Phylogenomics of Psocodea

Psocodea is an order of insects that includes parasitic and non-parasitic lice. The phylogenetic relationships of many groups have never been tested with phylogenetic methodology. Most species are small in body size and produce little amounts of genomic DNA. The era of phylogenomics has ushered in a new period of insight, based on the analysis of thousands of 1:1 single copy genes. These methods have the power to resolve many ambiguous relationships between insect groups once thought impossible. It is now possible to amplify thousands of gene sequences from the smallest insect species to understand phylogenetic relationships. In my thesis chapters, phylogenomic methods are employed to explore the relationships between and within several groups of Psocodea. To do this Illumina next generation sequencing and a Pediculus humanus reference are employed to identify single copy gene regions. The phylogenomic analyses produced provide resolution among and within the order Psocodea and provides insight into the evolution of a diverse group of insects that has both parasitic and non-parasitic members. In chapter one, the ordinal level relationships are explored among major lineages of Psocodea. The phylogenetic relationships between Psocoptera (non-parasitic lice) and Phthiraptera (parasitic lice) has been debated. Morphological and molecular data suggests that Phthiraptera is derived within the non-parasitic suborder Troctomorpha. However, molecular data has also suggested that Phthiraptera could possibly be a polyphyletic group with multiple origins of parasitism. A recent phylogenomic study analyzed a transcriptome data set of 2,395 genes to produce a phylogenetic hypothesis for hemipteroid orders. This study included the transcriptomes from parasitic and non-parasitic lice which can be combined with other next generation data. In chapter one, Illumina based whole genome and transcriptome data are combined to explore the phylogenetic relationships among all suborders and infraorders recognized in the traditional Psocoptera and Phthiraptera. With a total of 2,370 gene sequences a phylogenomic analysis is performed and a new ordinal level classification scheme is proposed for Psocodea. Analyses demonstrate that GC% biases at specific codon positions influence deep level relationships and the Amphientometae are most unstable. Phthiraptera is recovered as monophyletic across analyses and suggests a single origin of parasitism within Psocodea. For chapter two, the phylogenetic relationships and host-switching patterns are explored among the parasitic family Philopteridae (feather lice). A previous phylogenomic parasitic louse study analyzed a 1,107 gene set derived from Illumina whole genome sequencing that can be combined with the present study. With expanded taxonomic sampling of 61 feather louse species, and use of Illumina whole genome data, a phylogenomic analysis is performed. Dating and Jane based cophylogenetic analyses are performed using avian host input trees from two published studies. The placement of members found on long-branches are unstable between analyses of all nucleotide sites and when third codon positions are removed. Results suggest that feather lice began to diversify following the K-Pg boundary and radiated via host-switching to unrelated hosts. The ancestral host inferred from cophylogenetic analyses reconstruct Galloanserae across all isomorphic solutions. Several host-switch events are detected from the Galloanserae and Neoaves to the oldest extant lineage Palaeognathae, suggesting deep level host-switching patterns of feather lice among avian hosts. Results suggest that host-switching was more prevalent in the history of feather lice relative to cospeciation. For chapter three, the relationships of North American and European populations of Valenzuela flavidus are explored with phylogenomic methodology. Valenzuela flavidus is a species of non-parasitic louse that has a broad distribution across North America and Europe. In Europe, populations are all female and cytogenetic studies have demonstrated that these European populations are triploid. Males are reported in North America, but thelytoky has been reported for certain populations found in North America also. Populations found within North America were historically recognized as V. aurantiacus, however this became synonymized under V. flavidus because of reports of thelytoky in North America and females between the two continents are identical. However, provided all-females in Europe are triploid and males are reported in North America, the two populations could represent a distinct species. With the analysis of 2,124 gene sequences derived from Illumina whole genome sequencing, genetic diversity is explored between the two populations with phylogenomic methods. Analyses suggest the existence of two divergent lineages that have been isolated for an estimated mean of 4 million years based on dating results. Inspection of allele frequencies from read-mapped single copy genes suggests North American populations that contain males are a diploid species. The results suggest that European and North American populations are divergent warranting species recognition of North American populations as V. aurantiacus. For chapter four, a comprehensive phylogenomic analysis of feather lice is performed with expanded sampling from chapter two. Results are based on the analysis of 1,107 gene sequences and include 137 feather louse species. The results represent the most comprehensive phylogenetic analysis of feather lice performed to date. With this expanded feather louse set, a dating and Jane based cophylogenetic analysis was performed. Phylogenetic analyses recover high support among most derived groups of feather lice, however there is instability recovered among the relationships of the deepest positioned feather lice found on long-branches. Similar to previous results, analyses of all sites recover a monophyletic Philopteridae with high support, but paraphyly of feather lice was recovered when third codon positions are removed. Dating analyses are similar to previous results and estimate feather lice began to diversify during the Paleogene following the origin of their avian hosts. The ancestral host inferred from cophylogenetic analysis are ambiguous and suggested to be either a member of the Galloanserae or Aequornithes. High levels of host-switching are reconstructed among land bird groups relative to water bird hosts. Host-switching is detected among water bird groups, but deep level cospeciation is also reconstructed among water birds. Ancestral character estimation suggests a water bird host at the root of the feather louse tree and specialized lice evolved from a generalist form. These analyses represent the most comprehensive phylogenetic analysis performed for the group to date and provide a framework to understand feather louse diversity. Results suggest the importance of water bird hosts during feather louse diversification, with deep level cospeciation reconstructed among water birds found in the Galloanserae and Aequornithes.LimitedAuthor requested closed access (OA after 2yrs) in Vireo ETD syste