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Flack N, Hughes L, Cassens J, Enriquez M, Gebeyehu S, Alshagawi M, Hatfield J, Kauffman A, Brown B, Klaeui C, Mabrouk IF, Walls C, Yeater T, Rivas A, Faulk C. The genome of Przewalski's horse ( Equus ferus przewalskii). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581252. [PMID: 38464182 PMCID: PMC10925127 DOI: 10.1101/2024.02.20.581252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The Przewalski's horse (Equus ferus przewalskii) is an endangered equid native to the steppes of central Asia. After becoming extinct in the wild, multiple conservation efforts convened to preserve the species including captive breeding programs, reintroduction and monitoring systems, protected lands, and cloning. Availability of a highly contiguous reference genome is essential to support these continued efforts. We used Oxford Nanopore sequencing to produce a scaffold-level 2.5 Gb nuclear assembly and 16,002 bp mitogenome from a captive Przewalski's mare. All assembly drafts were generated from 111 Gb of sequence from a single PromethION R10.4.1 flow cell. The mitogenome contained 37 genes in the standard mammalian configuration and was 99.63% identical to the domestic horse (Equus caballus). The nuclear assembly, EquPr2, contained 2,146 scaffolds with an N50 of 85.1 Mb, 43X mean depth, and BUSCO quality score of 98.92%. EquPr2 successfully improves upon the existing Przewalski's horse reference genome (Burgud), with 25-fold fewer scaffolds, a 166-fold larger N50, and phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation and 2.1% hydroxymethylation globally. Allele-specific methylation analysis between pseudohaplotypes revealed 226 differentially methylated regions (DMRs) in known imprinted genes and loci not previously reported as imprinted. The heterozygosity rate of 0.165% matches previous estimates for the species and compares favorably to other endangered animals. This improved Przewalski's horse assembly will serve as a valuable resource for conservation efforts and comparative genomics investigations.
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Affiliation(s)
- Nicole Flack
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota Saint Paul, MN, USA
| | - Lauren Hughes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota Saint Paul, MN, USA
| | - Jacob Cassens
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota Minneapolis, MN, USA
| | - Maya Enriquez
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Samrawit Gebeyehu
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
| | | | - Jason Hatfield
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Anna Kauffman
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Baylor Brown
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Caitlin Klaeui
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Islam F. Mabrouk
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Carrie Walls
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
| | - Taylor Yeater
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | | | - Christopher Faulk
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
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Kang Z, Shi J, Liu T, Zhang Y, Zhang Q, Liu Z, Wang J, Cheng S. Genome-wide single-nucleotide polymorphism data and mitochondrial hypervariable region 1 nucleotide sequence reveal the origin of the Akhal-Teke horse. Anim Biosci 2023; 36:1499-1507. [PMID: 37170508 PMCID: PMC10475378 DOI: 10.5713/ab.23.0044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 04/10/2023] [Indexed: 05/13/2023] Open
Abstract
OBJECTIVE The study investigated the origin of the Akhal-Teke horse using genome-wide single-nucleotide polymorphism (SNP) data and mitochondrial hypervariable region 1 (HVR-1) nucleotide sequences. METHODS Genome-wide SNP data from 22 breeds (481 horses) and mitochondrial HVR-1 sequences from 24 breeds (544 sequences) worldwide to examine the origin of the Akhal- Teke horse. The data were analyzed using principal component analysis, linkage disequilibrium analysis, neighbor-joining dendrograms, and ancestry inference to determine the population relationships, ancestral source, genetic structure, and relationships with other varieties. RESULTS A close genetic relationship between the Akhal-Teke horse and horses from the Middle East was found. Analysis of mitochondrial HVR-1 sequences showed that there were no shared haplotypes between the Akhal-Teke and Tarpan horses, and the mitochondrial data indicated that the Akhal-Teke horse has not historically expanded its group. Ancestral inference suggested that Arabian and Caspian horses were the likely ancestors of the Akhal- Teke horse. CONCLUSION The Akhal-Teke horse originated in the Middle East.
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Affiliation(s)
- Zhoucairang Kang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
| | - Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
| | - Ting Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
| | - Yong Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070,
China
| | - Quanwei Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070,
China
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
| | - Jianfu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
| | - Shuru Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
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Sheikh A. Mitochondrial DNA sequencing of Kehilan and Hamdani horses from Saudi Arabia. Saudi J Biol Sci 2023; 30:103741. [PMID: 37575470 PMCID: PMC10413190 DOI: 10.1016/j.sjbs.2023.103741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/04/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023] Open
Abstract
The Arabian horse breed is well known for its purity and played a key role in the genetic improvement of other horses worldwide. The mitochondrial genome plays a vital role in maternal inheritance and it's helpful to evaluate its genetic diversity and conservation. It has higher mutation rates than nuclear DNA in vertebrates and therefore reveals phylogenetic relationships and haplotypes. In this study, the mitochondrial genome mutations in two Saudi horse strains, Kehilan and Hamdani demonstrated various changes in the gene and amino acid levels and included two other Saudi horses (Hadban and Seglawi) from the previous study for phylogenetic comparison. The whole mitochondrial genome sequencing resulted in intra and inter mtDNA variations between the studied horses. Interestingly, the Hamdani horse has nucleotide substitutions similar to those of the Hadban horse, which is reflected in the phylogenetic tree as a significantly close relationship. This type of study provides a better understanding of mitogenome structure and conservation of livestock species genetic data.
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Affiliation(s)
- Abdullah Sheikh
- Camel Research Center, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
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Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022; 13:genes13122272. [PMID: 36553539 PMCID: PMC9777570 DOI: 10.3390/genes13122272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Anna Tommasi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | | | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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Mitochondrial Whole D-Loop Variability in Polish Draft Horses of Sztumski Subtype. Animals (Basel) 2022; 12:ani12151870. [PMID: 35892520 PMCID: PMC9332387 DOI: 10.3390/ani12151870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
The Polish draft horse (PDH) breed is a result of crossing local mares with imported cold-blooded stallions, such as Belgians, Ardennes, Fjords, and others. A part of the broodmare stock investigated in this study was also imported from various countries, such as Denmark. In this study, we investigate the genetic composition of the PDH by analyzing the whole mitochondrial d-loop variability and comparing it to previously demonstrated whole d-loop sequences of other cold-blooded breeds: Ardennais, Belgian, Breton, Clydesdale, Noriker, Norwegian Fjord, Percheron, and Suffolk. Our results show high nucleotide diversity within the PDH population (π = 0.011), and the existence of two main haplogroups: one of relatively concise origin, with strong kinship to the Belgian breed, and the second showing close relation to the majority of other analyzed cold-blooded breeds. Some of the PDH maternal strains clustered separately, which can be a result of the influence of other unidentified breeds that served as a foundation stock for the present population. This present study explains the genetic relationship of the PDH to other cold-blooded breeds and indicates the high genetic diversity of the breed.
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Salek Ardestani S, Zandi MB, Vahedi SM, Mahboudi H, Mahboudi F, Meskoob A. Detection of common copy number of variation underlying selection pressure in Middle Eastern horse breeds using whole-genome sequence data. J Hered 2022; 113:421-430. [PMID: 35605262 DOI: 10.1093/jhered/esac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 05/21/2022] [Indexed: 11/14/2022] Open
Abstract
Dareshouri, Arabian, and Akhal-Teke are three Middle Eastern horse breeds that have been selected for endurance and adaptation to harsh climates. Deciphering the genetic characteristics of these horses by tracing selection footprints and copy number of variations will be helpful in improving our understanding of equine breeds' development and adaptation. For this purpose, we sequenced the whole-genome of four Dareshouri horses using Illumina Hiseq panels and compared them with publicly available whole-genome sequences of Arabian (n=3) and Akhal-Teke (n=3) horses . Three tests of FLK, hapFLK, and pooled heterozygosity were applied using a sliding window (window size=100kb, step size=50kb) approach to detect putative selection signals. Copy number variation analysis was applied to investigate copy number of variants (CNVs), and the results were used to suggest selection signatures involving CNVs. Whole-genome sequencing demonstrated 8,837,950 single nucleotide polymorphisms (SNPs) in autosomal chromosomes. We suggested 58 genes and three quantitative trait loci (QTLs), including some related to horse gait, insect bite hypersensitivity, and withers height, based on selective signals detected by adjusted p-value of Mahalanobis distance based on the rank-based P-values (Md-rank-P) method. We proposed 12 genomic regions under selection pressure involving CNVs which were previously reported to be associated with metabolism energy (SLC5A8), champagne dilution in horses (SLC36A1), and synthesis of polyunsaturated fatty acids (FAT2). Only 10 Middle Eastern horses were tested in this study; therefore, the conclusions are speculative. Our findings are useful to better understanding the evolution and adaptation of Middle Eastern horse breeds.
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Affiliation(s)
- Siavash Salek Ardestani
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Canada
| | - Hossein Mahboudi
- Department of Biotechnology, School of Pharmacy, Alborz University of Medical Sciences, Karaj, Iran
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Lovász L, Fages A, Amrhein V. Konik, Tarpan, European wild horse: An origin story with conservation implications. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses. Sci Rep 2021; 11:16057. [PMID: 34362995 PMCID: PMC8346562 DOI: 10.1038/s41598-021-95669-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/29/2021] [Indexed: 11/08/2022] Open
Abstract
The Thoroughbred breed was formed by crossing Oriental horse breeds and British native horses and is currently used in horseracing worldwide. In this study, we constructed a single-nucleotide variant (SNV) database using data from 101 Thoroughbred racehorses. Whole genome sequencing (WGS) revealed 11,570,312 and 602,756 SNVs in autosomal (1–31) and X chromosomes, respectively, yielding a total of 12,173,068 SNVs. About 6.9% of identified SNVs were rare variants observed only in one allele in 101 horses. The number of SNVs detected in individual horses ranged from 4.8 to 5.3 million. Individual horses had a maximum of 25,554 rare variants; several of these were functional variants, such as non-synonymous substitutions, start-gained, start-lost, stop-gained, and stop-lost variants. Therefore, these rare variants may affect differences in traits and phenotypes among individuals. When observing the distribution of rare variants among horses, one breeding stallion had a smaller number of rare variants compared to other horses, suggesting that the frequency of rare variants in the Japanese Thoroughbred population increases through breeding. In addition, our variant database may provide useful basic information for industrial applications, such as the detection of genetically modified racehorses in gene-doping control and pedigree-registration of racehorses using SNVs as markers.
