02250nas a2200277 4500008004100000245008100041210006900122300001000191490000800201520140800209653001401617653001901631653001601650653001401666653002701680653002101707653002901728100002401757700002401781700001901805700002101824700001701845700002301862700002101885856006601906 2004 eng d00aParasite escape mechanisms drive morphological diversification in avian lice0 aParasite escape mechanisms drive morphological diversification i a12 pp0 v2913 a

Organisms that have repeatedly evolved similar morphologies owing to the same selective pressures provide excellent cases in which to examine specific morphological changes and their relevance to the ecology and evolution of taxa. Hosts of permanent parasites act as an independent evolutionary experiment, as parasites on these hosts are thought to be undergoing similar selective pressures. Parasitic feather lice have repeatedly diversified into convergent ecomorphs in different microhabitats on their avian hosts. We quantified specific morphological characters to determine (i) which traits are associated with each ecomorph, (ii) the quantitative differences between these ecomorphs, and (iii) if there is evidence of displacement among co-occurring lice as might be expected under louse–louse competition on the host. We used nano-computed tomography scan data of 89 specimens, belonging to four repeatedly evolved ecomorphs, to examine their mandibular muscle volume, limb length and three-dimensional head shape data. Here, we find evidence that lice repeatedly evolve similar morphologies as a mechanism to escape host defences, but also diverge into different ecomorphs related to the way they escape these defences. Lice that co-occur with other genera on a host exhibit greater morphological divergence, indicating a potential role of competition in evolutionary divergence.

10aBird lice10aco-adaptations10aCT scanning10aEvolution10aGuimaraesiella antiqua10amicro-morphology10aNeopsittaconirmus bushae1 aKOLENCIK, STANISLAV1 aStanley, Edward, L.1 aPunnath, Aswaj1 aGrant, Avery, R.1 aDoña, Jorge1 aJohnson, Kevin, P.1 aAllen, Julie, M. uhttps://royalsocietypublishing.org/doi/10.1098/rspb.2023.266502946nas a2200385 4500008004100000022001400041245009600055210006900151260001600220300000900236490000600245520179600251653001402047653001902061653002802080653001302108653001302121100002602134700002202160700002302182700002102205700001702226700002102243700002002264700002302284700002302307700002302330700002702353700002402380700002302404700002002427700002402447700002502471856006402496 2023 eng d a2399-342100aBuilding a community-based taxonomic resource for digitization of parasites and their hosts0 aBuilding a communitybased taxonomic resource for digitization of cNov-01-2023 a9 pp0 v73 a

Classification of the biological diversity on Earth is foundational to all areas of research within the natural sciences. Reliable biological nomenclatural and taxonomic systems facilitate efficient access to information about organisms and their names over time. However, broadly sharing, accessing, delivering, and updating these resources remains a persistent problem. This barrier has been acknowledged by the biodiversity data sharing community, yet concrete efforts to standardize and continually update taxonomic names in a sustainable way remain limited. High diversity groups such as arthropods are especially challenging as available specimen data per number of species is substantially lower than vertebrate or plant groups. The Terrestrial Parasite Tracker Thematic Collections Network project developed a workflow for gathering expert-verified taxonomic names across all available sources, aligning those sources, and publishing a single resource that provides a model for future endeavors to standardize digital specimen identification data. The process involved gathering expert-verified nomenclature lists representing the full taxonomic scope of terrestrial arthropod parasites, documenting issues experienced, and finding potential solutions for reconciliation of taxonomic resources against large data publishers. Although discordance between our expert resources and the Global Biodiversity Information Facility are relatively low, the impact across all taxa affects thousands of names that correspond to hundreds of thousands of specimen records. Here, we demonstrate a mechanism for the delivery and continued maintenance of these taxonomic resources, while highlighting the current state of taxon name curation for biodiversity data sharing.

10aarthropod10aBioinformatics10abiological nomenclature10aparasite10ataxonomy1 aSullivan, Kathryn, A.1 aTucker, Erika, M.1 aDowdy, Nicolas, J.1 aAllen, Julie, M.1 aBarve, Vijay1 aBoone, James, H.1 aBush, Sarah, E.1 aEvenhuis, Neal, L.1 aHastriter, Michael1 aLight, Jessica, E.1 aMayfield-Meyer, Teresa1 aO'Connor, Barry, M.1 aPoelen, Jorrit, H.1 aRacz, Gabor, R.1 aSeltmann, Katja, C.1 aZaspel, Jennifer, M. uhttps://academic.oup.com/isd/article-abstract/7/6/1/743948301724nas a2200253 4500008004100000022002500041245006600066210006300132260001600195300000900211490000700220520096800227653001001195653001901205653003401224653002601258653001301284100002101297700002201318700001901340700002301359700002601382856006201408 2018 eng d a1176-9343, 1176-934300aaTRAM 2.0: An Improved, Flexible Locus Assembler for NGS Data0 aaTRAM 20 An Improved Flexible Locus Assembler for NGS Data cJan-01-2018 a4 pp0 v143 a

Massive strides have been made in technologies for collecting genome-scale data. However, tools for efficiently and flexibly assembling raw outputs into downstream analytical workflows are still nascent. aTRAM 1.0 was designed to assemble any locus from genome sequencing data but was neither optimized for efficiency nor able to serve as a single toolkit for all assembly needs. We have completely re-implemented aTRAM and redesigned its structure for faster read retrieval while adding a number of key features to improve flexibility and functionality. The software can now (1) assemble single- or paired-end data, (2) utilize both read directions in the database, (3) use an additional de novo assembly module, and (4) leverage new built-in pipelines to automate common workflows in phylogenomics. Owing to reimplementation of databasing strategies, we demonstrate that aTRAM 2.0 is much faster across all applications compared to the previous version

10aaTRAM10alocus assembly10amassively parallel sequencing10ashort-read sequencing10asoftware1 aAllen, Julie, M.1 aLaFrance, Raphael1 aFolk, Ryan, A.1 aJohnson, Kevin, P.1 aGuralnick, Robert, P. uhttps://journals.sagepub.com/doi/10.1177/117693431877454602217nas a2200253 4500008004100000022001400041245010100055210006900156260001600225490000600241520147400247653001301721653001301734653001701747653001801764653002401782653001801806653001701824100002101841700002101862700002301883700002001906856003701926 2016 eng d a2167-835900aEffects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice0 aEffects of 16S rDNA sampling on estimates of the number of endos cJul-19-20160 v43 a

Phylogenetic trees can reveal the origins of endosymbiotic lineages of bacteria and detect patterns of co-evolution with their hosts. Although taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships are based on few available bacterial sequences. Here we examined how different sampling strategies ofGammaproteobacteriasequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from otherGammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. Sampling of 16S rDNA sequences affects the estimates of endosymbiont diversity in sucking lice until we reach a threshold of genetic diversity, the size of which depends on the sampling strategy. Sampling by maximizing the diversity of 16S rDNA sequences is more efficient than randomly sampling available 16S rDNA sequences. Although simulation results validate estimates of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that the precise number of endosymbiont origins is still uncertain.

