SPAGeDi a program for Spatial Pattern Analysis of Genetic Diversity

Slides:

Advertisements

Similar presentations

RAPD markers Larisa Gustavsson (Garkava)

Advertisements

BIOL EVOLUTION AT MORE THAN ONE GENE SO FAR Evolution at a single locus No interactions between genes One gene - one trait REAL evolution: 10,000.

Population Genetics 2002 WORKSHOP GENETIC ESTIMATES OF DISPERSAL Joop Ouborg Dept. of Ecology Univ. of Nijmegen.

Confounding from Cryptic Relatedness in Association Studies Benjamin F. Voight (work jointly with JK Pritchard)

Planning breeding programs for impact

Sasha Gimelfarb died on May 11, 2004 A Multilocus Analysis of Frequency-Dependent Selection on a Quantitative Trait Reinhard Bürger Department of Mathematics,

Lab 3 : Exact tests and Measuring of Genetic Variation.

Lab 3 : Exact tests and Measuring Genetic Variation.

Chapter 6: Quantitative traits, breeding value and heritability Quantitative traits Phenotypic and genotypic values Breeding value Dominance deviation.

Cultivation of the blue mussel (Mytillus edulis) has grown strongly in Scotland over the last ten years. The further development of sustainable and productive.

Evaluation of a new tool for use in association mapping Structure Reinhard Simon, 2002/10/29.

Believing in MAGIC: Validation of a novel experimental breeding design Emma Huang, Ph.D. Biometrics on the Lake December 2, 2009.

Genetic diversity analysis of CWR in Portugal Joana Magos Brehm, Brian V. Ford-Lloyd, Nigel Maxted, Maria Amélia Martins-Loução Joint PGR Secure/ECPGR.

Quantitative Genetics Up until now, we have dealt with characters (actually genotypes) controlled by a single locus, with only two alleles: Discrete Variation.

Quantitative Genetics Theoretical justification Estimation of heritability –Family studies –Response to selection –Inbred strain comparisons Quantitative.

Conservation Genetics: Lessons from Population & Evolutionary Genetics.

Brian Kinlan UC Santa Barbara Integral-difference model simulations of marine population genetics.

Quantitative Genetics

Molecular Markers DNA & PROTEINS –mtDNA = often used in systematics; in general, no recombination = uniparental inheritance –cpDNA = often used in systematics;

Population Genetics What is population genetics?

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.

Procedures in RFLP. RFLP analysis can detect Point mutations Length mutations Inversions.

Population Genetics of Puccinia coronata f. sp. avenae Hattie Dambroski and Martin Carson USDA-ARS Cereal Disease Laboratory Saint Paul, MN.

Linkage Analysis in Merlin

Genetic Diversity of the Phaseolus acutifolius A. Gray Collection of the USDA National Plant Germplasm System Using Targeted Region Amplified Polymorphism.

Mating Programs Including Genomic Relationships and Dominance Effects

Lecture 5: Segregation Analysis I Date: 9/10/02  Counting number of genotypes, mating types  Segregation analysis: dominant, codominant, estimating segregation.

Creating a Kinship Matrix using Microsatellite Analyzer (MSA) Zhifen Zhang The Ohio State University.

Biodiversity IV: genetics and conservation

The appropriateness of three different association analysis models, the least square solution to the fixed effects General Linear Model (GLM-Q, Searle.

Maria Eugenia D’Amato Slide 1

Molecular phylogenetics

Targeted next generation sequencing for population genomics and phylogenomics in Ambystomatid salamanders Eric M. O’Neill David W. Weisrock Photograph.

Genes within Populations. What is a population? How are populations characterized? What does it mean to be diploid, haploid, polyploid? How can we characterize.

Lecture 13: Population Structure October 5, 2015.

Experimental Design and Data Structure Supplement to Lecture 8 Fall

Quantitative Genetics. Continuous phenotypic variation within populations- not discrete characters Phenotypic variation due to both genetic and environmental.

