01994nas a2200181 4500008004100000022001400041245008700055210006900142260001600211300001000227490000600237520142100243653002301664100002201687700002301709700002501732856005501757 2022 eng d a2399-364200aIndependent evolution of highly variable, fragmented mitogenomes of parasitic lice0 aIndependent evolution of highly variable fragmented mitogenomes  cJul-08-2022 a10 pp0 v53 a

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

Supplementary data files please visit the publisher's website, Under supplementary information https://www.nature.com/articles/s42003-022-03625-0. There are 6 supplementary data files

10aPessoaiella absita1 aSweet, Andrew, D.1 aJohnson, Kevin, P.1 aCameron, Stephen, L. uhttps://www.nature.com/articles/s42003-022-03625-004906nas a2200241 4500008004100000245008100041210006900122260007500191300001100266490000800277520413300285653002504418653002004443653002604463653001404489653001804503653002404521653003104545653000904576653001104585100002204596856004604618 2018 eng d00aUntangling the coevolutionary history between doves and their parasitic lice0 aUntangling the coevolutionary history between doves and their pa aUrbana, IllinoisbUniversity of Illinois at Urbana-ChampaigncMay 2018 a291 pp0 vPhd3 a

In host-parasite systems, any given host species can be associated with multiple types of parasites, each of which can have a unique ecological relationship with the host. However, it remains unclear how these ecological differences link to evolutionary patterns. What shapes the dynamics of a host-parasite interaction over evolutionary time? An ideal approach for addressing this question is to compare multiple lineages of similar parasites that are associated with the same group of hosts but have distinct ecological differences – or “ecological replicates.” For my dissertation, I applied this strategy by focusing on the wing and body lice of doves. These two “ecomorphs” of lice are not closely related yet exclusively parasitize the same group of hosts. Notably, wing lice have a greater capability for dispersal than body lice. Dispersal is an important ecological component of host-parasite interactions and speciation in general. The first part of my dissertation examined broad cophylogenetic patterns across the dove-louse system. I found that wing and body lice did not have correlated patterns, and body lice showed more cospeciation with their hosts. This pattern agreed with previous studies, the results of which suggested that the increased cospeciation in body lice was due to differences in dispersal ability. In contrast with previous work, I also found that both wing and body louse phylogenies are statistically congruent with the host phylogeny. However, the previous studies had limited taxon sampling compared to my study, indicating that taxon sampling can have a significant impact on the results of cophylogenetic comparisons, and that there can be variable cophylogenetic patterns within a host-parasite system. Cophylogenetic variation in dove lice was further highlighted by my study on lice from phabine doves, a clade native to Australia and Southeast Asia. In this system, wing lice have higher levels of cospeciation with their hosts than did body lice, which is the opposite pattern found in other dove louse systems. The second part of my dissertation focused on the wing and body lice of New World ground-doves. All three groups (wing lice, body lice, and doves) are monophyletic and have relatively few species, which makes the system ideal for obtaining a comprehensive taxonomic sample. As a group that straddles the population-species boundary, ground-dove lice are also useful for gaining insight into host-parasite evolution at phylogenetic and population scales. I used Sanger or whole-genome sequencing data to estimate phylogenetic and/or population patterns of the ground-dove hosts and both groups of lice. For the louse genomes, I developed a novel pipeline to assemble nuclear genes for phylogenetic analysis and call SNPs for population analysis. My results indicate that dispersal is a key factor in shaping the evolution of this host-parasite system. Body lice had higher levels of cospeciation with their hosts, were more host-specific, and had higher rates of divergence than wing lice. At the population level, some body lice also showed host-specific structure, whereas wing lice did not. Body lice also had lower levels of heterozygosity than wing lice, suggesting higher levels of inbreeding. However, dispersal is likely not the only factor that shapes this host-parasite system. Host phylogeny appears to have a significant effect as well. Both wing and body louse phylogenies were statistically congruent with the host phylogeny, and the congruence metrics for individual associations were correlated between the two types of lice. Biogeography may also dictate host-parasite interactions. The wing louse phylogeny was significantly structured according to biogeographic region, and both wing and body lice also showed some biogeographic structure at the population level. Together, these results show that host-parasite interactions can be dictated by many ecological factors over evolutionary time, even in the presence of a primary, dominant factor (e.g., parasite dispersal)

