{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T18:27:42Z","timestamp":1787509662998,"version":"build-2736575974"},"reference-count":84,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2021,6,19]],"date-time":"2021-06-19T00:00:00Z","timestamp":1624060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000104","name":"NASA","doi-asserted-by":"publisher","award":["17-EXO-17-2-0112"],"award-info":[{"award-number":["17-EXO-17-2-0112"]}],"id":[{"id":"10.13039\/100000104","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["IOS-1656514"],"award-info":[{"award-number":["IOS-1656514"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["DEB-1546049"],"award-info":[{"award-number":["DEB-1546049"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000270","name":"NERC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000270","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100003891","name":"IRF","doi-asserted-by":"publisher","award":["NE\/N014936\/1"],"award-info":[{"award-number":["NE\/N014936\/1"]}],"id":[{"id":"10.13039\/100003891","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"ERC","doi-asserted-by":"publisher","award":["758508"],"award-info":[{"award-number":["758508"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"publisher","award":["URF\\R1\\180682"],"award-info":[{"award-number":["URF\\R1\\180682"]}],"id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Major changes in chromosome number and structure are linked to a series of evolutionary phenomena, including intrinsic barriers to gene flow or suppression of recombination due to chromosomal rearrangements. However, chromosome rearrangements can also affect the fundamental dynamics of molecular evolution within populations by changing relationships between linked loci and altering rates of recombination. Here, we build chromosome-level assembly Eueides isabella and, together with a recent chromosome-level assembly of Dryas iulia, examine the evolutionary consequences of multiple chromosome fusions in Heliconius butterflies. These assemblies pinpoint fusion points on 10 of the 20 autosomal chromosomes and reveal striking differences in the characteristics of fused and unfused chromosomes. The ten smallest autosomes in D. iulia and E. isabella, which have each fused to a longer chromosome in Heliconius, have higher repeat and GC content, and longer introns than predicted by their chromosome length. When fused, these characteristics change to become more in line with chromosome length. The fusions also led to reduced diversity, which likely reflects increased background selection and selection against introgression between diverging populations, following a reduction in per-base recombination rate. We further show that chromosome size and fusion impact turnover rates of functional loci at a macroevolutionary scale. Together these results provide further evidence that chromosome fusion in Heliconius likely had dramatic effects on population level processes shaping rates of neutral and adaptive divergence. These effects may have impacted patterns of diversification in Heliconius, a classic example of an adaptive radiation.<\/jats:p>","DOI":"10.1093\/molbev\/msab185","type":"journal-article","created":{"date-parts":[[2021,6,18]],"date-time":"2021-06-18T07:07:57Z","timestamp":1624000077000},"page":"4449-4462","source":"Crossref","is-referenced-by-count":71,"title":["Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size"],"prefix":"10.1093","volume":"38","author":[{"given":"Francesco","family":"Cicconardi","sequence":"first","affiliation":[{"name":"School of Biological Sciences, University of Bristol Bristol\u2014Life Sciences Building, Bristol, United Kingdom"},{"name":"Department of Zoology, University of Cambridge, Cambridge, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4170-9118","authenticated-orcid":false,"given":"James J","family":"Lewis","sequence":"additional","affiliation":[{"name":"Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA"},{"name":"Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0747-7456","authenticated-orcid":false,"given":"Simon H","family":"Martin","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert D","family":"Reed","sequence":"additional","affiliation":[{"name":"Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles G","family":"Danko","sequence":"additional","affiliation":[{"name":"Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen H","family":"Montgomery","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Bristol Bristol\u2014Life Sciences Building, Bristol, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,6,19]]},"reference":[{"key":"2021092720222091000_msab185-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms5737","article-title":"The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera","volume":"5","author":"Ahola","year":"2014","journal-title":"Nat Commun"},{"issue":"2","key":"2021092720222091000_msab185-B2","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1093\/genetics\/140.2.821","article-title":"Linkage and the limits to natural