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Maternal Phylogenetic Relationships and Genetic Variation among Rare, Phenotypically Similar Donkey Breeds. Genes (Basel) 2021; 12:genes12081109. [PMID: 34440283 PMCID: PMC8392470 DOI: 10.3390/genes12081109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/02/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022] Open
Abstract
The mitochondrial DNA (mtDNA) D-loop of endangered and critically endangered breeds has been studied to identify maternal lineages, characterize genetic inheritance, reconstruct phylogenetic relations among breeds, and develop biodiversity conservation and breeding programs. The aim of the study was to determine the variability remaining and the phylogenetic relationship of Martina Franca (MF, with total population of 160 females and 36 males), Ragusano (RG, 344 females and 30 males), Pantesco (PT, 47 females and 15 males), and Catalonian (CT) donkeys by collecting genetic data from maternal lineages. Genetic material was collected from saliva, and a 350 bp fragment of D-loop mtDNA was amplified and sequenced. Sequences were aligned and evaluated using standard bioinformatics software. A total of 56 haplotypes including 33 polymorphic sites were found in 77 samples (27 MF, 22 RG, 8 PT, 19 CT, 1 crossbred). The breed nucleotide diversity value (π) for all the breeds was 0.128 (MF: 0.162, RG: 0.132, PT: 0.025, CT: 0.038). Principal components analysis grouped most of the haplogroups into two different clusters, I (including all haplotypes from PT and CT, together with haplotypes from MF and RG) and II (including haplotypes from MF and RG only). In conclusion, we found that the primeval haplotypes, haplogroup variability, and a large number of maternal lineages were preserved in MF and RG; thus, these breeds play putative pivotal roles in the phyletic relationships of donkey breeds. Maternal inheritance is indispensable genetic information required to evaluate inheritance, variability, and breeding programs.
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Engel L, Becker D, Nissen T, Russ I, Thaller G, Krattenmacher N. Exploring the Origin and Relatedness of Maternal Lineages Through Analysis of Mitochondrial DNA in the Holstein Horse. Front Genet 2021; 12:632500. [PMID: 34335677 PMCID: PMC8320364 DOI: 10.3389/fgene.2021.632500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/18/2021] [Indexed: 11/26/2022] Open
Abstract
Maternal lineages are important for the breeding decision in the Holstein horse breed. To investigate the genetic diversity of the maternal lineages and the relationships between founder mares, the maternal inherited mitochondrial genome (except the repetitive part of the non-coding region) of 271 mares representing 75 lineages was sequenced. The sequencing predominantly revealed complete homology in the nucleotide sequences between mares from one lineage with exceptions in 13 lineages, where differences in one to three positions are probably caused by de novo mutations or alternate fixation of heteroplasmy. We found 78 distinct haplotypes that have not yet been described in other breeds. Six of these occurred in two or three different lineages indicating a common ancestry. Haplotypes can be divided into eight clusters with all mares from one lineage belonging to the same cluster. Within a cluster, the average number of pairwise differences ranged from zero to 16.49 suggesting close maternal relationships between these mares. The results showed that the current breeding population originated from at least eight ancestral founder mares.
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Affiliation(s)
- Laura Engel
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Kiel, Germany
| | - Doreen Becker
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Thomas Nissen
- Verband der Züchter des Holsteiner Pferdes e.V., Kiel, Germany
| | - Ingolf Russ
- Tierzuchtforschung e.V. München, Grub, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Kiel, Germany
| | - Nina Krattenmacher
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Kiel, Germany
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Lee W, Mun S, Choi SY, Oh DY, Park YS, Han K. Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse. Animals (Basel) 2021; 11:ani11071924. [PMID: 34203473 PMCID: PMC8300358 DOI: 10.3390/ani11071924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary In modern times, horse breeds, mostly in horse racing, are the Thoroughbred varieties obtained by breeding three Godolphin Arabians with British mares in England. Especially in Jeju Island, Korea, Jeju horses have been introduced from Mongolia since the 13th century. They have contributed a lot to the agricultural community, but their population has been rapidly decreasing due to rapid agricultural industrialization. Therefore, we sympathize with Jeju horse-specific genetic variation and compare and analyze evolutionary correlations by utilizing Whole Genome Sequencing analysis to evaluate the genetic diversity of Jeju horses and preserve genetic information. We explored Jeju horse-specific genetic differences through a comparative analysis of large-capacity genomic data between the public database and a Thoroughbred variety. In order to adapt to the barren external environment, it is predicted that Jeju horses have experienced strong positive selection in the direction of accumulating many genetic variations, enough to cause functional differences in the eqCD1a6 gene to have an efficient immune function. In addition, we further validate the Jeju horse-specific single nucleotide polymorphisms in the aqCD1a6 gene by employing the digital PCR method, a diagnostic technique for genetic variations. Abstract The Jeju horse is a native Korean species that has been breeding on Jeju Island since the 13th century. Their shape has a distinct appearance from the representative species, Thoroughbred. Here, we performed a comparison of the Jeju horse and Thoroughbred horse for the identification of genome-wide structure variation by using the next-generation sequencing (NGS) technique. We generated an average of 95.59 Gb of the DNA sequence, resulting in an average of 33.74 X sequence coverage from five Jeju horses. In addition, reads obtained from WGRS data almost covered the horse reference genome (mapped reads 98.4%). Based on our results, we identified 1,244,064 single nucleotide polymorphisms (SNPs), 113,498 genomic insertions, and 114,751 deletions through bioinformatics analysis. Interestingly, the results of the WGRS comparison indicated that the eqCD1a6 gene contains signatures of positive natural selection in Jeju horses. The eqCD1a6 gene is known to be involved in immunity. The eqCD1a6 gene of Jeju horses commonly contained 296 variants (275 SNPs and 21 INDELs) that were compared with its counterpart of two Thoroughbred horses. In addition, we used LOAA, digital PCR, to confirm the possibility of developing a molecular marker for species identification using variant sites. As a result, it was possible to confirm the result of the molecular marker with high accuracy. Nevertheless, eqCD1a6 was shown to be functionally intact. Taken together, we have found significant genomic variation in these two different horse species.
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Affiliation(s)
- Wooseok Lee
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea; (W.L.); (S.M.)
| | - Seyoung Mun
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea; (W.L.); (S.M.)
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
| | - Song-Yi Choi
- Department of Pathology, Colleage of Medicine, Chungnam National University, Daejeon 34134, Korea;
| | - Dong-Yep Oh
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju 36052, Korea;
| | - Yong-Soo Park
- Department of Equine Industry, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea
- Correspondence: (Y.-S.P.); (K.H.); Tel.: +82-41-550-1298 (Y.-S.P. & K.H.)
| | - Kyudong Han
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea; (W.L.); (S.M.)
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan 31116, Korea
- Correspondence: (Y.-S.P.); (K.H.); Tel.: +82-41-550-1298 (Y.-S.P. & K.H.)
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From the Eurasian Steppes to the Roman Circuses: A Review of Early Development of Horse Breeding and Management. Animals (Basel) 2021; 11:ani11071859. [PMID: 34206575 PMCID: PMC8300240 DOI: 10.3390/ani11071859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 01/14/2023] Open
Abstract
Simple Summary Horses were domesticated later than any other major livestock species. Their role in shaping ancient civilizations cannot be overestimated. As a primary means of transportation, an essential asset in warfare, and later one of the key elements of circus entertainment, horses quickly became luxurious goods. Vast amounts of money were invested in the horse industry resulted resulting in the rapid development of horse breeding and husbandry. This review examines paleogenetic, archeological, and classical studies on managing horses in antiquity. Many ancient approaches and practices in horse management are still relevant today and some of them, now abandoned, are worth re-examination. Abstract The domestication of the horse began about 5500 years ago in the Eurasian steppes. In the following millennia horses spread across the ancient world, and their role in transportation and warfare affected every ancient culture. Ownership of horses became an indicator of wealth and social status. The importance of horses led to a growing interest in their breeding and management. Many phenotypic traits, such as height, behavior, and speed potential, have been proven to be a subject of selection; however, the details of ancient breeding practices remain mostly unknown. From the fourth millennium BP, through the Iron Age, many literature sources thoroughly describe horse training systems, as well as various aspects of husbandry, many of which are still in use today. The striking resemblance of ancient and modern equine practices leaves us wondering how much was accomplished through four thousand years of horse breeding.
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Vershinina AO, Heintzman PD, Froese DG, Zazula G, Cassatt-Johnstone M, Dalén L, Der Sarkissian C, Dunn SG, Ermini L, Gamba C, Groves P, Kapp JD, Mann DH, Seguin-Orlando A, Southon J, Stiller M, Wooller MJ, Baryshnikov G, Gimranov D, Scott E, Hall E, Hewitson S, Kirillova I, Kosintsev P, Shidlovsky F, Tong HW, Tiunov MP, Vartanyan S, Orlando L, Corbett-Detig R, MacPhee RD, Shapiro B. Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge. Mol Ecol 2021; 30:6144-6161. [PMID: 33971056 DOI: 10.1111/mec.15977] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/24/2021] [Accepted: 04/27/2021] [Indexed: 01/02/2023]
Abstract
The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0-0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875-625 and ~200-50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.
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Affiliation(s)
- Alisa O Vershinina
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Duane G Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada
| | - Grant Zazula
- Collections and Research, Canadian Museum of Nature, Station D, Ottawa, ON, Canada.,Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Clio Der Sarkissian
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Shelby G Dunn
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Luca Ermini
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Copenhagen, Denmark
| | - Cristina Gamba
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Copenhagen, Denmark
| | - Pamela Groves
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, CA, USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Daniel H Mann
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, CA, USA
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - John Southon
- Keck-CCAMS Group, Earth System Science Department, University of California, Irvine, CA, USA
| | - Mathias Stiller
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Division Molecular Pathology, Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Matthew J Wooller
- Alaska Stable Isotope Facility, Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, Fairbanks, AK, USA.,Department of Marine Biology, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Gennady Baryshnikov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Dmitry Gimranov
- Institute of Plant & Animal Ecology of the Russian Academy of Sciences, Ural Branch, Ekaterinburg, Russia.,Ural Federal University named after the first President of Russia B. N. Yeltsin, Ekaterinburg, Russia
| | - Eric Scott
- California State University, San Bernardino, CA, USA
| | - Elizabeth Hall
- Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | - Susan Hewitson
- Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | - Irina Kirillova
- Institute of Geography, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Kosintsev
- Institute of Plant & Animal Ecology of the Russian Academy of Sciences, Ural Branch, Ekaterinburg, Russia
| | | | - Hao-Wen Tong
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Mikhail P Tiunov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russia
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A. Shilo, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | | | | | - Beth Shapiro
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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14
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Tuniyazi M, He J, Guo J, Li S, Zhang N, Hu X, Fu Y. Changes of microbial and metabolome of the equine hindgut during oligofructose-induced laminitis. BMC Vet Res 2021; 17:11. [PMID: 33407409 PMCID: PMC7789226 DOI: 10.1186/s12917-020-02686-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/19/2020] [Indexed: 12/15/2022] Open
Abstract
Background Laminitis is a common and serve disease which caused by inflammation and pathological changes of the laminar junction. However, the pathologic mechanism remains unclear. In this study we aimed to investigate changes of the gut microbiota and metabolomics in oligofructose-induced laminitis of horses. Results Animals submitted to treatment with oligofructose had lower fecal pH but higher lactic acid, histamine, and Lipopolysaccharide (LPS) in serum. Meanwhile, oligofructose altered composition of the hindgut bacterial community, demonstrated by increasing relative abundance of Lactobacillus and Megasphaera. In addition, the metabolome analysis revealed that treatment with oligofructose decreased 84 metabolites while 53 metabolites increased, such as dihydrothymine, N3,N4-Dimethyl-L-arginine, 10E,12Z-Octadecadienoic acid, and asparagine. Pathway analysis revealed that aldosterone synthesis and secretion, regulation of lipolysis in adipocytes, steroid hormone biosynthesis, pyrimidine metabolism, biosynthesis of unsaturated fatty acids, and galactose metabolism were significantly different between healthy and laminitis horses. Furthermore, correlation analysis between gut microbiota and metabolites indicated that Lactobacillus and/or Megasphaera were positively associated with the dihydrothymine, N3,N4-Dimethyl-L-arginine, 10E,12Z-Octadecadienoic acid, and asparagine. Conclusions These results revealed that disturbance of gut microbiota and changes of metabolites were occurred during the development of equine laminitis, and these results may provide novel insights to detect biomarkers for a better understanding of the potential mechanism and prevention strategies for laminitis in horses. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-020-02686-9.
