The Theory of Gene Family Histories.
Best matches
Gene family
Horizontal gene transfer
Orthologs
Paralogs
Phylogeny
Protein family
Tree-free methods
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2024
2024
Historique:
medline:
31
5
2024
pubmed:
31
5
2024
entrez:
31
5
2024
Statut:
ppublish
Résumé
Most genes are part of larger families of evolutionary-related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.e., the precise dating of evolutionary events relative to phylogenetic tree of the underlying species has remained a challenging topic despite their importance as a basis for detailed investigations into adaptation and functional evolution of individual members of the gene family. The identification of orthologs, moreover, is a particularly important subproblem of the more general setting considered here. In the last few years, an extensive body of mathematical results has appeared that tightly links orthology, a formal notion of best matches among genes, and horizontal gene transfer. The purpose of this chapter is to broadly outline some of the key mathematical insights and to discuss their implication for practical applications. In particular, we focus on tree-free methods, i.e., methods to infer orthology or horizontal gene transfer as well as gene trees, species trees, and reconciliations between them without using a priori knowledge of the underlying trees or statistical models for the inference of phylogenetic trees. Instead, the initial step aims to extract binary relations among genes.
Identifiants
pubmed: 38819554
doi: 10.1007/978-1-0716-3838-5_1
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1-32Informations de copyright
© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151–1155
pubmed: 11073452
doi: 10.1126/science.290.5494.1151
Cutter AD, Jovelin R (2015) When natural selection gives gene function the cold shoulder. Bioessays 37(11):1169–1173
pubmed: 26411745
pmcid: 4751052
doi: 10.1002/bies.201500083
Innan H, Kondrashov F (2010) The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 11:97–108
pubmed: 20051986
doi: 10.1038/nrg2689
Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C (2012) Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Comp Biol 8:e1002514
doi: 10.1371/journal.pcbi.1002514
Studer RA, Robinson-Rechavi M (2009) How confident can we be that orthologs are similar, but paralogs differ? Trends Genet 25:210–216
pubmed: 19368988
doi: 10.1016/j.tig.2009.03.004
Gabaldón T, Koonin EV (2013) Functional and evolutionary implications of gene orthology. Nat Rev Genet 14(5):360–366
pubmed: 23552219
pmcid: 5877793
doi: 10.1038/nrg3456
Nehrt NL, Clark WT, Radivojac P, Hahn MW (2011) Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS Comput Biol 7:e1002073
pubmed: 21695233
pmcid: 3111532
doi: 10.1371/journal.pcbi.1002073
Sonnhammer E, Gabaldón T, da Silva AWS, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas P, Dessimoz C, the Quest for Orthologs Consortium (2014) Big data and other challenges in the quest for orthologs. Bioinformatics 30(21):2993–2998
doi: 10.1093/bioinformatics/btu492
Ballesteros JA, Hormiga G (2016) A new orthology assessment method for phylogenomic data: Unrooted phylogenetic orthology. Mol Biol Evol 33(8):2117–2134
pubmed: 27189539
doi: 10.1093/molbev/msw069
Menet H, Daubin V, Tannier E (2022) Phylogenetic reconciliation. PLoS Comp Biol 18:e1010621
doi: 10.1371/journal.pcbi.1010621
Fitch WM (1970) Distinguishing homologous from analogous proteins. Syst Zool 19:99–113
pubmed: 5449325
doi: 10.2307/2412448
Fitch WM (2000) Homology: a personal view on some of the problems. Trends Genet 16:227–231
pubmed: 10782117
