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Molecular Profiling of the Population Dynamics: Foundation and Expansion of an Archaic Domesticate
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

"An ‘exponential growth of science’ throughout modern history has been frequently boasted by numerous narcissistic accounts of ‘modern humanity.’ Nonetheless, ‘modern science’ seems to have overwhelmingly compromised on its original promises by fitting into an ‘industrial scheme.’ With this concern, ‘molecular phylogeographics with conservational ambitions’ would look an intact ground for research efforts in a ‘school of biotechnology.’ The dog (Canis familiaris) as an earliest domestic animal has a history of conflicts over its origins and dispersal. Having those disputes addressed, valuable knowledge could be acquired on the nature and dynamics of domestication, and of human societies particularly of pre-agricultural ages. We employed two most widely-used genealogical markers, the mitochondrial DNA (mtDNA) and the non-recombining portion of the Y-chromosome (NRY), to address dog demography. Through 582 bps of mtDNA Control Region, complemented with whole mitochondrial genomes, it was established that almost all maternal lineages of the domestic dog worldwide coalesce to a population of at least 51 and perhaps many more female wolves in Asia South of Yangtze River (ASY) approximately 16,000 years before present (BP). This was based on the presence of a maximal diversity in this area, a descending gradient of diversity outward it, and a ubiquitous population structure everywhere in the world. A closer examination of this portrait in Southwest Asia (SwAsia) and the Fertile Crescent (FC), a region which has supplied persuasive evidence on early presence of the domestic dog, retrieved the same information, with implications for backbreeding with the local wolf population. Meanwhile, analyses of mtDNA dispersal showed that dogs took the long way via land to Madagascar Island, and not together with humans via sea. By the other approach, the NRY data in 14,437 bps length supplemented the mtDNA in reporting the height of diversity from ASY with a founding population of at least 13 male wolves, but expectably produced lower inter-regional differentiation by diversity. Screening of NRY by a SNP assay in the dingoes of Australia Island as a population of feral dogs revealed restricted and similar dispersal patterns for sires and dams. Prospects of ancient, multilocus and whole genome assays with the emerging high-throughput technologies has still more to promise on finer elaborations of these issues."

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2012. , 47 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2012:7
Keyword [en]
Dog, wolf, dingo, mtDNA, NRY, SNP, Madagascar, Australia, domestication
National Category
Genetics
Identifiers
URN: urn:nbn:se:kth:diva-95688ISBN: 978-91-7501-349-7 (print)OAI: oai:DiVA.org:kth-95688DiVA: diva2:529026
Public defence
2012-06-08, Hilarp hörsal, Retzius väg 8, Solna, 13:00 (English)
Opponent
Supervisors
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council
Note

QC 20120529

Available from: 2012-05-29 Created: 2012-05-28 Last updated: 2013-09-24Bibliographically approved
List of papers
1. mtDNA Data Indicate a Single Origin for Dogs South of Yangtze River, Less Than 16,300 Years Ago, from Numerous Wolves
Open this publication in new window or tab >>mtDNA Data Indicate a Single Origin for Dogs South of Yangtze River, Less Than 16,300 Years Ago, from Numerous Wolves
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2009 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 26, no 12, 2849-2864 p.Article in journal (Refereed) Published
Abstract [en]

There is no generally accepted picture of where, when, and how the domestic dog originated. Previous studies of mitochondrial DNA (mtDNA) have failed to establish the time and precise place of origin because of lack of phylogenetic resolution in the so far studied control region (CR), and inadequate sampling. We therefore analyzed entire mitochondrial genomes for 169 dogs to obtain maximal phylogenetic resolution and the CR for 1,543 dogs across the Old World for a comprehensive picture of geographical diversity. Hereby, a detailed picture of the origins of the dog can for the first time be suggested. We obtained evidence that the dog has a single origin in time and space and an estimation of the time of origin, number of founders, and approximate region, which also gives potential clues about the human culture involved. The analyses showed that dogs universally share a common homogenous gene pool containing 10 major haplogroups. However, the full range of genetic diversity, all 10 haplogroups, was found only in southeastern Asia south of Yangtze River, and diversity decreased following a gradient across Eurasia, through seven haplogroups in Central China and five in North China and Southwest (SW)Asia, down to only four haplogroups in Europe. The mean sequence distance to ancestral haplotypes indicates an origin 5,400-16,300 years ago (ya) from at least 51 female wolf founders. These results indicate that the domestic dog originated in southern China less than 16,300 ya, from several hundred wolves. The place and time coincide approximately with the origin of rice agriculture, suggesting that the dogs may have originated among sedentary hunter-gatherers or early farmers, and the numerous founders indicate that wolf taming was an important culture trait.