selection","volume":"140","author":"Barton","year":"1995","journal-title":"Genetics"},{"issue":"D1","key":"2021092720222091000_msab185-B3","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"Bateman","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"2021092720222091000_msab185-B4","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1038\/s41559-016-0052","article-title":"Complex modular architecture around a simple toolkit of wing pattern genes","volume":"1","author":"Van Belleghem","year":"2017","journal-title":"Nat Ecol Evol"},{"issue":"1","key":"2021092720222091000_msab185-B5","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1038\/s41562-017-0189-z","article-title":"Redefine statistical significance","volume":"2","author":"Benjamin","year":"2017","journal-title":"Nat Hum Behav"},{"issue":"4702","key":"2021092720222091000_msab185-B6","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1126\/science.4001930","article-title":"The mosaic genome of warm-blooded vertebrates","volume":"228","author":"Bernardi","year":"1985","journal-title":"Science"},{"issue":"15","key":"2021092720222091000_msab185-B7","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2021092720222091000_msab185-B8","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1745-6150-7-12","article-title":"Domain enhanced lookup time accelerated BLAST","volume":"7","author":"Boratyn","year":"2012","journal-title":"Biol Direct"},{"issue":"21","key":"2021092720222091000_msab185-B9","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1093\/bioinformatics\/btn480","article-title":"F-Seq: a feature density estimator for high-throughput sequence tags","volume":"24","author":"Boyle","year":"2008","journal-title":"Bioinformatics"},{"key":"2021092720222091000_msab185-B10"},{"issue":"1","key":"2021092720222091000_msab185-B11","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1534\/genetics.119.301951","article-title":"The effects on neutral variability of recurrent selective sweeps and background selection","volume":"212","author":"Campos","year":"2019","journal-title":"Genetics"},{"issue":"3","key":"2021092720222091000_msab185-B12","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1017\/S0016672300025532","article-title":"Mutation-selection balance and the evolutionary advantage of sex and recombination","volume":"55","author":"Charlesworth","year":"1990","journal-title":"Genet Res"},{"issue":"23","key":"2021092720222091000_msab185-B13","doi-asserted-by":"crossref","first-page":"3996","DOI":"10.1016\/j.cub.2019.10.010","article-title":"Interplay between developmental flexibility and determinism in the evolution of mimetic Heliconius wing patterns","volume":"29","author":"Concha","year":"2019","journal-title":"Curr Biol"},{"issue":"4","key":"2021092720222091000_msab185-B14","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1371\/journal.pbio.1002112","article-title":"Natural selection constrains neutral diversity across a wide range of species","volume":"13","author":"Corbett-Detig","year":"2015","journal-title":"PLoS Biol"},{"issue":"4","key":"2021092720222091000_msab185-B15","doi-asserted-by":"crossref","first-page":"e1002112","DOI":"10.1038\/nrg3425","article-title":"Genomic signatures of selection at linked sites: unifying the disparity among species","volume":"14","author":"Cutter","year":"2013","journal-title":"Nat Rev Genet"},{"key":"2021092720222091000_msab185-B17","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1534\/g3.115.023655","article-title":"Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution","volume":"6","author":"Davey","year":"2016","journal-title":"G3 Genes Genomes Genet"},{"key":"2021092720222091000_msab185-B18","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"Depristo","year":"2011","journal-title":"Nat Genet"},{"issue":"1","key":"2021092720222091000_msab185-B19","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2021092720222091000_msab185-B20","volume-title":"Animal cytology and evolution","author":"Dobzhansky","year":"1977"},{"issue":"9","key":"2021092720222091000_msab185-B21","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"Eddy","year":"1998","journal-title":"Bioinformatics"},{"issue":"6465","key":"2021092720222091000_msab185-B22","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1126\/science.aaw2090","article-title":"Genomic architecture and introgression shape a butterfly radiation","volume":"366","author":"Edelman","year":"2019","journal-title":"Science"},{"issue":"D1","key":"2021092720222091000_msab185-B23","doi-asserted-by":"crossref","first-page":"D427","DOI":"10.1093\/nar\/gky995","article-title":"The Pfam protein families database in 2019","volume":"47","author":"El-Gebali","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"2021092720222091000_msab185-B24","doi-asserted-by":"crossref","first-page":"1488","DOI":"10.1111\/jeb.13101","article-title":"Genome evolution, structural rearrangements and speciation","volume":"30","author":"Feulner","year":"2017","journal-title":"J Evol Biol"},{"issue":"19","key":"2021092720222091000_msab185-B25","doi-asserted-by":"crossref","first-page":"2928","DOI":"10.1016\/j.cub.2017.08.038","article-title":"Genome architecture and evolution of a unichromosomal asexual Nematode","volume":"27","author":"Fradin","year":"2017","journal-title":"Curr