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  • 1.
    Angleby, Helen
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Oskarsson, Mattias
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pang, Junfeng
    Zhang, Ya-ping
    Leitner, Thomas
    Braham, Caitlyn
    Arvestad, Lars
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Webb, Kristen M.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Forensic Informativity of similar to 3000bp of Coding Sequence of Domestic Dog mtDNA2014In: Journal of Forensic Sciences, ISSN 0022-1198, E-ISSN 1556-4029, Vol. 59, no 4, p. 898-908Article in journal (Refereed)
    Abstract [en]

    The discriminatory power of the noncoding control region (CR) of domestic dog mitochondrial DNA alone is relatively low. The extent to which the discriminatory power could be increased by analyzing additional highly variable coding regions of the mitochondrial genome (mtGenome) was therefore investigated. Genetic variability across the mtGenome was evaluated by phylogenetic analysis, and the three most variable similar to 1kb coding regions identified. We then sampled 100 Swedish dogs to represent breeds in accordance with their frequency in the Swedish population. A previously published dataset of 59 dog mtGenomes collected in the United States was also analyzed. Inclusion of the three coding regions increased the exclusion capacity considerably for the Swedish sample, from 0.920 for the CR alone to 0.964 for all four regions. The number of mtDNA types among all 159 dogs increased from 41 to 72, the four most frequent CR haplotypes being resolved into 22 different haplotypes.

  • 2.
    Angleby, Helen
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Forensic informativity of domestic dog mtDNA control region sequences2005In: Forensic Science International, ISSN 0379-0738, E-ISSN 1872-6283, Vol. 154, no 03-feb, p. 99-110Article in journal (Refereed)
    Abstract [en]

    We have analysed the genetic information to be obtained from analysis of mitochondrial DNA (mtDNA) in domestic dogs studying the exclusion capacity in different populations and the correlation between mtDNA types and breeds or types of dogs. The exclusion capacities for a 573 bp sequence of the mitochondrial control region was between 0.86 and 0.95 for dogs in Sweden, the UK, Germany, Japan and China. The direct correlation between mtDNA type and breed, type of dog, and geographical origin of breed was generally low, but in some cases certain mtDNA types were overrepresented in one breed, and for wider groupings such as morphologically similar breeds, some mtDNA types were in many cases found in a distinct group of breeds, often originating from the same geographic region. This type of information may be used as an indication of the breed and, with some degree of probability, to include or exclude certain breeds from being the source of evidence materials.

  • 3.
    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 (closed 20130101).
    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, ISSN 2045-7758, 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.

  • 4.
    Ardalan, Arman
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. Division of Animal Biotechnology and Genomics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran.
    Oskarsson, Mattias C. R.
    KTH, School of Biotechnology (BIO), Gene Technology.
    van Asch, Barbara
    Rabakonandriania, Elisabeth
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    African origin for Madagascan dogs revealed by mtDNA analysis2015In: Royal Society Open Science, E-ISSN 2054-5703Article in journal (Refereed)
    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.

  • 5.
    Ardalan, Arman
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Oskarsson, Mattias
    KTH, School of Biotechnology (BIO), Gene Technology.
    Natanaelsson, Christian
    KTH, School of Biotechnology (BIO), Gene Technology.
    Wilton, Alan N.
    Ahmadian, Afshin
    KTH, School of Biotechnology (BIO), Gene Technology.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Narrow genetic basis for the Australian dingo confirmed through analysis of paternal ancestry2012In: Genetica, ISSN 0016-6707, E-ISSN 1573-6857, Vol. 140, no 1-3, p. 65-73Article in journal (Refereed)
    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.

  • 6. Arendt, M.
    et al.
    Cairns, K. M.
    Ballard, J. W. O.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Axelsson, E.
    Diet adaptation in dog reflects spread of prehistoric agriculture2016In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 117, no 5, p. 301-306Article in journal (Refereed)
    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.

  • 7.
    Arvestad, Lars
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
    Visa, N.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    Wieslander, L.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Expressed sequence tags from the midgut and an epithelial cell line of Chironomus tentans: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels2005In: Insect molecular biology (Print), ISSN 0962-1075, E-ISSN 1365-2583, Vol. 14, no 6, p. 689-695Article in journal (Refereed)
    Abstract [en]

    Expressed sequence tags (ESTs) were generated from two Chironomus tentans cDNA libraries, constructed from an embryo epithelial cell line and from larva midgut tissue. 8584 5'-end ESTs were generated and assembled into 3110 tentative unique transcripts, providing the largest contribution of C. tentans sequences to public databases to date. Annotation using BLAST gave 1975 (63.5%) transcripts with a significant match in the major gene/protein databases, 1170 with a best match to Anopheles gambiae and 480 to Drosophila melanogaster. 1091 transcripts (35.1%) had no match to any database. Studies of open reading frames suggest that at least 323 of these contain a coding sequence, indicating that a large proportion of the genes in C. tentans belong to previously unknown gene families.

