Population genomics of seal lice provides insights into the postglacial history of northern European seals.

Genetic analyses of host-specific parasites can elucidate the evolutionary histories and biological features of their hosts. Here, we used population-genomic analyses of ectoparasitic seal lice (Echinophthirius horridus) to shed light on the postglacial history of seals in the Arctic Ocean and the Baltic Sea region. One key question was the enigmatic origin of relict landlocked ringed seal populations in lakes Saimaa and Ladoga in northern Europe. We found that that lice of four postglacially diverged subspecies of the ringed seal (Pusa hispida) and Baltic gray seal (Halichoerus grypus), like their hosts, form genetically differentiated entities. Using coalescent-based demographic inference, we show that the sequence of divergences of the louse populations is consistent with the geological history of lake formation. In addition, local effective population sizes of the lice are generally proportional to the census sizes of their respective seal host populations. Genome-based reconstructions of long-term effective population sizes revealed clear differences among louse populations associated with gray versus ringed seals, with apparent links to Pleistocene and Holocene climatic variation as well as to the isolation histories of ringed seal subspecies. Interestingly, our analyses also revealed ancient gene flow between the lice of Baltic gray and ringed seals, suggesting that the distributions of Baltic seals overlapped to a greater extent in the past than is the case today. Taken together, our results demonstrate how genomic information from specialized parasites with higher mutation and substitution rates than their hosts can potentially illuminate finer scale population genetic patterns than similar data from their hosts.

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.

Detection of Bartonella schoenbuchensis (sub)species DNA in different louse fly species in Saxony, Germany: The proof of multiple PCR analysis necessity in case of ruminant-associated bartonellae determination.

BACKGROUND: Hippoboscid flies are bloodsucking arthropods that can transmit pathogenic microorganisms and are therefore potential vectors for pathogens such as Bartonella spp. These Gram-negative bacteria can cause mild-to-severe clinical signs in humans and animals; therefore, monitoring Bartonella spp. prevalence in louse fly populations appears to be a useful prerequisite for zoonotic risk assessment. METHODS: Using convenience sampling, we collected 103 adult louse flies from four ked species (Lipoptena cervi, n = 22; Lipoptena fortisetosa, n = 61; Melophagus ovinus, n = 12; Hippobosca equina, n = 8) and the pupae of M. ovinus (n = 10) in the federal state of Saxony, Germany. All the samples were screened by polymerase chain reaction (PCR) for Bartonella spp. DNA, targeting the citrate synthase gene (gltA). Subsequently, PCRs targeting five more genes (16S, ftsZ, nuoG, ribC and rpoB) were performed for representatives of revealed gltA genotypes, and all the PCR products were sequenced to identify the Bartonella (sub)species accurately. RESULTS AND CONCLUSIONS: The overall detection rates for Bartonella spp. were 100.0%, 59.1%, 24.6% and 75.0% in M. ovinus, L. cervi, L. fortisetosa and H. equina, respectively. All the identified bartonellae belong to the Bartonella schoenbuchensis complex. Our data support the proposed reclassification of the (sub)species status of this group, and thus we conclude that several genotypes of B. schoenbuchensis were detected, including Bartonella schoenbuchensis subsp. melophagi and Bartonella schoenbuchensis subsp. schoenbuchensis, both of which have previously validated zoonotic potential. The extensive PCR analysis revealed the necessity of multiple PCR approach for proper identification of the ruminant-associated bartonellae.

The genome of the blind bee louse fly reveals deep convergences with its social host and illuminates Drosophila origins.

Social insects' nests harbor intruders known as inquilines,1 which are usually related to their hosts.2,3 However, distant non-social inquilines may also show convergences with their hosts,4,5 although the underlying genomic changes remain unclear. We analyzed the genome of the wingless and blind bee louse fly Braula coeca, an inquiline kleptoparasite of the western honey bee, Apis mellifera.6,7 Using large phylogenomic data, we confirmed recent accounts that the bee louse fly is a drosophilid8,9 and showed that it had likely evolved from a sap-breeder ancestor associated with honeydew and scale insects' wax. Unlike many parasites, the bee louse fly genome did not show significant erosion or strict reliance on an endosymbiont, likely due to a relatively recent age of inquilinism. However, we observed a horizontal transfer of a transposon and a striking parallel evolution in a set of gene families between the honey bee and the bee louse fly. Convergences included genes potentially involved in metabolism and immunity and the loss of nearly all bitter-tasting gustatory receptors, in agreement with life in a protective nest and a diet of honey, pollen, and beeswax. Vision and odorant receptor genes also exhibited rapid losses. Only genes whose orthologs in the closely related Drosophila melanogaster respond to honey bee pheromone components or floral aroma were retained, whereas the losses included orthologous receptors responsive to the anti-ovarian honey bee queen pheromones. Hence, deep genomic convergences can underlie major phenotypic transitions during the evolution of inquilinism between non-social parasites and their social hosts.

