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2. Phylogenomics and the rise of the angiosperms

Author

Zuntini, Alexandre R., Carruthers, Tom, Maurin, Olivier, Bailey, Paul C., Leempoel, Kevin, Brewer, Grace E., Epitawalage, Niroshini, Françoso, Elaine, Gallego-Paramo, Berta, McGinnie, Catherine, Negrão, Raquel, Roy, Shyamali R., Simpson, Lalita, Toledo Romero, Eduardo, Barber, Vanessa M. A., Botigué, Laura, Clarkson, James J., Cowan, Robyn S., Dodsworth, Steven, Johnson, Matthew G., Kim, Jan T., Pokorny, Lisa, Wickett, Norman J., Antar, Guilherme M., DeBolt, Lucinda, Gutierrez, Karime, Hendriks, Kasper P., Hoewener, Alina, Hu, Ai-Qun, Joyce, Elizabeth M., Kikuchi, Izai A. B. S., Larridon, Isabel, Larson, Drew A., de Lírio, Elton John, Liu, Jing-Xia, Malakasi, Panagiota, Przelomska, Natalia A. S., Shah, Toral, Viruel, Juan, Allnutt, Theodore R., Ameka, Gabriel K., Andrew, Rose L., Appelhans, Marc S., Arista, Montserrat, Ariza, María Jesús, Arroyo, Juan, Arthan, Watchara, Bachelier, Julien B., Bailey, C. Donovan, Barnes, Helen F., Barrett, Matthew D., Barrett, Russell L., Bayer, Randall J., Bayly, Michael J., Biffin, Ed, Biggs, Nicky, Birch, Joanne L., Bogarín, Diego, Borosova, Renata, Bowles, Alexander M. C., Boyce, Peter C., Bramley, Gemma L. C., Briggs, Marie, Broadhurst, Linda, Brown, Gillian K., Bruhl, Jeremy J., Bruneau, Anne, Buerki, Sven, Burns, Edie, Byrne, Margaret, Cable, Stuart, Calladine, Ainsley, Callmander, Martin W., Cano, Ángela, Cantrill, David J., Cardinal-McTeague, Warren M., Carlsen, Mónica M., Carruthers, Abigail J. A., de Castro Mateo, Alejandra, Chase, Mark W., Chatrou, Lars W., Cheek, Martin, Chen, Shilin, Christenhusz, Maarten J. M., Christin, Pascal-Antoine, Clements, Mark A., Coffey, Skye C., Conran, John G., Cornejo, Xavier, Couvreur, Thomas L. P., Cowie, Ian D., Csiba, Laszlo, Darbyshire, Iain, Davidse, Gerrit, Davies, Nina M. J., Davis, Aaron P., van Dijk, Kor-jent, Downie, Stephen R., Duretto, Marco F., Duvall, Melvin R., Edwards, Sara L., Eggli, Urs, Erkens, Roy H. J., Escudero, Marcial, de la Estrella, Manuel, Fabriani, Federico, Fay, Michael F., Ferreira, Paola de L., Ficinski, Sarah Z., Fowler, Rachael M., Frisby, Sue, Fu, Lin, Fulcher, Tim, Galbany-Casals, Mercè, Gardner, Elliot M., German, Dmitry A., Giaretta, Augusto, Gibernau, Marc, Gillespie, Lynn J., González, Cynthia C., Goyder, David J., Graham, Sean W., Grall, Aurélie, Green, Laura, Gunn, Bee F., Gutiérrez, Diego G., Hackel, Jan, Haevermans, Thomas, Haigh, Anna, Hall, Jocelyn C., Hall, Tony, Harrison, Melissa J., Hatt, Sebastian A., Hidalgo, Oriane, Hodkinson, Trevor R., Holmes, Gareth D., Hopkins, Helen