Biol"},{"issue":"7","key":"2021092720222091000_msab185-B26","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat Biotechnol"},{"issue":"7374","key":"2021092720222091000_msab185-B27","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/nature10640","article-title":"The genome of Tetranychus urticae reveals herbivorous pest adaptations","volume":"479","author":"Grbi\u0107","year":"2011","journal-title":"Nature"},{"issue":"23","key":"2021092720222091000_msab185-B28","doi-asserted-by":"crossref","first-page":"4071","DOI":"10.1016\/j.cub.2019.09.056","article-title":"Dichotomy of dosage Compensation along the Neo Z chromosome of the Monarch butterfly","volume":"29","author":"Gu","year":"2019","journal-title":"Curr Biol"},{"issue":"10","key":"2021092720222091000_msab185-B29","first-page":"2747","article-title":"Local adaptation and the evolution of chromosome fusions","volume":"68","author":"Guerrero","year":"2014","journal-title":"Evolution (N.Y.)"},{"issue":"2","key":"2021092720222091000_msab185-B30","doi-asserted-by":"crossref","first-page":"R18","DOI":"10.1186\/gb-2007-8-2-r18","article-title":"Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over","volume":"8","author":"Haddrill","year":"2007","journal-title":"Genome Biol"},{"issue":"3","key":"2021092720222091000_msab185-B31","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1093\/genetics\/150.3.1143","article-title":"Chromosomal heterozygosity and fertility in house mice (Mus musculus domesticus) from Northern Italy","volume":"150","author":"Hauffe","year":"1998","journal-title":"Genetics"},{"issue":"3","key":"2021092720222091000_msab185-B32","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1017\/S0016672300010156","article-title":"The effect of linkage on limits to artificial selection","volume":"8","author":"Hill","year":"1966","journal-title":"Genet Res"},{"issue":"5","key":"2021092720222091000_msab185-B33","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1093\/bioinformatics\/btv661","article-title":"BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS","volume":"32","author":"Hoff","year":"2016","journal-title":"Bioinformatics"},{"issue":"W1","key":"2021092720222091000_msab185-B35","doi-asserted-by":"crossref","first-page":"W12","DOI":"10.1093\/nar\/gkx428","article-title":"CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features","volume":"45","author":"Kang","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2021092720222091000_msab185-B36","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2016.0458","article-title":"Coevolution between transposable elements and recombination","volume":"372","author":"Kent","year":"2017","journal-title":"Philos Trans R Soc B Biol Sci"},{"issue":"1","key":"2021092720222091000_msab185-B37","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-016-1071-4","article-title":"Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly","volume":"17","author":"Kim","year":"2016","journal-title":"Genome Biol"},{"issue":"3","key":"2021092720222091000_msab185-B38","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1534\/g3.115.023655","article-title":"Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution","volume":"6","author":"Davey","year":"2016","journal-title":"G3 (Bethesda)"},{"key":"2021092720222091000_msab185-B39","first-page":"1","author":"Koren","year":"2016"},{"key":"2021092720222091000_msab185-B40"},{"issue":"3","key":"2021092720222091000_msab185-B41","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1093\/sysbio\/syv007","article-title":"Multilocus species trees show the recent adaptive radiation of the mimetic heliconius butterflies","volume":"64","author":"Kozak","year":"2015","journal-title":"Syst Biol"},{"issue":"9","key":"2021092720222091000_msab185-B42","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res"},{"issue":"39","key":"2021092720222091000_msab185-B43","doi-asserted-by":"crossref","first-page":"eabb8617","DOI":"10.1126\/sciadv.abb8617","article-title":"Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone","volume":"6","author":"Lewis","year":"2020","journal-title":"Sci Adv"},{"issue":"11","key":"2021092720222091000_msab185-B44","doi-asserted-by":"crossref","first-page":"2855","DOI":"10.1016\/j.celrep.2016.08.042","article-title":"ChIP-Seq-annotated Heliconius erato genome highlights patterns of cis-regulatory evolution in Lepidoptera","volume":"16","author":"Lewis","year":"2016","journal-title":"Cell Rep"},{"key":"2021092720222091000_msab185-B45","author":"Lewis","year":"2021"},{"issue":"48","key":"2021092720222091000_msab185-B46","doi-asserted-by":"crossref","first-page":"24174","DOI":"10.1073\/pnas.1907068116","article-title":"Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry","volume":"116","author":"Lewis","year":"2019","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"2021092720222091000_msab185-B47","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1093\/molbev\/msy209","article-title":"Genome-wide regulatory adaptation shapes population-level genomic landscapes in Heliconius","volume":"36","author":"Lewis","year":"2019","journal-title":"Mol Biol