https://core.ac.uk/outputs/161953145

10aAerodramus salangana10aCOPHYLOGENETICS10aGoniocotes talegallae10aparasites10aPhylogenetics10apopulation genetics10aStronglyocotes orbicularis10atext10aThesis1 aSweet, Andrew, D. uhttps://core.ac.uk/download/161953145.pdf02460nas a2200277 4500008004100000022002500041245011600066210007100182260001600253300001400269490000700283520155200290653002601842653002401868653003301892653002801925653002301953653001501976100003101991700002302022700002202045700001702067700002302084700001702107856005802124 2022 eng d a0962-1083, 1365-294X00aHigh levels of inbreeding with spatial and host‐associated structure in lice of an endangered freshwater seal0 aHigh levels of inbreeding with spatial and host‐associated struc cJul-01-2022 a4593-46060 v313 a

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.

10aconservation genomics10agenome resequencing10ahost–parasite interactions10aPhoca hispida saimensis10aSaimaa ringed seal10aseal louse1 aVirrueta-Herrera, Stephany1 aJohnson, Kevin, P.1 aSweet, Andrew, D.1 aYlinen, Eeva1 aKunnasranta, Mervi1 aNyman, Tommi uhttps://onlinelibrary.wiley.com/doi/10.1111/mec.1656902040nas a2200301 4500008004100000022001400041245011200055210006900167260001600236300000900252490000800261520110000269653001201369653001901381653001401400653002901414653002301443653001401466100002201480700002301502700001701525700002401542700002401566700001601590700003101606700002501637856007601662 2021 eng d a0378-111900aStructure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera0 aStructure gene order and nucleotide composition of mitochondrial cFeb-01-2021 a7 pp0 v7683 a

Parasitic lice have unique mitochondrial (mt) genomes characterized by rearranged gene orders, variable genome structures, and less AT content compared to most other insects. However, relatively little is known about the mt genomes of Amblycera, the suborder sister to all other parasitic lice. Comparing among nine different genera (including representative of all seven families), we show that Amblycera have variable and highly rearranged mt genomes. Some genera have fragmented genomes that vary considerably in length, whereas others have a single mt chromosome. Notably, these genomes are more AT-biased than most other lice. We also recover genus-level phylogenetic relationships among Amblycera that are consistent with those reported from large nuclear datasets, indicating that mt sequences are reliable for reconstructing evolutionary relationships in Amblycera. However, gene order data cannot reliably recover these same relationships. Overall, our results suggest that the mt genomes of lice, already know to be distinctive, are even more variable than previously thought.

10aAT-bias10aCrotophaga ani10aEvolution10aMyiothylpis luteoviridis10aOrganelle genomics10aPhylogeny1 aSweet, Andrew, D.1 aJohnson, Kevin, P.1 aCao, Yanghui1 ade_Moya, Robert, S.1 aSkinner, Rachel, K.1 aTan, Milton1 aVirrueta-Herrera, Stephany1 aCameron, Stephen, L. uhttps://www.sciencedirect.com/science/article/abs/pii/S037811192030981102478nas a2200253 4500008004100000022001400041245014600055210006900201260001600270300001000286520160200296653001701898653001701915653004101932653001501973653001101988653001301999100002202012700002302034700002602057700002302083700002502106856009302131 2023 eng d a2160-183600aDraft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen0 aDraft genome assemblies of the avian louse iBrueelia nebulosai a cFeb-03-2023 a13 pp3 a

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

10aectoparasite10aEndosymbiont10ahistorical effective population size10amitogenome10aPacBio10aTELL-Seq1 aSweet, Andrew, D.1 aBrowne, Daniel, R.1 aHernandez, Alvaro, G.1 aJohnson, Kevin, P.1 aCameron, Stephen, L. uhttps://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkad030/702574102146nas 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.2022.004202689nas a2200205 4500008004100000022001400041245015900055210006900214260001600283300001000299490000600309520199700315653001902312653002502331653002002356100002202376700002302398700002502421856003702446 2020 eng d a2167-835900aMitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice0 aMitochondrial genomes of iColumbicolai feather lice are highly f cMar-23-2020 a27 pp0 v83 a

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 genusColumbicola(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 ofPediculus humanusfrom 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.