  • 8. Bulut, Z.
    et al.
    Tepeli, C.
    Nizamlioglu, M.
    Kurar, E.
    Erdogan, M.
    Yilmaz, A.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Microsatellite analysis of Kangal shepherd dogs in Turkey, Uzbekistan, Ajerbaijan and Iran2012In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 279, p. 349-349Article in journal (Other academic)
  • 9. Coward, K.
    et al.
    Ponting, C. P.
    Chang, H. Y.
    Hibbitt, O.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Jones, K. T.
    Parrington, J.
    Phospholipase C zeta, the trigger of egg activation in mammals, is present in a non-mammalian species2005In: Reproduction, ISSN 1470-1626, E-ISSN 1476-3990, Vol. 130, no 2, p. 157-163Article in journal (Refereed)
    Abstract [en]

    The activation of the egg to begin development into an embryo is triggered by a sperm-induced increase in intracellular egg Ca2+. There has been much controversy about how the sperm induces this fundamental developmental event, but recent studies suggest that, in mammals, egg activation is triggered by a testis-specific phospholipase C: PLC zeta. Since the discovery of PLC zeta, it has been unclear whether its role in triggering egg activation is common to all vertebrates, or is confined to mammals. Here, we demonstrate for the first time that PLC zeta is present in a non-mammalian vertebrate. Using genomic and cDNA databases, we have identified the cDNA encoding a PLC zeta orthologue in the domestic chicken that, like the mammalian isoforms, is a testis-specific gene. The chicken PLC zeta cDNA is 2152 bp in size and encodes an open reading frame of 639 amino acids. When injected into mouse oocytes, chicken PLC zeta cRNA triggers Ca2+ oscillations, indicating that it has functional properties similar to those of mammalian PLC zeta. Our findings suggest that PLC zeta may have a universal role in triggering egg activation in vertebrates.

  • 10.
    Dezfouli, Mahya
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Magnusson, M.
    Arvestad, L.
    Lohi, H.
    Van Asch, D.
    Fain, S.
    Kennedy, L. J.
    Ahmadian, Afshin
    KTH, School of Biotechnology (BIO), Gene Technology.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Massively Parallel MHC-Typing by Sequencing RevealedNovel Variants of Canine Leukocyte AntigenManuscript (preprint) (Other academic)
  • 11. Ding, Z. L.
    et al.
    Oskarsson, Mattias
    KTH, School of Biotechnology (BIO), Gene Technology.
    Ardalan, Arman
    KTH, School of Biotechnology (BIO), Gene Technology.
    Angleby, Helen
    KTH, School of Biotechnology (BIO), Gene Technology.
    Dahlgren, Lars-Göran
    KTH, School of Biotechnology (BIO), Gene Technology.
    Tepeli, C.
    Kirkness, E.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Zhang, Y. P.
    Origins of domestic dog in Southern East Asia is supported by analysis of Y-chromosome DNA2012In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 108, no 5, p. 507-514Article in journal (Refereed)
    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.

  • 12. Ellegren, H
    et al.
    Savolainen, Peter
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Rosen, B
    The genetical history of an isolated population of the endangered grey wolf Canis lupus: A study of nuclear and mitochondrial polymorphisms1996In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 351, no 1348, p. 1661-1669Article in journal (Refereed)
    Abstract [en]

    The grey wolf was thought to have been exterminated in the Scandinavian peninsula when the sudden appearance of a few animals in southern Sweden was reported in 1980. These wolves founded a new Swedish population which currently numbers at least 25 individuals, one of the world's smallest populations of the species. The sudden occurrence of the founder animals caused speculation that these had not appeared by 'natural' means but rather were Swedish zoo animals deliberately released by man. To analyse if this was the case and to elucidate the genetic status bi; this small and isolated population, we assessed nuclear and mitochondrial (mt) genetic variability in wild and captive grey wolves, using microsatellite typing and sequence analysis of the mtDNA D-loop. The new population was found to be monomorphic for a mtDNA haplotype which also was present in the Swedish zoo population. A total of four different mtDNA haplotypes were found among all captive and wild wolves (including two animals from an occasional establishment of a few wolves in northern Sweden in the late 1970s), with a maximum sequence divergence of 3.1 %. Despite the mtDNA congruence, animals from the zoo population could most likely be excluded as founders for the wild population since the latter group of animals displayed several unique microsatellite alleles (i.e. alleles not found in the zoo population). Moreover, a phylogenetic analysis of individual wolves, using microsatellite allele sharing as distance measure, placed all wild animals on a branch separated from that of the captive animals. The average degree of nuclear variability as well as allelic diversity was similar in the wild and the captive populations, respectively, but was lower than that reported for North-American populations of grey wolves. Polymorphism has declined in wild wolves born in recent years suggesting that this small population is currently suffering from a loss of genetic variability due to inbreeding. Inbreeding depression is documented in captive wolves and the long-term survival of the wild Swedish population may therefore depend on immigration of animals from Russia. This study illustrates the usefulness of microsatellites for dissecting close genetic relationships and for addressing the genetic status of individuals.

