Genetic diversity of a captive population of black muntjac revealed by a set of high polymorphism across-species microsatellites

2009 ◽  
Vol 59 (3) ◽  
pp. 273-281 ◽  
Author(s):  
Xiao-Wei Ni ◽  
Hai-Long Wu ◽  
Guo-Ping Zhu ◽  
Kai Meng
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Individual Identification ◽  
Source Population ◽  
Captive Population ◽  
Discrimination Power ◽  
Polymorphic Loci ◽  
D Loop ◽  
Population Genetic Variation ◽  
The Individual

AbstractEleven high polymorphic across-species loci were used to test the usefulness in the individual identification and parentage determination of black muntjac and to detect the genetic variation in a captive population of the animal. Discrimination power for individual locus ranged from 0.845 to 0.949 with the cumulative discrimination power across the eleven loci being up to 1. The combined exclusion probability across the eleven polymorphic loci in the absence and presence of genetic information on the second parent was 0.999 and 1, respectively. These results indicated that the eleven microsatellites would be highly diagnostic in individual identification and parentage testing for the species. The application of these polymorphic loci to evaluate population genetic variation indicated that the genetic diversity of the captive population (5.4 and 0.68 for A and He, respectively; n = 14) was significantly lower than that of the source population (7 and 0.785 for A and He, respectively; n=16). This supported our previous results discovered by mtDNA d-loop, i.e., the genetic diversity of the captive population had obviously declined over less than 20 years due to the paucity of founders. However, difference of observation heterozygosity between the captive and the source populations was not significant. These results indicated that loss of nuclear diversity in the captive population was first evidenced by A but not Ho. In order to retard the potential inbreeding effect, we suggested that some more wild animals should be introduced into the captive population and that a pedigree-based breeding program should be established.

scholarly journals Genetic analysis of silver-fir populations in the Beskids

2011 ◽  
Vol 72 (2) ◽  
pp. 115-119 ◽  
Author(s):  
Leon Mejnartowicz
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Abies Alba ◽  
Genetic Distances ◽  
Silver Fir ◽  
Geographical Distance ◽  
Polymorphic Loci ◽  
Expected Heterozygosity ◽  
Rare Alleles

Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (<em>Abies alba</em>): one in Beskid Makowski (BM) and three populations in Beskid Sądecki (BS). Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (<em>I</em> = <em>0.42</em>), percentage of polymorphic loci <em>(%PoL </em>= <em>64.29</em>) and number of rare alleles (<em>NoRa </em>= <em>5</em>). Besides, the BM population has the highest observed heterozygosity (<em>Ho </em>= <em>0.291</em>), which exceeds the expected heterozygosity (<em>He </em>= <em>0.254</em>), estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of <em>He </em>= <em>0.262 </em>and <em>Ho </em>= <em>0.264</em>.

Patterns of morphological and genetic variation in western Indian Ocean members of the Chaerephon 'pumilus' complex (Chiroptera: Molossidae), with the description of a new species from Madagascar

Zootaxa ◽  
2010 ◽  
Vol 2551 (1) ◽  
pp. 1 ◽  
Author(s):  
STEVEN M. GOODMAN ◽  
WAHEEDA BUCCAS ◽  
THESHNIE NAIDOO ◽  
FANJA RATRIMOMANARIVO ◽  
PETER J. TAYLOR ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Indian Ocean ◽  
Species Complex ◽  
Arabian Peninsula ◽  
Molecular Genetic ◽  
Western Indian Ocean ◽  
D Loop ◽  
Indian Ocean Island ◽  
The Individual ◽  
A New Species

