Usefulness of molecular-based methods for estimating effective population size in livestock assessed using data from the endangered black-coated Asturcón pony.
Abstract: Empirical evidence of the usefulness of different molecular-based methods to estimate the effective population size (N(e)) for conservation purposes in endangered livestock populations is reported. The black-coated Asturcón pony pedigree (1,981 individuals) was available. Additionally, a total of 267 Asturcón individuals born in 1998, 2002, and 2008 were typed for 15 microsatellites. These yearly cohorts (cohort(1998, 2002, 2008)) included almost all individuals kept for reproduction at the end of the corresponding foaling season. The genealogical realized N(e) was estimated for each cohort by using the individual increase in inbreeding. Molecular N(e) was computed by using 1) linkage disequilibrium [N(e)(()(D)())], 2) a temporal method based on F-statistics [N(e)(()(T)())], 3) an unbiased temporal method [N(e)(()(JR)())], and 4) a Bayesian temporal method [N(e)(()(B)())]. Estimates of increased from cohort(1998) (18.8 ± 5.1) to cohort(2008) (24.9 ± 5.2), illustrating the history of the population and its breeding policy of avoiding matings between close relatives. The estimates of N(e)(()(D)()) were highly biased upward, with the maximum N(e)(()(D)()) value obtained for cohort(2002) (137.0). The estimates of N(e)(()(T)()), N(e)(()(JR)()), and N(e)(()(B)()) showed similar performance. However, N(e)(()(JR)()) estimates were very consistent across cohorts, varying from 14.9 to 15.5 after correcting for the effect of overlapping generations. When the drift signal was not strong (pair cohort(1998)-cohort(2002)), estimates of N(e)(()(T)()) and N(e)(()(B)()) were not realistic. Estimates of N(e)(()(B)()) tended to be biased downward (being 9.0 or below for the sampling pairs including cohort(2008)). Results of N(e)(()(D)()) are more likely to be estimates of the effective number of breeders producing the sample, rather than the effective size for a generation. The temporal methods were strongly affected by a weak drift signal, particularly when samplings were not spaced a sufficient number of generations or a sufficient time apart. The use of molecular-based estimates of N(e) is not straightforward, and their use in livestock conservation programs should be carried out with caution. Sampling strategies (including sampling sizes, sampling periods, and the age structure of the sampled individuals) must be carefully planned to ensure that robust estimates of N(e) are obtained.
Publication Date: 2011-01-21 PubMed ID: 21257782DOI: 10.2527/jas.2010-3620Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The research investigates various molecular methods used to estimate effective population size in endangered livestock, specifically focusing on the black-coated Asturcón pony. The results demonstrate that molecular methods can be complex and must be applied with caution for reliable data.
Research Context and Methodology
- The study focused on the black-coated Asturcón pony, an endangered livestock population, to test the reliability of different molecular methods in estimating effective population size.
- Available data included the pony’s pedigree of 1,981 individuals and microsatellite typing for 267 Asturcón individuals born in 1998, 2002, and 2008. These individuals represented virtually all the ponies kept for reproduction at the end of each respective foaling season.
- The effective population size was calculated based on the increase in inbreeding in each cohort and was quantified using four molecular methods: linkage disequilibrium, temporal method based on F-statistics, an unbiased temporal method, and a Bayesian temporal method.
Key Findings
- Estimates showed an increase from 1998 to 2008, indicating the effects of the population’s breeding strategy, which aimed to prevent matings between close relatives.
- The method using linkage disequilibrium was found to be highly biased upwards, with the maximum value observed for the 2002 cohort.
- Estimates from the temporal method based on F-statistics, unbiased temporal method, and Bayesian temporal method exhibited similar trends. However, the unbiased temporal method showed more consistency across cohorts after adjusting for the effect of overlapping generations.
- Results were not realistic when the genetic drift signal was weak, as observed between 1998 and 2002 cohorts. In these cases, the Bayesian temporal method estimates were notably biased downwards.
- The linkage disequilibrium method is more likely to estimate the effective number of breeders producing the sample, rather than the lifespan effective size. Conversely, the temporal methods were strongly affected by weak genetic drift signals, especially when samples were not separated by a significant number of generations or duration.
Conclusions and Recommendations
- The use of molecular methods for estimating effective population size in livestock is complex and should be applied cautiously for accurate results.
- Proper planning is required for sampling strategies, including considerations for sample sizes, periods, and the age structure of the sampled individuals. This ensures the acquisition of robust estimates of effective population size.
Cite This Article
APA
Goyache F, Alvarez I, Fernández I, Pérez-Pardal L, Royo LJ, Lorenzo L.
(2011).
Usefulness of molecular-based methods for estimating effective population size in livestock assessed using data from the endangered black-coated Asturcón pony.
J Anim Sci, 89(5), 1251-1259.
https://doi.org/10.2527/jas.2010-3620 Publication
Researcher Affiliations
- Servicio Regional de Investigación y Desarrollo Agroalimentario de Principado de Asturias, (SERIDA-Deva), Camino de Rioseco 1225, E-33394 Gijón (Asturias), Spain. fgoyache@serida.org
MeSH Terms
- Animals
- Bayes Theorem
- Cohort Studies
- Conservation of Natural Resources / methods
- Endangered Species
- Female
- Horses / genetics
- Inbreeding
- Linkage Disequilibrium
- Male
- Microsatellite Repeats
- Pedigree
- Population Density
Citations
This article has been cited 4 times.- Ablondi M, Dadousis C, Vasini M, Eriksson S, Mikko S, Sabbioni A. Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data.. Animals (Basel) 2020 Jun 8;10(6).
- Menéndez J, Álvarez I, Fernandez I, Menéndez-Arias NA, Goyache F. Assessing performance of single-sample molecular genetic methods to estimate effective population size: empirical evidence from the endangered Gochu Asturcelta pig breed.. Ecol Evol 2016 Jul;6(14):4971-80.
- Mészáros G, Boison SA, Pérez O'Brien AM, Ferenčaković M, Curik I, Da Silva MV, Utsunomiya YT, Garcia JF, Sölkner J. Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle.. Front Genet 2015;6:173.
- Leroy G, Mary-Huard T, Verrier E, Danvy S, Charvolin E, Danchin-Burge C. Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse.. Genet Sel Evol 2013 Jan 2;45(1):1.
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