  • 13. Erdogan, Metin
    et al.
    Tepeli, Cafer
    Brenig, Bertram
    Akbulut, Mine Dosay
    Uguz, Cevdet
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ozbeyaz, Ceyhan
    Genetic variability among native dog breeds in Turkey2013In: Turkish Journal of Biology, ISSN 1300-0152, E-ISSN 1303-6092, Vol. 37, no 2, p. 176-183Article in journal (Refereed)
    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.

  • 14. Fitzsimmons, C. J.
    et al.
    Savolainen, Peter
    KTH, Superseded Departments, Biotechnology.
    Amini, Bahram
    KTH, Superseded Departments, Biotechnology.
    Hjalm, G.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Andersson, L.
    Detection of sequence polymorphisms in red junglefowl and White Leghorn ESTs2004In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 35, no 5, p. 391-396Article in journal (Refereed)
    Abstract [en]

    Over 16 000 high quality expressed sequence tags (ESTs) from red junglefowl (RJ) and White Leghorn (WL) brain and testis cDNA libraries were generated. Here, we have used this resource for detection of single nucleotide polymorphisms (SNPs), and also completed full-length sequencing of 46 pairs of clones, representing the same gene from both the RJ and WL libraries. From the main set of ESTs, which were assembled using Phrap, 746 putative SNPs were identified, of which 76% were transitions and 24% were transversions. A subset of SNPs was evaluated by sequence analysis of five RJ and five WL birds. Nine of 12 SNPs were verified in this limited sample, suggesting that a majority of the putative polymorphisms documented in this study represent real SNPs. During full-length sequencing of the 46 RJ/WL clones 100 SNPs were identified, which translated to a frequency of 1.90 SNPs/1000 bp. The number of transitions and transversions were 77% and 23%, respectively, and the proportion of non-synonymous vs. synonymous SNPs was 20% and 80%, respectively. Four large insertions/deletions were identified between the RJ and WL full-length sequences, and they appear to represent different splice variants.

  • 15. Guo, Songchang
    et al.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Su, Jianping
    Zhang, Qian
    Qi, Delin
    Zhou, Jie
    Zhong, Yang
    Zhao, Xinquan
    Liu, Jianquan
    Origin of mitochondrial DNA diversity of domestic yaks2006In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 6Article in journal (Refereed)
    Abstract [en]

    Background: The domestication of plants and animals was extremely important anthropologically. Previous studies have revealed a general tendency for populations of livestock species to include deeply divergent maternal lineages, indicating that they were domesticated in multiple, independent events from genetically discrete wild populations. However, in water buffalo, there are suggestions that a similar deep maternal bifurcation may have originated from a single population. These hypotheses have rarely been rigorously tested because of a lack of sufficient wild samples. To investigate the origin of the domestic yak (Poephagus grunnies), we analyzed 637 bp of maternal inherited mtDNA from 13 wild yaks (including eight wild yaks from a small population in west Qinghai) and 250 domesticated yaks from major herding regions. Results: The domestic yak populations had two deeply divergent phylogenetic groups with a divergence time of > 100,000 yrs BP. We here show that haplotypes clustering with two deeply divergent maternal lineages in domesticated yaks occur in a single, small, wild population. This finding suggests that all domestic yaks are derived from a single wild gene pool. However, there is no clear correlation of the mtDNA phylogenetic clades and the 10 morphological types of sampled yaks indicating that the latter diversified recently. Relatively high diversity was found in Qinghai and Tibet around the current wild distribution, in accordance with previous suggestions that the earliest domestications occurred in this region. Conventional molecular clock estimation led to an unrealistic early dating of the start of the domestication. However, Bayesian estimation of the coalescence time allowing a relaxation of the mutation rate Conclusion: The information gathered here and the previous studies of other animals show that the demographic histories of domestication of livestock species were highly diverse despite the common general feature of deeply divergent maternal lineages. The results further suggest that domestication of local wild prey ungulate animals was a common occurrence during the development of human civilization following the postglacial colonization in different locations of the world, including the high, arid Qinghai-Tibetan Plateau.

  • 16. Hillbertz, Nicolette H. C. Salmon
    et al.
    Isaksson, Magnus
    Karlsson, Elinor K.
    Hellmen, Eva
    Pielberg, Gerli Rosengren
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Wade, Claire M.
    Von Euler, Henrik
    Gustafson, Ulla
    Hedhammar, Ake
    Nilsson, Mats
    Lindblad-Toh, Kerstin
    Andersson, Leif
    Andersson, Goran
    Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in Ridgeback dogs2007In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 39, no 11, p. 1318-1320Article in journal (Refereed)
    Abstract [en]

    The dorsal hair ridge in Rhodesian and Thai Ridgeback dogs is caused by a dominant mutation that also predisposes to the congenital developmental disorder dermoid sinus. Here we show that the causative mutation is a 133-kb duplication involving three fibroblast growth factor (FGF) genes. FGFs play a crucial role in development, suggesting that the ridge and dermoid sinus are caused by dysregulation of one or more of the three FGF genes during development.