10a16S rDNA10aAnoplura10aEndosymbiont10aEndosymbiosis10aGammaproteobacteria10aPhylogenetics10asucking lice1 aAllen, Julie, M.1 aBurleigh, Gordon1 aLight, Jessica, E.1 aReed, David, L. uhttps://peerj.com/articles/2187/02146nas a2200313 4500008004100000022002500041245014900066210006900215260001600284300000900300490000800309520115400317653001501471653001701486653001701503653000901520653001801529100001901547700002301566700002101589700002701610700001701637700002201654700002201676700002001698700002501718700002301743856006601766 2022 eng d a0962-8452, 1471-295400aLong-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites0 aLongdistance dispersal of pigeons and doves generated new ecolog cMar-09-2022 a8 pp0 v2893 a

Adaptive radiation is an important mechanism of organismal diversification and can be triggered by new ecological opportunities. Although poorly studied in this regard, parasites are an ideal group in which to study adaptive radiations because of their close associations with host species. Both experimental and comparative studies suggest that the ectoparasitic wing lice of pigeons and doves have adaptively radiated, leading to differences in body size and overall coloration. Here, we show that long-distance dispersal by dove hosts was central to parasite diversification because it provided new ecological opportunities for parasites to speciate after host-switching. We further show that among extant parasite lineages host-switching decreased over time, with cospeciation becoming the more dominant mode of parasite speciation. Taken together, our results suggest that host dispersal, followed by host-switching, provided novel ecological opportunities that facilitated adaptive radiation by parasites.

Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.17108207.

10aColumbidae10acospeciation10aectoparasite10alice10aPhylogenomics1 aBoyd, Bret, M.1 aNguyen, Nam-phuong1 aAllen, Julie, M.1 aWaterhouse, Robert, M.1 aVo, Kyle, B.1 aSweet, Andrew, D.1 aClayton, Dale, H.1 aBush, Sarah, E.1 aShapiro, Michael, D.1 aJohnson, Kevin, P. uhttps://royalsocietypublishing.org/doi/10.1098/rspb.2022.004203138nas a2200361 4500008004100000022001400041245011200055210006900167260001600236300000900252490000800261520204700269653002402316653001702340653001902357653001502376653000802391653002102399653002202420653001902442653002002461653001302481653002302494653001702517100002402534700002302558700002102581700002502602700002702627700002502654700002102679856007602700 2022 eng d a1055-790300aMolecular phylogenetics of the avian feather louse Philopterus-complex (Phthiraptera: Philopteridae)0 aMolecular phylogenetics of the avian feather louse iPhilopterusi cSep-01-2022 a7 pp0 v1743 a

Highlights

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.

10aAustralophilopterus10aChewing lice10aCinclosomicola10aCorcorides10adna10aMayriphilopterus10aMolecular Biology10aPhilopteroides10aSpecies complex10ataxonomy10aTyranniphilopterus10aVinceopterus1 aKOLENCIK, STANISLAV1 aJohnson, Kevin, P.1 aGrant, Avery, R.1 aValim, Michel, Paiva1 aKuabara, Kamila, M. D.1 aWeckstein, Jason, D.1 aAllen, Julie, M. uhttps://www.sciencedirect.com/science/article/abs/pii/S105579032200169503306nas a2200241 4500008004100000245007600041210006900117260001400186300001000200490000700210520256400217653001802781653001902799653001902818653001902837653001902856100002302875700002702898700002102925700002202946700002002968856007602988 2010 eng d00aEvolutionary history of mammalian sucking lice (Phthiraptera: Anoplura)0 aEvolutionary history of mammalian sucking lice Phthiraptera Anop cSept 2010 a15 pp0 v103 a

Background

Sucking lice (Phthiraptera: Anoplura) are obligate, permanent ectoparasites of eutherian mammals, parasitizing members of 12 of the 29 recognized mammalian orders and approximately 20% of all mammalian species. These host specific, blood-sucking insects are morphologically adapted for life on mammals: they are wingless, dorso-ventrally flattened, possess tibio-tarsal claws for clinging to host hair, and have piercing mouthparts for feeding. Although there are more than 540 described species of Anoplura and despite the potential economical and medical implications of sucking louse infestations, this study represents the first attempt to examine higher-level anopluran relationships using molecular data. In this study, we use molecular data to reconstruct the evolutionary history of 65 sucking louse taxa with phylogenetic analyses and compare the results to findings based on morphological data. We also estimate divergence times among anopluran taxa and compare our results to host (mammal) relationships.

Results

This study represents the first phylogenetic hypothesis of sucking louse relationships using molecular data and we find significant conflict between phylogenies constructed using molecular and morphological data. We also find that multiple families and genera of sucking lice are not monophyletic and that extensive taxonomic revision will be necessary for this group. Based on our divergence dating analyses, sucking lice diversified in the late Cretaceous, approximately 77 Ma, and soon after the Cretaceous-Paleogene boundary (ca. 65 Ma) these lice proliferated rapidly to parasitize multiple mammalian orders and families.

Conclusions

The diversification time of sucking lice approximately 77 Ma is in agreement with mammalian evolutionary history: all modern mammal orders are hypothesized to have diverged by 75 Ma thus providing suitable habitat for the colonization and radiation of sucking lice. Despite the concordant timing of diversification events early in the association between anoplurans and mammals, there is substantial conflict between the host and parasite phylogenies. This conflict is likely the result of a complex history of host switching and extinction events that occurred throughout the evolutionary association between sucking lice and their mammalian hosts. It is unlikely that there are any ectoparasite groups (including lice) that tracked the early and rapid radiation of eutherian mammals.

10achewing louse10aCodon position10ahost switching10aMammalian host10aTaxon sampling1 aLight, Jessica, E.1 aSmith, Vincent, Stuart1 aAllen, Julie, M.1 aDurden, Lance, A.1 aReed, David, L. uhttps://bmcecolevol.biomedcentral.com/articles/10.1186/1471-2148-10-29202383nas a2200265 4500008004100000022002500041245011600066210007300182260001600255300001200271490000700283520156000290653001701850653000801867653001401875653001401889653001201903100002401915700002501939700002301964700002101987700002102008700002502029856006302054 2022 eng d a0307-6970, 1365-311300aPhylogenetics and host‐specificity of the mega‐diverse louse genus Myrsidea (Amblycera: Menoponidae)0 aPhylogenetics and host‐specificity of the mega‐diverse louse gen cJan-19-2022 a390-4010 v473 a

Myrsidea Waterston is the most diverse genus of chewing lice, primarily parasitizing perching birds (Passeriformes), which is the most speciose avian order. Myrsidea also 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 genus Myrsidea using DNA sequence data from two fragments of the mitochondrial COI gene and a fragment of the nuclear EF-1α gene for 152 Myrsidea specimens collected from 23 avian host families. Unlike other highly diverse louse genera, only a small proportion of Myrsidea species parasitize more than one host species. We found that host family has significant phylogenetic signal on the Myrsidea phylogeny. These results suggest that Myrsidea is generally highly host-specific, with some exceptions where host switching is important. We found that there are two separate groups of Myrsidea that parasitize toucans, and that both are nested within Myrsidea found on perching birds, suggesting that these toucan ectoparasites may have arisen from two independent host switching events. Lastly, representatives of the genus Ramphasticola Carriker, which was originally described as a distinct genus due to a suite of morphologically unique characters, falls in with a strongly supported clade of Myrsidea parasitizing Ramphastos toucans, and therefore we definitively place Ramphasticola as a synonym of Myrsidea.

