The power of coalescent methods for inferring recent and ancient gene flow in endangered Bactrian camels

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..., 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 ..., , # 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 ...