Y-chromosome diversity in Central Africa Aussois, September 2005 Gemma Berniell-Lee, Jaume Bertranpetit, David Comas.

Slides:

Advertisements

Similar presentations

Population Genetics 3 We can learn a lot about the origins and movements of populations from genetics Did all modern humans come from Africa? Are we derived.

Advertisements

Molecular Anthropology Genetics Research Tutorial 1

Y CHROMOSOME VARIATION Males from Cis-Baikal Sites of Lokomotiv, Shamanka II, and Ust’-Ida Examine the genetic relationships between prehistoric Cis- Baikal.

The Five Factors of Evolution

Genetic Genealogy A Report on The CLOUD DNA Project. 1.Our Data Examined 2.Intro to Genetic Genealogy & DNA Genealogical DNA and its Components 4.Examining.

Lecture 23: Introduction to Coalescence April 7, 2014.

Patterns of population structure and admixture among human populations Katarzyna Bryc OEB 275br February 19, 2013.

Sequencing Neanderthal DNA

Signatures of Selection

CS177 Lecture 9 SNPs and Human Genetic Variation Tom Madej

Tutorial #6 by Ma’ayan Fishelson Based on notes by Terry Speed.

Islands in Africa: a study of structure in the source population for modern humans Rosalind Harding Depts of Statistics, Zoology & Anthropology, Oxford.

A coalescent computational platform for tagging marker selection for clinical studies Gabor T. Marth Department of Biology, Boston College

Introduction to Linkage Analysis March Stages of Genetic Mapping Are there genes influencing this trait? Epidemiological studies Where are those.

Dispersal models Continuous populations Isolation-by-distance Discrete populations Stepping-stone Island model.

Human Migrations Saeed Hassanpour Spring Introduction Population Genetics Co-evolution of genes with language and cultural. Human evolution: genetics,

Salit Kark Department of Evolution, Systematics and Ecology The Silberman Institute of Life Sciences The Hebrew University of Jerusalem Conservation Biology.

MtDNA diversity in Central Africa: from hunter-gathering to agriculturalism CNRS-Institut Pasteur, Paris Lluis Quintana-Murci Blandine Massonnet Francesca.

A dynamic program algorithm for haplotype block partitioning Zhang, et. al. (2002) PNAS. 99, 7335.

Human population migrations Out of Africa, Replacement –Single mother of all humans (Eve) ~150,000yr –Single father of all humans (Adam) ~70,000yr –Humans.

PROCESS OF EVOLUTION I (Genetic Context). Since the Time of Darwin  Darwin did not explain how variation originates or passed on  The genetic principles.

Aussois The Berbers Linguistic and genetic diversity J.-M. DUGOUJON and G. PHILIPPSON UMR 8555 CNRS Toulouse UMR 5596 CNRS Lyon.

Forensics Chapter 8. Central Points  DNA testing can determine identity  DNA profiles are constructed in specialized laboratories  DNA profiles used.

Out-of-Africa Theory: The Origin Of Modern Humans

Haplotype Blocks An Overview A. Polanski Department of Statistics Rice University.

Conservation of genomic segments (haplotypes): The “HapMap” n In populations, it appears the the linear order of alleles (“haplotype”) is conserved in.

Biology 101 DNA: elegant simplicity A molecule consisting of two strands that wrap around each other to form a “twisted ladder” shape, with the.

CS177 Lecture 10 SNPs and Human Genetic Variation

Gene Hunting: Linkage and Association

blank  The Movement of Alleles  The Movement of Alleles Migration and Inter-breeding.

INTRODUCTION TO ASSOCIATION MAPPING

Recombination based population genomics Jaume Bertranpetit Marta Melé Francesc Calafell Asif Javed Laxmi Parida.

Lab 7. Estimating Population Structure. Goals 1.Estimate and interpret statistics (AMOVA + Bayesian) that characterize population structure. 2.Demonstrate.

H.J. Muller. T. Dobzhansky Mutation Rates at Human STR Loci, Measured in Paternity Tests STR SystemMaternal Meioses (%)Paternal Meioses (%) TH015/42100.

The new Y Chromosome Haplotype Reference Database (YHRD) and optimized approaches for the forensic Y-STR analysis Sascha Willuweit & Lutz Roewer Institut.

Y-STR POLYMORPHISMS IN FORENSIC CASEWORK Mgr. Jana Odlerová Institute of Forensic Science Slovak Police Corps.

Evolutionary Genome Biology Gabor T. Marth, D.Sc. Department of Biology, Boston College

Chapter 8 Additional DNA Markers: Amelogenin, Y-Chromosome STRs, mtDNA, SNPs, Alu Repeats ©2002 Academic Press.

Inferences on human demographic history using computational Population Genetic models Gabor T. Marth Department of Biology Boston College Chestnut Hill,

Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds Pontus Skoglund, Erik Ersmark, Eleftheria.

Population Genetics As we all have an interest in genomic epidemiology we are likely all either in the process of sampling and ananlysising genetic data.

High-resolution haplotype structure in the human genome

PLANT BIOTECHNOLOGY & GENETIC ENGINEERING (3 CREDIT HOURS)

Linkage: Statistically, genes act like beads on a string

Unit 7: Mechanisms of Evolution Mutation & Recombination

Population Genetics.