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Affiliation(s)
- Maimaiti Tuniyazi
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, 130062, People's Republic of China
| | - Junying He
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, 130062, People's Republic of China
| | - Jian Guo
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, 130062, People's Republic of China
| | - Shuang Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, 130062, People's Republic of China
| | - Naisheng Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, 130062, People's Republic of China
| | - Xiaoyu Hu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, 130062, People's Republic of China.
| | - Yunhe Fu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, 130062, People's Republic of China.
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15
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Orlando L. The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics. Annu Rev Genet 2020; 54:563-581. [PMID: 32960653 DOI: 10.1146/annurev-genet-021920-011805] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.
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Affiliation(s)
- Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse, Faculté de Médecine Purpan, Université Toulouse III-Paul Sabatier, 31000 Toulouse, France;
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16
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Vorobieva NV, Makunin AI, Druzhkova AS, Kusliy MA, Trifonov VA, Popova KO, Polosmak NV, Molodin VI, Vasiliev SK, Shunkov MV, Graphodatsky AS. High genetic diversity of ancient horses from the Ukok Plateau. PLoS One 2020; 15:e0241997. [PMID: 33180850 PMCID: PMC7660532 DOI: 10.1371/journal.pone.0241997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/24/2020] [Indexed: 11/18/2022] Open
Abstract
A growing number of researchers studying horse domestication come to a conclusion that this process happened in multiple locations and involved multiple wild maternal lines. The most promising approach to address this problem involves mitochondrial haplotype comparison of wild and domestic horses from various locations coupled with studies of possible migration routes of the ancient shepherds. Here, we sequenced complete mitochondrial genomes of six horses from burials of the Ukok plateau (Russia, Altai Mountains) dated from 2.7 to 1.4 thousand years before present and a single late Pleistocene wild horse from the neighboring region (Denisova cave). Sequencing data indicates that the wild horse belongs to an extinct pre-domestication lineage. Integration of the domestic horse data with known Eurasian haplotypes of a similar age revealed two distinct groups: the first one widely distributed in Europe and presumably imported to Altai, and the second one specific for Altai Mountains and surrounding area.
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Affiliation(s)
- Nadezhda V. Vorobieva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
- Paleogenomics Laboratory, Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Alexey I. Makunin
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Anna S. Druzhkova
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Mariya A. Kusliy
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
- * E-mail:
| | - Vladimir A. Trifonov
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Kseniya O. Popova
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Natalia V. Polosmak
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Vyacheslav I. Molodin
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Sergei K. Vasiliev
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Michael V. Shunkov
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
| | - Alexander S. Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Novosibirsk Oblast, Russia
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17
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Modern Northern Domestic Horses Carry Mitochondrial DNA Similar to Przewalski’s Horse. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09517-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractSeveral recent studies have suggested past gene flow between the Przewalski’s horse and modern domestic horse and questioned the wild origin of the Przewalski’s horse. Mitochondrial DNA has placed representatives of the Przewalski’s horse into three among the eighteen haplogroups detected from the modern horse. Of these, two haplogroups have so far been found exclusively in the Przewalski’s horse, while the one shared with the domestic horse includes captive individuals that have uncertain pedigrees. We recently found five domestic horse individuals of North European horse breeds to carry a mitochondrial haplogroup that was previously confined only to the Przewalski’s horse. These individuals were sequenced for 6039 bp of mitochondrial DNA and used, together with domestic and Przewalski’s horse sequences presenting all horse haplogroups, to examine the phylogenetic relationships and to date the divergence time between Przewalski’s and domestic horse clusters within this haplogroup. The divergence was dated to have likely occurred about 13,300–11,400 years ago, which coincides with the time of the Younger Dryas.
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18
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Guimaraes S, Arbuckle BS, Peters J, Adcock SE, Buitenhuis H, Chazin H, Manaseryan N, Uerpmann HP, Grange T, Geigl EM. Ancient DNA shows domestic horses were introduced in the southern Caucasus and Anatolia during the Bronze Age. SCIENCE ADVANCES 2020; 6:eabb0030. [PMID: 32938680 PMCID: PMC7494339 DOI: 10.1126/sciadv.abb0030] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/31/2020] [Indexed: 05/12/2023]
Abstract
Despite the important roles that horses have played in human history, particularly in the spread of languages and cultures, and correspondingly intensive research on this topic, the origin of domestic horses remains elusive. Several domestication centers have been hypothesized, but most of these have been invalidated through recent paleogenetic studies. Anatolia is a region with an extended history of horse exploitation that has been considered a candidate for the origins of domestic horses but has never been subject to detailed investigation. Our paleogenetic study of pre- and protohistoric horses in Anatolia and the Caucasus, based on a diachronic sample from the early Neolithic to the Iron Age (~8000 to ~1000 BCE) that encompasses the presumed transition from wild to domestic horses (4000 to 3000 BCE), shows the rapid and large-scale introduction of domestic horses at the end of the third millennium BCE. Thus, our results argue strongly against autochthonous independent domestication of horses in Anatolia.
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Affiliation(s)
- Silvia Guimaraes
- Institut Jacques Monod, CNRS, University of Paris, Paris, France
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joris Peters
- ArchaeoBioCenter and Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication and the History of Veterinary Medicine, Ludwig Maximilian University Munich, Kaulbachstraße 37/111, 80539 Munich, Germany
- State Collection of Anthropology and Palaeoanatomy Munich, Bavarian Natural History Collections, Karolinenplatz 2a, 80333 Munich, Germany
| | - Sarah E Adcock
- Department of Anthropology, University of Chicago, 1126 East 59th Street, Chicago, IL 60637, USA
| | - Hijlke Buitenhuis
- Groningen Institute of Archaeology, University of Groningen, 9712 ER Groningen, Netherlands
| | - Hannah Chazin
- Department of Anthropology, Columbia University, 1200 Amsterdam Avenue, New York, NY 10031, USA
| | - Ninna Manaseryan
- Scientific Center of Zoology and Hydroecology, Institute of Zoology, National Academy of Sciences of the Republic of Armenia, 7 Paruyr Sevak Str., Yerevan 0014, Armenia
| | - Hans-Peter Uerpmann
- Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung für Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Universität Tübingen, Rümelinstraße 23, 72070 Tübingen, Germany
| | - Thierry Grange
- Institut Jacques Monod, CNRS, University of Paris, Paris, France
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, University of Paris, Paris, France.
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19
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Ning T, Ling Y, Hu S, Ardalan A, Li J, Mitra B, Chaudhuri TK, Guan W, Zhao Q, Ma Y, Savolainen P, Zhang Y. Local origin or external input: modern horse origin in East Asia. BMC Evol Biol 2019; 19:217. [PMID: 31775623 PMCID: PMC6882189 DOI: 10.1186/s12862-019-1532-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite decades of research, the horse domestication scenario in East Asia remains poorly understood. RESULTS The study identified 16 haplogroups with fine-scale phylogenetic resolution using mitochondrial genomes of 317 horse samples. The time to the most recent common ancestor of the 16 haplogroups ranges from [0.8-3.1] thousand years ago (KYA) to [7.9-27.1] KYA. With combined analyses of the mitochondrial control region for 35 extant Przewalski's horses, 3544 modern and 203 ancient horses across the world, researchers provide evidence for that East Asian prevalent haplogroups Q and R were indigenously domesticated or they were involved in numerous distinct genetic components from wild horses in the southern part of East Asia. These events of haplotypes Q and R occurred during 4.7 to 16.3 KYA and 2.1 to 11.5 KYA, respectively. The diffusion of preponderant European haplogroups L from west to East Asia is consistent with the external gene input. Furthermore, genetic differences were detected between northern East Asia and southern East Asia cohorts by Principal Component Analysis, Analysis of Molecular Variance test, the χ2 test and phylogeographic analyses. CONCLUSIONS All results suggest a complex picture of horse domestication, as well as geographic pattern in East Asia. Both local origin and external input occurred in East Asia horse populations. And besides, there are at least two different domestication or hybridization centers in East Asia.
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Affiliation(s)
- Tiao Ning
- College of Agriculture, Kunming University, Kunming, 650214, Yunnan, China. .,Laboratory for Conservation and Utilization of Bio-resource and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, Yunnan, China.
| | - Yinghui Ling
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Shaoji Hu
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, 650214, Yunnan, China
| | - Arman Ardalan
- Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, SE-171 65, Solna, Sweden
| | - Jing Li
- College of Agriculture, Kunming University, Kunming, 650214, Yunnan, China.,The Research Center for Urban Modern Agricultural Engineering of Yunnan Tertiary Education, Kunming University, Kunming, 650214, Yunnan, China
| | - Bikash Mitra
- Department of Zoology, University of North Bengal, Cellular Immunology Laboratory, Siliguri, West Bengal, 734013, India
| | - Tapas Kumar Chaudhuri
- Department of Zoology, University of North Bengal, Cellular Immunology Laboratory, Siliguri, West Bengal, 734013, India
| | - Weijun Guan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Peter Savolainen
- Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, SE-171 65, Solna, Sweden.
| | - Yaping Zhang
- Laboratory for Conservation and Utilization of Bio-resource and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, Yunnan, China. .,State Key Laboratory of Genetic Resources and Evolution Kunming, Yunnan, Kunming Institute of Zoology, Chinese Academy of Sciences, Wuhua, 650223, Yunnan, China.
