02675nas a2200253 4500008004100000022002500041245010400066210006900170260001600239520181100255100003002066700001902096700002102115700003302136700001902169700001802188700001702206700002202223700001802245700003102263700002002294700002302314856008402337 2022 eng d a0737-4038, 1537-171900aAncient human genomes and environmental DNA from the cement attaching 2,000 year-old head lice nits0 aAncient human genomes and environmental DNA from the cement atta cDec-28-20213 a

Over the past few decades there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500–2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel Cell Polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield two-fold compared to a petrous bone, and four-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, while hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, non-destructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history.

Note: the attached 95612 pdf is not the final but a published review version of the paper. 95612 published copy.pdf is the final published paper.

1 aPedersen, Mikkel, Winther1 aAntunes, Catia1 aDe Cahsan, Binia1 aMoreno-Mayar, José, Víctor1 aSikora, Martin1 aVinner, Lasse1 aMann, Darren1 aKlimov, Pavel, B.1 aBlack, Stuart1 aMichieli, Catalina, Teresa1 aBraig, Henk, R.1 aPerotti, Alejandra uhttps://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab351/648155101625nas a2200217 4500008004100000022001400041245009700055210006900152260001400221300001200235490000700247520093900254653002001193653003001213653000901243100001801252700002001270700002301290700002001313856007401333 2011 eng d a0737-403800aOrigin of Clothing Lice Indicates Early Clothing Use by Anatomically Modern Humans in Africa0 aOrigin of Clothing Lice Indicates Early Clothing Use by Anatomic cSpet 2011 a29 - 320 v283 a

Clothing use is an important modern behavior that contributed to the successful expansion of humans into higher latitudes and cold climates. Previous research suggests that clothing use originated anywhere between 40,000 and 3 Ma, though there is little direct archaeological, fossil, or genetic evidence to support more specific estimates. Since clothing lice evolved from head louse ancestors once humans adopted clothing, dating the emergence of clothing lice may provide more specific estimates of the origin of clothing use. Here, we use a Bayesian coalescent modeling approach to estimate that clothing lice diverged from head louse ancestors at least by 83,000 and possibly as early as 170,000 years ago. Our analysis suggests that the use of clothing likely originated with anatomically modern humans in Africa and reinforces a broad trend of modern human developments in Africa during the Middle to Late Pleistocene.

10aHuman evolution10aisolation with migration.10alice1 aToups, M., A.1 aKitchen, Andrea1 aLight, Jessica, E.1 aReed, David, L. uhttps://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msq23402589nas 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/34/7/1743/309842002241nas a2200145 4500008004100000245012400041210006900165260000900234300001400243490000700257520171200264100002301976700002301999856007302022 2002 eng d00aAn insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks0 ainsect molecular clock dates the origin of the insects and accor c2002 a748 - 7610 v193 aA unified understanding of .390 Myr of insect evolution requires insight into their origin. Molecular clocks are widely applied for evolutionary dating, but clocks for the class Insecta have remained elusive. We now define a robust nucleotide and amino acid mitochondrial molecular clock encompassing five insect orders, including the Blattaria (cockroaches), Orthoptera (crickets and locusts), Hemiptera (true bugs), Diptera, and Lepidoptera (butterflies and moths). Calibration of the clock using one of the earliest, most extensive fossil records for insects (the early ancestors of extant Blattaria) was congruent with all available insect fossils, with biogeographic history, with the Cambrian explosion, and with independent dating estimates from Lepidopteran families. In addition, dates obtained from both nucleotide and amino acid clocks were congruent with each other.Of particular interest to vector biology is the early date of the emergence of triatomine bugs (99.8–93.5 MYA), coincident with the formation of the South American continent during the breakup of Gondwanaland. More generally, we reveal the insects arising from a common ancestor with the Anostraca (fairy shrimps) at around the Silurian-Ordovician boundary (434.2–421.1 MYA) coinciding with the earliest plant megafossil. We explore Tilyard’s theory proposing that the terrestrial transition of the aquatic arthropod ancestor to the insects is associated with a particular plant group (early vascular plants). The major output of the study is a comprehensive series of dates for deep-branching points within insect evolution that can act as calibration points for further dating studies within insect families and genera. 1 aGaunt, Michael, W.1 aMiles, Michael, A. uhttp://www.phthiraptera.info/sites/phthiraptera.info/files/47120.pdf00754nas a2200265 4500008004100000245007800041210006900119260000900188300001600197490000700213653001800220653001400238653001500252653001400267653000800281653001400289653001000303653001100313653001200324653001400336653001800350100002400368700002400392856007200416 1998 eng d00aAn unprecedented major rearrangement in an arthropod mitochondrial genome0 aunprecedented major rearrangement in an arthropod mitochondrial  c1998 a1786 - 17870 v1510aamplification10aarachnida10aArthropoda10aBoophilus10adna10aEvolution10agenes10agenome10aIxodida10amicroplus10amitochondrial1 aCampbell, N., J. H.1 aBarker, Stephen, C. uhttp://www.phthiraptera.info/sites/phthiraptera.info/files/3264.pdf00565nas a2200157 4500008004100000245010900041210006900150260000900219300001600228490000700244100001600251700002400267700002000291700002400311856007200335 2001 eng d00aIncreased rate of gene rearrangement in the mitochondrial genomes of three orders of hemipteroid insects0 aIncreased rate of gene rearrangement in the mitochondrial genome c2001 a1828 - 18320 v181 aShao, Renfu1 aCampbell, N., J. H.1 aSchmidt, E., R.1 aBarker, Stephen, C. uhttp://www.phthiraptera.info/sites/phthiraptera.info/files/3199.pdf01884nas a2200181 4500008004100000245011900041210006900160260000900229300001400238490000700252520127700259653001601536653001401552100001601566700002401582700002401606856007201630 2001 eng d00aNumerous gene rearrangements in the mitochondrial genome of the wallaby louse, Heterodoxus macropus (Phthiraptera)0 aNumerous gene rearrangements in the mitochondrial genome of the  c2001 a858 - 8650 v183 a