C. F., Jackson, Christopher J., James, Shelley A., Jobson, Richard W., Kadereit, Gudrun, Kahandawala, Imalka M., Kainulainen, Kent, Kato, Masahiro, Kellogg, Elizabeth A., King, Graham J., Klejevskaja, Beata, Klitgaard, Bente B., Klopper, Ronell R., Knapp, Sandra, Koch, Marcus A., Leebens-Mack, James H., Lens, Frederic, Leon, Christine J., Léveillé-Bourret, Étienne, Lewis, Gwilym P., Li, De-Zhu, Li, Lan, Liede-Schumann, Sigrid, Livshultz, Tatyana, Lorence, David, Lu, Meng, Lu-Irving, Patricia, Luber, Jaquelini, Lucas, Eve J., Luján, Manuel, Lum, Mabel, Macfarlane, Terry D., Magdalena, Carlos, Mansano, Vidal F., Masters, Lizo E., Mayo, Simon J., McColl, Kristina, McDonnell, Angela J., McDougall, Andrew E., McLay, Todd G. B., McPherson, Hannah, Meneses, Rosa I., Merckx, Vincent S. F. T., Michelangeli, Fabián A., Mitchell, John D., Monro, Alexandre K., Moore, Michael J., Mueller, Taryn L., Mummenhoff, Klaus, Munzinger, Jérôme, Muriel, Priscilla, Murphy, Daniel J., Nargar, Katharina, Nauheimer, Lars, Nge, Francis J., Nyffeler, Reto, Orejuela, Andrés, Ortiz, Edgardo M., Palazzesi, Luis, Peixoto, Ariane Luna, Pell, Susan K., Pellicer, Jaume, Penneys, Darin S., Perez-Escobar, Oscar A., Persson, Claes, Pignal, Marc, Pillon, Yohan, Pirani, José R., Plunkett, Gregory M., Powell, Robyn F., Prance, Ghillean T., Puglisi, Carmen, Qin, Ming, Rabeler, Richard K., Rees, Paul E. J., Renner, Matthew, Roalson, Eric H., Rodda, Michele, Rogers, Zachary S., Rokni, Saba, Rutishauser, Rolf, de Salas, Miguel F., Schaefer, Hanno, Schley, Rowan J., Schmidt-Lebuhn, Alexander, Shapcott, Alison, Al-Shehbaz, Ihsan, Shepherd, Kelly A., Simmons, Mark P., Simões, André O., Simões, Ana Rita G., Siros, Michelle, Smidt, Eric C., Smith, James F., Snow, Neil, Soltis, Douglas E., Soltis, Pamela S., Soreng, Robert J., Sothers, Cynthia A., Starr, Julian R., Stevens, Peter F., Straub, Shannon C. K., Struwe, Lena, Taylor, Jennifer M., Telford, Ian R. H., Thornhill, Andrew H., Tooth, Ifeanna, Trias-Blasi, Anna, Udovicic, Frank, Utteridge, Timothy M. A., Del Valle, Jose C., Verboom, G. Anthony, Vonow, Helen P., Vorontsova, Maria S., de Vos, Jurriaan M., Al-Wattar, Noor, Waycott, Michelle, Welker, Cassiano A. D., White, Adam J., Wieringa, Jan J., Williamson, Luis T., Wilson, Trevor C., Wong, Sin Yeng, Woods, Lisa A., Woods, Roseina, Worboys, Stuart, Xanthos, Martin, Yang, Ya, Zhang, Yu-Xiao, Zhou, Meng-Yuan, Zmarzty, Sue, Zuloaga, Fernando O., Antonelli, Alexandre, Bellot, Sidonie, Crayn, Darren M., Grace, Olwen M., Kersey, Paul J., Leitch, Ilia J., Sauquet, Hervé, Smith, Stephen A., Eiserhardt, Wolf L., Forest, Félix, and Baker, William J.

