Incomplete lineage sorting and phenotypic evolution in marsupials

Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS le...

Full description

Autores:: Feng, Shaohong
Bai, Ming
Rivas-González, Iker
Li, Cai
Liu, Shiping
Tong, Yijie
Yang, Haidong
Chen, Guangji
Xie, Duo
Sears, Karen E
Franco, Lida M
Gaitan-Espitia, Juan Diego

Tipo de recurso:: Article of journal

Fecha de publicación:: 2022

Institución:: Universidad de Ibagué

Repositorio:: Repositorio Universidad de Ibagué

Idioma:: eng

id	UNIBAGUE2_53b7fcb1b7d55fbdde1d88d8402e6e10
oai_identifier_str	oai:repositorio.unibague.edu.co:20.500.12313/3840
network_acronym_str	UNIBAGUE2
network_name_str	Repositorio Universidad de Ibagué
repository_id_str
dc.title.eng.fl_str_mv	Incomplete lineage sorting and phenotypic evolution in marsupials
title	Incomplete lineage sorting and phenotypic evolution in marsupials
spellingShingle	Incomplete lineage sorting and phenotypic evolution in marsupials Phylogenetic inference Rapid speciation Gene-phenotype incongruence Hemiplasy Incomplete lineage sorting CoalHMM Marsupial Monito del monte Trait evolution Biogeography
title_short	Incomplete lineage sorting and phenotypic evolution in marsupials
title_full	Incomplete lineage sorting and phenotypic evolution in marsupials
title_fullStr	Incomplete lineage sorting and phenotypic evolution in marsupials
title_full_unstemmed	Incomplete lineage sorting and phenotypic evolution in marsupials
title_sort	Incomplete lineage sorting and phenotypic evolution in marsupials
dc.creator.fl_str_mv	Feng, Shaohong Bai, Ming Rivas-González, Iker Li, Cai Liu, Shiping Tong, Yijie Yang, Haidong Chen, Guangji Xie, Duo Sears, Karen E Franco, Lida M Gaitan-Espitia, Juan Diego
dc.contributor.author.none.fl_str_mv	Feng, Shaohong Bai, Ming Rivas-González, Iker Li, Cai Liu, Shiping Tong, Yijie Yang, Haidong Chen, Guangji Xie, Duo Sears, Karen E Franco, Lida M Gaitan-Espitia, Juan Diego
dc.subject.proposal.eng.fl_str_mv	Phylogenetic inference Rapid speciation Gene-phenotype incongruence Hemiplasy Incomplete lineage sorting CoalHMM Marsupial Monito del monte Trait evolution Biogeography
topic	Phylogenetic inference Rapid speciation Gene-phenotype incongruence Hemiplasy Incomplete lineage sorting CoalHMM Marsupial Monito del monte Trait evolution Biogeography
description	Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya.
publishDate	2022
dc.date.issued.none.fl_str_mv	2022-05-12
dc.date.accessioned.none.fl_str_mv	2023-10-17T20:55:47Z
dc.date.available.none.fl_str_mv	2023-10-17T20:55:47Z
dc.type.none.fl_str_mv	Artículo de revista
dc.type.coar.fl_str_mv	http://purl.org/coar/resource_type/c_2df8fbb1
dc.type.coar.none.fl_str_mv	http://purl.org/coar/resource_type/c_6501
dc.type.coarversion.none.fl_str_mv	http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.content.none.fl_str_mv	Text
dc.type.driver.none.fl_str_mv	info:eu-repo/semantics/article
dc.type.redcol.none.fl_str_mv	http://purl.org/redcol/resource_type/ART
dc.type.version.none.fl_str_mv	info:eu-repo/semantics/publishedVersion
format	http://purl.org/coar/resource_type/c_6501
status_str	publishedVersion
dc.identifier.citation.none.fl_str_mv	Shaohong Feng, Ming Bai, Iker Rivas-González, Cai Li, Shiping Liu, Yijie Tong, Haidong Yang, Guangji Chen, Duo Xie, Karen E. Sears, Lida M. Franco, Juan Diego Gaitan-Espitia, Roberto F. Nespolo, Warren E. Johnson, Huanming Yang, Parice A. Brandies, Carolyn J. Hogg, Katherine Belov, Marilyn B. Renfree, Kristofer M. Helgen, Jacobus J. Boomsma, Mikkel Heide Schierup, Guojie Zhang, Incomplete lineage sorting and phenotypic evolution in marsupials, Cell, Volume 185, Issue 10, 2022, Pages 1646-1660.e18, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2022.03.034. (https://www.sciencedirect.com/science/article/pii/S0092867422003440)
dc.identifier.issn.none.fl_str_mv	00928674
dc.identifier.uri.none.fl_str_mv	https://hdl.handle.net/20.500.12313/3840
identifier_str_mv	Shaohong Feng, Ming Bai, Iker Rivas-González, Cai Li, Shiping Liu, Yijie Tong, Haidong Yang, Guangji Chen, Duo Xie, Karen E. Sears, Lida M. Franco, Juan Diego Gaitan-Espitia, Roberto F. Nespolo, Warren E. Johnson, Huanming Yang, Parice A. Brandies, Carolyn J. Hogg, Katherine Belov, Marilyn B. Renfree, Kristofer M. Helgen, Jacobus J. Boomsma, Mikkel Heide Schierup, Guojie Zhang, Incomplete lineage sorting and phenotypic evolution in marsupials, Cell, Volume 185, Issue 10, 2022, Pages 1646-1660.e18, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2022.03.034. (https://www.sciencedirect.com/science/article/pii/S0092867422003440) 00928674
url	https://hdl.handle.net/20.500.12313/3840
dc.language.iso.none.fl_str_mv	eng
language	eng
dc.relation.citationendpage.none.fl_str_mv	1660
dc.relation.citationissue.none.fl_str_mv	10
dc.relation.citationstartpage.none.fl_str_mv	1646
dc.relation.citationvolume.none.fl_str_mv	185
dc.relation.ispartofjournal.none.fl_str_mv	Cell
dc.relation.references.none.fl_str_mv	L. Almasy, J. Blangero Multipoint quantitative-trait linkage analysis in general pedigrees Am. J. Hum. Genet., 62 (1998), pp. 1198-1211 S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman Basic local alignment search tool J. Mol. Biol., 215 (1990), pp. 403-410 H. Amrine-Madsen, M. Scally, M. Westerman, M.J. Stanhope, C. Krajewski, M.S. Springer Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials Mol. Phylogenet. Evol., 28 (2003), pp. 186-196 J.C. Avise, T.J. Robinson Hemiplasy: a new term in the lexicon of phylogenetics Syst. Biol., 57 (2008), pp. 503-507 M. Bai, R.G. Beutel, K.-D. Klass, W. Zhang, X. Yang, B. Wipfler Alienoptera—a new insect order in the roach–mantodean twilight zone Gondwana Res., 39 (2016), pp. 317-326 M. Bai, R.G. Beutel, W. Zhang, S. Wang, M. Hörnig, C. Gröhn, E. Yan, X. Yang, B. Wipfler A new Cretaceous insect with a unique cephalo-thoracic scissor device Curr. Biol., 28 (2018), pp. 438-443.e1 M. Bai, X. Yang, J. Li, W. Wang Geometric morphometrics, a super scientific computing tool in morphology comparison Sci. Bull., 59 (2014), pp. 887-894 A.K. Behrensmeyer, A. Turner Taxonomic occurrences of Suidae recorded in the Paleobiology Database Fossilworks (2013) G. Benson Tandem repeats finder: a program to analyze DNA sequences Nucleic Acids Res., 27 (1999), pp. 573-580 E. Birney, M. Clamp, R. Durbin GeneWise and Genomewise Genome Res., 14 (2004), pp. 988-995 M. Blanchette, W.J. Kent, C. Riemer, L. Elnitski, A.F. Smit, K.M. Roskin, R. Baertsch, K. Rosenbloom, H. Clawson, E.D. Green, et al. Aligning multiple genomic sequences with the threaded blockset aligner Genome Res., 14 (2004), pp. 708-715 