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20
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Massacci FR, Clark A, Ruet A, Lansade L, Costa M, Mach N. Inter-breed diversity and temporal dynamics of the faecal microbiota in healthy horses. J Anim Breed Genet 2019; 137:103-120. [PMID: 31523867 DOI: 10.1111/jbg.12441] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/09/2019] [Accepted: 08/28/2019] [Indexed: 12/13/2022]
Abstract
Understanding gut microbiota similarities and differences across breeds in horses has the potential to advance approaches aimed at personalized microbial modifications, particularly those involved in improving sport athletic performance. Here, we explore whether faecal microbiota composition based on faecal 16S ribosomal RNA gene sequencing varies across six different sport breeds at two time points 8 months apart within a cohort of 189 healthy horses cared for under similar conditions. Lusitano horses presented the smallest and Hanoverians the greatest bacterial diversity. We found subtle but significant differences in β-diversity between Lusitano, Anglo Arabian and the central European breeds, and we reproduced these results across the two time points. Repeat sampling of subjects showed community to be temporally more stable in Lusitano and Anglo Arabian breeds. Additionally, we found that 27 genera significantly varied in abundance across breeds. Overall, 33% of these taxa overlapped with previously identified taxa that were associated with genetic variation in humans or other species. However, a non-significant correlation was observed between microbial composition and the host pedigree-based kinship. Despite a notable variation in the diversity and composition of the faecal microbiota, breed exerted limited effects on the equine faecal microbiota.
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Affiliation(s)
- Francesca Romana Massacci
- UMR 1313, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Research and Development Department, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche 'Togo Rosati', Perugia, Italy.,Agricultural and Food Sciences Department, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Allison Clark
- Gastroenterology Department, Vall d'Hebron Research Center, Barcelona, Spain
| | - Alice Ruet
- PRC, INRA, CNRS, IFCE, University of Tours, Nouzilly, France
| | - Léa Lansade
- PRC, INRA, CNRS, IFCE, University of Tours, Nouzilly, France
| | - Marcio Costa
- Biomedical Veterinary Sciences Department, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Núria Mach
- UMR 1313, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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21
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Kvist L, Niskanen M, Mannermaa K, Wutke S, Aspi J. Genetic variability and history of a native Finnish horse breed. Genet Sel Evol 2019; 51:35. [PMID: 31262246 PMCID: PMC6604459 DOI: 10.1186/s12711-019-0480-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/19/2019] [Indexed: 11/17/2022] Open
Abstract
Background The Finnhorse was established as a breed more than 110 years ago by combining local Finnish landraces. Since its foundation, the breed has experienced both strong directional selection, especially for size and colour, and severe population bottlenecks that are connected with its initial foundation and subsequent changes in agricultural and forestry practices. Here, we used sequences of the mitochondrial control region and genomic single nucleotide polymorphisms (SNPs) to estimate the genetic diversity and differentiation of the four Finnhorse breeding sections: trotters, pony-sized horses, draught horses and riding horses. Furthermore, we estimated inbreeding and effective population sizes over time to infer the history of this breed. Results We found a high level of mitochondrial genetic variation and identified 16 of the 18 haplogroups described in present-day horses. Interestingly, one of these detected haplogroups was previously reported only in the Przewalski’s horse. Female effective population sizes were in the thousands, but declines were evident at the times when the breed and its breeding sections were founded. By contrast, nuclear variation and effective population sizes were small (approximately 50). Nevertheless, inbreeding in Finnhorses was lower than in many other horse breeds. Based on nuclear SNP data, genetic differentiation among the four breeding sections was strongest between the draught horses and the three other sections (FST = 0.007–0.018), whereas based on mitochondrial DNA data, it was strongest between the trotters and the pony-sized and riding horses (ΦST = 0.054–0.068). Conclusions The existence of a Przewalski’s horse haplogroup in the Finnhorse provides new insights into the domestication of the horse, and this finding supports previous suggestions of a close relationship between the Finnhorse and eastern primitive breeds. The high level of mitochondrial DNA variation in the Finnhorse supports its domestication from a large number of mares but also reflects that its founding depended on many local landraces. Although inbreeding in Finnhorses was lower than in many other horse breeds, the small nuclear effective population sizes of each of its breeding sections can be considered as a warning sign, which warrants changes in breeding practices. Electronic supplementary material The online version of this article (10.1186/s12711-019-0480-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura Kvist
- Department of Ecology and Genetics, University of Oulu, POB 8000, 90014, Oulu, Finland.
| | - Markku Niskanen
- Research Unit of History, Culture and Communications, University of Oulu, POB 8000, 90014, Oulu, Finland
| | - Kristiina Mannermaa
- Department of Philosophy, History, Culture and Art Studies, University of Helsinki, POB 24, 00014, Helsinki, Finland
| | - Saskia Wutke
- Department of Environmental and Biological Sciences, University of Eastern Finland, POB 111, 80101, Joensuu, Finland
| | - Jouni Aspi
- Department of Ecology and Genetics, University of Oulu, POB 8000, 90014, Oulu, Finland
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22
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Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH, Allentoft M, Alquraishi S, Anthony D, Baimukhanov N, Barrett JH, Bayarsaikhan J, Benecke N, Bernáldez-Sánchez E, Berrocal-Rangel L, Biglari F, Boessenkool S, Boldgiv B, Brem G, Brown D, Burger J, Crubézy E, Daugnora L, Davoudi H, de Barros Damgaard P, de Los Ángeles de Chorro Y de Villa-Ceballos M, Deschler-Erb S, Detry C, Dill N, do Mar Oom M, Dohr A, Ellingvåg S, Erdenebaatar D, Fathi H, Felkel S, Fernández-Rodríguez C, García-Viñas E, Germonpré M, Granado JD, Hallsson JH, Hemmer H, Hofreiter M, Kasparov A, Khasanov M, Khazaeli R, Kosintsev P, Kristiansen K, Kubatbek T, Kuderna L, Kuznetsov P, Laleh H, Leonard JA, Lhuillier J, Liesau von Lettow-Vorbeck C, Logvin A, Lõugas L, Ludwig A, Luis C, Arruda AM, Marques-Bonet T, Matoso Silva R, Merz V, Mijiddorj E, Miller BK, Monchalov O, Mohaseb FA, Morales A, Nieto-Espinet A, Nistelberger H, Onar V, Pálsdóttir AH, Pitulko V, Pitskhelauri K, Pruvost M, Rajic Sikanjic P, Rapan Papeša A, Roslyakova N, Sardari A, Sauer E, Schafberg R, Scheu A, Schibler J, Schlumbaum A, Serrand N, Serres-Armero A, Shapiro B, Sheikhi Seno S, Shevnina I, Shidrang S, Southon J, Star B, Sykes N, Taheri K, Taylor W, Teegen WR, Trbojević Vukičević T, Trixl S, Tumen D, Undrakhbold S, Usmanova E, Vahdati A, Valenzuela-Lamas S, Viegas C, Wallner B, Weinstock J, Zaibert V, Clavel B, Lepetz S, Mashkour M, Helgason A, Stefánsson K, Barrey E, Willerslev E, Outram AK, Librado P, Orlando L. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series. Cell 2019; 177:1419-1435.e31. [PMID: 31056281 PMCID: PMC6547883 DOI: 10.1016/j.cell.2019.03.049] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/14/2019] [Accepted: 03/27/2019] [Indexed: 11/30/2022]
Abstract
Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.
