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Smith, B. P., Cairns, K. M., Adams, J. W., Newsome, T. M., Fillios, M., Deaux, E. C., . . . Crowther, M. S. (2019). Taxonomic status of the Australian dingo: the case for Canis dingo Meyer, 1793. Zootaxa, 4564(1), 173-197
Open this publication in new window or tab >>Taxonomic status of the Australian dingo: the case for Canis dingo Meyer, 1793
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2019 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, Vol. 4564, no 1, p. 173-197Article in journal (Refereed) Published
Abstract [en]

The taxonomic status and systematic nomenclature of the Australian dingo remain contentious, resulting in decades of inconsistent applications in the scientific literature and in policy. Prompted by a recent publication calling for dingoes to be considered taxonomically as domestic dogs (Jackson et al. 2017, Zootaxa 4317, 201-224), we review the issues of the taxonomy applied to canids, and summarise the main differences between dingoes and other canids. We conclude that (1) the Australian dingo is a geographically isolated (allopatric) species from all other Canis, and is genetically, phenotypically, ecologically, and behaviourally distinct; and (2) the dingo appears largely devoid of many of the signs of domestication, including surviving largely as a wild animal in Australia for millennia. The case of defining dingo taxonomy provides a quintessential example of the disagreements between species concepts (e.g., biological, phylogenetic, ecological, morphological). Applying the biological species concept sensu stricto to the dingo as suggested by Jackson et al. (2017) and consistently across the Canidae would lead to an aggregation of all Canis populations, implying for example that dogs and wolves are the same species. Such an aggregation would have substantial implications for taxonomic clarity, biological research, and wildlife conservation. Any changes to the current nomen of the dingo (currently Canis dingo Meyer, 1793), must therefore offer a strong, evidence-based argument in favour of it being recognised as a subspecies of Canis lupus Linnaeus, 1758, or as Canis familiaris Linnaeus, 1758, and a successful application to the International Commission for Zoological Nomenclature - neither of which can be adequately supported. Although there are many species concepts, the sum of the evidence presented in this paper affirms the classification of the dingo as a distinct taxon, namely Canis dingo.

Place, publisher, year, edition, pages
MAGNOLIA PRESS, 2019
Keywords
dingo, dog, canid, Canidae, domestication, hybridisation, nomenclature, species concept, taxonomy
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-247815 (URN)10.11646/zootaxa.4564.1.6 (DOI)000460137200006 ()2-s2.0-85062445940 (Scopus ID)
Note

QC 20190401

Available from: 2019-04-01 Created: 2019-04-01 Last updated: 2019-04-01Bibliographically approved
Arendt, M., Cairns, K. M., Ballard, J. W., Savolainen, P. & Axelsson, E. (2016). Diet adaptation in dog reflects spread of prehistoric agriculture. Heredity, 117(5), 301-306
Open this publication in new window or tab >>Diet adaptation in dog reflects spread of prehistoric agriculture
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2016 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 117, no 5, p. 301-306Article in journal (Refereed) Published
Abstract [en]

Adaptations allowing dogs to thrive on a diet rich in starch, including a significant AMY2B copy number gain, constituted a crucial step in the evolution of the dog from the wolf. It is however not clear whether this change was associated with the initial domestication, or represents a secondary shift related to the subsequent development of agriculture. Previous efforts to study this process were based on geographically limited data sets and low-resolution methods, and it is therefore not known to what extent the diet adaptations are universal among dogs and whether there are regional differences associated with alternative human subsistence strategies. Here we use droplet PCR to investigate worldwide AMY2B copy number diversity among indigenous as well as breed dogs and wolves to elucidate how a change in dog diet was associated with the domestication process and subsequent shifts in human subsistence. We find that AMY2B copy numbers are bimodally distributed with high copy numbers (median 2n AMY2B =11) in a majority of dogs but no, or few, duplications (median 2n AMY2B =3) in a small group of dogs originating mostly in Australia and the Arctic. We show that this pattern correlates geographically to the spread of prehistoric agriculture and conclude that the diet change may not have been associated with initial domestication but rather the subsequent development and spread of agriculture to most, but not all regions of the globe.

