Bayesian inference under the multispecies coalescent with ancient DNA sequences

Ancient DNA (aDNA) is increasingly being used to investigate questions such as the phylogenetic relationships and divergence times of extant and extinct species. If aDNA samples are sufficiently old, expected branch lengths (in units of DNA substitutions) are reduced relative to contemporary samples. This can be accounted for by incorporating sample ages into phylogenetic analyses. Existing methods that use tip (sample) dates infer gene trees rather than species trees, which can lead to incorrect or biased inferences of the species tree. Methods using a multispecies coalescent (MSC) model overcome these issues. We developed an MSC model with tip dates and implemented it in the program bpp. The method performed well for a range of biologically realistic scenarios, estimating calibrated divergence times and mutation rates precisely. Simulations suggest that estimation precision can be best improved by prioritizing sampling of many loci and more ancient samples. Incorrectly treating ancien..., , , # Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences [https://doi.org/10.5061/dryad.4mw6m90h0](https://doi.org/10.5061/dryad.4mw6m90h0) ## Description of the data and file structure This contains the supplemental information (on Zenodo) and the alignment of mammoth and elephant mitochondrial DNA. Most of the mtDNA was derived from the following source. The rest were downloaded from GenBank (accession numbers are included in the supplement): * [http://palaeogenetics.com/data-and-scripts/](http://palaeogenetics.com/data-and-scripts/)