Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. eeto,bcueedsmin tesi atal ikdwt otfins Wrere 02.Scn,host Second, host-level 2002). may (Wernegreen by fitness we affected host partially such, evolutionary with be hosts’ linked As will their partially genomes by is hosts. endosymbiont fitness shaped endosymbiont in respective partially because selection be their selection, First, to with endosymbionts histories. symbionts in demographic evolution as and molecular retention of continued patterns their expect (Chong for sizes necessary genome those degraded entirely resistance not but nutrition, Gil reduced, have host generally in endosymbionts Obligate implicated (Anbutsu Obligate often general 2020). are 2009). in Bordenstein (Kikuchi and & evolution Perlmutter obligate common and to particularly pathogens, facultative are (Clark from to hosts insects dependence their in in and endosymbioses range & microorganisms flow- commensalisms (Ehrlich between endosymbiotic or as species between mutualisms such or partner partners, pollinators Kiester between between codiversification their 2000; adaptations pop- in and another reciprocal result plants in may require change ering evolution evolutionary generally Mutualistic to will 1964). response Raven in 1980), population (Janzen one in ulation change evolutionary the Coevolution, loss. gene endosymbiont loss and INTRODUCTION gene demography of host patterns between across random relationship absence somewhat no and indicating found presence signal, we variable phylogenetic Lastly, toward exhibited exhibited shifts genomes. genes positive half endosymbiont and Blochmannia of about in demography the demography signatures those, host of host found Of between 10% between we relationship About genomes. relationship genes, no endosymbiont positive genes. Blochmannia but endosymbiont a in genes, in identified endosymbiont selection selection We in for relaxed phylogeny. selection tests the intensified multiple across toward Using rapidly, shifts strength evolved and hosts. selection have their in genes endosymbiont of shifts that that and found selection ˜30x We of endosymbionts. pace signatures their host (Genus a strong and how identified at ants ants we about phylogenomics, carpenter carpenter hypotheses genome between of test whole codiversification Using genomes and of endosymbionts. codiversification complete in their sequenced evolution demography investigate molecular we host to impacts of Here, demography endosymbionts impact Blochmannia lacking. the their many generally of and While investigations are Camponotus) detailed evolution. evolution endosymbiont endosymbionts, molecular of and codiversification course endosymbiont expect hosts the may on of affecting we discernibly cospeciation instances, demography these demonstrated host In have as endosymbiont. studies well obligate, and as are host endosymbionts that of and those evolution hosts especially the Endosymbioses, of link that taxa. interacting mutualism intimate more or an two are of evolution the connects discernibly Mutualism Abstract 2020 2, December 2 1 Manthey Joseph their and ants carpenter endosymbionts Camponotus Blochmannia in genome test endosymbiont a on evolution: history evolutionary host of Impact udeUniversity Purdue University Tech Texas tal. et 03 engen20) ugsigte eansm ee o hi w ucina elas well as function own their for genes some retain they suggesting 2002), Wernegreen 2003; tal. et 1 enfrGiron Jennifer , 94.Edsmissaecmo niscs a eita retaellr n the and extracellular, or intra- be may insects, in common are Endosymbioses 1984). 2 n akHruska Jack and , tal. et 1 07 rwle&Jhsn20;Mra 2020; Moreau 2009; Johnson & Brownlie 2017; 1 tal. et tal. et 2019; Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. 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All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. 