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Affiliation(s)
- Antoine Fages
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Kristian Hanghøj
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Naveed Khan
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Charleen Gaunitz
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Michela Leonardi
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Christian McCrory Constantz
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Cristina Gamba
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Silvia Albizuri
- Seminari d'Estudis i Recerques Prehistoriques, HAR2017-87695-P, Universitat de Barcelona, Barcelona, Spain
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Morten Allentoft
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Saleh Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - David Anthony
- Anthropology Department, Hartwick College 1, Oneonta, NY 13820, USA
| | | | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, UK
| | | | - Norbert Benecke
- Deutsches Archäologisches Institut (DAI), 14195 Berlin, Germany
| | - Eloísa Bernáldez-Sánchez
- Laboratorio de Paleontologia y Paleobiologia, Instituto Andaluz del Patrimonio Historico, Sevilla, Spain
| | - Luis Berrocal-Rangel
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fereidoun Biglari
- Department of Paleolithic, National Museum of Iran, 1136918111, Tehran, Iran
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Bazartseren Boldgiv
- Ecology Group, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | - Dorcas Brown
- Anthropology Department, Hartwick College 1, Oneonta, NY 13820, USA
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Eric Crubézy
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Linas Daugnora
- Osteological material research laboratory, Klaipėda university, Klaipėda 92294, Lithuania
| | - Hossein Davoudi
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran
| | | | | | - Sabine Deschler-Erb
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Cleia Detry
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Nadine Dill
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Maria do Mar Oom
- CE3C-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Anna Dohr
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, 80539 München, Germany; ArchaeoBioCenter, Ludwig-Maximilians-University Munich, 80539 München, Germany; Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | | | | | - Homa Fathi
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Sabine Felkel
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | | | - Esteban García-Viñas
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Mietje Germonpré
- Operational Direction, Earth and History of Life, Royal Belgian Institute of Natural Sciences, 1000, Brussels, Belgium
| | - José D Granado
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Jón H Hallsson
- Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
| | - Helmut Hemmer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Aleksei Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg 191186, Russia
| | | | - Roya Khazaeli
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Ekaterinburg 620144, Russia
| | | | - Tabaldiev Kubatbek
- Department of History, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Lukas Kuderna
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain
| | - Pavel Kuznetsov
- Samara State University of Social Science and Education, Samara, Russia
| | - Haeedeh Laleh
- Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Department of Archaeology, Faculty of Humanities, University of Tehran, Iran
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), 41092 Sevilla, Spain
| | - Johanna Lhuillier
- Laboratoire Archéorient, UMR 5133, Maison de l'Orient et de la Méditerranée, 69365 Lyon Cedex 7, France
| | | | - Andrey Logvin
- Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, 10130 Tallinn, Estonia
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany; Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University Berlin, 10115 Berlin, Germany
| | - Cristina Luis
- Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Lisboa, Portugal; Centro Interuniversitário de História das Ciências e da Tecnologia (CIUHCT), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Instituto Universitário de Lisboa (ISCTE-IUL), CIES-IUL, Lisboa, Portugal
| | - Ana Margarida Arruda
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain; Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Victor Merz
- S.Toraighyrov Pavlodar State University, Joint Research Center for Archeological Studies, 637000 Pavlodar, Kazakhstan
| | - Enkhbayar Mijiddorj
- Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar 51, Mongolia
| | - Bryan K Miller
- University of Oxford, Faculty of History, George Street, Oxford, OX1 2RL, UK
| | - Oleg Monchalov
- Samara State University of Social Science and Education, Samara, Russia
| | - Fatemeh A Mohaseb
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Arturo Morales
- Laboratory of Archaeozoology, Department Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ariadna Nieto-Espinet
- Archaeology of Social Dynamics Group (ADS), Institució Milà i Fontanals-Consejo Superior de Investigaciones Científicas (IMF-CSIC), 08001 Barcelona, Spain; Grup d'Investigació Prehistòrica, HAR2016-78277-R, Universitat de Lleida, 25003 Lleida, Spain
| | - Heidi Nistelberger
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, 34320, Avcılar, Istanbul, Turkey
| | - Albína H Pálsdóttir
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway; Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
| | - Vladimir Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg 191186, Russia
| | | | - Mélanie Pruvost
- Université de Bordeaux, CNRS, UMR 5199-PACEA, 33615 Pessac Cedex, France
| | | | | | | | - Alireza Sardari
- Iranian Center for Archaeological Research (ICAR), Iranian Cultural Heritage, Handicrafts, and Tourism Organization (ICHHTO), 1136918111, Tehran, Iran
| | - Eberhard Sauer
- School of History, Classics and Archaeology, The University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Renate Schafberg
- Central Natural Science Collections (ZNS), Martin Luther University Halle-Wittenberg, Domplatz 4, 06108 Halle (Saale), Germany
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Jörg Schibler
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Angela Schlumbaum
- Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland
| | - Nathalie Serrand
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France; INRAP Guadeloupe, Centre de recherches archéologiques, UMR 7209 CNRS/MNHN, 97113 Gourbeyre, Guadeloupe
| | - Aitor Serres-Armero
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology and Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Shiva Sheikhi Seno
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Irina Shevnina
- Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Sonia Shidrang
- Saeedi Institute for Advanced Studies, University of Kashan, Kashan 87317-51167, Iran
| | - John Southon
- Department Earth System Science, University of California, Irvine, Irvine, CA 92697, USA
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Naomi Sykes
- Department of Archaeology, University of Nottingham, Nottingham, NG7 2RD, UK; Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Kamal Taheri
- Kermanshah Regional Water Authority, Kermanshah 67145-1466, Iran
| | - William Taylor
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Wolf-Rüdiger Teegen
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, 80539 München, Germany; ArchaeoBioCenter, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | - Tajana Trbojević Vukičević
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, 10 000 Zagreb, Croatia
| | - Simon Trixl
- Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 München, Germany
| | - Dashzeveg Tumen
- Department of Anthropology and Archaeology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Sainbileg Undrakhbold
- Ecology Group, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Emma Usmanova
- Saryarka Archaeological Institute of Buketov Karaganda State University, Karaganda 100074, Kazakhstan
| | - Ali Vahdati
- Iranian Center for Archaeological Research (ICAR), Iranian Cultural Heritage, Handicrafts, and Tourism Organization (ICHHTO), 1136918111, Tehran, Iran
| | - Silvia Valenzuela-Lamas
- Archaeology of Social Dynamics Group (ADS), Institució Milà i Fontanals-Consejo Superior de Investigaciones Científicas (IMF-CSIC), 08001 Barcelona, Spain
| | - Catarina Viegas
- Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria
| | - Jaco Weinstock
- Faculty of Humanities (Archaeology), University of Southampton, Avenue Campus, Highfield, Southampton SO17 1BF, UK
| | - Victor Zaibert
- Scientific Research Institute of Archaeology and Steppe Civilizations, Al Farabi Kazakh National University, 050040 Almaty, Kazakhstan
| | - Benoit Clavel
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Sébastien Lepetz
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | - Marjan Mashkour
- Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France
| | | | | | - Eric Barrey
- GABI UMR1313, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark.
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Antonova EI, Solovyev AV, Vyazov LA, Semykin YA, Mishchenko AV. Reconstruction of the Mitochondrial Genome of the Ancient Horse from the Ashna-Pando Hillfort (Middle Volga). RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419050041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin CJ, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B. The horse Y chromosome as an informative marker for tracing sire lines. Sci Rep 2019; 9:6095. [PMID: 30988347 PMCID: PMC6465346 DOI: 10.1038/s41598-019-42640-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 04/04/2019] [Indexed: 12/31/2022] Open
Abstract
Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.
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Affiliation(s)
- Sabine Felkel
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Viktoria Dobretsberger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | | | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, 30559, Germany
| | - Ruedi Fries
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, 85354, Germany
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Jan E Janečka
- Department of Biological Sciences, Duquesne University, Pittsburgh, 15282, USA
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
- Department of Biosystems, KU Leuven, Leuven, 3001, Belgium
| | - Molly McCue
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, 55108, USA
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, 30559, Germany
| | | | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, USA
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, Avenches, 1580, Switzerland
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, 75123, Sweden
| | - Robert Schaefer
- Agroscope, Swiss National Stud Farm, Avenches, 1580, Switzerland
| | - Christian Schlötterer
- Institut fuer Populationsgenetik, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, 24098, Germany
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, 24098, Germany
- Functional Breeding Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, 37077, Germany
| | - Brandon Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
- School of Life and Environmental Sciences, University of Sydney, Sydney, 2006, Australia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria.
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The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data. Genes (Basel) 2019; 10:genes10030241. [PMID: 30901931 PMCID: PMC6471023 DOI: 10.3390/genes10030241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/03/2019] [Accepted: 03/04/2019] [Indexed: 01/19/2023] Open
Abstract
The Jinjiang horse is a unique Chinese indigenous horse breed distributed in the southern coastal areas, but the ancestry of Jinjiang horses is not well understood. Here, we used Equine SNP70 Bead Array technology to genotype 301 horses representing 10 Chinese indigenous horse breeds, and we integrated the published genotyped data of 352 individuals from 14 foreign horse breeds to study the relationships between Jinjiang horses and horse breeds from around the world. Principal component analysis (PCA), linkage disequilibrium (LD), runs of homozygosity (ROH) analysis, and ancestry estimating methods were conducted to study the population relationships and the ancestral sources and genetic structure of Jinjiang horses. The results showed that there is no close relationship between foreign horse breeds and Jinjiang horses, and Jinjiang horses shared a similar genetic background with Baise horses. TreeMix analysis revealed that there was gene flow from Chakouyi horses to Jinjiang horses. The ancestry analysis showed that Baise horses and Chakouyi horses are the most closely related ancestors of Jinjiang horses. In conclusion, our results showed that Jinjiang horses have a native origin and that Baise horses and Chakouyi horses were key ancestral sources of Jinjiang horses. The study also suggested that ancient trade activities and the migration of human beings had important effects on indigenous horse breeds in China.
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A genome-wide scan for diversifying selection signatures in selected horse breeds. PLoS One 2019; 14:e0210751. [PMID: 30699152 PMCID: PMC6353161 DOI: 10.1371/journal.pone.0210751] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/30/2018] [Indexed: 12/20/2022] Open
Abstract
The genetic differentiation of the current horse population was evolutionarily created by natural or artificial selection which shaped the genomes of individual breeds in several unique ways. The availability of high throughput genotyping methods created the opportunity to study this genetic variation on a genome-wide level allowing detection of genome regions divergently selected between separate breeds as well as among different horse types sharing similar phenotypic features. In this study, we used the population differentiation index (FST) that is generally used for measuring locus-specific allele frequencies variation between populations, to detect selection signatures among six horse breeds maintained in Poland. These breeds can be classified into three major categories, including light, draft and primitive horses, selected mainly in terms of type (utility), exterior, performance, size, coat color and appearance. The analysis of the most pronounced selection signals found in this study allowed us to detect several genomic regions and genes connected with processes potentially important for breed phenotypic differentiation and associated with energy homeostasis during physical effort, heart functioning, fertility, disease resistance and motor coordination. Our results also confirmed previously described association of loci on ECA3 (spanning LCORL and NCAPG genes) and ECA11 (spanning LASP1 gene) with the regulation of body size in our draft and primitive (small size) horses. The efficiency of the applied FST-based approach was also confirmed by the identification of a robust selection signal in the blue dun colored Polish Konik horses at the locus of TBX3 gene, which was previously shown to be responsible for dun coat color dilution in other horse breeds. FST-based method showed to be efficient in detection of diversifying selection signatures in the analyzed horse breeds. Especially pronounced signals were observed at the loci responsible for fixed breed-specific features. Several candidate genes under selection were proposed in this study for traits selected in separate breeds and horse types, however, further functional and comparative studies are needed to confirm and explain their effect on the observed genetic diversity of the horse breeds.
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Yoon SH, Lee W, Ahn H, Caetano-Anolles K, Park KD, Kim H. Origin and spread of Thoroughbred racehorses inferred from complete mitochondrial genome sequences: Phylogenomic and Bayesian coalescent perspectives. PLoS One 2018; 13:e0203917. [PMID: 30216366 PMCID: PMC6138400 DOI: 10.1371/journal.pone.0203917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 08/30/2018] [Indexed: 11/26/2022] Open
Abstract
The Thoroughbred horse breed was developed primarily for racing, and has a significant contribution to the qualitative improvement of many other horse breeds. Despite the importance of Thoroughbred racehorses in historical, cultural, and economical viewpoints, there was no temporal and spatial dynamics of them using the mitogenome sequences. To explore this topic, the complete mitochondrial genome sequences of 14 Thoroughbreds and two Przewalski’s horses were determined. These sequences were analyzed together along with 151 previously published horse mitochondrial genomes from a range of breeds across the globe using a Bayesian coalescent approach as well as Bayesian inference and maximum likelihood methods. The racing horses were revealed to have multiple maternal origins and to be closely related to horses from one Asian, two Middle Eastern, and five European breeds. Thoroughbred horse breed was not directly related to the Przewalski’s horse which has been regarded as the closest taxon to the all domestic horses and the only true wild horse species left in the world. Our phylogenomic analyses also supported that there was no apparent correlation between geographic origin or breed and the evolution of global horses. The most recent common ancestor of the Thoroughbreds lived approximately 8,100–111,500 years ago, which was significantly younger than the most recent common ancestor of modern horses (0.7286 My). Bayesian skyline plot revealed that the population expansion of modern horses, including Thoroughbreds, occurred approximately 5,500–11,000 years ago, which coincide with the start of domestication. This is the first phylogenomic study on the Thoroughbred racehorse in association with its spatio-temporal dynamics. The database and genetic history information of Thoroughbred mitogenomes obtained from the present study provide useful information for future horse improvement projects, as well as for the study of horse genomics, conservation, and in association with its geographical distribution.
