Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets

An obligate symbiont of Haematomyzus elephantis with a strongly reduced genome resembles symbiotic bacteria in sucking lice

The parvorder Rhynchophthirina with a single genus Haematomyzus is a small group of ectoparasites of unclear phylogenetic position, related to sucking and chewing lice. Previous screening based on the 16S rRNA gene indicated that Haematomyzus harbors a symbiotic bacterium whose DNA exhibits a strong shift in nucleotide composition typical of obligate mutualistic symbionts in insects. Within Phthiraptera, the smallest known genomes are found in the symbionts associated with sucking lice, which feed exclusively on mammal blood, compared to the generally larger genomes of the symbionts inhabiting chewing lice, which feed on skin derivatives. In this study, we investigate the genome characteristics of the symbiont associated with Haematomyzus elephantis. We sequenced and assembled the H. elephantis metagenome, extracted a genome draft of its symbiotic bacterium, and showed that the symbiont has a significantly reduced genome, which is with 0.39 Mbp the smallest genome among the symbionts known from Phthiraptera. Multigenic phylogenetic analysis places the symbiont into one of three clusters composed of long-branched symbionts from other insects. More specifically, it clusters together with symbionts from several other sucking lice and also with Wigglesworthia glossinidia, an obligate symbiont of tsetse flies. Consistent with the dramatic reduction of its genome, the H. elephantis symbiont lost many metabolic capacities. However, it retained functional pathways for four B vitamins, a trait typical for symbionts in blood-feeding insects. Considering genomic, metabolic, and phylogenetic characteristics, the new symbiont closely resembles those known from several sucking lice rather than chewing lice.IMPORTANCERhynchophthirina is a unique small group of permanent ectoparasites that is closely related to both sucking and chewing lice. These two groups of lice differ in their morphology, ecology, and feeding strategies. As a consequence of their different dietary sources, i.e., mammals' blood vs vertebrate skin derivatives, they also exhibit distinct patterns of symbiosis with obligate bacterial symbionts. While Rhynchophthirina shares certain traits with sucking and chewing lice, the nature of its obligate symbiotic bacterium and its metabolic role is not known. In this study, we assemble the genome of symbiotic bacterium from Haematomyzus elephantis (Rhynchophthirina), demonstrating its close similarity and phylogenetic proximity to several symbionts of sucking lice. The genome is highly reduced (representing the smallest genome among louse-associated symbionts) and exhibits a significant loss of metabolic pathways. However, similar to other sucking louse symbionts, it retains essential pathways for the synthesis of several B vitamins.

Biogeographic History of Pigeons and Doves Drives the Origin and Diversification of Their Parasitic Body Lice

Despite their extensive diversity and ecological importance, the history of diversification for most groups of parasitic organisms remains relatively understudied. Elucidating broad macroevolutionary patterns of parasites is challenging, often limited by the availability of samples, genetic resources, and knowledge about ecological relationships with their hosts. In this study, we explore the macroevolutionary history of parasites by focusing on parasitic body lice from doves. Building on extensive knowledge of ecological relationships and previous phylogenomic studies of their avian hosts, we tested specific questions about the evolutionary origins of the body lice of doves, leveraging whole genome data sets for phylogenomics. Specifically, we sequenced whole genomes from 68 samples of dove body lice, including representatives of all body louse genera from 51 host taxa. From these data, we assembled > 2300 nuclear genes to estimate dated phylogenetic relationships among body lice and several outgroup taxa. The resulting phylogeny of body lice was well supported, although some branches had conflicting signals across the genome. We then reconstructed ancestral biogeographic ranges of body lice and compared the body louse phylogeny to the phylogeny of doves, and also to a previously published phylogeny of the wing lice of doves. Divergence estimates placed the origin of body lice in the late Oligocene. Body lice likely originated in Australasia and dispersed with their hosts during the early Miocene, with subsequent codivergence and host switching throughout the world. Notably, this evolutionary history is very similar to that of dove wing lice, despite the stronger dispersal capabilities of wing lice compared to body lice. Our results highlight the central role of the biogeographic history of host organisms in driving the evolutionary history of their parasites across time and geographic space.

The first detailed morphological treatment of a Cretaceous psocid and the character evolution of Trogiomorpha (Insecta: Psocodea)

While new fossil psocid taxa are described every year, the morphology is generally not studied and documented in sufficient detail, limiting our understanding of the character evolution in this order. A new fossil species of the genus Psyllipsocus from mid-Cretaceous Kachin amber is described and its morphology reconstructed in detail using synchrotron-radiation micro-computed tomography (SR-μ-CT). We present the first cybertype of a Cretaceous fossil psocid. We also describe and discuss the putative evolution of previously unrecognized and underestimated exoskeletal characters for the suborder Trogiomorpha. Additionally, using our new observations, we critically evaluate the phylogeny of Trogiomorpha and the character evolution in this group. We also present a modified character matrix which we analyze using Bayesian inference and parsimony. Based on our results and previous studies we propose monophyletic Trogiomorpha s.l. (incl. †Brachyantennum) and Trogiomorpha s. str. (possibly incl. †Cormopsocidae), the latter comprising Prionoglarididae and monophyletic Spinaprocta. Spinaprocta contain Atropetae and Psyllipsocetae (incl. Psyllipsocus) as sister taxa. Some relationships on the genus level in Trogiomorpha are still strongly disputed and unclear. Here, we synonymize the extinct monotypic genus †Khatangia with Psyllipsocus and discuss the systematic position of †Sinopsyllipsocus, †Parapsyllipsocus, †Empheriopsis and †Concavapsocus. A key for all extinct species of Psyllipsocidae is provided.