10aBioinformatics10aConvergent evolution10agenome assembly1 aSweet, Andrew, D.1 aJohnson, Kevin, P.1 aCameron, Stephen, L. uhttps://peerj.com/articles/8759/02456nas a2200241 4500008004100000022001400041245017000055210006900225260001200294520160900306653001301915653001701928653001501945653002101960653002101981100002402002700002402026700002802050700002202078700003002100700002302130856006102153 2020 eng d a1063-515700aPhylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): Combining sequence data and Exploring compositional bias solutions in Next Generation Datasets0 aPhylogenomics of parasitic and nonparasitic lice Insecta Psocode c09-20203 a

The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.

Attachment 95246.pdf file is an Advance article, pre-print

Printed version is also attached.

10aIllumina10aPhthiraptera10aPsocoptera10aQuartet sampling10aRecoding methods1 ade_Moya, Robert, S.1 aYoshizawa, Kazunori1 aWalden, Kimberly, K. O.1 aSweet, Andrew, D.1 aDietrich, Christopher, H.1 aJohnson, Kevin, P. uhttps://academic.oup.com/sysbio/article/70/4/719/591202601633nas a2200181 4500008004100000245010100041210006900142260001300211300000800224490000600232520105700238653001601295653002401311100001701335700002201352700002301374856005401397 2020 eng d00aComparing rates of introgression in parasitic feather lice with differing dispersal capabilities0 aComparing rates of introgression in parasitic feather lice with  cOct-2020 a6pp0 v33 a

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.

The preprint version 1 entitled, Parasite dispersal influences introgression rate, can be found in http://phthiraptera.info/node/95185

 

10acoevolution10apopulation genetics1 aDoña, Jorge1 aSweet, Andrew, D.1 aJohnson, Kevin, P. uhttp://www.nature.com/articles/s42003-020-01345-x02192nas a2200145 4500008004100000245005300041210005300094260001200147490001400159520175800173100001701931700002201948700002301970856005301993 2019 eng d00aParasite dispersal influences introgression rate0 aParasite dispersal influences introgression rate c01-20190 vVersion 13 a

This is a preprint version 1.

Dispersal is a central process in biology with implications at multiple scales of organization1,2,3,4. Organisms vary in their dispersal abilities, and these differences can have important biological consequences, such as impacting the likelihood of hybridization events5. However, the factors shaping the frequency of hybridization are still poorly understood, and therefore how dispersal ability affects the opportunities for hybridization is still unknown. Here, using the ecological replicate system of dove wing and body lice (Insecta: Phthiraptera)6, 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 illustrate how differences in dispersal ability can drive differences in the extent of introgression through hybridization. The results from this study represent an important step for understanding the factors driving hybridization. We expect our approach will stimulate future studies on the ecological factors shaping hybridization to further understand this important process

The latest version of this with a change in title published in August 2020 https://www.biorxiv.org/content/10.1101/527226v8.article-info, under the title:  Comparing rates of introgression in parasitic feather lice with differing dispersal capabilities. Now published in Communications Biology doi: 10.1038/s42003-020-01345-x

Published version see also http://phthiraptera.info/node/95186

 

 

 

 

