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1. Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation

   https://doi.org/10.1146/annurev-animal-061220-023149  

   Murphy, William J.; Foley, Nicole M.; Bredemeyer, Kevin R.; Gatesy, John; Springer, Mark S. (February 2021, Annual Review of Animal Biosciences)

   null (Ed.)

   The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species. 

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2. Phylogenomics reveals the timescale of diversification in Amblycera

   https://doi.org/10.1111/syen.12668  

   Najer, Tomáš; Doña, Jorge; Buček, Aleš; Sweet, Andrew D; Sychra, Oldřich; Johnson, Kevin P (July 2025, Systematic Entomology)

   Abstract Recently, genomic approaches have helped to resolve phylogenetic questions in many groups of parasitic organisms, including lice (Phthiraptera). However, these approaches have still not been applied to one of the most diverse groups of lice, Amblycera. To fill this gap, we applied phylogenomic methods based on genome‐level exon sequence data to resolve the relationships within and among the families of Amblycera. Our phylogenomic trees support the monophyly of the families Ricinidae and Laemobothriidae. However, the families Trimenoponidae and Gyropidae are not monophyletic, indicating that they should be merged into a single family. The placement ofTrinotonis unstable with respect to Boopiidae and Menoponidae, and we suggest recognizing Trinotonidae as a separate family. At the genus level, the generaColpocephalum,Hohorstiella,MenacanthusandRicinuswere recovered as paraphyletic. Regarding generic complexes, the tree revealed theMenacanthuscomplex to be monophyletic, but theColpocephalumcomplex paraphyletic, including genera not traditionally placed in this group. Dating analysis suggests that the divergence among families of Amblycera occurred shortly after the Cretaceous–Paleogene boundary 66 Mya. Cophylogenetic analyses revealed many host‐switching events during the diversification of Amblycera, indicating that the evolutionary history of Amblycera does not tightly mirror that of its hosts. Ancestral host reconstructions revealed that the ancestral host of Amblycera was most likely a bird, with two host switching events to mammals. By combining phylogenomics, molecular dating and cophylogenetic analyses, we provide the first large‐scale picture of amblyceran evolution, which will serve as a basis for future studies of this group. 

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3. Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

   https://doi.org/10.7717/peerj.8759  

   Sweet, Andrew D.; Johnson, Kevin P.; Cameron, Stephen L. (January 2020, PeerJ)

   null (Ed.)

   Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between nine and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2–3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. Columbicola spp. genomes are highly fragmented into 15–17 minicircles between ∼1,100 and ∼3,100 bp in length, with 1–4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice. 

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4. Genomic Approaches to Uncovering the Coevolutionary History of Parasitic Lice

   https://doi.org/10.3390/life12091442  

   Johnson, Kevin P. (September 2022, Life)

   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. 

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5. Transcriptome and Evolutionary Analysis of Pseudotrichomonas keilini , a Free-Living Anaerobic Eukaryote

   https://doi.org/10.1093/gbe/evae262  

   Abu-Elmakarem, Hend; Taerum, Stephen_J; Petitjean, Celine; Kotyk, Michael; Kay, Christopher; Čepička, Ivan; Bass, David; Gile, Gillian_H; Williams, Tom_A; Katz, ed., Laura (December 2024, Genome Biology and Evolution)

   Abstract The early evolution of eukaryotes and their adaptations to low-oxygen environments are fascinating open questions in biology. Genome-scale data from novel eukaryotes, and particularly from free-living lineages, are the key to answering these questions. The Parabasalia are a major group of anaerobic eukaryotes that form the most speciose lineage of Metamonada. The most well-studied are parasitic parabasalids, including Trichomonas vaginalis and Tritrichomonas foetus, but very little genome-scale data are available for free-living members of the group. Here, we sequenced the transcriptome of Pseudotrichomonas keilini, a free-living parabasalian. Comparative genomic analysis indicated that P. keilini possesses a metabolism and gene complement that are in many respects similar to its parasitic relative T. vaginalis and that in the time since their most recent common ancestor, it is the T. vaginalis lineage that has experienced more genomic change, likely due to the transition to a parasitic lifestyle. Features shared between P. keilini and T. vaginalis include a hydrogenosome (anaerobic mitochondrial homolog) that we predict to function much as in T. vaginalis and a complete glycolytic pathway that is likely to represent one of the primary means by which P. keilini obtains ATP. Phylogenomic analysis indicates that P. keilini branches within a clade of endobiotic parabasalids, consistent with the hypothesis that different parabasalid lineages evolved toward parasitic or free-living lifestyles from an endobiotic, anaerobic, or microaerophilic common ancestor. 

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