The species delimitations of African, Arabian Peninsula, and western Indian Ocean island members of the Molossidae bat species complex Chaerephon pumilus remain largely unresolved. Based on genetic analyses this group is paraphyletic, with C. leucogaster nested within C. pumilus sensu lato, and the latter is composed of several distinct clades. DNA was isolated from a specimen of C. p. pumilus obtained at the type locality (Massawa, Eritrea). Although incomplete, this sequence allowed us to clearly define which clade is referable to nominate pumilus, a critical step in resolving the systematics of this species complex. Using morphological and molecular genetic (cytochrome b and D-loop sequences) characters, we establish that C. leucogaster and C. 'pumilus' on Madagascar represent two different lineages and that the Malagasy population referred to C. 'pumilus' is specifically distinct from those on Africa, the islands and mainland Africa. The population of C. pusillus from the western Seychelles atoll of Aldabra cluster with that of the Comoros, rather than Madagascar. For numerous other species of volant vertebrates (bats and birds), the origin of the Aldabra fauna is mixed between the Comoros and Madagascar (e.g., Goodman & Ranivo 2008; O'Brien et al. 2009; Pasquet et al. 2007; Warren et al. 2003). Hence, in the case of these 9-17 g Chaerephon bats, these water barriers have been associated with the isolation and subsequent differentiation of populations after successful dispersal and colonization events. In contrast, within the Comoros, there is no apparent genetic structure between with the individual islands, which are separated by 40 and 80 km, indicating that this distance is regularly traversed by these bats and giving rise to intra-archipelago panmixia of populations.

scholarly journals Genetic diversity in wild and hatchery populations of stinging catfish (Heteropneustes fossilis Bloch) revealed by RAPD analysis

2012 ◽  
Vol 19 ◽  
pp. 81-87
Author(s):  
Md Nazrul Islam ◽  
Abhishak Basak ◽  
Dr Ashrafullah ◽  
Md Samsul Alam
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Gene Diversity ◽  
Similarity Index ◽  
Heteropneustes Fossilis ◽  
Wild Populations ◽  
Polymorphic Loci

Context: DNA fingerprinting using genetic markers such as Random Amplification of Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), microsatellite (Simple sequence repeat), Amplified Fragment Length Polymorphism (AFLP) etc. can be successfully used to reveal genetic variation within and among different populations. Objective: The aim of the present study was to assess genetic diversity in two wild and one hatchery populations of stinging catfish Heteropneustes fossilis by RAPD fingerprinting. Materials and Methods: A total of 90 live fish (H. fossilis), 30 from each source, were collected from a beel in Patuakhali, a beel in Jessore and Rupali Hatchery, Mymensingh. Genomic DNA was extracted from fin tissues. The concentration of DNA was estimated using a spectrophotometer. Fifteen decamer primers of random sequence from three kits (six from kit A, seven from kit B and two from kit C) (Operon technologies, Inc., Alameda, CA, USA) were screened on sub-samples of one randomly chosen H. fossilis DNA sample from the each population to test their suitability for amplifying RAPDs. The amplified products from each sample were separated by electrophoresis on 1.4% agarose gel containing ethidium bromide. The sizes of the bands were calculated using the software DNAFRAG and the sizes in base pair (bp) were used for identification of the bands (RAPD markers). The similarity index values (SI) between the RAPD fingerprint of any two individuals on the same gel were calculated from RAPD band sharing. Results: A total of 28 RAPD bands were obtained using four decamer random primers, among which 21 bands were polymorphic. The percentage of polymorphic loci, intra-population similarity indices and Nei's gene diversity values were 85.71%, 78.75 and 0.304±0.183 for Jessore population, 83.71%, 82.62 and 0.280±0.159 for Patuakhali population, 82.14%, 85.25 and 0.271±0.165 for Rupali hatchery population, respectively. The overall gene flow (Nm) among the populations was 5.755. The highest inter-similarity (Sij) was found between Patuakhali - Rupali hatchery populations. Among the three populations, the highest genetic distance (0.069) was found between Jessore and Patuakhali population. Considering polymorphic loci, intrapopulation similarity index and gene diversity the genetic variation in the Jessore population was higher than the other two populations. The genetic variation of the hatchery population was found to be lower than the two wild populations. Conclusion: The result of the present study can be used as baseline information regarding the genetic variation and population structure before undertaking any breeding programme. Study indicated that the genetic variation in the hatchery populations were slightly lower than those of the wild populations. DOI: http://dx.doi.org/10.3329/jbs.v19i0.13005 J. bio-sci. 19 81-87, 2011

