B1_TreeRef6_MrBayesFile_Morph1-25

File_B1 (plain text). The MrBayes [10] executable file to infer branch lengths for the 25 candidate morphological partitions, using the total-evidence Maximum Likelihood topology from [6]. The matrix consists of only the 46 extant taxa from [6], since molecular branch lengths (to which these morphological branch lengths have to be compared) cannot be ascertained for extinct taxa

Genotype by Environment Interaction (GxE)

This project addresses the following: • Do we need to breed ewes specifically for hill country or can we breed “all-rounders”? • Do eBVs from stud farms stack up in commercial farms? • Can we routinely record commercial animals to get eBVs relevant to commercial farms (e.g. stayability

C10_8clocks_topolConvergence

File_C10 (pdf). Convergence diagnostics for tree topologies sampled in C8. (A) AWTY [20] plots demonstrating relatively good correlation (albeit with substantial variance) for all clades across 4 runs, and (A) high variation at different stages in a single run, but no obvious directional trends. The topology convergence statistics from MrBayes and AWTY (standard deviation of split frequencies across runs) were also relatively good ie being <0.093 across all comparisons (see top right cells of panel A). These results are consistent with convergence or near-convergence, i.e. runs sampling similar distributions but cycling very slowly through parameter space

C1_PartitionFinder

File_C1 (zipped, plain text). Matrix with molecular data for 46 extant taxa (extracted from [6]), in Phylip format (mammals.phy); PartitionFinder [12] command file (cfg) with 71 candidate partitions (by genes and by codons, with noncoding genes treated as single candidate partitions); best scheme with 7 partitions requiring separate substitution models, found by PartitionFinder using the Bayesian Information Criterion with unlinked branch lengths

C5_1clock_topologyConvergence

File_C5 (pdf). Convergence diagnostics for tree topologies sampled in C2. (A) AWTY [20] plots demonstrating similar posterior probabilities for all clades across 4 runs, and (B) at different stages in a single run. The topology convergence statistics from MrBayes and AWTY (standard deviation of split frequencies across runs) were also good ie low, being <0.031 across all comparisons (see top right cells of panel A). These patterns are consistent with good convergence. The kink in one of the fitted lines appears to be an artefact of a glitch in AWTY

B3_TreeRef6_Parts1-28branchlengths_newick

File_B3 (newick format). The ClockstaR [3] treefile containing the trees with the branch lengths for the 28 candidate partitions obtained from the MrBayes analysis in files B1, B2. Note: ClockstaR treats all trees as unrooted, so different rootings of trees are of no consequence

C11_8clocks_param_summary

File_C11 (plain text). Convergence diagnostics for numerical parameters from MrBayes [10] for the analysis in Files C7-9. PSRFs (ratio of within-run to between-run variance) is very 1 for most numerical parameters, but approaches ~1.7 for a single parameter (due to variance in 1 run). This single outlier is slightly higher than desirable. These diagnostics do not indicate convergence, though are consistent with convergence being approached

B11_ClockstaR_script

File_B11 (plain text). ClockstaR R script (and output) for the above analysis. Note filenames and paths need to be changed as appropriate

B11_ClockstaR_script

File_B11 (plain text). ClockstaR R script (and output) for the above analysis. Note filenames and paths need to be changed as appropriate

C7_8clocks MrBayes file

File_C7 (plain text). MrBayes executable file for a total-evidence dating analysis of all 86 taxa in the matrix in [6], using 8 separate relaxed clocks (independent gamma rates; 7 for morphology and 1 for molecular data), as found in analysis B-3. The sampled ancestor birth-death tree prior [17], and the Markov model of morphological evolution [18,19], were used. Optimal substitution models and substitution-model-partitions were found with PartitionFinder for molecular data (see C1) and with stepping-stone analysis in MrBayes for morphological data [10]. Numerous (>20) MCMC runs were initially performed for 20 million generations to investigate tuning, mixing and convergence. The final analysis was then performed with 4 runs and the trees from 10 million post-burnin generations retained Note: The burnin for each run varies considerably due to variation in time to reach (apparent) stationarity, from 20 million to 50 million. For computational efficiency, the 4 runs were performed separately and in all cases, the last 10 million steps (after stationarity) were retained. However, the step numbers have been readjusted in file C8 below so they are all identical across runs (ie to a common burnin of 50 million), to facilitate downstream analyses e.g. generating summary statistics in MrBayes