Published
2024
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4. The Soursop Genome (Annona muricata L., Annonaceae)

Author

Strijk, Joeri S., Hinsinger, Damien D., Roeder, Mareike M., Chatrou, Lars W., Couvreur, Thomas L. P., Erkens, Roy H. J., Sauquet, Hervé, Pirie, Michael D., Thomas, Daniel C., Cao, Kunfang, Kole, Chittaranjan, Series Editor, and Chapman, Mark A., editor

Published
2022
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5. (2786) Proposal to change the conserved type of Ipomoea , nom. cons. ( Convolvulaceae )

Author

Eserman, Lauren A., Sosef, Marc S.M., Simão-Bianchini, Rosângela, Utteridge, Timothy M.A., Barbosa, Juliana C.J., Buril, Maria Teresa, Chatrou, Lars W., Clay, Keith, Delgado, Geadelande, Desquilbet, Thibaut E., Ferreira, Priscila P.A., Allende, José R. Grande, Hernández, Alexis L., Huerta-Ramos, Guillermo, Jarret, Robert L., Kojima, Roberta K., Landrein, Sven, Lourenço, Juliana A.A.M., De Man, Ine, Miller, Richard E., More, Sushant, Moreira, André L.C., Mwanga-Mwanga, Ithe, Nhanala, Stella, Pastore, Mayara, Petrongari, Fernanda S., Pisuttimarn, Ponprom, Pornpongrungrueng, Pimwadee, Rifkin, Joanna, Santos, Francisco D.S., Shimpale, Vinod B., Silva, Simone S., Stinchcombe, John R., Traiperm, Paweena, Vasconcelos, Liziane V., Wang, Ming Li, Villordon, Arthur, Yang, Jun, Yencho, G. Craig, Heider, Bettina, and Simões, Ana Rita G.

Published
2020

7. Towards a collaborative approach to the systematics of Ipomoea: A response to the "Rebuttal to (2786) Proposal to change the conserved type of Ipomoea, nom. cons. (Convolvulaceae)".

Author

Eserman, Lauren A., Buril, Maria Teresa, Chatrou, Lars W., Clay, Keith, Desquilbet, Thibaut E., Ferreira, Priscila P.A., Grande Allende, José R., Huerta‐Ramos, Guillermo, Kojima, Roberta K., Miller, Richard E., More, Sushant, Moreira, André L.C., Pastore, Mayara, Petrongari, Fernanda S., Pisuttimarn, Ponprom, Pornpongrungrueng, Pimwadee, Rifkin, Joanna, Shimpale, Vinod B., Sosef, Marc S.M., and Stinchcombe, John R.

Subjects
IPOMOEA, CONVOLVULACEAE, SWEET potatoes, EXPERTISE, AUTHORSHIP collaboration
Abstract

A proposal to change the conserved type of Ipomoea was published in December 2020, and recommended by the Nomenclature Committee in 2023. This was done in the light of the possible negative consequences for a name change in the crop sweetpotato, which risk our proposal would significantly minimize. Recently, Muñoz‐Rodríguez & al. have published a rebuttal to this proposal, which we respond to here. The objections raised by these authors focus as much on the expertise and credibility of our group of authors as on the merits of our arguments. In this "rebuttal to the rebuttal", we respond to the scientific questions raised, highlight demonstrated misinterpretation of the specialised literature relevant to this discussion and counter the assertion that a reclassification of Ipomoeeae is impossible given existing evidence. While the currently recognised genera of Ipomoeeae are not all monophyletic, the proposal to change the conserved type of Ipomoea is a necessary step that will allow exploring an improved classification for the tribe Ipomoeeae, either in the form of a better recircumscription of the genera or an efficient infrageneric classification for Ipomoea. Previously published literature has not advocated for the integration of all genera into a single genus, as Muñoz‐Rodríguez and co‐authors have incorrectly suggested, and instead have recommended a reanalysis of the high morphological diversity of the group in the context of expanded phylogenetic studies, with the possible maintenance of some of the existing genera. We believe that, in a concerted collaborative approach and with the contribution of experts from different regions and scientific backgrounds, an improved classification of Ipomoeeae that integrates the principles of monophyly and diagnosability may soon be achieved, and until when some uncertainty may need to be accommodated, with the added reassurance that, regardless of the direction of future systematic rearrangements, the stability of the scientific name of sweetpotato would be preserved. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Towards a collaborative approach to the systematics of Ipomoea: A response to the “Rebuttal to (2786) Proposal to change the conserved type of Ipomoea, nom. cons. (Convolvulaceae)”

