Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites

Funk, Stephan M.; Guedaoura, Sonya; Juras, Rytis; Raziq, Absul; Landolsi, Faouzi; Luı́s, Cristina; Martínez, Amparo Martínez; Mayaki, Abubakar Musa; Mujica, Fernando; Oom, María do Mar; Ouragh, Lahoussine; Stranger, Yves-Marie; Vega‐Pla, J. L.; Cothran, E. Gus

doi:10.1002/ece3.6195

Cited by 22 publications

(22 citation statements)

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“…Evanno method of determining ΔK is best identify the highest level of genetic structure and may not be particularly reliable under complex evolutionary scenarios 59 . And although it is an elegant method from the statistic point of view, it always produces a "solution" for the given data and the solution may not be the best one 60 . The alterative assessment of clusters performed by DAPC revealed K DAPC = 14 inferred clusters, after 40 principal components and 4 discriminant functions were retained (Fig.…”

Section: Resultsmentioning

confidence: 99%

The future of endangered crayfish in light of protected areas and habitat fragmentation

Pârvulescu

Iorgu

Zaharia

et al. 2020

Sci Rep

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The long-term survival of a species requires, among other things, gene flow between populations. Approaches for the evaluation of fragmentation in the frame of freshwater habitats consider only a small amount of the information that combined demography and geography are currently able to provide. This study addresses two species of Austropotamobius crayfish in the light of population genetics, spatial ecology and protected areas of the Carpathians. Advancing the classical approaches, we defined ecological distances upon the rasterised river network as a surrogate of habitat resistance to migration, quantifying the deviations from the species´ suitability range for a set of relevant geospatial variables in each cell of the network. Molecular analyses revealed the populations of the two Austropotamobius crayfish species are clearly distinct, lacking hybridisation. Comparing pairs of populations, we found, in some cases, a strong disagreement regarding genetic and ecological distances, potentially due to human-mediated translocations or the geophysical phenomena of regressive erosion, which may have led to unexpected colonisation routes. Protected areas were found to offer appropriate local habitat conditions but failed to ensure connectivity. The methodology applied in this study allowed us to quantify the contribution of each geospatial (environmental) variable to the overall effect of fragmentation, and we found that water quality was the most important variable. A multilevel approach proved to reveal a better understanding of drivers behind the distribution patterns, which can lead to more adequate conservation measures.

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Section: Resultsmentioning

confidence: 99%

The future of endangered crayfish in light of protected areas and habitat fragmentation

Pârvulescu

Iorgu

Zaharia

et al. 2020

Sci Rep

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“…To ensure such a capability, however, we had to supply a priori information about the sample origin; without these data, there was only 58.03% accuracy yielded from the Bayesian approach that assigns individuals to source populations or facilitates the proportional assignment of ancestry to multiple (22 in this case) populations. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated (Funk et al 2020). STRUCTURe works best with a small number of discrete populations (Pritchard et al 2000), but the performance with large data sets was also evaluated (e.g.…”

Section: Breed Relationshipsmentioning

confidence: 99%

“…STRUCTURe works best with a small number of discrete populations (Pritchard et al 2000), but the performance with large data sets was also evaluated (e.g. Funk et al 2020).…”

Section: Breed Relationshipsmentioning

confidence: 99%

“…According to Cornuet et al (1999), the procedures exploiting the Bayesian approach yield the best results, but the populations must be in the Hardy-Weinberg and linkage equilibria; this necessity, however, can be eliminated by distance-based methodologies. Factors having an impact on the individual assignment success, such as the number and divergence of populations, sample size, and number of loci, were assessed from actual or simulated data and are widely reported in the literature (Bjornstad and Roed 2002;Koskinen 2003;Fan et al 2005;Talle et al 2005;Funk et al 2020).…”

Section: Breed Relationshipsmentioning

confidence: 99%

“…The International Studbook Committee (ISBC) relies on the International Society of Animal Genetics (ISAG). The DNA markers used by the Czech laboratories are based on the internationally recognised microsatellite testing panel operated by the ISAG; moreover, they have been endorsed by the Food and Agriculture Organization of the United Nations (FAO) as a tool to support diversity studies (Funk et al 2020).…”

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The assignment success for 22 horse breeds registered in the Czech Republic: The machine learning perspective

Putnová¹,

Štohl²

2021

Czech J. Anim. Sci.