Keyword
dog, Canis familiaris, domestication, mitochondrial DNA, domestic dog, world dogs, dna, genome, archaeology, sequences, ancestor, east
National Category
Genetics Medical Bioscience
Identifiers
urn:nbn:se:kth:diva-18962 (URN)10.1093/molbev/msp195 (DOI)000271818500018 ()2-s2.0-70450227389 (Scopus ID)
Note

QC 20100525

Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2016-12-09Bibliographically approved
2. Comprehensive study of mtDNA among Southwest Asian dogs contradicts independent domestication of wolf, but implies dog–wolf hybridization
Open this publication in new window or tab >>Comprehensive study of mtDNA among Southwest Asian dogs contradicts independent domestication of wolf, but implies dog–wolf hybridization
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2011 (English)In: Ecology and Evolution, ISSN 2045-7758, Vol. 1, no 3, 373-385 p.Article in journal (Refereed) Published
Abstract [en]

Studies of mitochondrial DNA (mtDNA) diversity indicate explicitly that dogs were domesticated, probably exclusively, in southern East Asia. However, Southwest Asia (SwAsia) has had poor representation and geographical coverage in these studies. Other studies based on archaeological and genome-wide SNP data have suggested an origin of dogs in SwAsia. Hence, it has been suspected that mtDNA evidence for this scenario may have remained undetected. In the first comprehensive investigation of genetic diversity among SwAsian dogs, we analyzed 582 bp of mtDNA for 345 indigenous dogs from across SwAsia, and compared with 1556 dogs across the Old World. We show that 97.4% of SwAsian dogs carry haplotypes belonging to a universal mtDNA gene pool, but that only a subset of this pool, five of the 10 principal haplogroups, is represented in SwAsia. A high frequency of haplogroup B, potentially signifying a local origin, was not paralleled with the high genetic diversity expected for a center of origin. Meanwhile, 2.6% of the SwAsian dogs carried the rare non-universal haplogroup d2. Thus, mtDNA data give no indication that dogs originated in SwAsia through independent domestication of wolf, but dog–wolf hybridization may have formed the local haplogroup d2 within this region. Southern East Asia remains the only region with virtually full extent of genetic variation, strongly indicating it to be the primary and probably sole center of wolf domestication. An origin of dogs in southern East Asia may have been overlooked by other studies due to a substantial lack of samples from this region.

Keyword
Canis familiaris, domestication, fertile crescent, hybridization, mitochondrial DNA
National Category
Ecology
Identifiers
urn:nbn:se:kth:diva-49714 (URN)10.1002/ece3.35 (DOI)000312441000009 ()
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish Research CouncilKnut and Alice Wallenberg Foundation
Note

QC 20111130

Available from: 2011-11-29 Created: 2011-11-29 Last updated: 2013-12-12Bibliographically approved
3. Origins of domestic dog in Southern East Asia is supported by analysis of Y-chromosome DNA
Open this publication in new window or tab >>Origins of domestic dog in Southern East Asia is supported by analysis of Y-chromosome DNA
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2012 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 108, no 5, 507-514 p.Article in journal (Refereed) Published
Abstract [en]

Global mitochondrial DNA (mtDNA) data indicates that the dog originates from domestication of wolf in Asia South of Yangtze River (ASY), with minor genetic contributions from dog-wolf hybridisation elsewhere. Archaeological data and autosomal single nucleotide polymorphism data have instead suggested that dogs originate from Europe and/or South West Asia but, because these datasets lack data from ASY, evidence pointing to ASY may have been overlooked. Analyses of additional markers for global datasets, including ASY, are therefore necessary to test if mtDNA phylogeography reflects the actual dog history and not merely stochastic events or selection. Here, we analyse 14 437 bp of Y-chromosome DNA sequence in 151 dogs sampled worldwide. We found 28 haplotypes distributed in five haplogroups. Two haplogroups were universally shared and included three haplotypes carried by 46% of all dogs, but two other haplogroups were primarily restricted to East Asia. Highest genetic diversity and virtually complete phylogenetic coverage was found within ASY. The 151 dogs were estimated to originate from 13-24 wolf founders, but there was no indication of post-domestication dog-wolf hybridisations. Thus, Y-chromosome and mtDNA data give strikingly similar pictures of dog phylogeography, most importantly that roughly 50% of the gene pools are shared universally but only ASY has nearly the full range of genetic diversity, such that the gene pools in all other regions may derive from ASY. This corroborates that ASY was the principal, and possibly sole region of wolf domestication, that a large number of wolves were domesticated, and that subsequent dog-wolf hybridisation contributed modestly to the dog gene pool.

