{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T16:08:42Z","timestamp":1743005322192,"version":"3.40.3"},"publisher-location":"Cham","reference-count":35,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783031062193"},{"type":"electronic","value":"9783031062209"}],"license":[{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022]]},"DOI":"10.1007\/978-3-031-06220-9_10","type":"book-chapter","created":{"date-parts":[[2022,5,14]],"date-time":"2022-05-14T12:10:26Z","timestamp":1652530226000},"page":"168-186","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["On Partial Gene Transfer and\u00a0Its Impact on\u00a0Gene Tree Reconstruction"],"prefix":"10.1007","author":[{"given":"Sumaira","family":"Zaman","sequence":"first","affiliation":[]},{"given":"Mukul S.","family":"Bansal","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,5,15]]},"reference":[{"issue":"8","key":"10_CR1","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1093\/bioinformatics\/btu806","volume":"31","author":"MS Bansal","year":"2015","unstructured":"Bansal, M.S., Wu, Y.C., Alm, E.J., Kellis, M.: Improved gene tree error correction in the presence of horizontal gene transfer. Bioinformatics 31(8), 1211\u20131218 (2015). https:\/\/doi.org\/10.1093\/bioinformatics\/btu806","journal-title":"Bioinformatics"},{"key":"10_CR2","doi-asserted-by":"crossref","unstructured":"Bay, R.A., Bielawski, J.P.: Recombination detection under evolutionary scenarios relevant to functional divergence. J. Mol. Evol. 73, 273\u2013286 (2011)","DOI":"10.1007\/s00239-011-9473-0"},{"issue":"21","key":"10_CR3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr735","volume":"39","author":"A Boc","year":"2011","unstructured":"Boc, A., Makarenkov, V.: Towards an accurate identification of mosaic genes and partial horizontal gene transfers. Nucleic Acids Res. 39(21), e144 (2011)","journal-title":"Nucleic Acids Res."},{"key":"10_CR4","doi-asserted-by":"publisher","first-page":"67","DOI":"10.4137\/EBO.S2242","volume":"5","author":"B Boussau","year":"2009","unstructured":"Boussau, B., Gu\u00e9guen, L., Gouy, M.: A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies. Evol. Bioinform. Online 5, 67\u201379 (2009)","journal-title":"Evol. Bioinform. Online"},{"key":"10_CR5","doi-asserted-by":"publisher","first-page":"1994","DOI":"10.1038\/s41396-018-0150-9","volume":"12","author":"H Brinkmann","year":"2018","unstructured":"Brinkmann, H., G\u00f6ker, M., Kobl\u00edzek, M., Wagner-D\u00f6bler, I., Petersen, J.: Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae. ISME J. 12, 1994\u20132010 (2018)","journal-title":"ISME J."},{"key":"10_CR6","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1093\/gbe\/evp044","volume":"1","author":"CX Chan","year":"2009","unstructured":"Chan, C.X., Beiko, R.G., Darling, A.E., Ragan, M.A.: Lateral transfer of genes and gene fragments in prokaryotes. Genome Biol. Evol. 1, 429\u2013438 (2009). https:\/\/doi.org\/10.1093\/gbe\/evp044","journal-title":"Genome Biol. Evol."},{"key":"10_CR7","doi-asserted-by":"publisher","unstructured":"Chan, C.X., Darling, A.E., Beiko, R.G., Ragan, M.A.: Are protein domains modules of lateral genetic transfer? PLoS ONE 4(2), e4524 (2009). https:\/\/doi.org\/10.1371\/journal.pone.0004524","DOI":"10.1371\/journal.pone.0004524"},{"key":"10_CR8","doi-asserted-by":"crossref","unstructured":"David, L.A., Alm, E.J.: Rapid evolutionary innovation during an archaean genetic expansion. Nature 469, 93\u201396 (2011)","DOI":"10.1038\/nature09649"},{"key":"10_CR9","doi-asserted-by":"publisher","unstructured":"Dunning, L.T., et al.: Lateral transfers of large DNA fragments spread functional genes among grasses. Proc. Natl. Acad. Sci. 116(10), 4416\u20134425 (2019). https:\/\/doi.org\/10.1073\/pnas.1810031116","DOI":"10.1073\/pnas.1810031116"},{"issue":"3","key":"10_CR10","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1093\/bioinformatics\/bth500","volume":"21","author":"GJ Etherington","year":"2004","unstructured":"Etherington, G.J., Dicks, J., Roberts, I.N.: Recombination analysis tool (RAT): a program for the high-throughput detection of recombination. Bioinformatics 21(3), 278\u2013281 (2004)","journal-title":"Bioinformatics"},{"issue":"12","key":"10_CR11","doi-asserted-by":"publisher","first-page":"2226","DOI":"10.1093\/oxfordjournals.molbev.a004046","volume":"19","author":"JP Gogarten","year":"2002","unstructured":"Gogarten, J.P., Doolittle, W.F., Lawrence, J.G.: Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19(12), 2226\u20132238 (2002)","journal-title":"Mol. Biol. Evol."},{"issue":"13","key":"10_CR12","doi-asserted-by":"publisher","first-page":"2056","DOI":"10.1093\/bioinformatics\/btw105","volume":"32","author":"E Jacox","year":"2016","unstructured":"Jacox, E., Chauve, C., Szollosi, G.J., Ponty, Y., Scornavacca, C.: ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. Bioinformatics 32(13), 2056 (2016). https:\/\/doi.org\/10.1093\/bioinformatics\/btw105","journal-title":"Bioinformatics"},{"issue":"6","key":"10_CR13","doi-asserted-by":"publisher","first-page":"2639","DOI":"10.1093\/molbev\/msab043","volume":"38","author":"L Kloub","year":"2021","unstructured":"Kloub, L., Gosselin, S., Fullmer, M., Graf, J., Gogarten, J.P., Bansal, M.S.: Systematic detection of large-scale multigene horizontal transfer in prokaryotes. Mol. Biol. Evol. 38(6), 2639\u20132659 (2021). https:\/\/doi.org\/10.1093\/molbev\/msab043","journal-title":"Mol. Biol. Evol."},{"issue":"21","key":"10_CR14","doi-asserted-by":"publisher","first-page":"6688","DOI":"10.1093\/nar\/gkn668","volume":"36","author":"EV Koonin","year":"2008","unstructured":"Koonin, E.V., Wolf, Y.I.: Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res. 36(21), 6688\u20136719 (2008). https:\/\/doi.org\/10.1093\/nar\/gkn668","journal-title":"Nucleic Acids Res."},{"key":"10_CR15","doi-asserted-by":"publisher","unstructured":"Kordi, M., Bansal, M.S.: TreeSolve: Rapid Error-Correction of Microbial Gene Trees. In: Mart\u00edn-Vide, C., Vega-Rodr\u00edguez, M.A., Wheeler, T. (eds.) AlCoB 2020. LNCS, vol. 12099, pp. 125\u2013139. Springer, Cham (2020). https:\/\/doi.org\/10.1007\/978-3-030-42266-0_10","DOI":"10.1007\/978-3-030-42266-0_10"},{"issue":"18","key":"10_CR16","doi-asserted-by":"publisher","first-page":"3496","DOI":"10.1093\/bioinformatics\/btz081","volume":"35","author":"S Kundu","year":"2019","unstructured":"Kundu, S., Bansal, M.S.: SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution. Bioinformatics 35(18), 3496\u20133498 (2019)","journal-title":"Bioinformatics"},{"issue":"6","key":"10_CR17","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1093\/sysbio\/syw042","volume":"65","author":"PO Lewis","year":"2016","unstructured":"Lewis, P.O., Chen, M.H., Kuo, L., Lewis, L.A., Fucikova, K., Neupane, S., Wang, Y.B., Shi, D.: Estimating bayesian phylogenetic information content. Syst. Biol. 65(6), 1009\u20131023 (2016). https:\/\/doi.org\/10.1093\/sysbio\/syw042","journal-title":"Syst. Biol."},{"key":"10_CR18","doi-asserted-by":"crossref","unstructured":"Lole, K.S., et al.: Full-length human immunodeficiency virus type 1 genomes from subtype c-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73(1), 152\u2013160 (1999)","DOI":"10.1128\/JVI.73.1.152-160.1999"},{"issue":"6","key":"10_CR19","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1111\/j.1755-0998.2011.03026.x","volume":"11","author":"DP Martin","year":"2011","unstructured":"Martin, D.P., Lemey, P., Posada, D.: Analysing recombination in nucleotide sequences. Mol. Ecol. Resour. 