MolKin v2.0: A Computer Program for Genetic Analysis of Populations Using Molecular Coancestry Information

Gutiérrez, Juan Pablo; Royo, Luis J.; Álvarez, Isabel; Goyache, F.

doi:10.1093/jhered/esi118

Cited by 175 publications

(126 citation statements)

References 21 publications

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“…Private alleles were accounted for utilizing the GDA software (Lewis and Zaykin, 2001). Polymorphic information content (PIC) and the rarefacted allelic richness were estimated in MOLKIN 3.0 (Gutierrez et al, 2005), using bootstrapping to standardize among different sample size populations. Hulbert's rarefaction correction and sample size correction were based on 50 diploid individuals.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and differentiation of 12 eastern Adriatic and western Dinaric native sheep breeds using microsatellites

Šalamon

Gutiérrez-Gil

Arranz

et al. 2014

Animal

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Nuclear genetic diversity and differentiation of 341 sheep belonging to 12 sheep breeds from Croatia and Bosnia and Herzegovina were examined. The aim of the study was to provide the understanding of the genetic structure and variability of the analysed pramenka sheep populations, and to give indications for conservation strategies based on the population diversity and structure information. The genetic variation of the sheep populations, examined at the nuclear level using 27 microsatellite loci, revealed considerable levels of genetic diversity, similar to the diversity found in other European indigenous low-production sheep breeds. Population-specific alleles were detected at most loci and in breeds analysed. The observed heterozygosity ranged from 0.643 (in Lika pramenka) to 0.743 (in Vlasic pramenka), and the expected heterozygosity ranged from 0.646 (in Lika pramenka) to 0.756 (in Dalmatian pramenka). Significant inbreeding coefficients were found for half of the populations studied and ranged from 0.040 (Pag island sheep) to 0.091 (Kupres pramenka). Moderate genetic differentiation was found between the studied sheep populations. The total genetic variability observed between different populations was 5.29%, whereas 94.71% of the variation was found within populations. Cres island sheep, Lika pramenka and Istrian sheep were identified as the most distinct populations, which was confirmed by the factorial analysis of correspondence and supported through a bootstrapping adjustment to correct for the difference in the sample sizes. The population structure analysis distinguished 12 clusters for the 12 sheep breeds analysed. However, the cluster differentiation was low for Dalmatian, Vlasic, Stolac and Krk pramenka. This systematic study identified Lika pramenka and Rab island sheep as those with the lowest diversity, whereas Istrian sheep and Pag island sheep had the highest. Conservation actions are proposed for Istrian, Rab and Cres island sheep, Lika and Kupres pramenka because of high estimated coefficients of inbreeding.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity and differentiation of 12 eastern Adriatic and western Dinaric native sheep breeds using microsatellites

Šalamon

Gutiérrez-Gil

Arranz

et al. 2014

Animal

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“…In addition, the loss in genetic diversity from the data set was also assessed using the Petit et al's (1998) approach and molecular kinship analyses as proposed by Caballero and Toro (2002) and implemented in MOLKIN version 2 (Gutié rrez et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations

Prystupa

Juras

Cothran

et al. 2012

Animal

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As part of the requirements of the Convention on Biological Diversity, Canada has been investigating the genetic diversity of its native equine and pony populations. Along with examining four indigenous Canadian equine populations (Canadian horse, Lac La Croix pony, Newfoundland pony and Sable Island population), another 10 Mountain and Moorland, three Nordic, four horse and two feral equine populations (thought to have influenced some pony breeds) were also investigated. In total, 821 individuals were genotyped at 38 microsatellite loci. Results of the analysis of molecular variance indicated that 13.3% of genetic diversity was explained by breed differences, whereas 84.6% and 2.1% of diversity came from within and among individuals, respectively. The average effective number of alleles and allelic richness was the lowest in the Eriskay (2.51 and 3.98) and Lac La Croix (2.83 and 4.01) populations, whereas it was highest in the New Forest (4.31 and 6.01) and Welsh (4.33 and 5.87) breeds, followed closely by the Newfoundland-CDN (4.23 and 5.86) population. Expected heterozygosities varied from 0.61 in the Lac La Croix to 0.74 in the Welsh and in Newfoundland. Observed heterozygosities ranged from 0.57 in the Exmoor and 0.58 in the Sable Island herd to 0.77 in the Kerry Bog and 0.76 in the New Forest breeds. Structure and admixture analyses revealed that the most likely number of clusters was 21, although some substructure was also observed when K 5 16, compared with the 24 predefined populations. Information gathered from this study should be combined with other available phenotypic and pedigree data to develop, or amend, a suitable conservation strategy for all populations examined.

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“…The following parameters were computed using the program MolKin 3.0 (Gutiérrez et al, 2005): number of observed alleles, expected heterozygosity (He), Wright's F-statistics and raw (A) and rarefacted (Ag) average number of alleles per locus (allelic richness). Here, g was fitted to 38, which is twice the minimum number of individuals within a population with genotype known for all the microsatellites.…”

Section: Statistical Analysesmentioning

confidence: 99%

“…Here, g was fitted to 38, which is twice the minimum number of individuals within a population with genotype known for all the microsatellites. See Gutiérrez et al (2005) and the User's Guide of the program MolKin (freely available at http://www.ucm.es/info/prodanim/html/JP Web.htm) for a detailed description of the methodologies used. The statistical significance of the obtained values was estimated by bootstrapping using 1000 replications.…”

Section: Statistical Analysesmentioning

confidence: 99%

Microsatellite analysis of the Rousse de Maradi (Red Sokoto) goat of Burkina Faso

Álvarez

Traoré

Kaboré

et al. 2012

Small Ruminant Research

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a b s t r a c tA total of 33 reproductive individuals of the Rousse de Maradi (Red Sokoto) goat breed of Burkina Faso were genotyped for 19 microsatellites and compared with 154 samples from four different populations of Burkinabé Sahelian and Djallonké goat. The betweenpopulations molecular coancestry for the Rousse de Maradi-pairs varied from 0.420 (with the Northern Sahelian population) to 0.459 (with the Eastern Djallonké population). The between-populations genetic differentiation assessed using F ST varied from 0.018 for the pair formed by the two Sahelian populations to 0.050 for the pairs formed between the Rousse de Maradi population and each of the Djallonké populations. Both correspondence and STRUCTURE analyses showed that the Rousse de Maradi breed: (a) has a particular genetic background; and (b) it is genetically nearer to the Sahelian goat. Overall, the present analysis characterise the Rousse de Maradi breed as a part the goat metapopulation exploited in the Sahel area rather than a population derived from the West African Dwarf goat. Implementation of strategies to further characterise production and reproduction performance of the Burkinabé Rousse de Maradi goat breed can be advised.

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MolKin v2.0: A Computer Program for Genetic Analysis of Populations Using Molecular Coancestry Information

Cited by 175 publications

References 21 publications

Genetic diversity and differentiation of 12 eastern Adriatic and western Dinaric native sheep breeds using microsatellites

Genetic diversity and differentiation of 12 eastern Adriatic and western Dinaric native sheep breeds using microsatellites

Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations

Microsatellite analysis of the Rousse de Maradi (Red Sokoto) goat of Burkina Faso

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