10aChewing lice10adna10aparasites10aPhylogeny10atoucans1 aKOLENCIK, STANISLAV1 aCacioppo, Joseph, A.1 aJohnson, Kevin, P.1 aAllen, Julie, M.1 aSychra, Oldřich1 aWeckstein, Jason, D. uhttps://onlinelibrary.wiley.com/doi/abs/10.1111/syen.1253601514nas a2200253 4500008004100000022001400041245012700055210006900182260001300251300001000264490000800274520069900282653001600981653003100997653002601028653002401054653001501078653001401093653001401107100002401121700002101145700002101166856007301187 2021 eng d a2118-977300aAnother puzzle piece in the systematics of the chewing louse genus Myrsidea, with a description of a new genus Apomyrsidea0 aAnother puzzle piece in the systematics of the chewing louse gen cMay-2021 a36-500 v7483 a

A new avian chewing louse genus Apomyrsidea gen. nov. is described based on species parasitizing birds in the family Formicariidae. Diagnostic characteristics and phylogenetic analyses were used to evaluate and confirm the generic status and merit its recognition as unique and different from Myrsidea Waterston, 1915. Three species previously belonging to the genus Myrsidea are placed in the new genus Apomyrsidea gen. nov. and are discussed: Apomyrsidea circumsternata (Valim & Weckstein, 2013) gen. et comb. nov., Apomyrsidea isacantha (Valim & Weckstein, 2013) gen. et comb. nov. and Apomyrsidea klimesi (Sychra in Sychra et al., 2006) gen. et comb. nov.

10aApomyrsidea10aApomyrsidea circumsternata10aApomyrsidea isacantha10aApomyrsidea klimesi10amorphology10anew genus10aPhylogeny1 aKOLENCIK, STANISLAV1 aSychra, Oldřich1 aAllen, Julie, M. uhttps://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/133902481nas a2200229 4500008004100000022001300041245011800054210006900172260001200241300001000253490000800263520176400271653001402035653000902049653001802058100002002076700002102096700002302117700002302140700002102163856006702184 2020 eng d a1055790300aDisentangling lousy relationships: Comparative phylogenomics of two sucking louse lineages parasitizing chipmunks0 aDisentangling lousy relationships Comparative phylogenomics of t c10-2020 a11 pp0 v1553 a

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 Neo-haematopinus 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.

10aChipmunks10alice10aPhylogenomics1 aBell, Kayce, C.1 aAllen, Julie, M.1 aJohnson, Kevin, P.1 aDemboski, John, R.1 aCook, Joseph, A. uhttps://linkinghub.elsevier.com/retrieve/pii/S105579032030270002156nas a2200253 4500008004100000022001400041245006700055210006200122260001200184300000900196490000800205520138400213653001601597653002201613653003301635653001801668100003101686700002201717700002101739700002801760700002501788700002301813856006601836 2020 eng d a0962-845200aExtensive in situ radiation of feather lice on tinamous0 aExtensive iin situi radiation of feather lice on tinamous c02-2020 a7 pp0 v2873 a

Tinamous host the highest generic diversity of lice of any group of birds, as well as hosting representatives of all four avian feather louse ecomorphs. Although the generic diversity of tinamou feather lice is well documented, few attempts have been made to reconstruct the phylogenetic relationships among these lice. To test whether tinamou feather lice form a monophyletic group as a whole, we used whole-genome sequencing to estimate a higher-level phylogeny of tinamou feather lice, together with a broad diversity of other avian feather louse groups. In total, we analysed sequences from over 1000 genes for 48 genera of avian lice using both concatenated and coalescent approaches to estimate the phylogeny of this diverse group of avian feather lice. Although the body louse ecomorph of tinamou feather lice formed a monophyletic group, they did not strictly form a monophyletic group together with the other three ecomorphs of tinamou feather lice. In particular, a clade comprised of several feather louse genera, mainly from South America, is nested phylogenetically within tinamou lice, which also have their main centre of diversity in South America. These results suggest in situ radiation of these parasites in South America.

Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.4840287.

10acoevolution10agenome sequencing10ahost–parasite interactions10aPhylogenomics1 aVirrueta-Herrera, Stephany1 aSweet, Andrew, D.1 aAllen, Julie, M.1 aWalden, Kimberly, K. O.1 aWeckstein, Jason, D.1 aJohnson, Kevin, P. uhttps://royalsocietypublishing.org/doi/10.1098/rspb.2019.300502193nas a2200301 4500008004100000245010800041210006900149260001200218300000900230490000600239520126200245653001701507653001701524653001201541653001801553100002401571700002101595700002201616700002801638700002301666700002701689700002501716700002501741700002401766700002501790700002301815856005301838 2019 eng d00aExtensive host-switching of avian feather lice following the Cretaceous-Paleogene mass extinction event0 aExtensive hostswitching of avian feather lice following the Cret c11-2019 a6 pp0 v23 a

Nearly all lineages of birds host parasitic feather lice. Based on recent phylogenomic studies, the three major lineages of modern birds diverged from each other before the Cretaceous- Paleogene (K-Pg) mass extinction event. In contrast, studies of the phylogeny of feather lice on birds, indicate that these parasites diversified largely after this event. However, these studies were unable to reconstruct the ancestral avian host lineage for feather lice. Here we use genome sequences of a broad diversity of lice to reconstruct a phylogeny based on 1,075 genes. By comparing this louse evolutionary tree to the avian host tree, we show that feather lice began diversifying on the common ancestor of waterfowl and landfowl, then radiated onto other avian lineages by extensive host-switching. Dating analyses and cophylogenetic comparisons revealed that two of three lineages of birds that diverged before the K-Pg boundary acquired their feather lice after this event via host-switching.

Data availability

Data generated during this study are available through the Illinois Databank (https://doi.org/10.13012/B2IDB-0440388_V1)39. Raw read sequences are available in the NCBI SRA database (Supplementary Table 3).

10aFeather lice10aGalloanserae10aNeoaves10aPalaeognathae1 ade_Moya, Robert, S.1 aAllen, Julie, M.1 aSweet, Andrew, D.1 aWalden, Kimberly, K. O.1 aPalma, Ricardo, L.1 aSmith, Vincent, Stuart1 aCameron, Stephen, L.1 aValim, Michel, Paiva1 aGalloway, Terry, D.1 aWeckstein, Jason, D.1 aJohnson, Kevin, P. uhttp://www.nature.com/articles/s42003-019-0689-701803nas a2200229 4500008004100000022001400041245012300055210006900178260001200247300001600259490000700275520107700282100002301359700002101382700002101403700002201424700001701446700001901463700001901482700002001501856005201521 2008 eng d a0022-339500aGeographic Distributions and Origins of Human Head Lice (Pediculus humanus capitis) Based on Mitochondrial Data0 aGeographic Distributions and Origins of Human Head Lice iPedicul c12-2008 a1275 - 12810 v943 a

Human head lice (Pediculus humanus capitis) are subdivided into 3 deeply divergent mitochondrial clades (Clades A, B, and C), each having unique geographical distributions. Determining the evolutionary history and geographic distribution of these mitochondrial clades can elucidate the evolutionary history of the lice as well as their human hosts. Previous data suggest that lice belonging to mitochondrial Clade B may have originated in North America or Asia; however, geographic sampling and sample sizes have been limited. With newly collected lice, we calculate the relative frequency, geographic distribution, and genetic diversity of louse mitochondrial clades to determine the geographic origin of lice belonging to Clade B. In agreement with previous studies, genetic diversity data support a North American origin of Clade B lice. It is likely that lice belonging to this mitochondrial clade recently migrated to other geographic localities, e.g., Europe and Australia, and, if not already present, may disperse further to occupy all geographic regions.