1 aDoña, Jorge1 aSweet, Andrew, D.1 aJohnson, Kevin, P. uhttps://www.biorxiv.org/content/10.1101/527226v102457nas a2200277 4500008004100000022001400041245015200055210006900207260001300276300001300289490000700302520151100309653002301820653001901843653001801862653003401880653002701914653002801941653002701969100001701996700001902013700002102032700002202053700002302075856008102098 2021 eng d a0022-258500aCombining Nuclear and Mitochondrial Loci Provides Phylogenetic Information in the Philopterus Complex of Lice (Psocodea: Ischnocera: Philopteridae)0 aCombining Nuclear and Mitochondrial Loci Provides Phylogenetic I cJan 2021 a252–260 v583 a

The Philopterus Complex includes several lineages of lice that occur on birds. The complex includes the genera Philopterus (Nitzsch, 1818; Psocodea: Philopteridae), Philopteroides (Mey, 2004; Psocodea: Philopteridae), and many other lineages that have sometimes been regarded as separate genera. Only a few studies have investigated the phylogeny of this complex, all of which are based on morphological data. Here we evaluate the utility of nuclear and mitochondrial loci for recovering the phylogeny within this group. We obtained phylogenetic trees from 39 samples of the Philopterus Complex (Psocodea: Philopteridae), using sequences of two nuclear (hyp and TMEDE6) and one mitochondrial (COI) marker. We evaluated trees derived from these genes individually as well as from concatenated sequences. All trees show 20 clearly demarcated taxa (i.e., putative species) divided into five well-supported clades. Percent sequence divergence between putative species (~5–30%) for the COI gene tended to be much higher than those for the nuclear genes (~1–15%), as expected. In cases where species are described, the lineages identified based on molecular divergence correspond to morphologically defined species. In some cases, species that are host generalists exhibit additional underlying genetic variation and such cases need to be explored by further future taxonomic revisions of the Philopterus Complex.

Attachment 95111.pdf -Advance access version published in August 2020

10agenetic divergence10amolecular data10aPasseriformes10aPhilopteroides cucphuongensis10aPhilopteroides flavala10aPhilopterus gustafssoni10aTyranniphilopterus sp.1 aNajer, Tomas1 aPapoušek, Ivo1 aSychra, Oldřich1 aSweet, Andrew, D.1 aJohnson, Kevin, P. uhttps://academic.oup.com/jme/advance-article/doi/10.1093/jme/tjaa166/589602702661nas a2200229 4500008004100000022001400041245013700055210006900192260001200261300001000273520192600283653001602209653001302225653001102238653001402249653001602263100002202279700001902301700002602320700002302346856006202369 2020 eng d a2045-775800aLousy grouse: Comparing evolutionary patterns in Alaska galliform lice to understand host evolution and host–parasite interactions0 aLousy grouse Comparing evolutionary patterns in Alaska galliform c07-2021 a15 pp3 a

Understanding both sides of host–parasite relationships can provide more complete insights into host and parasite biology in natural systems. For example, phylogenetic and population genetic comparisons between a group of hosts and their closely associated parasites can reveal patterns  of host dispersal, interspecies interactions, and population structure that might not be evident from host data alone. These comparisons are also useful for understanding factors that drive host–parasite coevolutionary patterns (e.g., codivergence or host switching) over different periods of time. However, few studies have compared the evolutionary histories between multiple groups of parasites from the same group of hosts at a  regional geographic scale. Here, we used genomic data to compare phylogenomic and population genomic patterns of Alaska ptarmigan and grouse species (Aves: Tetraoninae) and two genera of their associated feather lice: Lagopoecus and Goniodes . We used whole‐genome sequencing to obtain hundreds of genes and thousands of single‐nucleotide polymorphisms (SNPs) for the lice and double‐digest restriction‐associated DNA sequences to obtain SNPs from Alaska populations of two species of ptarmigan. We found that both genera of lice have some codivergence with their galliform hosts, but these relationships are primarily characterized by host switching and phylogenetic incongruence. Population structure was also uncorrelated between the hosts and lice. These patterns suggest that grouse, and ptarmigan in particular, share habitats and have likely had historical and ongoing dispersal within Alaska. However, the two genera of lice also have sufficient dissimilarities in the relationships with their hosts to suggest there are other factors, such as differences in louse dispersal ability, that shape the evolutionary patterns with their hosts.