Unveiling the chewing lice (Menoponidae and Philopteridae) fauna of the Brazilian Northeast: new records for Maranhão and Piauí States

Lice (Phthiraptera) are obligate ectoparasites of birds and mammals found worldwide. Chewing lice, belonging to the families Menoponidae and Philopteridae, are particularly diverse in Brazil, although their distribution is unevenly documented across states. This study focused on recent collections from protected areas in Maranhão and Piauí, the sampling involved mist netting and comprehensive ectoparasite examination, with specimens identified using both light microscopy and Scanning Electron Microscopy. A total of 239 birds were collected, 63 (26.35%) of which were infested with chewing lice. Seventeen distinct species were identified, including seven that had not been previously recorded in Brazil. Our findings contribute to the growing knowledge of chewing lice diversity in Brazil, with particular emphasis on the underrepresented states of Maranhão and Piauí.

Insect Mitochondrial Genomics: A Decade of Progress

The past decade has seen the availability of insect genomic data explode, with mitochondrial (mt) genome data seeing the greatest growth. The widespread adoption of next-generation sequencing has solved many earlier methodological limitations, allowing the routine sequencing of whole mt genomes, including from degraded or museum specimens and in parallel to nuclear genomic projects. The diversity of available taxa now allows finer-scale comparisons between mt and nuclear phylogenomic analyses; high levels of congruence have been found for most orders, with some significant exceptions (e.g., Odonata, Mantodea, Diptera). The evolution of mt gene rearrangements and their association with haplodiploidy have been tested with expanded taxonomic sampling, and earlier proposed trends have been largely supported. Multiple model systems have been developed based on findings unique to insects, including mt genome fragmentation (lice and relatives) and control region duplication (thrips), allowing testing of hypothesized evolutionary drivers of these aberrant genomic phenomena. Finally, emerging research topics consider the contributions of mt genomes to insect speciation and habitat adaption, with very broad potential impacts. Integration between insect mt genomic research and other fields within entomology continues to be our field's greatest opportunity and challenge.

Nudiviruses in free-living and parasitic arthropods: evolutionary taxonomy

The nudiviruses (family: Nudiviridae) are large double-stranded DNA (dsDNA) viruses that infect insects and crustaceans, and have most recently been identified from ectoparasitic members (fleas and lice). This virus family was created in 2014 and has since been expanded via the discovery of multiple novel viral candidates or accepted members, sparking the need for a new taxonomic and evolutionary overview. Using current information (including data from public databases), we construct a new comprehensive phylogeny, encompassing 49 different nudiviruses. We use this novel phylogeny to propose a new taxonomic structure of the Nudiviridae by suggesting two new viral genera (Zetanudivirus and Etanudivirus), from ectoparasitic lice. We detail novel emerging relationships between nudiviruses and their hosts, considering their evolutionary history and ecological role.

Morphology of the pterothoracic musculature in Paraneoptera and its phylogenetic implication (Insecta: Neoptera)

Although the monophyly of Paraneoptera (=hemipteroid orders or Acercaria, composed of Psocodea, Thysanoptera and Hemiptera) has been widely accepted morphologically, the results from molecular phylogenetic and phylogenomic analyses contradict this hypothesis. In particular, phylogenomic analyses provide strong bootstrap support for the sister group relationship between Psocodea and Holometabola, that is, paraphyly of Paraneoptera. Here, we examined the pterothoracic musculature of Paraneoptera, as well as a wide range of other neopterous insect orders, and analysed its phylogenetic implication. By using the synchrotron microcomputed tomography (µCT) and parsimony-based ancestral state reconstruction, several apomorphic conditions suggesting the monophyly of Paraneoptera, such as the absence of the II/IIItpm7, IIscm3, IIIspm2 and IIIscm3 muscles, were identified. In contrast, no characters supporting Psocodea + Holometabola were recovered from the thoracic muscles. These results provide additional support for the monophyly of Paraneoptera, together with the previously detected morphological apomorphies of the head, wing base, and abdomen.