  • 17. Ka, S.
    et al.
    Fitzsimmons, C.
    Jacobsson, L.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    Siegel, P. B.
    Andersson, L.
    Hallböök, F.
    Expression analysis of growth and energy regulation-associated genes in two divergent chicken strains2005In: Trends in Comparative Endocrinology and Neurobiology, New York Academy of Sciences, 2005, p. 357-359Conference paper (Refereed)
    Abstract [en]

    We have studied differential expression of genes using cDNA arrays in the hypothalamic region of two divergent chicken lines, which differ in body weight and feeding behavior. Several transcripts from genes in metabolic networks as well as from retroviruses were differentially expressed.

  • 18.
    Kahles, André
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Sarqume, Fahad
    KTH, School of Biotechnology (BIO).
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Arvestad, Lars
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholms universitet.
    Excap: maximization of haplotypic diversity of linked markers2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 11, p. e79012-Article in journal (Refereed)
    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.

  • 19.
    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.

  • 20.
    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 (Print), 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.

  • 21. Koban, Evren
    et al.
    Sarac, Cigdem Goekcek
    Acan, Sinan Can
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Togan, Inci
    Genetic relationship between Kangal, Akbash and other dog populations2009In: Discrete Applied Mathematics, ISSN 0166-218X, E-ISSN 1872-6771, Vol. 157, no 10, p. 2335-2340Article in journal (Refereed)
    Abstract [en]

    Kangal and Akbash dogs are the two well-known shepherd dog breeds in Turkey. In order to contribute to the understanding of the genetic relationship between Kangal dogs, Akbash dogs and the dogs from different regions of Eurasia, 585 base pair (bp) segment of mitochondrial DNA (mtDNA) control region was sequenced from Kangals and Akbashes. Sequences of the Kangal and Akbash dogs examined in the present study were comparatively examined with those of previous studies on dogs. Consensus neighbour-joining tree with bootstrapping, which is constructed based on pairwise F-ST values between populations, indicated that Kangal dogs and Akbash dogs are on different branches of the tree. Furthermore, the nodes of these branches were supported with high bootstrap values. In conclusion, the present study indicated that Kangal and Akbash dogs might have descended maternally from different origins along the evolutionary history of domestic dogs.

  • 22.
    Natanaelsson, Christian
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Oskarsson, Mattias C. R.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Angleby, Helen
    KTH, School of Biotechnology (BIO), Gene Technology.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    Kirkness, Ewen
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery2006In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 7Article in journal (Refereed)
    Abstract [en]

    Background: Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results: The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion: We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and giving a first description of the dog Y-chromosome phylogeny.

  • 23.
    Neiman, Mårten
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundin, Sverker
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Molecular Biotechnology (closed 20130101).
    Ahmadian, Afshin
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Decoding a substantial set of samples in parallel by massive sequencing2011In: Plos One, ISSN 1932-6203, Vol. 6, no 3Article in journal (Refereed)
    Abstract [en]

    The dramatic increase of throughput seen in the eld of sequenceanalysis during the last years has opened up new possibilities of se-quencing a multitude of samples in parallel. Here we present a novelstrategy where the combination of two tags is used to link reads totheir origins in a pool of samples. The two tags are incorporated intwo steps leading to lowering of sample handling complexity by nearly100 times. The method described here enables accurate identi cationand typing of thousands of samples in parallel and is scalable. In thisstudy the system was designed to test 4992 samples using only 122 tags.

    To proof the concept of two tagging method the highly polymor-phic 2nd exon of DLA-DRB1 in dogs and wolves was sequenced usingthe 454 GS FLX Titanium Chemistry. By requiring a minimum se-quence depth of 20 reads per sample, 94% of the successfully ampli edsamples were genotyped. In addition, the method allowed digital de-tection of chimeric fragments. These results demonstrate that it ispossible to sequence thousands of samples in parallel without complexpooling patterns or primer combinations. Furthermore, the method isscalable and increasing the sample size by 960 samples requires only10 additional tags.

  • 24. Niskanen, A. K.
    et al.
    Hagström, Erik
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lohi, H.
    Ruokonen, M.
    Esparza-Salas, R.
    Aspi, J.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    MHC variability supports dog domestication from a large number of wolves: high diversity in Asia2013In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 110, no 1, p. 80-85Article in journal (Refereed)
    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.

  • 25. Nizamlioglu, M.
    et al.
    Bulut, Z.
    Erdogan, M.
    Tepeli, C.
    Yilmaz, A.
    Kurar, E.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Genetic characterization of Akbas shepherd dogs in Turkey, Uzbekistan and Iran using STR markers2012In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 279, p. 349-349Article in journal (Other academic)
  • 26.
    Oskarsson, Mattias
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Ardalan, Arman
    KTH, School of Biotechnology (BIO), Gene Technology.
    Rabakonandriania, Elisabeth
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    African origin for Madagascan dogs revealed by mtDNA analysisManuscript (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.

  • 27.
    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.

  • 28. 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.