10acoevolution10agenomics10agrouse10aptarmigan10aTetraoninae1 aSweet, Andrew, D.1 aWilson, R., E.1 aSonsthagen, Sarah, A.1 aJohnson, Kevin, P. uhttps://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.654502156nas 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/s42003-019-0689-701988nas a2200157 4500008004100000245010100041210006900142260001300211300001600224490000700240520140900247653007101656100002201727700002301749856005801772 2018 eng d00aThe role of parasite dispersal in shaping a host-parasite system at multiple evolutionary scales0 arole of parasite dispersal in shaping a hostparasite system at m cDec 2018 a5104 - 51190 v273 a

Parasite dispersal can shape host–parasite interactions at both deep and shallow timescales. One approach to understanding the effects of dispersal is to study para‐ site lineages that differ in dispersal capability but are from the same group of hosts. In this study, we compared phylogenetic and population genetic patterns of wing and body lice from ground‐doves. Wing lice are more capable of dispersal than body lice. We sequenced full genomes of individual lice for multiple representatives of several wing and body louse species. From these data, we assembled genes for phylogenetic analysis and called SNPs for population genetic analysis. At the phylogenetic level, body lice showed more codivergence with their hosts than did wing lice. However, both wing and body lice exhibited some phylogenetic congruence with their hosts. Within species, body lice showed more population genetic structure than wing lice, although both types of lice showed some structure according to biogeography. Body lice also had significantly lower heterozygosity than wing lice, suggesting more in‐ breeding. Our results demonstrate that dispersal can shape a host–parasite system across evolutionary time, but also that other factors (e.g., host association and bioge‐ ography) can have varying degrees of influence on different groups of parasites and at different evolutionary scales.

10aavian lice; coevolution; doves; phylogenomics; population genomics1 aSweet, Andrew, D.1 aJohnson, Kevin, P. uhttps://onlinelibrary.wiley.com/doi/10.1111/mec.1493702616nas a2200181 4500008004100000245007700041210006900118260001200187300001200199490000700211520204600218100003002264700003102294700002202325700002002347700002302367856004402390 2019 eng d00aPhylogenomic analysis of seal lice reveals codivergence with their hosts0 aPhylogenomic analysis of seal lice reveals codivergence with the c10-2019 a699-7080 v443 a

Lice are considered a model system for studying the process of cospeciation because they are obligate and permanent parasites and are often highly host‐specific. Among lice, species in the family Echinophthiriidae Enderlein (Anoplura) are unique in that they infest mammalian hosts with an amphibious lifestyle, i.e. pinnipeds and the river otter. There is evidence that the ancestor of this group infested the terrestrial ancestor of pinnipeds, which suggests these parasites coevolved with their hosts during the transition to marine environments. However, there has been no previous study investigating the phylogenetic relationships among sucking lice parasitizing seals and sea lions. To uncover the evolutionary history of these parasites, we obtained genomic data for Antarctophthirus microchir Trouessart and Neumann (from two hosts), Antarctophthirus carlinii Leonardi et al., Antarctophthirus lobodontis Enderlein, Antarctophthirus ogmorhini Enderlein, Lepidophthirus macrorhini Enderlein, and Proechinophthirus fluctus Ferris. From genomic sequence reads, we assembled > 1000 nuclear genes and used these data to infer a phylogenetic tree for these lice. We also used the assembled genes in combination with read‐mapping to estimate heterozygosity and effective population size from individual lice. Our analysis supports the monophyly of lice from pinnipeds and uncovers phylogenetic relationships within the group. Surprisingly, we found that A. carlinii, A. lobodontis, and A. ogmorhini have very little genetic divergence among them, whereas the divergence between different geographic representatives of A. microchir indicate that they are possibly different species. Nevertheless, our phylogeny of Echinophthiriidae suggests that these lice have consistently codiverged with their hosts with minimal host switching. Population genomic metrics indicate that louse effective population size is linked to host demographics, which further highlights the close association between pinnipeds and their lice.