1 aLight, Jessica, E.1 aAllen, Julie, M.1 aLong, Lauren, M.1 aCarter, Tamar, E.1 aBarrow, Lisa1 aSuren, Ganbold1 aRaoult, Didier1 aReed, David, L. uhttp://www.bioone.org/doi/abs/10.1645/GE-1618.103003nas a2200517 4500008004100000022001400041245005900055210005900114260001600173300001800189490000800207520154000215653001401755653001401769653001301783653001601796653001901812100002301831700003001854700002101884700002101905700002201926700002201948700002101970700002001991700002202011700002802033700002302061700002402084700002102108700002102129700003102150700002702181700002502208700002502233700002402258700002102282700002002303700001702323700001702340700001402357700002002371700002402391700002402415856004602439 2018 eng d a0027-842400aPhylogenomics and the evolution of hemipteroid insects0 aPhylogenomics and the evolution of hemipteroid insects cNov-12-2018 a12775 - 127800 v1153 a

Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.

10aHemiptera10aPhylogeny10aPsocodea10asystematics10atranscriptomes1 aJohnson, Kevin, P.1 aDietrich, Christopher, H.1 aFriedrich, Frank1 aBeutel, Rolf, G.1 aWipfler, Benjamin1 aPeters, Ralph, S.1 aAllen, Julie, M.1 aPetersen, Malte1 aDonath, Alexander1 aWalden, Kimberly, K. O.1 aKozlov, Alexey, M.1 aPodsiadlowski, Lars1 aMayer, Christoph1 aMeusemann, Karen1 aVasilikopoulos, Alexandros1 aWaterhouse, Robert, M.1 aCameron, Stephen, L.1 aWeirauch, Christiane1 aSwanson, Daniel, R.1 aPercy, Diana, M.1 aHardy, Nate, B.1 aTerry, Irene1 aLiu, Shanlin1 aZhou, Xin1 aMisof, Bernhard1 aRobertson, Hugh, M.1 aYoshizawa, Kazunori uhttps://www.pnas.org/content/115/50/1277502346nas a2200277 4500008004100000022001400041245015100055210006900206300001100275490000600286520143400292653001801726653001701744653002101761100002601782700002501808700002301833700002501856700003001881700002601911700002201937700002101959700002401980700002102004856004302025 2018 eng d a1314-283600aComposition and distribution of lice (Insecta: Phthiraptera) on Colombian and Peruvian birds: New data on louse-host association in the Neotropics0 aComposition and distribution of lice Insecta Phthiraptera on Col ae216350 v63 a

The diversity of permanent ectoparasites is likely underestimated due to the difficulty of collecting samples. Lice (Insecta: Phthiraptera) are permanent ectoparasites of birds and mammals; there are approximately 5,000 species described and many more undescribed, particularly in the Neotropics. We document the louse genera collected from birds sampled in Peru (2006–2007) and Colombia (2009–2016), from 22 localities across a variety of ecosystems, ranging from lowland tropical forest and Llanos to high elevation cloud forest. We identified 35 louse genera from a total of 210 bird species belonging to 37 avian families and 13 orders. These genera belong to two suborders and three families of lice: Amblycera, families Menoponidae (present on 131 bird species) and Ricinidae (39 bird species); and Ischnocera, family Philopteridae (119 bird species). We compared our bird-louse associations with data in Price et al. (2003) and recently published Neotropical studies. The majority of bird-louse associations (51.9%) were new, with most of these coming from Passeriformes, the most diverse avian order, with the most poorly known louse fauna. Finally, we found geographical variation in louse infestation and prevalence rates. With this study, we report the first comprehensive documentation of bird-louse associations for Colombia and substantially increase the known associations documented for Peru.

10aectoparasites10aFeather lice10aTropical Forests1 aSoto-Patiño, Juliana1 aLondoño, Gustavo, A1 aJohnson, Kevin, P.1 aWeckstein, Jason, D.1 aAvendaño, Jorge, Enrique1 aCatanach, Therese, A.1 aSweet, Andrew, D.1 aCook, Andrew, T.1 aJamkowski, Jill, E.1 aAllen, Julie, M. uhttps://bdj.pensoft.net/article/21635/02369nas a2200301 4500008004100000022001300041245009200054210006900146260001600215300001400231490000700245520145000252653001501702653002101717653002801738653001701766653001401783653002401797100002201821700002001843700002601863700002101889700001901910700002301929700002501952700002301977856006702000 2018 eng d a0020751900aHost and parasite morphology influence congruence between host and parasite phylogenies0 aHost and parasite morphology influence congruence between host a cJan-07-2018 a641 - 6480 v483 a

Comparisons of host and parasite phylogenies often show varying degrees of phylogenetic congruence. However, few studies have rigorously explored the factors driving this variation. Multiple factors such as host or parasite morphology may govern the degree of phylogenetic congruence. An ideal analysis for understanding the factors correlated with congruence would focus on a diverse host–parasite system for increased variation and statistical power. In this study, we focused on the Brueelia-complex, a diverse and widespread group of feather lice that primarily parasitise songbirds. We generated a molecular phy- logeny of the lice and compared this tree with a phylogeny of their avian hosts. We also tested for the contribution of each host–parasite association to the overall congruence. The two trees overall were sig- nificantly congruent, but the contribution of individual associations to this congruence varied. To under- stand this variation, we developed a novel approach to test whether host, parasite or biogeographic factors were statistically associated with patterns of congruence. Both host plumage dimorphism and parasite ecomorphology were associated with patterns of congruence, whereas host body size, other plu- mage traits and biogeography were not. Our results lay the framework for future studies to further elu- cidate how these factors influence the process of host–parasite coevolution.

10aAvian lice10aBrueelia complex10acophylogenetic analysis10acospeciation10aEctomorph10asexual dichromatism1 aSweet, Andrew, D.1 aBush, Sarah, E.1 aGustafsson, Daniel, R1 aAllen, Julie, M.1 aDiBlasi, Emily1 aSkeen, Heather, R.1 aWeckstein, Jason, D.1 aJohnson, Kevin, P. uhttps://linkinghub.elsevier.com/retrieve/pii/S002075191830059601593nas a2200253 4500008004100000022001400041245007900055210006900134260001600203300001300219490000700232520082600239653001601065653003301081653001801114653001601132100002301148700002301171700002201194700001901216700001801235700002101253856006501274 2018 eng d a1744-956100aSimultaneous radiation of bird and mammal lice following the K-Pg boundary0 aSimultaneous radiation of bird and mammal lice following the KPg cMar-19-2018 a201801410 v143 a

The diversification of parasite groups often occurs at the same time as the diversification of their hosts. However, most studies demonstrating this concordance only examine single host–parasite groups. Multiple diverse lineages of ectoparasitic lice occur across both birds and mammals. Here, we describe the evolutionary history of lice based on analyses of 1107 single-copy orthologous genes from sequenced genomes of 46 species of lice. We identify three major diverse groups of lice: one exclusively on mammals, one almost exclusively on birds and one on both birds and mammals. Each of these groups radiated just after the Cretaceous–Paleogene (K-Pg) boundary, the time of the mass extinction event of the dinosaurs and rapid diversification of most of the modern lineages of birds and mammals.