Evol"},{"issue":"21","key":"2021092720222091000_msab185-B48","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"2021092720222091000_msab185-B49","first-page":"1","author":"Li","year":"2013"},{"issue":"18","key":"2021092720222091000_msab185-B50","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"issue":"16","key":"2021092720222091000_msab185-B51","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"20","key":"2021092720222091000_msab185-B52","doi-asserted-by":"crossref","first-page":"6494","DOI":"10.1093\/nar\/gki937","article-title":"Gene identification in novel eukaryotic genomes by self-training algorithm","volume":"33","author":"Lomsadze","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2021092720222091000_msab185-B53","doi-asserted-by":"crossref","first-page":"e356","DOI":"10.7717\/peerj.356","article-title":"The complex hybrid origins of the root knot nematodes revealed through comparative genomics","volume":"2","author":"Lunt","year":"2014","journal-title":"PeerJ"},{"issue":"7384","key":"2021092720222091000_msab185-B54","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nature10811","article-title":"The Drosophila melanogaster genetic reference panel","volume":"482","author":"MacKay","year":"2012","journal-title":"Nature"},{"issue":"1)","key":"2021092720222091000_msab185-B55","doi-asserted-by":"crossref","first-page":"3466","DOI":"10.1038\/s41467-019-11308-4","article-title":"The determinants of genetic diversity in butterflies","volume":"10","author":"Mackintosh","year":"2019","journal-title":"Nat Commun"},{"issue":"7","key":"2021092720222091000_msab185-B56","doi-asserted-by":"crossref","first-page":"e1008918","DOI":"10.1371\/journal.pgen.1008918","article-title":"Holocentric chromosomes","volume":"16","author":"Mandrioli","year":"2020","journal-title":"PLoS Genet"},{"issue":"12","key":"2021092720222091000_msab185-B57","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giy131","article-title":"Efficient and accurate detection of splice junctions from RNA-seq with Portcullis","volume":"7","author":"Mapleson","year":"2018","journal-title":"Gigascience"},{"issue":"2","key":"2021092720222091000_msab185-B58","doi-asserted-by":"crossref","first-page":"e2006288","DOI":"10.1371\/journal.pbio.2006288","article-title":"Recombination rate variation shapes barriers to introgression across butterfly genomes","volume":"17","author":"Martin","year":"2019","journal-title":"PLoS Biol"},{"issue":"1","key":"2021092720222091000_msab185-B59","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1534\/genetics.115.183285","article-title":"Natural selection and genetic diversity in the butterfly Heliconius melpomene","volume":"203","author":"Martin","year":"2016","journal-title":"Genetics"},{"issue":"2","key":"2021092720222091000_msab185-B60","doi-asserted-by":"crossref","first-page":"e3000597","DOI":"10.1371\/journal.pbio.3000597","article-title":"Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation","volume":"18","author":"Moest","year":"2020","journal-title":"PLoS Biol"},{"issue":"3","key":"2021092720222091000_msab185-B61","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat Biotechnol"},{"issue":"18","key":"2021092720222091000_msab185-B62","doi-asserted-by":"crossref","first-page":"1651","DOI":"10.1016\/j.cub.2005.07.065","article-title":"Recombination enhances protein adaptation in Drosophila melanogaster","volume":"15","author":"Presgraves","year":"2005","journal-title":"Curr Biol"},{"key":"2021092720222091000_msab185-B63","author":"Qin","year":"2018"},{"issue":"9","key":"2021092720222091000_msab185-B64","doi-asserted-by":"crossref","first-page":"e3000636","DOI":"10.1371\/journal.pbio.3000636","article-title":"Millipede genomes reveal unique adaptations during myriapod evolution","volume":"18","author":"Qu","year":"2020","journal-title":"PLoS Biol"},{"key":"2021092720222091000_msab185-B65","article-title":"The BEDTools manual","author":"Quinlan","year":"2010","journal-title":"Genome"},{"issue":"23","key":"2021092720222091000_msab185-B66","doi-asserted-by":"crossref","first-page":"3726","DOI":"10.1093\/bioinformatics\/btx494","article-title":"Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data","volume":"33","author":"Rastas","year":"2017","journal-title":"Bioinformatics"},{"issue":"8","key":"2021092720222091000_msab185-B67","doi-asserted-by":"crossref","first-page":"2162","DOI":"10.1093\/gbe\/evz125","article-title":"Simultaneous TE analysis of 19 Heliconiine butterflies yields novel insights into rapid TE-based genome diversification and multiple SINE births and deaths","volume":"11","author":"Ray","year":"2019","journal-title":"Genome Biol Evol"},{"key":"2021092720222091000_msab185-B68","author":"Roach","year":"2018"},{"issue":"11","key":"2021092720222091000_msab185-B69","doi-asserted-by":"crossref","first-page":"1928","DOI":"10.1016\/j.biochi.2011.07.014","article-title":"Exonization of transposed elements: a challenge and opportunity for evolution","volume":"93","author":"Schmitz","year":"2011","journal-title":"Biochimie"},{"issue":"6","key":"2021092720222091000_msab185-B70","doi-asserted-by":"crossref","first-page":"R59","DOI":"10.1186\/gb-2010-11-6-r59","article-title":"The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates","volume":"11","author":"Sela","year":"2010","journal-title":"Genome