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.

Co-phylogeny of a hyper-symbiotic system: Endosymbiotic bacteria (Gammaproteobacteria), chewing lice (Insecta: Phthiraptera) and birds (Passeriformes).

Chewing lice are hosts to endosymbiotic bacteria as well as themselves being permanent parasites. This offers a unique opportunity to examine the cophylogenetic relationships between three ecologically interconnected organismal groups: birds, chewing lice, and bacteria. Here, we examine the cophylogenetic relationships between lice in the genus Guimaraesiella Eichler, 1949, their endosymbiotic Sodalis-allied bacteria, and a range of bird species from across South China. Both event and distance-based cophylogenetic analyses were explored to compare phylogenies of the three organismal groups. Pair-wise comparisons between lice-endosymbionts and bird-endosymbionts indicated that their evolutionary histories are not independent. However, comparisons between lice and birds, showed mixed results; the distance-based method of ParaFit indicated that their evolutionary histories are not independent, while the event-based method of Jane indicated that their phylogenies were no more congruent than expected by chance. Notably, louse host-switching does not seem to have affected bacterial strains, as conspecific lice sampled from distantly related hosts share bacteria belonging to the same clade.

Molecular quantification of parasitic sea louse larvae depends on species and life stage.

Sea lice cause substantial economic and environmental harm to Norway's aquaculture industry and wild salmonid populations. Rapid, accurate quantification of lice larval densities in coastal waters remains the greatest bottleneck for providing empirical data on infestation risk within wild salmon habitats and aquaculture production regions. We evaluated the capability of droplet digital PCR (ddPCR) as an absolute quantification method for the planktonic stages of two parasitic louse species, Lepeophtheirus salmonis (Krøyer) and Caligus elongatus (von Nordman). Results demonstrated linear relationships between the DNA quantity measured and the number of spiked larvae for both species and life stages. However, L. salmonis contained a significantly greater number of DNA copies than C. elongatus individuals and for C. elongatus, nauplii displayed a significantly higher number of DNA copies than copepodids. Our results suggest that ddPCR can effectively enumerate louse larvae, but interpreting ddPCR results differ between the two louse species. Obtaining larval abundance estimates from marine plankton samples will depend on the nauplii to copepodid ratio for C. elongatus, but not for L. salmonis.

Development of a novel molecular tool to study molecular ecology of Ornithomya (Hippoboscidae) avian louse flies.

Louse flies (Diptera: Hippoboscidae) are obligatory hematophagous ectoparasites of birds and mammals. These widely distributed parasitic flies may have a significant impact on wild and farm animals by feeding on their blood and transmitting bloodborne pathogens. However, despite their ecological importance, louse flies are clearly underrepresented in host-parasite research and implementation of genetic approaches in this group is generally hampered by lacking molecular tools. In addition, louse flies that parasitize long-distance migrants can travel long distances with their avian hosts, facilitating the large-scale spread of pathogens across landscapes and geographic regions. Given the wide diversity of louse flies that parasitize a variety of avian hosts, their direct negative impact on host survival, and their high potential to transmit bloodborne pathogens even along avian migration routes, it is surprising that our knowledge of louse fly ecology is rather modest and incomplete. Here, we aimed to develop a novel molecular tool for polyxenous avian louse flies from the genus Ornithomya, which are among the most common and widely distributed representatives of Hippoboscidae family, to improve research of their genetic population structure and molecular ecology. Using the Illumina Mi-seq sequencing, we conducted a genome-wide scan in Ornithomya avicularia to identify putative microsatellite markers. A panel of 26 markers was selected to develop amplification protocols and assess polymorphism in the Central European population of O. avicularia, as well as to test for cross-amplification in a congeneric species (O. chloropus). A genome-scan in O. avicularia identified over 12 thousand putative microsatellite markers. Among 26 markers selected for a population-wide screening; one did not amplify successfully and three were monomorphic. 22 markers were polymorphic with at least two alleles detected. Two markers showed presence of null alleles. A cross-amplification of microsatellite markers in O. chloropus revealed allelic polymorphism at 14 loci, with the mean allelic richness of 3.78 alleles per locus (range: 2-8). Our genome-wide scan in O. avicularia provides a novel and powerful tool for molecular research in Ornithomya louse flies. Our panel of polymorphic microsatellite loci should allow genotyping of louse flies from geographically distinct populations and from a wide spectrum of avian hosts, enhancing population genetic and phylogeographic research in Ornithomya.