M. Boetzer, C.V. Henkel, H.J. Jansen, D. Butler, W. Pirovano Scaffolding pre-assembled contigs using SSPACE Bioinformatics, 27 (2011), pp. 578-579 P.A. Brandies, S. Tang, R.S.P. Johnson, C.J. Hogg, K. Belov The first Antechinus reference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies Gigabyte, 1 (2020), p. 7 G.A. Bravo, A. Antonelli, C.D. Bacon, K. Bartoszek, M.P.K. Blom, S. Huynh, G. Jones, L.L. Knowles, S. Lamichhaney, T. Marcussen, et al. Embracing heterogeneity: coalescing the tree of life and the future of phylogenomics PeerJ, 7 (2019), p. e6399 A.A. Burbidge, J. Woinarski Macropus eugenii. The IUCN Red List of Threatened Species 2016 (2016), A. Burk, M. Westerman, D.J. Kao, J.R. Kavanagh, M.S. Springer An analysis of marsupial interordinal relationships based on 12S rRNA, tRNA valine, 16S rRNA, and cytochrome b sequences J. Mamm. Evol., 6 (1999), pp. 317-334 S. Burnett, C. Dickman Antechinus stuartii. The IUCN Red List of Threatened Species 2016 (2016), C. Darwin The Origin of Species John Murray (1859) L.M. Dávalos, A.L. Cirranello, J.H. Geisler, N.B. Simmons Understanding phylogenetic incongruence: lessons from phyllostomid bats Biol. Rev. Camb. Philos. Soc., 87 (2012), pp. 991-1024 J.H. Degnan, N.A. Rosenberg Gene tree discordance, phylogenetic inference and the multispecies coalescent Trends Ecol. Evol., 24 (2009), pp. 332-340 D.A. Duchêne, J.G. Bragg, S. Duchêne, L.E. Neaves, S. Potter, C. Moritz, R.N. Johnson, S.Y.W. Ho, M.D.B. Eldridge Analysis of phylogenomic tree space resolves relationships among marsupial families Syst. Biol., 67 (2018), pp. 400-412 J.Y. Dutheil, G. Ganapathy, A. Hobolth, T. Mailund, M.K. Uyenoyama, M.H. Schierup Ancestral population genomics: the coalescent hidden Markov model approach Genetics, 183 (2009), pp. 259-274 N.B. Edelman, P.B. Frandsen, M. Miyagi, B. Clavijo, J. Davey, R.B. Dikow, G. García-Accinelli, S.M. Van Belleghem, N. Patterson, D.E. Neafsey, et al. Genomic architecture and introgression shape a butterfly radiation Science, 366 (2019), pp. 594-599 D. Flores, N. de la Sancha Monodelphis domestica. The IUCN Red List of Threatened Species. Version 2016.2 (2016) M.C. Fontaine, J.B. Pease, A. Steele, R.M. Waterhouse, D.E. Neafsey, I.V. Sharakhov, X. Jiang, A.B. Hall, F. Catteruccia, E. Kakani, et al. Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics Science, 347 (2015), p. 1258524 G.J. Frankham, P.D. Temple-Smith Absence of mammary development in male Dromiciops gliroides: another link to the Australian marsupial fauna J. Mammal., 93 (2012), pp. 572-578 M.H. Gallardo, B.D. Patterson An additional 14-chromosome karyotype and sex-chromosome mosaicism in South American marsupials Fieldiana Zool., 39 (1987), pp. 111-116 S. Gallus, A. Janke, V. Kumar, M.A. Nilsson Disentangling the relationship of the Australian marsupial orders using retrotransposon and evolutionary network analyses Genome Biol. Evol., 7 (2015), pp. 985-992 P. Gaubert, W.C. Wozencraft, P. Cordeiro-Estrela, G. Veron Mosaics of convergences and noise in morphological phylogenies: what's in a viverrid-like carnivoran? Syst. Biol., 54 (2005), pp. 865-894 F.J. Goin, M.A. Abello Los Metatheria sudamericanos de comienzos del Neógeno (Mioceno temprano, edad mamífero Colhuehuapense): Microbiotheria y Polydolopimorphia Ameghiniana, 50 (2013), pp. 51-78 R.E. Green, J. Krause, A.W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, M.H. Fritz, et al. A draft sequence of the Neandertal genome Science, 328 (2010), pp. 710-722 Y. Gurovich, K.W. Ashwell Brain and behavior of Dromiciops gliroides J. Mamm. Evol., 27 (2020), pp. 177-197 M. Haeussler, A.S. Zweig, C. Tyner, M.L. Speir, K.R. Rosenbloom, B.J. Raney, C.M. Lee, B.T. Lee, A.S. Hinrichs, J.N. Gonzalez, et al. The UCSC Genome Browser database: 2019 update Nucleic Acids Res., 47 (2019), pp. D853-D858 R.S. Harris Improved Pairwise Alignment Of Genomic DNA The Pennsylvania State University (2007) C. Hawkins, H. McCallum, N. Mooney, M. Jones, M. Holdsworth Sarcophilus harrisii IUCN red list of threatened species. Version 2009.1 (2008) K. Henderson, J. Pantinople, K. McCabe, H.L. Richards, N. Milne Forelimb bone curvature in terrestrial and arboreal mammals PeerJ, 5 (2017), p. e3229 A. Hobolth, O.F. Christensen, T. Mailund, M.H. Schierup Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model PLoS Genet., 3 (2007), p. e7 A. Hobolth, J.Y. Dutheil, J. Hawks, M.H. Schierup, T. Mailund Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection Genome Res., 21 (2011), pp. 349-356 R. Hope, S. Cooper, B. Wainwright Globin macromolecular sequences in marsupials and monotremes Aust. J. Zool., 37 (1989), pp. 289-313 I. Horovitz, M.R. Sánchez-Villagra A morphological analysis of marsupial mammal higher-level phylogenetic relationships Cladistics, 19 (2003), pp. 181-212 E.D. Jarvis, S. Mirarab, A.J. Aberer, B. Li, P. Houde, C. Li, S.Y. Ho, B.C. Faircloth, B. Nabholz, J.T. Howard, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds Science, 346 (2014), pp. 1320-1331 R.N. Johnson, D. O'Meally, Z. Chen, G.J. Etherington, S.Y.W. Ho, W.J. Nash, C.E. Grueber, Y. Cheng, C.M. Whittington, S. Dennison, et al. Adaptation and conservation insights from the koala genome Nat. Genet., 50 (2018), pp. 1102-1111 S. Kalyaanamoorthy, B.Q. Minh, T.K.F. Wong, A. von Haeseler, L.S. Jermiin ModelFinder: fast model selection for accurate phylogenetic estimates Nat. Methods, 14 (2017), pp. 587-589 K. Katoh, D.M. Standley MAFFT multiple sequence alignment software version 7: improvements in performance and usability Mol. Biol. Evol., 30 (2013), pp. 772-780 D. Katz, M. Friess Technical note: 3D from standard digital photography of human crania-a preliminary assessment Am. J. Phys. Anthropol., 154 (2014), pp. 152-158 M. Kearse, R. Moir, A. Wilson, S. Stones-Havas, M. Cheung, S. Sturrock, S. Buxton, A. Cooper, S. Markowitz, C. Duran, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data Bioinformatics, 28 (2012), pp. 1647-1649 H. Kiyonari, M. Kaneko, T. Abe, A. Shiraishi, R. Yoshimi, K.I. Inoue, Y. Furuta Targeted gene disruption in a marsupial, Monodelphis domestica, by CRISPR/Cas9 genome editing Curr. Biol., 31 (2021), pp. 3956-3963.e4 A. Kuritzin, T. Kischka, J. Schmitz, G. Churakov Incomplete lineage sorting and hybridization statistics for large-scale retroposon insertion data PLoS Comput. Biol., 12 (2016), p. e1004812 S. Lamichhaney, J. Berglund, M.S. Almén, K. Maqbool, M. Grabherr, A. Martinez-Barrio, M. Promerová, C.