Reconciling the conflicts between mitochondrial DNA haplogroup trees of  Canis lupus

Song, Jiao-Jiao; Wang, Wenzhi; Otecko, Newton O.; Peng, Min‐Sheng; Zhang, Yaping

doi:10.1016/j.fsigen.2016.03.008

Cited by 9 publications

(12 citation statements)

References 19 publications

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“…About 120 sequences, including recent Balkan dogs and wolf populations, as well as ancient Bulgarian and Italian samples, were analyzed by a median-joining network (Figure 4, Table S3). All samples (dogs and wolves) were explored as described previously, from position 15,595–15,784 bp (189 bp) of the first amplified region of HVR1 , according to reference sequence EU789787 [9]; haplotypes were determined according to the classifications of [10] and [42], as well as the MitoToolPy program [43]. The results show that most of the ancient and recent dog haplotypes from clades A and B are similar to recent Balkan wolf haplotypes.…”

Section: Resultsmentioning

confidence: 99%

“…The obtained sequences were manually edited and aligned by MEGA software version 7.0 [41], using the dog mtDNA sequence NC_002008 [40] and EU789787 [9] as references. Sequences were analyzed by polymorphic SNPs, and haplogroups were determined according to [10,42], as well as the MitoToolPy program [43] () with reference sequence EU789787 [9]. The phylogenetic analysis was based on the archaeological dog samples used in this study, as well as on all available ancient DNA dog sequences in GenBank and the Dome tree [5,6,12,13,15,16,17,22,31,32,33,44] (Table S3).…”

Section: Methodsmentioning

confidence: 99%

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Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages

Yankova

Marinov

Neov

et al. 2019

Genes

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The history of dog domestication is still under debate, but it is doubtless the process of an ancient partnership between dogs (Canis familiaris) and humans. Although data on ancient DNA for dog diversity are still incomplete, it is clear that several regional dog populations had formed in Eurasia up to the Holocene. During the Neolithic Revolution and the transition from hunter-gatherer to farmer societies, followed by civilization changes in the Antiquity period, the dog population structure also changed. This process was due to replacement with newly formed dog populations. In this study, we present for the first time mitochondrial data of ancient dog remains from the Early Neolithic (8000 years before present (BP)) to Late Antiquity (up to 3th century AD) from southeastern Europe (the Balkans). A total of 16 samples were analyzed, using the mitochondrial D-loop region (HVR1). The results show the presence of A (70%) and B (25%) clades throughout the Early and Late Neolithic Period. In order to clarify the position of our results within the ancient dog population in Eneolithic Eurasia, we performed phylogenetic analysis with the available genetic data sets. This data showed a similarity of the ancient Bulgarian dogs to Italian (A, B, and C clades) and Iberian (clades A and C) dogs’ populations. A clear border can be seen between southern European genetic dog structure, on the one hand, and on the other hand, central-western (clade C), eastern (clade D) and northern Europe (clades A and C). This corresponds to genetic data for European humans during the same period, without admixture between dog populations. Also, our data have shown the presence of clade B in ancient Eurasia. This is not unexpected, as the B haplogroup is widely distributed in extant Balkan dogs and wolves. The presence of this clade both in dogs and in wolves on the Balkans may be explained with hybridization events before the Neolithic period. The spreading of this clade across Europe, together with the A clade, is related to the possible dissemination of newly formed dog breeds from Ancient Greece, Thrace, and the Roman Empire.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages

Yankova

Marinov

Neov

et al. 2019

Genes

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show abstract

“…Sequences were aligned using the dog mtDNA sequences NC_002008 and EU789787 as reference, following the steps of previously published papers [6,9,51,52]. Haplogroup assignments were determined through a phylogenetic analysis by creating UPGMA trees in MEGA X (Penn State University, PA, USA) [53], using reference samples with well-defined dog matrilines, available from previous studies [54,55]. The haplogroup of the ancient samples analyzed was also tested through the MitoToolPy program [56], with reference sequence EU789787 [57].…”

Section: Haplotype Identification and Phylogenetic Analysesmentioning

confidence: 99%

Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age

Koupadi

Fontani

Ciucani

et al. 2020

Genes

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Dog domestication is still largely unresolved due to time-gaps in the sampling of regions. Ancient Italian canids are particularly understudied, currently represented by only a few specimens. In the present study, we sampled 27 canid remains from Northern Italy dated between the Late Pleistocene and Bronze Age to assess their genetic variability, and thus add context to dog domestication dynamics. They were targeted at four DNA fragments of the hypervariable region 1 of mitochondrial DNA. A total of 11 samples had good DNA preservation and were used for phylogenetic analyses. The dog samples were assigned to dog haplogroups A, C and D, and a Late Pleistocene wolf was set into wolf haplogroup 2. We present our data in the landscape of ancient and modern dog genetic variability, with a particular focus on the ancient Italian samples published thus far. Our results suggest there is high genetic variability within ancient Italian canids, where close relationships were evident between both a ~24,700 years old Italian canid, and Iberian and Bulgarian ancient dogs. These findings emphasize that disentangling dog domestication dynamics benefits from the analysis of specimens from Southern European regions.

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“…The 79 Tibetan Mastiff mtDNA genomes were classified into specific haplogroups by using MitoToolPy (Peng et al, 2015) with reference to DomeTree (http://dometree.kiz.ac.cn) – dog mtDNA haplogroup tree build 2 (Song et al, 2016). The variants for each of mtDNA genomes were also scored with MitoToolPy.…”

Section: Methodsmentioning

confidence: 99%

Long amplicon HiFi sequencing for mitochondrial DNA genomes

Cai

Yin

et al. 2023

Molecular Ecology Resources

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Long‐read sequencing technology is a powerful approach with application in various genetic and genomic research. Herein, we developed the pipeline for long amplicon high‐fidelity (HiFi) sequencing and then applied it for sequencing mitochondrial DNA (mtDNA) genomes from pools of 79 Tibetan Mastiffs. We amplified the mtDNA genome with long‐range PCR using two pairs of primers. Two rounds of circular consensus sequencing (CCS) were conducted and their accuracy was evaluated. The results indicate that the second round of CCS can improve the accuracy of HiFi reads. In addition, the analysis of 79 high‐quality mtDNA genomes shows the Tibetan Mastiffs from outside of the Tibetan Plateau experienced hybridization with other dogs. The high quality reads generator (HQGR) software is provided to facilitate data analyses, which is publicly accessible on GitHub (https://github.com/Caizf-script/HQGR). Our long amplicon HiFi sequencing pipeline can also be applied in various target enrichment strategies for small genomes and candidate genes.

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Reconciling the conflicts between mitochondrial DNA haplogroup trees of Canis lupus

Cited by 9 publications

References 19 publications

Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages

Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages

Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age

Long amplicon HiFi sequencing for mitochondrial DNA genomes

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