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Affiliation(s)
- Sook Hee Yoon
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Wonseok Lee
- Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyeonju Ahn
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kelsey Caetano-Anolles
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kyoung-Do Park
- The Animal Molecular Genetics & Breeding Center, Chonbuk National University, Jeonju, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
- * E-mail:
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Cozzi MC, Strillacci MG, Valiati P, Rogliano E, Bagnato A, Longeri M. Genetic variability of Akhal-Teke horses bred in Italy. PeerJ 2018; 6:e4889. [PMID: 30202639 PMCID: PMC6129384 DOI: 10.7717/peerj.4889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/14/2018] [Indexed: 12/13/2022] Open
Abstract
Background The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. Methods Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences. Results Nucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.
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Affiliation(s)
- Maria C Cozzi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Maria G Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Paolo Valiati
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Elisa Rogliano
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Maria Longeri
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
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Ovchinnikov IV, Dahms T, Herauf B, McCann B, Juras R, Castaneda C, Cothran EG. Genetic diversity and origin of the feral horses in Theodore Roosevelt National Park. PLoS One 2018; 13:e0200795. [PMID: 30067807 PMCID: PMC6070244 DOI: 10.1371/journal.pone.0200795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/03/2018] [Indexed: 11/19/2022] Open
Abstract
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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Affiliation(s)
- Igor V. Ovchinnikov
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, United States of America
- Forensic Science Program, University of North Dakota, Grand Forks, North Dakota, United States of America
- * E-mail:
| | - Taryn Dahms
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, United States of America
| | - Billie Herauf
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, United States of America
| | - Blake McCann
- Resource Management, Theodore Roosevelt National Park, Medora, North Dakota, United States of America
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Bioscience, Texas A&M University, College Station, Texas, United States of America
| | - Caitlin Castaneda
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Bioscience, Texas A&M University, College Station, Texas, United States of America
| | - E. Gus Cothran
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Bioscience, Texas A&M University, College Station, Texas, United States of America
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Yang L, Kong X, Yang S, Dong X, Yang J, Gou X, Zhang H. Haplotype diversity in mitochondrial DNA reveals the multiple origins of Tibetan horse. PLoS One 2018; 13:e0201564. [PMID: 30052677 PMCID: PMC6063445 DOI: 10.1371/journal.pone.0201564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/17/2018] [Indexed: 12/11/2022] Open
Abstract
The Tibetan horse is a species endemic to the Tibetan plateau, with considerable economic value in the region. However, we currently have little genetic evidence to verify whether the breed originated in Tibet or if it entered the area via an ancient migratory route. In the present study, we analyzed the hypervariable segment I sequences of mitochondrial DNA (mtDNA) in 2,050 horses, including 290 individuals from five Tibetan populations and 1,760 from other areas across Asia. Network analysis revealed multiple maternal lineages in the Tibetan horse. Component analysis of sub-lineage F3 indicated that it decreased in frequency from east to west, a trend reflected both southward and northward from Inner Mongolia. Analysis of population genetics showed that the Deqen horse of eastern Tibet was more closely related to the Ningqiang horse of northern China than to other Tibetan horses or the Yunnan horse. These results indicated that the Tibetan horse migrated first from Central Asia to Mongolia, moved south to eastern Tibet (near Deqen), then finally westward to other regions of Tibet. We also identified a novel lineage K that mainly comprises Tibetan and Yunnan horses, suggesting autochthonous domesticated origin for some Tibetan horse breeds from local wild horses. In conclusion, our study demonstrated that modern Tibetan horse breeds originated from the introgression of local wild horses with exotic domesticated populations outside China.
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Affiliation(s)
- Lin Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaoyan Kong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Shuli Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xinxing Dong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jianfa Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xiao Gou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
- * E-mail: (HZ); (XG)
| | - Hao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail: (HZ); (XG)
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31
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Liu LL, Fang C, Liu WJ. Identification on novel locus of dairy traits of Kazakh horse in Xinjiang. Gene 2018; 677:105-110. [PMID: 30257803 DOI: 10.1016/j.gene.2018.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/21/2018] [Accepted: 07/02/2018] [Indexed: 01/23/2023]
Abstract
The utility of high-density single nucleotide polymorphism (SNP) data help to accurately identify genomic regions that have undergone positive selection. In this study, the Affymetrix Equine 670 K high-density SNP array was used to genotype Kazakh and Yili horse population. After quality control, 370,227 autosomal SNPs were used to detect selection signatures by using global fixation index (FST) and cross-population extended haplotype homozygosity (XP-EHH). The database of Ensemble, Genecards, and NCBI were used to make gene annotation and functional analysis. The results showed that there were 134 candidate SNPs overlapped between FST and XP-EHH in Kazakh horse. We also discovered some potential selective sweep regions associated with milk trait, including NUMB, LGALS2, ADCY8, SLC25A30, and CA8 genes. New findings from this research have potential value for milk traits selecting in horse.
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Affiliation(s)
- Ling-Ling Liu
- Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
| | - Chao Fang
- Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
| | - Wu-Jun Liu
- Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China.
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Ma H, Wu Y, Xiang H, Yang Y, Wang M, Zhao C, Wu C. Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences. PeerJ 2018; 6:e4896. [PMID: 29868288 PMCID: PMC5985762 DOI: 10.7717/peerj.4896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/13/2018] [Indexed: 11/20/2022] Open
Abstract
Objectives There are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses. Methods To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed. Results Eightteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35-10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe. Conclusions Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.
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Affiliation(s)
- Hongying Ma
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China
| | - Yajiang Wu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China
| | - Hai Xiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yunzhou Yang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Min Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China
| | - Chunjiang Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing, China
| | - Changxin Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China
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Tong KJ, Duchêne DA, Duchêne S, Geoghegan JL, Ho SYW. A comparison of methods for estimating substitution rates from ancient DNA sequence data. BMC Evol Biol 2018; 18:70. [PMID: 29769015 PMCID: PMC5956955 DOI: 10.1186/s12862-018-1192-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 05/04/2018] [Indexed: 12/02/2022] Open
Abstract
Background Phylogenetic analysis of DNA from modern and ancient samples allows the reconstruction of important demographic and evolutionary processes. A critical component of these analyses is the estimation of evolutionary rates, which can be calibrated using information about the ages of the samples. However, the reliability of these rate estimates can be negatively affected by among-lineage rate variation and non-random sampling. Using a simulation study, we compared the performance of three phylogenetic methods for inferring evolutionary rates from time-structured data sets: regression of root-to-tip distances, least-squares dating, and Bayesian inference. We also applied these three methods to time-structured mitogenomic data sets from six vertebrate species. Results Our results from 12 simulation scenarios show that the three methods produce reliable estimates when the substitution rate is high, rate variation is low, and samples of similar ages are not all grouped together in the tree (i.e., low phylo-temporal clustering). The interaction of these factors is particularly important for least-squares dating and Bayesian estimation of evolutionary rates. The three estimation methods produced consistent estimates of rates across most of the six mitogenomic data sets, with sequence data from horses being an exception. Conclusions We recommend that phylogenetic studies of ancient DNA sequences should use multiple methods of inference and test for the presence of temporal signal, among-lineage rate variation, and phylo-temporal clustering in the data. Electronic supplementary material The online version of this article (10.1186/s12862-018-1192-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- K Jun Tong
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
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Wutke S, Sandoval-Castellanos E, Benecke N, Döhle HJ, Friederich S, Gonzalez J, Hofreiter M, Lõugas L, Magnell O, Malaspinas AS, Morales-Muñiz A, Orlando L, Reissmann M, Trinks A, Ludwig A. Decline of genetic diversity in ancient domestic stallions in Europe. SCIENCE ADVANCES 2018; 4:eaap9691. [PMID: 29675468 PMCID: PMC5906072 DOI: 10.1126/sciadv.aap9691] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/01/2018] [Indexed: 05/12/2023]
Abstract
Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.
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Affiliation(s)
- Saskia Wutke
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Department of Environmental and Biological Sciences, University of Eastern Finland, 80101 Joensuu, Finland
| | | | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, 14195 Berlin, Germany
| | - Hans-Jürgen Döhle
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt—Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt—Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Javier Gonzalez
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Michael Hofreiter
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, Rüütli 10, 10130 Tallinn, Estonia
| | - Ola Magnell
- National Historical Museums, Contract Archaeology, 226 60 Lund, Sweden
| | | | | | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
- Université de Toulouse, Université Paul Sabatier, Laboratoire Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Toulouse, France
| | - Monika Reissmann
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University Berlin, 10115 Berlin, Germany
| | - Alexandra Trinks
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Corresponding author.
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Gaunitz C, Fages A, Hanghøj K, Albrechtsen A, Khan N, Schubert M, Seguin-Orlando A, Owens IJ, Felkel S, Bignon-Lau O, de Barros Damgaard P, Mittnik A, Mohaseb AF, Davoudi H, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Crubézy E, Benecke N, Olsen S, Brown D, Anthony D, Massy K, Pitulko V, Kasparov A, Brem G, Hofreiter M, Mukhtarova G, Baimukhanov N, Lõugas L, Onar V, Stockhammer PW, Krause J, Boldgiv B, Undrakhbold S, Erdenebaatar D, Lepetz S, Mashkour M, Ludwig A, Wallner B, Merz V, Merz I, Zaibert V, Willerslev E, Librado P, Outram AK, Orlando L. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 2018; 360:111-114. [DOI: 10.1126/science.aao3297] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/31/2018] [Indexed: 12/28/2022]
Abstract
The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.
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Csizmár N, Mihók S, Jávor A, Kusza S. Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing. PeerJ 2018; 6:e4198. [PMID: 29404201 PMCID: PMC5797449 DOI: 10.7717/peerj.4198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 12/05/2017] [Indexed: 11/20/2022] Open
Abstract
Background The Hungarian draft is a horse breed with a recent mixed ancestry created in the 1920s by crossing local mares with draught horses imported from France and Belgium. The interest in its conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks. Methods To genetically characterize the breed and to set up the basis for a conservation program, in the present study a hypervariable region of the mitochrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed. Results One hundred and sixty-four haplotypes and thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (Hd = 0.954 ± 0.004; π = 0.028 ± 0.0004) were identified in Hungarian population, although they were higher within than among the different populations (Hd = 0.972 ± 0.002; π = 0.03097 ± 0.002). Fourteen of the previously observed seventeen haplogroups were detected. Discussion Our samples showed a large intra- and interbreed variation. There was no clear clustering on the median joining network figure. The overall information collected in this work led us to consider that the genetic scenario observed for Hungarian draft breed is more likely the result of contributions from ‘ancestrally’ different genetic backgrounds. This study could contribute to the development of a breeding plan for Hungarian draft horses and help to formulate a genetic conservation plan, avoiding inbreeding while.
