系統解析論演習１（梶田担当分） †
Major evolutionary transitions in ant agriculture †
- Ted R. Schultz and Sean G. Brady. 2008
PNAS. 105(14): 5435-5440.
Data †
- 2,459 aligned nucleotide sites from the coding regions of four nuclear genes:
- elongation factor 1- F1 (EF1F1) (1,075 bp)
- elongation factor 1- F2 (EF1F2) (517 bp)
- wingless (409 bp)
- long-wavelength rhodopsin (opsin) (458 bp)
- All data in this study represent protein-coding (exon) sequences
intervening introns in opsin and EF1F1 were not used because they could not be aligned confidently.
- Sample: 65 attine taxa and 26 nonattine outgroups.
Primers used for PCR amplification and sequencing are found in supporting information (SI) Table S1.
- Of the total 2,459 included nucleotide positions from all genes, 952 were variable and 847 parsimony informative. Sequences are deposited in GenBank; taxa and accession numbers are listed in Table S2.
Phylogenetic Analyses †
- (i) Maximum parsimony (MP) analyses
- PAUP* v4.0b10
- heuristic searches with tree bisection.reconnection (TBR) and 1,000 random-taxon-addition replicates.
Analyses identified 12 most-parsimonious trees (MPTs) of length 4,383, CI 0.270, RI 0.704. Successive-approximations-weighting analyses identified a single tree, one of the MPTs.
- Nonparametric bootstrap analyses used TBR branch-swapping and consisted of 1,000 pseudoreplicates, with 10 random-taxon-addition replicates per pseudoreplicate.
- (ii) Maximum likelihood (ML)
- ModelTest v3.06
The data and the MPT identified by weighting were evaluated under the Akaike information criterion (AIC) as calculated in,
- identifying the GTRI model of evolution.
- GARLI v0.951 using the GTRI model (with six rate categories), with a heuristiclosuccessiveapproximationsg likelihood of 24,868.84927.
- Nonparametric bootstrap analyses consisted of 500 pseudoreplicates in GARLI under the same conditions as the ML search.
- A subsequent search in PAUP* using the most likely tree identified by the GARLI searches as the starting tree and employing TBR branch-swapping and the GTRI model (with six rate categories) resulted in exactly the same topology and likelihood score.
- (iii) Bayesian nucleotide-model Markov Chain Monte Carlo (MCMC):
MrBayes v3.1.2 (59).
- Burn-in and run convergence were assessed by comparing the mean and variance of log likelihoods, both by eye and by using the program
- Tracer v1.3
- MrBayes e e.stat f f output file
- MrBayes bthe split frequencies diagnostic.
- Eight character partitions for nucleotide-model analyses:
- four partitions consisting of the combined first and second codon positions for each of the four genes
- four partitions consisting of the third codon position for each of the four genes.
- based on ModelTest results
the wingless third-position - GTR model
opsin and EF1F2 third positions - separately assigned the HKYI model
all other character partitions - separately assigned the GTRI model
- (iv) Bayesian codon-model MCMC
Phylogenetic Mapping of Agricultural Systems. †
- Terminal taxa were assigned states for a single six-state character representing the four attine agricultural systems and leaf-cutter agriculture (i.e., no agriculture, lower agriculture, yeast agriculture, higher agriculture, leaf-cutter agriculture, coral-fungus agriculture).
- Five species (Myrmicocrypta n. sp. Brazil, Mycetagroicus triangularis, Cyphomyrmex n. sp., Cyphomyrmex morschi, Trachymyrmex irmgardae, and Pseudoatta n. sp.) received e eunknown f f (i.e., e e? f f) state assignments, and @Trachymyrmex papulatus received a e elower agriculture f f state assignment based on a single garden collection from Argentina (a second colony from the same locality cultivated a typical higher attine garden).
- Character evolution was optimized onto the Bayesian codon-model consensus tree (with branch lengths) under both parsimony using MacClade and maximum likelihood using the StochChar module provided in the Mesquite package.
- Under parsimony, ancestral-state optimizations were unambiguous.
- Under the Markov k-state 1-parameter model, the likelihood that each agricultural system arose in the most recent common ancestor of the corresponding ant clade was, as a proportion of the total probability ( 1.0) distributed across the six character states, 0.9831 for lower agriculture, 0.9995 for yeast agriculture, 0.9905 for higher agriculture, 0.9924 for leaf-cutter agriculture, and 0.9998 for coral-fungus agriculture.
Divergence Dating †
- We inferred divergence dates using both semiparametric and Bayesian relaxed clock methods.
- The first method used was the semiparametric penalized likelihood approach implemented in r8s v1.7 (64, 65).
- Branch lengths were first estimated on the ML topology using PAUP* under a GTRI model.
- The Pogonomyrmex and two Myrmica species were used to root the tree during branch length estimation and were subsequently removed from all dating analyses.
- Thus, the root of the tree for all dating analyses represents the origin of the e ecore myrmicines, f f a well supported clade established by previous work (33).
- Smoothing parameters were estimated by using the cross-validation feature in r8s.
- Confidence intervals were calculated by using 100 nonparametric bootstrap replicates of the dataset generated by Mesquite, followed by reestimation of branch lengths and divergence times for each replicate.
- We calibrated three nodes with minimum-age constraints using attine Dominican amber fossils.
^^These fossils are
- (i) Apterostigma electropilosum, a member of the A. pilosum group
- (ii) Cyphomyrmex maya and Cyphomyrmex taino, both members of the C. rimosus group
- (iii) Trachymyrmex primaevus, a fossil of uncertain placement within the genus (but see below).
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