  • 29. Rubin, Carl-Johan
    et al.
    Lindberg, Johan
    Fitzsimmons, Carolyn
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Jensen, Per
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    Andersson, Leif
    Kindmark, Andreas
    Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits2007In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 8, p. 208-Article in journal (Refereed)
    Abstract [en]

    Background: Osteoporosis is frequently observed among aging hens from egg-producing strains (layers) of domestic chicken. White Leghorn (WL) has been intensively selected for egg production and it manifests striking phenotypic differences for a number of traits including several bone phenotypes in comparison with the wild ancestor of chicken, the red junglefowl (RJ). Previously, we have identified four Quantitative Trait Loci (QTL) affecting bone mineral density and bone strength in an intercross between RJ and WL. With the aim of further elucidating the genetic basis of bone traits in chicken, we have now utilized cDNA-microarray technology in order to compare global RNA-expression in femoral bone from adult RJ and WL (five of each sex and population). Results: When contrasting microarray data for all WL-individuals to that of all RJ-individuals we observed differential expression (False discovery rate adjusted p-values < 0.015) for 604 microarray probes. In corresponding male and female contrasts, differential expression was observed for 410 and 270 probes, respectively. Altogether, the three contrasts between WL and RJ revealed differential expression of 779 unique transcripts, 57 of which are located to previously identified QTL-regions for bone traits. Some differentially expressed genes have previously been attributed roles in bone metabolism and these were: WNT inhibitory factor I (WIFI), WD repeat-containing protein 5 (WDR5) and Syndecan 3 (SDC3). Among differentially expressed transcripts, those encoding structural ribosomal proteins were highly enriched and all 15 had lower expression in WL. Conclusion: We report the identification of 779 differentially expressed transcripts, several residing within QTL-regions for bone traits. Among differentially expressed transcripts, those encoding structural ribosomal proteins were highly enriched and all had lower expression levels in WL. In addition, transcripts encoding four translation initiation and translation elongation factor proteins also had lower expression levels in WL, possibly indicating perturbation of protein biosynthesis pathways between the two populations. Information derived from this study could be relevant to the bone research field and may also aid in further inference of genetic changes accompanying animal domestication.

  • 30. Sajantila, A
    et al.
    Salem, H
    Savolainen, Peter
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Bauer, K
    Gierig, C
    Paabo, S
    Paternal and maternal DNA lineages reveal a bottleneck in the founding of the Finnish population1996In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 93, no 21, p. 12035-12039Article in journal (Refereed)
    Abstract [en]

    An analysis of Y-chromosomal haplotypes in several European populations reveals an almost monomorphic pattern in the Finns, whereas Y-chromosomal diversity is significantly higher in other populations. Furthermore, analyses of nucleotide positions in the mitochondrial control region that evolve slowly show a decrease in genetic diversity in Finns. Thus, relatively few men and women have contributed the genetic lineages that today survive in the Finnish population. This is likely to have caused the so-called ''Finnish disease heritage''-i.e., the occurrence of several genetic diseases in the Finnish population that are rare elsewhere. A preliminary analysis of the mitochondrial mutations that have accumulated subsequent to the bottleneck suggests that it occurred about 4000 years ago, presumably when populations using agriculture and animal husbandry arrived in Finland.

  • 31.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Domestication of dogs2007In: The Behavioural Biology of Dogs, CABI Publishing, 2007, p. 21-37Chapter in book (Refereed)
  • 32.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Extensive phenotypic diversity among South Chinese dogs2013In: ISRN Evolutionary Biology, ISSN 2314-4033, Vol. 2013, no Article ID 621836Article in journal (Refereed)
    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.

  • 33.
    Savolainen, Peter
    KTH, Superseded Departments, Biotechnology.
    Mitochondrial DNA: analysis of the control region in forensic and population genetic studies1999Doctoral thesis, comprehensive summary (Other scientific)
  • 34.
    Savolainen, Peter
    et al.
    KTH, Superseded Departments, Biotechnology.
    Arvestad, Lars
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    A novel method for forensic DNA investigations: Repeat-type sequence analysis of tandemly repeated mtDNA in domestic dogs2000In: Journal of Forensic Sciences, ISSN 0022-1198, E-ISSN 1556-4029, Vol. 45, no 5, p. 990-999Article in journal (Refereed)
    Abstract [en]

    A highly variable and heteroplasmic tandem repeat region situated in the mitochondrial mt DNA control region (CR) in domestic dogs and wolves was studied to evaluate its suitability as a forensic genetic marker for analysis of single hairs. The tandem repeat array is composed of three 10-bp repeat types that are distributed so that a secondary DNA sequence is formed. Thus, the region presents two levels of variation: variation in the number of repeats and variation in the secondary DNA sequence of repeat types. Two analysis methods were therefore tested; fragment length analysis and analysis of the sequence of repeat types. Fragment analysis produced unique profiles that could be used to discriminate between blood samples from maternally closely related individuals. However, different hairs from one individual did not have the same fragment profile, and the method is, therefore, not suitable for analysis of single hairs. In contrast, analysis of the repeat type sequences (array types) is highly informative. When different hairs from one individual were studied, identical array types were found. The repeat-type sequence variation was studied among individuals having identical nonrepetitive CR mtDNA sequence variants. Seven, six, and two individuals, representing three different sequence variants, respectively, were analyzed. All these individuals had different array types, which implies a very high genetic variation between individuals in this region. The analysis method considerably improves the exclusion capacity of mtDNA analysis of domestic dogs compared with sequence analysis of non-repetitive DNA.