Author

Eserman, Lauren A., primary, Buril, Maria Teresa, additional, Chatrou, Lars W., additional, Clay, Keith, additional, Desquilbet, Thibaut E., additional, Ferreira, Priscila P.A., additional, Grande Allende, José R., additional, Huerta‐Ramos, Guillermo, additional, Kojima, Roberta K., additional, Miller, Richard E., additional, More, Sushant, additional, Moreira, André L.C., additional, Pastore, Mayara, additional, Petrongari, Fernanda S., additional, Pisuttimarn, Ponprom, additional, Pornpongrungrueng, Pimwadee, additional, Rifkin, Joanna, additional, Shimpale, Vinod B., additional, Sosef, Marc S.M., additional, Stinchcombe, John R., additional, and Simões, Ana Rita G., additional

Published
2023
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14. Angiosperm Phylogeny Based on matK Sequence Information

Author

Hilu, Khidir W., Borsch, Thomas, Müller, Kai, Soltis, Douglas E., Soltis, Pamela S., Savolainen, Vincent, Chase, Mark W., Powell, Martyn P., Alice, Lawrence A., Sauquet, Hervé, Rohwer, Jens G., Campbell, Christopher S., and Chatrou, Lars W.

Published
2003

22. Distimake vitifolius (Convolvulaceae): reclassification of a widespread species in view of phylogenetics and convergent pollen evolution

Author

Pisuttimarn, Ponprom, primary, Simões, Ana Rita Giraldes, additional, Petrongari, Fernanda Satori, additional, Simão-Bianchini, Rosângela, additional, Barbosa, Juliana Cruz Jardim, additional, de Man, Ine, additional, Fonseca, Luiz Henrique Martins, additional, Janssens, Steven B, additional, Patil, Sujit B, additional, Shimpale, Vinod B, additional, Pornpongrungrueng, Pimwadee, additional, Leliaert, Frederik, additional, and Chatrou, Lars W, additional

Published
2023
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38. The evolutionary history of the Caribbean magnolias (Magnoliaceae): Testing species delimitations and biogeographical hypotheses using molecular data

Author

Veltjen, Emily, primary, Testé, Ernesto, additional, Palmarola Bejerano, Alejandro, additional, Asselman, Pieter, additional, Hernández Rodríguez, Majela, additional, Roberto González Torres, Luis, additional, Chatrou, Lars W., additional, Goetghebeur, Paul, additional, Larridon, Isabel, additional, and Samain, Marie-Stéphanie, additional

Published
2022
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39. Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes

Author

Qiu, Yin‐Long, Dombrovska, Olena, Lee, Jungho, Li, Libo, Whitlock, Barbara A., Bernasconi‐Quadroni, Fabiana, Rest, Joshua S., Davis, Charles C., Borsch, Thomas, Hilu, Khidir W., Renner, Susanne S., Soltis, Douglas E., Soltis, Pamela S., Zanis, Michael J., Cannone, Jamie J., Gutell, Robin R., Powell, Martyn, Savolainen, Vincent, Chatrou, Lars W., and Chase, Mark W.

Published
2005
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44. Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcl, atpB, and matK DNA sequences

Author

Cuenoud, Philippe, Savolainen, Vincent, Chatrou, Lars W., Powell, Martyn, Grayer, Renee J., and Chase, Mark W.

Subjects
Phylogeny (Botany) -- Analysis, Plant genetics -- Analysis, Plants -- Evolution, Biological sciences
Abstract

To study the inter- and infrafamilial phylogenetic relationships in the order Caryophyllales sensu lato (s.1.), ~930 base pairs of the matK plastid gene have been sequenced and analyzed for 127 taxa. In addition, these sequences have been combined with the rbcL plastid gene for 53 taxa and with the rbcL and atpB plastid genes as well as the nuclear 18S rDNA for 26 taxa to provide increased support for deeper branches. The red pigments of Corbichonia, Lophiocarpus, and Sarcobatus have been tested and shown to belong to the betacyanin class of compounds. Most taxa of the order are clearly grouped into two main clades (i.e., 'core' and 'noncore' Caryophyllales) which are, in turn, divided into well-defined subunits. Phytolaccaceae and Molluginaceae are polyphyletic, and Portulacaceae are paraphyletic, whereas Agdestidaceae, Barbeuiaceae, Petiveriaceae, and Sarcobataceae should be given familial recognition. Two additional lineages are potentially appropriate to be elevated to the family level in the future: the genera Lophiocarpus and Corbichonia form a well-supported clade on the basis of molecular and chemical evidence, and Limeum appears to be separated from other Molluginaceae based on both molecular and ultrastructural data. Key words: betalain; Caryophyllales; DNA evolution; matK; phylogeny.