-J. Rubin, C. Wang, N. Zamani, et al. Evolution of Darwin’s finches and their beaks revealed by genome sequencing Nature, 518 (2015), pp. 371-375 A. Larson The comparison of morphological and molecular data in phylogenetic systematics. Molecular Approaches to Ecology and Evolution Springer (1998), pp. 275-296 J.M. Lee, H.J. Song, S.I. Park, Y.M. Lee, S.Y. Jeong, T.O. Cho, J.H. Kim, H.G. Choi, C.G. Choi, W.A. Nelson, et al. Mitochondrial and plastid genomes from coralline red algae provide insights into the incongruent evolutionary histories of organelles Genome Biol. Evol., 10 (2018), pp. 2961-2972 Y.S. Lee, S.J. Lee Regulation of GDF-11 and myostatin activity by GASP-1 and GASP-2 Proc. Natl. Acad. Sci. USA, 110 (2013), pp. E3713-E3722 R. Li, W. Fan, G. Tian, H. Zhu, L. He, J. Cai, Q. Huang, Q. Cai, B. Li, Y. Bai, et al. The sequence and de novo assembly of the giant panda genome Nature, 463 (2010), pp. 311-317 R. Livermore, A. Nankivell, G. Eagles, P. Morris Palaeogene opening of Drake Passage Earth Planet. Sci. Lett., 236 (2005), pp. 459-470 F. Lopes, L.R. Oliveira, A. Kessler, Y. Beux, E. Crespo, S. Cárdenas-Alayza, P. Majluf, M. Sepúlveda, R.L. Brownell, V. Franco-Trecu, et al. Phylogenomic discordance in the eared seals is best explained by incomplete lineage sorting following explosive radiation in the Southern hemisphere Syst. Biol., 70 (2021), pp. 786-802 J.B. Losos Adaptive radiation, ecological opportunity, and evolutionary determinism. American Society of Naturalists E.O. Wilson award address Am. Nat., 175 (2010), pp. 623-639 R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang, J. Yuan, G. He, Y. Chen, Q. Pan, Y. Liu, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler GigaScience, 1 (2012), p. 18 Z.X. Luo, Q. Ji, J.R. Wible, C.X. Yuan An Early Cretaceous tribosphenic mammal and metatherian evolution Science, 302 (2003), pp. 1934-1940 Z.X. Luo, C.X. Yuan, Q.J. Meng, Q. Ji A Jurassic eutherian mammal and divergence of marsupials and placentals Nature, 476 (2011), pp. 442-445 N. MacLeod Automated Taxon Identification in Systematics: Theory, Approaches and APPLICATIONs CRC Press (2007) N. MacLeod Morphometrics: history, development methods and prospects Syst. Zool., 42 (2017), pp. 4-33 U. Mai, S. Mirarab TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees BMC Genom., 19 (2018), p. 272 T. Mailund, K. Munch, M.H. Schierup Lineage sorting in apes Annu. Rev. Genet., 48 (2014), pp. 519-535 T.S. Mikkelsen, M.J. Wakefield, B. Aken, C.T. Amemiya, J.L. Chang, S. Duke, M. Garber, A.J. Gentles, L. Goodstadt, A. Heger, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences Nature, 447 (2007), pp. 167-177 J. Mistry, S. Chuguransky, L. Williams, M. Qureshi, G.A. Salazar, E.L.L. Sonnhammer, S.C.E. Tosatto, L. Paladin, S. Raj, L.J. Richardson, et al. Pfam: the protein families database in 2021 Nucleic Acids Res., 49 (2021), pp. D412-D419 K.J. Mitchell, R.C. Pratt, L.N. Watson, G.C. Gibb, B. Llamas, M. Kasper, J. Edson, B. Hopwood, D. Male, K.N. Armstrong, et al. Molecular phylogeny, biogeography, and habitat preference evolution of marsupials Mol. Biol. Evol., 31 (2014), pp. 2322-2330 D. Moen, H. Morlon From dinosaurs to modern bird diversity: extending the time scale of adaptive radiation PLoS Biol., 12 (2014), p. e1001854 O. Monestier, V. Blanquet WFIKKN1 and WFIKKN2: “Companion” proteins regulating TGFB activity Cytokine Growth Factor Rev., 32 (2016), pp. 75-84 M. Muschick, A. Indermaur, W. Salzburger Convergent evolution within an adaptive radiation of cichlid fishes Curr. Biol., 22 (2012), pp. 2362-2368 L.T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies Mol. Biol. Evol., 32 (2015), pp. 268-274 M.A. Nilsson, U. Arnason, P.B. Spencer, A. Janke Marsupial relationships and a timeline for marsupial radiation in south Gondwana Gene, 340 (2004), pp. 189-196 M.A. Nilsson, G. Churakov, M. Sommer, N.V. Tran, A. Zemann, J. Brosius, J. Schmitz Tracking marsupial evolution using archaic genomic retroposon insertions PLoS Biol., 8 (2010), p. e1000436 M.A. Nilsson, A. Gullberg, A.E. Spotorno, U. Arnason, A. Janke Radiation of extant marsupials after the K/T boundary: evidence from complete mitochondrial genomes J. Mol. Evol., 57 (Suppl. 1) (2003), pp. S3-S12 M.A. Nilsson, Y. Zheng, V. Kumar, M.J. Phillips, A. Janke Speciation generates mosaic genomes in kangaroos Genome Biol. Evol., 10 (2018), pp. 33-44 E. Oda, G.B. Rodríguez-Gómez, F. Fontúrbel, M. Soto-Gamboa, R. Nespolo Southernmost records of Dromiciops gliroides: extending its distribution beyond the Valdivian rainforest Gayana, 83 (2019), pp. 145-149 U. Olsson, P. Alström, L. Svensson, M. Aliabadian, P. Sundberg The Lanius excubitor (Aves, Passeriformes) conundrum—Taxonomic dilemma when molecular and non-molecular data tell different stories Mol. Phylogenet. Evol., 55 (2010), pp. 347-357 G. Parra, K. Bradnam, I. Korf CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes Bioinformatics, 23 (2007), pp. 1061-1067 J.B. Pease, D.C. Haak, M.W. Hahn, L.C. Moyle Phylogenomics reveals three sources of adaptive variation during a rapid radiation PLoS Biol., 14 (2016), p. e1002379 J.B. Pease, M.W. Hahn Detection and polarization of introgression in a five-taxon phylogeny Syst. Biol., 64 (2015), pp. 651-662 D.A. Pollard, V.N. Iyer, A.M. Moses, M.B. Eisen Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting PLoS Genet., 2 (2006), p. e173 K.S. Pollard, M.J. Hubisz, K.R. Rosenbloom, A. Siepel Detection of nonneutral substitution rates on mammalian phylogenies Genome Res., 20 (2010), pp. 110-121 A.L. Price, N.C. Jones, P.A. Pevzner De novo identification of repeat families in large genomes Bioinformatics, 21 (Suppl. 1) (2005), pp. i351-i358 R Core Team R: A language and environment for statistical computing R Foundation for Statistical Computing (2021) M.B. Renfree, A.T. Papenfuss, J.E. Deakin, J. Lindsay, T. Heider, K. Belov, W. Rens, P.D. Waters, E.A. Pharo, G. Shaw, et al. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Genome Biol., 12 (2011), p. R81 M.B. Renfree, E.S. Robinson, R.V. Short, J.L. Vandeberg Mammary glands in male marsupials: I. Primordia in neonatal opossums Didelphis virginiana and Monodelphis domestica Development, 110 (1990), pp. 385-390 A. Rhie, S.A. McCarthy, O. Fedrigo, J. Damas, G. Formenti, S. Koren, M. Uliano-Silva, W. Chow, A. Fungtammasan, J. Kim, et al. Towards complete and error-free genome assemblies of all vertebrate species Nature, 592 (2021), pp. 737-746 A. Rokas, B.L. Williams, N. King, S.B. Carroll Genome-scale approaches to resolving incongruence in molecular phylogenies Nature, 425 (2003), pp. 798-804 T.B. Sackton, N. Clark Convergent evolution in the genomics era: new insights and directions Philos. Trans. R. Soc. Lond. B Biol. Sci., 374 (2019), p. 20190102 W. Salzburger, S. Baric, C. Sturmbauer Speciation via introgressive hybridization in East African cichlids? Mol. Ecol., 11 (2002), pp. 619-625 E. Sayyari, J.B. Whitfield, S. Mirarab DiscoVista: interpretable visualizations of gene tree discordance Mol. Phylogenet. Evol., 122 (2018), pp. 110-115 A. Scally, J.Y. Dutheil, L.W. Hillier, G.E. Jordan, I. Goodhead, J. Herrero, A. Hobolth, T. Lappalainen, T. Mailund, T. Marques-Bonet, et al. Insights into hominid evolution from the gorilla genome sequence Nature, 483 (2012), pp. 169-175 D. Schluter The Ecology of Adaptive Radiation OUP Oxford (2000) G. Sharman Karyotypic similarities between Dromiciops australis (Microbiotheriidae, marsupialia) and some Australian marsupials M. Archer (Ed.), Carnivorous Marsupials, Royal Society of New South Wales (1982), pp. 711-714 A.F.A. Smit, R. Hubley, P. Green RepeatMasker (1996) C.L. Smith, J.T. Eppig The mammalian phenotype ontology: enabling robust annotation and comparative analysis Wiley Interdiscip. Rev. Syst. Biol. Med., 1 (2009), pp. 390-399 C.M. Smith, T.F. Hayamizu, J.H. Finger, S.M. Bello, I.J. McCright, J. Xu, R.M. Baldarelli, J.S. Beal, J. Campbell, L.E. Corbani, et al. The mouse Gene Expression Database (GXD): 2019 update Nucleic Acids Res., 47 (2019), pp. D774-D779 M.S. Springer, E.K. Molloy, D.B. Sloan, M.P. Simmons, J. Gatesy ILS-aware analysis of low-homoplasy retroelement insertions: inference of species trees and introgression using quartets J. Hered., 111 (2020), pp. 147-168 M.S. Springer, M. Westerman, J.R. Kavanagh, A. Burk, M.O. Woodburne, D.J. Kao, C. Krajewski The origin of the Australasian marsupial fauna and the phylogenetic affinities of the enigmatic monito del monte and marsupial mole Proc. Biol. Sci., 265 (1998), pp. 2381-2386 D. Stalling, M. Westerhoff, H.-C. Hege Amira: a highly interactive system for visual data analysis Vis. Handb., 38 (2005), pp. 749-767 A. Stamatakis RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Bioinformatics, 22 (2006), pp. 2688-2690 M. Stanke, O. Keller, I. Gunduz, A. Hayes, S. Waack, B. Morgenstern AUGUSTUS: ab initio prediction of alternative transcripts Nucleic Acids Res., 34 (2006), pp. W435-W439 C. Stelzer, A. Brimmer, P. Hermanns, B. Zabel, U.H. Dietz Expression profile of Papss2 (3′-phosphoadenosine 5′-phosphosulfate synthase 2) during cartilage formation and skeletal development in the mouse embryo Dev. Dyn., 236 (2007), pp. 1313-1318 D.L. Stern The genetic causes of convergent evolution Nat. Rev. Genet., 14 (2013), pp. 751-764 A. Suh, L. Smeds, H. Ellegren The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds PLoS Biol., 13 (2015), p. e1002224 Y.B. Sun, T.T. Fu, J.Q. Jin, R.W. Murphy, D.M. Hillis, Y.P. Zhang, J. Che Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations Proc. Natl. Acad. Sci. USA, 115 (2018), pp. E10634-E10641 F.S. Szalay A new appraisal of marsupial phylogeny and classification M. Archer (Ed.), Carnivorous Marsupials, Royal Zoological Society (1982), pp. 621-640 F.S. Szalay Evolutionary History of the Marsupials and an Analysis of Osteological Characters Cambridge University Press (1994) G.J. Szöllősi, E. Tannier, V. Daubin, B. Boussau The inference of gene trees with species trees Syst. Biol., 64 (2015), pp. e42-e62 P.D. Temple-Smith Sperm structure and marsupial phylogeny Possums Opossums Stud. Evol., 1 (1987), pp. 171-193 P.D. Temple-Smith Comparative structure and function of marsupial spermatozoa Reprod. Fertil. Dev., 6 (1994), pp. 421-435 A.A. Tikku, S.C. Cande The oldest magnetic anomalies in the Australian–Antarctic Basin: are they isochrons? J. Geophys. Res. Solid Earth, 104 (1999), pp. 661-677 A.A. Tikku, S.C. Cande On the fit of broken ridge and Kerguelen Plateau Earth Planet. Sci. Lett., 180 (2000), pp. 117-132 Y.-J. Tong, H.-D. Yang, J. Jenkins Shaw, X.-K. Yang, M. Bai The relationship between genus/species richness and morphological diversity among subfamilies of jewel beetles Insects, 12 (2021), p. 24 C.H. Tyndale-Biscoe, M.B. Renfree Reproductive Physiology of Marsupials Cambridge University Press (1987), p. 476 C. Van Den Ende, L.T. White, P.C. van Welzen The existence and break-up of the Antarctic land bridge as indicated by both amphi-Pacific distributions and tectonics Gondwana Res., 44 (2017), pp. 219-227 S.F. Vizcaíno, R. Pascual, M.A. Reguero, F.J. Goin Antarctica as background for mammalian evolution Paleógeno de América del sur y de la Península Antártica (Asociación Paleontológica Argentina, Publicación Especial) (1998), pp. 199-209 L.T. White, G.M. Gibson, G.S. Lister A reassessment of paleogeographic reconstructions of eastern Gondwana: bringing geology back into the equation Gondwana Res., 24 (2013), pp. 984-998 D.F. Wiley, N. Amenta, D.A. Alcantara, D. Ghosh, Y.J. Kil, E. Delson, W. Harcourt-Smith, F.J. Rohlf, K. St John, B. Hamann Evolutionary Morphing IEEE (2005) S.E. Williams, J.M. Whittaker, J.A. Halpin, R.D. Müller Australian-Antarctic breakup and seafloor spreading: balancing geological and geophysical constraints Earth Sci. Rev., 188 (2019), pp. 41-58 J. Woinarski, A. Burbidge Phascolarctos cinereus (amended version of 2016 assessment). The IUCN Red List of Threatened Species 2020: e.T16892A166496779 (2021) Y.I. Wolf, I.B. Rogozin, N.V. Grishin, E.V. Koonin Genome trees and the tree of life Trends Genet., 18 (2002), pp. 472-479 Z. Xu, H. Wang LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons Nucleic Acids Res., 35 (2007), pp. W265-W268 Z. Yang PAML: a program package for phylogenetic analysis by maximum likelihood Comput. Appl. Biosci., 13 (1997), pp. 555-556 C. Zhang, M. Rabiee, E. Sayyari, S. Mirarab ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees BMC Bioinformatics, 19 (2018), p. 153 M. Zhang, Y. Ruan, X. Wan, Y. Tong, X. Yang, B. Ming Bai Geometric morphometric analysis of the pronotum and elytron in stag beetles: insight into its diversity and evolution ZooKeys, 833 (2019), pp. 21-40 Y. Zhou, L. Shearwin-Whyatt, J. Li, Z. Song, T. Hayakawa, D. Stevens, J.C. Fenelon, E. Peel, Y. Cheng, F. Pajpach, et al. Platypus and echidna genomes reveal mammalian biology and evolution Nature, 592 (2021), pp. 756-762 Z. Zou, J. Zhang Morphological and molecular convergences in mammalian phylogenetics Nat. Commun., 7 (2016), p. 12758
dc.rights.accessrights.none.fl_str_mv	info:eu-repo/semantics/openAccess
dc.rights.coar.none.fl_str_mv	http://purl.org/coar/access_right/c_abf2
dc.rights.license.none.fl_str_mv	Atribución-NoComercial-SinDerivadas 4.0 Internacional (CC BY-NC-ND 4.0)
dc.rights.uri.none.fl_str_mv	https://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv	openAccess
