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Admixture Dynamics, Natural Selection and Diseases in Admixed Populations 2015 ed. [Hardback]

  • Formāts: Hardback, 114 pages, height x width: 235x155 mm, weight: 3564 g, 29 Illustrations, color; 3 Illustrations, black and white; XIX, 114 p. 32 illus., 29 illus. in color., 1 Hardback
  • Sērija : Springer Theses
  • Izdošanas datums: 09-Oct-2015
  • Izdevniecība: Springer
  • ISBN-10: 9401774064
  • ISBN-13: 9789401774062
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Admixture Dynamics, Natural Selection and Diseases in Admixed Populations 2015 ed.Palielināt
  • Formāts: Hardback, 114 pages, height x width: 235x155 mm, weight: 3564 g, 29 Illustrations, color; 3 Illustrations, black and white; XIX, 114 p. 32 illus., 29 illus. in color., 1 Hardback
  • Sērija : Springer Theses
  • Izdošanas datums: 09-Oct-2015
  • Izdevniecība: Springer
  • ISBN-10: 9401774064
  • ISBN-13: 9789401774062
Citas grāmatas par šo tēmu:
Permanent link: https://www.kriso.lv/db/9789401774062.html
Keywords:

In this thesis, Dr. Jin presents the distribution of ancestral chromosomal segments in the admixed genome, which could provide the information needed to explore population admixture dynamics. The author derives accurate population histories of African Americans and Mexicans using genome-wide single nucleotide polymorphisms (SNPs) data. Mapping the genetic background facilitates the study of natural selection in the admixed population, and the author identifies the signals of selection in African Americans since their African ancestors left for America. He further demonstrates that many of the selection signals were associated with African American-specific high-risk diseases such as prostate cancer and hypertension, suggesting an important role these disease-related genes might have played in adapting to their new environment. Lastly, the author reveals the complexity of natural selection in shaping human susceptibility to disease. The thesis significantly advances our understanding of the recent population admixture, adaptation to local environment and its health implications.

1 Introduction
1(22)
1.1 Origin of Modern Human
1(2)
1.2 Human Populations and Population Structure
3(3)
1.3 Human Adaptation to Local Environment
6(5)
1.3.1 Adaptation to High-Latitude Climates
8(1)
1.3.2 Adaptation to High Altitude
8(1)
1.3.3 Adaptation to Shifted Diet
9(1)
1.3.4 Adaptation to Pathogens and Its Impact on Human Genome
10(1)
1.4 Human Population Admixture and Admixture Mapping
11(3)
1.5 Disease-Associated Genes and Genetic Variants
14(9)
References
17(6)
2 Distribution of Length of Ancestral Chromosomal Segments in Admixed Genomes
23(12)
2.1 Ancestral Chromosomal Segments in Admixed Genome
23(1)
2.2 Two Classic Admixture Models
24(1)
2.3 Distribution of LACS in HI Model
25(1)
2.4 Distribution of LACS in GA Model
26(1)
2.5 Consistency Between Theoretical and Simulated Distributions
27(1)
2.6 Comparison of Distribution of LACS Between HI and GA Models
27(4)
2.7 Influence of Distribution of LACS on Admixture Mapping
31(4)
References
32(3)
3 Exploring Population Admixture Dynamics via Distribution of LACS
35(18)
3.1 Different Admixture Dynamics, Distinct Distribution of LACS
35(2)
3.2 Parental Populations of African Americans
37(5)
3.3 Admixture Dynamics of African Americans
42(3)
3.4 Substructure in African American Admixture
45(1)
3.5 Admixture Dynamics of Mexicans
46(2)
3.6 Genetics Difference Between Mexican Americans and Mestizos
48(1)
3.7 Implication for Future Study
49(4)
References
50(3)
4 Genome-Wide Search for Signatures of Natural Selection in African Americans
53(20)
4.1 Potential Natural Selection Events in African Americans
53(2)
4.2 Identification of Genomic Regions with Biased Ancestry
55(4)
4.3 African/European Ancestral Components in African Americans
59(1)
4.4 Identifying Highly Differentiated Regions Between AAF and Indigenous African
60(4)
4.5 Reconstituted African Americans and Its Difference with African Americans
64(1)
4.6 Further Evidences for Positive Selection in African Ancestral Components
65(2)
4.7 Relaxed Natural Selection in African Americans
67(1)
4.8 Disease Susceptibility Genes Enriched Among Signatures of Selection
68(1)
4.9 Implication for the Future Study
68(5)
References
69(4)
5 Complex Selective Forces Shaping the Genes Underlying Human Diseases
73(20)
5.1 Genes Underlying Genetic Diseases
73(2)
5.2 Monogenic Disease Genes Are More Likely to Be Involved in Complex Diseases
75(1)
5.3 MC Genes Are Associated with More Diseases and Phenotypes
76(1)
5.4 MC Genes Involved in More Complex Interaction Network Than that of Monogenic or Complex Genes
76(2)
5.5 MC Genes Have the Longest Coding Sequence (CDS)
78(1)
5.6 MC Genes Have the Highest Tissue Specificity
79(2)
5.7 Recent Natural Selection on Different Gene Categories
81(2)
5.8 Relative Evolutionary Rate Changed at Different Timescales
83(3)
5.9 Over-representation Analysis with CNV Regions
86(1)
5.10 Distinct Functional Characteristics of Different Genes Categories
87(1)
5.11 Summary and Genetic Implication
88(5)
References
89(4)
6 Materials and Methods
93(18)
6.1 Population Admixture Models
93(1)
6.2 Data Simulation and Comparison with Theoretical LACS Distribution
94(1)
6.3 Simulation of Susceptibility Locus in Admixed Population and Admixture Mapping
95(1)
6.4 Genetic Data of African Americans
95(2)
6.5 Genetic Data of Mexicans
97(1)
6.6 Linkage Disequilibrium Correction and PCA Analysis
97(1)
6.7 Population Genetic Analysis and Inference of Ancestral Chromosomal Segments
98(1)
6.8 Earth Mover's Distance (EMD)
99(1)
6.9 Measurement of the Differences Between Two Distributions
99(1)
6.10 Analysis of African Americans Admixture Dynamics
100(1)
6.11 Admixture Time and Admixture Proportion for Each Individual
101(1)
6.12 Analysis of Mexican Admixture Dynamics
101(1)
6.13 Simulation of African Americans and Its Parental Populations
102(1)
6.14 Function Annotations and Ingenuity Pathway Analysis (IPA)
103(1)
6.15 Databases for Genes Underlying Monogenic and Complex Diseases
103(1)
6.16 Protein--Protein Interaction Data
104(1)
6.17 Analysis of Gene Expression Pattern
104(1)
6.18 Gene Ontology Annotation Analysis Using DAVID
105(1)
6.19 Structural Annotations and Evolutionary Rates of Human Genes
105(1)
6.20 Human Polymorphism Data Analysis
106(1)
6.21 Statistical Analyses
107(4)
References
107(4)
Web Resource 111(2)
Epilogue 113
Wenfei Jin obtained his Ph.D. from Shanghai Institute of Biological Sciences (SIBS), Chinese Academy of Sciences (CAS). He was supervised by Prof. Li Jin from Fudan University and Prof. Shuhua Xu from SIBS. During his Ph.D. study, Wenfei Jin published 11 research articles, of which 6 articles are as first or co-first author. He received SIBS-Eli Lilly Outstanding Ph.D. Thesis Awards from Eli Lilly, China, in 2012, and won the Excellent Doctoral Dissertation of CAS in 2013. Dr. Wenfei Jin is now a visiting fellow at NHLBI, National Institute of Health in the USA.