10acoevolution10ahost–parasite interactions10aPhylogenomics10asystematics1 aJohnson, Kevin, P.1 aNguyen, Nam-phuong1 aSweet, Andrew, D.1 aBoyd, Bret, M.1 aWarnow, Tandy1 aAllen, Julie, M. uhttp://rsbl.royalsocietypublishing.org/content/14/5/2018014102729nas a2200313 4500008004100000022001400041245014100055210006900196260001600265300001200281490000700293520176300300653001002063653001502073653001602088653001802104653001802122100001902140700002102159700002302180700002202203700001802225700002502243700002102268700002002289700002202309700002302331856006102354 2017 eng d a1063-515700aPhylogenomics using Target-restricted Assembly Resolves Intra-generic Relationships of Parasitic Lice (Phthiraptera: Columbicola)0 aPhylogenomics using Targetrestricted Assembly Resolves Intragene cJul-01-2018 a896-9110 v663 a

Parasitic “wing lice” (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species. Understanding the ecological and evolutionary factors that influence coadaptation and codiversification in this system will substantially improve our understanding of coevolution in general. However, further work is hampered by the lack of a robust phylogenetic framework for Columbicola spp. and their hosts. Previous attempts to resolve the phylogeny of Columbicola based on sequences from a few genes provided limited support. Here, we apply a new approach, target restricted assembly, to assemble 977 orthologous gene sequences from whole-genome sequence data generated from very small, ethanol-preserved specimens, representing up to 61 species of wing lice. Both concatenation and coalescent methods were used to estimate the species tree. These two approaches yielded consistent and well-supported trees with 90% of all relationships receiving 100% support, which is a substantial improvement over previous studies. We used this new phylogeny to show that biogeographic ranges are generally conserved within clades of Columbicola wing lice. Limited inconsistencies are probably attributable to intercontinental dispersal of hosts, and host switching by some of the lice.

10aaTRAM10acoalescent10acoevolution10aconcatenation10aspecies tree.1 aBoyd, Bret, M.1 aAllen, Julie, M.1 aNguyen, Nam-phuong1 aSweet, Andrew, D.1 aWarnow, Tandy1 aShapiro, Michael, D.1 aVilla, Scott, M.1 aBush, Sarah, E.1 aClayton, Dale, H.1 aJohnson, Kevin, P. uhttps://academic.oup.com/sysbio/article/66/6/896/292940202589nas a2200301 4500008004100000022001400041245009800055210006900153260001600222300001600238490000700254520168400261653001501945653002901960653001701989653001302006653001202019100001902031700002102050700002302071700002402094700002702118700001802145700002202163700002302185700002002208856005902228 2017 eng d a0737-403800aPrimates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice0 aPrimates Lice and Bacteria Speciation and Genome Evolution in th cDec-30-2017 a1743 - 17570 v343 a

Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood- sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here, we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement. Examination of the highly reduced symbiont genomes (0.53–0.57 Mb) reveals much of the genomes are dedicated to vitamin synthesis. This is unchanged in the smallest symbiont genome and one that appears to have been reorganized. Specifically, symbionts from human lice, chimpanzee lice, and gorilla lice carry a small plasmid that encodes synthesis of vitamin B5, a vitamin critical to the bacteria-louse symbiosis. This plasmid is absent in an old world monkey louse symbiont, where this pathway is on its primary chromosome. This suggests the unique genomic configuration brought about by the plasmid is not essential for symbiosis, but once obtained, it has persisted for up to 25 My. We also find evidence that human, chimpanzee, and gorilla louse endosymbionts have lost a pathway for synthesis of vitamin B1, whereas the monkey louse symbiont has retained this pathway. It is unclear whether these changes are adaptive, but they may point to evolutionary responses of louse symbionts to shifts in primate biology.

10aCa. Riesia10aendosymbiont replacement10apantothenate10aplasmid.10athiamin1 aBoyd, Bret, M.1 aAllen, Julie, M.1 aNguyen, Nam-phuong1 aVachaspati, Pranjal1 aQuicksall, Zachary, S.1 aWarnow, Tandy1 aMugisha, Lawrence1 aJohnson, Kevin, P.1 aReed, David, L. uhttps://academic.oup.com/mbe/article/34/7/1743/309842003087nas a2200217 4500008004100000245018800041210006900229260001600298300001600314490000600330520230100336653002502637653001402662653001902676653002502695100001902720700002102739700003102760700002002791856005802811 2014 eng d00aGenome Sequence of Candidatus Riesia pediculischaeffi, Endosymbiont of Chimpanzee Lice, and Genomic Comparison of Recently Acquired Endosymbionts from Human and Chimpanzee Lice0 aGenome Sequence of iCandidatusi Riesia pediculischaeffi Endosymb cFeb-15-2014 a2189 - 21950 v43 a

The obligate-heritable endosymbionts of insects possess some of the smallest known bacterial genomes. This is likely due to loss of genomic material during symbiosis. The mode and rate of this erosion may change over evolutionary time; faster in newly formed associations and slower in long-established ones. The endosymbionts of human and anthropoid primate lice present a unique opportunity to study genome erosion in newly established (or young) symbionts. This is because we have a detailed phylogenetic history of these endosymbionts with divergence dates for closely related species. This allows for genome evolution to be studied in detail and rates of change to be estimated in a phylogenetic framework. Here we sequenced the genome of the chimpanzee louse endosymbiont (Candidatus Riesia pediculischaeffi) and compared it to the closely related genome of the human body louse endosymbiont. From this comparison we found evidence for recent genome erosion leading to gene loss in these endosymbionts. While gene loss was detected, it was not significantly higher than in older endosymbionts from aphids and ants. Additionally, we searched for genes associated with B-vitamin synthesis in the two louse endosymbiont genomes because these endosymbionts are believed to synthesize essential B-vitamins absent in the louse's diet. All of the expected genes were present, except those involved in thiamin synthesis. We failed to find genes encoding for proteins involved in the biosynthesis of thiamin or any exogenous means of salvaging thiamin, suggesting there is an undescribed mechanism for the salvage of thiamin. Finally, genes encoding for the pantothenate de novo biosynthesis pathway were located on a plasmid in both taxa along with a heat shock protein. Movement of these genes onto a plasmid may be functionally and evolutionarily significant, potentially increasing production and guarding against the deleterious effects of mutation. These data add to a growing resource of obligate endosymbiont genomes and to our understanding of the rate and mode of genome erosion in obligate animal-associated bacteria. Ultimately sequencing additional louse p-endosymbiont genomes will provide a model system for studying genome evolution in obligate host associated bacteria.

