Molecular Stream Ecology

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Molecular Stream Ecology
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Topics

• Genetic diversity
• How is it defined ?
• How is it measured ?
• Population Substructure
• Applying population genetics tools to stream
  ecology

Paper Discussion Waples et al. 2001
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Population Genetics a pedigree
Evolutionary Genetics Biology 1859
1866 (1900)
http//instruct.uwo.ca/zoology/441a/hist1.html
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What is biodiversity?

• In Conservation
• The variety of life in all its forms, levels,
  and combinations.
• Includes
• Ecosystem diversity
• Species diversity
• Genetic diversity
• (IUCN, UNEP, and WWF, 1991)

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Quantification Conservation

• Ecosystem diversity
• Scale-dependent groupings of broadly similar
  assemblages and habitats
• Species diversity
• Number and relative abundances of species or
  other taxa in a particular ecological unit
• Genetic diversity
• DNA-based measures of genetic variation within
  and among populations

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The unifying process Evolution

• Ecosystem the environmental context of evolution
• Genes the raw material of evolution
• ? Species (and interactions) products of
  evolution

Loosely speaking, habitat diversity and genetic
diversity interact through the process of
evolution to create species diversity
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Evolution
a process that results in heritable changes
in a population over multiple generations.
Kingdom  Phylum  Class Order
Family Genus  Species
__________
Genetic divergence
Biodiversity
Population
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What is a population?
a local group of conspecific organisms sharing
a common gene pool.
You collected the same mayfly species in 3
adjacent headwater streams.
How many populations are here?

• A) 1
• B) 2
• C) 3

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The answer could be a, b, or c
But how would you know?
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Population Genetics
is the study of genetic variation within and
among populations, and the evolutionary and
ecological processes that produce and maintain
(or eliminate) that variation.

• Genetic Variation among species Divergence
• Genetic Variation within species Polymorphism

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Polymorphism
..is rampant at every level of genetic
analysis

• Morphological polymorphism
• Protein polymorphism (amino acid sequence)
• DNA polymorphism (nucleotide sequence or
  chromosomal structure)
• Is the basis for measuring genetic diversity
• Provides a rich source of data for ecology and
  conservation

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What is DNA polymorphism?

• A genetic locus at which the frequency of the
  most common allele is lt 0.95
• Two or more genetically different classes
  co-existing within a population

Example Population sample showing multi-locus
polymorphism in a 100 base pair (bp) gene
fragment Site Allele 13 19 46 52 87 a T C
T A G b T C C T G c C T C C T d C T C C G
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DNA Polymorphisms

• Arise from multiple evolutionary and population
  processes
• Accumulate at significantly different rates as a
  result of differences in (a) DNA type (b)
  environmental conditions (c) rates of
  emigration/immigation, etc.
• May increase or decrease in a given population
  over time.

The Natural History of DNA
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Quantifying polymorphism

• Nucleotide diversity (p)
• Average proportion of nucleotide differences
  between all possible pairs of sequences in the
  sample (differences / (n(n-1)/2)sites

Site Allele (n4) 13 19 46 52 87 a
T C T A G b T C C T G c C T C C T d
C T C C G
------------------------------------ Differences
4 4 3 5 3
19 p 19 / (6
100) 0.032

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Quantifying polymorphism

• Allelle (or gene) frequency
• Genotype frequency

For allele A p xAA ½ xAa For allele
a q 1- p xaa ½ xAa
For alleles A and a Genotype AA
Aa aa Frequency xAA
xAa xaa 1

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Heterozygosity a key measure of diversity

• Hardy Weinberg Equilibrium
• The relative frequency of heterozygotes in a
  randomly mating population
• The expected heterozygosity at a locus (HE)

Frequencies in offspring under Hardy-Weinburg
Equilibrium
AA p2 Aa 2pq aa
q2
p2 2pq q2 1
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Wrights F statistic Inbreeding Coefficient
SINGLE POPULATION

• Reduction in heterozygosity relative to a
  randomly-mating population with the same allele
  frequencies

HS HI HS
FIS
p2 (1-F) pF p2 pqF 2pq (1-F)
2pq 2pqF q2 (1-F) qF
q2 pqF
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The classic example
We sample a mouse population that has become
subdivided in a barn, and look at a single locus
with 2 alleles in the population (A,a)
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Using deviations from HWE to detect population
substructure (or inbreeding)
East p(A)0 q(a)1
West p(A)1 q(a)0

• If you sampled the barn mice as one population
• You would find p0.5 and q0.5, but HO0 (no
  heterozygotes observed in the population).
• Since you expect HE 2pq 0.5 under HWE, you
  know that this population is not randomly mating.
  It is substructured, or inbred (related
  concepts)

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The FST statistic Fixation Index
Multiple Populations

• (Remote inbreeding) The average reduction in
  HWE heterozygosity among two or more
  subpopulations (HS) relative to the combined
  population (HT).

For single locus
p2
p3
p1
p4
p5
(Recall that q1-p)
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Interpreting FST

• The theoretical range of FST 0..1, but in
  reality it is usually much smaller than one

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Effects of population substructure

• Reduction in heterozygosity
• Genetic divergence
• Selection pressures may be different across
  subpopulations
• Reduced gene flow, which spreads novel alleles
  (mutations) that arise into the total population
• Genetic drift causes random fixation and loss of
  alleles within subpopulations

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Genetic Drift

• The random fluctuations of allele frequencies due
  to sampling of gametes at reproduction. Alleles
  are fixed or lost from a population simply by
  chance.
• Without gene flow, every allele in every
  population will eventually become lost or fixed.
  However, the rate of drift is much faster in
  small populations

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Consider stream geomorphology

• Stream habitats are hierarchically structured by
• Nested drainage basin morphology
• Unidirectional streamflow

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A hypothetical stream network
Stream p q 2pq 1 0.6 0.4 0.48 2
0.3 0.7 0.42 3 0.2 0.8 0.32
Avg 0.37 0.63 0.41
(Single locus, 2 alleles)
HT - HS HT
(0.46 0.41) / 0.45 0.11
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Physical network structure

• limits dispersal options

• can be highly branched

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Invertebrate population genetic structure
Physical network structure
Stream Order

• Isolation-by-distance
• Peltoperlidae1 (Rocky Mtns)
• Peltoperlidae (Appalachians)
• Baetidae 2 (Swiss Alps)
• Glass shrimp3 (Queensland)
• Inversion of I-by-D
• Baetidae 4 (Queensland)
• Tasimiidae 4 (Queensland)

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Evolutionary processes at work

• Mutation
  A5
• random introduction of novel alleles A4
• Heterozygotes_____
• A1 A4 A2 A5

A2
A1
A3
A0
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300 M years of evolution