Download Species trees and gene trees

Species trees and gene trees
Fundamentals of molecular phylogenies
Genetic distances
•
Comparison of 50 amino acids (fig 9.6)
Constructing trees
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2
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1
0
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8
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22
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14
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Molecular clocks
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DNA fixes substitutions at
a roughly clock-like rate
Distantly related Related pairs
of species have a large number
of substitutions in the
cytochome c gene
Number of substitutions in
cytochrome c gene
Different types of DNA
segments evolve at
different rates
Time since last common ancestor (millions of years)
Coalescing genes
• Gene trees and species trees
Species tree
Gene tree
Coalescing genes
• Genetic loci have their own genealogy
10 haploid individuals pass down their
copies of alleles at a particular gene
locus
Alleles coalesce
Fig 9.2, 9.3
Coalescing genes
• Coalescence of alleles varies
Coalescence of alleles
in human genes
(Templeton, 2006)
Gene trees versus species trees: rates of evolution
1. Monomorphic founding population
Constant rate of evolution
A
B
C
2. Monomorphic founding population
Unequal rates of evolution
A
A
B
C
B
C
A
B
C
Gene trees versus species trees
A
A
B
C
B
C
A
B
2. Polymorphic founding population
Constant rate of evolution
C
Gene trees versus species trees
Three biological factors that can produce true genealogical
discordance between a gene tree and a species tree
“Non-canonical” trees
• Horizontal gene transfer
• Example: The ACR3 gene
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•
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an arsenic permease involved in the cell’s response to
arsenic toxicity
effluxes arsenite from the cell
The gene is often found on plasmids
Mega - http://www.megasoftware.net/
Silva - http://www.arb-silva.de/
“Non-canonical” trees
• What might explain this result?
Clymene dolphins
Median-joining network of cytochrome b haplotypes of Stenella clymene (red circles),
S. coeruleoalba (green circles) and S. longirostris (blue circles). Circle size is
proportional to the number of individuals exhibiting the correspondent haplotype.
Length of lines separating the haplotypes is proportional to the number of mutational
steps. White circles indicate missing, intermediate haplotypes. (Amaral 2014)
Non-canonical trees
Stenella
coeruleoalba
Stenella clymene
Stenella
longirostris
Stenella
clymene
“Non-canonical” trees
• Gene duplication
Orthologs
Paralogs
Pelagic species
Substrate spawner
Most extant marine teleosts spawn highly
hydrated pelagic eggs, due to differential
proteolysis of vitellogenin (Vtg)-derived
yolk proteins. This tree represents
sequences of vitellogenin sequences
extracted from species that spawn in the
pelagic zone and one that spawns against
substrate