#Code for recreating the analyses used in Hamm et al. 2013, Journal of Heredity. There are six .nex files, one for each locus. Each file has the same order of individuals. The files are: #MrBayes and subsequent BUCKy analysis AL15_sort.nex (anonymous locus 15) AL21_sort.nex (anonymous locus 21) COI_sort.nex (cytochrome oxidase 1) EF1a_sort.nex (elongation factor 1a) GAPDH_sort.nex (glyceradehyde phosphate dehydrogenase) RpS5_sort.nex (ribsomal protein S5) MrBayes code for each data file : mcmc nchains=6 ngen=2000000 samplefreq=5000 printfreq=250000 diagnfreq=5000 This generates two files (one for each run), which need to be combined for BUCKy ./mbsum -n 501 AL15_sort.run1.t AL15_sort.run2.t ./mbsum -n 501 AL21_sort.run1.t AL21_sort.run2.t ./mbsum -n 501 COI_sort.run1.t COI_sort.run2.t ./mbsum -n 501 EF1a_sort.run1.t EF1a_sort.run2.t ./mbsum -n 501 GAPDH_sort.run1.t GAPDH_sort.run2.t ./mbsum -n 501 RpS5_sort.run1.t RpS5_sort.run2.t Code for BUCKy runs across values of a: ./bucky -n 1000000 -c 4 -a 0.1 -s 1000 *.in ./bucky -n 1000000 -c 4 -a 1 -s 1000 *in ./bucky -n 1000000 -c 4 -a 100 -s 1000 *.in #Code for RAxML gene1=ef1a, gene2=coi, gene3=gapdh, gene4=Rps5, gene5=Al15, gene6=AL21 This is the partition file needed by RAxML patition file = MSB_OG2_part DNA, gene1 = 1-590 DNA, gene2 = 591-1261 DNA, gene3 = 1262-1896 DNA, gene4 = 1897-2145 DNA, gene5= 2146-2721 DNA, gene6= 2722-2933 The concatenated nexus file needed for RAxML is called MSB_OG2.nex ./raxmlHPC-PTHREADS -T 3 -f a -m GTRGAMMA -s MSB_OG2.nex -q MSB_OG2_part -n MSB_OG2_run1 -o Taydebis -x 12345 -#10000 #IMa2 code, the -i files correspond to the input file relative to that comparison. ./IMa2 -iMSB_IM_9 -oMSB_IM_9h.out -b100000 -l100000 -q10 -m200 -t8 -p5 -s123 ./IMa2 -iMSB_IM_11 -oMSB_IM_11m.out -b100000 -l1000 -q 20 -m 10 -t8 -p5 -j7 -s123 ./IMa2 -iMSB_IM_14.txt -oMSB_IM_14a.out -b100000 -l1000 -q 10 -m 10 -t 8 -p25 -j7 -s123 ./IMa2 -iMSB_IM_10 -oMSB_IM_10j.out -b100000 -l1000 -q 20 -m 10 -t10 -p25 -j7 -s123 ./IMa2 -iMSB_IM_12 -oMSB_IM_12n.out -b100000 -l1000 -q 20 -m 8 -t 8 -p25 -j7 -s123 ./IMa2 -iMSB_IM_13 -oMSB_IM_13d.out -b100000 -l100000 -q10 -m150 -t8 -p5 -s123 The code for generating the map, deltaK plot, and IMa2 plot are in the R script associated with this paper.