Place, publisher, year, edition, pages
The Genetics Society, 2012
Keyword
dog, canis familiaris, domestication, Y-chromosome DNA, genetic diversity, phylogeography
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:kth:diva-49715 (URN)10.1038/hdy.2011.114 (DOI)000303001600008 ()22108628 (PubMedID)2-s2.0-84860013652 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish Research CouncilKnut and Alice Wallenberg Foundation
Note
QC 20120509Available from: 2011-11-29 Created: 2011-11-29 Last updated: 2012-05-29Bibliographically approved
4. Narrow genetic basis for the Australian dingo confirmed through analysis of paternal ancestry
Open this publication in new window or tab >>Narrow genetic basis for the Australian dingo confirmed through analysis of paternal ancestry
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2012 (English)In: Genetica, ISSN 0016-6707, E-ISSN 1573-6857, Vol. 140, no 1-3, 65-73 p.Article in journal (Refereed) Published
Abstract [en]

The dingo (Canis lupus dingo) is an iconic animal in the native culture of Australia, but archaeological and molecular records indicate a relatively recent history on the continent. Studies of mitochondrial DNA (mtDNA) imply that the current dingo population was founded by a small population of already tamed dogs from Southeast Asia. However, the maternal genetic data might give a unilateral picture, and the gene pool has yet to be screened for paternal ancestry. We sequenced 14,437 bp of the Y-chromosome (Y-chr) from two dingoes and one New Guinea Singing Dog (NGSD). This positioned dingo and NGSD within the domestic dog Y-chr phylogeny, and produced one haplotype not detected before. With this data, we characterized 47 male dingoes in 30 Y-chr single-nucleotide polymorphism sites using protease-mediated allele-specific extension technology. Only two haplotypes, H3 and H60, were found among the dingoes, at frequencies of 68.1 and 31.9 %, respectively, compared to 27 haplotypes previously established in the domestic dog. While H3 is common among Southeast Asian dogs, H60 was specifically found in dingoes and the NGSD, but was related to Southeast Asian dog Y-chr haplotypes. H3 and H60 were observed exclusively in the western and eastern parts of Australia, respectively, but had a common range in Southeast. Thus, the Y-chr diversity was very low, similar to previous observations for d-loop mtDNA. Overall genetic evidence suggests a very restricted introduction of the first dingoes into Australia, possibly from New Guinea. This study further confirms the dingo as an isolated feral dog.

Keyword
Dingo, Canis familiaris, New Guinea Singing Dog, Y-chromosome, Single Nucleotide Polymorphism (SNP), Protease-mediated Allele-specific Extension (PrASE), Short Interspersed Element (SINE)
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-94527 (URN)10.1007/s10709-012-9658-5 (DOI)000305886800006 ()2-s2.0-84863336209 (Scopus ID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20120730

Available from: 2012-05-10 Created: 2012-05-09 Last updated: 2013-04-15Bibliographically approved
5. African origin for Madagascan dogs revealed by mtDNA analysis
Open this publication in new window or tab >>African origin for Madagascan dogs revealed by mtDNA analysis
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Dogs were the only domestic animals accompanying humans to every continent in ancient time, and was along with pig and chicken part of the Austronesian Neolithic culture. Madagascar was one of the last major land masses to be occupied by humans, 1,500-2,000 years ago. It was initially colonized by Austronesian speaking Indonesians but subsequent migration from Africa has resulted in approximately equal genetic contribution from Indonesia and Africa, and the material culture has mainly African influences. To track the initial worldwide dispersal of dogs and illuminate this part of Madagascan cultural origins we here investigate the ancestry of Malagasy dogs. We analysed mtDNA control region sequences in dogs from Madagascar (n=145) and compared with dogs from potential ancestral populations in Island Southeast Asia (n=219) and sub-Saharan Africa (n=493). We found that 90% of the Madagascan dogs carried a haplotype present also in sub-Saharan Africa, and the remaining lineages could all be attributed to a likely origin in Africa. In contrast, only 26% of Malagasy dogs shared a haplotype with Indonesian dogs, all of which universally occurring haplotypes, and three haplotypes typical for Austronesian dogs, carried by >50% of Indonesian and Polynesian dogs, were carried by only 1% of the Madagscan dogs. Thus, in contrast to the human population, the Madagscan dogs seem to trace its origin entirely from Africa. This indicates that dogs were not brought with the initial Austronesian speaking colonizers on their trans-ocean voyage but introduced at a later stage with the migration and cultural influence from Africa.

National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-94475 (URN)
Note
QS 2012Available from: 2012-05-09 Created: 2012-05-09 Last updated: 2012-05-29Bibliographically approved

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