Mitochondrial genome fragmentation is correlated with increased rates of molecular evolution

While mitochondrial genome content and organization is quite diverse across all Eukaryotes, most bilaterian animal mitochondrial genomes (mitogenomes) exhibit highly conserved gene content and organisation, with genes typically encoded on a single circular chromosome. However, many species of parasitic lice (Insecta: Phthiraptera) are among the notable exceptions, having mitogenomes fragmented into multiple circular chromosomes. To better understand the process of mitogenome fragmentation, we conducted a large-scale genomic study of a major group of lice, Amblycera, with extensive taxon sampling. Analyses of the evolution of mitogenome structure across a phylogenomic tree of 90 samples from 53 genera revealed evidence for multiple independent origins of mitogenome fragmentation, some inferred to have occurred less than five million years ago. We leveraged these many independent origins of fragmentation to compare the rates of DNA substitution and gene rearrangement, specifically contrasting branches with fragmented and non-fragmented mitogenomes. We found that lineages with fragmented mitochondrial genomes had significantly higher rates of mitochondrial sequence evolution. In addition, lineages with fragmented mitochondrial genomes were more likely to have mitogenome gene rearrangements than those with single-chromosome mitochondrial genomes. By combining phylogenomics and mitochondrial genomics we provide a detailed portrait of mitogenome evolution across this group of insects with a remarkably unstable mitogenome structure, identifying processes of molecular evolution that are correlated with mitogenome fragmentation.

Highly Resolved Genomes of Two Closely Related Lineages of the Rodent Louse Polyplax serrata with Different Host Specificities

Sucking lice of the parvorder Anoplura are permanent ectoparasites with specific lifestyle and highly derived features. Currently, genomic data are only available for a single species, the human louse Pediculus humanus. Here, we present genomes of two distinct lineages, with different host spectra, of a rodent louse Polyplax serrata. Genomes of these ecologically different lineages are closely similar in gene content and display a conserved order of genes, with the exception of a single translocation. Compared with P. humanus, the P. serrata genomes are noticeably larger (139 vs. 111 Mbp) and encode a higher number of genes. Similar to P. humanus, they are reduced in sensory-related categories such as vision and olfaction. Utilizing genome-wide data, we perform phylogenetic reconstruction and evolutionary dating of the P. serrata lineages. Obtained estimates reveal their relatively deep divergence (∼6.5 Mya), comparable with the split between the human and chimpanzee lice P. humanus and Pediculus schaeffi. This supports the view that the P. serrata lineages are likely to represent two cryptic species with different host spectra. Historical demographies show glaciation-related population size (Ne) reduction, but recent restoration of Ne was seen only in the less host-specific lineage. Together with the louse genomes, we analyze genomes of their bacterial symbiont Legionella polyplacis and evaluate their potential complementarity in synthesis of amino acids and B vitamins. We show that both systems, Polyplax/Legionella and Pediculus/Riesia, display almost identical patterns, with symbionts involved in synthesis of B vitamins but not amino acids.

Mitochondrial genome sequence comparisons indicate that the elephant louse Haematomyzus elephantis (Piaget, 1869) contains cryptic species

The parvorder Rhynchopthirina contains three currently recognised species of lice that parasitize elephants (both African savanna elephant Loxodonta africana and Asian elephant Elephas maximus), desert warthogs (Phacochoerus aethiopicus) and Red River hogs (Potamochoerus porcus), respectively. The Asian elephant lice and the African savanna elephant lice are currently treated as the same species, Haematomyzus elephantis (Piaget, 1869), based on morphology despite the fact that their hosts diverged 8.4 million years ago. In the current study, we sequenced 23 mitochondrial (mt) genes of African savanna elephant lice collected in South Africa and analysed the sequence divergence between African savanna elephant lice and previously sequenced Asian elephant lice. Sequence comparisons revealed >23% divergence for the 23 mt genes as a whole and ~17% divergence for cox1 gene between African savanna and Asian elephant lice, which were far higher than the divergence expected within a species. Furthermore, the mt gene sequence divergences between these lice are 3.76-4.6 times higher than that between their hosts, the African savanna and Asian elephants, which are expected for the co-divergence and co-evolution between lice and their elephant hosts. We conclude that (1) H. elephantis (Piaget, 1869) contains cryptic species and (2) African savanna and Asian elephant lice are different species genetically that may have co-diverged and co-evolved with their hosts.

Stem chewing lice on Cretaceous feathers preserved in amber

Phthirapteran lice (true lice or parasitic lice) are a major group of ectoparasitic insects living on their bird or mammal hosts during their entire life cycle.1 Due to their highly specialized lifestyles, they are extremely poorly represented in fossil records.2 Molecular clock estimations have speculated extensively about the origin time of parasitic lice,3,4 yet none have been confirmed unequivocally. Herein, we report a new family of stem chewing lice, based on two adult insects associated with several semiplume feathers preserved within a piece of Kachin amber from the mid-Cretaceous. They display some defining characteristics of the Amblycera, an early-diverging lineage of the crown lice group. These features include a wingless body, chewing mouthparts, narrow and small thorax, and short tarsus with elongated euplantulae. Our phylogenetic analysis places the new taxa in the Amblycera, and the discovery thus pushes back the lice fossil records by at least 55 million years. Furthermore, the new specimens show primitive characters such as compressed and club-shaped terminal segments of antennae, maxillary and labial palps, and unmodified femora of hind legs, providing key information for the evolutionary relationship between free-living booklice and parasitic lice. This suggests that some ectoparasitic characters defining the crown lice group might have evolved among amblyceran and non-amblyceran lice in parallel. These newly described fossil specimens imply at least a Cretaceous age of Phthiraptera.

