Title: Gene-tree/species-tree discordance and diversification
1Gene-tree/species-tree discordance and
diversification
Sara Ruane CUNY (CSI, GC)
R. Alex Pyron The GW Univ.
Frank Burbrink CUNY (CSI, GC)
2Understanding patterns of diversification
- Ecological Opportunity
- Key Innovations
- Competition
- Extinction
- Ecological Limits
3History of the study
- Paleontological Research
- Understand patterns of speciation and extinction
through time - Simpson (1944, 1953)
- Sloss (1950)
- Sepkoski (1979)
- Stanley (1979)
- Raup (1985)
- Foote (1993)
4Sloss 1950
5Molecular Phylogenetic Approaches
- Waiting times between speciation
- Slowinski and Guiher (1989)
- Harvey et al. (1991, 1994)
- Nee et al. (1992, 1994)
- Pybus and Harvey (2000)
- Rabosky (2006, 2008)
- Purvis et al. (2009)
6Gamma and Rate Variable Models
- Gamma (?) examines the density of nodes relative
to time - Models of diversification
- 1 ) Constant
- Yule, Birth-Death
- 2) Variable
- Yule2, Yule3, DDL, DDX
7Plethodon ouachitae Complex
Early
Late
Even (Yule)
Log(Lineages)
Time
Gamma 2.2 (LB/Ext)
Gamma -4.5 (DDL)
Gamma -1.3 (Yule)
8External Problems with Molecular Trees
- Only Looking at the winners
- Extinction dynamics must come from data external
to the tree or tame diversification rate
variation across a tree - Can we see all speciation events?
Quental and Marshall (2010)
9Internal Problems Gene-Tree/Species-Tree
Discordance
A
B
(See Edwards and Beerli 2000)
10What does ?t tell us?
- Increasing 2Ne (T/2) increases ?t
- Gene div gt Species div
- ?t will be small as div time between species
becomes large, because ?t will be a small
fraction of the total gene divergence - At deep div SG
- At shallow div SltltG
11Simulating gene trees from species trees
?t
Tree Depth
12Impact on diversification estimation
- Disproportionally pushes younger nodes towards to
the root - Density of nodes increases gt root.
- Decreasing ? (early burst!)
- Variable diversification models
- Impact of T (4Neµ)?
13Simulations
- In R
- (Phybase, Ape, Geiger, Laser, Phangorn)
- Simulate Species Trees (ST)
- Yule ?0 and BD
- Taxa 25-100
- Simulate Gene Trees (GT)
- T 0.0001-100
- T G distribution
Burbrink Pyron 2011
14What are we looking for?
- Impact of T on ?-error (GT ST)
- Topology (RF Distance)
15Simulation Results
16Implications
- T gt 1 yields a pattern of early burst (-?)
- T gt 1 also increases topological discordance
- Is T gt 1 likely?
- Most studies of extant populations are well below
1.0.
17Empirical Study
- Group with all species sampled
- Enough genes to construct a species trees
- Lampropeltis
- 21 species of snakes
- Throughout North America and South America
- 12 Loci
18Comparisons
- Tested fit of model for all genes and partitions
- Species Trees (Beast) 3-7 individuals /species
- Individual Gene Trees (Beast)
- Concatenated gene trees with mtDNA
- Concatenated gene trees nuclear genes only
- Two calibration points
19Lampropeltis Concat Gene Tree Depth Error
R20.87 Plt4.36x10-7
?t
Tree Depth
20Null Distribution Yule
21SpeciesTree -0.169 Yule
22SpeciesTree -0.169 Yule
Nucl Gene Trees -1.512 to 0.415 Yule
23SpeciesTree -0.169 Yule
Nucl GT -1.512 to 0.415 Yule
mtDNA GT -2.19 DDL
24SpeciesTree -0.169 Yule
Concat GT mtdna and nuc -2.474 DDL
25SpeciesTree -0.169 Yule
Concat mtdna and nuc -2.474 DDL
Concat nuc -2.11 Yule2
26Is ?-errorassociated with topological
discordance?
R20.083 P0.787
?-error
RF
27Issues
- Increasing T increases ?-error
- Mean T for Lampropeltis 0.0055 (Max0.04)
- GT/ST divergence and ? discordance shouldnt be
high - Nuclear gene trees ? are similar to ST
- mtDNA estimates (alone or with other genes)
- of ? are underestimated (early burst)
28Why mtDNA Problems?
- Model underparametrization decreases ? (Revell et
al. 2005) - Saturation Driven Compression
- Deeper nodes are
- artificially compressed
- Decreases ?
- Usually at very old time scales
- In Lampropeltis, mtDNA
- ? (substitutions) increases
- towards terminal branches
- (W 604.5, P 0.0002477)
Hugall et al. 2007, Sanders et al. 2008, Zheng
et al. 2011
29Conclusions
- mtDNA GTs poorly estimate diversification
dynamics - Use Species Trees!
- And include fossils (if possible)
- Investigate Impact on other comparative methods
- Simulations account for
- T
- Substitution variation
- GT uncertainty
30Thanks to
- My coauthors (Sara and Alex), PSC-CUNY, and NSF.
31Simulation Results
32Sloss 1950