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Mitochondrial DNA: analysis of the control region in forensic and population genetic studies
KTH, Superseded Departments, Biotechnology.ORCID iD: 0000-0002-1495-8338
1999 (English)Doctoral thesis, comprehensive summary (Other scientific)
Place, publisher, year, edition, pages
Stockholm: KTH , 1999. , 49 p.
Keyword [en]
mitochondrial DNA, control region, tandem repeats, D-loop, homoplasmy, hair, forensic, microsatellites, evolution, DNA sequencing, PCR, domestic dog, wolf
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-2824ISBN: 91-7170-408-6 (print)OAI: oai:DiVA.org:kth-2824DiVA: diva2:8547
Public defence
1999-06-11, 00:00
Note
QC 20100702Available from: 2000-01-01 Created: 2000-01-01 Last updated: 2010-07-02Bibliographically approved
List of papers
1. Sequence analysis of domestic dog mitochondrial DNA for forensic use
Open this publication in new window or tab >>Sequence analysis of domestic dog mitochondrial DNA for forensic use
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1997 (English)In: Journal of Forensic Sciences, ISSN 0022-1198, E-ISSN 1556-4029, Vol. 42, no 4, 593-600 p.Article in journal (Refereed) Published
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.

Keyword
forensic science, DNA typing, dog, Canis familiaris, mitochondrial DNA, sequence analysis, hair, SINGLE HAIRS, IDENTIFICATION, VARIABILITY, POPULATION, FAMILY, PCR
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:kth:diva-13928 (URN)A1997XL34800004 ()
Note
QC 20100702Available from: 2010-07-02 Created: 2010-07-02 Last updated: 2017-12-12Bibliographically approved
2. Multiple and ancient origins of the domestic dog
Open this publication in new window or tab >>Multiple and ancient origins of the domestic dog
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1997 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 276, no 5319, 1687-1689 p.Article in journal (Refereed) Published
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.

Keyword
MITOCHONDRIAL-DNA, EVOLUTION, HAPLOTYPES, CARNIVORES, SEQUENCE, REGION, WOLF
National Category
Social Sciences Interdisciplinary
Identifiers
urn:nbn:se:kth:diva-13924 (URN)A1997XD94700039 ()
Note
QC 20100702Available from: 2010-07-02 Created: 2010-07-02 Last updated: 2017-12-12Bibliographically approved
3. Paternal and maternal DNA lineages reveal a bottleneck in the founding of the Finnish population
Open this publication in new window or tab >>Paternal and maternal DNA lineages reveal a bottleneck in the founding of the Finnish population
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1996 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 93, no 21, 12035-12039 p.Article in journal (Refereed) Published
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.

Keyword
HUMAN MITOCHONDRIAL-DNA, Y-CHROMOSOME, EVOLUTION, FINLAND, ASPARTYLGLUCOSAMINURIA, SEQUENCE, EUROPE, GENES
National Category
Social Sciences Interdisciplinary
Identifiers
urn:nbn:se:kth:diva-13926 (URN)A1996VM68100132 ()
Note
20100702Available from: 2010-07-02 Created: 2010-07-02 Last updated: 2017-12-12Bibliographically approved
4. The genetical history of an isolated population of the endangered grey wolf Canis lupus: A study of nuclear and mitochondrial polymorphisms
Open this publication in new window or tab >>The genetical history of an isolated population of the endangered grey wolf Canis lupus: A study of nuclear and mitochondrial polymorphisms
1996 (English)In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 351, no 1348, 1661-1669 p.Article in journal (Refereed) Published
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.

National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-13927 (URN)A1996WB72600001 ()
Note
QC 20100702Available from: 2010-07-02 Created: 2010-07-02 Last updated: 2017-12-12Bibliographically approved
5. mtDNA tandem repeats in domestic dogs and wolves: Mutation mechanism studied by analysis of the sequence of imperfect repeats
Open this publication in new window or tab >>mtDNA tandem repeats in domestic dogs and wolves: Mutation mechanism studied by analysis of the sequence of imperfect repeats
2000 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 17, no 4, 474-488 p.Article in journal (Refereed) Published
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.

Keyword
mitochondrial DNA, tandem repeats, mutation, Canis, DNA CONTROL REGION, MAMMALIAN MITOCHONDRIAL-DNA, D-LOOP REGION, EVOLUTION, HETEROPLASMY, GENERATION, MODEL
National Category
Biochemistry and Molecular Biology Biochemistry and Molecular Biology Developmental Biology
Identifiers
urn:nbn:se:kth:diva-13922 (URN)000086337700002 ()
Note
QC 20100702Available from: 2010-07-02 Created: 2010-07-02 Last updated: 2017-12-12Bibliographically approved
6. Forensic evidence based on mtDNA from dog and wolf hairs
Open this publication in new window or tab >>Forensic evidence based on mtDNA from dog and wolf hairs
1999 (English)In: Journal of Forensic Sciences, ISSN 0022-1198, E-ISSN 1556-4029, Vol. 44, no 1, 77-81 p.Article in journal (Refereed) Published
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.

Keyword
forensic science, DNA typing, dog, wolf, Canis familiaris, mitochondrial DNA, sequence analysis, hair, MITOCHONDRIAL-DNA, CONTROL REGION, DOMESTIC DOG, IDENTIFICATION, FAMILY
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:kth:diva-13923 (URN)000085830100011 ()
Note
QC 20100702Available from: 2010-07-02 Created: 2010-07-02 Last updated: 2017-12-12Bibliographically approved
7. A novel method for forensic DNA investigations: Repeat-type sequence analysis of tandemly repeated mtDNA in domestic dogs
Open this publication in new window or tab >>A novel method for forensic DNA investigations: Repeat-type sequence analysis of tandemly repeated mtDNA in domestic dogs
2000 (English)In: Journal of Forensic Sciences, ISSN 0022-1198, E-ISSN 1556-4029, Vol. 45, no 5, 990-999 p.Article in journal (Refereed) Published
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.

Keyword
forensic science, DNA typing, dog, wolf, Canis familiaris, mitochondrial DNA, tandem repeat, sequence analysis, hair, MITOCHONDRIAL-DNA, CONTROL REGION, HETEROPLASMY, IDENTIFICATION, AMPLIFICATION, POLYMORPHISMS, SEGREGATION
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:kth:diva-13925 (URN)000089267500004 ()
Note
QC 20100702Available from: 2010-07-02 Created: 2010-07-02 Last updated: 2017-12-12Bibliographically approved

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