The complete arrangement of genes in the mitochondrial (mt) genome is known for 12 species of insects, and part of the gene arrangement in the mt genome is known for over 300 other species of insects. The arrangement of genes in the mt genome is very conserved in insects studied, since all of the protein-coding and rRNA genes and most of the tRNA genes are arranged in the same way. We sequenced the entire mt genome of the wallaby louse, Heterodoxus macropus, which is 14,670 bp long and has the 37 genes typical of animals and some noncoding regions. The largest noncoding region is 73 bp long (93% A+T), and the second largest is 47 bp long (92% A+T). Both of these noncoding regions seem to be able to form stem-loop structures. The arrangement of genes in the mt genome of this louse is unlike that of any other animal studied. All tRNA genes have moved and/or inverted relative to the ancestral gene arrangement of insects, which is present in the fruit fly Drosophila yakuba. At least nine protein-coding genes (atp6, atp8, cox2, cob, nad1-nad3, nad5, and nad6) have moved; moreover, four of these genes (atp6, atp8, nad1, and nad3) have inverted. The large number of gene rearrangements in the mt genome of H. macropus is unprecedented for an arthropod.

10aHeterodoxus10amolecular1 aShao, Renfu1 aCampbell, N., J. H.1 aBarker, Stephen, C. uhttp://www.phthiraptera.info/sites/phthiraptera.info/files/2268.pdf02110nas a2200325 4500008004100000245005700041210005700098260000900155300001400164490000700178520128300185653001001468653000901478653001001487653000801497653001401505653001501519653001101534653001201545653002201557653001401579653001201593653001401605653001001619653001701629653001001646100001601656700001601672856009601688 1998 eng d00aEstimating divergence dates from molecular sequences0 aEstimating divergence dates from molecular sequences c1998 a442 - 4480 v153 aThe ability to date the time of divergence between lineages using molecular data provides the opportunity to answer many important questions in evolutionary biology. However, molecular dating techniques have previously been criticized for failing to adequately account for variation in the rate of molecular evolution. We present a maximum-likelihood approach to estimating divergence times that deals explicitly with the problem of rate variation. This method has many advantages over previous approaches including the following: (1) a rate constancy test excludes data for which rate heterogeneity is detected; (2) date estimates are generated with confidence intervals that allow the explicit testing of hypotheses regarding divergence times; and (3) a range of sequences and fossil dates are used, removing the reliance on a single calculated calibration rate. We present tests of the accuracy of our method, which show it to be robust to the effects of some modes of rate variation. In addition, we test the effect of substitution model and length of sequence on the accuracy of the dating technique. We believe that the method presented here offers solutions to many of the problems facing molecular dating and provides a platform for future improvements to such analyses.10aavian10abird10aclock10adna10aEvolution10alikelihood10amammal10amaximum10amitochondrial dna10amolecular10aorigins10aPhylogeny10asites10asubstitution10atrees1 aRambaut, A.1 aBromham, L. uhttps://phthiraptera.myspecies.info/content/estimating-divergence-dates-molecular-sequences02331nas a2200301 4500008004100000245013400041210006900175260000900244300001600253490000700269520140600276653000901682653000901691653001101700653001401711653000801725653001201733653002301745653001701768653001701785653001201802653001301814653001201827653001201839100001901851700001801870856014101888 1999 eng d00aPhylogenetic relationships of the enigmatic hoatzin (Opisthocomus hoazin) resolved using mitochondrial and nuclear gene sequences0 aPhylogenetic relationships of the enigmatic hoatzin Opisthocomus c1999 a1300 - 13070 v163 aThe hoatzin (Opisthocomus hoazin) is a bizarre, long-tailed, crested bird that inhabits the riparian lowlands of South America. Among its peculiar attributes are (1) microbial foregut fermentation to convert plant cellulose in consumed foliage into simple sugars, (2) a highly modified skeleton to