DO PARASITIC LICE EXHIBIT ENDEMISM IN PARALLEL WITH THEIR AVIAN HOSTS? A COMPARISON ACROSS NORTHERN AMAZONIAN AREAS OF ENDEMISM.

Areas of endemism are the smallest units in biogeography and can be defined as biologically unique areas comprising taxa with common geographic limits to their distributions. High beta diversity within Amazonia is often related to turnover among these areas. For decades, evolutionary biologists have tried to comprehend the mechanisms generating and maintaining the spatial structure and high diversity of free-living Amazonian organisms, particularly birds. However, few studies have tried to analyze these patterns among their parasites. Host and parasite associations involve shared history that may allow us to better understand the fine-scale evolutionary history of the host. Here we compare the coevolutionary patterns among 2 avian host species with distinct patterns of genetic structure in northern Amazonia, Dendrocincla fuliginosa (Aves: Dendrocolaptidae) and Dixiphia pipra (Aves: Pipridae), and their ectoparasitic lice (Insecta: Phthiraptera), Furnaricola sp. ex Dendrocincla fuliginosa, Myrsidea sp. ex Dixiphia pipra, and Tyranniphilopterus sp. ex Dixiphia pipra. We obtained sequences of the mitochondrial gene cytochrome oxidase subunit I from hosts and parasites collected on opposite banks of the Negro and Japurá rivers, which delimit 3 areas of endemism in northern Amazonia: Napo, Jau, and Guiana. Our results demonstrate that the Negro River is a geographical barrier for both Furnaricola sp. and its avian host, Dendrocincla fuliginosa. Phylogenies of both hosts, Dendrocincla fuliginosa, and the parasites, Furnaricola sp., show monophyletic clades on opposite margins of the river that are not sister taxa. These clades have a mean uncorrected p-distance of 17.8% for Furnaricola sp. and 6.0% for Dendrocincla fuliginosa. Thus, these parasite clades constitute distinct evolutionary lineages and may even be distinct species. In contrast, Dixiphia pipra has no population structure associated with either river. Accordingly, data from their lice Myrsidea sp. indicate weak support for different clades on opposite margins of the Negro River, whereas data from their lice Tyranniphilopterus sp. indicate weak structure across the Japurá. This study is a first step toward understanding the effects of biogeographic history on permanent ectoparasites and suggests that host biogeographic history is to some extent a determinant of the parasite's history. Furthermore, the parasite's evolutionary history is an additional source of information about their hosts' evolution in this highly diverse region of northern Amazonia.

Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen.

Sequencing high molecular weight (HMW) DNA with long-read and linked-read technologies has promoted a major increase in more complete genome sequences for nonmodel organisms. Sequencing approaches that rely on HMW DNA have been limited to larger organisms or pools of multiple individuals, but recent advances have allowed for sequencing from individuals of small-bodied organisms. Here, we use HMW DNA sequencing with PacBio long reads and TELL-Seq linked reads to assemble and annotate the genome from a single individual feather louse (Brueelia nebulosa) from a European Starling (Sturnus vulgaris). We assembled a genome with a relatively high scaffold N50 (637 kb) and with BUSCO scores (96.1%) comparable to louse genomes assembled from pooled individuals. We annotated a number of genes (10,938) similar to the human louse (Pediculus humanus) genome. Additionally, calling phased variants revealed that the Brueelia genome is more heterozygous (∼1%) then expected for a highly obligate and dispersal-limited parasite. We also assembled and annotated the mitochondrial genome and primary endosymbiont (Sodalis) genome from the individual louse, which showed evidence for heteroplasmy in the mitogenome and a reduced genome size in the endosymbiont compared to its free-living relative. Our study is a valuable demonstration of the capability to obtain high-quality genomes from individual small, nonmodel organisms. Applying this approach to other organisms could greatly increase our understanding of the diversity and evolution of individual genomes.

