DOI: 10.5061/dryad.prr4xgxj2
title: Genomic signatures of domestication in Old World camels

description: Domestication begins with the selection of animals showing less fear of
 humans.  In most domesticates, selection signals for
 tameness have been superimposed by intensive breeding for economical or
 other desirable traits. Old World camels, conversely, have maintained high
 genetic variation and lack these secondary bottlenecks associated with
 breed development.  By re-sequencing multiple genomes
 from dromedaries, Bactrian camels, and their endangered wild relatives, we
 show that positive selection for candidate genes underlying traits
 collectively referred to as ‘domestication syndrome’ is consistent with
 neural crest deficiencies and altered thyroid hormone-based
 signaling.  Comparing our results with other domestic
 species, we postulate that the core set of domestication genes is
 considerably smaller than the pan-domestication set – and overlapping
 genes are likely a result of chance and
 redundancy.  These results, along with the extensive
 genomic resources provided, are an important contribution to understanding
 the evolutionary history of camels and the genomic features of their
 domestication.
description: All methods that either utilize or generate the files in this
 repository are documented on GitHub
 (https://github.com/rfitak/Camel_Genomics).
description: ######################################################<br>
 ### This README file contains a list of the files  ###<br> ### and
 descriptions for each file in this Dryad   ###<br> ### repository.
 NOTE: The md5sum is also given for ###<br> ### each file.  You can
 verify that you do not     ###<br> ### have a corrupted file by
 matching the md5sum   ###<br> ### for each file given below with the
 output of   ###<br> ### UNIX terminal commands like "md5
 file" or      ###<br> ### "md5sum file". The various
 file formats are    ###<br> ### described in appendix 1 at the
 bottom.  The    ###<br> ### computer code and commands used to
 generate    ###<br> ### the results are available at my GitHub page:
   ###<br> ###
    https://github.com/rfitak/Camel_Genomics    ###<br> ###
      Thanks for promoting data-sharing!!!      ###<br> ###
            Bob Fitak 4/28/2020                 ###<br>
 ######################################################
 # Note 1 #<br> As mentioned in the manuscript associated
 with this<br> dataset, all raw sequencing data can be
 obtained<br> through the NCBI BioProject database, under
 accession<br> PRJNA276064. # Note 2 #<br>
 Files compressed using gzip (suffix .gz) can be uncompressed<br> a
 variety of ways:  by double clicking, or in the UNIX<br> terminal
 typing the command `gunzip &lt;file.gz&gt;`
 ####################################################<br>
 ###################### Files #######################<br>
 ####################################################
 FILE:  SraRunTable.csv<br> MD5SUM:
 2c6448024189128e762e353ba1fc7c7f<br> DESCRIPTION:  This file
 contains the full list of<br> sequencing data (raw + aligned to
 reference) accession<br> numbers in NCBI's SRA database
 (https://www.ncbi.nlm.nih.gov/sra).<br> FORMAT: CSV
 FILE:  CB1.fasta.gz<br> MD5SUM:
 57ed0e8fcefb09637a9cea54221f0568<br> DESCRIPTION:  This file
 contains the CB1 reference<br> genome sequence for Camelus ferus
 (also<br> available from NCBI).<br> FORMAT: FASTA (compressed
 with gzip) FILE:  ref_CB1_proteins.fa.gz<br>
 MD5SUM: e94c1316e57d3a47de4fec9b40fc6a0b<br> DESCRIPTION:  This file
 contains all the protein <br> sequences annotated in the CB1
 reference<br> genome for Camelus ferus (also available<br>
 from NCBI).<br> FORMAT: FASTA (compressed with gzip)
 FILE:  ref_CB1_scaffolds.gff3.gz<br> MD5SUM:
 51e3a17b0bce6e4ee74534eb65ebb93f<br> DESCRIPTION:  This file
 contains the annotation<br> information of the reference genome for
 Camelus<br> ferus (CB1; from NCBI).<br> FORMAT: GFF3
 (compressed with gzip) FILE:
  BLAST2GO_CFERUS.tar.gz<br> MD5SUM:
 0c81429b505896e37ab0c66343c906fc<br> DESCRIPTION:  This file
 contains all the<br> output annotations created for the C.