  • 35.
    Savolainen, Peter
    et al.
    KTH, Superseded Departments, Biotechnology.
    Arvestad, Lars
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    mtDNA tandem repeats in domestic dogs and wolves: Mutation mechanism studied by analysis of the sequence of imperfect repeats2000In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 17, no 4, p. 474-488Article in journal (Refereed)
    Abstract [en]

    The mitochondrial (mt) DNA control region (CR) of dogs and wolves contains an array of imperfect 10 bp tandem repeats. This region was studied for 14 domestic dogs representing the four major phylogenetic groups of nonrepetitive CR and for 5 wolves. Three repeat types were found among these individuals, distributed so that different sequences of the repeat types were formed in different molecules. This enabled a detailed study of the arrays and of the mutation events that they undergo. Extensive heteroplasmy was observed in all individuals; 85 different array types were found in one individual, and the total number of types was estimated at 384. Among unrelated individuals, no identical molecules were found, indicating a high rate of evolution of the region. By performing a pedigree analysis, array types which had been inherited from mother to offspring and array types which were the result of somatic mutations, respectively, could be identified, showing that about 20% of the molecules within an individual had somatic mutations. By direct pairwise comparison of the mutated and the original array types, the physiognomy of the inserted or deleted elements (indels) and the approximate positions of the mutations could be determined. All mutations could be explained by replication slippage or point mutations. The majority of the indels were 1-5 repeats long, but deletions of up to 17 repeats were found. Mutations were found in all parts of the arrays, but at a higher frequency in the 5' end. Furthermore, the inherited array types within the mother-offspring pair were aligned and compared so that germ line mutations could be studied. The pattern of the germ line mutations was approximately the same as that of the somatic mutations.

  • 36.
    Savolainen, Peter
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Fitzsimmons, C.
    Arvestad, Lars
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
    Andersson, L.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    ESTs from brain and testis of White Leghorn and red junglefowl: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels2005In: Cytogenetic and Genome Research, ISSN 1424-8581, E-ISSN 1424-859X, Vol. 111, no 1, p. 79-87Article in journal (Refereed)
    Abstract [en]

    We report the generation, assembly and annotation of expressed sequence tags (ESTs) from four chicken cDNA libraries, constructed from brain and testis tissue dissected from red junglefowl and White Leghorn. 21,285 5'-end ESTs were generated and assembled into 2,813 contigs and 9,737 singletons, giving 12,549 tentative unique transcripts. The transcripts were annotated using BLAST by matching to known chicken genes or to putative homologues in other species using the major gene/protein databases. The results for these similarity searches are available on www.sbc.su.se/ -arve/chicken. 4,129 (32.9%) of the transcripts remained without a significant match to gene/protein databases, a proportion of unmatched transcripts similar to earlier non-mammalian EST studies. To estimate how many of these transcripts may represent novel genes, they were studied for the presence of coding sequence. It was shown that most of the unique chicken transcripts do not contain coding parts of genes, but it was estimated that at least 400 of the transcripts contain coding sequence, indicating that 3.2% of avian genes belong to previously unknown gene families. Further BLAST search against dbEST left 1,649 (13.1 %) of the transcripts unmatched to any library. The number of completely unmatched transcripts containing coding sequence was estimated at 180, giving a measure of the number of putative novel chicken genes identified in this study. 84.3 % of the identified transcripts were found only in testis tissue, which has been poorly studied in earlier chicken EST studies. Large differences in expression levels were found between the brain and testis libraries for a large number of transcripts, and among the 525 most frequently represented transcripts, there were at least 20 transcripts with significant difference in expression levels between red junglefowl and White Leghorn

  • 37.
    Savolainen, Peter
    et al.
    KTH, Superseded Departments, Biotechnology.
    Leitner, T.
    Wilton, A. N.
    Matisoo-Smith, E.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA2004In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 101, no 33, p. 12387-12390Article in journal (Refereed)
    Abstract [en]

    To determine the origin and time of arrival to Australia of the dingo, 582 bp of the mtDNA control region were analyzed in 211 Australian dingoes sampled in all states of Australia, 676 dogs from all continents, and 38 Eurasian wolves, and 263 bp were analyzed in 19 pre-European archaeological dog samples from Polynesia. We found that all mtDNA sequences among dingoes were either identical to or differing by a single substitution from a single mtDNA type, A29. This mtDNA type, which was present in >50% of the dingoes, was found also among domestic dogs, but only in dogs from East Asia and Arctic America, whereas 18 of the 19 other types were unique to dingoes. The mean genetic distance to A29 among the dingo mtDNA sequences indicates an origin approximate to5,000 years ago. From these results a detailed scenario of the origin and history of the dingo can be derived: dingoes have an origin from domesticated dogs coming from East Asia, possibly in connection with the Austronesian expansion into Island Southeast Asia. They were introduced from a small population of dogs, possibly at a single occasion, and have since lived isolated from other dog populations.