Detailed morphological structure and phylogenetic relationships of Degeeriella punctifer (Phthiraptera: Philopteridae), a parasite of the bearded vulture Gypaetus barbatus (Accipitriformes: Accipitridae).

Habitat loss is one of the main threats to species survival and, in the case of parasites, it is their hosts that provide their habitat. Therefore, extinction even at local scale of host taxa also implies the extinction of their parasites in a process known as co-extinction. This is the case of the bearded vulture (Gypaetus barbatus), which almost became extinct at the beginning of the twentieth century. After several attempts, this species was successfully reintroduced into the Alps at the end of the twentieth century. We collected 25 lice specimens from an electrocuted bearded vulture from Susa (Italian Alps) that were morphologically identified as Degeeriella punctifer. Six individuals were studied by scanning electron microscopy, with particular emphasis on their cephalic sensorial structures, while four further specimens were characterized at molecular level by amplifying partial regions of the 12SrRNA, COX1 and elongation factor 1 alpha (EF-1) genes. From a morphological perspective, the number, type and arrangement of the sensillae on the two distal antennal segments is quite similar to that of other species of the family Philopteridae (Phthiraptera: Ischnocera). The mandibles and tarsal claws allow lice to cling firmly to their host's feathers. Phylogenetic analyses help unravel the paraphyletic nature of the genus Degeeriella and demonstrate the clear differentiation between lice parasitizing Accipitriformes and Falconiformes, as well as the close relationship between D. punctifer, D. fulva, D. nisus and Capraiella sp. that, along with other genera, parasitize rollers (Aves: Coraciiformes).

A chromosome-level genome of the booklouse, Liposcelis brunnea, provides insight into louse evolution and environmental stress adaptation.

BACKGROUND: Booklice (psocids) in the genus Liposcelis (Psocoptera: Liposcelididae) are a group of important storage pests, found in libraries, grain storages, and food-processing facilities. Booklice are able to survive under heat treatment and typically possess high resistance to common fumigant insecticides, hence posing a threat to storage security worldwide. RESULTS: We assembled the genome of the booklouse, L. brunnea, the first genome reported in Psocoptera, using PacBio long-read sequencing, Illumina sequencing, and chromatin conformation capture (Hi-C) methods. After assembly, polishing, haplotype purging, and Hi-C scaffolding, we obtained 9 linkage groups (174.1 Mb in total) ranging from 12.1 Mb to 27.6 Mb (N50: 19.7 Mb), with the BUSCO completeness at 98.9%. In total, 15,543 genes were predicted by the Maker pipeline. Gene family analyses indicated the sensing-related gene families (OBP and OR) and the resistance-related gene families (ABC, EST, GST, UGT, and P450) expanded significantly in L. brunnea compared with those of their closest relatives (2 parasitic lice). Based on transcriptomic analysis, we found that the CYP4 subfamily from the P450 gene family functioned during phosphine fumigation; HSP genes, particularly those from the HSP70 subfamily, were upregulated significantly under high temperatures. CONCLUSIONS: We present a chromosome-level genome assembly of L. brunnea, the first genome reported for the order Psocoptera. Our analyses provide new insights into the gene family evolution of the louse clade and the transcriptomic responses of booklice to environmental stresses.

Independent evolution of highly variable, fragmented mitogenomes of parasitic lice.

The mitochondrial genomes (mitogenomes) of bilaterian animals are highly conserved structures that usually consist of a single circular chromosome. However, several species of parasitic lice (Insecta: Phthiraptera) possess fragmented mitogenomes, where the mitochondrial genes are present on separate, circular chromosomes. Nevertheless, the extent, causes, and consequences of this structural variation remain poorly understood. Here, we combined new and existing data to better understand the evolution of mitogenome fragmentation in major groups of parasitic lice. We found strong evidence that fragmented mitogenomes evolved many times within parasitic lice and that the level of fragmentation is highly variable, including examples of heteroplasmic arrangements. We also found a significant association between mitochondrial fragmentation and signatures of relaxed selection. Mitochondrial fragmentation was also associated with changes to a lower AT%, possibly due to differences in mutation biases. Together, our results provide a significant advance in understanding the process of mitogenome fragmentation and provide an important perspective on mitochondrial evolution in eukaryotes.

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.