rights_invalid_str_mv	http://purl.org/coar/access_right/c_abf2 Atribución-NoComercial-SinDerivadas 4.0 Internacional (CC BY-NC-ND 4.0) https://creativecommons.org/licenses/by-nc-nd/4.0/
dc.format.mimetype.none.fl_str_mv	application/pdf
dc.publisher.place.none.fl_str_mv	Estados Unidos
dc.source.none.fl_str_mv	https://www.sciencedirect.com/science/article/pii/S0092867422003440
institution	Universidad de Ibagué
bitstream.url.fl_str_mv	https://repositorio.unibague.edu.co/bitstreams/6132c865-05b9-4acb-9340-3f66fa3a2fac/download https://repositorio.unibague.edu.co/bitstreams/d7ae8997-d7f2-4f31-9afa-f3c50ceaa288/download https://repositorio.unibague.edu.co/bitstreams/1368c7ce-dbb8-46df-9eff-35615e94058f/download https://repositorio.unibague.edu.co/bitstreams/a41cc8ca-97da-4302-9a3a-5b9aa50bfc43/download
bitstream.checksum.fl_str_mv	423b8a145cc7c7b5390caa84a4b51178 3fac1e3ddb4778c8cb2187b2b06e2bb1 added9e92d589cdab8efc0604b265cfd 2fa3e590786b9c0f3ceba1b9656b7ac3
bitstream.checksumAlgorithm.fl_str_mv	MD5 MD5 MD5 MD5
repository.name.fl_str_mv	Repositorio Institucional Universidad de Ibagué
repository.mail.fl_str_mv	bdigital@metabiblioteca.com
_version_	1814204117422178304
spelling	Feng, Shaohong7a72ec96-dbac-446b-8a60-71f215e58d82-1Bai, Mingffa0d64b-5ad6-43ad-91fc-ccf361da2548-1Rivas-González, Iker56c58ad1-9fc2-4780-8db1-660bcd2f49d6-1Li, Cai997cf0a3-9822-4e64-9cb2-9802763d012c-1Liu, Shipingdf685187-6457-4850-b0db-d5aae0b10f99-1Tong, Yijie119f9fa8-9e09-4eed-95cd-e2bafc90f44d-1Yang, Haidong34f51834-2230-4689-afd8-437d9d8e1706-1Chen, Guangji70cc8679-5ccf-4f2f-8561-44e3fcfb9160-1Xie, Duo75e7815a-5461-43f9-9933-dd252e9b24c7-1Sears, Karen E37ef386a-66a2-4e6f-afb1-2ca5385eb792-1Franco, Lida Mf0957cf0-877f-43bd-827c-6bbb3e67502c-1Gaitan-Espitia, Juan Diego5caa5ba2-bd6a-4435-b042-a46e99c34111-12023-10-17T20:55:47Z2023-10-17T20:55:47Z2022-05-12Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya.application/pdfShaohong Feng, Ming Bai, Iker Rivas-González, Cai Li, Shiping Liu, Yijie Tong, Haidong Yang, Guangji Chen, Duo Xie, Karen E. Sears, Lida M. Franco, Juan Diego Gaitan-Espitia, Roberto F. Nespolo, Warren E. Johnson, Huanming Yang, Parice A. Brandies, Carolyn J. Hogg, Katherine Belov, Marilyn B. Renfree, Kristofer M. Helgen, Jacobus J. Boomsma, Mikkel Heide Schierup, Guojie Zhang, Incomplete lineage sorting and phenotypic evolution in marsupials, Cell, Volume 185, Issue 10, 2022, Pages 1646-1660.e18, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2022.03.034. (https://www.sciencedirect.com/science/article/pii/S0092867422003440)00928674https://hdl.handle.net/20.500.12313/3840engEstados Unidos1660101646185CellL. Almasy, J. Blangero Multipoint quantitative-trait linkage analysis in general pedigrees Am. J. Hum. Genet., 62 (1998), pp. 1198-1211S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman Basic local alignment search tool J. Mol. Biol., 215 (1990), pp. 403-410H. Amrine-Madsen, M. Scally, M. Westerman, M.J. Stanhope, C. Krajewski, M.S. Springer Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials Mol. Phylogenet. Evol., 28 (2003), pp. 186-196J.C. Avise, T.J. Robinson Hemiplasy: a new term in the lexicon of phylogenetics Syst. Biol., 57 (2008), pp. 503-507M. Bai, R.G. Beutel, K.-D. Klass, W. Zhang, X. Yang, B. Wipfler Alienoptera—a new insect order in the roach–mantodean twilight zone Gondwana Res., 39 (2016), pp. 317-326M. Bai, R.G. Beutel, W. Zhang, S. Wang, M. Hörnig, C. Gröhn, E. Yan, X. Yang, B. Wipfler A new Cretaceous insect with a unique cephalo-thoracic scissor device Curr. Biol., 28 (2018), pp. 438-443.e1M. Bai, X. Yang, J. Li, W. Wang Geometric morphometrics, a super scientific computing tool in morphology comparison Sci. Bull., 59 (2014), pp. 887-894A.K. Behrensmeyer, A. Turner Taxonomic occurrences of Suidae recorded in the Paleobiology Database Fossilworks (2013)G. Benson Tandem repeats finder: a program to analyze DNA sequences Nucleic Acids Res., 27 (1999), pp. 573-580E. Birney, M. Clamp, R. Durbin GeneWise and Genomewise Genome Res., 14 (2004), pp. 988-995M. Blanchette, W.J. Kent, C. Riemer, L. Elnitski, A.F. Smit, K.M. Roskin, R. Baertsch, K. Rosenbloom, H. Clawson, E.D. Green, et al. Aligning multiple genomic sequences with the threaded blockset aligner Genome Res., 14 (2004), pp. 708-715M. Boetzer, C.V. Henkel, H.J. Jansen, D. Butler, W. Pirovano Scaffolding pre-assembled contigs using SSPACE Bioinformatics, 27 (2011), pp. 578-579P.A. Brandies, S. Tang, R.S.P. Johnson, C.J. Hogg, K. Belov The first Antechinus reference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies Gigabyte, 1 (2020), p. 7G.A. Bravo, A. Antonelli, C.D. Bacon, K. Bartoszek, M.P.K. Blom, S. Huynh, G. Jones, L.L. Knowles, S. Lamichhaney, T. Marcussen, et al. Embracing heterogeneity: coalescing the tree of life and the future of phylogenomics PeerJ, 7 (2019), p. e6399A.A. Burbidge, J. Woinarski Macropus eugenii. The IUCN Red List of Threatened Species 2016 (2016),A. Burk, M. Westerman, D.J. Kao, J.R. Kavanagh, M.S. Springer An analysis of marsupial interordinal relationships based on 12S rRNA, tRNA valine, 16S rRNA, and cytochrome b sequences J. Mamm. Evol., 6 (1999), pp. 317-334S. Burnett, C. Dickman Antechinus stuartii. The IUCN Red List of Threatened Species 2016 (2016),C. Darwin The Origin of Species John Murray (1859)L.M. Dávalos, A.L. Cirranello, J.H. Geisler, N.B. Simmons Understanding phylogenetic incongruence: lessons from phyllostomid bats Biol. Rev. Camb. Philos. Soc., 87 (2012), pp. 991-1024J.H. Degnan, N.A. Rosenberg Gene tree discordance, phylogenetic inference and the multispecies coalescent Trends Ecol. Evol., 24 (2009), pp. 332-340D.A. Duchêne, J.G. Bragg, S. Duchêne, L.E. Neaves, S. Potter, C. Moritz, R.N. Johnson, S.Y.W. Ho, M.D.B. Eldridge Analysis of phylogenomic tree space resolves relationships among marsupial families Syst. Biol., 67 (2018), pp. 400-412J.Y. Dutheil, G. Ganapathy, A. Hobolth, T. Mailund, M.K. Uyenoyama, M.H. Schierup Ancestral population genomics: the coalescent hidden Markov model approach Genetics, 183 (2009), pp. 259-274N.B. Edelman, P.B. Frandsen, M. Miyagi, B. Clavijo, J. Davey, R.B. Dikow, G. García-Accinelli, S.M. Van Belleghem, N. Patterson, D.E. Neafsey, et al. Genomic architecture and introgression shape a butterfly radiation Science, 366 (2019), pp. 594-599D. Flores, N. de la Sancha Monodelphis domestica. The IUCN Red List of Threatened Species. Version 2016.2 (2016)M.C. Fontaine, J.B. Pease, A. Steele, R.M. Waterhouse, D.E. Neafsey, I.V. Sharakhov, X. Jiang, A.B. Hall, F. Catteruccia, E. Kakani, et al. Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics Science, 347 (2015), p. 1258524G.J. Frankham, P.D. Temple-Smith Absence of mammary development in male Dromiciops gliroides: another link to the Australian marsupial fauna J. Mammal., 93 (2012), pp. 572-578M.H. Gallardo, B.D. Patterson An additional 14-chromosome karyotype and sex-chromosome mosaicism in South American marsupials Fieldiana Zool., 39 (1987), pp. 111-116S. Gallus, A. Janke, V. Kumar, M.A. Nilsson Disentangling the relationship of the Australian marsupial orders using retrotransposon and evolutionary network analyses Genome Biol. Evol., 7 (2015), pp. 985-992P. Gaubert, W.C. Wozencraft, P. Cordeiro-Estrela, G. Veron Mosaics of convergences and noise in morphological phylogenies: what's in a viverrid-like carnivoran? Syst. Biol., 54 (2005), pp. 865-894F.J. Goin, M.A. Abello Los Metatheria sudamericanos de comienzos del Neógeno (Mioceno temprano, edad mamífero Colhuehuapense): Microbiotheria y Polydolopimorphia Ameghiniana, 50 (2013), pp. 51-78R.E. Green, J. Krause, A.W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, M.H. Fritz, et al. A draft sequence of the Neandertal genome Science, 328 (2010), pp. 710-722Y. Gurovich, K.W. Ashwell Brain and behavior of Dromiciops gliroides J. Mamm. Evol., 27 (2020), pp. 177-197M. Haeussler, A.S. Zweig, C. Tyner, M.L. Speir, K.R. Rosenbloom, B.J. Raney, C.M. Lee, B.T. Lee, A.S. Hinrichs, J.N. Gonzalez, et al. The UCSC Genome Browser database: 2019 update Nucleic Acids Res., 47 (2019), pp. D853-D858R.S. Harris Improved Pairwise Alignment Of Genomic DNA The Pennsylvania State University (2007)C. Hawkins, H. McCallum, N. Mooney, M. Jones, M. Holdsworth Sarcophilus harrisii IUCN red list of threatened species. Version 2009.1 (2008)K. Henderson, J. Pantinople, K. McCabe, H.L. Richards, N. Milne Forelimb bone curvature in terrestrial and arboreal mammals PeerJ, 5 (2017), p. e3229A. Hobolth, O.F. Christensen, T. Mailund, M.H. Schierup Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model PLoS Genet., 3 (2007), p. e7A. Hobolth, J.Y. Dutheil, J. Hawks, M.H. Schierup, T. Mailund Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection Genome Res., 21 (2011), pp. 349-356R. Hope, S. Cooper, B. Wainwright Globin macromolecular sequences in marsupials and monotremes Aust. J. Zool., 37 (1989), pp. 289-313I. Horovitz, M.R. Sánchez-Villagra A morphological analysis of marsupial mammal higher-level phylogenetic relationships Cladistics, 19 (2003), pp. 181-212E.D. Jarvis, S. Mirarab, A.J. Aberer, B. Li, P. Houde, C. Li, S.Y. Ho, B.C. Faircloth, B. Nabholz, J.T. Howard, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds Science, 346 (2014), pp. 1320-1331R.N. Johnson, D. O'Meally, Z. Chen, G.J. Etherington, S.Y.W. Ho, W.J. Nash, C.E. Grueber, Y. Cheng, C.M. Whittington, S. Dennison, et al. Adaptation and conservation insights from the koala genome Nat. Genet., 50 (2018), pp. 1102-1111S. Kalyaanamoorthy, B.Q. Minh, T.K.F. Wong, A. von Haeseler, L.S. Jermiin ModelFinder: fast model selection for accurate phylogenetic estimates Nat. Methods, 14 (2017), pp. 587-589K. Katoh, D.M. Standley MAFFT multiple sequence alignment software version 7: improvements in performance and usability Mol. Biol. Evol., 30 (2013), pp. 772-780D. Katz, M. Friess Technical note: 3D from standard digital photography of human crania-a preliminary assessment Am. J. Phys. Anthropol., 154 (2014), pp. 152-158M. Kearse, R. Moir, A. Wilson, S. Stones-Havas, M. Cheung, S. Sturrock, S. Buxton, A. Cooper, S. Markowitz, C. Duran, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data Bioinformatics, 28 (2012), pp. 1647-1649H. Kiyonari, M. Kaneko, T. Abe, A. Shiraishi, R. Yoshimi, K.I. Inoue, Y. Furuta Targeted gene disruption in a marsupial, Monodelphis domestica, by CRISPR/Cas9 genome editing Curr. Biol., 31 (2021), pp. 3956-3963.e4A. Kuritzin, T. Kischka, J. Schmitz, G. Churakov Incomplete lineage sorting and hybridization statistics for large-scale retroposon insertion data PLoS Comput. Biol., 12 (2016), p. e1004812S. Lamichhaney, J. Berglund, M.S. Almén, K. Maqbool, M. Grabherr, A. Martinez-Barrio, M. Promerová, C.-J. Rubin, C. Wang, N. Zamani, et al. Evolution of Darwin’s finches and their beaks revealed by genome sequencing Nature, 518 (2015), pp. 371-375A. Larson The comparison of morphological and molecular data in phylogenetic systematics. Molecular Approaches to Ecology and Evolution Springer (1998), pp. 275-296J.M. Lee, H.J. Song, S.I. Park, Y.M. Lee, S.Y. Jeong, T.O. Cho, J.H. Kim, H.G. Choi, C.G. Choi, W.A. Nelson, et al. Mitochondrial and plastid genomes from coralline red algae provide insights into the incongruent evolutionary histories of organelles Genome Biol. Evol., 10 (2018), pp. 2961-2972Y.S. Lee, S.J. Lee Regulation of GDF-11 and myostatin activity by GASP-1 and GASP-2 Proc. Natl. Acad. Sci. USA, 110 (2013), pp. E3713-E3722R. Li, W. Fan, G. Tian, H. Zhu, L. He, J. Cai, Q. Huang, Q. Cai, B. Li, Y. Bai, et al. The sequence and de novo assembly of the giant panda genome Nature, 463 (2010), pp. 311-317R. Livermore, A. Nankivell, G. Eagles, P. Morris Palaeogene opening of Drake Passage Earth Planet. Sci. Lett., 236 (2005), pp. 459-470F. Lopes, L.R. Oliveira, A. Kessler, Y. Beux, E. Crespo, S. Cárdenas-Alayza, P. Majluf, M. Sepúlveda, R.L. Brownell, V. Franco-Trecu, et al. Phylogenomic discordance in the eared seals is best explained by incomplete lineage sorting following explosive radiation in the Southern hemisphere Syst. Biol., 70 (2021), pp. 786-802J.B. Losos Adaptive radiation, ecological opportunity, and evolutionary determinism. American Society of Naturalists E.O. Wilson award address Am. Nat., 175 (2010), pp. 623-639R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang, J. Yuan, G. He, Y. Chen, Q. Pan, Y. Liu, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler GigaScience, 1 (2012), p. 18Z.X. Luo, Q. Ji, J.R. Wible, C.X. Yuan An Early Cretaceous tribosphenic mammal and metatherian evolution Science, 302 (2003), pp. 1934-1940Z.X. Luo, C.X. Yuan, Q.J. Meng, Q. Ji A Jurassic eutherian mammal and divergence of marsupials and placentals Nature, 476 (2011), pp. 442-445N. MacLeod Automated Taxon Identification in Systematics: Theory, Approaches and APPLICATIONs CRC Press (2007)N. MacLeod Morphometrics: history, development methods and prospects Syst. Zool., 42 (2017), pp. 4-33U. Mai, S. Mirarab TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees BMC Genom., 19 (2018), p. 272T. Mailund, K. Munch, M.H. Schierup Lineage sorting in apes Annu. Rev. Genet., 48 (2014), pp. 