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(perhaps 09 una al21)t xrc eoi ein matching regions genomic extract to 2010) Hall & Quinlan 2009; p 1JM eoe 1 dniyd oorpasadover- and repeats novo de identify (1) genome: (1-JDM) sp. omc selysi Formica p 1JM eoei w tgs is,w sdCanu used we First, stages. two in genome (1-JDM) sp. tal. et enovo de edcddt sebetegnm famme fthe of member a of genome the assemble to decided We . .novaeboracensis C. 3 05 n hncetn osnu eune fnovel of sequences consensus creating then and 2005) seby(a dy20;Bno 99 Price 1999; Benson 2002; Eddy & (Bao assembly Camponotus eoe(CI GCA (NCBI: genome Camponotus pce nthe in species )gnrlyfudi otenor northern in found generally ?) Camponotus tal. et 0893.;Brelsford 009859135.1; p 1JM eoe we genome, (1-JDM) sp. enovo de Camponotus 07 Durand 2017; pce odt is date to species sebyo a of assembly subgenus tal. et tal. et et et Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. 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No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. o s nMM,w akdgnmcrgosntgntpd steewudohrieb itknfor mistaken be otherwise would these as genotyped, not 2014). regions Durbin genomic & (Schiffels masked v1.1.0 we MSMC2 program MSMC, the in used we use individual, For each for demography estimate To (R samples hereafter. found ingroup We heterozygosity in of scores. correlated quality estimates highly per-base raw be and genetic to depth of sequencing estimates estimates two for each (Renaud accounting impact the for while ROHan to heterozygosity sites potential program of invariant the rates the to has estimate used bi-allelic depth sequencing of also Because we proportion diversity, sites. the genotyped as all simply for heterozygosity individual observed estimated coalescent-based we the demography. 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Data may be preliminary. hnei hlgntccnetb esrn eaiebac egh ntehs pce revru the versus tree species host the in lengths branch relative measuring and by tree context species phylogenetic host a (Paradis the ape in package between R change distance the in (1994) implemented Kuhner-Felsenstein trees, gene the calculated we in variation each this examined for we First, matrix ways. absence / rates. presence Evolutionary gene a coevolution from tabulated Blochmannia annotated we and genes Camponotus coding results, from analysis sequences BLAST acid the amino Blochmannia all From of (blastp) samples. BLAST all protein for all-to-all once an times, formed six RELAX loss. branches ran Gene test we followed such, of selection As set positive a strength. outgroup). requires for selection the RELAX tested in are shifts testing. identify branches multiple each to all for branches 1979) where reference (Holm mode and correction exploratory Holm-Bonferroni in a aBSREL by ran We 2015). al. 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Camponotus Blochmannia Blochmannia Blochmannia tal. et ns eue osraiepoygnrto ieused time generation proxy conservative a used we ants, eepyoeisrltv otehs pce re odo To tree. species host the to relative phylogenies gene 6 lcmni floridanus Blochmannia tal. et ee.Fo hs eetes eetmtdaspecies a estimated we trees, gene these From genes. 06.Bcueo hs oecuinsol eused be should caution some this, of Because 2016). oooymxbarbatus Pogonomyrmex Blochmannia eoe sebe o hssuy is,w per- we First, study. this for assembled genomes 04.Scn,w xlrdrtso evolutionary of rates explored we Second, 2004). eoeuigbdol.W hnused then We bedtools. using genome Blochmannia tal. et oietf uaieyhomolo- putatively identify to ooiskp ncaptivity in kept colonies ) 05.In 2015). eoe nmultiple in genomes tal. et .ocreatus C. Camponotus Blochmannia 2018). tal. et and et , Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ewe niiul ihnseis(ooe rnei i.2.I otatt ayn rprin fgene of of proportions majority relationships varying a some to hosts, were contrast ant differences In only the 2). The in relationships 2). Fig. tree in (Fig. species orange tree matching (colored species trees species host within the individuals to between topology identical nearly a h pce re hl ahnd a 0%spoti SRLaaye Fg 2). 