11(6), 943\u2013955 (2011). https:\/\/doi.org\/10.1111\/j.1755-0998.2011.03026.x","journal-title":"Mol. Ecol. Resour."},{"key":"10_CR20","doi-asserted-by":"crossref","unstructured":"Martin, D.P., Murrell, B., Golden, M., Khoosal, A., Muhire, B.: RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1(1) (2015)","DOI":"10.1093\/ve\/vev003"},{"issue":"9","key":"10_CR21","doi-asserted-by":"publisher","first-page":"2763","DOI":"10.1093\/molbev\/msaa141","volume":"37","author":"B Morel","year":"2020","unstructured":"Morel, B., Kozlov, A.M., Stamatakis, A., Szollosi, G.J.: GeneRax: a tool for species-tree-aware maximum likelihood-based gene family tree inference under gene duplication, transfer, and loss. Mol. Biol. Evol. 37(9), 2763\u20132774 (2020). https:\/\/doi.org\/10.1093\/molbev\/msaa141","journal-title":"Mol. Biol. Evol."},{"key":"10_CR22","doi-asserted-by":"publisher","unstructured":"Nguyen, T.H., Doyon, J.-P., Pointet, S., Arigon Chifolleau, A.-M., Ranwez, V., Berry, V.: Accounting for gene tree uncertainties improves gene trees and reconciliation inference. In: Raphael, B., Tang, J. (eds.) WABI 2012. LNCS, vol. 7534, pp. 123\u2013134. Springer, Heidelberg (2012). https:\/\/doi.org\/10.1007\/978-3-642-33122-0_10","DOI":"10.1007\/978-3-642-33122-0_10"},{"key":"10_CR23","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.3389\/fmicb.2017.01350","volume":"8","author":"J Petersen","year":"2017","unstructured":"Petersen, J., Wagner-Dobler, I.: Plasmid transfer in the ocean - a case study from the roseobacter group. Front. Microbiol. 8, 1350 (2017). https:\/\/doi.org\/10.3389\/fmicb.2017.01350","journal-title":"Front. Microbiol."},{"issue":"3","key":"10_CR24","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1016\/j.tig.2012.12.006","volume":"29","author":"MF Polz","year":"2013","unstructured":"Polz, M.F., Alm, E.J., Hanage, W.P.: Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet. 29(3), 170\u2013175 (2013)","journal-title":"Trends Genet."},{"key":"10_CR25","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1007\/s00239-001-0034-9","volume":"54","author":"D Posada","year":"2002","unstructured":"Posada, D., Crandall, K.: The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54, 396\u2013402 (2002)","journal-title":"J. Mol. Evol."},{"key":"10_CR26","doi-asserted-by":"publisher","unstructured":"Rambaut, A., Grass, N.C.: Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Bioinformatics 13(3), 235\u2013238 (1997). https:\/\/doi.org\/10.1093\/bioinformatics\/13.3.235","DOI":"10.1093\/bioinformatics\/13.3.235"},{"key":"10_CR27","doi-asserted-by":"publisher","unstructured":"Rangel, L.T., Marden, J., Colston, S., Setubal, J.C., Graf, J., Gogarten, J.P.: Identification and characterization of putative Aeromonas spp. T3SS effectors. PLOS ONE 14(6), 1\u201320 (2019). https:\/\/doi.org\/10.1371\/journal.pone.0214035","DOI":"10.1371\/journal.pone.0214035"},{"key":"10_CR28","doi-asserted-by":"publisher","unstructured":"Ravenhall, M., \u0160kunca, N., Lassalle, F., Dessimoz, C.: Inferring horizontal gene transfer. PLOS Comput. Biol. 11(5), 1\u201316 (2015). https:\/\/doi.org\/10.1371\/journal.pcbi.1004095","DOI":"10.1371\/journal.pcbi.1004095"},{"issue":"1","key":"10_CR29","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/0025-5564(81)90043-2","volume":"53","author":"DF Robinson","year":"1981","unstructured":"Robinson, D.F., Foulds, L.R.: Comparison of phylogenetic trees. Math. Biosci. 53(1), 131\u2013147 (1981)","journal-title":"Math. Biosci."