Comparative genetic diversity in a sample of pony breeds from the U.K. and North America: a case study in the conservation of global genetic resources

Winton, Clare Louise; Plante, Y.; Hind, Pamela; McMahon, Robert; Hegarty, Matthew J.; McEwan, Neil R.; Davies-Morel, Mina Clare Gwynne; Morgan, Charly; Powell, W.; Nash, Deborah

doi:10.1002/ece3.1562

Cited by 6 publications

(5 citation statements)

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“…The founder effect resulted from improper management is a major cause of genetic drift in conservation programs [69,70,71,72]. Its negative impact is associated with the number and genetic makeup of founders, number of generations (time between founding and sampling), gene flow, reproductive variance, etc [69,71,73]. Ex-situ daughter populations of the same origin may evolve divergently under respective founder effects [71,72].…”

Section: Discussionmentioning

confidence: 99%

“…Its negative impact is associated with the number and genetic makeup of founders, number of generations (time between founding and sampling), gene flow, reproductive variance, etc [69,71,73]. Ex-situ daughter populations of the same origin may evolve divergently under respective founder effects [71,72]. Thus, it is necessary to investigate and interpret the population structure of the crested ibis after 38 years of conservation practices, thereby evaluating and guiding the captive management [74].…”

Section: Discussionmentioning

confidence: 99%

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Genetic Diversity and Differentiation at Structurally Varying MHC Haplotypes and Microsatellites in Bottlenecked Populations of Endangered Crested Ibis

Zhou

Wan

et al. 2019

Cells

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Investigating adaptive potential and understanding the relative roles of selection and genetic drift in populations of endangered species are essential in conservation. Major histocompatibility complex (MHC) genes characterized by spectacular polymorphism and fitness association have become valuable adaptive markers. Herein we investigate the variation of all MHC class I and II genes across seven populations of an endangered bird, the crested ibis, of which all current individuals are offspring of only two pairs. We inferred seven multilocus haplotypes from linked alleles in the Core Region and revealed structural variation of the class II region that probably evolved through unequal crossing over. Based on the low polymorphism, structural variation, strong linkage, and extensive shared alleles, we applied the MHC haplotypes in population analysis. The genetic variation and population structure at MHC haplotypes are generally concordant with those expected from microsatellites, underlining the predominant role of genetic drift in shaping MHC variation in the bottlenecked populations. Nonetheless, some populations showed elevated differentiation at MHC, probably due to limited gene flow. The seven populations were significantly differentiated into three groups and some groups exhibited genetic monomorphism, which can be attributed to founder effects. We therefore propose various strategies for future conservation and management.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Differentiation at Structurally Varying MHC Haplotypes and Microsatellites in Bottlenecked Populations of Endangered Crested Ibis

Zhou

Wan

et al. 2019

Cells

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“…Mitochondrial DNA (mtDNA) has been analyzed to understand the origin and relationship of several feral equine herds in North America [ 14 , 15 , 16 ]. These studies were based on the analysis of a 5’ end section of the mtDNA control region [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and origin of the feral horses in Theodore Roosevelt National Park

et al. 2018

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Feral horses in Theodore Roosevelt National Park (TRNP) represent an iconic era of the North Dakota Badlands. Their uncertain history raises management questions regarding origins, genetic diversity, and long-term genetic viability. Hair samples with follicles were collected from 196 horses in the Park and used to sequence the control region of mitochondrial DNA (mtDNA) and to profile 12 autosomal short tandem repeat (STR) markers. Three mtDNA haplotypes found in the TRNP horses belonged to haplogroups L and B. The control region variation was low with haplotype diversity of 0.5271, nucleotide diversity of 0.0077 and mean pairwise difference of 2.93. We sequenced one mitochondrial genome from each haplotype determined by the control region. Two complete mtDNA sequences of haplogroup L were closely related to the mtDNA of American Paint horse. The TRNP haplotype B did not have close matches in GenBank. The phylogenetic test placed this sequence in a group consisting of two horses from China, one from Yakutia, and one from Italy raising a possibility of historical transportation of horses from Siberia and East Asia to North America. Autosomal STR loci were polymorphic and indicated that the TRNP horses were distinctly different from 48 major horse breeds. Heterozygosity, mean number of alleles, and other measures of diversity indicated that TRNP herd diversity was below that observed for most other feral herds and domestic breeds. Both mtDNA and STRs demonstrated that the existing genetic data sets of horses are insufficient to determine the exact origins of the TRNP horses. However, measures of nuclear and mitochondrial diversity have elucidated management needs. It is recommended that new genetic stock be introduced and that adaptive management principles are employed to ensure that unique mitochondrial lineages are preserved and genetic diversity is increased and maintained over time.

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“…It is interesting to note that several studies have regarded haplogroup D as an old clade characteristic of the small ponies distributed in Northern Europe (Exmoor, Fjord, Icelandic, Scottish Highland, etc. ) (Winton et al, 2015(Winton et al, , 2020. These observations represent a convenient possibility for the high frequency of haplogroup D in the Serbian Nonius.…”

Section: The Enigmatic Haplogroup D In the Serbian Noniusmentioning

confidence: 66%

Sequence analysis of the mitochondrial D-loop region throws a new light on the origin of Hungarian Nonius, Danubian Horse and Serbian Nonius

Yordanov

Zlatanovic²,

Palova

et al. 2021

AVet

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The objective of our study was to investigate the genetic structure of yet uninvestigated populations of three closely related horse breeds – the Danubian Horse, the Hungarian Nonius and the Serbian Nonius – in order to clarify their origin and genetic diversity. A 640-bp-long fragment of the mtDNA D-loop region was amplified and sequenced. The results showed that the investigated breeds have different genetic profiles although they share some common characteristics. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fall into the M, L, G, and O’P lineages, which is indicative of the genetic profile of the ancestral mares that had probably been used at the initial stages of the formation of the breeds. The population of the Danubian Horse is characterised by a high prevalence of the Anatolian specific haplogroup G (45%), followed by the Western Eurasian specific haplogroups L and M (both about 21%). In the Hungarian Nonius breed we found the highest frequency of the Western Eurasian haplogroup M (44%), followed by the Middle Eastern O’P (26%) and the Central Asian specific E (13%) and G (13%). The Serbian Nonius showed a distinct genetic profile, characterised by a high prevalence of the rare European haplogroup D (67%), followed by the Central Asian specific haplogroup G (17%). The high percentage of haplogroups shared especially between the Danubian and the Hungarian Nonius indicates the possibility of a common origin of the two breeds. In contrast, the Serbian Nonius showed a specific genetic profile, which can be explained by a different and independent origin.

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Comparative genetic diversity in a sample of pony breeds from the U.K. and North America: a case study in the conservation of global genetic resources

Cited by 6 publications

References 54 publications

Genetic Diversity and Differentiation at Structurally Varying MHC Haplotypes and Microsatellites in Bottlenecked Populations of Endangered Crested Ibis

Genetic Diversity and Differentiation at Structurally Varying MHC Haplotypes and Microsatellites in Bottlenecked Populations of Endangered Crested Ibis

Genetic diversity and origin of the feral horses in Theodore Roosevelt National Park

Sequence analysis of the mitochondrial D-loop region throws a new light on the origin of Hungarian Nonius, Danubian Horse and Serbian Nonius

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