DOI: 10.5061/dryad.3xsj3txrk
title: The power of coalescent methods for inferring recent and ancient gene flow in endangered Bactrian camels

description: Genomic sequence data harbour valuable information concerning the history
 of species divergence and interspecific gene flow, and may offer important
 insights into conservation of endangered species. However, extracting such
 information from genomic data requires powerful statistical inference
 methods. A recent analysis of genomic sequence data found little evidence
 for gene flow from domestic Bactrian camels into the endangered wild
 Bactrian species. Nevertheless, the methods used to infer gene flow are
 based on data summaries and lack the power and precision to represent the
 complex phylogenetic history of the species with gene flow. Here we apply
 newly developed Bayesian methods to genomic sequence data to test for both
 recent and ancient gene flow among the three species in the genus Camelus,
 and to estimate the strength and timing of gene flow. We detect strong
 signal of gene flow from domestic into wild Bactrian camels, confirming
 early evidence based on mitochondrial DNA and the Y chromosome. Overall
 gene flow appears to affect the autosomal genome uniformly, with similar
 effective rates of gene flow for exonic and noncoding regions. Estimation
 of species divergence times is seriously affected if gene flow is not
 accommodated in the analysis. Our results highlight the power of the
 coalescent model in analysis of genomic data and the utility of the coding
 as well as noncoding parts of the genome in elucidating the evolutionary
 history of modern species.
description: The data were generated from the genomic sequence data of Ming et
 al. (2020) ##Descriptions #
 exon-data We used the genome annotation of C. ferus
 (GCF_000311805.1) to identify known exons, and included all exons except
 short ones of less than 100bp. A total of 120,720 exons (loci) were
 collected. Each exon was treated as an independent locus in the MSC model.
 The raw data with 120,720 exons loci is divided into 13 partitions, named
 (**CDS_fil.seq.aa**) to (**CDS_fil.seq.am**). To ensure the convergence of
 numerical calculations, We further separated them into 48 subsets, each of
 2500 loci, named (**seq-01**) to (**seq-48**). #
 mitochondrion data We assembled an alignment of whole
 mitochondrial genomes for 15 Bactrians (C. bactrianus),4 wild Bactrian
 species (C. ferus), and 11 dromedaries (C. dromedarius). We included two
 domestic South American species as well: one Vicugna pacos and one Lama
 Glama. In BPP analysis under the MSC, we treated the whole mitochondrial
 genome as one locus as all sites in the genome share the same genealogical
 tree. The data is (**camel-mt.txt**). We inferred the
 maximum likelihood tree using raxml-ng, and the related file is
 (**camel-mt-raxml.tre**). The mapfile and control file
 needed for BPP analysis of mitochondrion data are (**camel-mt-imap.txt*
 and (**bpp-msc-r1.ctl**). # non-coding
 The dataset *data1.txt* consists of 10,000 non-coding genomic
 segments of length 1kb (referred to as loci), separated by a gap of at
 least 30kb between loci. We further separated the
 10,000 non-coding loci into four random subsets, each of 2500 loci, and
 the related files are (**data1.quarter1.txt**), (**data1.quarter2.txt**),
 (**data1.quarter3.txt**) and
 (**data1.quarter4.txt**)<em>.</em>
   # other-files This folder
 include four files which are necessary for non-coding data and exon data
 analysis with BPP. (The files corresponding to the chromosomal data are
 located in folder # mitochondrion data.)  
 **bpp-msc.ctl** is the control file to run analysis under MSC
 model, which does not specify any gene flow.
   **bpp-msci-6rates.ctl** is the control file
 to run analysis under MSC-I model with six introgression events showed in
 fig.1a. To conduct analysis with other numbers of rates (such as I5, I4
 and I4-final), the Newick tree specified for the ‘species&tree’
 option must be edited accordingly.  
 **bpp-mscm-6rates.ctl** is the control file for running analysis
 under MSC-M model which incorporates six migration events as depicted in
 fig. 1a. To conduct an analysis with other numbers of migration events,
 one needs to edit the option ‘migration’, including the number and the
 directions of the migration events.  