Place, publisher, year, edition, pages
Nature Publishing Group, 2016
Keywords
Canidae, Canis familiaris
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-195211 (URN)10.1038/hdy.2016.48 (DOI)000385835900001 ()2-s2.0-84978160744 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20161118

Available from: 2016-11-18 Created: 2016-11-02 Last updated: 2017-11-29Bibliographically approved
Wang, G.-D., Zhai, W., Yang, H.-C., Wang, L., Zhong, L., Liu, Y.-H., . . . Zhang, Y.-P. (2016). Out of southern East Asia: the natural history of domestic dogs across the world. Cell Research, 26(1), 21-33
Open this publication in new window or tab >>Out of southern East Asia: the natural history of domestic dogs across the world
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2016 (English)In: Cell Research, ISSN 1001-0602, E-ISSN 1748-7838, Vol. 26, no 1, p. 21-33Article in journal (Refereed) Published
Abstract [en]

The origin and evolution of the domestic dog remains a controversial question for the scientific community, with basic aspects such as the place and date of origin, and the number of times dogs were domesticated, open to dispute. Using whole genome sequences from a total of 58 canids (12 gray wolves, 27 primitive dogs from Asia and Africa, and a collection of 19 diverse breeds from across the world), we find that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern East Asia 33 000 years ago. Around 15 000 years ago, a subset of ancestral dogs started migrating to the Middle East, Africa and Europe, arriving in Europe at about 10 000 years ago. One of the out of Asia lineages also migrated back to the east, creating a series of admixed populations with the endemic Asian lineages in northern China before migrating to the New World. For the first time, our study unravels an extraordinary journey that the domestic dog has traveled on earth.

Place, publisher, year, edition, pages
Nature Publishing Group, 2016
Keywords
dog domestication, demography, Chinese indigenous dog, gene flow, artificial selection
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-181365 (URN)10.1038/cr.2015.147 (DOI)000367615200005 ()26667385 (PubMedID)2-s2.0-84953360034 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation
Note

QC 20160205

Available from: 2016-02-05 Created: 2016-02-01 Last updated: 2017-11-30Bibliographically approved
Wang, G.-D., Peng, M.-S., Yang, H.-C., Savolainen, P. & Zhang, Y.-P. (2016). Questioning the evidence for a Central Asian domestication origin of dogs [Letter to the editor]. Proceedings of the National Academy of Sciences of the United States of America, 113(19), E2554-E2555
Open this publication in new window or tab >>Questioning the evidence for a Central Asian domestication origin of dogs
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2016 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 19, p. E2554-E2555Article in journal, Letter (Refereed) Published
Place, publisher, year, edition, pages
National Academy of Sciences, 2016
National Category
Other Biological Topics
Identifiers
urn:nbn:se:kth:diva-187779 (URN)10.1073/pnas.1600225113 (DOI)000375478800003 ()2-s2.0-84966354993 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20160530

Available from: 2016-05-30 Created: 2016-05-30 Last updated: 2017-11-30Bibliographically approved
Ardalan, A., Oskarsson, M. C. R., van Asch, B., Rabakonandriania, E. & Savolainen, P. (2015). African origin for Madagascan dogs revealed by mtDNA analysis. Royal Society Open Science
Open this publication in new window or tab >>African origin for Madagascan dogs revealed by mtDNA analysis
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2015 (English)In: Royal Society Open Science, E-ISSN 2054-5703Article in journal (Refereed) Published
Abstract [en]

Madagascar was one of the last major land masses to be inhabited by humans. It was initially colonized by Austronesian speaking Indonesians 1500–2000 years ago, but subsequent migration from Africa has resulted in approximately equal genetic contributions from Indonesia and Africa, and the material culture has mainly African influences. The dog, along with the pig and the chicken, was part of the Austronesian Neolithic culture, and was furthermore the only domestic animal to accompany humans to every continent in ancient times. To illuminate Madagascan cultural origins and track the initial worldwide dispersal of dogs, we here investigated the ancestry of Madagascan dogs. We analysed mtDNA control region sequences in dogs from Madagascar (n=145) and compared it with that 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 that was also present in sub-Saharan Africa and that the remaining lineages could all be attributed to a likely origin in Africa. By contrast, only 26% of Madagascan dogs shared haplotypes with Indonesian dogs, and one haplotype typical for Austronesian dogs, carried by more than 40% of Indonesian and Polynesian dogs, was absent among the Madagascan dogs. Thus, in contrast to the human population, Madagascan dogs seem to trace their origin entirely from Africa. These results suggest that dogs were not brought to Madagascar by the initial Austronesian speaking colonizers on their transoceanic voyage, but were introduced at a later stage, together with human migration and cultural influence from Africa.