 ferus<br> reference (CB1) genome using Blast2GO.<br> FORMAT:
 TAR.GZ FILE:  CB1.repeats.bed<br> MD5SUM:
 2380e59d10ed550707a59b980f8b7b92<br> DESCRIPTION:  This file
 contains the annotation<br> of repetitive elements (masked
 coordinates) for the<br> reference Camelus ferus genome (CB1; from
 NCBI).<br> FORMAT: BED FILE:
  Drom.repeats.bed<br> MD5SUM:
 f63983517d7accbaa462388a4ddd3a3b<br> DESCRIPTION:  This file
 contains the annotation<br> of repetitive elements (masked
 coordinates) for the<br> reference dromedary genome (Drom64k; from
 NCBI).<br> FORMAT: BED FILE:
  XY.exclude.bed<br> MD5SUM:
 e2e45f398017243357f1bbe56cbc7671<br> DESCRIPTION:  This file
 contains the annotation<br> intervals of putative X and Y
 chromosomal<br> scaffolds for the reference genome (CB1; from
 NCBI).<br> FORMAT: BED FILE:
  All.SNPs.filtered.vcf.gz<br> MD5SUM:
 e6c459c8ec6c1e3831b7a55fdd738744<br> DESCRIPTION:  This file
 contains all the filtered SNPs<br> identified among all three camel
 species aligned to the<br> Camelus ferus (CB1) reference
 genome.<br> FORMAT: VCF v4.1 (compressed with gzip)
 FILE:  All.SNPs.filtered.EFF.vcf.gz<br> MD5SUM:
 d4a725d29dca4047427b4ab20d7c8fbf<br> DESCRIPTION:  This file
 contains all the filtered SNPs<br> identified among all three camel
 species aligned to the<br> Camelus ferus (CB1) reference genome, and
 annotated<br> using SNPEFF (same SNPs as
 All.SNPs.filtered.vcf.gz).<br> FORMAT: VCF v4.1 (compressed with
 gzip) FILE:  Drom.SNPs.filtered.vcf.gz<br>
 MD5SUM: ed9251a94e04424046c3015fd0f8e99c<br> DESCRIPTION:  This file
 contains all the filtered SNPs<br> identified among just dromedaries
 aligned to the<br> Camelus dromedarius (Cdrom64k) reference
 genome.<br> FORMAT: VCF v4.1 (compressed with gzip)
 FILE:  *.windowed.pi<br> DESCRIPTION:  These files contains
 the nucleotide<br> diversity across non-overlapping 10-kb windows
 in<br> each camel species (see file name).<br> FORMAT:
 WINDOWED.PI FILE:  *.Tajima.D<br> DESCRIPTION:
  These files contains the Tajima's D<br> across non-overlapping
 10-kb windows in each camel<br> species (see file name).<br>
 FORMAT: WINDOWED.PI FILE:  *.snpden<br>
 DESCRIPTION:  These files contains the SNP density<br> across
 non-overlapping 10-kb windows in either<br> individual camels or
 across species (see file name).<br> FORMAT: SNPDEN
 FILE:  PSMC.tar.gz<br> MD5SUM:
 8471a445f6d1d2fb6c37012cf4ba3237<br> DESCRIPTION:  This file
 contains the output of the<br> PSMC program written by Heng
 Li<br> (https://github.com/lh3/psmc).<br> FORMAT: TAR.GZ
 (containing PSMC and PSMCFA files) FILE:
  Final.100kb.csv.gz<br> MD5SUM:
 084936273909cf4e26255a1531ecb8a3<br> DESCRIPTION:  This file
 contains the full table of<br> output from the genomics_general
 python scripts.<br> Various measures of genetic variation (pi,
 theta,<br> heterozygosity, Fst, etc) are calculated in
 100-kb<br> windows with a step size of 50 kb.<br> FORMAT: CSV
 (compressed with gzip) FILE:
  Drom.selected.genes.gff3<br> MD5SUM:
 65c301f5ae958f650dbd7e3120b1297c<br> DESCRIPTION:  This file
 contains the annotation<br> information of the genes overlapping
 windows<br> putatively determined to be under selection in<br>
 Camelus dromedarius.<br> FORMAT: GFF3 FILE:
  WC.selected.genes.gff3<br> MD5SUM:
 9780ff52c3de8935ca4cc128ec0b1d0b<br> DESCRIPTION:  This file
 contains the annotation<br> information of the genes overlapping
 windows<br> putatively determined to be under selection in<br>
 Camelus ferus.<br> FORMAT: GFF FILE:
  ADMIXTURE.tar.gz<br> MD5SUM:
 0b47fa35f63368a3477ae3bc81597647<br> DESCRIPTION:  This file
 contains all the<br> input and output files used to LD
 prune<br> the SNP dataset, generate the principal<br>
 components analysis, and determine ancestry<br> using the program
 ADMIXTURE. It is recommended<br> to see the code/methods
