Phylogeography
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Phylogeography. John Brookfield Ecology Club 11 th February 2010. Circular DNAs derived from bacterial symbionts 16kb, 37 genes (in humans) Rapid evolutionary rates in warm blooded vertebrates (particularly in “D loop”) Maternally transmitted and non-recombining. Mitochondrial DNAs.

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Phylogeography

Phylogeography

John Brookfield

Ecology Club

11th February 2010


Mitochondrial dnas

Circular DNAs derived from bacterial symbionts

16kb, 37 genes (in humans)

Rapid evolutionary rates in warm blooded vertebrates (particularly in “D loop”)

Maternally transmitted and non-recombining

Mitochondrial DNAs


Phylogeography avise 1994 molecular markers natural history and evolution chapman and hall

Phylogeography (Avise 1994*)Molecular Markers, Natural History and Evolution. Chapman and Hall


Mitochondrial dnas in an undivided population

Mitochondrial DNAs in an undivided population

2Nf


Mutations enable the tree to be estimated average divergence 2 nf n

Mutations enable the tree to be estimated-Average divergence=2NfN

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2Nf

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Animals from northern and southern populations

Animals from Northern and Southern Populations

Nor Nor Nor Nor Sou Sou Sou Sou


Animals from northern and southern populations complete migration and mixing

Animals from Northern and Southern Populations (complete migration and mixing)

Sou Nor Sou Nor Sou Nor Sou Nor


Animals from northern and southern populations1

Animals from Northern and Southern Populations

MRCA

MRCA

Nor Nor Nor Nor Nor Sou Sou Sou Sou Sou


A complementary approach f st

A complementary approach- FST

  • Hardy-Weinberg Formula: q=1-p

  • AA: p2

  • Aa: 2pq

  • aa: q2

    Random Mating

    Inbreeding (specified by F ), when homozygotes exceed p2 +q2


Two islands

Two Islands

p=0.8

q=0.2

p=0.2

q=0.8


A complementary approach f st1

A complementary approach- FST

  • FST=(p1-p2)2/4(p(1-p))

  • -scaled squared difference in allele frequency between the populations

  • -averaged over alleles and loci


Two islands1

Two Islands

p=0.8

q=0.2

p=0.2

q=0.8

FST = (0.8-0.2)2/(4x0.5x0.5)=0.36


What does f st mean

What does FST mean

  • FST=(p1-p2)2/4(p(1-p))

    =(0.8-0.2)2/(4x0.5X0.5)=0.36

    How many heterozygotes expected (Hardy-Weinberg)=2p(1-p)=0.50

    How many seen=

    2p1(1-p1)/2

    +2p2(1-p2)/2

    =0.8x0.2+0.2x0.8 =0.32


Two islands2

Two Islands

p=0.9

q=0.1

p=0.1

q=0.9

FST = (0.9-0.1)2/(4x0.5x0.5)=0.64


Two islands3

Two Islands

p=1.0

q=0.0

p=0.0

q=1.0

FST = (1.0-0.0)2/(4x0.5x0.5)=1.00


Two islands4

Two Islands

p=0.6

q=0.4

p=0.4

q=0.6

FST = (0.6-0.4)2/(4x0.5x0.5)=0.04


Two islands two loci a and b

Two Islands-Two Loci, A and B

pA=0.6

qa=0.4

pB=0.7

qb=0.3

pA=0.4

qa=0.6

pB=0.3

qb=0.7

Linkage Disequilibrium: Association of A and B and association of a and b


The island model f st 1 1 4 n e m

The Island Model: FST =1/(1+4Nem)


Linear stepping stone model

Linear Stepping Stone Model


Isolation by distance

Isolation By Distance


Table of f st values

Table of FST Values


Interpretation 1 gene flow inferred migration rates n e m

Interpretation 1-Gene FlowInferred Migration Rates- Nem


Table of f st values1

Table of FST Values


Interpretation 2 ancestral population splitting upgma tree of population ancestry

Interpretation 2-Ancestral Population SplittingUPGMA Tree of Population Ancestry


Methods

Methods

  • AMOVA-Laurent Excoffier ARLEQUIN

  • http://cmpg.unibe.ch/software/arlequin3/

  • Designed for mtDNAs initially

  • Takes various levels-populations and subpopulations, etc. molecular variation between them as a proportion of total molecular variance


Phylogeography

Methods-Nested Clade Analysis (1)Templeton, A. (2006) Population genetics and microevolutionary theory. Wiley


Nested clade analysis 2

Nested Clade Analysis (2)

  • Dc: Clade distance: Geographical separation of individuals within a clade

  • Dn: Nested clade distance: Distance from the centre of a clade and the mean location of individuals in related clades (all those within the same higher level of nesting)

  • Isolation by distance: A clade-defining mutation arises in a single location, and its spread will increase with age. Clades within that clade (nested clades) will have a geographic distribution within that of the ancestral clade.

  • Fragmentation: Strict correlation of clades with geography-which breaks down as older clades are considered.

  • Range Expansion: Subclades can be more widespread geographically than their ancestral clades.


Methods structure jonathan pritchard

Samples individuals and genotypes at many loci

Creates subpopulations where there are Hardy-Weinberg proportions and linkage equilibrium within subpopulations

Assigns individuals to subpopulations

http://pritch.bsd.uchicago.edu/structure.html

Methods: STRUCTURE- Jonathan Pritchard


Methods geneland

G. Guillot, Estoup, A., Mortier, F. Cosson, J.F. A spatial statistical model for landscape genetics. Genetics, 170, 1261-1280, 2005.

http://www2.imm.dtu.dk/~gigu/Geneland/

Methods-GENELAND


Natural selection

Selective Sweeps

Complete or partial

Locus-specific

Natural Selection


Natural selection1

Natural Selection

  • Effects on FST

    • Balanced polymorphism throughout species range gives low FST

    • Geographically localised selection gives high FST


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