Cophylogenetic analysis of New World ground-doves (Aves: Columbidae) and their parasitic wing lice (Insecta: Phthiraptera: Columbicola)

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.

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.

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.

Biogeographical events, not cospeciation, might be the main drivers in the historical association between Noctiliostrebla species (Streblidae) and their bulldog bat hosts

The genus Noctiliostrebla Wenzel (Diptera: Streblidae) stands out for its high degree of specificity exhibited in relation to bat species of the genus Noctilio Linnaeus and provides an exciting system for understanding the history behind host–parasite associations. Here, we present a phylogeny of Noctiliostrebla based on an analysis of DNA sequences and morphological characters, along with cophylogenetic and biogeographical analyses. Our results strongly support the monophyly of Noctiliostrebla, but with uncertainties within the genus. With a low frequency of cospeciation events explaining the associations between hosts and parasites, cophylogenetic analyses did not show an overall congruence between the host and parasite phylogenies. Indeed, two parallel histories were recovered in the host–parasite associations, which might indicate that niche segregation is determined evolutionarily, facilitating the coexistence of parasites and promoting diversification. Biogeographical analysis showed a strong spatial congruence between disjunct distributions of Noctiliostrebla and major river basins in South America and with areas of higher elevation, which might be associated with the glacial periods throughout the Pliocene and Pleistocene. Overall, our findings suggest an agreement with the expectations of the ‘Stockholm paradigm’ framework, in which biogeographical events and ecological factors act as important components to explain the associations, instead of cospeciation events.

Cophylogenetic analyses of Trachymyrmex ant-fungal specificity: "One to one with some exceptions"

Over the past few decades, large-scale phylogenetic analyses of fungus-gardening ants and their symbiotic fungi have depicted strong concordance among major clades of ants and their symbiotic fungi, yet within clades, fungus sharing is widespread among unrelated ant lineages. Sharing has been explained using a diffuse coevolution model within major clades. Understanding horizontal exchange within clades has been limited by conventional genetic markers that lack both interspecific and geographic variation. To examine whether reports of horizontal exchange were indeed due to symbiont sharing or the result of employing relatively uninformative molecular markers, samples of Trachymyrmex arizonensis and Trachymyrmex pomonae and their fungi were collected from native populations in Arizona and genotyped using conventional marker genes and genome-wide single nucleotide polymorphisms (SNPs). Conventional markers of the fungal symbionts generally exhibited cophylogenetic patterns that were consistent with some symbiont sharing, but most fungal clades had low support. SNP analysis, in contrast, indicated that each ant species exhibited fidelity to its own fungal subclade with only one instance of a colony growing a fungus that was otherwise associated with a different ant species. This evidence supports a pattern of codivergence between Trachymyrmex species and their fungi, and thus a diffuse coevolutionary model may not accurately predict symbiont exchange. These results suggest that fungal sharing across host species in these symbioses may be less extensive than previously thought.

Analysis of phoretic relation between chewing lice and hippoboscid flies of Columba livia

Phoresy is a biologically mechanical phenomena where an immobile organism hitches on a other mobile organism to translocate. This behaviour is not studied very well on the field level especially between two important parasites infesting the same host. Parasite/parasite interaction is rarely studied through most biological host-parasite systems. Here, we evaluated the phoretic relation between parasitic chewing lice and hippoboscid flies (Pseudolynchia canariensis) on rock pigeons. A total of 69 captivated rock pigeons, Columba livia, were examined for the parasitic chewing lice and hippoboscid flies in Giza Zoo and two local farms near Cairo, Egypt. Results indicated that there is a positive correlation between infestation of hippoboscid flies and chewing lice. Also, the analysis of louse/louse interaction using ANOVA indicated a significant difference between the three chewing louse species which were recorded on the rock pigeons with relatively high abundance of two species, Columbicola columbae and Campanulotes compar. The analysis of hippoboscid flies' abundance and its relation with chewing lice infestation indicate a significant increase of lice intensity in case of high infestation with the fly. The level of hygiene of nest may be inversely related to level of parasite infestation. This work forms a step in the process of understanding parasite/parasite and host/parasite interactions using two parasitic species with a characteristic phoretic behaviour in nature.

Diversity and host associations of Myrsidea chewing lice (Phthiraptera: Menoponidae) in the tropical rainforest of Malaysian Borneo