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Data may be preliminary. lcmni eoeszs eecmoiin ae fmlclrevolution molecular of The rates composition, entire as gene the concordance, sizes, across phylogenetic genome consistent the Blochmannia were general, metric, In KF94 signal. the phylogenomic by overall measured the from divergent relatively were B i.S0.A rvosymnind oegn osi noybotgnmsehbtdphylogenetic exhibited genomes endosymbiont in (Fig. loss demography we gene host contrast, some and In mentioned, strength selection previously S10). relaxed As of Fig. as with number 5A, S10). well genes and as of (Fig. estimates Fig. multiple number strength pressures size without 5B, between selection selection and population relationship with all intensified in host no tests toward between shifts for found selection shifts relationship of lineages for with positive numbers tested results host genes a relative also report endosymbiont found the we identify We We strength, among both selection correction. S5). to relaxed) in Table testing trying shifts or S9; extreme were intensified with we (Fig. loci (i.e., as phylogeny strength Here, the selection in genes. in randomly somewhat shifts appeared for selection and positive traits estimates. 19 endosymbiont of size tests, between selection population correlations positive mean for observed In due harmonic looked estimates with these we in using variance correlated such, sizes (e.g., As highly trends population size host was structure). population years population simply however, the not differential Overall, million if therefore to even half and mind. history, population in last panmixia), reflect this of the estimates (R lack with individual through each interpreted a for size be (i.e., heterozygosity flow should population gene individual mean each population harmonic for among species within trends in couple histories a demographic variation demographic with in overall of Variation and, indicative 300,000 S8). to be (Fig. ˜20,000 may species from within ranged consistent sizes largely were population 3B. exceptions, effective Fig. host in these of estimates rates evolution in of Contemporary genic endosymbiont alignments rates the on the high-quality than say, demography any to higher host much Needless recover of likely in alignments). Impacts to are the identity unable regions of were intergenic sequence regions these these we (Darling percent in in progressiveMauve that evolution and sections using non-overlapping species, evolution large alignments host host (e.g., of genome between of regions rates whole scale cases relative taxonomic some performed identify the we in at to this, genome al. tried do the et To also of We regions. most 3C). intergenic across acting (Fig. forces clades evolutionary similar of suggestive 10 Blochmannia x 1.454 = (range year / mean the context, absolute timed S7). Fig. 4, myrmex (Fig. loss samples gene the subgenus of among signal phylogenetic absence exhibited / the 37 presence genes, variable 65 exhibited those The genes Of 65 4). total, (Fig. In here sequenced while annotated. were kbp, genes 781 to coding kbp 775 from The size in for ranged GenBank genomes from the subgenussequence the of in Five with individuals consistent contrast, sizes. is In This kbp]. 3). 791 (Fig. = [ kbp GenBank 792 on to already ˜783 subgenus from size in varied genomes between distance KF94 the measured We node). each for support 99% to each (67% tree species the of relationships Blochmannia Blochmannia Blochmannia Blochmannia Blochmannia 00.Hwvr noybotitrei eune ees iegn ewe otsbeea and subgenera, host between divergent so were sequences intergenic endosymbiont However, 2010). Fg B.I euethe use we If 3B). (Fig. Camponotus eeiett ihnhs ugnr a eeal ossetars h noybotgenome, endosymbiont the across consistent generally was subgenera host within identity gene eoe(i.3) diinly tapae that appeared it Additionally, 3B). (Fig. genome eoe otie ewe 7 n 0 ee,adi oa cosalgnms 0 unique 607 genomes, all across total in and genes, 601 and 576 between contained genomes eoe sebe eelreyvre e ugns ntesubgenus the In subgenus. per varied largely here assembled genomes eete n h otseiste oietf fayrgoso the of regions any if identify to tree species host the and tree gene ee vle t˜03xtert fteathss ihsih aito across variation slight with hosts, ant the of rate the ˜20–30x at evolved genes a lgtysoe aeo vlto hntoeo h n otsubgenus host ant the of those than evolution of rate slower slightly a had -8 .vafer B. o126x10 x 1.256 to Blochmannia .pennsylvanicus B. Blochmannia Camponotus 2 (NC .47 p 0.7497, = -7 1992 a 72kp(i.3D). (Fig. kbp ˜722 was 014909.2) ee hwdeiec o eeto TbeS) hs signatures These S4). 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Data may be preliminary. 