Lecture 8 Power and Promise of DNA. Flashcards
LAST LECTURE - TAKEAWAYS
6 pathways of plant domestication
Cereal pathway – adaptive introgression
Weed pathway – Vavilovian mimicry
Tuber pathway – high phenotypic plasticity
Ecosystem engineering – landscape management rather than ‘domestication’
Fruit tree pathway – propagation through layering, sucker removal, stem cutting and
grafting
Directed fiber pathway – prior knowledge of cereal domestication
REVIEW OF GENETICS
Genome: the complete set of inheritable genetic material of an organism
- Genes (coding DNA– 3%) – units of heredity - component of gnome
- Non-coding sequences (97%) contain most genetic variation between groups and individuals
NUCLEAR GENOMES
(nDNA)
- Pairs of chromosomes (autosomes, sex chromosomes)
- Inherited from both parents
- Undergoes recombination
- NRY: Non-recombining area of the Y (sex) chromosome
MITOCHONDRIAL DNA
(mtDNA)
- 37 genes and non-coding DNA
- ~1000 mitochondria in each cell
- Circular genome
- Non-recombinant - stable gene component
- Used to track maternal lineages
GENETIC ANALYSIS IN DOMESTICATION STUDIES
Analyze similarities and differences across the genomes(differences between wild and domesticated species)
Single nucleotide polymorphisms (SNPS)
GENETIC ANALYSIS IN DOMESTICATION STUDIES
mtDNA for phylogenetic analysis
(i.e., evolutionary relationships)
nDNA usually required to track:
- Gene flow
- Genetic drift
- Bottlenecks
- Reproductive isolation
- Artificial selection
DNA GLOSSARY
Phylogenetics: Study of evolutionary relationships among groups of organisms (three like diagram)
Phylogeography: historical processes responsible for the geographic distributions of individuals
Nuclear DNA/Genome: DNA contained within a nucleus of eukaryotic (cells have a nucleus) organisms, with information from both parents (recombinant)
Mitochondrial DNA: Maternally inherited DNA located in mitochondria (non- recombinant)
Regulatory gene: A gene involved in controlling the expression of one or more other genes (important for epigenetic)
Quantitative Trait Loci: Stretches of DNA containing or linked to the genes that underlie a quantitative trait (typically vary along a gradient/spectrum) ex: fur color
WHY DNA IS SO POWERFUL?
- to track wild phenotypes and domestic phenotype
WHY DNA IS SO POWERFUL?
Genetic change often precedes morphological changes visible in the archaeological record.
Provides insight into the early stages of domestication
TRADITIONAL APPROACHES
Geographic centres of diversity or wild progenitor range identified as origin of domestication (Vavilovian approach)
Primarily based on earliest archaeological evidence or on morphological evidence
✔May be valid for species with a restricted geographic range (e.g., teosinte)
✘ Difficult for widely distributed species (e.g., grey wolf) or when animals are domesticated on the periphery of range
Genetic approch
- compare DNA from domestic population to various wild populations and assess their evolutionary relationships(Phylogeography)
- traditionally focused on mitchondrial DNA
- now-
PROGENITOR OF SW DOMESTIC TURKEY
Who is the progenitor of the
Southwest domestic turkey?
- Local wild turkey stocks?
- Imported from Mexico?
Analysis of modern wild turkey
mtDNA and extinct domestic
turkey DNA
results
SW turkey is distinct from Mexican turkeys
Also distinct from local wild turkeys
Wild progenitor populations still unknown
LESSON 1(cons of genetic reserch)
Modern wild populations have
complex histories and it may be impossible to identify progenitor
populations based on modern DNA alone
example
WHERE & HOW
MANY TIMES
WERE PIGS
DOMESTICATED?
Extensive archaeological evidence for domestic pigs across Eurasia
DNA analysis of modern
wild and domestic pigs worldwide, suggested at least 6 different independent centers of domestication.
NOW WITH ANCIENT DNA…
DNA analysis of archaeological pigs in Europe and Near East reveals extensive gene flow
- Near Eastern domestic pigs are
introduced to Europe ~5,500BC - Domestic pigs interbreed extensively with European wild boars (gene flow)
- ‘European’ domestic pigs return to
Near East ca. 700BC.
ADAPTIVE INTROGRESSION
Gene flow between wild and domestic populations that increases diversity, facilitates adaptions to various environments, and/or increases the fitness of the recipient population.
- e.g., gene flow from European aurochs and wild boar into introduced domestic populations.
Gene flow can be difficult to differentiate from independent domestication events
Lesson 2 (cons)
There is frequently gene
flow (introgression) between introduced domestic populations and
local wild animals.
Without ancient DNA
analysis, this introgression can be mistaken for an independent
domestication event
MOLECULAR CLOCK
Regular rate of random DNA mutations
Estimate divergence times between taxa
try ro understand when domestication happened - as precise as it cans
DOG/WOLF MOLECULAR CLOCK
- mtDNA set divergence at
~135,000BP (too old!) - Full genome analysis set date at
11,000–16,000BP (too recent!) - Ancient genome study suggests
60,000-20,000 BP (just right?)
Frantz et al. 2016. Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science 352, 1228–1231.
LESSON 3
DNA mutation rates can differ by orders of magnitudes
Different DNA loci can produce wildly different results
Best scaled for divergences >1mya
TIMING OF MAIZE DOMESTICATION
Archaeological evidence for maize
domestication10,000-6,250 BP in S. Mexico
Genome sequence of a 5,310-year-old maize cob, modern teosinte and maize landraces
Similar to modern maize, but with several ancestral traits (mosaic)
Suggests slow, gradual adoption of
domestication syndrome.
LESSON 4
Ancient DNA analysis of intermediate forms can (sometimes) be useful for tracking the timing of domestication
and the strength of artificial selection
helpful to written
THE AGE OF CLONES
Grape vines are vegetatively propagated, producing clonal varieties for wine
DNA of 28 grape seeds from archaeological sites in France
Roman grapes closely related to cultivars used for winemaking today: syrah, pinot noir
One ~1100AD grape was identical to
modern ‘Savagnin Blanc’
there is a citation in the slide
