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All causes of death assignments in this dataset were made using the InterVA-4 model version 4.02 (8).
Phylogenetic trees for the complete dataset were made using both neighbor-joining (1000 replicates, pairwise deletion, Tamura-Nei, in MEGA4) and parsimony (1000 replicates in Paup).
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Numerical comparisons across conditions for the same datasets were made using pairwise t-tests (with a significance level of 0.05).
Comparisons between microarray datasets were made using Microsoft Excel and Access.
In addition to the three phylogenetic trees estimated from each of the WG, 3G and 3G-WG datasets, estimations were made using ML for alignments based on single gene regions from both the WG and 3G datasets.
For two nonnormal datasets, comparisons were made using the Mann-Whitney U test.
Dataset analysis and visualization were made using EASANA® (GenoSplice technology, http://www.genosplice.com), based on the GenoSplice's FAST DB® annotations.
In the Brisbane dataset, all tacrolimus concentration measurements were made using liquid chromatography-tandem mass spectrometry assay (LC-MS/MS) 24.
SAS® version 9.1 (Cary, NC, USA) was used to create the datasets and analyze them; graphs were made using Microsoft Excel®.
Dental microwear comparisons were made using a dataset [ 14] partitioned into the leaf browsing (n = 7), fruit browsing (n = 3), grazing (n = 7), mountain grazer (n = 1), seasonal (n = 6) and non-seasonal mixed feeder (n = 4) categories.
In cases where multiple tests were made using single datasets, alpha levels were adjusted using step-down sequential Bonferroni correction.
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