accommodate its large crop, and (3) in the young of this species, wing claws at the wrist joint which are used to climb among the branches of the nest tree. Consequently, the taxonomic position of this unusual bird has perplexed systematists since its description over 200 years ago. Traditionally classified among the fowl-like birds (Galliformes), recent studies have favored its placement with the cuckoos (Cuculiformes: Cuculidae). To help resolve this systematic uncertainty, we sequenced six mitochondrial genes (cytochrome oxidase I, II, and III, ATPase 8, ATPase 6, and cytochrome b) and one nuclear gene (c-mos), totaling 5,487 base pairs. With this large data set and an appropriate range of outgroup taxa, we demonstrate that the hoatzin should not be classified among the cuckoos or Galliformes. Instead, our analyses indicate that the hoatzin is most closely related to the turacos (Musophagiformes: Musophagidae), a small family of arboreal, frugivorous birds inhabiting sub-Saharan Africa. This phylogenetic relationship is also supported by osteological, behavioral, and fossil evidence.10aacid10abird10acuckoo10aCuculidae10adna10ahoatzin10amaximum likelihood10aMusophagidae10aOpisthocomus10aprotein10asequence10astomach10aturacos1 aHughes, J., M.1 aBaker, A., J. uhttps://phthiraptera.myspecies.info/content/phylogenetic-relationships-enigmatic-hoatzin-opisthocomus-hoazin-resolved-using-mitochondria02968nas a2200397 4500008004100000245008100041210006900122260000900191300001600200490000700216520189200223653001002115653001002125653001402135653001502149653001002164653001502174653001402189653001902203653002202222653001402244653001202258653001502270653001602285653002202301653001302323653000902336653001702345653001602362653001102378653000902389653001602398100001702414700002002431856011902451 1998 eng d00aBody size effects and rates of cytochrome b evolution in tube-nosed seabirds0 aBody size effects and rates of cytochrome b evolution in tubenos c1998 a1360 - 13710 v153 aVariation in rates of molecular evolution now appears to be widespread. The demonstration that body size is correlated with rates of molecular evolution suggests that physiological and ecological factors may be involved in molecular rate variation, but large-scale comparative studies are still lacking. Here, we use complete cytochrome b sequences from 85 species of tube-nosed seabirds (order Procellariiformes) and 5 outgroup species of penguins (order Sphenisciformes) to test for an association between body mass and rates of molecular evolution within the former avian order. Cladistic analysis of the 90 sequences estimates a phylogeny largely consistent with the traditional taxonomy of the Procellariiformes. The Diomedeidae, Procellariidae, and Pelecanoldidae are monophyletic, while the Hydrobatidae are basal and paraphyletic. However, the two subfamilies within the Hydrobatidae (Hydrobatinae and Oceanitinae) are monophyletic. A Likelihood ratio test detects significant deviation from clocklike evolution in our data. Using a sign test for an association between body mass and branch length in the seabird phylogeny, we find that larger taxa tend to have shorter terminal branch lengths than smaller taxa. This observation suggests that rates of mitochondrial DNA evolution are slower for larger taxa. Rate calibrations based on the fossil record reveal concordant body size effects. We interpret these results as evidence for a metabolic rate effect, as the species in this order exhibit large differences in metabolic rates, which are known to be highly correlated with body mass in this group. Our results support previous findings of body size effects and show that this effect can be significant even within a single avian order. This suggests that even lineage-specific molecular clocks may not be tenable if calibrations involve taxa with different metabolic rates.10aavian10aclock10aEvolution10ageneration10agenes10ahypothesis10ametabolic10ametabolic rate10amitochondrial dna10amolecular10aneutral10anucleotide10apopulations10aProcellariiformes10asequence10asize10asubstitution10asystematics10atheory10atime10avertebrates1 aNunn, G., B.1 aStanley, S., E. uhttps://phthiraptera.myspecies.info/content/body-size-effects-and-rates-cytochrome-b-evolution-tube-nosed-seabirds