02,w a aeanl xetto hths eorpi atrsprilyiflec endosymbiont influence partially endosymbiont patterns of factors demographic two Wernegreen host influenced 2002; demography that Moran host whether & expectation investigated (Mira we null sizes Here, a population evolution. have molecular effective may host effective endosymbiont with we and linked size, 2002), intrinsically population is effective by size influenced population are processes genomic population Because evolution? endosymbiont bacterial shape free-living demography their to host and Does hosts their of both rates to relative evolution specific evolution molecular of relatives. host-lineage by rates corroborated have faster have are may endosymbionts results that and previous in These here genome identified 2009). the Ochman rates relatives, endosymbiont across & However, free-living (Kuo somewhat their 1996). evolution varies (Moran to molecular sites rate compared coding rates nonsynonymous evolution 2002). at Wernegreen evolutionary molecular evolution 2002; insect relative of Moran faster histories; rates & increased have (Mira life including evolution also their fast endosymbionts relatively inheritance of of and such, mode because sizes As their populations endosymbionts of effective because in small bottlenecks to here expected regular This lead identified undergo are evolution to propensity of rates properly. and rates evolution asexuality them endosymbionts’ the fast scale, align Relatively absolute to an On 1999). able (1995). not colleagues were and in Moran we in by reported that (˜36x) level the aphids lineages to of similar across is rate divergent evolution relative so endosymbiont-host were regions intergenic that found endosymbionts We Blochmannia generally in statistic a KF94 evolution found the molecular of we of estimate Rates Indeed, stable a by genome. evidenced as the genome the across the across across pressures overall sorting similar selective lineage relatively of variable pattern with by consistent genome as the caused across trees incongruence signal species and consistent across supported (1) evolution strongly patterns: of two obtain rates of to one sequencing able across expected by were sorting we contrast, lineage we Here, in in endosymbionts, variation markers; and estimate molecular hosts as few well both a for or genomes one using full phylogenies (Degnan inferred ants have carpenter codiversification in studies previous and vertically- 2000), and been hosts has al. endosymbionts between (Toju et and and co-speciation hosts weevils completely host between of in were between codiversification expectations found relationships of incongruence with evidence species-level phylogenetic consistent similar all endosymbionts; are some transmitted but patterns was species, These There within identified congruent. individuals we 2). endosymbionts, amongst bacterial trees their (Fig. endosymbiont and codiversification hosts ant strict carpenter generally both of sequencing endosymbionts demog- whole-genome Blochmannia host Using and of hosts effects selection. ant (3) natural carpenter and and of variation loss genome, Codiversification (2) endosymbiont gene endosymbionts, of the and patterns across endosymbiont hosts evolution on of molecular raphy codiversification and (1) sorting available to lineage related publicly in questions of investigated a number we for the sources, resource doubled genome whole than a more added We endosymbiont dynamics. and size coevolutionary host population ant carpenter host several between sequenced S11). relationship We a (Fig. for contrasts independent evidence phylogenetic no using found DISCUSSION genomes we endosymbiont this, in Despite loss S7). gene and Fig. 4, (Fig. signal Blochmannia 01 Lo 2001; Blochmannia Blochmannia tal. et vrg bu nodro antd atrta hs eotdin reported those than faster magnitude of order an about average 03,bvle (Distel bivalves 2003), Blochmannia genome. tal. et Blochmannia ee vle tart 3xfse hntehs eoe(i.3.I addition, In 3). (Fig. genome host the than faster ˜30x rate a at evolved genes 03,fle (Chen flies 2013), eoe Fg ) vrl,teerslscrooaepeiu evidence previous corroborate results these Overall, 3). (Fig. genomes ee,o 2 ihyvral adcp fpyoeei congruence phylogenetic of landscape variable highly a (2) or genes, tal. et