519-535T.S. Mikkelsen, M.J. Wakefield, B. Aken, C.T. Amemiya, J.L. Chang, S. Duke, M. Garber, A.J. Gentles, L. Goodstadt, A. Heger, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences Nature, 447 (2007), pp. 167-177J. Mistry, S. Chuguransky, L. Williams, M. Qureshi, G.A. Salazar, E.L.L. Sonnhammer, S.C.E. Tosatto, L. Paladin, S. Raj, L.J. Richardson, et al. Pfam: the protein families database in 2021 Nucleic Acids Res., 49 (2021), pp. D412-D419K.J. Mitchell, R.C. Pratt, L.N. Watson, G.C. Gibb, B. Llamas, M. Kasper, J. Edson, B. Hopwood, D. Male, K.N. Armstrong, et al. Molecular phylogeny, biogeography, and habitat preference evolution of marsupials Mol. Biol. Evol., 31 (2014), pp. 2322-2330D. Moen, H. Morlon From dinosaurs to modern bird diversity: extending the time scale of adaptive radiation PLoS Biol., 12 (2014), p. e1001854O. Monestier, V. Blanquet WFIKKN1 and WFIKKN2: “Companion” proteins regulating TGFB activity Cytokine Growth Factor Rev., 32 (2016), pp. 75-84M. Muschick, A. Indermaur, W. Salzburger Convergent evolution within an adaptive radiation of cichlid fishes Curr. Biol., 22 (2012), pp. 2362-2368L.T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies Mol. Biol. Evol., 32 (2015), pp. 268-274M.A. Nilsson, U. Arnason, P.B. Spencer, A. Janke Marsupial relationships and a timeline for marsupial radiation in south Gondwana Gene, 340 (2004), pp. 189-196M.A. Nilsson, G. Churakov, M. Sommer, N.V. Tran, A. Zemann, J. Brosius, J. Schmitz Tracking marsupial evolution using archaic genomic retroposon insertions PLoS Biol., 8 (2010), p. e1000436M.A. Nilsson, A. Gullberg, A.E. Spotorno, U. Arnason, A. Janke Radiation of extant marsupials after the K/T boundary: evidence from complete mitochondrial genomes J. Mol. Evol., 57 (Suppl. 1) (2003), pp. S3-S12M.A. Nilsson, Y. Zheng, V. Kumar, M.J. Phillips, A. Janke Speciation generates mosaic genomes in kangaroos Genome Biol. Evol., 10 (2018), pp. 33-44E. Oda, G.B. Rodríguez-Gómez, F. Fontúrbel, M. Soto-Gamboa, R. Nespolo Southernmost records of Dromiciops gliroides: extending its distribution beyond the Valdivian rainforest Gayana, 83 (2019), pp. 145-149U. Olsson, P. Alström, L. Svensson, M. Aliabadian, P. Sundberg The Lanius excubitor (Aves, Passeriformes) conundrum—Taxonomic dilemma when molecular and non-molecular data tell different stories Mol. Phylogenet. Evol., 55 (2010), pp. 347-357G. Parra, K. Bradnam, I. Korf CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes Bioinformatics, 23 (2007), pp. 1061-1067J.B. Pease, D.C. Haak, M.W. Hahn, L.C. Moyle Phylogenomics reveals three sources of adaptive variation during a rapid radiation PLoS Biol., 14 (2016), p. e1002379J.B. Pease, M.W. Hahn Detection and polarization of introgression in a five-taxon phylogeny Syst. Biol., 64 (2015), pp. 651-662D.A. Pollard, V.N. Iyer, A.M. Moses, M.B. Eisen Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting PLoS Genet., 2 (2006), p. e173K.S. Pollard, M.J. Hubisz, K.R. Rosenbloom, A. Siepel Detection of nonneutral substitution rates on mammalian phylogenies Genome Res., 20 (2010), pp. 110-121A.L. Price, N.C. Jones, P.A. Pevzner De novo identification of repeat families in large genomes Bioinformatics, 21 (Suppl. 1) (2005), pp. i351-i358R Core Team R: A language and environment for statistical computing R Foundation for Statistical Computing (2021)M.B. Renfree, A.T. Papenfuss, J.E. Deakin, J. Lindsay, T. Heider, K. Belov, W. Rens, P.D. Waters, E.A. Pharo, G. Shaw, et al. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Genome Biol., 12 (2011), p. R81M.B. Renfree, E.S. Robinson, R.V. Short, J.L. Vandeberg Mammary glands in male marsupials: I. Primordia in neonatal opossums Didelphis virginiana and Monodelphis domestica Development, 110 (1990), pp. 385-390A. Rhie, S.A. McCarthy, O. Fedrigo, J. Damas, G. Formenti, S. Koren, M. Uliano-Silva, W. Chow, A. Fungtammasan, J. Kim, et al. Towards complete and error-free genome assemblies of all vertebrate species Nature, 592 (2021), pp. 737-746A. Rokas, B.L. Williams, N. King, S.B. Carroll Genome-scale approaches to resolving incongruence in molecular phylogenies Nature, 425 (2003), pp. 798-804T.B. Sackton, N. Clark Convergent evolution in the genomics era: new insights and directions Philos. Trans. R. Soc. Lond. B Biol. Sci., 374 (2019), p. 20190102W. Salzburger, S. Baric, C. Sturmbauer Speciation via introgressive hybridization in East African cichlids? Mol. Ecol., 11 (2002), pp. 619-625E. Sayyari, J.B. Whitfield, S. Mirarab DiscoVista: interpretable visualizations of gene tree discordance Mol. Phylogenet. Evol., 122 (2018), pp. 110-115A. Scally, J.Y. Dutheil, L.W. Hillier, G.E. Jordan, I. Goodhead, J. Herrero, A. Hobolth, T. Lappalainen, T. Mailund, T. Marques-Bonet, et al. Insights into hominid evolution from the gorilla genome sequence Nature, 483 (2012), pp. 169-175D. Schluter The Ecology of Adaptive Radiation OUP Oxford (2000)G. Sharman Karyotypic similarities between Dromiciops australis (Microbiotheriidae, marsupialia) and some Australian marsupials M. Archer (Ed.), Carnivorous Marsupials, Royal Society of New South Wales (1982), pp. 711-714A.F.A. Smit, R. Hubley, P. Green RepeatMasker (1996)C.L. Smith, J.T. Eppig The mammalian phenotype ontology: enabling robust annotation and comparative analysis Wiley Interdiscip. Rev. Syst. Biol. Med., 1 (2009), pp. 390-399C.M. Smith, T.F. Hayamizu, J.H. Finger, S.M. Bello, I.J. McCright, J. Xu, R.M. Baldarelli, J.S. Beal, J. Campbell, L.E. Corbani, et al. The mouse Gene Expression Database (GXD): 2019 update Nucleic Acids Res., 47 (2019), pp. D774-D779M.S. Springer, E.K. Molloy, D.B. Sloan, M.P. Simmons, J. Gatesy ILS-aware analysis of low-homoplasy retroelement insertions: inference of species trees and introgression using quartets J. Hered., 111 (2020), pp. 147-168M.S. Springer, M. Westerman, J.R. Kavanagh, A. Burk, M.O. Woodburne, D.J. Kao, C. Krajewski The origin of the Australasian marsupial fauna and the phylogenetic affinities of the enigmatic monito del monte and marsupial mole Proc. Biol. Sci., 265 (1998), pp. 2381-2386D. Stalling, M. Westerhoff, H.