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  Evolutionary Biology and Forensics
Summary
Ahmadian
Lundeberg
Nilsson
Odeberg
Savolainen
Sterky

Principal Investigator (PI): Dr Peter Savolainen

Summary and objectives
Background
This group has worked extensively with sequence analysis of mitochondrial DNA (mtDNA) from mainly domestic dogs, but also wolves and humans. The genetic variation has been studied with two main objectives: to draw population genetic conclusions and to evaluate its value for forensic use. We have also worked with development of forensic DNA analysis methods.
Origin and history of the domestic dog
Several 10-15,000 year old archaeological finds in Eastern Europe and the Middle East of domestic dog-looking canids indicate that the dog was the first domestic animal. Apart from this, however, archaeological studies have not produced any detailed facts about the origin of the domestic dog. Such basic questions as the number of founding events, and where and when these occurred, have remained unsolved. To address these questions we initiated a study of mtDNA sequence variation among domestic dogs, based on our comprehensive collection of more than 1,000 DNA samples from dogs from most parts of the world. We could thereby show that the geographic variation of mtDNA among domestic dogs indicate that the dog originates from East Asia, probably about 15,000 years ago (9, note link to article). We are now refining the results of this study by analysing more individuals from some important geographic regions. This will give a more precise place of origin and dating of the first origin of the dog, and will show by what routes dogs spread from East Asia to the other parts of the world. We have also, in a recent article, given a detailed picture of the origin of the Australian dingo (10). We could show that the dingo originates from domesticated dogs, originally from East Asia, which came in small numbers to Australia approximately 5,000 years ago. We are now turning to analysis also of the Y chromosome and of autosomal markers, in order to get a more complete picture of the genetic history of the dog. We will test whether the history of male and female lines are congruent, and the number of male founders of the dog and dingo populations and their geographic origin will be determined, and the influence of later crossings of female dogs with male wolves for the formation of local morphologic types of dog breeds, e.g. some Arctic breeds, will be studied. In order to explain our population-genetic work to the dog interested public, we have written some popular-science articles describing our studies of the geographic origin of the domestic dog (23, 24, 25).
Forensics
Based on the genetic information from our population genetic studies, forensic techniques for the analysis of mtDNA from dogs and wolves have been developed (5, 8). These methods have been used in forensic casework for the analysis of dog and wolf hairs, using the population studies as a reference (5, 18). We have recently written an article describing the correlation between mtDNA types and breeds of dogs, and its potential for forensic analyses (13). Techniques using nuclear Single Nucleotide Polymorphisms (SNPs) for forensic analyses of human, as well as canine, samples are now under development, aiming at improving analysis of hair samples. The methods are based on multiplex PCR and chip-based SNP-analysis.
Mitochondrial repeats
This group has also in detail studied a hypervariable repetitive unit in canine mtDNA. The extreme genetic variation has been studied both in pedigrees and in the dog population. The mechanisms creating the extreme genetic variation were analyzed and the possibility of using this region for forensic analysis was shown (7, 8).

Positions available
Postdoc position available!
There are several opportunities for “examensarbete” in this group, both for dog population genetics and forensic method develoment.