Blochmannia tal. et 94,ahd (Clark aphids 1994), 9 Blochmannia tal. et 99 Hosokawa 1999; Blochmannia 04.Gnrly rvossuisinvestigating studies previous Generally, 2004). ee Fg A ihpyoeei statistics. phylogenetic with 3A) (Fig. genes Camponotus ulgnm eune.Wt hs re- these With sequences. full-genome eoe oadesqetosabout questions address to genomes tal. et Buchnera tal. et 00,pyld (Thao psyllids 2000), ( 02,ccrahs(Clark cockroaches 2012), Camponotus atra endosymbionts bacterial Buchnera pce and species ) (Clark tal. et tal. et Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. CS,rpttv n rnpsbeeeet,adG otn.Pit niaesmaysaitc n100 in statistics summary indicate Points content. GC and elements, transposable for and Jisha repetitive John (CDS), thanks 1. JDM Figure JDM. to funds TABLES & startup FIGURES University Tech Texas in interested by him supported getting was work be This to taxon, those new https://github.com/jdmanthey/camponotus including a files, GithHub: ACKNOWLEDGEMENTS as on Output available it to are archive. in describe uploaded project Genome loss or this gene NCBI’s be species and in to will selection the genome for assemblies place tests the from either format uploading GFA to by followed us all subsequently allows while investigation GenBank, novo taxonomic de NCBI’s further The to All SRA. submitted NCBI’s Dryad. to being submitted are being currently first format is the data sequencing wrote specimens. raw and ant All data of the photos and analyzed macro samples, JDM took collecting JDM work. AVAILABILITY for DATA and lab fieldwork JCG performed (2) manuscript. JPH project, the the drafts. of in writing draft ideas initial of of development revisions (1) (3) to contributed somewhat authors all, found All histories. not we demographic Lastly, but host history. some, to demographic that related CONTRIBUTIONS host not found AUTHOR We by was that shaped phylogeny. loss part host gene in the endosymbiont were across random selection strength natural selection of in patterns shifts and selection itive the their across investigate rates to of evolutionary endosymbionts codiversification their and strict hosts bionts. identified ant We carpenter both of coevolution. sequencing whole-genome used We a with phylogeny; consistent 2015). the is Wernegreen in This & CONCLUSIONS loss 4). (Williams smallest gene drift (Fig. the of genetic losses with patterns and rest gene constraints random the species singleton selection while relatively were the informative, suggests signal in phylogenetically but phylogenetic This was research lacking loss dataset, previous S4). loss gene entire Table the gene S7; of the of half 4, majority in about that case (Figs. to found not the We leading was drift— not 4). thereby genetic was (Fig. of sizes, loss estimates This population gene and along host sizes loss. faster, small population occur gene with estimated would drift of endosymbionts genetic in rates significant that no part anticipated pressures, faster found in initially and selection We loss least gene decreased at S11). endosymbiont of may with (Fig. patterns pressures two on demography the selection host between in of relationship effect shifts an that in for tested appears patterns also but We it processes. to S10), endosymbionts, demographic relative 5, host insect selection by (Figs. in (Alleman influenced results relaxed identified genes be our expect often of on may fraction is Based small we selection 2012). a general, Indeed, in in only endosymbionts 2002). generally in (Wernegreen In pressures bacteria selection S6). free-living intensified Table toward relaxation shifts S10; and and 5, selection sizes positive population of host signatures between both loss. in and gene strength demography of selection host patterns of between (2) relationship and no selection, found We natural of patterns (1) evolution: genome Blochmannia Camponotus Blochmannia Camponotus ee r vligaot3xfse hnhs eoe,wt eaieyconsistent relatively with genomes, host than faster 30x about evolving are genes Blochmannia p (1-JDM) sp. 