-C. Hege Amira: a highly interactive system for visual data analysis Vis. Handb., 38 (2005), pp. 749-767A. Stamatakis RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Bioinformatics, 22 (2006), pp. 2688-2690M. Stanke, O. Keller, I. Gunduz, A. Hayes, S. Waack, B. Morgenstern AUGUSTUS: ab initio prediction of alternative transcripts Nucleic Acids Res., 34 (2006), pp. W435-W439C. Stelzer, A. Brimmer, P. Hermanns, B. Zabel, U.H. Dietz Expression profile of Papss2 (3′-phosphoadenosine 5′-phosphosulfate synthase 2) during cartilage formation and skeletal development in the mouse embryo Dev. Dyn., 236 (2007), pp. 1313-1318D.L. Stern The genetic causes of convergent evolution Nat. Rev. Genet., 14 (2013), pp. 751-764A. Suh, L. Smeds, H. Ellegren The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds PLoS Biol., 13 (2015), p. e1002224Y.B. Sun, T.T. Fu, J.Q. Jin, R.W. Murphy, D.M. Hillis, Y.P. Zhang, J. Che Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations Proc. Natl. Acad. Sci. USA, 115 (2018), pp. E10634-E10641F.S. Szalay A new appraisal of marsupial phylogeny and classification M. Archer (Ed.), Carnivorous Marsupials, Royal Zoological Society (1982), pp. 621-640F.S. Szalay Evolutionary History of the Marsupials and an Analysis of Osteological Characters Cambridge University Press (1994)G.J. Szöllősi, E. Tannier, V. Daubin, B. Boussau The inference of gene trees with species trees Syst. Biol., 64 (2015), pp. e42-e62P.D. Temple-Smith Sperm structure and marsupial phylogeny Possums Opossums Stud. Evol., 1 (1987), pp. 171-193P.D. Temple-Smith Comparative structure and function of marsupial spermatozoa Reprod. Fertil. Dev., 6 (1994), pp. 421-435A.A. Tikku, S.C. Cande The oldest magnetic anomalies in the Australian–Antarctic Basin: are they isochrons? J. Geophys. Res. Solid Earth, 104 (1999), pp. 661-677A.A. Tikku, S.C. Cande On the fit of broken ridge and Kerguelen Plateau Earth Planet. Sci. Lett., 180 (2000), pp. 117-132Y.-J. Tong, H.-D. Yang, J. Jenkins Shaw, X.-K. Yang, M. Bai The relationship between genus/species richness and morphological diversity among subfamilies of jewel beetles Insects, 12 (2021), p. 24C.H. Tyndale-Biscoe, M.B. Renfree Reproductive Physiology of Marsupials Cambridge University Press (1987), p. 476C. Van Den Ende, L.T. White, P.C. van Welzen The existence and break-up of the Antarctic land bridge as indicated by both amphi-Pacific distributions and tectonics Gondwana Res., 44 (2017), pp. 219-227S.F. Vizcaíno, R. Pascual, M.A. Reguero, F.J. Goin Antarctica as background for mammalian evolution Paleógeno de América del sur y de la Península Antártica (Asociación Paleontológica Argentina, Publicación Especial) (1998), pp. 199-209L.T. White, G.M. Gibson, G.S. Lister A reassessment of paleogeographic reconstructions of eastern Gondwana: bringing geology back into the equation Gondwana Res., 24 (2013), pp. 984-998D.F. Wiley, N. Amenta, D.A. Alcantara, D. Ghosh, Y.J. Kil, E. Delson, W. Harcourt-Smith, F.J. Rohlf, K. St John, B. Hamann Evolutionary Morphing IEEE (2005)S.E. Williams, J.M. Whittaker, J.A. Halpin, R.D. Müller Australian-Antarctic breakup and seafloor spreading: balancing geological and geophysical constraints Earth Sci. Rev., 188 (2019), pp. 41-58J. Woinarski, A. Burbidge Phascolarctos cinereus (amended version of 2016 assessment). The IUCN Red List of Threatened Species 2020: e.T16892A166496779 (2021)Y.I. Wolf, I.B. Rogozin, N.V. Grishin, E.V. Koonin Genome trees and the tree of life Trends Genet., 18 (2002), pp. 472-479Z. Xu, H. Wang LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons Nucleic Acids Res., 35 (2007), pp. W265-W268Z. Yang PAML: a program package for phylogenetic analysis by maximum likelihood Comput. Appl. Biosci., 13 (1997), pp. 555-556C. Zhang, M. Rabiee, E. Sayyari, S. Mirarab ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees BMC Bioinformatics, 19 (2018), p. 153M. Zhang, Y. Ruan, X. Wan, Y. Tong, X. Yang, B. Ming Bai Geometric morphometric analysis of the pronotum and elytron in stag beetles: insight into its diversity and evolution ZooKeys, 833 (2019), pp. 21-40Y. Zhou, L. Shearwin-Whyatt, J. Li, Z. Song, T. Hayakawa, D. Stevens, J.C. Fenelon, E. Peel, Y. Cheng, F. Pajpach, et al. Platypus and echidna genomes reveal mammalian biology and evolution Nature, 592 (2021), pp. 756-762Z. Zou, J. Zhang Morphological and molecular convergences in mammalian phylogenetics Nat. Commun., 7 (2016), p. 12758All rights are reserved, including those for text and data mining, AI training, and similar technologies. For all open access content, the Creative Commons licensing terms apply.info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Atribución-NoComercial-SinDerivadas 4.0 Internacional (CC BY-NC-ND 4.0)https://creativecommons.org/licenses/by-nc-nd/4.0/https://www.sciencedirect.com/science/article/pii/S0092867422003440Phylogenetic inferenceRapid speciationGene-phenotype incongruenceHemiplasyIncomplete lineage sortingCoalHMMMarsupialMonito del monteTrait evolutionBiogeographyIncomplete lineage sorting and phenotypic evolution in marsupialsArtículo de revistahttp://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1http://purl.org/coar/version/c_970fb48d4fbd8a85Textinfo:eu-repo/semantics/articlehttp://purl.org/redcol/resource_type/ARTinfo:eu-repo/semantics/publishedVersionPublicationTEXTIncomplete lineage sorting and phenotypic evolution in marsupials.pdf.txtIncomplete lineage sorting and phenotypic evolution in marsupials.pdf.txtExtracted texttext/plain1498https://repositorio.unibague.edu.co/bitstreams/6132c865-05b9-4acb-9340-3f66fa3a2fac/download423b8a145cc7c7b5390caa84a4b51178MD53THUMBNAILIncomplete lineage sorting and phenotypic evolution in marsupials.pdf.jpgIncomplete lineage sorting and phenotypic evolution in marsupials.pdf.jpgGenerated Thumbnailimage/jpeg12522https://repositorio.unibague.edu.co/bitstreams/d7ae8997-d7f2-4f31-9afa-f3c50ceaa288/download3fac1e3ddb4778c8cb2187b2b06e2bb1MD54ORIGINALIncomplete lineage sorting and phenotypic evolution in marsupials.pdfIncomplete lineage sorting and phenotypic evolution in marsupials.pdfapplication/pdf225003https://repositorio.unibague.edu.co/bitstreams/1368c7ce-dbb8-46df-9eff-35615e94058f/downloadadded9e92d589cdab8efc0604b265cfdMD51LICENSElicense.txtlicense.txttext/plain; charset=utf-8134https://repositorio.unibague.edu.co/bitstreams/a41cc8ca-97da-4302-9a3a-5b9aa50bfc43/download2fa3e590786b9c0f3ceba1b9656b7ac3MD5220.500.12313/3840oai:repositorio.unibague.edu.co:20.500.12313/38402023-10-18 03:00:39.339https://creativecommons.org/licenses/by-nc-nd/4.0/All rights are reserved, including those for text and data mining, AI training, and similar technologies. For all open access content, the Creative Commons licensing terms apply.https://repositorio.unibague.edu.coRepositorio Institucional Universidad de Ibaguébdigital@metabiblioteca.comQ3JlYXRpdmUgQ29tbW9ucyBBdHRyaWJ1dGlvbi1Ob25Db21tZXJjaWFsLU5vRGVyaXZhdGl2ZXMgNC4wIEludGVybmF0aW9uYWwgTGljZW5zZQ0KaHR0cHM6Ly9jcmVhdGl2ZWNvbW1vbnMub3JnL2xpY2Vuc2VzL2J5LW5jLW5kLzQuMC8=

Incomplete lineage sorting and phenotypic evolution in marsupials

Publicaciones similares