DOI: 10.5061/dryad.rfj6q577d
title: Supplementary data for: Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

description: Our understanding of the evolutionary history of primates is undergoing
 continual revision due to ongoing genome sequencing efforts. Bolstered by
 growing fossil evidence, these data have led to increased acceptance of
 once controversial hypotheses regarding phylogenetic relationships,
 hybridization and introgression, and the biogeographical history of
 primate groups. Among these findings is a pattern of recent introgression
 between species within all major primate groups examined to date, though
 little is known about introgression deeper in time. To address this and
 other phylogenetic questions, here we present new reference genome
 assemblies for three Old World Monkey species: Colobus angolensis
 ssp. palliatus (the black and white colobus), Macaca
 nemestrina (southern pig-tailed macaque), and Mandrillus
 leucophaeus (the drill). We combine these data with 23 additional
 primate genomes to estimate both the species tree and individual gene
 trees using thousands of loci. While our species tree is largely
 consistent with previous phylogenetic hypotheses, the gene trees reveal
 high levels of genealogical discordance associated with multiple primate
 radiations. We use strongly asymmetric patterns of gene tree discordance
 around specific branches to identify multiple instances of introgression
 between ancestral primate lineages. In addition, we exploit recent fossil
 evidence to perform fossil-calibrated molecular dating analyses across the
 tree. Taken together, our genome-wide data help to resolve multiple
 contentious sets of relationships among primates, while also providing
 insight into the biological processes and technical artifacts that led to
 the disagreements in the first place.
description: ***********************************************
 ALIGNMENTS Aligned single-copy orthologs from
 primate datasets obtained via NCBI.  Alignments were performed using
 GUIDANCE2 with Mafft.   An example of an alignment
 script is below. #!/bin/bash #PBS -k
 o<br> #PBS -l nodes=1:ppn=8,vmem=40gb,walltime=45:00:00<br>
 #PBS -M ddvanderpool@gmail.com<br> #PBS -m abe<br> #PBS -N
 1_CODON_AlignQSUB<br> #PBS -j oe cd
 /N/u/danvand/Carbonate/work_Primates/ALIGN_all_PRIMATE_GROUPS_4TAX/CODON_UNALIGNED <br> for file in *unalign.fa;<br> do<br>    dest="/N/u/danvand/Carbonate/work_Primates/ALIGN_all_PRIMATE_GROUPS_4TAX/CODON_UNALIGNED/";<br>    f=${file%\_TRANS_unalign.fa}; <br>    /N/u/danvand/Carbonate/src/guidance.v2.02/www/Guidance/guidance.pl --seqFile "$dest""$file" --dataset "$f" --msaProgram MAFFT --out Order as_input --proc_num 10 --seqCutoff 0.93 --colCutoff 0.95 --seqType codon --bootstraps 60 --outDir $PWD; ## The above line runs the file through GUIDANCE2 which generates column and seq scores using 60 bootstrap replicates from MAFFT codon alignments.   <br>    /N/u/danvand/Carbonate/bin/maskLowScoreResidues.pl "$f".MAFFT.aln.With_Names "$f".MAFFT.Guidance2_res_pair_res.scr "$f".GUIDANCE.MASK_SEQ.fa 0.93 nuc; ##The above line uses the scores file to mask low confidence residues <br>    /N/u/danvand/Carbonate/bin/trimal -in "$dest""$f".GUIDANCE.MASK_SEQ.fa -out "$dest""$f".GUIDANCE.MASK_SEQ_TRIMal.fa -gt 0.5 -cons 50; ##The above lineTrimAl to cut out sites not present in at least 50% of the taxa or conserved in 50%     /N/u/danvand/Carbonate/pythonscripts/Clean.N.py  "$dest""$f".GUIDANCE.MASK_SEQ_TRIMal.fa; ## The above line is just an adhoc fix because I realized Trimal was was counting the masked sequence and not trimming them.  the easiest fix was to convert the N’s to gaps.    /N/u/danvand/Carbonate/pythonscripts/remove_aln_gaps_update.pl "$dest""$f".GUIDANCE.MASK_SEQ_TRIMal.fa.NoNs.fa  .5 .9 200 &gt; "$dest""$f”_NO_GAP.fa; ## The above line now takes the new “gapped” sequence and deletes a site  if more than 1/2 of the taxa don’t have, Masks the whole sequence if more than 10% of the sequence is missing or if it is under 200bp.    /N/u/danvand/Carbonate/pythonscripts/ReplaceString.py "$f"_NO_GAP.fa "_.5_.9_200" ""  "$f”_TRANS_GUIDANCE_TRIMAL_NoNcol_CODON.fa; ## The Above line just deletes fasta headerline annotation left from the previous script    /N/u/danvand/Carbonate/pythonscripts/Remove_All_N_Taxa.py "$f”_TRANS_GUIDANCE_TRIMAL_NoNcol_CODON.fa; ## The Above line just takes out taxa that composed only of N’s, this turns out to matter and is more of a double check for all seqs before they are finalized. <br>    mv "$dest"*GUIDANCE* "$dest"../CODON_ALIGNED;<br>    rm "$dest"*MAFFT* "$dest"*Seqs* "$dest"COS* "$dest"END* "$dest"Sample* "$dest"log "$dest”*NO_GAP.fa ##The above lines just cut down build up and only keeps the most relevant last couple of steps, just in case you want to change something.  You don’t have to realign everything.   done;<br>   ***********************************************  
description: Alignments were then analyzed using IQ-TREE2, ASTRAL, PhyloBayes,
 and PAUP*.  Commands available in manuscript except for PAUP* commands
 which are included in a PAUP block with the concatenated alignment
 (1730_ALIGNMENT_CONCAT.paup.nex) Parsimony
 gene trees were generated with MPBoot using the following
 command for file in *SAME.fa;<br> do<br>  
 mpboot -s "$file" -pre
 ../PARSIMONY_GENE_TREES/${file%\_TRANS_GUIDANCE_TRIMAL_NoNcol_*.SAME.fa}_PARS.tre;<br> done;<br>