10agamma-proteobacteria10aGene loss10agenome erosion10aprimary-endosymbiont1 aBoyd, Bret, M.1 aAllen, Julie, M.1 ade Crécy-Lagard, Valérie1 aReed, David, L. uhttp://g3journal.org/lookup/doi/10.1534/g3.114.01256703205nas a2200313 4500008004100000022001400041245005800055210005800113260001600171300001200187490000700199520223300206653006002439100002102499700001902520700002302539700002402562700001802586700002102604700002502625700002002650700002202670700002202692700002702714700003002741700002002771700002302791856007702814 2017 eng d a1063-515700aPhylogenomics from Whole Genome Sequences Using aTRAM0 aPhylogenomics from Whole Genome Sequences Using aTRAM cJan-01-2019 a786-7980 v663 a

Abstract.—Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (<1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10−30×). Computational challenges for handling these large data sets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix. Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1107 single-copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and out-groups. We developed a pipeline to extract exon sequences from the aTRAM assemblies by annotating them with respect to the original target protein. We aligned these protein sequences with the inferred amino acids and then performed phylogenetic analyses on both the concatenated matrix of genes and on each gene separately in a coalescent analysis. Finally, we tested the limits of successful assembly in aTRAM by assembling 100 genes from close- to distantly related taxa at high to low levels of coverage.
Both the concatenated analysis and the coalescent-based analysis produced the same tree topology, which was consistent with previously published results and resolved weakly supported nodes. These results demonstrate that this approach is successful at developing phylogenomic data sets from raw genome sequencing reads. Further, we found that with coverages above 5−10×, aTRAM was successful at assembling 80–90% of the contigs for both close and distantly related taxa. As sequencing costs continue to decline, we expect full genome sequencing will become more feasible for a wider array of organisms, and aTRAM will enable mining of these genomic data sets for an extensive variety of applications, including phylogenomics.

10aaTRAM; gene assembly; genome sequencing; phylogenomics.1 aAllen, Julie, M.1 aBoyd, Bret, M.1 aNguyen, Nam-phuong1 aVachaspati, Pranjal1 aWarnow, Tandy1 aHuang, Daisie, I1 aGrady, Patrick, G.S.1 aBell, Kayce, C.1 aCronk, Quentin, C1 aMugisha, Lawrence1 aPittendrigh, Barry, R.1 aLeonardi, María, Soledad1 aReed, David, L.1 aJohnson, Kevin, P. uhttps://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syw10502338nas a2200253 4500008004100000245013000041210006900171260001600240300001300256490000700269520153400276653002001810653001001830653001401840100002201854700001901876700002101895700002101916700002501937700002701962700001901989700002302008856005302031 2018 eng d00aIntegrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution0 aIntegrating phylogenomic and population genomic patterns in avia cJan-01-2018 a95 - 1120 v723 a

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.

10aDiversification10adoves10aparasites1 aSweet, Andrew, D.1 aBoyd, Bret, M.1 aAllen, Julie, M.1 aVilla, Scott, M.1 aValim, Michel, Paiva1 aRivera-Parra, Jose, L.1 aWilson, R., E.1 aJohnson, Kevin, P. uhttp://doi.wiley.com/10.1111/evo.2018.72.issue-102357nas a2200289 4500008004100000022001400041245013200055210006900187260001400256300001600270490000700286520141100293653001801704653001501722653000901737653001201746653002301758100001901781700002101800700001801821700002001839700002201859700002301881700002001904700002301924856012001947 2016 eng d a0099-224000aTwo Bacterial Genera, Sodalis and Rickettsia, Associated with the Seal Louse Proechinophthirus fluctus (Phthiraptera: Anoplura)0 aTwo Bacterial Genera Sodalis and Rickettsia Associated with the  cJune 2016 a3185 - 31970 v823 a

Roughly 10% to 15% of insect species host heritable symbiotic bacteria known as endosymbionts. The lice parasitizing mammals rely on endosymbionts to provide essential vitamins absent in their blood meals. Here, we describe two bacterial associates from a louse, Proechinophthirus fluctus, which is an obligate ectoparasite of a marine mammal. One of these is a heritable endosymbi- ont that is not closely related to endosymbionts of other mammalian lice. Rather, it is more closely related to endosymbionts of the genus Sodalis associated with spittlebugs and feather-chewing bird lice. Localization and vertical transmission of this endo- symbiont are also more similar to those of bird lice than to those of other mammalian lice. The endosymbiont genome appears to be degrading in symbiosis; however, it is considerably larger than the genomes of other mammalian louse endosymbionts. These patterns suggest the possibility that this Sodalis endosymbiont might be recently acquired, replacing a now-extinct, an- cient endosymbiont. From the same lice, we also identified an abundant bacterium belonging to the genus Rickettsia that is closely related to Rickettsia ricketsii, a human pathogen vectored by ticks. No obvious masses of the Rickettsia bacterium were observed in louse tissues, nor did we find any evidence of vertical transmission, so the nature of its association remains unclear.

10aendosymbionts10aRickettsia10aseal10aSodalis10asymbiotic bacteria1 aBoyd, Bret, M.1 aAllen, Julie, M.1 aKoga, Ryuichi1 aFukatsu, Takema1 aSweet, Andrew, D.1 aJohnson, Kevin, P.1 aReed, David, L.1 aGoodrich-Blair, H. uhttp://aem.asm.org/lookup/doi/10.1128/AEM.00282-16https://syndication.highwire.org/content/doi/10.1128/AEM.00282-1602245nas a2200241 4500008004100000022001300041245011400054210006900168260001600237300001400253490000700267520146600274100002001740700002501760700002601785700002101811700001901832700002201851700001801873700002301891700002301914856006601937 2016 eng d a1055790300aUnlocking the black box of feather louse diversity: A molecular phylogeny of the hyper-diverse genus Brueelia0 aUnlocking the black box of feather louse diversity A molecular p cJan-01-2016 a737 - 7510 v943 a

Songbirds host one of the largest, and most poorly understood, groups of lice: the Brueelia-complex. The Brueelia-complex contains nearly one-tenth of all known louse species (Phthiraptera), and the genus Brueelia has over 300 species. To date, revisions have been confounded by extreme morphological variation, convergent evolution, and periodic movement of lice between unrelated hosts. Here we use Bayesian inference based on mitochondrial (COI) and nuclear (EF-1a) gene fragments to analyze the phylogenetic relationships among 333 individuals within the Brueelia-complex. We show that the genus Brueelia, as it is currently recognized, is paraphyletic. Many well-supported and morphologically unified clades within our phylogenetic reconstruction of Brueelia were previously described as genera. These genera should be recognized, and the erection of several new genera should be explored. We show that four distinct ecomorphs have evolved repeatedly within the Brueelia-complex, mirroring the evolutionary history of feather-lice across the entire order. We show that lice in the Brueelia-complex, with some notable exceptions, are extremely host specific and that the host family associations and geographic distributions of these lice are significantly correlated with our understanding of their phylogenetic history. Several ecological phenomena, including phoresis, may be responsible for the macroevolutionary patterns in this diverse group.