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Affiliation(s)
- Nikolett Csizmár
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
| | - Sándor Mihók
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
| | - András Jávor
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
| | - Szilvia Kusza
- Institute of Animal Husbandry, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
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38
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Heintzman PD, Zazula GD, MacPhee RDE, Scott E, Cahill JA, McHorse BK, Kapp JD, Stiller M, Wooller MJ, Orlando L, Southon J, Froese DG, Shapiro B. A new genus of horse from Pleistocene North America. eLife 2017; 6. [PMID: 29182148 PMCID: PMC5705217 DOI: 10.7554/elife.29944] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/02/2017] [Indexed: 11/19/2022] Open
Abstract
The extinct ‘New World stilt-legged’, or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here, we report complete mitochondrial and partial nuclear genomes from NWSL equids from across their geographic range. Although multiple NWSL equid species have been named, our palaeogenomic and morphometric analyses support the idea that there was only a single species of middle to late Pleistocene NWSL equid, and demonstrate that it falls outside of crown group Equus. We therefore propose a new genus, Haringtonhippus, for the sole species H. francisci. Our combined genomic and phenomic approach to resolving the systematics of extinct megafauna will allow for an improved understanding of the full extent of the terminal Pleistocene extinction event. The horse family – which also includes zebras, donkeys and asses – is often featured on the pages of textbooks about evolution. All living horses belong to a group, or genus, called Equus. The fossil record shows how the ancestors of these animals evolved from dog-sized, three-toed browsers to larger, one-toed grazers. This process took around 55 million years, and many members of the horse family tree went extinct along the way. Nevertheless, the details of the horse family tree over the past 2.5 million years remain poorly understood. In North America, horses from this period – which is referred to as the Pleistocene – have been classed into two major groups: stout-legged horses and stilt-legged horses. Both groups became extinct near the end of the Pleistocene in North America, and it was not clear how they relate to one another. Based on their anatomy, many scientists suggested that stilt-legged horses were most closely related to modern-day asses living in Asia. Yet, other studies using ancient DNA placed the stilt-legged horses closer to the stout-legged horses. Heintzman et al. set out to resolve where the stilt-legged horses sit within the horse family tree by examining more ancient DNA than the previous studies. The analyses showed that the stilt-legged horses were much more distinct than previously thought. In fact, contrary to all previous findings, these animals actually belonged outside of the genus Equus. Heintzman et al. named the new genus for the stilt-legged horses Haringtonhippus, and showed that all stilt-legged horses belonged to a single species within this genus, Haringtonhippus francisci. Together these new findings provide a benchmark for reclassifying problematic fossil groups across the tree of life. A similar approach could be used to resolve the relationships in other problematic groups of Pleistocene animals, such as mammoths and bison. This would give scientists a more nuanced understanding of evolution and extinction during this period.
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Affiliation(s)
- Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States.,Tromsø University Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Grant D Zazula
- Yukon Palaeontology Program, Government of Yukon, Whitehorse, Canada
| | - Ross DE MacPhee
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, United States
| | - Eric Scott
- Cogstone Resource Management, Incorporated, Riverside, United States.,California State University San Bernardino, San Bernardino, United States
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States
| | - Brianna K McHorse
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States
| | - Mathias Stiller
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States.,Department of Translational Skin Cancer Research, German Consortium for Translational Cancer Research, Essen, Germany
| | - Matthew J Wooller
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, United States.,Alaska Stable Isotope Facility, Water and Environmental Research Center, University of Alaska Fairbanks, Fairbanks, United States
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, København K, Denmark.,Université Paul Sabatier, Université de Toulouse, Toulouse, France
| | - John Southon
- Keck-CCAMS Group, Earth System Science Department, University of California, Irvine, Irvine, United States
| | - Duane G Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States.,UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, United States
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Cieslak J, Wodas L, Borowska A, Cothran EG, Khanshour AM, Mackowski M. Characterization of the Polish Primitive Horse (Konik) maternal lines using mitochondrial D-loop sequence variation. PeerJ 2017; 5:e3714. [PMID: 28852595 PMCID: PMC5572418 DOI: 10.7717/peerj.3714] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/28/2017] [Indexed: 11/20/2022] Open
Abstract
The Polish Primitive Horse (PPH, Konik) is a Polish native horse breed managed through a conservation program mainly due to its characteristic phenotype of a primitive horse. One of the most important goals of PPH breeding strategy is the preservation and equal development of all existing maternal lines. However, until now there was no investigation into the real genetic diversity of 16 recognized PPH dam lines using mtDNA sequence variation. Herein, we describe the phylogenetic relationships between the PPH maternal lines based upon partial mtDNA D-loop sequencing of 173 individuals. Altogether, 19 mtDNA haplotypes were detected in the PPH population. Five haplotypes were putatively novel while the remaining 14 showed the 100% homology with sequences deposited in the GenBank database, represented by both modern and primitive horse breeds. Generally, comparisons found the haplotypes conformed to 10 different recognized mtDNA haplogroups (A, B, E, G, J, M, N, P, Q and R). A multi-breed analysis has indicated the phylogenetic similarity of PPH and other indigenous horse breeds derived from various geographical regions (e.g., Iberian Peninsula, Eastern Europe and Siberia) which may support the hypothesis that within the PPH breed numerous ancestral haplotypes (found all over the world) are still present. Only in the case of five maternal lines (Bona, Dzina I, Geneza, Popielica and Zaza) was the segregation of one specific mtDNA haplotype observed. The 11 remaining lines showed a higher degree of mtDNA haplotype variability (2-5 haplotypes segregating in each line). This study has revealed relatively high maternal genetic diversity in the small, indigenous PPH breed (19 haplotypes, overall HapD = 0.92). However, only some traditionally distinguished maternal lines can be treated as genetically pure. The rest show evidence of numerous mistakes recorded in the official PPH pedigrees. This study has proved the importance of maternal genetic diversity monitoring based upon the application of molecular mtDNA markers and can be useful for proper management of the PPH conservation program in the future.
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Affiliation(s)
- Jakub Cieslak
- Department of Horse Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Lukasz Wodas
- Department of Horse Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Alicja Borowska
- Department of Horse Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Ernest G Cothran
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Science, Texas A&M University, College Station, TX, United States of America
| | - Anas M Khanshour
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Science, Texas A&M University, College Station, TX, United States of America.,Texas Scottish Rite Hospital for Children, Dallas, TX, United States of America
| | - Mariusz Mackowski
- Department of Horse Breeding, Poznan University of Life Sciences, Poznan, Poland.,Horse Genetic Markers Laboratory, Poznan University of Life Sciences, Poznan, Poland
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40
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Wallner B, Palmieri N, Vogl C, Rigler D, Bozlak E, Druml T, Jagannathan V, Leeb T, Fries R, Tetens J, Thaller G, Metzger J, Distl O, Lindgren G, Rubin CJ, Andersson L, Schaefer R, McCue M, Neuditschko M, Rieder S, Schlötterer C, Brem G. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions. Curr Biol 2017; 27:2029-2035.e5. [PMID: 28669755 DOI: 10.1016/j.cub.2017.05.086] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/19/2017] [Accepted: 05/26/2017] [Indexed: 11/25/2022]
Abstract
The Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence diversity in horses has prevented the reconstruction of stallion genealogies [1, 2]. Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the male-specific region of the Y chromosome (MSY) in 52 horses from 21 breeds. Based on highly accurate pedigree data, we estimated the de novo mutation rate of the horse MSY and showed that various modern horse Y chromosome lineages split much later than the domestication of the species. Apart from few private northern European haplotypes, all modern horse breeds clustered together in a roughly 700-year-old haplogroup that was transmitted to Europe by the import of Oriental stallions. The Oriental horse group consisted of two major subclades: the Original Arabian lineage and the Turkoman horse lineage. We show that the English Thoroughbred MSY was derived from the Turkoman lineage and that English Thoroughbred sires are largely responsible for the predominance of this haplotype in modern horses.
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Affiliation(s)
- Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria.
| | - Nicola Palmieri
- Institut für Populationsgenetik, University of Veterinary Medicine Vienna, Vienna 1210, Austria; Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Elif Bozlak
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Thomas Druml
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Ruedi Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising 85354, Germany
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel 24098, Germany; Functional Breeding Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen 37077, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel 24098, Germany
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover 30559, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover 30559, Germany
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Leif Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4461, USA
| | - Robert Schaefer
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN 55108, USA
| | - Molly McCue
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, Avenches 1580, Switzerland
| | - Christian Schlötterer
- Institut für Populationsgenetik, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
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41
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The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics 2017; 204:423-434. [PMID: 27729493 DOI: 10.1534/genetics.116.194860] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/17/2016] [Indexed: 12/21/2022] Open
Abstract
The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses.