Place, publisher, year, edition, pages
ROYAL SOCIETY OPEN SCIENCE, 2015
Keywords
Canis familiaris; mtDNA; Madagascar; Austronesian expansion; Indian Ocean exchange; cultural diffusion
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-206337 (URN)10.1098/rsos.140552 (DOI)000377965600012 ()2-s2.0-84951157864 (Scopus ID)
Note

QC 20170502

Available from: 2017-04-28 Created: 2017-04-28 Last updated: 2017-05-02Bibliographically approved
Kahles, A., Sarqume, F., Savolainen, P. & Arvestad, L. (2013). Excap: maximization of haplotypic diversity of linked markers. PLoS ONE, 8(11), e79012
Open this publication in new window or tab >>Excap: maximization of haplotypic diversity of linked markers
2013 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 11, p. e79012-Article in journal (Refereed) Published
Abstract [en]

Genetic markers, defined as variable regions of DNA, can be utilized for distinguishing individuals or populations. As long as markers are independent, it is easy to combine the information they provide. For nonrecombinant sequences like mtDNA, choosing the right set of markers for forensic applications can be difficult and requires careful consideration. In particular, one wants to maximize the utility of the markers. Until now, this has mainly been done by hand. We propose an algorithm that finds the most informative subset of a set of markers. The algorithm uses a depth first search combined with a branch-and-bound approach. Since the worst case complexity is exponential, we also propose some data-reduction techniques and a heuristic. We implemented the algorithm and applied it to two forensic caseworks using mitochondrial DNA, which resulted in marker sets with significantly improved haplotypic diversity compared to previous suggestions. Additionally, we evaluated the quality of the estimation with an artificial dataset of mtDNA. The heuristic is shown to provide extensive speedup at little cost in accuracy.

Place, publisher, year, edition, pages
PLOS, 2013
Keywords
Mitochondrial-Dna, Coding Region, Mtdna, Identification, Sequence, Genome
National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:kth:diva-136427 (URN)10.1371/journal.pone.0079012 (DOI)000327162900030 ()24244403 (PubMedID)2-s2.0-84892418349 (Scopus ID)
Funder
Swedish e‐Science Research CenterKnut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20140403

Available from: 2013-12-05 Created: 2013-12-05 Last updated: 2018-01-11Bibliographically approved
Savolainen, P. (2013). Extensive phenotypic diversity among South Chinese dogs. ISRN Evolutionary Biology, 2013(Article ID 621836)
Open this publication in new window or tab >>Extensive phenotypic diversity among South Chinese dogs
2013 (English)In: ISRN Evolutionary Biology, ISSN 2314-4033, Vol. 2013, no Article ID 621836Article in journal (Refereed) Published
Abstract [en]

We describe here a broad diversity in phenotype among dogs in southern China’s rural areas, previously relatively unknown outside of China. These dogs display a much broader spectrum of diversity than is observed for the Indian Pariah Dog and the Australian Dingo, which are of a more uniform type and popularly thought to be typical for South Asian dogs and to represent the primitive morphology of the earliest domestic dogs. We show here that the village dog population of southern China harbors a broad diversity of morphological features, for color, body structure and size, coat texture, ear, and tail set, that are otherwise typically associated with the wide variety of Western dog breeds and assumed to be the result of intense selective breeding. The diversity of southern China’s dogs is cast in the light of mtDNA and Y-chromosome DNA studies showing that the genetic diversity is distinctly higher in southern East Asia than in the rest of the world, indicating that this was the geographical origins of today’s dog. These data suggest that the diverse morphologies of European dogs may have been formed from genetic “building blocks" still present in the dog population of rural southern China.

Place, publisher, year, edition, pages
Hindawi Publishing Corporation, 2013
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-108085 (URN)10.5402/2013/621836 (DOI)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20130122

Available from: 2013-01-22 Created: 2012-12-19 Last updated: 2013-04-15Bibliographically approved
Erdogan, M., Tepeli, C., Brenig, B., Akbulut, M. D., Uguz, C., Savolainen, P. & Ozbeyaz, C. (2013). Genetic variability among native dog breeds in Turkey. Turkish Journal of Biology, 37(2), 176-183
Open this publication in new window or tab >>Genetic variability among native dog breeds in Turkey
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2013 (English)In: Turkish Journal of Biology, ISSN 1300-0152, E-ISSN 1303-6092, Vol. 37, no 2, p. 176-183Article in journal (Refereed) Published
Abstract [en]

In this study, the genetic structures and relationships of native Turkish dog breeds were investigated using 20 polymorphic loci (17 microsatellites and 3 proteins). For this aim, a total of 141 blood samples were taken from Turkish shepherd dogs and Turkish Greyhounds located in several geographical regions of Turkey. Multilocus F-ST values indicated that around 1.92% of the total genetic variation could be explained by breed differences and the remaining 98.08% by differences among individuals. The gene flow between populations within each generation varied between 8.4 (Akbash-White Kars Shepherd dog pairs) and 62.3 (Black-Grey Kars Shepherd dog pairs). Four different groups appeared in the 3-dimensional factorial correspondence analysis, and among these, dogs from the Akbash, Kangal, Kars Shepherd, and Turkish Greyhound breeds grouped in clearly separated clusters in distant parts of the 3-dimensional graph. These results clearly show that Akbash and Kangal Shepherd dogs are different populations with different genetic structures. Therefore, the generalised grouping of Turkish shepherd dogs into a single breed called Anatolian or Turkish shepherd dogs is incorrect.