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S9, 5, (Figs. genes oeta eaeaowt ot-ogfil trip. field month-long a with ago decade a than more enovo de Blochmannia eoe In genome. eoeasml hrceitc,icuigcdn content coding including characteristics, assembly genome 10 tal. et ilb poddt ra.Alcd sdfranalyses for used code All Dryad. to uploaded be will , Blochmannia Camponotus 08 Chong 2018; .laevigatus C. ot n their and hosts ee,w on oeeiec o pos- for evidence some found we genes, tal. et ddhv h otendosymbiont most the have —did Blochmannia 09 ilas&Wernegreen & Williams 2019; Blochmannia Blochmannia sebisi FASTA in assemblies genomes1. ee (Figs. genes endosym- Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. hlgne n xiie 0%qattspotfreeyrltosi.Hs re eeroe ihthe with phylogenies. rooted endosymbiont were and host trees the Host between vary these relationship. that branches to every identical indicate for were tree support topologies tree quartet niger species 100% Cataglyphis of ASTRAL proportion exhibited indicate The and labels Branch hypothesis. phylogenies phylogenetic endosymbionts. their this and ants supporting host trees of congruence Phylogenetic 2. Figure estimates. mean Mbp) 1 (i.e., window ten indicate lines solid while windows, sliding non-overlapping kbp ape The sample. Blochmannia rewsmdon otd rnebace nthe in branches Orange rooted. midpoint was tree 11 Blochmannia Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ee o lgmnswt nesrmvd o l ttsis ie niaema ausars idw of windows across values mean indicate these lines (NC for statistics, GenBank all on For published (D) molecular of removed. rates genes. indels Relative (B) ten with alignments tree. identical for an genes is zero of value in a evolution where lengths, branch including and topologies tree the species across host evolution the molecular in Variation 3. Figure 007292.1), Blochmannia .vafer B. Blochmannia (NC Blochmannia ee eaiet h otseiste.()Gn dniypretg in percentage identity Gene (C) tree. species host the to relative genes 014909.2), eoeasml ie o l e sebisi hssuya ela those as well as study this in assemblies new all for sizes assembly genome Camponotus ee.TeK9 itnemaue ieecsbtenphylogenetic between differences measures distance KF94 The genes. .chromaiodes B. ugnr.Gnaksequences: GenBank subgenera. 12 Blochmannia (NC 020075.1). eoe.()TeK9 itnebetween distance KF94 The (A) genomes. lcmni pennsylvanicus Blochmannia Blochmannia Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. eut ihmlil etn orcinaecnitn ihteerslsadpeetdi iueS10. Figure in presented and results. results corrected these testing with non-multiple were consistent for strength are selection are correction in here testing Shifts presented multiple demography. Results with host aBSREL. and Results program strength the selection in using shifts obtained of Relationships 5. Figure exhibit individual absence. one indicates least yellow at light in while lost presence, genes indicates 65 green of Dark 37 S7). S4). (Table (Fig. samples signal among phylogenetic absence / presence in varied 4. Figure Blochmannia eepeec asnepyoeei eta.O 0 oa ee noae,65 annotated, genes total 607 Of heatmap. phylogenetic /absence presence gene 13 Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. nlresaepyoeei analyses. phylogenetic trimming large-scale alignment automated in for tool a trimAl: Silla-Mart´ınez Gabald´onCapella-Guti´errez (2009) S, JM, T SM genomes. organism Robb model I, emerging Korf BL, Cantarel Berkeley Lawrence V Orlando Avagyan Ernest formatics G, Coulouris Aligner. C, Splice-Aware Camacho Accurate, (US). Fast, CA A Berkeley, Laboratory, BBMap: National (2014) B Bushnell hosts. insect in protection Symbiont-mediated 348-354. (2009) , KN Johnson JC, Brownlie A ants. Avril Formica J, Purcell A, Brelsford C Ye saltator. G, Harpegnathos Zhang finch. R, zebra in Bonasio retrotransposons M LTR Santos of dos diversity Silva hidden da uncovers C, Frankl-Vilches J, Boman ants. formicine of study case a history: 15 evolutionary deep resolving in TR approaches Schultz SG, sequences. Brady BB, DNA Blaimer analyze to program a to approach finder: 573-580. powerful repeats , and Tandem practical (1999) a G Benson rate: discovery false the Controlling testing. genomes. (1995) multiple sequenced Y in Hochberg families Y, sequence Benjamini repeat of identification novo de Research Automated (2002) Genome SR Eddy Z, Bao N Nikoh Shaping Pressures M, beetles. Selective Moriyama and H, Drift Anbutsu Genetic Random (2018) Genome. S Blattabacterium Kambhampati the KL, Hertweck A, Alleman CITED LITERATURE 271. , rceig fteNtoa cdm fSine,USA Sciences, of Academy National the of Proceedings 10 1. , urn Biology Current ora fterylsaitclscey eisB(Methodological) B Series society. statistical royal the of Journal 12 1269-1276. , Science tal. et , cetfi Reports Scientific tal. et , 30 329 tal. et , 0-1.e304. 