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  Mus musculus helgolandicus: insights into their origin. A study based on genetic and morphometrics analysis

Babiker, H. M. A. (2014). Mus musculus helgolandicus: insights into their origin. A study based on genetic and morphometrics analysis. PhD Thesis, Christian-Albrechts-Universität, Kiel.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-001A-1071-D Version Permalink: http://hdl.handle.net/11858/00-001M-0000-001A-1073-9
Genre: Thesis

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Babiker, Hiba Mohammed Ali1, Author              
Tautz, Diethard1, Referee              
Schulenburg, Hinrich, Referee
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1Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              

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 Abstract: Islands are a center of interest in evolutionary biology since the emergence of evolutionary theory itself. They are studied to understand the molecular mechanisms of evolution, adaptation and speciation. Invasive species are of particular interest since they may garner clues and evidence about the processes that took place during the onset of colonization and for understanding mechanisms of adaptation. The aim of this project is to study the evolutionary processes that altogether with isolation shaped the phenotypically known house mouse Mus musculus helgolandicus inhabiting the island of Heligoland. Heligoland is a small island located in the South-East corner of the North Sea and was first colonized by humans in the dawn of the fifteenth century. M. m. helgolandicus were first described by Zimmermann in 1953. Since then they have been thought to form a separate subspecies, which is morphologically different from its continental counterpart M. m. domesticus inhabiting the Western European region. Here, four nuclear diagnostic markers (Abpa, D11 cenB2, Btk and Zfy2 ) and the discriminatory relative tail length (TBLR) were used to differentiate these mice from the other two subspecies M. m. musculus and M. m. domesticus. In addition, the possible routes of colonization and population structure for the invasive mice were investigated using mitochondrial (mt)D-loop DNA sequence and (21) microsatellite loci respectively. Furthermore, whole mtDNA genome was sequenced for 11 individual mice to estimate the onset of colonization on the island from the calculation of mutation frequency in comparison to that of house mouse from Kerguelen archipelago, which has a documented colonization history. Moreover, the whole genome sequence of three individuals was generated and analysed for single nucleotide polymorphisms (SNPs) which were then used along with data for two po- tential source populations from the two subspecies inhabiting Europe to assign the possible patterns of introgression of haplotypes in M. m. helgolandicus. This study also revisits the morphology of M. m. helgolandicus, in particular, the mandible to assign morphological differences among Heligoland mice on one side and among Heligoland and mainland populations on the other side. Based on the results from diagnostic markers, relative tail length, microsatellites and mtDNA analyses, M. m. helgolandicus are predominantly of M. m. domesticus origin. M. m. helgolandicus population on Heligoland exhibited low genetic diversity compared with other populations from the mainland. The mtDNA data shows that there is a major mtDNA haplotype specic to Heligoland and a minor haplotype represented by a single individual presumably introgressed. Hence, there was a single primary colonization into the island a few hundred years ago and more interestingly, the isolated island shows a case of recent migration from the mainland revealing a signal of refractory to immigration. M. m. helgolandicus displays an elongated mandible which is distinctive for Heligoland. Most likely it was acquired by adaptive forces due to diet changes from a novel environment, with particular a shift to carnivory. The genome is highly intermixed with M. m. musculus haplotypes, pointing to a possible hybrid speciation scenario during the colonization phase.