The tropical rainforests of Sundaland are a global biodiversity hotspot increasingly threatened by human activities. While parasitic insects are an important component of the ecosystem, their diversity and parasite-host relations are poorly understood in the tropics. We investigated parasites of passerine birds, the chewing lice of the speciose genus MyrsideaWaterston, 1915 (Phthiraptera: Menoponidae) in a natural rainforest community of Malaysian Borneo. Based on morphology, we registered 10 species of lice from 14 bird species of six different host families. This indicated a high degree of host specificity and that the complexity of the system could be underestimated with the potential for cryptic lineages/species to be present. We tested the species boundaries by combining morphological, genetic and host speciation diversity. The phylogenetic relationships of lice were investigated by analyzing the partial mitochondrial cytochrome oxidase I (COI) and the nuclear elongation factor alpha (EF-1α) genes sequences of the species. This revealed a monophyletic group of Myrsidea lineages from seven hosts of the avian family Pycnonotidae, one host of Timaliidae and one host of Pellorneidae. However, species delimitation methods supported the species boundaries hypothesized by morphological studies and confirmed that four species of Myrsidea are not single host specific. Cophylogenetic analysis by both distance-based test ParaFit and event-based method Jane confirmed overall congruence between the phylogenies of Myrsidea and their hosts. In total we recorded three cospeciation events for 14 host-parasite associations. However only one host-parasite link (M. carmenae and their hosts Terpsiphone affinis and Hypothymis azurea) was significant after the multiple testing correction in ParaFit.

Four new species are described: Myrsidea carmenaesp.n. ex Hypothymis azurea and Terpsiphone affinis, Myrsidea franciscaesp.n. ex Rhipidura javanica, Myrsidea ramonisp.n. ex Copsychus malabaricus stricklandii, and Myrsidea victoriaesp.n. ex. Turdinus sepiarius.

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We newly resolved the species boundaries of representatives of chewing lice genus Myrsidea in a rainforest avian community.

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Ten species of Bornean Myrsidea from 14 bird species were registered, and four new species of Myrsidea were described.

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We analyzed phylogenetic relations of Myrsidea species studied and showed partial congruence of host-parasite phylogenies.

Disentangling lousy relationships: Comparative phylogenomics of two sucking louse lineages parasitizing chipmunks

The evolution of obligate parasites is often interpreted in light of their hosts' evolutionary history. An expanded approach is to examine the histories of multiple lineages of parasites that inhabit similar environments on a particular host lineage. Western North American chipmunks (genus Tamias) have a broad distribution, a history of divergence with gene flow, and host two species of sucking lice (Anoplura), Hoplopleura arboricola and Neohaematopinus pacificus. From total genomic sequencing, we obtained sequences of over 1100 loci sampled across the genomes of these lice to compare their evolutionary histories and examine the roles of host association in structuring louse relationships. Within each louse species, clades are largely associated with closely related chipmunk host species. Exceptions to this pattern appear to have a biogeographic component, but differ between the two louse species. Phylogenetic relationships among these major louse clades, in both species, are not congruent with chipmunk relationships. In the context of host associations, each louse lineage has a different evolutionary history, supporting the hypothesis that host-parasite assemblages vary both across the landscape and with the taxa under investigation. In addition, the louse Hoplopleura erratica (parasitizing the eastern Tamias striatus) is embedded within H. arboricola, rendering it paraphyletic. This phylogenetic result, together with comparable divergences within H. arboricola, indicate a need for taxonomic revision. Both host divergence and biogeographic components shape parasite diversification as demonstrated by the distinctive diversification patterns of these two independently evolving lineages that parasitize the same hosts.

Patterns of host-parasite associations in tropical lice and their passerine hosts in Cameroon

Coevolutionary processes that drive the patterns of host-parasite associations can be deduced through congruence analysis of their phylogenies. Feather lice and their avian hosts have previously been used as typical model systems for congruence analysis; however, such analyses are strongly biased toward nonpasserine hosts in the temperate zone. Further, in the Afrotropical region especially, cospeciation studies of lice and birds are entirely missing. This work supplements knowledge of host-parasite associations in lice using cospeciation analysis of feather lice (genus Myrsidea and the Brueelia complex) and their avian hosts in the tropical rainforests of Cameroon. Our analysis revealed a limited number of cospeciation events in both parasite groups. The parasite-host associations in both louse groups were predominantly shaped by host switching. Despite a general dissimilarity in phylogeny for the parasites and hosts, we found significant congruence in host-parasite distance matrices, mainly driven by associations between Brueelia lice and passerine species of the Waxbill (Estrildidae) family, and Myrsidea lice and their Bulbul (Pycnonotidae) host species. As such, our study supports the importance of complex biotic interactions in tropical environments.

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

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.

Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution

Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g., cospeciation, host switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly resolved species-level relationships for the lice. By comparing the louse and ground-dove phylogenies, we found that over long-term evolutionary scales their phylogenies were largely congruent. Many louse lineages (both species and populations) also demonstrated high host-specificity, suggesting ground-dove divergence is a primary driver of their parasites' diversity. However, the few louse taxa that are generalists are structured according to biogeography at the population level. This suggests dispersal among sympatric hosts has some effect on body louse diversity, but over deeper time scales the parasites eventually sort according to host species. Overall, our results demonstrate that multiple factors explain the patterns of diversity in this group of parasites, and that the effects of these factors can vary over different evolutionary scales. The integrative approach we employed was crucial for uncovering these patterns, and should be broadly applicable to other studies.