doi: 10.1016/S0168-9525(00)02005-9
Darby CA, Stolzer M, Ropp PJ, Barker D, Durand D (2017) Xenolog classification. Bioinformatics 33:640–649
pubmed: 27998934
doi: 10.1093/bioinformatics/btw686
Geiß M, González Laffitte ME, López Sánchez A, Valdivia DI, Hellmuth M, Hernández Rosales M, Stadler PF (2020) Best match graphs and reconciliation of gene trees with species trees. J Math Biol 80:1459–1495
pubmed: 32002659
pmcid: 7052050
doi: 10.1007/s00285-020-01469-y
Geiß M, Stadler PF, Hellmuth M (2020) Reciprocal best match graphs. J Math Biol 80:865–953
pubmed: 31691135
doi: 10.1007/s00285-019-01444-2
Stadler PF, Geiß M, Schaller D, López Sánchez A, González Laffitte M, Valdivia DI, Hellmuth M, Hernández Rosales M (2020) From pairs of most similar sequences to phylogenetic best matches. Algorithms Mol Biol 15:5
pubmed: 32308731
pmcid: 7147060
doi: 10.1186/s13015-020-00165-2
Geiß M, Chávez E, González Laffitte M, López Sánchez A, Stadler BMR, Valdivia DI, Hellmuth M, Hernández Rosales M, Stadler PF (2019) Best match graphs. J Math Biol 78(7):2015–2057
pubmed: 30968198
pmcid: 6534531
doi: 10.1007/s00285-019-01332-9
Novichkov PS, Omelchenko MV, Gelfand Mikhail S, Mironov AA, Wolf YI, Koonin EV (2004) Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol 186:6575–6585
pubmed: 15375139
pmcid: 516599
doi: 10.1128/JB.186.19.6575-6585.2004
Schaller D, Lafond M, Stadler PF, Wiesecke N, Hellmuth M (2021) Indirect identification of horizontal gene transfer. J Math Biol 83:10
pubmed: 34218334
pmcid: 8254804
doi: 10.1007/s00285-021-01631-0
Schaller D, Hartmann T, Lafond M, Wieseke N, Hellmuth M, Stadler PF (2023) Relative timing information and orthology in evolutionary scenarios. Alg Mol Biol (in press), preprint arXiv.2212.02201
Doyle VP, Young RE, Naylor GJ, Brown JM (2015) Can we identify genes with increased phylogenetic reliability? Syst Biol 64(5):824–837
pubmed: 26099258
doi: 10.1093/sysbio/syv041
Boussau B, Szöllősi GJ, Duret L, Gouy M, Tannier E, Daubin V (2013) Genome-scale coestimation of species and gene trees. Genome Res 23(2):323–330
Szöllősi GJ, Tannier E, Daubin V, Boussau B (2015) The inference of gene trees with species trees. Syst Biol 64:e42–e62
Altenhoff AM, Dessimoz C (2009) Phylogenetic and functional assessment of orthologs inference projects and methods. PLOS Comp Biol 5:e1000262
doi: 10.1371/journal.pcbi.1000262
Altenhoff AM, Glover NM, Dessimoz C (2019) Inferring orthology and paralogy. In: Evolutionary Genomics, Methods in Molecular Biology, vol 1910. Humana, New York, pp 149–175
doi: 10.1007/978-1-4939-9074-0_5
Ravenhall M, Škunca N, Lassalle F, Dessimoz C (2015) Inferring horizontal gene transfer. PLoS Comp Biol 11:e1004095
doi: 10.1371/journal.pcbi.1004095
Tofigh A, Hallett M, Lagergren J (2011) Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM Trans Comp Biol Bioinf 8(2):517–535
doi: 10.1109/TCBB.2010.14
Chen ZZ, Deng F, Wang L (2012) Simultaneous identification of duplications losses and lateral gene transfers. IEEE/ACM Trans Comp Biol Bioinf 9:1515–1528
doi: 10.1109/TCBB.2012.79
Ma W, Smirnov D, Forman J, Schweickart A, Slocum C, Srinivasan S, Libeskind-Hadas R (2018) DTL-RnB: algorithms and tools for summarizing the space of DTL reconciliations. IEEE/ACM Trans Comp Biol Bioinf 15:411–421
doi: 10.1109/TCBB.2016.2537319
Dufraigne C, Fertil B, Lespinats S, Giron A, Deschavanne P (2005) Detection and characterization of horizontal transfers in prokaryotes using genomic signature. Nucleic Acids Res 33:e6
pubmed: 15653627
pmcid: 546175
doi: 10.1093/nar/gni004
Becq J, Churlaud C, Deschavanne P (2010) A benchmark of parametric methods for horizontal transfers detection. PLoS ONE 5:e9989