1 aBush, Sarah, E.1 aWeckstein, Jason, D.1 aGustafsson, Daniel, R1 aAllen, Julie, M.1 aDiBlasi, Emily1 aShreve, Scott, M.1 aBoldt, Rachel1 aSkeen, Heather, R.1 aJohnson, Kevin, P. uhttp://linkinghub.elsevier.com/retrieve/pii/S105579031500281X01314nas a2200241 4500008004100000022001300041245007800054210006900132260001600201300001600217490000600233520057000239100002000809700002500829700002600854700002100880700001900901700002200920700001800942700002300960700002300983856006601006 2015 eng d a2352340900aData supporting a molecular phylogeny of the hyper-diverse genus Brueelia0 aData supporting a molecular phylogeny of the hyperdiverse genus  cJan-12-2015 a1078 - 10910 v53 a

Data is presented in support of a phylogenetic reconstruction of one of the largest, and most poorly understood, groups of lice: the Brueelia-complex (Bush et al., 2015 [1]). Presented data include the voucher information and molecular data (GenBank accession numbers) of 333 ingroup taxa within the Brueelia-complex and 30 outgroup taxa selected from across the order Phthiraptera. Also included are phylogenetic reconstructions based on Bayesian inference analyses of combined COI and EF-1α sequences for Brueelia-complex species and outgroup taxa.

1 aBush, Sarah, E.1 aWeckstein, Jason, D.1 aGustafsson, Daniel, R1 aAllen, Julie, M.1 aDiBlasi, Emily1 aShreve, Scott, M.1 aBoldt, Rachel1 aSkeen, Heather, R.1 aJohnson, Kevin, P. uhttp://linkinghub.elsevier.com/retrieve/pii/S235234091500270X00702nas a2200217 4500008004100000020001800041022002600059245006000085210005600145260004200201300001400243100002000257700002100277700001800298700001900316700002400335700001800359700002300377700002800400856005600428 2015 eng d a9781107037656 aOnline: 978113979474900aThe study of primate evolution from a lousy perspective0 astudy of primate evolution from a lousy perspective aCambridgebCambridge University Press a202 - 2141 aReed, David, L.1 aAllen, Julie, M.1 aToups, M., A.1 aBoyd, Bret, M.1 aAscunce, Marina, S.1 aMorand, Serge1 aKrasnov, Boris, R.1 aLittlewood, Timothy, J. uhttp://ebooks.cambridge.org/ref/id/CBO978113979474902535nas a2200229 4500008004100000245015000041210006900191260001600260490000700276520173200283653003702015653003102052653001802083653001802101653002302119653002702142100002102169700002102190700002202211700002302233856004902256 2015 eng d00aaTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data0 aaTRAM automated target restricted assembly method a fast method  cJan-12-20150 v163 a

Background: Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome using de novo approaches can take days, even on a powerful computer, and these assemblies typically require data from a variety of genomic libraries. Here we describe software that will alleviate these issues by rapidly assembling genes from distantly related taxa using a single library of paired-end reads: aTRAM, automated Target Restricted Assembly Method. The aTRAM pipeline uses a reference sequence, BLAST, and an iterative approach to target and locally assemble the genes of interest.
Results: Our results demonstrate that aTRAM rapidly assembles genes across distantly related taxa. In comparative tests with a closely related taxon, aTRAM assembled the same sequence as reference-based and de novo approaches taking on average < 1 min per gene. As a test case with divergent sequences, we assembled >1,000 genes from six taxa ranging from 25 – 110 million years divergent from the reference taxon. The gene recovery was between 97 – 99% from each taxon.
Conclusions: aTRAM can quickly assemble genes across distantly-related taxa, obviating the need for draft genome assembly of all taxa of interest. Because aTRAM uses a targeted approach, loci can be assembled in minutes depending on the size of the target. Our results suggest that this software will be useful in rapidly assembling genes for phylogenomic projects covering a wide taxonomic range, as well as other applications. The software is freely available http://www.github.com/juliema/aTRAM.

10aMassively parallel sequence data10aNext-generation sequencing10aPhylogenetics10aPhylogenomics10aShort-read archive10aTargeted gene assembly1 aAllen, Julie, M.1 aHuang, Daisie, I1 aCronk, Quentin, C1 aJohnson, Kevin, P. uhttp://www.biomedcentral.com/1471-2105/16/9801743nas a2200169 4500008004100000022001300041245010600054210006900160260001600229300001600245490000700261520106000268100002201328700002101350700002301371856017901394 2014 eng d a0022258500aNovel Primers From Informative Nuclear Loci for Louse Molecular Phylogenetics (Insecta: Phthiraptera)0 aNovel Primers From Informative Nuclear Loci for Louse Molecular  cJan-11-2014 a1122 - 11260 v513 a

While parasitic lice (Insecta: Phthiraptera) have historically been an important model taxon for understanding hostÐparasite coevolution, very few molecular markers have been developed for phylogenetic analysis. The current markers are insufÞcient to resolve many of the deeper nodes in this group; therefore, sequences from additional genetic loci are necessary. Here, we design primers targeting several nuclear protein coding genes based on a complete genome and transcriptome of Pediculus humanus L. plus transcriptomes and modest coverage genomic data from Þve genera of avian feather lice. These primers were tested on 32 genera of avian feather lice (Ischnocera), including multiple species within some genera. All of the new primer combinations produced sequences for the majority of the genera and had similar or higher divergences than the most widely used nuclear protein-coding gene in lice, EF-1?. These results indicate that these new loci will be useful in resolving phylogenetic relationships among parasitic lice.

1 aSweet, Andrew, D.1 aAllen, Julie, M.1 aJohnson, Kevin, P. uhttp://openurl.ingenta.com/content/xref?genre=article&issn=0022-2585&volume=51&issue=6&spage=1122http://www.ingentaconnect.com/content/esa/jme/2014/00000051/00000006/art0000402004nas a2200265 4500008004100000022001400041245007000055210006900125260001600194490000800210520120700218653001601425653001301441653002401454653002401478653001401502100002301516700002101539700001701560700002201577700002001599700001801619700002701637856007401664 2014 eng d a0962-845200aRates of genomic divergence in humans, chimpanzees and their lice0 aRates of genomic divergence in humans chimpanzees and their lice cJan-08-20140 v2813 a

The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their hosts when comparing single genes. However, the variation in this relative rate of molecular evolution across different genes in the genome is unknown. We compared the rate of DNA sequence divergence between humans, chim- panzees and their ectoparasitic lice for 1534 protein-coding genes across their genomes. The rate of DNA substitution in these orthologous genes was on average 14 times faster for lice than for humans and chimpanzees. In addition, these rates were positively correlated across genes. Because this correlation only occurred for substitutions that changed the amino acid, this pattern is probably produced by similar functional constraints across the same genes in humans, chimpanzees and their ectoparasites.