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The paper demonstrates the dependability of assignment testing in the identification of an appropriate breed to monitor comprehensive genetic information from molecular markers to analyse the collection of real population data covering 22 horse breeds registered in the Czech Republic, including native breeds and genetic resources. If 17 microsatellites are used, the mean number of alleles per locus corresponds to 10.4. The count of alleles at the individual loci ranges between five (HTG07) and 17 (ASB17). The loci ASB02, ASB23, HMS03, HTG10, and VHL20 exhibit the highest gene diversity and observed heterozygosity (both above 80%), with the mean value of 0.77 and 0.73, respectively. The moderate total inbreeding coefficient (5.2%) is estimated across all the loci and breeds. The levels of apparent breed differentiation span from zero between the Czech Warmblood and Slovak Warmblood to 0.15 between the Shetland Pony and Standardbred. The phylogenetic breed relationships are revealed via the NeighbourNet dendrogram constructed from Reynolds’ genetic distances, which clearly separate the Coldblood draught, Hot/Warmblood, and Pony horses. Our results reveal that the Bayesian approach (the Rannala and Mountain technique) provides the most intensive prediction power (83.6%) out of the GeneClass tools and that the Bayes Net algorithm exhibits the best efficiency (78.4%) from the WEKA machine learning workbench options, considering the use of the five-fold cross validation technique. The algorithms could be trained on large real reference data sets, and thus there appears another viable perspective for machine learning in horse ancestry testing. In this context, it is also important to stress the fact that innovated computational tools will potentially lead towards structuring a novel web server to allow the identification of horse breeds.

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Population genomics provide insight into ancestral relationships and diversity of the feral horses of Theodore Roosevelt National Park

Thompson,

McCann,

Rhen

et al. 2024

Ecology and Evolution

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Theodore Roosevelt National Park (TRNP) manages a herd of feral horses (Equus caballus) which was present on the landscape prior to the establishment of the park. The population presents a unique scenario in that it has experienced fairly intensive and well‐documented management since the park's establishment, including herd size reductions, intentional introduction of diversity, and subsequent attempts to remove introduced lineages. This provides an interesting case study on the genetic effects of diverse evolutionary forces on an isolated feral population. To explore the effects of these forces and clarify the relationship of this feral herd with other horses, we used genome‐wide markers to examine the population structure of a combined dataset containing common established breeds. Using the Illumina Equine 70k BeadChip, we sampled SNPs across the genome for 118 TRNP horses and evaluated the inbreeding coefficient f and runs of homozygosity (RoH). To identify breed relationships, we compared 23 representative TRNP samples with 792 horses from 35 different breeds using genomic population structure analyses. Mean f of TRNP horses was 0.180, while the mean f for all other breeds in the dataset was 0.116 (SD 0.079). RoH analysis indicates that the TRNP population has experienced recent inbreeding in a timeframe consistent with their management. With Bayesian clustering, PCA, and maximum likelihood phylogeny, TRNP horses show genetic differentiation from other breeds, likely due to isolation, historical population bottlenecks, and genetic drift. However, maximum likelihood phylogeny places them with moderate confidence (76.8%) among draft breeds, which is consistent with the known history of breeds used on early North Dakota ranches and stallions subsequently introduced to the park herd. These findings will help resolve speculation about the origins of the herd and inform management decisions for the TRNP herd.

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Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites

Cited by 22 publications

References 110 publications

The future of endangered crayfish in light of protected areas and habitat fragmentation

The future of endangered crayfish in light of protected areas and habitat fragmentation

The assignment success for 22 horse breeds registered in the Czech Republic: The machine learning perspective

Population genomics provide insight into ancestral relationships and diversity of the feral horses of Theodore Roosevelt National Park

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