pubmed: 20376325
pmcid: 2848678
doi: 10.1371/journal.pone.0009989
Kanhere A, Vingron M (2009) Horizontal gene transfers in prokaryotes show differential preferences for metabolic and translational genes. BMC Evol Biol 9:9
pubmed: 19134215
pmcid: 2651853
doi: 10.1186/1471-2148-9-9
Setubal JC, Stadler PF (2018) Gene phylogenies and orthologous groups. In: Setubal JC, Stadler PF, Stoye J (eds) Comparative Genomics, vol 1704. Springer, Heidelberg, pp 1–28
doi: 10.1007/978-1-4939-7463-4_1
Aho AV, Sagiv Y, Szymanski TG, Ullman JD (1981) Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J Comput 10:405–421
doi: 10.1137/0210030
He YJ, Huynh TND, Jansson J, Sung WK (2006) Inferring phylogenetic relationships avoiding forbidden rooted triplets. J Bioinf Comp Biol 4:59–74
doi: 10.1142/S0219720006001709
Rutschmann F (2006) Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Divers Distrib 12:35–48
doi: 10.1111/j.1366-9516.2006.00210.x
Sauquet H (2013) A practical guide to molecular dating. Comptes Rendus Palevol 12:355–367
doi: 10.1016/j.crpv.2013.07.003
Ford D, Matsen FA, Stadler T (2009) A method for investigating relative timing information on phylogenetic trees. Syst Biol 58:167–183
pubmed: 20525576
doi: 10.1093/sysbio/syp018
Szöllősi G, Höhna S, Williams TA, Schrempf D, Daubin V, Boussau B (2022) Relative time constraints improve molecular dating. Syst Biol 71:797–809
Marques DA, Meier JI, Seehausen O (2019) A combinatorial view on speciation and adaptive radiation. Trends Ecol Evol 34:531–544
pubmed: 30885412
doi: 10.1016/j.tree.2019.02.008
Zheng Y, Zhang L (2014) Effect of incomplete lineage sorting on tree-reconciliation-based inference of gene duplication. IEEE/ACM Trans Comput Biol Bioinform 11:477–485
pubmed: 26356016
doi: 10.1109/TCBB.2013.2297913
Chan YB, Ranwez V, Scornavacca CJ (2017) Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations. Theor Biol 432:1–13
doi: 10.1016/j.jtbi.2017.08.008
Bansal MS, Alm EJ, Kellis M (2012) Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics 28:i283–i291
pubmed: 22689773
pmcid: 3371857
doi: 10.1093/bioinformatics/bts225
Stolzer M, Lai H, Xu M, Sathaye D, Vernot B, Durand D (2012) Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics 28:i409–i415
pubmed: 22962460
pmcid: 3436813
doi: 10.1093/bioinformatics/bts386
Guigó R, Muchnik I, Smith TF (1996) Reconstruction of ancient molecular phylogeny. Mol Phylogenet Evol 6:189–213
pubmed: 8899723
doi: 10.1006/mpev.1996.0071
Page RDM, Charleston MA (1997) From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Mol Phylog Evol 7:231–240
doi: 10.1006/mpev.1996.0390
Zhang L (1997) On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. J Comp Biol 4:177–187
doi: 10.1089/cmb.1997.4.177
Chen K, Durand D, Farach-Colton M (2000) NOTUNG: a program for dating gene duplications and optimizing gene family trees. J Comput Biol 7:e429–e447
doi: 10.1089/106652700750050871
Zmasek CM, Eddy SR (2001) A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17:821–828
pubmed: 11590098
doi: 10.1093/bioinformatics/17.9.821
Górecki P, Burleigh GJ, Eulenstein O (2011) Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. BMC Bioinform 12:S15
doi: 10.1186/1471-2105-12-S1-S15
Arvestad L (2003) Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 19:i7–i15
pubmed: 12855432
doi: 10.1093/bioinformatics/btg1000
Nøjgaard N, Geiß M, Merkle D, Stadler PF, Wieseke N, Hellmuth M (2018) Time-consistent reconciliation maps and forbidden time travel. Alg Mol Biol 13:2
Lafond M, Hellmuth M (2020) Reconstruction of time-consistent species trees. Alg Mol Biol 15:16
Górecki P, Tiuryn J (2006) DLS-trees: a model of evolutionary scenarios. Theor Comp Sci 359:378–399