The genetic crisis of the Mexican Bolson Tortoise (Gopherus flavomarginatus: Testudinidae)

2012 ◽  
Vol 33 (1) ◽  
pp. 45-53 ◽  
Author(s):  
Cinthya Alejandra Ureña-Aranda ◽  
Alejandro Espinosa de los Monteros
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
20Th Century ◽  
Chihuahuan Desert ◽  
Haplotype Diversity ◽  
Genetic Homogeneity ◽  
Significant Percentage ◽  
Tectonic Processes ◽  
D Loop ◽  
Demographic Growth

Gopherus flavomarginatus (Testudinidae) is endemic to a series of discontinuous, isolated basins collectively known as the Bolson de Mapimí in the Chihuahuan Desert. Its numbers declined after catastrophic levels of exploitation during the mid-20th century. However currently, the Bolson Tortoise appears to be on a path to recovery owing to intensive, sustained conservation efforts. We sequenced an 842-bp-long fragment of the D-loop from 76 individuals distributed throughout the species’ range. The results revealed only two haplotypes. An AMOVA showed that 95% of the variance occurred among populations, whereas the remaining 5% was explained by genetic differences within populations. Tectonic processes together with ecological transformation during the Pleistocene and Holocene may be responsible for the reduction in this species’ genetic variation. A bottleneck during which a significant percentage of the haplotype diversity was lost would result in genetic homogeneity. Although there is demographic growth, the lack of genetic diversity is indicative of the potential crisis that the Bolson Tortoise is facing, and awareness must be brought to this situation.

Genetic variation in populations of the endemic Achillea millefolium ssp. megacephala from the Athabasca sand dunes and the widespread ssp. lanulosa in western North America

1996 ◽  
Vol 74 (7) ◽  
pp. 1138-1146 ◽  
Author(s):  
Brett G. Purdy ◽  
Randall J. Bayer
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Diversity ◽  
Sand Dunes ◽  
Achillea Millefolium ◽  
Starch Gel Electrophoresis ◽  
Widespread Species ◽  
Polymorphic Loci ◽  
Endemic Taxon ◽  
Starch Gel

As part of an analysis of genetic diversity in endemic taxa of the Athabasca sand dunes in northern Saskatchewan, Canada, genetic variation was examined by starch gel electrophoresis in six populations of the endemic Achillea millefolium ssp. megacephala, and 13 populations of the closely related widespread taxon, A. millefolium ssp. lanulosa. Endemic populations had more alleles per locus, a higher percentage of polymorphic loci, and greater genetic diversity than did populations of the widespread taxon. At polymorphic loci, total gene diversity was comparable in both taxa, although within-population gene diversity was higher in the endemic taxon. Population differentiation (GST) was considerably lower in ssp. megacephala than in ssp. lanulosa, although GST values were reduced when the parameter was calculated separately for geographic subdivisions of the widespread taxon. Our results differ from previous studies in which the endemic is typically depauperate of genetic variation relative to related widespread species. We suggest that obligate sexual reproduction and the absence of long-term asexual reproduction may be one of a number of factors that help populations of ssp. megacephala maintain higher levels of genetic variation on the Athabasca sand dunes. Keywords: genetic variation, endemic, rare species, Athabasca sand dunes, Achillea millefolium.

RAPD analysis on genetic diversity of typical tea populations in Hunan Province

2008 ◽  
Vol 5 (1) ◽  
pp. 67-72
Author(s):  
Shen Cheng-Wen ◽  
Huang Yi-Huan ◽  
Huang Jian-An ◽  
Luo Jun-Wu ◽  
Liu Chun-Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Genetic ◽  
Diversity Index ◽  
Gene Diversity ◽  
Population Variation ◽  
Hunan Province ◽  
Rapid Amplification ◽  
Population Genetic Variation ◽  
Shannon’S Diversity Index