Complex Traits Most neurobehavioral traits are complex Multifactorial

Quantitative Genetics

INTRODUCTION TO ASSOCIATION MAPPING

Bottlenecks reduce genetic variation – Genetic Drift Northern Elephant Seals were reduced to ~30 individuals in the 1800s.

Estimating Genealogies from Marker Data Dario Gasbarra Matti Pirinen Mikko Sillanpää Elja Arjas Biometry Group Department of Mathematics and Statistics.

Lecture 12: Linkage Analysis V Date: 10/03/02  Least squares  An EM algorithm  Simulated distribution  Marker coverage and density.

Lecture 13: Population Structure

Lecture 24: Asscociation Genetics November 20, 2015.

Molecular markers Non-PCR based 1courtesy of Carol Ritland.

Errors in Genetic Data Gonçalo Abecasis. Errors in Genetic Data Pedigree Errors Genotyping Errors Phenotyping Errors.

Populations: defining and identifying. Two major paradigms for defining populations Ecological paradigm A group of individuals of the same species that.

Lab 4: Inbreeding and Kinship. Inbreeding Reduces heterozygosity Does not change allele frequencies.

Using Merlin in Rheumatoid Arthritis Analyses Wei V. Chen 05/05/2004.

Types of genome maps Physical – based on bp Genetic/ linkage – based on recombination from Thomas Hunt Morgan's 1916 ''A Critique of the Theory of Evolution'',

Statistical Genomics Zhiwu Zhang Washington State University Lecture 26: Kernel method.

1 Chapter 8: Fingerprints, diversity analysis, specific markers Cultivar identification (fingerprint) Specific markers Distance analysis (genetic relatedness)

Genetic mapping and QTL analysis - JoinMap and QTLNetwork -

Association Mapping in Families Gonçalo Abecasis University of Oxford.

Quantitative genetics

Bottlenecks reduce genetic variation – Genetic Drift

Washington State University

Washington State University

DNA Marker Lecture 10 BY Ms. Shumaila Azam

Mapping Quantitative Trait Loci

Genome-wide Association Studies

Washington State University

Linkage analysis and genetic mapping

Barley (Hordeum vulgare subsp. vulgare)

IBD Estimation in Pedigrees

Washington State University

mtDNA genotypes correlate with gut microbiota composition.

Presentation transcript:

SPAGeDi a program for Spatial Pattern Analysis of Genetic Diversity by Olivier J. Hardy and Xavier Vekemans http://www.ulb.ac.be/sciences/lagev/ Goal: characterise spatial genetic structure of mapped individuals or populations using genotype data of any ploidy level Compute: - inbreeding coef - pairwise relatedness/differentiation coef between indiv/pop  averages / distance classes  association with distance (regression with lin/log distance) ( isolation by distance, neighbourhood size estimates) - actual variance of relatedness coef  Ritland’s approach for marker based estimate of h2 Tests: - permutations (of genes, individuals, or spatial locations) - jackknife over loci ( SE for multilocus estimates) Option: - restricted analysis within or among categories of ind/pop

Input data Input file with : format #’s (#ind, #categ, #spat coord, #loci, #digits/allele, ploidy) distance intervals for each ind : name category (facultative) spatial coordinates genotype at each locus Analyses defined on keyboard while running the program : indiv vs pop level stat to compute (+ within/among categ) tests, …

Statistics computed: "relatedness" coef at the individual level 2-genes coef : - "kinship" coef (Loiselle 1995; Ritland 1996) - "relationship" coef (Moran’s I; Lynch & Ritland 1999; Wang 2002) - kinship type coef based on allele size (Streiff et al. 1999) - ar distance measure (Rousset 2000) 4-genes coef : - "fraternity" coef (Lynch & Ritland 1999; Wang 2002) also for dominant marker (Hardy 2003)

Estimates of the actual variance of pairwise kinship coef in natural populations

Consistency among kinship coef estimators

Reliable estimates of the actual variance of pairwise relatedness require large data set (300 – 1000 individuals) very polymorphic markers and/or many loci  SSR  AFLP ???