Prevalence and diversity of parasitic bird lice (Insecta: Psocodea) in northeast Arkansas

Many groups of parasites lack basic information on biodiversity and host associations, which poses challenges for conservation and understanding the ecological relationships between hosts and their parasites. This gap in knowledge is particularly relevant for parasitic species with obscure lifestyles. Ectoparasitc bird lice (Insecta: Psocodea: Phthiraptera) are a group of parasites that has received a relatively substantial research focus, yet patterns of bird-louse relationships and louse diversity remain understudied in many geographic regions, including in parts of the southeastern United States. In this study, we assessed the diversity, prevalence, abundance, and intensity of lice from live and salvaged birds in northeastern Arkansas. We also focused on the frequency of co-occurrence of lice and symbiotic feather mites. Finally, we used nuclear and mitochondrial genes to assess the phylogenic relationships among the most common genera of lice in our sample. We found a total louse prevalence of 10.57% with the highest prevalence on the Passeriformes families Turdidae, Passerellidae, and Parulidae. We also found the louse genera Myrsidea and Brueelia to be the most prevalent and abundant in our sample. Additionally, we reported several novel associations among well-studied bird species. We also found that louse phylogenic patterns tend to reflect host taxonomy and/or ecology. Overall, our results provide important insight into the biodiversity, community structure, and host interactions of parasitic lice from North American birds.

Ectoparasitic mites, ticks (Acari: Trombidiformes, Mesostigmata, Ixodida) and insects (Insecta: Psocodea, Siphonaptera) of ground-dwelling small mammals in the Baltic States. An annotated checklist

This paper presents an annotated checklist of 77 species of ectoparasitic mites, ticks (Acari: Trombidiformes, Mesostigmata, Ixodida) and insects (Insecta: Psocodea, Siphonaptera) found on ground-dwelling small mammals in the Baltic States (Estonia, Latvia, Lithuania). Eight species of five genera of chigger mites (Trombidiformes: Trombiculidae), 26 species of eight genera of laelapid mites (Mesostigmata: Laelapidae), six species of two genera of ixodid ticks (Ixodida: Ixodidae), 11 species of three genera of blood-sucking lice (Psocodea: Hoplopleuridae, Pediculidae, Polyplacidae) and 26 species of 15 genera of fleas (Siphonaptera: Ceratophyllidae, Ctenophthalmidae, Hystrichopsyllidae, Pulicidae) were recorded on ground-dwelling small mammals in the Baltic States. Neotrombicula japonica (Tanaka, Kaiwa, Teramura & Kagaya), Neotrombicula vulgaris (Schluger), Miyatrombicula muris (Oudemans), Hoplopleura edentula Fahrenholz and Polyplax hannswrangeli Eichler are recorded for the first time in the Baltic States.

Bridging two insect flight modes in evolution, physiology and robophysics

Since taking flight, insects have undergone repeated evolutionary transitions between two seemingly distinct flight modes1-3. Some insects neurally activate their muscles synchronously with each wingstroke. However, many insects have achieved wingbeat frequencies beyond the speed limit of typical neuromuscular systems by evolving flight muscles that are asynchronous with neural activation and activate in response to mechanical stretch2-8. These modes reflect the two fundamental ways of generating rhythmic movement: time-periodic forcing versus emergent oscillations from self-excitation8-10. How repeated evolutionary transitions have occurred and what governs the switching between these distinct modes remain unknown. Here we find that, despite widespread asynchronous actuation in insects across the phylogeny3,6, asynchrony probably evolved only once at the order level, with many reversions to the ancestral, synchronous mode. A synchronous moth species, evolved from an asynchronous ancestor, still preserves the stretch-activated muscle physiology. Numerical and robophysical analyses of a unified biophysical framework reveal that rather than a dichotomy, these two modes are two regimes of the same dynamics. Insects can transition between flight modes across a bridge in physiological parameter space. Finally, we integrate these two actuation modes into an insect-scale robot11-13 that enables transitions between modes and unlocks a new self-excited wingstroke strategy for engineered flight. Together, this framework accounts for repeated transitions in insect flight evolution and shows how flight modes can flip with changes in physiological parameters.

Emerging bacterial infectious diseases/pathogens vectored by human lice

Human lice have always been a major public health concern due to their vector capacity for louse-borne infectious diseases, like trench fever, louse-borne relapsing fever, and epidemic fever, which are caused by Bartonella quintana, Borrelia recurrentis, and Rickettsia prowazekii, respectively. Those diseases are currently re-emerging in the regions of poor hygiene, social poverty, or wars with life-threatening consequences. These louse-borne diseases have also caused outbreaks among populations in jails and refugee camps. In addition, antibodies and DNAs to those pathogens have been steadily detected in homeless populations. Importantly, more bacterial pathogens have been detected in human lice, and some have been transmitted by human lice in laboratories. Here, we provide a comprehensive review and update on louse-borne infectious diseases/bacterial pathogens.

