Unit 6 Part 10001 Genetic Diversity PDF

Characterizing genetic diversity in single loci and by quantitative variation  Unit 3 Characterizing genetic diversity in single loci and by quantitative variation. ✓ What is genetic diversity? ✓ How do you measure genetic diversity? ✓ What are DNA markers...

Characterizing genetic diversity in single loci and by quantitative variation  Unit 3 Characterizing genetic diversity in single loci and by quantitative variation. ✓ What is genetic diversity? ✓ How do you measure genetic diversity? ✓ What are DNA markers and their properties (microsatellites, SNPs, allozymes, etc.)? ✓ Types of DNA (nuclear vs mtDNA) and why would you choose one over the other? ✓ What are the characteristics of nuclear (nDNA) and mtDNA? ✓ Forms of genetic diversity (allelic, heterozygous, etc.)? ✓ How to you get samples – types of samples - to conduct genetic diversity? ✓ Lab procedures to extract DNA? PCR process and function? ✓ Differences when working on different labs – invasive versus non-invasive? Characterizing GD in single loci and by quantitative variation Measuring genetic diversity Genetic diversity and variation Traits = alleles, genes, chromosomes, proteins, SNPs, heritable traits DNA Markers SNPs, Microsatellites, allozymes and chromosomal variants Quantitative markers Morphological/Phenotypic traits What is genetic variation? ✓Genetic variation “GV” ✓The raw material upon which natural selection acts ✓Reflects a taxa/spp evolutionary potential ✓Genetic variation has 3 components: ✓Genetic diversity (GD) = alleles and proportion of heterozygous inds ✓Genetic differentiation ✓Genetic distance ✓GV with respect to natural selection can be: ✓Neutral ✓Adaptive Types of DNA Characteristics of types of animal DNA Genetic markers: DNA based Nuclear (nDNA or gDNA) DNA sequencing Microsatellite (simple sequence repeats SSR or short tandem repeats STR) Amplified fragment length polymorphism (AFLP) Single nucleotide polymorphism (SNP) Randomly amplified polymorphic DNA (RAPD) DNA fingerprints (variable number tandem repeats VNTR) Restriction fragment length polymorphism (RFLP) Mitochondrial DNA (mtDNA) DNA primers that work for most species are now available for the control region (also known as the D-loop), for the cytochrome b locus and the 12S rRNA locus Trace female lines of descent, or migration patterns Bar/metabarcoding Assignment: characteristics of types of flora DNA Assignment: 1. Description of chloroplast genome 2. 2 main molecular analysis methods used to infer relationships among plant populations using chloroplast genomes 3. Properties of cpDNA 4. Example of an application of cpDNA to assist with the conservation/management of a plant species of conservation concern Questions that can be answered using molecular genetics Other charasteristics of molecular markers Molecular/DNA-based genetic marker Is any visible character or otherwise assayable phenotype Heritable DNA sequence differences (polymorphisms) Desirable characteristics of a genetic marker Inexpensive to develop and apply Unaffected by environmental and developmental variation; Highly robust and repeatable across different tissue types and different laboratories Polymorphic, i.e. reveal high levels of allelic variability Codominant in its expression  Where do we get DNA from (biological samples)? Invasive Non-invasive or remotely sampling Requires handling of sampling Does not require physical handling unit (ind) Scat/urine Tissue – kidney, spleen, brain, Hair lung, heart, blood Blood Larger amounts of highly pure DNA Tissue Lower/degraded amounts of highly pure DNA Genotyping error Fail to correct identify genotypes Fail to distinguish different individuals “shadow effect” Shed hair, skin, feathers, egg shell, fish scales, museum specimens and even fossils  Where do we get DNA from and how do we preserve them? Source of biological material per marker/techniques Stages Study objectives Data Sample analysis collection PCR Laboratory DNA extraction