doi: 10.1016/j.tcs.2006.05.019
Vernot B, Stolzer M, Goldman A, Durand D (2008) Reconciliation with non-binary species trees. J Comput Biol 15:981–1006
pubmed: 18808330
pmcid: 3205801
doi: 10.1089/cmb.2008.0092
Doyon JP, Ranwez V, Daubin V, Berry V (2011) Models, algorithms and programs for phylogeny reconciliation. Brief Bioinform 12:392–400
pubmed: 21949266
doi: 10.1093/bib/bbr045
Rusin LY, Lyubetskaya E, Gorbunov KY, Lyubetsky V (2014) Reconciliation of gene and species trees. BioMed Res Int 2014:642089
pubmed: 24800245
pmcid: 3985182
doi: 10.1155/2014/642089
Hellmuth M (2017) Biologically feasible gene trees, reconciliation maps and informative triples. Alg Mol Biol 12:23
Lechner M, Findeiß S, Steiner L, Marz M, Stadler PF, Prohaska SJ (2011) Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinform 12:124
Schaller D, Geiß M, Chávez E, González Laffitte M, López Sánchez A, Stadler BMR, Valdivia DI, Hellmuth M, Hernández Rosales M, Stadler PF (2021) Corrigendum to “Best Match Graphs”. J Math Biol 82:47
pubmed: 33818665
pmcid: 8021527
doi: 10.1007/s00285-021-01601-6
Schaller D, Stadler PF, Hellmuth M (2021) Complexity of modification problems for best match graphs. Theor Comp Sci 865:63–84
doi: 10.1016/j.tcs.2021.02.037
Maddison W (1989) Reconstructing character evolution on polytomous cladograms. Cladistics 5:365–377
pubmed: 34933477
doi: 10.1111/j.1096-0031.1989.tb00569.x
DeSalle R, Absher R, Amato G (1994) Speciation and phylogenetic resolution. Trends Ecol Evol 9:297–298
pubmed: 21236859
doi: 10.1016/0169-5347(94)90034-5
Walsh HE, Kidd MG, Moum T, Friesen VL (1999) Polytomies and the power of phylogenetic inference. Evolution 53:932–937
pubmed: 28565639
doi: 10.2307/2640732
Schaller D, Geiß M, Stadler PF, Hellmuth M (2021) Complete characterization of incorrect orthology assignments in best match graphs. J Math Biol 82:20
pubmed: 33606106
pmcid: 7894253
doi: 10.1007/s00285-021-01564-8
Schaller D, Geiß M, Hellmuth M, Stadler PF (2021) Best match graphs with binary trees. In: Martín-Vide C, Vega-Rodríguez MA, Wheeler T (eds) Algorithms for Computational Biology, 8th AlCoB, Lect. Notes Comp. Sci., vol 12715, pp 82–93
Schaller D, Geiß M, Hellmuth M, Stadler PF (2021) Heuristic algorithms for best match graph editing. Alg Mol Biol 16:19
Hellmuth M, Hernandez-Rosales M, Huber KT, Moulton V, Stadler PF, Wieseke N (2013) Orthology relations, symbolic ultrametrics, and cographs. J Math Biol 66:399–420
pubmed: 22456957
doi: 10.1007/s00285-012-0525-x
Corneil DG, Lerchs H, Burlingham LS (1981) Complement reducible graphs. Discr Appl Math 3(3):163–174
doi: 10.1016/0166-218X(81)90013-5
Hellmuth M, Geiß M, Stadler PF (2020) Complexity of modification problems for reciprocal best match graphs. Theor Comput Sci 809:384–393
doi: 10.1016/j.tcs.2019.12.033
Liu Y, Wang J, Guo J, Chen J (2012) Complexity and parameterized algorithms for cograph editing. Theor Comp Sci 461:45–54
doi: 10.1016/j.tcs.2011.11.040
White WTJ, Ludwig M, Böcker S (2018) Exact and heuristic algorithms for cograph editing. Tech. Rep. 1711.05839 v3, arXiv
Hellmuth M, Fritz A, Wieseke N, Stadler PF (2020) Techniques for the cograph editing problem: Module merge is equivalent to edit [Formula: see text]’s. Art Discr Appl Math 3:#P2.01
Crespelle C (2021) Linear-time minimal cograph editing. In: Bampis E, Pagourtzis A (eds) Fundamentals of Computation Theory (FCT 2021). Lect. Notes Comp. Sci., vol 12867. Springer, Cham, pp 176–189
doi: 10.1007/978-3-030-86593-1_12
Hernandez-Rosales M, Hellmuth M, Wieseke N, Huber KT, Moulton V, Stadler PF (2012) From event-labeled gene trees to species trees. BMC Bioinform 13(Suppl. 19):S6
