DOI: 10.5061/dryad.71tv1
title: Data from: Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus)

description: The geographical range of extant peccaries extends from the southwestern
 United States through Central America and into northern Argentina.
 However, from the Miocene until the Pleistocene now-extinct peccary
 species inhabited the entirety of North America. Relationships among the
 living and extinct species have long been contentious. Similarly, how and
 when peccaries moved from North to South America is unclear. The North
 American flat-headed peccary (Platygonus compressus) became extinct at the
 end of the Pleistocene and is one of the most abundant subfossil taxa
 found in North America, yet despite this extensive fossil record its
 phylogenetic position has not been resolved. This study is the first to
 present DNA data from the flat-headed peccary and full mitochondrial
 genome sequences of all the extant peccary species. We performed a
 molecular phylogenetic analysis to determine the relationships among
 ancient and extant peccary species. Our results suggested that the
 flat-headed peccary is sister-taxon to a clade comprising the extant
 peccary species. Divergence date estimates from our molecular dating
 analyses suggest that if extant peccary diversification occurred in South
 America then their common ancestor must have dispersed from North America
 to South America well before the establishment of the Isthmus of Panama.
 We also investigated the genetic diversity of the flat-headed peccary by
 performing a preliminary population study on specimens from Sheriden Cave,
 Ohio. Flat-headed peccaries from Sheriden Cave appear to be genetically
 diverse and show no signature of population decline prior to extinction.
 Including additional extinct Pleistocene peccary species in future
 phylogenetic analyses will further clarify peccary evolution.
description: BEAST_filesBEAST files, including input .xml and final maximum clade credibility tree.RAxML_filesRAxML files, including input alignment & partition file and final treePartitionFinder_filesInput & output from PartitionFinder analyses.12Files_Platygonus_compressus_SeqData_Filtered_Collapsed.fastqFASTQ files containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the 12 Platygonus compressus enriched genomic libraries. See main publication for full details on data processing.3Files_Pecari_tajacu_SeqData_Filtered_Collapsed.fastqFASTQ files containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the 3 Pecari tajacu enriched genomic libraries. See main publication for full details on data processing.Catagonus_wagneri_KY987545_SeqData_Filtered_Collapsed.fastqFASTQ file containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the Catagonus wagneri enriched genomic library. See main publication for full details on data processing.Tayassu_pecari_KY987556_SeqData_Filtered_Collapsed.fastqFASTQ file containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the Tayassu pecari enriched genomic library. See main publication for full details on data processing.HTS_pipeline_scriptsScripts for analysis of high-throughput sequencing data.Consensus sequence from sample ACAD2865Consensus sequence generated in Geneious. Final sequence too fragmentary for upload to GenBank due to poor DNA preservation. This sequence was excluded from most analyses.ACAD2865_ConsensusSequence.fasta