1 aLeonardi, María, Soledad1 aVirrueta-Herrera, Stephany1 aSweet, Andrew, D.1 aNegrete, Javier1 aJohnson, Kevin, P. uhttp://doi.wiley.com/10.1111/syen.1235002346nas 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/66/6/896/292940202338nas 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.00282-1602511nas a2200217 4500008004100000022001300041245013800054210006900192260001600261300001400277490000700291520180100298653001402099653001402113653002202127653001402149100002202163700001902185700002302204856006602227 2017 eng d a0020751900aComparative cophylogenetics of Australian phabine pigeons and doves (Aves: Columbidae) and their feather lice (Insecta: Phthiraptera)0 aComparative cophylogenetics of Australian phabine pigeons and do cJan-05-2017 a347 - 3560 v473 a

Host–parasite coevolutionary histories can differ among multiple groups of parasites associated with the same group of hosts. For example, parasitic wing and body lice (Insecta: Phthiraptera) of New World pigeons and doves (Aves: Columbidae) differ in their cophylogenetic patterns, with body lice exhibiting higher phylogenetic congruence with their hosts than wing lice. In this study, we focus on the wing and body lice of Australian phabine pigeons and doves to determine whether the patterns in New World pigeons and doves are consistent with those of pigeons and doves from other regions. Using molecular sequence data for most phabine species and their lice, we estimated phylogenetic trees for all three groups (pigeons and doves, wing lice and body lice), and compared the phabine (host) tree with both par- asite trees using multiple cophylogenetic methods. We found a pattern opposite to that found for New World pigeons and doves, with Australian wing lice showing congruence with their hosts, and body lice exhibiting a lack of congruence. There are no documented records of hippoboscid flies associated with Australian phabines, thus these lice may lack the opportunity to disperse among host species by attaching to hippoboscid flies (phoresis), which could explain these patterns. However, additional sampling for flies is needed to confirm this hypothesis. Large differences in body size among phabine pigeons and doves may also help to explain the congruence of the wing lice with their hosts. It may be more difficult for wing lice than body lice to switch among hosts that vary more dramatically in size. The results from this study highlight how host–parasite coevolutionary histories can vary by region, and how local factors can shape the relationship.

10aAustralia10abody lice10aHippoboscid flies10aWing lice1 aSweet, Andrew, D.1 aChesser, Terry1 aJohnson, Kevin, P. uhttp://linkinghub.elsevier.com/retrieve/pii/S002075191730037101846nas a2200193 4500008004100000245007800041210006900119260001600188300001400204490000700218520124000225100002201465700002201487700002201509700002601531700001901557700002301576856005301599 2016 eng d00aPatterns of cryptic host specificity in duck lice based on molecular data0 aPatterns of cryptic host specificity in duck lice based on molec cJan-06-2016 a200 - 2080 v303 a

Documenting patterns of host specificity in parasites relies on the adequate definition of parasite species. In many cases, parasites have simplified morphology, making species delimitation based on traditional morphological characters difficult. Molecular data can help in assessing whether widespread parasites harbour cryptic species and, alternatively, in guiding further taxonomic revision in cases in which there is morphological variation. The duck louse genus Anaticola (Phthiraptera: Philopteridae), based on current taxonomy, contains both host-specific and widespread species. Mitochondrial and nuclear DNA sequences of samples from this genus were used to document patterns of host specificity. The comparison of these patterns with morphological variations in Anaticola revealed a general correspondence between the groups identified by DNA sequences and morphology, respectively. These results suggest that a more thorough taxonomic review of this genus is needed. In general, the groups identified on the basis of molecular data were associated with particular groups of waterfowl (e.g. dabbling ducks, sea ducks, geese) or specific biogeographic regions (e.g. North America, South America, Australia, Eurasia).