Publications
Refereed articles
1.
Holgersson S, Karlsson JA, Kihlgren A, Rosen B, Savolainen P, Gyllensten U. Fluorescent-based typing of the two short tandem repeat loci HUMTH01 and HUMACTBP2: reproducibility of size measurements and genetic variation in the Swedish population. Electrophoresis. 1994:15,890-895.
2.
Sajantila A, Salem A-H, Savolainen P, Bauer K, Gierig C and Pääbo S. Paternal and maternal DNA lineages reveal a bottleneck in the founding of the Finnish population. Proc. Natl. Acad. Sci. USA 1996:93,12035-12039.
3.
Ellegren H, Savolainen P and Rosén B. The genetical history of an isolated population of the endangered grey wolf Canis lupus: a study of nuclear and mitochondrial polymorphisms. Phil. Trans. R Soc. Lond. B. 1996:352,1161-1169.
4.
Vilà C, Savolainen P, Maldonado JE, Amorim IR, Rice JE, Honeycutt RL, Crandal KA, Lundeberg J and Wayne RK. Multiple and ancient origin of the domestic dog. Science 1997:276,1687-1689.
5.
Savolainen P, Rosén B, Holmberg A, Leitner T, Uhlén M and Lundeberg J. Analysis of domestic dog mitochondrial DNA for forensic use. J. Forensic Sci. 1997:42,593-600.
6.
Savolainen P and Lundeberg J. Forensic evidence based on mtDNA from Dog Hairs. J. Forensic Sci. 1999:44,77-81.
7.
Savolainen P, Arvestad L, Lundeberg J. mtDNA tandem repeats in domestic dogs and wolves: mutation mechanism studied by analysis of the sequence of imperfect repeats. Mol. Biol. Evol. 2000:17,474-488.
8.
Savolainen P, Arvestad L, Lundeberg J. A novel method for forensic DNA investigations, based on repeat type sequence analysis of domestic dog mtDNA. J Forensic Sci. 2000:45,990-999.
9.
Savolainen P, Zhang Y-P, Luo J, Lundeberg J, Leitner T. Genetic evidence for an East Asian origin of domestic dogs. Science 2002:298,1610-1613. Link to abstract and full article
10.
Savolainen P, Leitner T, Wilton A, Matisoo-Smith E, Lundeberg J. A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proc. Natl. Acad. Sci. USA 2004:101,12387-12390.
11.
Tellgren Å, Berglund AC, Savolainen P, Janis CM, Liberles DA. Myostatin rapid sequence evolution in ruminants predates domestication. Mol Phylogenet Evol. 2004:33:782-790.
12.
Fitzsimmons CJ, Savolainen P, Amini B, Hjälm G, Lundeberg J, Andersson L. Detection of sequence polymorphisms in red junglefowl and White Leghorn ESTs. Anim Genet. 2004:35,391-396.
13.
Angleby H, Savolainen P. A study of the forensic usefulness of the mitochondrial DNA variation among and within populations, breeds and types of domestic dogs. Forensic Sci Int. 2005:154,99-110
14.
Savolainen P, Fitzsimmons CJ, Arvestad L, Andersson L, Lundeberg J. ESTs from brain and testis of White Leghorn and red junglefowl: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels. Cytogenet. Genome Res 2005:111,79-87.
15.
Coward K, Ponting CP, Chang H-Y, Hibbitt O, Savolainen P, Jones KT, Parrington J. Phospholipase C zeta, the trigger of egg activation in mammals, is present in a non-mammalian species. Reproduction 2005:130,157-63.
16.
Ka S, Fitzsimmons C, Jacobsson L, Savolainen P, Lundeberg J, Siegel PB, Andersson L, Hallbook F. Expression analysis of growth and energy regulation-associated genes in two divergent chicken strains. Ann. N. Y. Acad. Sci. 2005:1040,357-9.
17.
Arvestad L, Visa N, Lundeberg J, Wieslander L, Savolainen P. ESTs from midgut and an epithelial cell line of Chironomus tentans: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels. Insect Mol Biol. 2005:14,689-95.
Book chapter
18.
Savolainen P and Lundeberg J. Dog genetic data and forensic evidence. In: Eds. Ruvinsky A, Sampson J. The Genetics of the dog. 2001. CABI Publishing, New York.
19.
Savolainen P. mtDNA studies of the origin of dogs. In: Eds. Ostrander EA, Giger U, Lindbladh-Toh K. The dog and its genome. Cold Spring Harbor Laboratory Press, New York.
20.
Savolainen P. Domestication of dogs. In: Ed. Jensen P. The behavioural biology of dogs. CABI Publishing, New York: in press.
Computer program
21.
Arvestad L and Savolainen P. Binary Repeat Align: Software for comparing marked repeats under a model including replication slippage. Source code (under the Gnu Public License) is distributed over WWW at http://repeatalign.cgb.ki.se, where also online analysis can be done through a Web-based interface.
22.
Arvestad L and Savolainen P. estzmate: Finding coding ESTs using a Z-score approach. Source code available from http://www.nada.kth.se/~arve/estzmate under the GNU Public Licence.
Popular science
23.
Cederlund B and Savolainen P. Från Asiatisk varg till både pekingeser och schäfer. Hundsport 2003:9,18-22.
24.
Savolainen P. Asien – die Wiege aller Hunde? Studie über den Ursprung der Hunde. Teil 1/2. Hundemagazin WUFF 2004:3,38-41
25.
Savolainen P. Asien – die Wiege aller Hunde? Studie über den Ursprung der Hunde. Teil 2/2. Hundemagazin WUFF 2004:4,42-45
Last updated: 2013-05-24