  • 38.
    Savolainen, Peter
    et al.
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Forensic evidence based on mtDNA from dog and wolf hairs1999In: Journal of Forensic Sciences, ISSN 0022-1198, E-ISSN 1556-4029, Vol. 44, no 1, p. 77-81Article in journal (Refereed)
    Abstract [en]

    In six forensic cases involving murder, bank robbery, theft and poaching, evidence material comprising shed hairs supposedly originating from dogs or wolves was analyzed by mitochondrial (mt) DNA sequencing. A 79 bp segment of the control region was amplified, sequenced, and compared with an established database of the domestic dog and wolf populations. In three murder cases exclusions of all eight suspects could be made. Furthermore, two of the murders could be linked to each other by a rare sequence variant, and the breed of the dog was indicated. In a theft case and a bank robbery a link could be established between the evidence material and the suspects. In a case of suspected wolf poaching, it could be established that the evidential material was of dog rather than wolf origin. We conclude that single hairs from common pets are suitable fur DNA analysis and that the described method has proved to be a valuable tool for forensic investigations.

  • 39.
    Savolainen, Peter
    et al.
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Rosen, B
    Holmberg, Anders
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Leitner, T
    Uhlen, Mathias
    Lundeberg, Joachim
    Sequence analysis of domestic dog mitochondrial DNA for forensic use1997In: Journal of Forensic Sciences, ISSN 0022-1198, E-ISSN 1556-4029, Vol. 42, no 4, p. 593-600Article in journal (Refereed)
    Abstract [en]

    A method has been developed for the direct sequencing of hypervariable region 1 (HV1) of domestic dog (Canis familiaris) and wolf (Canis lupus) mitochondrial DNA (mtDNA) using single hairs as template. The method uses a robotic work-station and an automated sequencer to allow for robust routine analysis. A population data base was created in order to investigate the forensic and population-genetic informativeness of domestic dog HV1. Sequence variation, partitioning of dog breeds among sequence variants and phylogenetic relations between the variants were determined. Samples from 102 domestic dogs of 52 different breeds and two captive wolves were analyzed. Nineteen dog sequence variants were found and the frequencies of the variants ranged from 1 to 21%. The calculated discrimination power of the region, i.e., the exclusion capacity, implied that nine out of ten disputed individuals can be excluded by this analysis. The sequence variants were found to cluster into four phylogenetic groups.

  • 40.
    Savolainen, Peter
    et al.
    KTH, Superseded Departments, Biotechnology.
    Zhang, Y. P.
    Luo, J.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Leitner, T.
    Genetic evidence for an East Asian origin of domestic dogs2002In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 298, no 5598, p. 1610-1613Article in journal (Refereed)
    Abstract [en]

    The origin of the domestic dog from wolves has been established, but the number of founding events, as well as where and when these occurred, is not known. To address these questions, we examined the mitochondrial DNA (mtDNA) sequence variation among 654 domestic dogs representing all major dog populations worldwide. Although our data indicate several maternal origins from wolf, >95% of all sequences belonged to three phylogenetic groups universally represented at similar frequencies, suggesting a common origin from a single gene pool for all dog populations. A larger genetic variation in East Asia than in other regions and the pattern of phylogeographic variation suggest an East Asian origin for the domestic dog, similar to15,000 years ago.

  • 41. Tellgren, A.
    et al.
    Berglund, A. C.
    Savolainen, Peter
    KTH, Superseded Departments, Biotechnology.
    Janis, C. M.
    Liberles, D. A.
    Myostatin rapid sequence evolution in ruminants predates domestication2004In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 33, no 3, p. 782-790Article in journal (Refereed)
    Abstract [en]

    Myostatin (GDF-8) is a negative regulator of skeletal muscle development. This gene has previously been implicated in the double muscling phenotype in mice and cattle. A systematic analysis of myostatin sequence evolution in ruminants was performed in a phylogenetic context. The myostatin coding sequence was determined from duiker (Sylvicapra grimmia caffra), eland (Taurotragus derbianus), gaur (Bos gaurus), ibex (Capra ibex), impala (Aepyceros melampus rednilis), pronghorn (Antilocapra americana), and tahr (Hemitragus jemlahicus). Analysis of nonsynonymous to synonymous nucleotide substitution rate ratios (K-a/K-s) indicates that positive selection may have been operating on this gene during the time of divergence of Bovinae and Antilopinae, starting from approximately 23 million years ago, a period that appears to account for most of the sequence difference between myostatin in these groups. These periods of positive selective pressure on myostatin may correlate with changes in skeletal muscle mass during the same period.

