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Backbones of evolutionary history
test biodiversity theory for microbes
James P. O’Dwyer, Steven W. Kembel,
and Thomas J. Sharpton
Proceedings of the national Academy of
Sciences (PNAS) (2015)
Sweetie Kuehu
Central Goal in Ecology
Patterns of Biodiversity
Central Goal in Ecology
Patterns of Biodiversity
Central Goal in Ecology
Patterns of Biodiversity
Mechanism
Central Goal in Ecology
Patterns of Biodiversity
Mechanism
Central Goal in Ecology
Patterns of Biodiversity
Mechanism
Data
Microbial Community Challenges
Microbial Community Challenges
• Unambiguous species
concept
Microbial Community Challenges
• Unambiguous species
concept
– ecological species is a set
of organisms adapted to
a particular set of
resources, a niche in the
environment
Microbial Community Challenges
• Unambiguous species
concept
– ecological species is a set
of organisms adapted to
a particular set of
resources, a niche in the
environment
– biological species is a
group of individuals
reproductively isolated
from other groups
Microbial Community Challenges
• Unambiguous species
concept
– ecological species is a set
of organisms adapted to
a particular set of
resources, a niche in the
environment
– biological species is a
group of individuals
reproductively isolated
from other groups
• Ecological mechanisms
Microbial Community Challenges
• Unambiguous species
concept
– ecological species is a set
of organisms adapted to
a particular set of
resources, a niche in the
environment
– biological species is a
group of individuals
reproductively isolated
from other groups
• Ecological mechanisms
– mechanism is a system
of causally interacting
parts and processes that
produce one or more
effects
Microbial Community Challenges
• Unambiguous species
concept
– ecological species is a set
of organisms adapted to
a particular set of
resources, a niche in the
environment
– biological species is a
group of individuals
reproductively isolated
from other groups
• Ecological mechanisms
– mechanism is a system
of causally interacting
parts and processes that
produce one or more
effects
– relations of organisms to
one another and to their
physical surroundings
Microbial Community Challenges
• Unambiguous species
concept
– ecological species is a set
of organisms adapted to
a particular set of
resources, a niche in the
environment
– biological species is a
group of individuals
reproductively isolated
from other groups
• Ecological mechanisms
– mechanism is a system
of causally interacting
parts and processes that
produce one or more
effects
– relations of organisms to
one another and to their
physical surroundings
– Ex: natural selection,
genetic drift, mutation,
and gene flow
Obstacles Linking Microbial
Theory
Data
Obstacles Linking Microbial
Theory
Data
1. Ecologically
meaningful microbe
species vary and
depend critically on
history and
environment
Obstacles Linking Microbial
Theory
Data
1. Ecologically
meaningful microbe
species vary and
depend critically on
history and
environment
- testing theories
rely on species
concept vs.
phylogenetics
Obstacles Linking Microbial
Theory
Data
1. Ecologically
meaningful microbe
species vary and
depend critically on
history and
environment
- testing theories
rely on species
concept vs.
phylogenetics
2. Theoretical models for
macroscopic
organisms are used for
microbes
Obstacles Linking Microbial
Theory
Data
1. Ecologically
meaningful microbe
species vary and
depend critically on
history and
environment
- testing theories
rely on species
concept vs.
