6.000). The F‐statistics for the six populations were FIS = ?0.172, FIT = ?0.082 and FST = 0.077, respectively. Furthermore, the pair‐wise FIS revealed a moderate genetic differentiation among populations (P < 0.01), indicating that all breeds can be considered genetically independent entities. The lowest genetic differentiation was between Tengchong (TC) and UQ (FST = 0.041), and the highest one was between TC and Fat‐tailed Han (FST = 0.111). In comparing the three statistical models, we note that the seven microsatellite loci (MAF65, OarJMP58, SRCRSP9, MCM140, OarAE129, BM8125 and SRCRSP5) commonly used for individual assignment will ensure a powerful detection of individual origin, with accuracy up to 91.87%, when the likelihood‐based method is used. Overall, these findings shed light onto the genetic characteristics of Chinese indigenous sheep and offer a set of microsatellite loci that is simple, economic and highly informative for individual assignment of Chinese sheep. 相似文献
19.
This study used polymerase chain reaction (PCR) and dideoxy direct sequencing methods to analyze the genetic structure of the chukar partridge (Alectoris chukar) in the Longdong Loess Plateau, northwestern China. A total of 491 nucleotides of mitochondrial DNA from the control region gene were sequenced for 78 chukar partridges from eight different populations. The 24 variable positions defined 25 haplotypes. The high gene flow (Nm=3.75) implied little genetic differentiation between the eight populations. All the populations shared the haplotype C1, which suggested that they all came from a common ancestor. The 25 haplotypes were spread through the populations, but could be clustered into two groups. The haplotype similar index between the two groups was only 0.15, with a genetic distance of 0.43%. The genetic variation was significantly different between the two groups, which had been isolated for all of recorded history. The genetic structure of chukar partridge populations in the Plateau appears to be the result of the synergistic effect of a glacier, along with debris flow and human activities since the middle of the Pleistocene.Communicated by F. Bairlein 相似文献
20.
Habitat fragmentation is known to generally reduce the size of plant populations and increase their isolation, leading to
genetic erosion and increased between-population genetic differentiation. In Flanders (northern Belgium) Primula vulgaris is very rare and declining. Populations have incurred strong fragmentation for the last decades and are now restricted to
a few highly fragmented areas in an intensively used agricultural landscape. Previous studies showed that small populations
of this long-lived perennial herb still maintained high levels of genetic variation and low genetic differentiation. This
pattern can either indicate recent gene flow or represent historical variation. Therefore, we used polymorphic microsatellite
loci to investigate genetic variation and structure in adult (which may still reflect historical variation) and seedling (recent
generation, thus affected by current processes) life stages. The recent generation (seedlings) showed a significant loss of
observed heterozygosity (H
o) together with lower expected heterozygosity (H
e), a trend for higher inbreeding levels (F
IS) and higher differentiation (F
ST) between populations compared to the adult generation. This might result from (1) a reduction in effective population size,
(2) higher inbreeding levels in the seedlings, (3) a higher survival of heterozygotes over time due to a higher fitness of
heterozygotes (heterosis) and/or a lower fitness of homozygotes (inbreeding depression), (4) overlapping generations in the
adult life stage, or (5) a lack of establishment of new (inbred) adults from seedlings due to degraded habitat conditions.
Combining restoration of both habitat quality and gene flow between populations may be indispensable to ensure a sustainable
conservation of fragmented populations. 相似文献