 at:<br>
 https://github.com/rfitak/Camel_Genomics/blob/master/admixture.md<br> FORMAT: TAR.GZ ####################################################<br> ############ Appendix 1:  File Formats #############<br> #################################################### Format:  CSV<br> This format stores tabulated data in plain text format<br> Each line of this format is a record, with fields, or<br> columns separated by a comma (",").  Can be opened<br> in any text editor or spreadsheet software, e.g.<br> MS Excel, R. Format:  TSV<br> This format stores tabulated data in plain text format<br> Each line of this format is a record, with fields, or<br> columns separated by a tab ("\t").  Can be opened<br> in any text editor or spreadsheet software, e.g.<br> MS Excel, R Format:  VCF v4.1<br> This is the standard format for representing genomic<br> variation data.  It is a tab-delimited text file that<br> also contains a header.  All header lines begin with<br> a "#".  A complete description is available at:<br> https://samtools.github.io/hts-specs/VCFv4.1.pdf Format:  WINDOWED.PI<br> This format stores tabulated data in plain text format.<br> The data are the nucleotide diversity (pi) outputs from<br> VCFtools v1.12b. Each line of this format is a record,<br> with fields, or columns separated by a tab ("\t").  Can<br> be opened in any text editor or spreadsheet software, e.g.<br> MS Excel, R. Format:  SNPDEN<br> This format stores tabulated data in plain text format.<br> The data are the SNP density output from VCFtools v1.12b.<br> Each line of this format is a record, with fields, or<br> columns separated by a tab ("\t").  Can be opened<br> in any text editor or spreadsheet software, e.g.<br> MS Excel, R. Format:  TAJIMA.D<br> This format stores tabulated data in plain text format.<br> The data are the Tajima's D outputs from<br> VCFtools v1.12b. Each line of this format is a record,<br> with fields, or columns separated by a tab ("\t").  Can<br> be opened in any text editor or spreadsheet software, e.g.<br> MS Excel, R. Format:  PSMCFA<br> This is a text-based format specific to the PSMC<br> program by Heng Li.  See the program website at:<br> https://github.com/lh3/psmc<br> Specifically, "the program 'fq2psmcfa' in PSMC<br> transforms the DNA consensus sequence into a<br> fasta-like format where the i-th character in the<br> output sequence indicates whether there is at least<br> one heterozygote in the bin [100i, 100i+100)." Format:  PSMC<br> This is a text -based format specific to the PSMC<br> program by Heng Li.  See the program website at:<br> https://github.com/lh3/psmc Format:  FASTA<br> This format represents DNA sequences without quality<br> scores.  See https://en.wikipedia.org/wiki/FASTA_format<br> for more specific information. Format:  GFF3<br> The General Feature Format (GFF) is one of the standard<br> formats for representing various elements in a genome.<br> The format is a tab-delimited text file with 9 columns.<br> See a complete description of the format and<br> the associated 9 columns here:<br> https://www.ensembl.org/info/website/upload/gff.html Format:  BED<br> BED format is a tab-delimited text file that represents<br> regions in a genome.  Only three columns are required,<br> 1) chromosome/scaffold, 2) start position, 3) stop position.<br> Positions are zero-based. See a complete description of<br> the format here:<br> https://useast.ensembl.org/info/website/upload/bed.html Format:  TAR.GZ<br> The format represents a folder of files that have<br> been archived together (.tar) then compressed (.gz).<br> Most computers can unpack this file into a folder of<br> files by double-clicking automatically.  In most unix<br> machines, it can easily be unpacked from the command<br> line using:<br> tar -zxvf file.tar.gz