Molecular phylogenetics of the avian feather louse Philopterus-complex (Phthiraptera: Philopteridae).

The avian feather louse Philopterus-complex (Phthiraptera: Ischnocera: Philopteridae) currently contains 12 genera that have been grouped together because of shared morphological characteristics. Although previously lumped into a single genus (Philopterus), more recent morphological treatments have separated the group into several different genera. Here we evaluate the status of these genera using DNA sequence data from 118 ingroup specimens belonging to ten genera in the Philopterus-complex: Australophilopterus Mey, 2004, Cinclosomicola Mey 2004, Clayiella Eichler, 1940, Corcorides Mey, 2004, Mayriphilopterus Mey, 2004, Paraphilopterus Mey 2004, Philopteroides Mey 2004, Philopterus Nitzsch, 1818, Tyranniphilopterus Mey, 2004, and Vinceopterus Gustafsson, Lei, Chu, Zou, and Bush, 2019. Our sampling includes 97 new louse-host association records. Our analyses suggest that the genus Debeauxoecus Conci, 1941, parasitic on pittas (Aves: Pittidae), is outside of the Philopterus-complex, and that there is strong support for the monophyly of a group containing the remaining genera from the complex. Some diverse genera, such as Philopterus (sensu stricto) and Mayriphilopterus are supported as monophyletic, whereas the genera Australophilopterus, Philopteroides, and Tyranniphilopterus are not. The present study is the largest phylogenetic reconstruction of avian lice belonging to the Philopterus-complex to date and suggests that further generic revision is needed in the group to integrate molecular and morphological information.

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.

Daily patterns in parasite processes: diel variation in fish louse transcriptomes.

Parasites, similar to all other organisms, time themselves to environmental cues using a molecular clock to generate and maintain rhythms. Chronotherapeutic (timed treatment) techniques based on such rhythms offer great potential for improving control of chronic, problematic parasites. Fish lice are a key disease threat in aquaculture, with current control insufficient. Assessing the rhythmicity of fish lice transcriptomes offers not only insight into the viability of chronotherapy, but the opportunity to identify new drug targets. Here, for the first known time in any crustacean parasite, diel changes in gene transcription are examined, revealing that approximately half of the Argulus foliaceus annotated transcriptome displays significant daily rhythmicity. We identified rhythmically transcribed putative clock genes including core clock/cycle and period/timeless pairs, alongside rhythms in feeding-associated genes and processes involving immune response, as well as fish louse drug targets. A substantial number of gene pathways showed peak transcription in hours immediately preceding onset of light, potentially in anticipation of peak host anti-parasite responses or in preparation for increased feeding activity. Genes related to immune haemocyte activity and chitin development were more highly transcribed 4 h post light onset, although inflammatory gene transcription was highest during dark periods. Our study provides an important resource for application of chronotherapy in fish lice; timed application could increase efficacy and/or reduce dose requirement, improving the current landscape of drug resistance and fish health while reducing the economic cost of infection.

Interacting Effects of Sea Louse (Lepeophtheirus salmonis) Infection and Formalin-Killed Aeromonas salmonicida on Atlantic Salmon Skin Transcriptome.

Lepeophtheirus salmonis (sea lice) and bacterial co-infection threatens wild and farmed Atlantic salmon performance and welfare. In the present study, pre-adult L. salmonis-infected and non-infected salmon were intraperitoneally injected with either formalin-killed Aeromonas salmonicida bacterin (ASAL) or phosphate-buffered saline (PBS). Dorsal skin samples from each injection/infection group (PBS/no lice, PBS/lice, ASAL/no lice, and ASAL/lice) were collected at 24 h post-injection and used for transcriptome profiling using a 44K salmonid microarray platform. Microarray results showed no clear inflammation gene expression signatures and revealed extensive gene repression effects by pre-adult lice (2,189 down and 345 up-regulated probes) in the PBS-injected salmon (PBS/lice vs. PBS/no lice), which involved basic cellular (e.g., RNA and protein metabolism) processes. Lice repressive effects were not observed within the group of ASAL-injected salmon (ASAL/lice vs. ASAL/no lice); on the contrary, the observed skin transcriptome changes -albeit of lesser magnitude (82 up and 1 down-regulated probes)- suggested the activation in key immune and wound healing processes (e.g., neutrophil degranulation, keratinocyte differentiation). The molecular skin response to ASAL was more intense in the lice-infected (ASAL/lice vs. PBS/lice; 272 up and 11 down-regulated probes) than in the non-infected fish (ASAL/no lice vs. PBS/no lice; 27 up-regulated probes). Regardless of lice infection, the skin's response to ASAL was characterized by the putative activation of both antibacterial and wound healing pathways. The transcriptomic changes prompted by ASAL+lice co-stimulation (ASAL/lice vs. PBS/no lice; 1878 up and 3120 down-regulated probes) confirmed partial mitigation of lice repressive effects on fundamental cellular processes and the activation of pathways involved in innate (e.g., neutrophil degranulation) and adaptive immunity (e.g., antibody formation), as well as endothelial cell migration. The qPCR analyses evidenced immune-relevant genes co-stimulated by ASAL and lice in an additive (e.g., mbl2b, bcl6) and synergistic (e.g., hampa, il4r) manner. These results provided insight on the physiological response of the skin of L. salmonis-infected salmon 24 h after ASAL stimulation, which revealed immunostimulatory properties by the bacterin with potential applications in anti-lice treatments for aquaculture. As a simulated co-infection model, the present study also serves as a source of candidate gene biomarkers for sea lice and bacterial co-infection.