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Language(s): eng - English
 Dates: 2014-09-292014
 Publication Status: Published in print
 Pages: XVI, 155 Bl.
 Publishing info: Kiel : Christian-Albrechts-Universität
 Table of Contents: Contents iv
Acknowledgements vii
Zusammenfassung ix
Abstract xi
Declaration xiii
List of Figures xiv
List of Tables xvi
1 General introduction 1
1.1 Evolution on islands . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 House mice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3 The hybrid zone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.4 The island of Heligoland . . . . . . . . . . . . . . . . . . . . . . . . . 9
1.5 Possible colonization routes of house mouse into Heligoland . . . . . . 11
1.6 Genetic studies on M. m. heligolandicus . . . . . . . . . . . . . . . . 13
1.7 Aims of the study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2 Genetic analysis and insights into the origin of M. m. helgolandi-
cus 16
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.2 Materials and methods . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.2.1 Sample collection . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.2.2 DNA extraction . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.2.3 Diagnostic nuclear markers . . . . . . . . . . . . . . . . . . . . 20
2.2.4 Microsatellite typing . . . . . . . . . . . . . . . . . . . . . . . 21
2.2.5 Microsatellite data analysis . . . . . . . . . . . . . . . . . . . 21
2.2.6 mtDNA control region . . . . . . . . . . . . . . . . . . . . . . 22
2.2.7 Complete mtDNA sequencing . . . . . . . . . . . . . . . . . . 23
2.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.3.1 Subspecies-diagnostic nuclear markers . . . . . . . . . . . . . . 24
2.3.2 Population genetic diversity . . . . . . . . . . . . . . . . . . . 25
2.3.3 mtDNA analysis . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.3.3.1 mtDNA D-loop . . . . . . . . . . . . . . . . . . . . . 29
2.3.3.2 mtDNA genome . . . . . . . . . . . . . . . . . . . . 31
2.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3 Aspects of Insular evolution and adaptation in the mandible of M.
m. helgolandicus 37
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.2 Materials and methods . . . . . . . . . . . . . . . . . . . . . . . . . . 44
3.2.1 Tail measurements and coat coloration . . . . . . . . . . . . . 44
3.2.2 Geometric morphometrics . . . . . . . . . . . . . . . . . . . . 44
3.2.2.1 Animal specimens . . . . . . . . . . . . . . . . . . . 44
3.2.2.2 Specimens preparation . . . . . . . . . . . . . . . . . 45
3.2.2.3 Mandible landmarking . . . . . . . . . . . . . . . . . 45
3.2.2.4 Geometric morphometrics analysis . . . . . . . . . . 47
3.2.2.5 Centroid size . . . . . . . . . . . . . . . . . . . . . . 48
3.2.2.6 Statistical analysis . . . . . . . . . . . . . . . . . . . 49
3.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
3.3.1 Mandible size among populations . . . . . . . . . . . . . . . . 50
3.3.2 Mandible shape differentiation . . . . . . . . . . . . . . . . . . 51
3.3.2.1 Mandible shape of the house mouse from Heligoland 51
3.3.2.2 Mandible shape of house mouse between Heligoland
and mainland populations . . . . . . . . . . . . . . . 53
3.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
4 Patterns of introgression in M. m. helgolandicus 69
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
4.2 Materials and methods . . . . . . . . . . . . . . . . . . . . . . . . . . 77
4.2.1 Whole genome sequencing . . . . . . . . . . . . . . . . . . . . 77
4.2.1.1 DNA Extraction . . . . . . . . . . . . . . . . . . . . 77
4.2.1.2 DNA Library construction and genome sequencing . 77
4.2.2 Sequence analysis . . . . . . . . . . . . . . . . . . . . . . . . . 78
4.2.2.1 Trimming of the reads . . . . . . . . . . . . . . . . . 78
4.2.2.2 Indexing of the reference genome . . . . . . . . . . . 78
4.2.2.3 Sequence mapping and alignment to the reference
genome . . . . . . . . . . . . . . . . . . . . . . . . . 78
4.2.2.4 SNP calling and detection . . . . . . . . . . . . . . . 79
4.2.2.5 Identification of SNPs and analysis of variants . . . . 79
4.2.3 Introgression analysis . . . . . . . . . . . . . . . . . . . . . . . 80
4.2.3.1 Hapmix-Inference of local ancestry in admixed populations
. . . . . . . . . . . . . . . . . . . . . . . . . 80
4.2.3.2 Reference data for introgression analysis . . . . . . . 80
4.2.3.3 Patterns of introgression . . . . . . . . . . . . . . . . 81
4.2.3.4 Data visualization and GO of introgressed regions . . 81
4.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
4.3.1 Whole genome sequence analysis . . . . . . . . . . . . . . . . 82
4.3.2 Detection of SNPs . . . . . . . . . . . . . . . . . . . . . . . . 82
4.3.3 Genome annotations . . . . . . . . . . . . . . . . . . . . . . . 83
4.3.4 Patterns of introgression . . . . . . . . . . . . . . . . . . . . . 84
4.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
5 Concluding remarks 92
References 94
Appendix 111
Affdavit 154
Curriculum Vitae 155
 Rev. Method: -
 Identifiers: Other: Diss/12564
 Degree: PhD

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