Extensive in situ radiation of feather lice on tinamous

Tinamous host the highest generic diversity of lice of any group of birds, as well as hosting representatives of all four avian feather louse ecomorphs. Although the generic diversity of tinamou feather lice is well documented, few attempts have been made to reconstruct the phylogenetic relationships among these lice. To test whether tinamou feather lice form a monophyletic group as a whole, we used whole genome sequencing to estimate a higher-level phylogeny of tinamou feather lice, together with a broad diversity of other avian feather louse groups. In total, we analyzed sequences from over 1000 genes for 48 genera of avian lice using both concatenated and coalescent approaches to estimate the phylogeny of this diverse group of avian feather lice. Although the body louse ecomorph of tinamou feather lice formed a monophyletic group, they did not strictly form a monophyletic group together with the other three ecomorphs of tinamou feather lice. In particular, a clade comprised of several feather louse genera, mainly from South America, are nested phylogenetically within tinamou lice, which also have their main center of diversity in South America. These results suggest in situ radiation of these parasites in South America.The concatentated data matrix created using SequenceMatrix. tinamou_concat_nexus_naked.phy Tinamou Louse IQ Tree consensus tree file. tinamou_concat_nexus_naked.phy.contree Gene tree files from nuclear data, all trees were estimated in RAxML. gene_trees.zip Tinamou Louse gene alignment files gene_alignements.zip ASTRAL output tree Tinamou_ASTRAL.tree Maximum likelihood tree RAxML output RAxML_bipartitions.tinamou_concatenated.tree Maximum likelihood tree with partitions RAxML output and PartitionFinder best scheme output RAxML_bipartitions.Tinamou_concat_with_partitions.tree Tinamou_partitions_best_scheme.txt Maximum likelihood tree after Degen recoding analysis RAxML output RAxML_bipartitions.tinamou_recoding.tree Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-1239788Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-1342604Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-185581