Phylogenomics and host-switching patterns of Philopteridae (Psocodea: Phthiraptera) feather lice.

Philopteridae feather lice are a group of ectoparasitic insects which have intimate relationships with their avian hosts. Feather lice include an enormous number of described species; however, the relationships of major lineages have been clouded by homoplasious characters due to convergent evolution. In this study, a comprehensive phylogenomic analysis of the group is performed which includes 137 feather louse species. Several other analyses are also completed including dating analysis, cophylogenetic reconstructions, and ancestral character estimation to understand the evolution of complex morphological and ecological traits. Phylogenetic results recover high support for the placement of major feather louse lineages, but with lower support for long-branched enigmatic genera found at the base of the tree. The results of dating analyses suggest modern feather lice began to diversify approximately 49 million years ago following the adaptive radiation of their avian hosts. Cost-based cophylogenetic reconstructions recover a high frequency of host switching, while congruence-based methods indicate a significant level of congruence between host and parasite trees. Ancestral state reconstructions favour a generalist ancestor and water bird host at the root. The analyses completed provide insight into the evolution of a diverse group of ectoparasitic insects which infest a wide variety of avian hosts. The results represent the most comprehensive phylogenetic hypothesis of the group to date and provide a framework for future classification of the family into natural groupings.

Phylogenetic analysis of lice infested chicken (Gallus gallus domisticus) with new records in Kurdistan of Iraq.

The domestic chickens are the most important protein sources of human populations in every part of the world; many parasites' species may affect birds. Ectoparasites can be found practically in all birds. They feed on their body components like blood, feathers. The effects of louse parasitism on birds are often severe, including retarded growth, low egg production and susceptibility to other infections and due to lice possess chewing mouthpart, it feeds on dry skin scales, scab tissues, and feather parts and it causes skin irritation and sucks blood (anemia), discomfort, loss of plumage, and decrease in productivity of the host. The aim of this study is to investigate lice genera and create the phylogenetic tree among the sequenced lice, using both mitochondrial DNA (COI gene) and nuclear gene (18S rRNA gene). Sequencing data were aligned with the sequences available in the NCBI GenBank. From October 2017 until July 2018, two hundred outdoor local chickens from three governorates (Duhok, Erbil and Sulaymaniyah), were examined for lice collection. After the morphological identification of the lice, the total genomic DNA of each louse was extracted individually and universal primers L6625, H7005 were used to amplify the DNA of mitochondrial gene COI (Cytochrome Oxidase Subunit I) and three designed specific primers (18SrRSHM1, 18SrRSHM2 and 18SrRSHM3) were applied to amplify the DNA of the nuclear gene 18S rRNA. Sequencing DNA results were submitted to the GenBank, For the first time in Iraq, twelve species of chicken lice have been submitted in a GenBank with accession numbers of MN531684 from Menopon gallinae; MN524167, MN588078, MN588079 belonged to the species of Menacanthus stramineus; MN524168, MN524182, MN588080 belonged to the species of Goniocotes gallinae; MN524180, MN588092 belonged to the species of Lipeurus caponis; MN524181, MN588091 belonged to the species of Goniocotes gigas and MN588089 belonged to the species of Goniodes dissimilis.