304-311. , tal. et , eoeResearch Genome Bioinformatics 1068-1071. , tal. et , 21)Gnmccmaio fteat apntsflrdnsand floridanus Camponotus ants the of comparison Genomic (2010) tal. et , 22)A nin n rddsca uegn swdsra across widespread is supergene social eroded and ancient An (2020) 20)MKR nes-oueantto ieiedsge for designed pipeline annotation easy-to-use an MAKER: (2008) 21)Pyoeoi ehd upromtaiinlmulti-locus traditional outperform methods Phylogenomic (2015) 21)Salgnm ybotudrisctcehrns in hardness cuticle underlies symbiont genome Small (2017) 20)BAT:acietr n applications. and architecture BLAST+: (2009) 8 tal. et , 1-12. , 25 14 18 1972-1973. , 188-196. , 21)Tegnm fBu-apdCordon-Bleu Blue-capped of genome The (2019) 114 Genes E8382-E8391. , 10 301. , M vltoayBiology Evolutionary BMC uli cd Research Acids Nucleic rnsi Microbiology in Trends 289-300. , M Bioin- BMC 17 27 Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. olrH 18)Plmrhs n ooyotgn nNrhAeia apne ns(Hymenoptera: ants carpenter American North ferrugineus). in Camponotus f ontogeny and colony pennsylvanicus and Camponotus Formicidae: Polymorphism (1986) method. HG comparative Fowler the and Phylogenies (1985) J Felsenstein coevolution. Blochmannia. in M endosymbiont Krischke study J, a Straka plants: H, and Feldhaar Butterflies (1964) PH Raven PR, Ehrlich zoom. MS unlimited with Shamim maps JT, contact Robinson NC, Durand scaffolds. chromosome-length AD sulfur-oxidizing yields Omer among SS, Batra congruence O, Dudchenko phylogenetic hosts. for bivalve Evidence their (1994) and 533-542. C endosymbionts Cavanaugh bacterial host. 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All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. oN ad ,Wtnb ,Nlp ,Bnnt 20)Eiec o oldgnssbtendiverse between cocladogenesis for Evidence (2003) T Beninati C, endosymbionts. Nalepa intracellular H, their and Watanabe lineages C, transform. dictyopteran Burrows–Wheeler Bandi with N, alignment Lo read short accurate and Fast (2009) matics assemblies. R genome Durbin of H, Interrogation Li in BlobTools: evolution (2017) molecular ML of Blaxter rates DR, variable Laetsch the rocks: lacking when clocks Inferring bacteria. (2009) H unequal Ochman and C-H, equal Kuo under algorithms phylogeny of comparison simulation rates. A evolutionary (1994) J Felsenstein genomes. 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C, PhyML Guyomar of performance V the assessing Lefort phylogenies: J-F, likelihood Dufayard S, Guindon genomes. reduced of E Zientz FJ, Silva R, Gil 0908180109-0908180109. , 25 h mrcnNaturalist American The ilg Direct Biology cec eotTkoKok agk eto B Section Daigaku Kyoiku Tokyo Report Science yoeei n eoeResearch Genome and Cytogenetic 1754-1760. , oeua ilg n Evolution and Biology Molecular 15 rceig fteNtoa cdm fSine,USA Sciences, of Academy National the of Proceedings ora fAia Ecology Animal of Journal 64-66. , 4 tal. et , 35. , A eoisadBioinformatics and Genomics NAR oeua ilg n Evolution and Biology Molecular 20)Tegnm euneo lcmni oiau:cmaaieanalysis comparative floridanus: Blochmannia of sequence genome The (2003) tal. et , tal. et , tal. et , 124 tal. et , tal. et , 220-243. , 21)Rdciegnm vlto,hs–ybotc-pcainand co-speciation host–symbiont evolution, genome Reductive (2012) 21)Cn:saal n cuaeln-edasml i adaptive via assembly long-read accurate and scalable Canu: (2017) eoeResearch Genome 22)MnS ieYu ybotb agtdgnm assembly genome targeted by Symbiont Your Mine MinYS: (2020) Evolution 21)Nwagrtm n ehd oetmt maximum- estimate to methods and algorithms New (2010) 110 20)RpaeUdt,adtbs fekroi repetitive eukaryotic of database a Update, Repbase (2005) M Bioinformatics BMC 82 462-467. , 16 11 540-550. , 34 459-468. , 611-612. , 215087.215116. , 14 h SEjournal ISME The oeua ilg n Evolution and Biology Molecular 30 27-46. , 2 772-780. , ytmtcBiology Systematic lqaa047. , 5 nulrpr fteNtoa Institute National the of report Annual 59. , cniainjunlo