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  • 1.
    Ardalan, Arman
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kluetsch, Cornelya F. C.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
    Zhang, Ai-bing
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Erdogan, Metin
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Houshmand, Massoud
    Tepeli, Cafer
    Ashtiani, Seyed Reza Miraei
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Comprehensive study of mtDNA among Southwest Asian dogs contradicts independent domestication of wolf, but implies dog–wolf hybridization2011In: Ecology and Evolution, E-ISSN 2045-7758, Vol. 1, no 3, p. 373-385Article in journal (Refereed)
    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.

  • 2. Gvozdik, Vaclav
    et al.
    Moravec, Jiri
    Klütsch, Cornelya
    KTH, School of Biotechnology (BIO), Gene Technology.
    Kotlik, Petr
    Phylogeography of the Middle Eastern tree frogs (Hyla, Hylidae, Amphibia) as inferred from nuclear and mitochondrial DNA variation, with a description of a new species2010In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 55, no 3, p. 1146-1166Article in journal (Refereed)
    Abstract [en]

    Evolutionary relationships of the tree frogs from the Middle East and the demographic histories of their populations were studied using a combination of mitochondrial and nuclear genes. Hyla savignyi and neighboring populations of H. orientalis (former eastern populations of H. arborea) were the main focus taxa. Within H. savignyi, a deep phylogenetic divergence dated about 8.4 Ma was discovered. Southern populations from Yemen, Jordan, southern Syria and extreme north-eastern Israel are hereby described as a new species, H. felixarabica sp. nov. Our study points to a biogeographic connection of the south-western Arabian Peninsula and southern Levant and to the importance of the Dead Sea Rift as a historical barrier geographically separating the new species from H. savignyi. Major genetic breaks revealed within species (H. felixarabica: Yemen vs. Jordan-Syria; H. savignyi sensu stricto: Levant vs. Turkey-Iran) are probably connected to climate changes during the Plio-Pleistocene boundary, while the finer phylogeographic structuring probably resulted from the Quaternary climate oscillations. The Cypriote population of H. savignyi originated from southern Anatolia relatively recently. Hyla orientalis from the southern Black Sea region seems to be genetically quite uniform, although two phylogeographic units with western Turkish and Caucasus-Caspian affinities might be detected. Hyla savignyi and H. orientalis carry signals of population expansions dated to the middle to late Pleistocene, while populations of H. felixarabica seem to have rather been constant in size, which might indicate more stable climatic conditions in the southern regions during the Quaternary.

  • 3.
    Klutsch, Cornelya F. C.
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    de Caprona, M. Dominique Crapon
    The IGF1 small dog haplotype is derived from Middle Eastern grey wolves: a closer look at statistics, sampling, and the alleged Middle Eastern origin of small dogs2010In: BMC Biology, E-ISSN 1741-7007, Vol. 8, p. 119-Article in journal (Refereed)
    Abstract [en]

    This paper is a response to Gray MM, Sutter NB, Ostrander EA, Wayne RK: The IGF1 small dog haplotype is derived from Middle Eastern grey wolves. BMC Biology 2010, 8:16. See research article at http://www.biomedcentral.com/1741-7007/8/16.

  • 4.
    Klütsch, Cornelya
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Misof, B.
    Grosse, W. -R
    Moritz, R. F. A.
    Genetic and morphometric differentiation among island populations of two Norops lizards (Reptilia: Sauria : Polychroticlae) on independently colonized islands of the Islas de Bahia (Honduras)2007In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 34, no 7, p. 1124-1135Article in journal (Refereed)
    Abstract [en]

    Aim: Anole lizards (Reptilia: Sauria: Polychrotidae) display remarkable morphological and genetic differentiation between island populations. Morphological differences between islands are probably due to both adaptive (e.g. differential resource exploitation and intra- or interspecific competition) and non-adaptive differentiation in allopatry. Anoles are well known for their extreme diversity and rapid adaptive speciation on islands. The main aim of this study was to use tests of morphological and genetic differentiation to investigate the population structure and colonization history of islands of the Islas de Bahia, off the coast of Honduras. Location Five populations of Norops bicaorum and Norops lemurinus were sampled, four from islands of the Islas de Bahia and one from the mainland of Honduras. Methods Body size and weight differentiation were measured in order to test for significant differences between sexes and populations. In addition, individuals were genotyped using the amplified fragment length polymorphism technique. Bayesian model-based and assignment/exclusion methods were used to study genetic differentiation between island and mainland populations and to test colonization hypotheses. Results Assignment tests suggested migration from the mainland to the Cayos Cochinos, and from there independently to both Utila and Roatan, whereas migration between Utila and Roatan was lacking. Migration from the mainland to Utila was inferred, but was much less frequent. Morphologically, individuals from Utila appeared to be significantly different in comparison with all other localities. Significant differentiation between males of Roatan and the mainland was found in body size, whereas no significant difference was detected between the mainland and the Cayos Cochinos. Main conclusions Significant genetic and morphological differentiation was found among populations. A stepping-stone model for colonization, in combination with an independent migration to Utila and Roatan, was suggested by assignment tests and was compatible with the observed morphological differentiation.

