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Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.]

 

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.

 

We applied an integrative taxonomic framework to evaluate the systematics of the Neotropical Black-and-white Becard (Pachyramphus albogriseusSclater 1857). Combining phylogenomic (ultraconserved elements), morphological, and vocalization data, we confirmed that this species is polyphyletic; some individuals form a clade sister to P. polychopterus and should be afforded species rank as P. salviniRichmond 1899 (Slender-billed Becard), whereas the remaining subspecies of P. albogriseus (Broad-banded Becard) are sister to P. major. We found that P. salvini differs from P. albogriseus in song, color of the lores, wing-bar width, body size, and bill width. Whereas P. albogriseus occurs in montane forest in Costa Rica and Panama (ssp. ornatus) and along the eastern slope of the Andes from northern Venezuela to southern Peru (ssp. albogriseus), P. salvini is found in the lowlands from Pacific Colombia south to northwest Peru and in the Río Marañón drainage. The latter also occurs, possibly only seasonally, along the eastern slope of the Andes, where the two species’ ranges approach closely. We treat P. a. guayaquilensisZimmer 1936 as a junior synonym of P. salviniRichmond 1899, and P. a. coronatusPhelps and Phelps 1953 as a junior synonym of P. a. albogriseusSclater 1857. This study provides a striking example of a major problem for comparative biology: underestimated and mischaracterized diversity. We argue that there are likely many more cases like this awaiting discovery.

 

Lachesillidae is one of the largest families of bark lice and includes more than 420 described species, in 26 genera and three subfamilies. This family belongs in the suborder Psocomorpha, infraorder Homilopsocidea. The classification of Lachesillidae is based on male and female genital morphologies, but questions remain regarding the monophyly of the family and some of its genera. Here, we used whole genome and transcriptome data to generate a 2060 orthologous gene data matrix of 2,438,763 aligned bp and used these data to reconstruct the phylogenetic relationships of species of Lachesillidae and relatives. Taxon sampling included 24 species from Lachesillidae and 23 additional species belonging to related families from the infraorders Homilopsocidea and Caeciliusetae. Phylogenetic relationships reconstructed with maximum likelihood and coalescent‐based analyses indicated paraphyly of Lachesillidae, and monophyly of the tribe Graphocaeciliini and the genusLachesillawere also never recovered. Instability was observed in the position ofEolachesilla chilensis, which was recovered either as sister to Elipsocidae or to Mesopsocidae species, so we cannot conclusively determine the position of this genus within the Homilopsocidea. Given our results, a reclassification is necessary, but more taxon sampling of other species in Mesopsocidae and Peripsocidae would be useful to add to a tree in future before proposing a new classification.

 

MyrsideaWaterston is the most diverse genus of chewing lice, primarily parasitizing perching birds (Passeriformes), which is the most speciose avian order.Myrsideaalso parasitize several hosts from non‐passerine groups, including toucans, barbets, woodpeckers (Piciformes) and hummingbirds (Apodiformes). To examine host specificity, host switching and generic limits, we reconstructed a phylogeny of the avian feather louse genusMyrsideausing DNA sequence data from two fragments of the mitochondrial COI gene and a fragment of the nuclear EF‐1α gene for 152Myrsideaspecimens collected from 23 avian host families. Unlike other highly diverse louse genera, only a small proportion ofMyrsideaspecies parasitize more than one host species. We found that host family has significant phylogenetic signal on theMyrsideaphylogeny. These results suggest thatMyrsideais generally highly host‐specific, with some exceptions where host switching is important. We found that there are two separate groups ofMyrsideathat parasitize toucans, and that both are nested withinMyrsideafound on perching birds, suggesting that these toucan ectoparasites may have arisen from two independent host switching events. Lastly, representatives of the genusRamphasticolaCarriker, which was originally described as a distinct genus due to a suite of morphologically unique characters, falls in with a strongly supported clade ofMyrsideaparasitizingRamphastostoucans, and therefore we definitively placeRamphasticolaas a synonym ofMyrsidea.

 

Organisms vary in their dispersal abilities, and these differences can have important biological consequences, such as impacting the likelihood of hybridization events. However, there is still much to learn about the factors influencing hybridization, and specifically how dispersal ability affects the opportunities for hybridization. Here, using the ecological replicate system of dove wing and body lice (Insecta: Phthiraptera), we show that species with higher dispersal abilities exhibited increased genomic signatures of introgression. Specifically, we found a higher proportion of introgressed genomic reads and more reticulated phylogenetic networks in wing lice, the louse group with higher dispersal abilities. Our results are consistent with the hypothesis that differences in dispersal ability might drive the extent of introgression through hybridization.