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Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. Ancient genomic changes associated with domestication of the horse. Science 2017; 356:442-445. [DOI: 10.1126/science.aam5298] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Ancient genomics of horse domesticationThe domestication of the horse was a seminal event in human cultural evolution. Libradoet al.obtained genome sequences from 14 horses from the Bronze and Iron Ages, about 2000 to 4000 years ago, soon after domestication. They identified variants determining coat color and genes selected during the domestication process. They could also see evidence of admixture with archaic horses and the demography of the domestication process, which included the accumulation of deleterious variants. The horse appears to have undergone a different type of domestication process than animals that were domesticated simply for food.Science, this issue p.442
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Affiliation(s)
- Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Charleen Gaunitz
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Mélanie Pruvost
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris Diderot, 75205 Paris cedex 13, France
| | - Anders Albrechtsen
- Bioinformatics Center, Department of Biology, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Antoine Fages
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Naveed Khan
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | | | - Aitor Serres-Armero
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Lukas F. K. Kuderna
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Inna S. Povolotskaya
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- National High-Throughput DNA Sequencing Center, Copenhagen, Denmark
| | - Sébastien Lepetz
- Centre National de la Recherche Scientifique, Muséum national d’histoire naturelle, Sorbonne Universités, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 55 rue Buffon, 75005 Paris, France
| | | | - Catherine Thèves
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Saleh Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed H. Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khaled Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, 1580 Avenches, Switzerland
| | - Zainolla Samashev
- Branch of Institute of Archaeology Margulan, Republic Avenue 24-405, 010000 Astana, Republic of Kazakhstan
| | - Henri-Paul Francfort
- CNRS, UMR 7041 Archéologie et Sciences de l’Antiquité, Archéologie de l'Asie Centrale, Maison René Ginouvès, 21 allée de l’Université, 92023 Nanterre, France
| | - Norbert Benecke
- German Archaeological Institute, Department of Natural Sciences, Berlin, 14195 Berlin, Germany
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin 10315, Germany
| | - Christine Keyser
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - Bertrand Ludes
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut Médico-Légal, Université Paris Descartes, Paris, France
| | - Eric Crubézy
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
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Yoon SH, Kim J, Shin D, Cho S, Kwak W, Lee HK, Park KD, Kim H. Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics. Mol Biol Rep 2017; 44:233-242. [PMID: 28432484 DOI: 10.1007/s11033-017-4101-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 08/16/2016] [Indexed: 11/30/2022]
Abstract
The Korean native horse (Jeju horse) is one of the most important animals in Korean historical, cultural, and economical viewpoints. In the early 1980s, the Jeju horse was close to extinction. The aim of this study is to explore the phylogenomics of Korean native horse focusing on spatio-temporal dynamics. We determined complete mitochondrial genome sequences for the first Korean native (n = 6) and additional Mongolian (n = 2) horses. Those sequences were analyzed together with 143 published ones using Bayesian coalescent approach as well as three different phylogenetic analysis methods, Bayesian inference, maximum likelihood, and neighbor-joining methods. The phylogenomic trees revealed that the Korean native horses had multiple origins and clustered together with some horses from four European and one Middle Eastern breeds. Our phylogenomic analyses also supported that there was no apparent association between breed or geographic location and the evolution of global horses. Time of the most recent common ancestor of the Korean native horse was approximately 13,200-63,200 years, which was much younger than 0.696 My of modern horses. Additionally, our results showed that all global horse lineages including Korean native horse existed prior to their domestication events occurred in about 6000-10,000 years ago. This is the first study on phylogenomics of the Korean native horse focusing on spatio-temporal dynamics. Our findings increase our understanding of the domestication history of the Korean native horses, and could provide useful information for horse conservation projects as well as for horse genomics, emergence, and the geographical distribution.
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Affiliation(s)
- Sook Hee Yoon
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Jaemin Kim
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Donghyun Shin
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Seoae Cho
- C&K Genomics, Seoul National University Mt.4-2, Main Bldg. #514, SNU Research Park, NakSeoungDae, Gwanakgu, Seoul, 151-919, Republic of Korea
| | - Woori Kwak
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Hak-Kyo Lee
- The Animal Genomics and Breeding Center, Chonbuk National University, Jeonju, 561-756, Republic of Korea
| | - Kyoung-Do Park
- Genomic Informatics Center, Hankyong National University, Anseong, 456-749, Republic of Korea.
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea. .,C&K Genomics, Seoul National University Mt.4-2, Main Bldg. #514, SNU Research Park, NakSeoungDae, Gwanakgu, Seoul, 151-919, Republic of Korea.
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44
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Lin X, Zheng HX, Davie A, Zhou S, Wen L, Meng J, Zhang Y, Aladaer Q, Liu B, Liu WJ, Yao XK. Association of low race performance with mtDNA haplogroup L3b of Australian thoroughbred horses. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:323-330. [PMID: 28129729 DOI: 10.1080/24701394.2016.1278535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mitochondrial DNA (mtDNA) encodes the genes for respiratory chain sub-units that determine the efficiency of oxidative phosphorylation in mitochondria. The aim of this study was to determine if there were any haplogroups and variants in mtDNA that could be associated with athletic performance of Thoroughbred horses. The whole mitochondrial genomes of 53 maternally unrelated Australian Thoroughbred horses were sequenced and an association study was performed with the competition histories of 1123 horses within their maternal lineages. A horse mtDNA phylogenetic tree was constructed based on a total of 195 sequences (including 142 from previous reports). The association analysis showed that the sample groups with poor racing performance history were enriched in haplogroup L3b (p = .0003) and its sub-haplogroup L3b1a (p = .0007), while those that had elite performance appeared to be not significantly associated with haplogroups G2 and L3a1a1a (p > .05). Haplogroup L3b and L3b1a bear two and five specific variants of which variant T1458C (site 345 in 16s rRNA) is the only potential functional variant. Furthermore, secondary reconstruction of 16s RNA showed considerable differences between two types of 16s RNA molecules (with and without T1458C), indicating a potential functional effect. The results suggested that haplogroup L3b, could have a negative association with elite performance. The T1458C mutation harboured in haplogroup L3b could have a functional effect that is related to poor athletic performance.
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Affiliation(s)
- Xiang Lin
- a Tianjin Key Laboratory of Exercise Physiology and Sports Medicine , Tianjin University of Sports , Tianjin , P.R. China
| | - Hong-Xiang Zheng
- b State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences , Fudan University , Shanghai , P.R.China
| | - Allan Davie
- c School of Health and Human Sciences , Southern Cross University , Lismore , New South Wales , Australia
| | - Shi Zhou
- c School of Health and Human Sciences , Southern Cross University , Lismore , New South Wales , Australia
| | - Li Wen
- a Tianjin Key Laboratory of Exercise Physiology and Sports Medicine , Tianjin University of Sports , Tianjin , P.R. China
| | - Jun Meng
- d College of Animal Sciences , Xinjiang Agricultural University , Urumuqi , China
| | - Yong Zhang
- a Tianjin Key Laboratory of Exercise Physiology and Sports Medicine , Tianjin University of Sports , Tianjin , P.R. China
| | - Qimude Aladaer
- e Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences , Urumqi , China
| | - Bin Liu
- e Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences , Urumqi , China
| | - Wu-Jun Liu
- d College of Animal Sciences , Xinjiang Agricultural University , Urumuqi , China
| | - Xin-Kui Yao
- d College of Animal Sciences , Xinjiang Agricultural University , Urumuqi , China
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Guo X, Bao P, Pei J, Ding X, Liang C, Yan P, Lu D. Complete mitochondrial genome of Qingyang donkey (Equus asinus). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-016-0670-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wutke S, Benecke N, Sandoval-Castellanos E, Döhle HJ, Friederich S, Gonzalez J, Hallsson JH, Hofreiter M, Lõugas L, Magnell O, Morales-Muniz A, Orlando L, Pálsdóttir AH, Reissmann M, Ruttkay M, Trinks A, Ludwig A. Spotted phenotypes in horses lost attractiveness in the Middle Ages. Sci Rep 2016; 6:38548. [PMID: 27924839 PMCID: PMC5141471 DOI: 10.1038/srep38548] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/09/2016] [Indexed: 01/08/2023] Open
Abstract
Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in ~3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.
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Affiliation(s)
- Saskia Wutke
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, 10315 Berlin, Germany
| | - Norbert Benecke
- German Archaeological Institute, Department of Natural Sciences, Berlin, 14195 Berlin, Germany
| | | | - Hans-Jürgen Döhle
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Javier Gonzalez
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Jón Hallsteinn Hallsson
- The Agricultural University of Iceland, Faculty of Land and Animal Resources, IS-112 Reykjavik, Iceland
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, Rüütli 10, 10130 Tallinn, Estonia
| | - Ola Magnell
- National Historical Museums, Contract Archaeology, 226 60 Lund, Sweden
| | | | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Albína Hulda Pálsdóttir
- The Agricultural University of Iceland, Faculty of Land and Animal Resources, IS-112 Reykjavik, Iceland
| | - Monika Reissmann
- Humboldt University Berlin, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, 10115 Berlin, Germany
| | - Matej Ruttkay
- Slovak Academy of Sciences, Institute of Archaeology, 949 21 Nitra, Slovak Republic
| | - Alexandra Trinks
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Arne Ludwig
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, 10315 Berlin, Germany
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Di Lorenzo P, Lancioni H, Ceccobelli S, Curcio L, Panella F, Lasagna E. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Yang Y, Zhu Q, Liu S, Zhao C, Wu C. The origin of Chinese domestic horses revealed with novel mtDNA variants. Anim Sci J 2016; 88:19-26. [PMID: 27071843 DOI: 10.1111/asj.12583] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 09/29/2015] [Accepted: 11/09/2015] [Indexed: 11/27/2022]
Abstract
The origin of domestic horses in China was a controversial issue and several hypotheses including autochthonous domestication, introduction from other areas, and multiple-origins from both introduction and local wild horse introgression have been proposed, but none of them have been fully supported by DNA data. In the present study, mitochondrial DNA (mtDNA) sequences of 714 Chinese indigenous horses were analyzed. The results showed that Chinese domestic horses harbor some novel mtDNA haplogroups and suggested that local domestication events may have occurred, but they are not the dominant haplogroups and the geographical distributions of the novel mtDNA haplogroups were rather restricted. Conclusively, our results support the hypothesis that the domestic horses in China originated from both the introduced horses from outside of China and the local wild horses' introgression into the domestic populations. Results of genetic diversity analysis suggested a possibility that the introduced horses entered China through northern regions from the Eurasian steppe.
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Affiliation(s)
- Yunzhou Yang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Qiyun Zhu
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | - Shuqin Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chunjiang Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key laboratory of Animal Breeding and Genetics of Ministry of Agriculture, P.R. China
| | - Changxin Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key laboratory of Animal Breeding and Genetics of Ministry of Agriculture, P.R. China
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Colli L, Lancioni H, Cardinali I, Olivieri A, Capodiferro MR, Pellecchia M, Rzepus M, Zamani W, Naderi S, Gandini F, Vahidi SMF, Agha S, Randi E, Battaglia V, Sardina MT, Portolano B, Rezaei HR, Lymberakis P, Boyer F, Coissac E, Pompanon F, Taberlet P, Ajmone Marsan P, Achilli A. Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomics 2015; 16:1115. [PMID: 26714643 PMCID: PMC4696231 DOI: 10.1186/s12864-015-2342-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/22/2015] [Indexed: 01/31/2023] Open
Abstract
Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago. Conclusions Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2342-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Licia Colli
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy.
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy.
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Marco Rosario Capodiferro
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. .,Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Marco Pellecchia
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Marcin Rzepus
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Institute of Food Science and Nutrition - ISAN, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Wahid Zamani
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. .,Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran, 46414-356, Iran.
| | - Saeid Naderi
- Natural Resources Faculty, University of Guilan, Guilan, 41335-1914, Iran.
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. .,School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK.
| | | | - Saif Agha
- Department of Animal Production, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt.
| | - Ettore Randi
- Laboratorio di Genetica, Istituto per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, 40064, Italy. .,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, DK-9000, Denmark.
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy.
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy.
| | - Hamid Reza Rezaei
- Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Gorgan, 49138-15739, Iran.
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Iraklio, Crete, 71409, Greece.
| | - Frédéric Boyer
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Eric Coissac
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - François Pompanon
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Pierre Taberlet
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Paolo Ajmone Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. .,Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
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