Mitochondrial Genome Fragmentation Occurred Multiple Times Independently in Bird Lice of the Families Menoponidae and Laemobothriidae

Mitochondrial (mt) genome fragmentation has been discovered in all five parvorders of parasitic lice (Phthiraptera). To explore whether minichromosomal characters derived from mt genome fragmentation are informative for phylogenetic studies, we sequenced the mt genomes of 17 species of bird lice in Menoponidae and Laemobothriidae (Amblycera). Four species of Menoponidae (Actornithophilus sp. 1 ex [pied oystercatcher], Act. sp. 2 ex [masked lapwing], Austromenopon sp. 2 ex [sooty tern and crested tern], Myr. sp. 1 ex [satin bowerbird]) have fragmented mt genomes, whereas the other 13 species retain the single-chromosome mt genomes. The two Actornithophilus species have five and six mt minichromosomes, respectively. Aus. sp. 2 ex [sooty tern and crested tern] has two mt minichromosomes, in contrast to Aus. sp. 1 ex [sooty shearwater], which has a single mt chromosome. Myr. sp. 1 ex [satin bowerbird] has four mt minichromosomes. When mapped on the phylogeny of Menoponidae and Laemobothriidae, it is evident that mt genome fragmentation has occurred multiple times independently among Menoponidae and Laemobothriidae species. We found derived mt minichromosomal characters shared between Myrsidea species, between Actornithophilus species, and between and among different ischnoceran genera, respectively. We conclude that while mt genome fragmentation as a general feature does not unite all the parasitic lice that have this feature, each independent mt genome fragmentation event does produce minichromosomal characters that can be informative for phylogenetic studies of parasitic lice at different taxonomic levels.

The evolution of sanguivory in vampire bats: origins and convergences

Blood-feeding (sanguivory) has evolved more than two dozen times among birds, fishes, insects, arachnids, molluscs, crustaceans, and annelids; however, among mammals, it is restricted to the vampire bats. Here, the authors revisit the question of how it evolved in that group. Evidence to date suggests that the ancestors of phyllostomids were insectivorous, and that carnivory, omnivory, and nectarivory evolved among phyllostomids after vampire bats diverged. Frugivory likely also evolved after vampire bats diverged, but the phylogeny is ambiguous on that point. However, vampire bats lack any genetic evidence of a frugivorous past, and the behavioural progression from frugivory to sanguivory is difficult to envision. Thus, the most parsimonious scenario is that sanguivory evolved in an insectivorous ancestor to vampire bats via ectoparasite-eating, wound-feeding, or some combination of the two—all feeding habits found among blood-feeding birds today. Comparing vampire bats with other sanguivores, the authors find several remarkable examples of convergence. Further, it was found that blood-feeding has been ca. 50 times more likely to evolve in a vertebrate lineage than in an invertebrate one. The authors hypothesize that this difference exists because vertebrates are more likely than invertebrates to have the biochemical necessities required to assimilate the components of vertebrate blood.

Supergroup F Wolbachia with extremely reduced genome: transition to obligate insect symbionts

BACKGROUND

Wolbachia belong to highly abundant bacteria which are frequently found in invertebrate microbiomes and manifest by a broad spectrum of lifestyles from parasitism to mutualism. Wolbachia supergroup F is a particularly interesting clade as it gave rise to symbionts of both arthropods and nematodes, and some of its members are obligate mutualists. Investigations on evolutionary transitions among the different symbiotic stages have been hampered by a lack of the known diversity and genomic data for the supergroup F members.

RESULTS

Based on amplicon screening, short- and long-read WGS approaches, and laser confocal microscopy, we characterize five new supergroup F Wolbachia strains from four chewing lice species. These strains reached different evolutionary stages and represent two remarkably different types of symbiont genomes. Three of the genomes resemble other known members of Wolbachia F supergroup, while the other two show typical signs of ongoing gene inactivation and removal (genome size, coding density, low number of pseudogenes). Particularly, wMeur1, a symbiont fixed in microbiomes of Menacanthus eurysternus across four continents, possesses a highly reduced genome of 733,850 bp. The horizontally acquired capacity for pantothenate synthesis and localization in specialized bacteriocytes suggest its obligate nutritional role.

CONCLUSIONS

The genome of wMeur1 strain, from the M. eurysternus microbiome, represents the smallest currently known Wolbachia genome and the first example of Wolbachia which has completed genomic streamlining as known from the typical obligate symbionts. This points out that despite the large amount and great diversity of the known Wolbachia strains, evolutionary potential of these bacteria still remains underexplored. The diversity of the four chewing lice microbiomes indicates that this vast parasitic group may provide suitable models for further investigations. Video Abstract.

