Genomic Approaches to Uncovering the Coevolutionary History of Parasitic Lice

Simple Summary

New sequencing technologies have now made it possible to sequence entire genomes for a diversity of life on earth. Parasites comprise nearly half of all species. Lice are one important group of parasites of birds and mammals, including humans. Genome sequencing approaches have been applied to this group of parasites to uncover patterns of diversification. These patterns can be compared to the patterns of diversification in their hosts. Key findings from these studies have revealed that parasitic lice likely originated on birds and then switched to mammals multiple times. Within groups of birds and mammals, the evolutionary trees of lice match those for mammal hosts more than those for birds. Genomic approaches have also revealed that individual birds and mammals harbor distinct populations of lice. Thus, these new techniques allow for the study of patterns of diversification at a wide variety of scales.

Abstract

Next-generation sequencing technologies are revolutionizing the fields of genomics, phylogenetics, and population genetics. These new genomic approaches have been extensively applied to a major group of parasites, the lice (Insecta: Phthiraptera) of birds and mammals. Two louse genomes have been assembled and annotated to date, and these have opened up new resources for the study of louse biology. Whole genome sequencing has been used to assemble large phylogenomic datasets for lice, incorporating sequences of thousands of genes. These datasets have provided highly supported trees at all taxonomic levels, ranging from relationships among the major groups of lice to those among closely related species. Such approaches have also been applied at the population scale in lice, revealing patterns of population subdivision and inbreeding. Finally, whole genome sequence datasets can also be used for additional study beyond that of the louse nuclear genome, such as in the study of mitochondrial genome fragmentation or endosymbiont function.

Examination of vertical transmission of Bartonella quintana in body lice following multiple infectious blood meals

Bartonella quintana is a re-emerging louse-borne pathogen. Horizontal transmission from the body louse vector (Pediculus humanus humanus) to a human host occurs through contact with infectious louse feces containing a high concentration of the bacteria. However, questions have remained about whether vertical transmission from infected vectors to their progeny, which could significantly influence the dynamics of transmission to humans, occurs in body lice. To address this subject, we performed a series of controlled laboratory experiments that examined the presence of B. quintana on the surface of and within eggs produced by female body lice that were provisioned multiple infectious blood meals to recapitulate the natural pathogen acquisition process. Our results demonstrate that B. quintana DNA can be detected from the surface of eggs by qPCR due to vertical transfer of infectious feces to the egg sheath during or after oviposition. However, viable B. quintana could not be cultured from the hemolymph of adult female lice or from within eggs that were surface sterilized, indicating a lack of true transovarial transmission. Based on this evidence, vertical transfer of B. quintana from infected adult lice to their eggs probably has a limited impact on the dynamics of transmission to humans.

Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites

While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.

Rigorous quantification of bacterial richness in ticks: A case study

Kwan et al. (2017) published an informative study comparing results obtained by next-generation sequencing (NGS) of mean bacterial genera richness among different life stages, male and female adults, and rearing conditions (field vs. laboratory) for Ixodes pacificus. The current paper examines Kwan et al. (2017) as a case study to provide guidance on statistical design and analysis for estimation of richness, derived from next generation sequencing technology, of the bacterial microbiome in field-collected I. pacificus. Suggestions are provided to further strengthen quantification of microbiome richness in studies in ticks, with focus on sampling design. In-depth treatment is provided of the relative merits of estimating mean richness versus median richness. Research on microbiome diversity in ticks can be made quantitatively rigorous; although, more research on methods is needed.