doi: 10.1186/1471-2105-13-S19-S6
Lafond M, Dondi R, El-Mabrouk N (2016) The link between orthology relations and gene trees: a correction perspective. Alg Mol Biol 11:4
Lafond M, El-Mabrouk N (2014) Orthology and paralogy constraints: satisfiability and consistency. BMC Genomics 15 S6:S12
Nøjgaard N, El-Mabrouk N, Merkle D, Wieseke N, Hellmuth M (2018) Partial homology relations – satisfiability in terms of di-cographs. In: Wang L, Zhu D (eds) Computing and Combinatorics COCOON’18. Lect. Notes Comp. Sci., vol 10976. Springer, Cham, pp 403–415
doi: 10.1007/978-3-319-94776-1_34
Hellmuth M, Wieseke N, Lechner M, Lenhof HP, Middendorf M, Stadler PF (2015) Phylogenetics from paralogs. Proc Natl Acad Sci USA 112:2058–2063
pubmed: 25646426
pmcid: 4343152
doi: 10.1073/pnas.1412770112
Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631–637
pubmed: 9381173
doi: 10.1126/science.278.5338.631
Roth ACJ, Gonnet GH, Dessimoz C (2008) Algorithm of OMA for large-scale orthology inference. BMC Bioinform 9:518
doi: 10.1186/1471-2105-9-518
Rahmann S, Wittkop T, Baumbach J, Martin M, Truß A, Böcker S (2007) Exact and heuristic algorithms for weighted cluster editing. In: Proceedings of the 6th LSS Conference on Computational Systems Bioinformatics (CSB2007), Life Sciences Society, pp 391–401
Falls C, Powell B, Snœyink J (2008) Computing high-stringency COGs using Turán-type graphs. Tech. rep., U. North Carolina
Tremblay-Savard O, Swenson KM (2012) A graph-theoretic approach for inparalog detection. BMC Bioinform 13:S16
doi: 10.1186/1471-2105-13-S19-S16
Geiß M, Anders J, Stadler PF, Wieseke N, Hellmuth M (2018) Reconstructing gene trees from Fitch’s xenology relation. J Math Biol 77(5):1459–1491
pubmed: 29951855
doi: 10.1007/s00285-018-1260-8
Hellmuth M, Seemann CR (2019) Alternative characterizations of Fitch’s xenology relation. J Math Biol 79(3):969–986
pubmed: 31111195
doi: 10.1007/s00285-019-01384-x
Hellmuth M, Long Y, Geiß M, Stadler PF (2018) A short note on undirected fitch graphs. Art Discr Appl Math 1(1):#P1.08
Hellmuth M, Michel M, Nøjgaard NN, Schaller D, Stadler PF (2021) Combining orthology and xenology data in a common phylogenetic tree. In: Stadler PFS, Walter MEMT, Hernández-Rosales M, Brigido MM (eds) Advances in Bioinformatics and Computational Biology, 14th BSB. Lect. Notes Bioinf, vol 13063. Springer, Cham, pp 53–64
doi: 10.1007/978-3-030-91814-9_5
Shamir R, Sharan R, Tsur D (2004) Cluster graph modification problems. Discrete Appl Math 144(1-2):173–182
doi: 10.1016/j.dam.2004.01.007
Gao Y, Hare DR, Nastos J (2013) The cluster deletion problem for cographs. Discrete Math 313(23):2763–2771
doi: 10.1016/j.disc.2013.08.017
Hellmuth M, Schaller D, Stadler PF (2022) Compatibility of partitions with trees, hierarchies, and split systems. Discr Appl Math 314:265–283
doi: 10.1016/j.dam.2022.03.014
Schaller D, Hellmuth M, Stadler PF (2023) Orientation of Fitch graphs and detection of horizontal gene transfer in gene trees. SIAM J Discr Math 37(3):2172–2207
doi: 10.1137/22M150736X
Gray GS, Fitch WM (1983) Evolution of antibiotic resistance genes: The DNA sequence of a kanamycin resistance gene from Staphylococcus aureus. Mol Biol Evol 1:57–66
pubmed: 6100986
Åkerborg Ö, Sennblad B, Arvestad L, Lagergren J (2009) Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci USA 106(14):5714–5719
pubmed: 19299507
pmcid: 2667006
doi: 10.1073/pnas.0806251106
Larget BR, Kotha SK, Dewey CN, Ané C (2010) BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26(22):2910–2911
pubmed: 20861028
doi: 10.1093/bioinformatics/btq539
Elias I (2006) Settling the intractability of multiple alignment. J Comp Biol 13:1323–1339