  • 5.
    Klütsch, Cornelya
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Seppälä, E. H.
    Fall, T.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Gene Technology.
    Hedhammar, Å.
    Lohi, H.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Regional occurrence, high frequency but low diversity of mitochondrial DNA haplogroup d1 suggests a recent dog-wolf hybridization in Scandinavia2011In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 42, no 1, p. 100-103Article in journal (Refereed)
    Abstract [en]

    P>The domestic dog mitochondrial DNA (mtDNA)-gene pool consists of a homogenous mix of haplogroups shared among all populations worldwide, indicating that the dog originated at a single time and place. However, one small haplogroup, subclade d1, found among North Scandinavian/Finnish spitz breeds at frequencies above 30%, has a clearly separate origin. We studied the genetic and geographical diversity for this phylogenetic group to investigate where and when it originated and whether through independent domestication of wolf or dog-wolf crossbreeding. We analysed 582 bp of the mtDNA control region for 514 dogs of breeds earlier shown to harbour d1 and possibly related northern spitz breeds. Subclade d1 occurred almost exclusively among Swedish/Finnish Sami reindeer-herding spitzes and some Swedish/Norwegian hunting spitzes, at a frequency of mostly 60-100%. Genetic diversity was low, with only four haplotypes: a central, most frequent, one surrounded by two haplotypes differing by an indel and one differing by a substitution. The substitution was found in a single lineage, as a heteroplasmic mix with the central haplotype. The data indicate that subclade d1 originated in northern Scandinavia, at most 480-3000 years ago and through dog-wolf crossbreeding rather than a separate domestication event. The high frequency of d1 suggests that the dog-wolf hybrid phenotype had a selective advantage.

  • 6.
    Klütsch, Cornelya
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Seppälä, Eija H.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Gene Technology.
    Lohi, Hannes
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Segregation of point mutation heteroplasmy in the control region of dog mtDNA studied systematically in deep generation pedigrees2011In: International journal of legal medicine, ISSN 0937-9827, E-ISSN 1437-1596, Vol. 125, no 4, p. 527-535Article in journal (Refereed)
    Abstract [en]

    Heteroplasmy, the presence of two or more variants in an organism, may render mitochondrial DNA (mtDNA)-based individual identification challenging in forensic analysis. However, the variation of heteroplasmic proportions and the segregation of heteroplasmic variants through generations and within families have not been systematically described at a large scale in animals such as the domestic dog. Therefore, we performed the largest study to date in domestic dogs and screened a 582-bp-long fragment of the mtDNA control region in 180 individuals in 58 pedigrees for signs of heteroplasmy. We identified three pedigrees (5.17%) with heteroplasmic point mutations. To follow the segregation of the point mutations, we then analyzed 131 samples from these three independent pedigrees and found significant differences in heteroplasmy between generations and among siblings. Frequently (10% of cases), the proportion of one base changed from 0-10% to 80-90% (as judged from Sanger electropherograms) between generations and varied to a similar extent among siblings. We included also a literature review of heteroplasmic and potential mutational hot spot positions in the studied region which showed that all heteroplasmic positions appear to be mutational hot spots. Thus, although heteroplasmy may be used to increase the significance of a match in forensic case work, it may also cause erroneous exclusion of related individuals because of sharp switches from one state to the other within a single generation or among siblings especially in the presented mutational hot spots.

  • 7.
    Oskarsson, Mattias C. R.
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
    Klütsch, Cornelya F. C.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
    Boonyaprakob, Ukadej
    Wilton, Alan
    Tanabe, Yuichi
    Savolainen, Peter
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
    Mitochondrial DNA data indicate an introduction through Mainland Southeast Asia for Australian dingoes and Polynesian domestic dogs2012In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 279, no 1730, p. 967-974Article in journal (Refereed)
    Abstract [en]