Morphological and molecular evidence reveals a new species of chewing louse Pancola ailurus n. sp. (Phthiraptera: Trichodectidae) from the endangered Chinese red panda Ailurus styani

Lice are six-legged, wingless, insect parasites of mammals and birds, and include two main functional groups: blood-sucking lice and chewing lice. However, it is still not clear whether the Chinese red panda Ailurus styani is infested with the parasitic louse. In the present study, we describe a new genus and a species of chewing louse, Pancola ailurus (Phthiraptera: Trichodectidae) based on morphological and molecular datasets. The morphological features showed that Pancola is closer to Paratrichodectes. The genetic divergence of cox1 and 12S rRNA among the Pancola ailurus n. sp. and other Trichodectidae lice was 29.7 - 34.6% and 38.9 - 43.6%, respectively. Phylogenetic analyses based on the available mitochondrial gene sequences showed that P. ailurus n. sp. is more closely related to Trichodectes canis and Geomydoecus aurei than to Felicola subrostratus and together nested within the family Trichodectidae. This study is the first record of parasitic lice from the endangered Chinese red panda A. styani and highlights the importance of integrating morphological and molecular datasets for the identification and discrimination of new louse species.

A New Genus and Species of the Suborder Trogiomorpha (Insecta, Psocodea) from Mid-Cretaceous Amber of Myanmar

We established a new genus with a new species Brachyantennum spinosum Liang et Liu, gen. et sp. nov. from mid-Cretaceous Burmese Kachin amber. It is tentatively placed into the suborder Trogiomorpha, based on the strong external valve, the reduced dorsal and ventral valve, and the short subgenital plate covering the basal part of the external valve. This new genus is apparently close to the family Cormopsocidae, based on the well-developed and very long hindwing Sc vein. However, its familial placement is ambiguous and it can be excluded from the established families of Trogiomorpha by the presence of the tarsal ctenidiobothria on the mid- and hindleg.

A Novel Mitochondrial Genome Fragmentation Pattern in the Buffalo Louse Haematopinus tuberculatus (Psocodea: Haematopinidae)

Sucking lice are obligate ectoparasites of mammalian hosts, causing serious public health problems and economic losses worldwide. It is well known that sucking lice have fragmented mitochondrial (mt) genomes, but many remain undetermined. To better understand patterns of mt genome fragmentation in the sucking lice, we sequenced the mt genome of the buffalo louse Haematopinus tuberculatus using next-generation sequencing (NGS). The mt genome of H. tuberculatus has ten circular minichromosomes containing a total of 37 genes. Each minichromosome is 2.9-5.0 kb long and carries one to eight genes plus one large non-coding region. The number of mt minichromosomes of H. tuberculatus (ten) is different from those of congeneric species (horse louse H. asini, domestic pig louse H. suis and wild pig louse H. apri) and other sucking lice. Two events (gene translocation and merger of mt minichromosome) are observed in Haematopinus. Compared to other studies, our phylogeny generated from mt genome datasets showed a different topology, suggesting that inclusion of data other than mt genomes would be required to resolve phylogeny of sucking lice. To our knowledge, this is the first report of a ten mt minichromosomes genome in sucking lice, which opens a new outlook into unexplored mt genome fragmentation patterns in sucking lice.

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.

Morphology and phylogenetic significance of the thoracic muscles in Psocodea (Insecta: Paraneoptera)

The thoracic musculature of the insect order Psocodea has been examined in only a few species of a single suborder to date. In the present study, we examined the thoracic musculature of species selected from all three suborders of Psocodea to elucidate the ground plan of the order and to examine the phylogenetic utility of the character system. The sister-group relationship between the suborders Troctomorpha and Psocomorpha received support from two novel nonhomoplasious synapomorphies, although the support from other morphological characters for this relationship is ambiguous. The sister-group relationship between the infraorders Epipsocetae and Psocetae also received support from one nonhomoplasious synapomorphy, although no other morphological characters supporting this relationship have been identified to date. The present examination revealed the potential of thoracic muscle characters for estimating deep phylogeny, possibly including interordinal relationships.

Phylogenomics reveals the origin of mammal lice out of Afrotheria

Mammals host a wide diversity of parasites. Lice, comprising more than 5,000 species, are one group of ectoparasites whose major lineages have a somewhat patchwork distribution across the major groups of mammals. Here we explored patterns in the diversification of mammalian lice by reconstructing a higher-level phylogeny of these lice, leveraging whole genome sequence reads to assemble single-copy orthologue genes across the genome. The evolutionary tree of lice indicated that three of the major lineages of placental mammal lice had a single common ancestor. Comparisons of this parasite phylogeny with that for their mammalian hosts indicated that the common ancestor of elephants, elephant shrews and hyraxes (that is, Afrotheria) was the ancestral host of this group of lice. Other groups of placental mammals obtained their lice via host-switching out of these Afrotherian ancestors. In addition, reconstructions of the ancestral host group (bird versus mammal) for all parasitic lice supported an avian ancestral host, indicating that the ancestor of Afrotheria acquired these parasites via host-switching from an ancient avian host. These results shed new light on the long-standing question of why the major groups of parasitic lice are not uniformly distributed across mammals and reveal the origins of mammalian lice.