 **camel-imap-3s.txt** is the map file required for BPP
 analysis.   ## Sharing/Access
 information The sequence alignment files and BPP
 control files are available in the following archive:
 http://abacus.gene.ucl.ac.uk/ziheng/data/2024Zhu-camel-data.tgz.   ## Code/Software The analysis in the paper is done by software BPP, which is available at: http://abacus.gene.ucl.ac.uk/software/#bpp-bayesian-analysis-of-genomic-sequence-data-under-the-multispecies-coalescent-model   Ming, L. et al., 2020. Whole-genome sequencing of 128 camels across Asia reveals origin and migration of domestic Bactrian camels. Commun Biol.<br>3, 1.  
description: # The power of coalescent methods for inferring recent and ancient gene
 flow in endangered Bactrian camels
 [https://doi.org/10.5061/dryad.3xsj3txrk](https://doi.org/10.5061/dryad.3xsj3txrk) ## Description of the data and file structure ### File: 2024Zhu-camel-data.tgz Archive containing files that are described in detail below. ### exon-data We used the genome annotation of C. ferus (GCF_000311805.1) to identify known exons, and included all exons except short ones of less than 100bp. A total of 120,720 exons (loci) were collected. Each exon was treated as an independent locus in the MSC model. The raw data with 120,720 exons loci is divided into 13 partitions, named (**CDS_fil.seq.aa**) to (**CDS_fil.seq.am**). To ensure the convergence of numerical calculations, We further separated them into 49 subsets, each of 2500 loci, named (**seq-01**) to (**seq-49**). ### mitochondrion data We assembled an alignment of whole mitochondrial genomes for 15 Bactrians (C. bactrianus),4 wild Bactrian species (C. ferus), and 11 dromedaries (C. dromedarius). We included two domestic South American species as well: one Vicugna pacos and one Lama Glama. In BPP analysis under the MSC, we treated the whole mitochondrial genome as one locus as all sites in the genome share the same genealogical tree. The data is (**camel-mt.txt**). We inferred the maximum likelihood tree using raxml-ng, and the related file is (**camel-mt-raxml.tre**). The mapfile and control file needed for BPP analysis of mitochondrion data are (**camel-mt-imap.txt** and **bpp-msc-r1.ctl**). ### non-coding The dataset **data1.txt** consists of 10,000 non-coding genomic segments of length 1kb (referred to as loci), separated by a gap of at least 30kb between loci. We further separated the 10,000 non-coding loci into four random subsets, each of 2500 loci, and the related files are (**data1.quarter1.txt**), (**data1.quarter2.txt**), (**data1.quarter3.txt**) and (**data1.quarter4.txt**)*.* ### other-files This folder include four files which are necessary for non-coding data and exon data analysis with BPP. (The files corresponding to the chromosomal data are located in folder # mitochondrion data.) **bpp-msc.ctl**: the control file to run analysis under MSC model, which does not specify any gene flow. **bpp-msci-6rates.ctl**: control file to run analysis under MSC-I model with six introgression events showed in fig.1a. To conduct analysis with other numbers of rates (such as I5, I4 and I4-final), the Newick tree specified for the ‘species&tree’ option must be edited accordingly. **bpp-mscm-6rates.ctl**: control file for running analysis under MSC-M model which incorporates six migration events as depicted in fig. 1a. To conduct an analysis with other numbers of migration events, one needs to edit the option ‘migration’, including the number and the directions of the migration events. **camel-imap-3s.txt**: map file required for BPP analysis. ## Code/Software The analysis in the paper is done by software BPP, which is available at: [http://abacus.gene.ucl.ac.uk/software/#bpp-bayesian-analysis-of-genomic-sequence-data-under-the-multispecies-coalescent-model](http://abacus.gene.ucl.ac.uk/software/#bpp-bayesian-analysis-of-genomic-sequence-data-under-the-multispecies-coalescent-model)