Biol"},{"issue":"1","key":"2021092720222091000_msab185-B71","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/1471-2105-6-31","article-title":"Automated generation of heuristics for biological sequence comparison","volume":"6","author":"Slater","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2021092720222091000_msab185-B72","author":"Smit","year":"2013"},{"issue":"5","key":"2021092720222091000_msab185-B73","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1093\/bioinformatics\/btn013","article-title":"Using native and syntenically mapped cDNA alignments to improve de novo gene finding","volume":"24","author":"Stanke","year":"2008","journal-title":"Bioinformatics"},{"key":"2021092720222091000_msab185-B74","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.cpb.2014.09.002","article-title":"Plant speciation through chromosome instability and ploidy change: cellular mechanisms, molecular factors and evolutionary relevance","volume":"1","author":"De Storme","year":"2014","journal-title":"Curr Plant Biol."},{"issue":"1","key":"2021092720222091000_msab185-B75","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s13059-014-0573-1","article-title":"ALLMAPS: robust scaffold ordering based on multiple maps","volume":"16","author":"Tang","year":"2015","journal-title":"Genome Biol"},{"issue":"3","key":"2021092720222091000_msab185-B76","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat Protoc"},{"issue":"5","key":"2021092720222091000_msab185-B77","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat Biotechnol"},{"issue":"4","key":"2021092720222091000_msab185-B78","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1534\/genetics.120.303680","article-title":"Variation in genetic relatedness is determined by the aggregate recombination process","volume":"216","author":"Veller","year":"2020","journal-title":"Genetics"},{"issue":"5","key":"2021092720222091000_msab185-B79","doi-asserted-by":"crossref","first-page":"1659","DOI":"10.1073\/pnas.1817482116","article-title":"A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel\u2019s second law","volume":"116","author":"Veller","year":"2019","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"2021092720222091000_msab185-B80","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/j.cell.2015.01.006","article-title":"Enhancer evolution across 20 mammalian species","volume":"160","author":"Villar","year":"2015","journal-title":"Cell"},{"issue":"1806","key":"2021092720222091000_msab185-B81","doi-asserted-by":"crossref","first-page":"20190539","DOI":"10.1098\/rstb.2019.0539","article-title":"Speciation through chromosomal fusion and fission in Lepidoptera","volume":"375","author":"de Vos","year":"2020","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"11","key":"2021092720222091000_msab185-B82","doi-asserted-by":"crossref","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"key":"2021092720222091000_msab185-B83","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1111\/j.2041-210X.2011.00153.x","article-title":"smatr 3- an R package for estimation and inference about allometric lines","volume":"3","author":"Warton","year":"2012","journal-title":"Methods Ecol Evol"},{"key":"2021092720222091000_msab185-B84","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1038\/s41587-018-0004-z","article-title":"Errors in long-read assemblies can critically affect protein prediction","volume":"37","author":"Watson","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"1","key":"2021092720222091000_msab185-B85","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giy157","article-title":"LR-Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly","volume":"8","author":"Xu","year":"2019","journal-title":"Gigascience"},{"issue":"1","key":"2021092720222091000_msab185-B86","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-018-4567-3","article-title":"P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads","volume":"19","author":"Zhu","year":"2018","journal-title":"BMC Genomics"}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/mbe\/advance-article-pdf\/doi\/10.1093\/molbev\/msab185\/39726263\/msab185.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/mbe\/article-pdf\/38\/10\/4449\/40449452\/msab185.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/mbe\/article-pdf\/38\/10\/4449\/40449452\/msab185.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,4]],"date-time":"2023-11-04T22:41:14Z","timestamp":1699137674000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article\/38\/10\/4449\/6306414"}},"subtitle":[],"editor":[{"given":"Kelley","family":"Harris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,6,19]]},"references-count":84,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2021,6,19]]},"published-print":{"date-parts":[[2021,9,27]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msab185","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.01.06.425547","asserted-by":"object"}]},"ISSN":["1537-1719"],"issn-type":[{"value":"1537-1719","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,10,1]]},"published":{"date-parts":[[2021,6,19]]}}}