1 aESCALANTE, G., C.1 aSweet, Andrew, D.1 aMCCRACKEN, K., G.1 aGustafsson, Daniel, R1 aWilson, R., E.1 aJohnson, Kevin, P. uhttp://doi.wiley.com/10.1111/mve.2016.30.issue-202673nas a2200157 4500008004100000022001300041245014000054210006900194260001600263300001400279490000800293520210300301100002202404700002302426856006602449 2016 eng d a1055790300aCophylogenetic analysis of New World ground-doves (Aves: Columbidae) and their parasitic wing lice (Insecta: Phthiraptera: Columbicola)0 aCophylogenetic analysis of New World grounddoves Aves Columbidae cJan-10-2016 a122 - 1320 v1033 a

Hosts-parasite interactions are plentiful and diverse, and understanding the patterns of these interactions can provide great insight into the evolutionary history of the organisms involved. Estimating the phylo- genetic relationships of a group of parasites and comparing them to that of their hosts can indicate how factors such as host or parasite life history, biogeography, or climate affect evolutionary patterns. In this study we compare the phylogeny generated for a clade of parasitic chewing lice (Insecta: Phthiraptera) within the genus Columbicola to that of their hosts, the small New World ground-doves (Aves: Columbidae). We sampled lice from the majority of host species, including samples from multiple geo- graphic locations. From these samples we sequenced mitochondrial and nuclear loci for the lice, and used these data to estimate phylogenetic trees and population networks. After estimating the appropriate number of operational taxonomic units (OTUs) for the lice, we used cophylogenetic analyses to compare the louse phylogeny to an existing host phylogeny. Our phylogenetic analysis recovered significant struc- ture within the louse clade, including evidence for potentially cryptic species. All cophylogenetic analyses indicated an overall congruence between the host and parasite trees. However, we only recovered a sin- gle cospeciation event. This finding suggests that certain branches in the trees are driving the signal of congruence. In particular, lice with the highest levels of congruence are associated with high Andean spe- cies of ground-doves that are well separated altitudinally from other related taxa. Other host-parasite associations are not as congruent, and these often involved widespread louse taxa. These widespread lice did, however, have significant phylogeographic structure, and their phylogenetic relationships are per- haps best explained by biogeographic patterns. Overall these results indicate that both host phylogeny and biogeography can be simultaneously important in influencing the patterns of diversification of parasites.

1 aSweet, Andrew, D.1 aJohnson, Kevin, P. uhttp://linkinghub.elsevier.com/retrieve/pii/S105579031630174901904nas a2200169 4500008004100000245009700041210006900138260001600207300001400223490000800237520130900245653007301554100002201627700001901649700002301668856004301691 2016 eng d00aCophylogenetic patterns are uncorrelated between two lineages of parasites on the same hosts0 aCophylogenetic patterns are uncorrelated between two lineages of cJan-02-2016 a813–8280 v1183 a

Free-living organisms are often host to multiple lineages of closely related parasites. Different lineages of obligate parasites living on the same hosts might potentially be expected to display similar cophylogenetic patterns. However, there are also reasons why these lineages might have different evolutionary histories (e.g. host switching, host geography). In the present study, we use mitochondrial and nuclear DNA sequence data to evaluate the cophylogenetic patterns between doves and their wing and body lice. Previous studies have found that the wing and body lice of doves have different levels of congruence between their phylogenetic histories. However, these studies are limited in scope, either taxonomically or geographically. We used both new and existing data to generate a worldwide and taxonomically diverse data set for doves and two independent groups of lice: wing and body lice. Using event and topology-based methods, we found that cophylogenetic patterns were not correlated between wing and body lice, even though both groups showed evidence of cospeciation with their hosts. These results indicate that external factors vary in their impact on different groups of parasites and also that broad sampling is critical for identifying patterns in cophylogenetic analyses.

10aclade-limited host switching;cospeciation;host ecology;sampling bias1 aSweet, Andrew, D.1 aBoyd, Bret, M.1 aJohnson, Kevin, P. uhttp://doi.wiley.com/10.1111/bij.1277101743nas 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/art00004