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Extensive in situ radiation of feather lice on tinamous

Citation

Virrueta Herrera, Stephany et al. (2020), Extensive in situ radiation of feather lice on tinamous, Dryad, Dataset, https://doi.org/10.5061/dryad.s1rn8pk4b

Abstract

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.

Usage Notes

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

National Science Foundation, Award: DEB-1239788

National Science Foundation, Award: DEB-1342604

National Science Foundation, Award: DEB-1855812