phylogenetics
2. Theoretical models for
macroscopic
organisms are used for
microbes
- temporal and
spatial scales are
fundamentally
different
Alternative Framework for Microbes
Alternative Framework for Microbes
• Neutral Biodiversity
Theory
Alternative Framework for Microbes
• Neutral Biodiversity
Theory
– patterns in the
distribution and
abundance of similar
organisms supposes that
all individuals have the
same probabilities of
birth and death
Alternative Framework for Microbes
• Neutral Biodiversity
Theory
– patterns in the
distribution and
abundance of similar
organisms supposes that
all individuals have the
same probabilities of
birth and death
– Outputs: abundance
distributions, speciesarea curves and rangeabundance relationships
Alternative Framework for Microbes
• Neutral Biodiversity
Theory
– patterns in the
distribution and
abundance of similar
organisms supposes that
all individuals have the
same probabilities of
birth and death
– Outputs: abundance
distributions, speciesarea curves and rangeabundance relationships
• Phylogenetic Diversity
Alternative Framework for Microbes
• Neutral Biodiversity
Theory
– patterns in the
distribution and
abundance of similar
organisms supposes that
all individuals have the
same probabilities of
birth and death
– Outputs: abundance
distributions, speciesarea curves and rangeabundance relationships
• Phylogenetic Diversity
Theory
– Circumvents the need to
define microbial species
Alternative Framework for Microbes
• Neutral Biodiversity
Theory
– patterns in the
distribution and
abundance of similar
organisms supposes that
all individuals have the
same probabilities of
birth and death
– Outputs: abundance
distributions, speciesarea curves and rangeabundance relationships
• Phylogenetic Diversity
Theory
– Circumvents the need to
define microbial species
– Explores patterns across
multiple habitats
Alternative Framework for Microbes
• Neutral Biodiversity
Theory
– patterns in the
distribution and
abundance of similar
organisms supposes that
all individuals have the
same probabilities of
birth and death
– Outputs: abundance
distributions, speciesarea curves and rangeabundance relationships
• Phylogenetic Diversity
Theory
– Circumvents the need to
define microbial species
– Explores patterns across
multiple habitats
– Outputs: cladogram
Central Findings
Central Findings
1. Empirical trees
Central Findings
1. Empirical trees
- on fine scale, very
individualistic
Central Findings
1. Empirical trees
- on fine scale, very
individualistic
- on coarse scale,
backbone is simple,
robust, consistent
across habitats,
bursts of
diversification
throughout
Central Findings
1. Empirical trees
- on fine scale, very
individualistic
- on coarse scale,
backbone is simple,
robust, consistent
across habitats,
bursts of
diversification
throughout
2. Data was not
predictable by using
the standard neutral
theories of biodiversity
Results
Results
Theoretical Framework for Microbes
Results
Theoretical Framework for Microbes
Ecological
Mechanisms
Results
Theoretical Framework for Microbes
Ecological
Mechanisms
Phylogenetic
Patterns
Documenting Patterns of PD
Documenting Patterns of PD
1. Quantify the increase
in PD with number of
individual sequences
sampled
Documenting Patterns of PD
1. Quantify the increase
in PD with number of
individual sequences
sampled
2. Explore heterogeneity
in diversification rates
across the same trees
Documenting Patterns of PD
1. Quantify the increase
in PD with number of
individual sequences
sampled
2. Explore heterogeneity
in diversification rates
across the same trees
Documenting Patterns of PD
1. Quantify the increase
in PD with number of
individual sequences
sampled
2. Explore heterogeneity
in diversification rates
across the same trees
Central Conclusion
Documenting Patterns of PD
1. Quantify the increase
in PD with number of
individual sequences
sampled
2. Explore heterogeneity
in diversification rates
across the same trees
Central Conclusion
PD increases approximately as a power law
with sample size across all habitats.
Empirical Scaling of PD
Edge length abundance distribution(EAD)
Power Law
Expected sample size
Abundance of a clade
Community size
Empirical EAD
Coarse Graining
Coalescent Theory
A model of the effect of genetic drift, viewed backwards
in time, on the genealogy of antecedents
How long ago the two genes shared
their most recent common ancestor.
Gene genealogies represent patterns of
descent among genes within species.
Λ-Coalescents
• Stochastic-Random
FastTree
•
•
•
•
Open source software
The Arkin Laboratory (UC Berkeley)
http://genomics.lbl.gov/
http://www.microbesonline.org/fasttree/
RAxML
•
•
•
•
•
Randomized Axelerated Maximum Likelihood
Open source software
The Exelixis Lab (Heidelberg Institute)
http://sco.h-its.org/exelixis/index.html
http://sco.h-its.org/exelixis/web/software/
raxml/hands_on.html
Multiple Sequence Alignment and
Phylogenetic tree (Bioinformatics)
• https://www.youtube.com/watch?v=I90MJShs
mmk
This video is about how to make Multiple sequence
alignment using NCBI and Clustal Omega. (5:27)