Keywords
Turkish dog breeds, microsatellite, F-statistics, genetic variability, factorial correspondence analysis, genetic distance
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-125787 (URN)10.3906/biy-1203-64 (DOI)000321227800008 ()2-s2.0-84875490484 (Scopus ID)
Funder
Knut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20130813

Available from: 2013-08-13 Created: 2013-08-13 Last updated: 2017-12-06Bibliographically approved
Niskanen, A. K., Hagström, E., Lohi, H., Ruokonen, M., Esparza-Salas, R., Aspi, J. & Savolainen, P. (2013). MHC variability supports dog domestication from a large number of wolves: high diversity in Asia. Heredity, 110(1), 80-85
Open this publication in new window or tab >>MHC variability supports dog domestication from a large number of wolves: high diversity in Asia
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2013 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 110, no 1, p. 80-85Article in journal (Refereed) Published
Abstract [en]

The process of dog domestication is still somewhat unresolved. Earlier studies indicate that domestic dogs from all over the world have a common origin in Asia. So far, major histocompatibility complex (MHC) diversity has not been studied in detail in Asian dogs, although high levels of genetic diversity are expected at the domestication locality. We sequenced the second exon of the canine MHC gene DLA-DRB1 from 128 Asian dogs and compared our data with a previously published large data set of MHC alleles, mostly from European dogs. Our results show that Asian dogs have a higher MHC diversity than European dogs. We also estimated that there is only a small probability that new alleles have arisen by mutation since domestication. Based on the assumption that all of the currently known 102 DLA-DRB1 alleles come from the founding wolf population, we simulated the number of founding wolf individuals. Our simulations indicate an effective population size of at least 500 founding wolves, suggesting that the founding wolf population was large or that backcrossing has taken place.

Keywords
Asia, MHC, DLA-DRB1, dog, domestication, founding population
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-108089 (URN)10.1038/hdy.2012.67 (DOI)000312496900011 ()2-s2.0-84871089764 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceKnut and Alice Wallenberg Foundation
Note

QC 20140613

Available from: 2012-12-19 Created: 2012-12-19 Last updated: 2017-12-06Bibliographically approved
van Asch, B., Zhang, A.-b., Oskarsson, M. C. R., Klütsch, C. F. C., Amorim, A. & Savolainen, P. (2013). Pre-Columbian origins of Native American dog breeds, with only limited replacement by European dogs, confirmed by mtDNA analysis. Proceedings of the Royal Society of London. Biological Sciences, 280(1766), 20131142
Open this publication in new window or tab >>Pre-Columbian origins of Native American dog breeds, with only limited replacement by European dogs, confirmed by mtDNA analysis
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2013 (English)In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 280, no 1766, p. 20131142-Article in journal (Refereed) Published
Abstract [en]

Dogs were present in pre-Columbian America, presumably brought by early human migrants from Asia. Studies of free-ranging village/street dogs have indicated almost total replacement of these original dogs by European dogs, but the extent to which Arctic, North and South American breeds are descendants of the original population remains to be assessed. Using a comprehensive phylogeographic analysis, we traced the origin of the mitochondrial DNA lineages for Inuit, Eskimo and Greenland dogs, Alaskan Malamute, Chihuahua, xoloitzcuintli and perro sin pelo del Peru, by comparing to extensive samples of East Asian (n = 984) and European dogs (n = 639), and previously published pre-Columbian sequences. Evidence for a pre-Columbian origin was found for all these breeds, except Alaskan Malamute for which results were ambigous. No European influence was indicated for the Arctic breeds Inuit, Eskimo and Greenland dog, and North/South American breeds had at most 30% European female lineages, suggesting marginal replacement by European dogs. Genetic continuity through time was shown by the sharing of a unique haplotype between the Mexican breed Chihuahua and ancient Mexican samples. We also analysed free-ranging dogs, confirming limited pre-Columbian ancestry overall, but also identifying pockets of remaining populations with high proportion of indigenous ancestry, and we provide the first DNA-based evidence that the Carolina dog, a free-ranging population in the USA, may have an ancient Asian origin.

Place, publisher, year, edition, pages
The Royal Society Publishing, 2013
Keywords
dog, mitochondrial DNA, mtDNA, haplotype, America, pre-Columbian
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-125534 (URN)10.1098/rspb.2013.1142 (DOI)000321621000007 ()2-s2.0-84880056979 (Scopus ID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20130812

Available from: 2013-08-12 Created: 2013-08-09 Last updated: 2017-12-06Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-1495-8338

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