10acoevolution10agenomics10ahosts and parasites10amolecular evolution10aPediculus1 aJohnson, Kevin, P.1 aAllen, Julie, M.1 aOlds, B., P.1 aMugisha, Lawrence1 aReed, David, L.1 aPaige, K., N.1 aPittendrigh, Barry, R. uhttp://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2013.217402385nas a2200193 4500008004100000022001400041245010600055210006900161260001200230300001400242490000700256520175000263100001902013700002102032700002602053700002302079700002002102856006902122 2012 eng d a0022-339500aVariable Microsatellite Loci for Population Genetic Analysis of Old World Monkey Lice (Pedicinus sp.)0 aVariable Microsatellite Loci for Population Genetic Analysis of  c10/2012 a930 - 9370 v983 a

Parasitic lice have been valuable informants of their host's evolutionary history because they complete their entire life cycle on the host and move between hosts primarily through direct host-to-host contact. Therefore, lice are confined to their hosts both in ecological and evolutionary time. Lice on great apes have been studied to examine details of their host's evolutionary history; however, species of Pedicinus, which parasitize the Old World monkeys, are less well known. We sampled lice from 2 groups of red colobus (Procolobus spp.) in Kibale National Park in Uganda and from red colobus and black and white colobus (Procolobus polycomos) in Taï National Park in Côte d'Ivoire. We used next-generation sequencing data analysis and the human body louse (Pediculus humanus humanus) genome to search for microsatellites for population genetic studies of Pedicinus lice. The 96 primer sets for microsatellite loci designed from the human body louse genome failed to amplify microsatellites in Pedicinus sp., perhaps due to the fast rate of evolution in parasitic lice. Of 63 microsatellites identified by next-generation sequencing data analysis of Pedicinus sp., 12 were variable among populations and 9 were variable within a single population. Our results suggest that these loci will be useful across the genus Pedicinus. We found that the lice in Uganda are not structured according to their hosts' social group; rather, 2 non-interbreeding populations of lice were found on both groups of red colobus. Because direct host-to-host contact is usually required for lice to move among hosts, these lice could be useful for identification and study of behavioral interactions between primate species.

1 aScholl, Katlyn1 aAllen, Julie, M.1 aLeendertz, Fabian, H.1 aChapman, Colin, A.1 aReed, David, L. uhttp://phthiraptera.info/sites/phthiraptera.info/files/68774.pdf02199nas a2200169 4500008004100000245013400041210006900175260000900244300001600253490000700269520159600276100002101872700002001893700002301913700002001936856007301956 2007 eng d00aEvolutionary Relationships of "Candidatus Riesia spp.," Endosymbiotic Enterobacteriaceae Living within Hematophagous Primate Lice0 aEvolutionary Relationships of Candidatus Riesia spp Endosymbioti c2007 a1659 - 16640 v733 a

The primary endosymbiotic bacteria from three species of parasitic primate lice were characterized molecularly. We have confirmed the characterization of the primary endosymbiont (P-endosymbiont) of the human head/body louse Pediculus humanus and provide new characterizations of the P-endosymbionts from Pediculus schaeffi from chimpanzees and Pthirus pubis, the pubic louse of humans. The endosymbionts show an average percent sequence divergence of 11 to 15% from the most closely related known bacterium "Candidatus Arsenophonus insecticola." We propose that two additional species be added to the genus "Candidatus Riesia." The new species proposed within "Candidatus Riesia" have sequence divergences of 3.4% and 10 to 12% based on uncorrected pairwise differences. Our Bayesian analysis shows that the branching pattern for the primary endosymbionts was the same as that for their louse hosts, suggesting a long coevolutionary history between primate lice and their primary endosymbionts. We used a calibration of 5.6 million years to date the divergence between endosymbionts from human and chimpanzee lice and estimated an evolutionary rate of nucleotide substitution of 0.67% per million years, which is 15 to 30 times faster than previous estimates calculated for Buchnera, the primary endosymbiont in aphids. Given the evidence for cospeciation with primate lice and the evidence for fast evolutionary rates, this lineage of endosymbiotic bacteria can be evaluated as a fast-evolving marker of both louse and primate evolutionary histories.

1 aAllen, Julie, M.1 aReed, David, L.1 aPerotti, Alejandra1 aBraig, Henk, R. uhttp://www.phthiraptera.info/sites/phthiraptera.info/files/46874.pdf01958nas a2200169 4500008004100000245008600041210006900127260000900196300001600205490000700221520140800228100002301636700002101659700002001680700002001700856006801720 2007 eng d00aHost-symbiont interaction of the primary endosymbiont of human head and body lice0 aHostsymbiont interaction of the primary endosymbiont of human he c2007 a1058 - 10660 v213 a

The first mycetome was discovered more than 340 yr ago in the human louse. Despite the remarkable biology and medical and social importance of human lice, its primary endosymbiont has eluded identification and characterization. Here, we report the host-symbiont interaction of the mycetomic bacterium of the head louse Pediculus humanus capitis and the body louse P. h. humanus. The endosymbiont represents a new bacterial lineage in the -Proteobacteria. Its closest sequenced relative is Arsenophonus nasoniae, from which it differs by more than 10%. A. nasoniae is a male-killing endosymbiont of jewel wasps. Using microdissection and multiphoton confocal microscopy, we show the remarkable interaction of this bacterium with its host. This endosymbiont is unique because it occupies sequentially four different mycetomes during the development of its host, undergoes three cycles of proliferation, changes in length from 2–4 µm to more than 100 µm, and has two extracellular migrations, during one of which the endosymbionts have to outrun its host’s immune cells. The host and its symbiont have evolved one of the most complex interactions: two provisional or transitory mycetomes, a main mycetome and a paired filial mycetome. Despite the close relatedness of body and head lice, differences are present in the mycetomic provisioning and the immunological response.

1 aPerotti, Alejandra1 aAllen, Julie, M.1 aReed, David, L.1 aBraig, Henk, R. uhttps://faseb.onlinelibrary.wiley.com/doi/10.1096/fj.06-6808com02780nas a2200169 4500008004100000245009700041210006900138260000900207300000600216490000600222520222000228100002002448700002302468700002102491700002502512856007302537 2007 eng d00aPair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice0 aPair of lice lost or parasites regained the evolutionary history c2007 a70 v53 a

Background: The parasitic sucking lice of primates are known to have undergone at least 25 million years of coevolution with their hosts. For example, chimpanzee lice and human head/body lice last shared a common ancestor roughly six million years ago, a divergence that is contemporaneous with their hosts. In an assemblage where lice are often highly host specific, humans host two different genera of lice, one that is shared with chimpanzees and another that is shared with gorillas. In this study, we reconstruct the evolutionary history of primate lice and infer the historical events that explain the current distribution of these lice on their primate hosts.RESULTS: Phylogenetic and cophylogenetic analyses suggest that the louse genera Pediculus and Pthirus are each monophyletic, and are sister taxa to one another. The age of the most recent common ancestor of the two Pediculus species studied matches the age predicted by host divergence (ca. 6 million years), whereas the age of the ancestor of Pthirus does not. The two species of Pthirus (Pthirus gorillae and Pthirus pubis) last shared a common ancestor ca. 3-4 million years ago, which is considerably younger than the divergence between their hosts (gorillas and humans, respectively), of approximately 7 million years ago. CONCLUSIONS: Reconciliation analysis determines that there are two alternative explanations that account for the current distribution of anthropoid primate lice. The more parsimonious of the two solutions suggests that a Pthirus species switched from gorillas to humans. This analysis assumes that the divergence between Pediculus and Pthirus was contemporaneous with the split (i.e., a node of cospeciation) between gorillas and the lineage leading to chimpanzees and humans. Divergence date estimates, however, show that the nodes in the host and parasite trees are not contemporaneous. Rather, the shared coevolutionary history of the anthropoid primates and their lice contains a mixture of evolutionary events including cospeciation, parasite duplication, parasite extinction, and host switching. Based on these data, the coevolutionary history of primates and their lice has been anything but parsimonious.

1 aReed, David, L.1 aLight, Jessica, E.1 aAllen, Julie, M.1 aKirchman, Jeremy, J. uhttp://www.phthiraptera.info/sites/phthiraptera.info/files/46801.pdf