AbstractGenetic diversity and genetic variation of 240 adult plants of four tea populations in Hunan – Camellia sinensis var. sinensis, C. sinensis var. assamica cv. Duntsa, C. ptilophylla and C. sinensis var. assamica cv. Jianghua – were studied by rapid amplification of polymorphic DNA (RAPD) markers. The results showed 226 loci using 21 random primers (10 bp), of which 201 (88.9%) were polymorphic. The genetic diversity analysis indicated that Shannon's index was 0.43; 74.7% of which was within-population genetic diversity while 25.3% was among-population variation. The gene diversity indexes of total populations (HT), within populations (HS) and among populations (HST) were, respectively, 0.37, 0.28 and 0.09. The coefficient of gene differentiation (GST) among populations was 0.23, indicating a 76.7% variation within populations and 23.3% among populations. These results displayed a rich within-population genetic variation, as in Shannon's diversity index. Interpopulation gene flow (Nm) was 0.74, which indicates the limited genetic exchange between populations.

Analysis of genetic diversity of four quails by microsatellite markers

2016 ◽  
Author(s):  
Jun.Yan. Bai ◽  
You.Zhi. Pang ◽  
Sheng.Jun. Wu ◽  
Mei.Qin. Yu ◽  
Xiao.Hui. Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Microsatellite Markers ◽  
Egg Production ◽  
Total Population ◽  
Polymorphic Information Content ◽  
Scientific Basis ◽  
Protection And Utilization ◽  
The Mean ◽  
Population Genetic Variation

Genetic diversity of four quail populations, including Korean quails (maroon quails), Peking white quails, Chinese yellow quails and Chinese black quails, were analyzed by microsatellite markers, aiming to provide scientific basis for new breeds of Chinese black quails for egg production as well as the assessment, protection and utilization of Chinese quail’s genetic resources. The results showed that 48 alleles were detected by nine microsatellite markers in the four quail populations, with the mean of 5.33 alleles in each locus. The average effective number of alleles marked by the nine microsatellite markers in Chinese black quails, Peking white quails, Chinese yellow quails and maroon quails were 3.5338, 3.6135, 4.0312 and 3.6508 respectively. The average heterozygosity of the four quail populations were 0.6952, 0.7046, 0.7353 and 0.7096 respectively. The average polymorphic information content of nine microsatellite loci in four quail populations were 0.6204, 0.6587, 0.6942 and 0.6639, respectively, all of which were greater than 0.5, indicating the four populations’ copious genetic diversity. In this study, the average genetic differentiation coefficient among populations was 0.0349, so the genetic variation among populations accounted for 3.49%, which demonstrated that genetic variation among populations was just a small proportion of the total population genetic variation, and there was little differentiation among the four populations. Cluster analysis indicated that Chinese black quails and Peking white quails were firstly clustered, and then Chinese yellow quails and maroon quails were clustered, and finally the two were clustered together.

scholarly journals A Study on the Genetic Variation in Licorice (Glycyrrhiza glabra) Iran by Molecular DNA Markers (RAPD)

2021 ◽  
Vol 2 (4) ◽  
pp. 89-97
Author(s):  
Mahboobeh Ahangaran ◽  
Mahmood Gharaviri ◽  
Majid Masoumian
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Medicinal Plant ◽  
Genetic Distance ◽  
Dna Markers ◽  
Genomic Dna ◽  
Rapd Marker ◽  
Glycyrrhiza Glabra ◽  
Polymorphic Loci ◽  
Ctab Method

Thirty ecotypes of licorice (a medicinal plant) from all of Iran were collected and genetically evaluated. To assess the genetic diversity of licorice, genomic DNA was extracted using Winnepenninckx method (CTAB method). 12 random primers were used to perform PCR. All 12 primers showed obvious and repeatable bands. Totally, 1343 bands were produced. Bands size varied from 250 to 5000 bp. Percentage of polymorphism and polymorphic loci was 88.83% and 95.5%, respectively. The highest number of band was related to primer OPN-08 (band 188). The highest similarity between Esfaraien and Bojnourd ecotypes is equal to 0.647. Kermanshah and Orumieh ecotypes had the lowest similarity that was 0.3. Dendrogram divided 30 ecotypes into 5 groups in terms of genetic distance. Generally, surveying the variation in genotypes of licorice using RAPD marker showed that this marker can be useful in identifying the polymorphism, estimating the genetic distance, and managing germplasm.