Volume 26, Issue 7, Pages (April 2016)

The Central Siberian Origin for Native American Y Chromosomes

The Genetic Legacy of Religious Diversity and Intolerance: Paternal Lineages of Christians, Jews, and Muslims in the Iberian Peninsula Susan M. Adams,

A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes Fulvio Cruciani, Piero Santolamazza,

Forensic significance and Population structure based on the 11-loci SWGDAM recommended Y-STR haplotypes in some Nigerian Population.

There is a Great Diversity of Organisms

Gene Discovery for Complex Traits: Lessons from Africa

Hong Shi, Yong-li Dong, Bo Wen, Chun-Jie Xiao, Peter A

A Predominantly Indigenous Paternal Heritage for the Austronesian-Speaking Peoples of Insular Southeast Asia and Oceania Cristian Capelli, James F. Wilson,

Linkage Genes that are physically located on the same chromosome are said to be “linked”. Linked genes are said to be “mapped” to the same chromosome.

Maternal History of Oceania from Complete mtDNA Genomes: Contrasting Ancient Diversity with Recent Homogenization Due to the Austronesian Expansion Ana T.

High-Resolution Analysis of Human Y-Chromosome Variation Shows a Sharp Discontinuity and Limited Gene Flow between Northwestern Africa and the Iberian.

Independent Origins of Indian Caste and Tribal Paternal Lineages

A Genetic Landscape Reshaped by Recent Events: Y-Chromosomal Insights into Central Asia Tatiana Zerjal, R. Spencer Wells, Nadira Yuldasheva, Ruslan Ruzibakiev,

E. Wang, Y. -C. Ding, P. Flodman, J. R. Kidd, K. K. Kidd, D. L

F. Mégraud, P. Lehours, F.F. Vale Clinical Microbiology and Infection

What evidence do we have for evolution? (5)

Shuhua Xu, Wei Huang, Ji Qian, Li Jin

Introducing a latent variable approach for finding populations in a forensic DNA database Maarten Kruijver Forensic Science International: Genetics.

Richard Howey, Chrysovalanto Mamasoula, Ana Töpf, Ron Nudel, Judith A

Y-Chromosomal Diversity in Lebanon Is Structured by Recent Historical Events Pierre A. Zalloua, Yali Xue, Jade Khalife, Nadine Makhoul, Labib Debiane,

Stephen Wooding, Un-kyung Kim, Michael J

Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds Pontus Skoglund, Erik Ersmark, Eleftheria.

Haplotypes in the Dystrophin DNA Segment Point to a Mosaic Origin of Modern Human Diversity Ewa Ziętkiewicz, Vania Yotova, Dominik Gehl, Tina Wambach,

Presentation transcript:

Y-chromosome diversity in Central Africa Aussois, September 2005 Gemma Berniell-Lee, Jaume Bertranpetit, David Comas

A HAPLOID SYSTEM THE Y CHROMOSOME Inherited via the father No recombination Variation passed on in the form of a block

STRs and SNPs THE Y CHROMOSOME TACGTAGCTAGCTAGCTAGCTAATGCAC TTCGTAGCTAGCTAGCTAATGCACGCTA TACGTAGCTAGCTAGCTAGCTAATGCAC TTCGTAGCTAGCTAGCTAATGCACGCTA TACGTAGCTAGCTAGCTAGCTAATGCAC TTCGTAGCTAGCTAGCTAATGCACGCTA Set of alleles for a number of STRsHAPLOTYPES HAPLOGROUPSSet of alleles for a number of SNPs

METHODS DYS 388 DYS 389 I/II DYS A7.1 DYS A7.2 DYS 385 DYS 390 DYS 391 DYS 392 DYS 434 DYS 435 DYS 436 DYS 437 DYS 438 DYS 439 DYS 462 DYS 19 DYS 393 EBF MULTIPLEX MSI MULTIPLEX CTS MULTIPLEX

RESULTS GENETIC DIVERSITY INDICES

RESULTS FOUNDER BANTU HAPLOTYPE Thomas et al.(2000) DYS DYS DYS DYS DYS Pereira et al.(2002) described three one-step neighbour haplotypes High frequencies of founder Bantu haplotype and its one-step neighbours in all Bantu populations and identified 3 new ones. Founder Bantu haplotype in 2 pygmy samples and a one-step neighbour in one pygmy sample.

RESULTS POPULATION GENETIC RELATIONHIPS Multidimensional Scaling Plots of R ST genetic distances Stress 0.11

Stress 0.08 RESULTS POPULATION GENETIC RELATIONHIPS Multidimensional Scaling Plots of R ST genetic distances

POPULATION STRUCTURE RESULTS

PHYLOGENETIC RELATIONSHIPS Phylogenetic network of Y-chromosome haplotypes carrying the allele 13.2 of DYS 385 Estimated date of appearance ~5,500 +/- 1,300 years ago.

CONCLUSIONS Bantu populations from Central Africa are very homogeneous, whilst Pygmy populations seem to be quite diverse. Bantu populations are statistically different from Pygmy populations Evidence of possible admixture events between Pygmy and Bantu populations, pointing towards a Bantu-to-Pygmy flow of paternal lineages No evidence of the Fang population or any of the Bantu populations in our sample set having an origin other than Bantu

FUTURE WORK Define genetic diversity present at Y-SNP level 48 Y-SNP multiplex reaction FUTURE WORK