doi: 10.1089/cmb.2006.13.1323
Day WHE (1983) Computationally difficult parsimony problems in phylogenetic systematics. J Theor Biol 103:429–438
doi: 10.1016/0022-5193(83)90296-5
Day WHE (1987) Computational complexity of inferring phylogenies from dissimilarity matrices. Bull Math Biol 49:461–467
pubmed: 3664032
doi: 10.1016/S0092-8240(87)80007-1
Roch S (2006) A short proof that phylogenetic tree reconstruction by maximum likelihood is hard. IEEE/ACM Trans Comp Biol Bioinf 3:92–94
doi: 10.1109/TCBB.2006.4
Schaller D, Hellmuth M, Stadler PF (2022) AsymmeTree: A flexible Python package for the simulation of complex gene family histories. Software 1:276–298
doi: 10.3390/software1030013
Merkle D, Middendorf M, Wieseke N (2010) A parameter-adaptive dynamic programming approach for inferring cophylogenies. BMC Bioinform 11(Suppl 1):S60
doi: 10.1186/1471-2105-11-S1-S60
Penel S, Menet H, Tricou T, Daubin V, Tannier E (2022) Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation. Bioinformatics 38(8):2350–2352
pubmed: 35139153
doi: 10.1093/bioinformatics/btac062
Du P, Nakhleh L (2018) Species tree and reconciliation estimation under a duplication-loss-coalescence model. In: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, pp 376–385
Ansarifar J, Markin A, Górecki P, Eulenstein O (2020) Integer linear programming formulation for the unified duplication-loss-coalescence model. In: Cai Z, Mandoiu I, Narasimhan G, Skums P, Guo X (eds) Bioinformatics Research and Applications (ISBRA 2020). Lect. Notes Comp. Sci., vol 12304. Springer, Cham, pp 229–242
doi: 10.1007/978-3-030-57821-3_20
LeMay M, Wu YC, Libeskind-Hadas R (2021) The most parsimonious reconciliation problem in the presence of incomplete lineage sorting and hybridization is NP-hard. In: Carbone A, El-Kebir M (eds) 21st International Workshop on Algorithms in Bioinformatics (WABI 2021), Schloss Dagstuhl – Leibniz-Zentrum für Informatik, Dagstuhl, Germany, Leibniz International Proceedings in Informatics (LIPIcs), vol 201, p 1
Hellmuth M, Huber KT, Moulton V (2019) Reconciling event-labeled gene trees with MUL-trees and species networks. J Math Biol 79(5):1885–1925
pubmed: 31410552
doi: 10.1007/s00285-019-01414-8
Huson DH, Rupp R, Scornavacca C (2010) Phylogenetic networks: concepts, algorithms and applications. Cambridge University Press, Cambridge
doi: 10.1017/CBO9780511974076
To TH, Scornavacca C (2015) Efficient algorithms for reconciling gene trees and species networks via duplication and loss events. BMC Genomics 16(Suppl 10):S6
pubmed: 26449687
pmcid: 4603766
doi: 10.1186/1471-2164-16-S10-S6
Scornavacca C, Pons Mayol JC, Cardona G (2017) Fast algorithm for the reconciliation of gene trees and LGT networks. J Theor Biol 418:129–137
pubmed: 28111320
doi: 10.1016/j.jtbi.2017.01.024
Chan YB, Robin C (2019) Reconciliation of a gene network and species tree. J Theor Biol 472:54–66
pubmed: 30951730
doi: 10.1016/j.jtbi.2019.04.001
Byrka J, Guillemot S, Jansson J (2010) New results on optimizing rooted triplets consistency. Discr Appl Math 158:1136–1147
doi: 10.1016/j.dam.2010.03.004
Morel B, Kozlov AM, Stamatakis A, Szöllősi GJ (2020) 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):2763–2774
Morel B, Schade P, Lutteropp S, Williams TA, Szölloősi GJ, Stamatakis A (2022) SpeciesRax: A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss. Mol Biol Evol 39(2):msab365
Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, Lindblad-Toh K, Haussler D, Karlsson E, Jarvis ED, Zhang G, Paten B (2020) Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 587:246–251
pubmed: 33177663
pmcid: 7673649
doi: 10.1038/s41586-020-2871-y