Published
2002

46. Macromorphological variation of recent invaders in northern Central America: the case of Malmea (Annonaceae)

Author

Chatrou, Lars W.

Subjects
Central America -- Natural history, Biogeography -- Research, Cluster analysis -- Research, Biological sciences
Abstract

Cluster analysis is used to reveal patterns of macromorphological variation in a species complex of Malmea (Annonaceae) distributed in eastern Mexico, Guatemala, Belize, and Honduras. Of 53 characters, 24 are important for the clustering of 238 herbarium specimens into 12 clusters. No cluster is exclusively specified by any character or combination of characters. Neither can any geographical pattern be detected, except for the clustering of specimens from Los Tuxtlas Tropical Biological Station, Veracruz. A new subspecies from this area, M. depressa subsp. abscondita, is described. Malmea gaumeri and M. leiophylla are brought into synonymy with M. depressa. Distribution patterns of Mexican and Central American taxa of Malmea are largely concordant with those of South American taxa, which spread into Cental America after the Pliocene closure of the Isthmus of Panama. A phytogeographical novelty is presented, however, as the distribution of M. depressa subsp. abscondita within the Sierra de los Tuxtlas shows an hitherto unknown pattern: the new subspecies is distributed only on the northeastern slopes of this mountain range, and is geographically separated from M. depressa subsp. depressa, which occurs only on the southwestern slopes. Key words: Annonaceae; biogeography; cluster analysis; macromorphology; Malmea; northern Central America.

Published
1997

49. Should we be concerned about incomplete taxon sampling when assessing the evolutionary history of regional biotas?

Author

Molina‐Venegas, Rafael, Lima, Herlander, and Chatrou, Lars

Subjects
BIOTIC communities, TIME perception, KNOWLEDGE gap theory, MACROECOLOGY
Abstract

Region‐specific phylogenies are increasingly used in biogeography and macroecology. However, there is debate as to whether incomplete taxon sampling inherent in these phylogenies can bias divergence time estimations. Here, we draw on a global genus‐level plant phylogeny and 345 regional phylogenies derived from the global tree to fill in this gap of knowledge. Genus ages as obtained from the regional phylogenies were significantly older than those extracted from the global tree across all regions, yet the correlation between both types of ages was overall high, particularly in taxon‐rich regions. Thus, comparing divergence time estimates from taxon‐rich regional phylogenies within regions and in a relative manner seems reasonable. However, comparisons among regional biotas could be misleading if taxon ages are inferred from their respective regional phylogenies because differences in divergence times between the biotas may appear greater than they are regardless of taxon richness. [ABSTRACT FROM AUTHOR]

Published
2021
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50. Chromosome‐level reference genome of the soursop (Annonamuricata): A new resource for Magnoliid research and tropical pomology.

Author

Strijk, Joeri S., Hinsinger, Damien D., Roeder, Mareike M., Chatrou, Lars W., Couvreur, Thomas L. P., Erkens, Roy H. J., Sauquet, Hervé, Pirie, Michael D., Thomas, Daniel C., and Cao, Kunfang

Subjects
AGROFORESTRY, FRUIT, GENOMES, DNA sequencing, TROPICAL crops, FLOWERING of plants
Abstract

The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome‐level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676× sequencing depth) from PacBio and Illumina short‐reads, in combination with 10× Genomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo‐chromosomes using Hi‐C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein‐coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA‐seq and homology‐based approaches. Reconstruction of the historical population size showed a slow continuous contraction, probably related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome‐assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry. [ABSTRACT FROM AUTHOR]

Published
2021
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