statistics of journal Scandinavian 100 6 9388-9393. , F1000Research 577-587. , 59 irbsadEnviron- and Microbes netsSociaux Insectes 307-321. , 20 6 907-913. , Bioinfor- 1287. , 30 , Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. usl A adr G oeuC 21)Htpt o yboi:fnto,eouin n pcfiiyof specificity and evolution, Formicidae). function, (Hymenoptera: phylogeny symbiosis: ant for the of Hotspots short tips (2017) News of to trunk CS assembly from Moreau and associations JG, detection ant-microbe integrated Sanders MindTheGap: JA, (2014) Russell C Lemaitre R, insertions. Heterozygosity Chikhi long of and A, Estimates Samples. Gouin Joint Ancient G, (2019) and L Rizk Modern Orlando for E, Homozygosity features. Willerslev of genomic TS, Runs comparing Korneliussen and for K, Hanghøj utilities G, of Renaud suite flexible a BEDTools: (2010) formatics ant. 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All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. hn ,Rbe ,SyaiE iaa 21)ATA-I:plnma ieseiste reconstruction tree species time polynomial ASTRAL-III: (2018) trees. S gene Mirarab resolved E, partially Sayyari from M, Rabiee likelihood. C, maximum Zhang by analysis phylogenetic for package program 13 a genera. PAML: ant (1997) prevalent Z gene most Yang the parallel Camponotini. are symbiosis: tribe Which ant bacteria-ant (1976) the ancient EO of an Wilson origin in the evolution spanning Genome Blochmannia among (2015) loss JJ Wernegreen indel LE, endosymbiont. context-specific Williams genome bacterial and novo a composition, de in sequence of variation selection, 44-51. visualization intraspecific Purifying interactive (2012) shape Bandage: JJ mutations Wernegreen (2015) LE, KE Williams Holt J, relaxed Zobel detecting MB, RELAX: assemblies. (2015) Schultz K RR, Scheffler Wick SL, Pond framework. phylogenetic Kosakovsky a MD, in Smith selection B, insects. Murrell sap-feeding JO, tending Wertheim Blochmanniaby Phylo- acquired another: begat Camponotini symbiosis tribe Biology nutritional ant One Evolutionary the (2009) that PS Ward evidence SG, genetic Brady SN, Kauppinen JJ, insects. Wernegreen replacements, of endosymbiosis: endosymbionts bacterial of in Diversification evolution 850-861. (2013) Genome T (2002) weevils. Fukatsu JJ in Wernegreen T, symbionts Sota bacteriocyte of Y, promiscuity Notsu and AS, co-speciation Tanabe H, Toju P Abbot symbionts. NA, Moran ML, Thao submodel. Research A Acids computing. intron Badretdin phylogenetic M, new DiCuccio for T, a library Tatusova and Python a model DendroPy: Markov (2010) hidden 26 MT Holder a J, with Sukumaran prediction Gene (2003) S Bioinformatics Waack phylogenies. 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Systems for Institute auervesgenetics reviews Nature 31 19 3 e881. , 3210-3212. , 187-200. , 7 32 1378-1390. , 1342-1353. , Bioinformatics Bioinformatics . Nucleic BMC 4 3 , , Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. camponotus-carpenter-ants-and-their-blochmannia-endosymbionts 496575-impact-of-host-evolutionary-history-on-endosymbiont-genome-evolution-a-test-in- Fig_2_camponotus_tree_reduced.pdf file Hosted

C Relative B A Gene % Identity Evolution Rate KF94 Distance Prop. GC Prop. Repetitive Prop. CDS 60 70 80 90 100 0 10 20 30 40 50 0.05 0.15 0.25 0.35 0.25 0.35 0.45 0.0 0.4 0.8 0.0 0.2 0.4 0 Position inBlochmanniaGenome(thousandsofbp) 100 1 200 2 3 300 vial at available 4 5 400 6 7 Scaffold 500 19 8 https://authorea.com/users/380686/articles/ Index Index 9 600 10 11 12 700 13 14 D Blochmannia Genome Size (1000s of bp) Tanaemyrmex Full Dataset Camponotus 720 740 760 780 Camponotus

Tanaemyrmex 15 -31 B. ocreatus B. vafer Posted on Authorea 2 Dec 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160689628.80980759/v1 — This a preprint and has not been peer reviewed. Data may be preliminary.

# Blochmannia Genes w/ A Intensified Selection Strength 10 15 20 25 30 35 40 50 C−005 C−039 C−028 C−029 C−024 C−018 C−016 C−010 C−056 C−050 C−049 C−036 C−019 C−002 C−003 C−046 C−006 100 150 Host SpeciesHarmonicMeanPop.Size(1000s) R 200 p =0.0011 2 =0.9332 250 20

# Blochmannia Genes w/ B Relaxed Selection Strength 10 15 20 25 50 100 150 R 200 p =0.5613 2 =0.0910 C. vicinus C. sp.(2-JDM) C. sp.(1-JDM) C. herculeanus C. modoc C. laevigatus C. ocreatus 250