  • 42. Tellgren-Roth, Asa
    et al.
    Dittmar, Katharina
    Massey, Steven E.
    Kemi, Cecilia
    KTH, School of Biotechnology (BIO), Gene Technology.
    Tellgren-Roth, Christian
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Lyons, Leslie A.
    Liberles, David A.
    Keeping the blood flowing-plasminogen activator genes and feeding behavior in vampire bats2009In: Die Naturwissenschaften, ISSN 0028-1042, E-ISSN 1432-1904, Vol. 96, no 1, p. 39-47Article in journal (Refereed)
    Abstract [en]

    The blood feeding vampire bats emerged from New World leaf-nosed bats that fed on fruit and insects. Plasminogen activator, a serine protease that regulates blood coagulation, is known to be expressed in the saliva of Desmodus rotundus (common vampire bat) and is thought to be a key enzyme for the emergence of blood feeding in vampire bats. To better understand the evolution of this biological function, we studied the plasminogen activator (PA) genes from all vampire bat species in light of their feeding transition to bird and subsequently mammalian blood. We include the rare species Diphylla ecaudata and Diaemus youngi, where plasminogen activator had not previously been studied and demonstrate that PA gene duplication observed in Desmodus is not essential to the vampire phenotype, but relates to the emergence of predominant mammalian blood feeding in this species. Plasminogen activator has evolved through gene duplication, domain loss, and sequence evolution leading to change in fibrin-specificity and susceptibility to plasminogen activator inhibitor-1. Before undertaking this study, only the four plasminogen activator isoforms from Desmodus were known. The evolution of vampire bat plasminogen activators can now be linked phylogenetically to the transition in feeding behavior among vampire bat species from bird to mammalian blood.

  • 43. 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.

  • 44. 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.

  • 45. Vila, C
    et al.
    Savolainen, Peter
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Maldonado, E
    Amorim, R
    Rice, E
    Honeycutt, L
    Crandall, A
    Lundeberg, Joakim
    Wayne, K
    Multiple and ancient origins of the domestic dog1997In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 276, no 5319, p. 1687-1689Article in journal (Refereed)
    Abstract [en]

    Mitochondrial DNA control region sequences were analyzed from 162 wolves at 27 localities worldwide and from 140 domestic dogs representing 67 breeds. Sequences from both dogs and wolves showed considerable diversity and supported the hypothesis that wolves were the ancestors of dogs. Most dog sequences belonged to a divergent monophyletic clade sharing no sequences with wolves. The sequence divergence within this clade suggested that dogs originated more than 100,000 years before the present. Associations of dog haplotypes with other wolf lineages indicated episodes of admixture between wolves and dogs. Repeated genetic exchange between dog and wolf populations may have been an important source of variation for artificial selection.

  • 46. Wang, Guo-Dong
    et al.
    Peng, Min-Sheng
    Yang, He-Chuan
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Zhang, Ya-Ping
    Questioning the evidence for a Central Asian domestication origin of dogs2016In: 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 (Refereed)
  • 47. Wang, Guo-dong
    et al.
    Zhai, Weiwei
    Yang, He-chuan
    Fan, Ruo-xi
    Cao, Xue
    Zhong, Li
    Wang, Lu
    Liu, Fei
    Wu, Hong
    Cheng, Lu-guang
    Poyarkov, Andrei D.
    Poyarkov, Nikolai A., Jr.
    Tang, Shu-sheng
    Zhao, Wen-ming
    Gao, Yun
    Lv, Xue-mei
    Irwin, David M.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Wu, Chung-I
    Zhang, Ya-ping
    The genomics of selection in dogs and the parallel evolution between dogs and humans2013In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, p. 1860-Article in journal (Refereed)
    Abstract [en]

    The genetic bases of demographic changes and artificial selection underlying domestication are of great interest in evolutionary biology. Here we perform whole-genome sequencing of multiple grey wolves, Chinese indigenous dogs and dogs of diverse breeds. Demographic analysis show that the split between wolves and Chinese indigenous dogs occurred 32,000 years ago and that the subsequent bottlenecks were mild. Therefore, dogs may have been under human selection over a much longer time than previously concluded, based on molecular data, perhaps by initially scavenging with humans. Population genetic analysis identifies a list of genes under positive selection during domestication, which overlaps extensively with the corresponding list of positively selected genes in humans. Parallel evolution is most apparent in genes for digestion and metabolism, neurological process and cancer. Our study, for the first time, draws together humans and dogs in their recent genomic evolution.

  • 48. Wang, Guo-Dong
    et al.
    Zhai, Weiwei
    Yang, He-Chuan
    Wang, Lu
    Zhong, Li
    Liu, Yan-Hu
    Fan, Ruo-Xi
    Yin, Ting-Ting
    Zhu, Chun-Ling
    Poyarkov, Andrei D.
    Irwin, David M.
    Hytonen, Marjo K.
    Lohi, Hannes
    Wu, Chung-I
    Savolainen, Peter
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
    Zhang, Ya-Ping
    Out of southern East Asia: the natural history of domestic dogs across the world2016In: Cell Research, ISSN 1001-0602, E-ISSN 1748-7838, Vol. 26, no 1, p. 21-33Article in journal (Refereed)
    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.

  • 49.
    Zhang, Ai-bing
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    BPSI2.0: a C/C++ interface program for species identification via DNA barcoding with a BP-neural network by calling the Matlab engine2009Article in journal (Refereed)
    Abstract [en]

    BP-Species Identification (BPSI2.0) is a computer program that performs species identification by training a Back-Propagation Neural Network. A short DNA barcoding segment is used as input for training a three-layer BP network. The trained network can assign an unknown query sequence to a known species in the user's database, and provide the corresponding subvector value of the output vector as a relative probability value.

1 - 49 of 49
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