 

Psocodea (booklice and parasitic lice) is an order of insects containing species with extensive mitochondrial genome rearrangements, particularly within the suborder Troctomorpha, in which some species possess an extremely fragmented mitochondrial genome with several small minichromosomes. In the remaining suborders of Psocodea, there are groups with the ancestral pancrustacean arrangement, quite extensive rearrangements (e.g. Trogiomorpha), or in which the small number of species analysed to date have rearrangements of only a few protein‐coding genes and/or tRNAs (e.g. Psocomorpha). Despite the apparent high rate of rearrangements in the order as a whole, a small number of complete mitochondrial genomes are available, especially for suborder Psocomorpha, the largest free‐living suborder. To understand the evolution of the gene arrangement of the mitochondrial genome within Psocomorpha and its phylogenetic implications, we assembled and analysed the mitochondrial genomes of 33 species of bark lice belonging to nine families in two infraorders. Within the infraorder Homilopsocidea, four families were analysed, mainly from Lachesillidae (which included 22 species of this family). Within the infraorder Caeciliusetae, seven species representing five families were analysed. Mitochondrial gene rearrangements were identified in seven of the nine families. Some of these rearrangements were unique to a single species, while some contained phylogenetic signal, being shared by related species. These rearrangements typically corresponded to transpositions and inversions of tRNAs, possibly caused by tandem duplication–random loss (TDRL) and/or recombination events. Phylogenetic analyses of mitochondrial gene sequences provided phylogenetic resolution for several branches of the tree, including monophyly of Lachesillinae. The genusHemicaeciliusEnderlein was found to be embedded within the genusLachesillaWestwood, rending the latter paraphyletic. Monophyly was also never recovered for Lachesillidae and Elipsocidae as currently defined. However, instability was observed for some higher level relationships within Psocomorpha, including the relationships among the major clades of Lachesillidae.

 

This paper provides a catalogue of the type specimens of lice (Insecta: Psocodea: Phthiraptera) held in the collection of the Field Museum of Natural History (FMNH), Chicago, Illinois, USA. There are 178 nominal species, four of which are represented by holotype only; 14 by holotype, allotype and paratypes; 29 by holotype and paratypes; 127 by paratypes only; three by neoparatypes, and one by paralectotype. The main goal of this type catalog is to make the louse type specimens and their metadata more readily available to biodiversity researchers. 

Abstract The order Psocodea includes the two historically recognized groups Psocoptera (free-living bark lice) and Phthiraptera (parasitic lice) that were once considered separate orders. Psocodea is divided in three suborders: Trogiomorpha, Troctomorpha, and Psocomorpha, the latter being the largest within the free-living groups. Despite the increasing number of transcriptomes and whole genome sequence (WGS) data available for this group, the relationships among the six known infraorders within Psocomorpha remain unclear. Here, we evaluated the utility of a bait set designed specifically for parasitic lice belonging to suborder Troctomorpha to extract UCE loci from transcriptome and WGS data of 55 bark louse species and explored the phylogenetic relationships within Psocomorpha using these UCE loci markers. Taxon sampling was heavily focused on the families Lachesillidae and Elipsocidae, whose relationships have been problematic in prior phylogenetic studies. We successfully recovered a total of 2,622 UCE loci, with a 40% completeness matrix containing 2,081 UCE loci and an 80% completeness matrix containing 178 UCE loci. The average number of UCE loci recovered for the 55 species was 1,401. The WGS data sets produced a larger number of UCE loci (1,495) on average than the transcriptome data sets (972). Phylogenetic relationships reconstructed with Maximum Likelihood and coalescent-based analysis were concordant regarding the paraphyly of Lachesillidae and Elipsocidae. Branch support values were generally lower in analyses that used a fewer number of loci, even though they had higher matrix completeness. 

Abstract Background Feather feeding lice are abundant and diverse ectoparasites that complete their entire life cycle on an avian host. The principal or sole source of nutrition for these lice is feathers. Feathers appear to lack four amino acids that the lice would require to complete development and reproduce. Several insect groups have acquired heritable and intracellular bacteria that can synthesize metabolites absent in an insect’s diet, allowing insects to feed exclusively on nutrient-poor resources. Multiple species of feather feeding lice have been shown to harbor heritable and intracellular bacteria. We expected that these bacteria augment the louse’s diet with amino acids and facilitated the evolution of these diverse and specialized parasites. Heritable symbionts of insects often have small genomes that contain a minimal set of genes needed to maintain essential cell functions and synthesize metabolites absent in the host insect’s diet. Therefore, we expected the genome of a bacterial endosymbiont in feather lice would be small, but encode pathways for biosynthesis of amino acids. Results We sequenced the genome of a bacterial symbiont from a feather feeding louse ( Columbicola wolffhuegeli ) that parasitizes the Pied Imperial Pigeon ( Ducula bicolor ) and used its genome to predict metabolism of amino acids based on the presence or absence of genes. We found that this bacterial symbiont has a small genome, similar to the genomes of heritable symbionts described in other insect groups. However, we failed to identify many of the genes that we expected would support metabolism of amino acids in the symbiont genome. We also evaluated other gene pathways and features of the highly reduced genome of this symbiotic bacterium. Conclusions Based on the data collected in this study, it does not appear that this bacterial symbiont can synthesize amino acids needed to complement the diet of a feather feeding louse. Our results raise additional questions about the biology of feather chewing lice and the roles of symbiotic bacteria in evolution of diverse avian parasites.