High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal

Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (Echinophthirius horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis), which is endemic to Lake Saimaa in Finland, and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.

New Genus and Species of Empheriidae (Insecta: Psocodea: Trogiomorpha) and Their Implication for the Phylogeny of Infraorder Atropetae

Two species of psocids discovered from the Mid-Cretaceous Burmese amber, Latempheria kachinensis Li, Yoshizawa, and Yao, gen. et sp. nov. and Burmempheria curvatavena Li, Yoshizawa, and Yao, sp. nov., are described and assigned to the Empheriidae (Trogiomorpha: Atropetae) family. A phylogenetic analysis of the infraorder Atropetae is conducted based on 38 morphological characters of three outgroups and fifteen ingroups, which supported the monophyly of Atropetae including fossil and extant taxa. In the phylogenetic result, all the genera of fossil families Empheriidae and Archaeatropidae form a monophyletic group, sister to the extant members of Atropetae. The two fossil families also share a lot of similarities in morphology, locality, and geological period. Recently discovered fossil species exhibited combined morphological characters of both families. Based on these observations and the results of the phylogenetic analysis, Archaeatropidae is treated here as a new junior synonym of Empheriidae.

Autosomal recessive cutis laxa type 1C with a homozygous LTBP4 splicing variant: a case report and update of literature

BACKGROUND

Autosomal recessive cutis laxa (ARCL) is a heterogeneous disorder with three primary forms (ARCL 1, ARCL 2 and ARCL 3). Latent transforming growth factor beta binding protein 4 (LTBP4) anomalies cause ARCL1C and are connected to different problems in the skin and other organs. Herein, we present a seven month old Iranian boy with a clinical manifestation of ARCL1 with literature review of previous cases with attributes of ARCL1C.

METHODS

Considering the craniofacial characteristics and respiratory distress of the proband, cutis laxa (CL) was expected and whole-exome sequencing (WES) was performed.

RESULTS

In the proband, signs of CL were mainly located in the face, thorax, and abdomen. The prenatal investigation revealed a diaphragmatic hernia and certain uncommon signs, such as an atrial septal defect and pyloric stenosis. The WES showed a novel homozygous mutation (c.533-1G > A) in exon six of the LTBP4 gene.

CONCLUSION

This report showed a new variant with uncommon clinical features, such as a stenosis atrial septal defect and pyloric stenosis, which causes ARCL1C. Unfortunately, the proband developed several heart problems and died at the age of seven months and seven days. Thus, a more in-depth evaluation is needed to clarify the different aspects of CL related to LTBP4 disorder.

Fragmented mitochondrial genomes of seal lice (family Echinophthiriidae) and gorilla louse (family Pthiridae): frequent minichromosomal splits and a host switch of lice between seals

Background

The mitochondrial (mt) genomes of 15 species of sucking lice from seven families have been studied to date. These louse species have highly dynamic, fragmented mt genomes that differ in the number of minichromosomes, the gene content, and gene order in a minichromosome between families and even between species of the same genus.

Results

In the present study, we analyzed the publicly available data to understand mt genome fragmentation in seal lice (family Echinophthiriidae) and gorilla louse, Pthirus gorillae (family Pthiridae), in particular the role of minichromosome split and minichromosome merger in the evolution of fragmented mt genomes. We show that 1) at least three ancestral mt minichromosomes of sucking lice have split in the lineage leading to seal lice, 2) one minichromosome ancestral to primate lice has split in the lineage to the gorilla louse, and 3) two ancestral minichromosomes of seal lice have merged in the lineage to the northern fur seal louse. Minichromosome split occurred 15-16 times in total in the lineages leading to species in six families of sucking lice investigated. In contrast, minichromosome merger occurred only four times in the lineages leading to species in three families of sucking lice. Further, three ancestral mt minichromosomes of sucking lice have split multiple times independently in different lineages of sucking lice. Our analyses of mt karyotypes and gene sequences also indicate the possibility of a host switch of crabeater seal louse to Weddell seals.

Conclusions

We conclude that: 1) minichromosome split contributes more than minichromosome merger in mt genome fragmentation of sucking lice, and 2) mt karyotype comparison helps understand the phylogenetic relationships between sucking louse species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08530-8.

The Complete Mitochondrial Genome of the Chicken Body Louse, Menacanthus cornutus, and Evolutionary Patterns of Extensive Gene Rearrangements in the Mitochondrial Genomes of Amblycera (Psocodea: Phthiraptera)

Animal mitochondrial (mt) genomes are typically double-strand circular DNA molecules, but diverse structural variations have been widely found in multiple groups. In parasitic lice (Phthiraptera), the structure of mt genomes varies remarkably across all five suborders. In this study, we reported the complete mt genome of a chicken body louse, Menacanthus cornutus, which has a typical single circular mt chromosome and drastic mt gene rearrangements. This mt genome is 15,693 bp in length, consisting of 13 protein-coding genes, 23 tRNA genes, 2 rRNA genes, and a control region. A comparison with a typical insect mt genome suggested that two highly similar trnM are present in the mt genome of M. cornutus. Moreover, almost every single gene was rearranged, and over half of mt genes were inverted. Phylogenetic analyses inferred from the mt genome sequences supported the monophyly and position of Amblycera. Mapped over the phylogenetic relationships of Amblycera, we identified two inversion events for the conserved gene blocks in Boopidae and Menoponidae. The inverted ND4L-ND4 was likely a synapomorphic rearrangement in Menoponidae. Our study demonstrated the importance of sequencing mt genomes for additional taxa to uncover the mechanism underlying the structural evolution of the mt genome in parasitic lice.