    In the late stages of the global dispersal of dogs, dingoes appear in the Australian archaeological record 3500 years BP, and dogs were one of three domesticates brought with the colonization of Polynesia, but the introduction routes to this region remain unknown. This also relates to questions about human history, such as to what extent the Polynesian culture was introduced with the Austronesian expansion from Taiwan or adopted en route, and whether pre-Neolithic Australia was culturally influenced by the surrounding Neolithic world. We investigate these questions by mapping the distribution of the mtDNA founder haplotypes for dingoes (A29) and ancient Polynesian dogs (Arc1 and Arc2) in samples across Southern East Asia (n = 424) and Island Southeast Asia (n = 219). All three haplotypes were found in South China, Mainland Southeast Asia and Indonesia but absent in Taiwan and the Philippines, and the mtDNA diversity among dingoes indicates an introduction to Australia 4600-18 300 years BP. These results suggest that Australian dingoes and Polynesian dogs originate from dogs introduced to Indonesia via Mainland Southeast Asia before the Neolithic, and not from Taiwan together with the Austronesian expansion. This underscores the complex origins of Polynesian culture and the isolation from Neolithic influence of the pre-Neolithic Australian culture.

  • 8. Pang, Jun-Feng
    et al.
    Klütsch, Cornelya
    KTH, School of Biotechnology (BIO), Gene Technology.
    Zou, Xiao-Ju
    Zhang, Ai-bing
    KTH, School of Biotechnology (BIO), Gene Technology.
    Luo, Li-Yang
    Angleby, Helen
    KTH, School of Biotechnology (BIO), Gene Technology.
    Ardalan, Arman
    KTH, School of Biotechnology (BIO), Gene Technology.
    Ekström, Camilla
    KTH, School of Biotechnology (BIO), Gene Technology.
    Sköllermo, Anna
    KTH, School of Biotechnology (BIO), Gene Technology.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    Matsumura, Shuichi
    Leitner, Thomas
    Zhang, Ya-Ping
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    mtDNA Data Indicate a Single Origin for Dogs South of Yangtze River, Less Than 16,300 Years Ago, from Numerous Wolves2009In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 26, no 12, p. 2849-2864Article in journal (Refereed)
    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.

  • 9. Stöck, Matthias
    et al.
    Dubey, Sylvain
    Klütsch, Cornelya
    KTH, School of Biotechnology (BIO), Gene Technology.
    Litvinchuk, Spartak N.
    Scheidt, Ulrich
    Perrin, Nicolas
    Mitochondrial and nuclear phylogeny of circum-Mediterranean tree frogs from the Hyla arborea group2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 49, no 3, p. 1019-1024Article in journal (Refereed)
  • 10. van Asch, Barbara
    et al.
    Zhang, Ai-bing
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Oskarsson, Mattias C. R.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Klütsch, Cornelya F. C.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Amorim, Antonio
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pre-Columbian origins of Native American dog breeds, with only limited replacement by European dogs, confirmed by mtDNA analysis2013In: 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)
    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.

  • 11. van Asch, Barbara
    et al.
    Zhang, Ai-bing
    KTH, School of Biotechnology (BIO), Gene Technology.
    Oskarsson, Mattias
    KTH, School of Biotechnology (BIO), Gene Technology.
    Klütsch, Cornelya
    KTH, School of Biotechnology (BIO), Gene Technology.
    Amorim, António
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    MtDNA analysis confirms early Pre‐Colombian origins of Native AmericandogsManuscript (preprint) (Other academic)
    Abstract [en]

    Dogs were present in Pre‐Columbian America, presumably brought to the New World by early human migrants of Asian origin. However, the extent to which historical Arctic, North and South American breeds, e.g. the Alaskan Malamute, Inuit, Eskimo and Greenland dogs, Xoloitzcuintli, Chihuahua and Perro Sín Pelo del Peru, are descendants of these original dogs or were replaced by European dogs remains to be assessed. Using a comprehensive phylogeographic analysis to trace the origin of their mitochondrial (mt) DNA lineages, these breeds were analysed for 582 bp of the mtDNA control region and compared 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 putative American breeds based on the detection of haplotypes phylogenetically distinct from European haplotypes, exclusive to America, shared only with East Asia, or identical to ancient American sequences. Identical rare haplotypes in ancient and modern samples showed geographic continuity over time in Mexico (Chihuahua) and Alaska (Alaskan Malamute). A European origin for at most 15% of the female lineages was indicated, suggesting marginal replacement by European dogs. We also analysed free‐ranging dogs from the USA and South America. In agreement with a previous study, free ranging dogs in general showed little pre‐Columbian ancestry. However, for several populations an appreciable proportion of indigenous ancestry was indicated. Specifically, we provide the first DNA‐based evidence for an ancient Asian origin of the Carolina Dog, a dingo‐like free‐ranging population in the USA. Numerous dogs were probably brought from Asia, since totally 13 mtDNA haplotypes among extant and ancient American dogs were distinct from haploypes found in Europe.

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