*&color(,yellow){このページは編集中です}; [#hf6160ea] *演習2 [#p1e5cf33] **Major evolutionary transitions in ant agriculture [#ma7c1896] -Ted R. Schultz and Sean G. Brady. 2008~ [[PNAS. 105(14): 5435-5440.>http://www.pnas.org/content/105/14/5435.full]] ***Data [#l57a712c] -2,459 aligned nucleotide sites from the coding regions of four nuclear genes: --elongation factor 1-F1 (EF1-F1) (1,075 bp) --elongation factor 1-F2 (EF1-F2) (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 [#u92e7045] -(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 GTR model of evolution. --GARLI v0.951 using the GTR 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. [#m346c506] //-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 [#gae0451f] //-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).