Exploration of the homology among the muscles associated with the female genitalia of the three suborders of Psocodea (Insecta)

By using μCT technology, we reconstructed 3D models of the female genital structures and associated muscles of seven species from three suborders of Psocodea (free-living species only, formerly known as independent insect order "Psocoptera"). The homology of the female genital structures and associated muscles of different species is discussed. A total of 21 muscle groups were observed, and except for one muscle, all were homologized throughout the order. Moreover, some of the homologous muscles could be identified confidently in holometabolan insects. Using the muscles as landmarks, we discuss the homology of the ovipositor valves between Psocodea and other neopteran insects. Most importantly, the ovipositor of the suborder Trogiomorpha was identified to consist of the well-developed external valve (V3) plus a remnant of the dorsal valve (V2). We also examined the phylogenetic information included in the female genital muscles and found that certain muscles provide useful information and support deeper nodes (e.g., monophyly of the suborder Psocomorpha). The present study of female genital muscles not only helps us to better understand the phylogeny of Psocodea but also provides a solid foundation for research on muscle evolution.

The Acari Hypothesis, II: Interspecies Operability of Pattern Recognition Receptors

Hypersensitivity to galactose-α-1,3-galactose (α-gal) is an informative example of a pathologic IgE-mediated process. By way of their saliva, ticks are able to sensitize humans to tick dietary elements that express α-gal. Mites, which along with ticks constitute the phyletic subclass Acari, feed on proteinaceous foodstuffs that represent most, if not all, human allergens. Given: (1) the gross nature of the pathophysiological reactions of allergy, especially anaphylaxis, (2) the allergenicity of acarian foodstuffs, and (3) the relatedness of ticks and mites, it has been hypothesized that human-acarian interactions are cardinal to the pathogenesis of allergy. In this report, a means by which such interactions contribute to that pathogenesis is proposed.

The interplay between host biogeography and phylogeny in structuring diversification of the feather louse genus Penenirmus

Parasite diversification is influenced by many of the same factors that affect speciation of free-living organisms, such as biogeographic barriers. However, the ecology and evolution of the host lineage also has a major impact on parasite speciation. Here we explore the interplay between biogeography and host-association on the pattern of diversification in a group of ectoparasitic lice (Insecta: Phthiraptera: Penenirmus) that feeds on the feathers of woodpeckers, barbets, and honeyguides (Piciformes) and some songbirds (Passeriformes). We use whole genome sequencing of 41 ingroup and 12 outgroup samples to develop a phylogenomic dataset of DNA sequences from a reference set of 2395 single copy ortholog genes, for a total of nearly four million aligned base positions. The phylogenetic trees resulting from both concatenated and gene-tree/species-tree coalescent analyses were nearly identical and highly supported. These trees recovered the genus Penenirmus as monophyletic and identified several major clades, which tended to be associated with one major host group. However, cophylogenetic analysis revealed that host-switching was a prominent process in the diversification of this group. This host-switching generally occurred within single major biogeographic regions. We did, however, find one case in which it appears that a rare dispersal event by a woodpecker lineage from North America to Africa allowed its associated louse to colonize a woodpecker in Africa, even though the woodpecker lineage from North America never became established there.

Highly rearranged mitochondrial genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from endangered eagles

Background

Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is known about the mt genomes from the family Philopteridae, the most species-rich family within the suborder Ischnocera.

Methods

Herein, we use next-generation sequencing to decode the mt genome of Falcolipeurus suturalis and compare it with the mt genome of F. quadripustulatus. Phylogenetic relationships within the family Philopteridae were inferred from the concatenated 13 protein-coding genes of the two Falcolipeurus lice and members of the family Philopteridae using Bayesian inference (BI) and maximum likelihood (ML) methods.

Results

The complete mt genome of F. suturalis is a circular, double-stranded DNA molecule 16,659bp in size that contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and three non-coding regions. The gene order of the F. suturalis mt genome is rearranged relative to that of F. quadripustulatus, and is radically different from both other louse species and the putative ancestral insect. Phylogenetic analyses revealed clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities=1.0 and bootstrapping frequencies=100), and that the genus Falcolipeurus is sister to the genus Ibidoecus (Bayesian posterior probabilities=1.0 and bootstrapping frequencies=100).

Conclusions

These datasets help to better understand gene rearrangements in lice and the phylogenetic position of Falcolipeurus and provide useful genetic markers for systematic studies of bird lice.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04776-5.