},{"issue":"3","key":"10_CR30","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1093\/sysbio\/syu007","volume":"63","author":"J Sjostrand","year":"2014","unstructured":"Sjostrand, J., Tofigh, A., Daubin, V., Arvestad, L., Sennblad, B., Lagergren, J.: A bayesian method for analyzing lateral gene transfer. Syst. Biol. 63(3), 409\u2013420 (2014). https:\/\/doi.org\/10.1093\/sysbio\/syu007","journal-title":"Syst. Biol."},{"issue":"9","key":"10_CR31","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"A Stamatakis","year":"2014","unstructured":"Stamatakis, A.: RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9), 1312\u20131313 (2014)","journal-title":"Bioinformatics"},{"issue":"6","key":"10_CR32","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1093\/sysbio\/syt054","volume":"62","author":"GJ Szollosi","year":"2013","unstructured":"Szollosi, G.J., Rosikiewicz, W., Boussau, B., Tannier, E., Daubin, V.: Efficient exploration of the space of reconciled gene trees. Syst. Biol. 62(6), 901\u2013912 (2013)","journal-title":"Syst. Biol."},{"issue":"10","key":"10_CR33","doi-asserted-by":"publisher","first-page":"5889","DOI":"10.1128\/IAI.68.10.5889-5900.2000","volume":"68","author":"EI Tuomanen","year":"2000","unstructured":"Tuomanen, E.I., Hollingshead, S.K., Becker, R., Briles, D.E.: Diversity of PspA: mosaic genes and evidence for past recombination in streptococcus pneumoniae. Infect. Immun. 68(10), 5889\u20135900 (2000). https:\/\/doi.org\/10.1128\/IAI.68.10.5889-5900.2000","journal-title":"Infect. Immun."},{"issue":"3","key":"10_CR34","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1093\/oxfordjournals.molbev.a025929","volume":"15","author":"GF Weiller","year":"1998","unstructured":"Weiller, G.F.: Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol. Biol. Evol. 15(3), 326\u2013335 (1998)","journal-title":"Mol. Biol. Evol."},{"issue":"5","key":"10_CR35","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1016\/j.tig.2004.03.009","volume":"20","author":"O Zhaxybayeva","year":"2004","unstructured":"Zhaxybayeva, O., Lapierre, P., Gogarten, J.P.: Genome mosaicism and organismal lineages. Trends Genet. 20(5), 254\u2013260 (2004)","journal-title":"Trends Genet."}],"container-title":["Lecture Notes in Computer Science","Comparative Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-031-06220-9_10","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,14]],"date-time":"2022-05-14T12:12:02Z","timestamp":1652530322000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-06220-9_10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022]]},"ISBN":["9783031062193","9783031062209"],"references-count":35,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-06220-9_10","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2022]]},"assertion":[{"value":"15 May 2022","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"RECOMB-CG","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"RECOMB International Workshop on Comparative Genomics","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"La Jolla, CA","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"USA","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2022","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"20 May 2022","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"21 May 2022","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"19","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"rcg2022","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/recombcg2022.usask.ca\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"28","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"18","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"64% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"4","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"2","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"No","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}