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演習2:Unixライク環境での系統解析：実際のデータを用いて †
この演習では実際の研究論文を参考にして、
- DNAデータベースからの塩基配列データのダウンロード
- ダウンロードした塩基配列データのアラインメント
Windows用の解析ソフトウェア †
以下のソフトウェアは、Windowsのグラフィカルインターフェースで使用でき、Cygwinと組み合わせて使うと便利なものばかりです。この演習で使うので、ダウンロードしてインストールしておきましょう。
Major evolutionary transitions in ant agriculture †
Data †
- 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 †
- (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. †
Divergence Dating †
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