Effective population size of koala populations under different population management regimes including contraception

2009 ◽  
Vol 36 (7) ◽  
pp. 601 ◽  
Author(s):  
Mark M. Tanaka ◽  
Romane Cristescu ◽  
Desmond W. Cooper
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Equal Opportunity ◽  
Management Strategies ◽  
Effective Population ◽  
Population Sizes ◽  
Wildlife Populations ◽  
Population Genetic Variation

Context. The management of wildlife populations aiming to control population size should also consider the preservation of genetic diversity. Some overabundant koala populations, for example, have low genetic variation. Different management strategies will affect population genetic variation differently. Aims. Here, we compare four strategies with respect to their effects on the effective population size, Ne , and therefore on genetic variation. Methods. The four strategies of interest are: (1) sterilisation or culling (which have the same effect on genetic variation); (2) random contraception of females with replacement; (3) random contraception of females without replacement; and (4) regular contraception, giving every female equal opportunity to reproduce. We develop mathematical models of these alternative schemes to evaluate their impact on Ne . We also consider the effect of changing population sizes by investigating a model with geometric population growth in which females are removed by sterilisation or culling. Key results. We find that sterilisation/culling at sexual maturity has the most detrimental effect on Ne , whereas regular contraception has no impact on Ne . Random contraception lies between these two extremes, leading to a moderate reduction in Ne . Removal of females from a growing population results in a higher Ne than the removal of females from a static population. Conclusions. Different strategies for controlling a population lead to different effective population sizes. Implications. To preserve genetic diversity in a wildlife population under control, the effective population size should be kept as large as possible. We suggest that a suitable approach in managing koala populations may be to prevent reproduction by all females older than a particular age.

scholarly journals GENETIC POLYMORPHISM AND SEED DIFFERENTIATION SCOTS PINE SEEDS OF DIFFERENT SELECTION CATEGORIES USING ISSR-MARKERS

2020 ◽  
Vol 9 (4) ◽  
pp. 15-24
Author(s):  
Olga Sheikina ◽  
Tat'yana Krivorotova ◽  
Yuriy Gladkov
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Polymerase Chain Reaction Method ◽  
Issr Markers ◽  
Effective Number ◽  
Polymorphic Loci ◽  
Expected Heterozygosity ◽  
Polymerase Chain ◽  
The Republic ◽  
Issr Primers

The purpose of the study is a comparative assessment of the genetic diversity and differentiation of common pine seeds of different breeding categories. The object of the study was seeds harvested on permanent forest seed plots and clone forest seed plantations in the Penza region, the Chuvash Republic and the Republic of Mari El. A polymerase chain reaction method with ISSR primers has been used to assess the level of genetic diversity and differentiation. A total of 250 loci have been amplified using 6 ISSR primers, 210 of which were polymorphic ones. The studied seed batches were characterized by different levels of genetic variation. Indicators of genetic diversity of seeds (improved breeding category) have varied within the following limits: the percentage of polymorphic loci from 56.3 to 72.6; the number of alleles per locus from 1.56 to 1.73; effective number of alleles from 1.26 to 1.38; expected heterozygosity from 0.17 to 0.23. Seeds of the normal selection category are characterized by the following indicators of genetic diversity: the percentage of polymorphic loci is 57.2–72.6; the number of alleles per locus 1.57–1.68; the effective number of alleles is 1.25–1.33; expected heterozygosity - 0.16–0.19. Dependence of the level of genetic diversity on the selection category of seeds has not been identified. Generalized indicators of the genetic diversity of improved seeds have been close or higher in comparison with normal seeds. Ney's genetic distance between 8 batches of seeds has ranged from 0.027 to 0.113. The genetic subdivision index (GSI) was 0.25. Therefore, a large proportion of the genetic variation is located inside seed batches (75%).

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