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1. 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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3. Global beta-diversity of angiosperm trees is shaped by Quaternary climate change

Author

Xu, Wu-Bing, Guo, Wen-Yong, Serra-Diaz, Josep M, Schrodt, Franziska, Eiserhardt, Wolf L, Enquist, Brian J, Maitner, Brian S, Merow, Cory, Violle, Cyrille, Anand, Madhur, Belluau, Michaël, Bruun, Hans Henrik, Byun, Chaeho, Catford, Jane A, Cerabolini, Bruno EL, Chacón-Madrigal, Eduardo, Ciccarelli, Daniela, Cornelissen, J Hans C, Dang-Le, Anh Tuan, de Frutos, Angel, Dias, Arildo S, Giroldo, Aelton B, Gutiérrez, Alvaro G, Hattingh, Wesley, He, Tianhua, Hietz, Peter, Hough-Snee, Nate, Jansen, Steven, Kattge, Jens, Komac, Benjamin, Kraft, Nathan JB, Kramer, Koen, Lavorel, Sandra, Lusk, Christopher H, Martin, Adam R, Ma, Ke-Ping, Mencuccini, Maurizio, Michaletz, Sean T, Minden, Vanessa, Mori, Akira S, Niinemets, Ülo, Onoda, Yusuke, Onstein, Renske E, Peñuelas, Josep, Pillar, Valério D, Pisek, Jan, Pound, Matthew J, Robroek, Bjorn JM, Schamp, Brandon, Slot, Martijn, Sun, Miao, Sosinski, Ênio E, Soudzilovskaia, Nadejda A, Thiffault, Nelson, van Bodegom, Peter M, van der Plas, Fons, Zheng, Jingming, Svenning, Jens-Christian, and Ordonez, Alejandro

Subjects
Life Below Water, Climate Action, Humans, Phylogeny, Magnoliopsida, Climate Change, Biodiversity
Abstract

As Earth's climate has varied strongly through geological time, studying the impacts of past climate change on biodiversity helps to understand the risks from future climate change. However, it remains unclear how paleoclimate shapes spatial variation in biodiversity. Here, we assessed the influence of Quaternary climate change on spatial dissimilarity in taxonomic, phylogenetic, and functional composition among neighboring 200-kilometer cells (beta-diversity) for angiosperm trees worldwide. We found that larger glacial-interglacial temperature change was strongly associated with lower spatial turnover (species replacements) and higher nestedness (richness changes) components of beta-diversity across all three biodiversity facets. Moreover, phylogenetic and functional turnover was lower and nestedness higher than random expectations based on taxonomic beta-diversity in regions that experienced large temperature change, reflecting phylogenetically and functionally selective processes in species replacement, extinction, and colonization during glacial-interglacial oscillations. Our results suggest that future human-driven climate change could cause local homogenization and reduction in taxonomic, phylogenetic, and functional diversity of angiosperm trees worldwide.

Published
2023

4. High exposure of global tree diversity to human pressure

Author

Guo, Wen-Yong, Serra-Diaz, Josep M, Schrodt, Franziska, Eiserhardt, Wolf L, Maitner, Brian S, Merow, Cory, Violle, Cyrille, Anand, Madhur, Belluau, Michaël, Bruun, Hans Henrik, Byun, Chaeho, Catford, Jane A, Cerabolini, Bruno EL, Chacón-Madrigal, Eduardo, Ciccarelli, Daniela, Cornelissen, J Hans C, Dang-Le, Anh Tuan, de Frutos, Angel, Dias, Arildo S, Giroldo, Aelton B, Guo, Kun, Gutiérrez, Alvaro G, Hattingh, Wesley, He, Tianhua, Hietz, Peter, Hough-Snee, Nate, Jansen, Steven, Kattge, Jens, Klein, Tamir, Komac, Benjamin, Kraft, Nathan JB, Kramer, Koen, Lavorel, Sandra, Lusk, Christopher H, Martin, Adam R, Mencuccini, Maurizio, Michaletz, Sean T, Minden, Vanessa, Mori, Akira S, Niinemets, Ülo, Onoda, Yusuke, Peñuelas, Josep, Pillar, Valério D, Pisek, Jan, Robroek, Bjorn JM, Schamp, Brandon, Slot, Martijn, Sosinski, Ênio Egon, Soudzilovskaia, Nadejda A, Thiffault, Nelson, van Bodegom, Peter, van der Plas, Fons, Wright, Ian J, Xu, Wu-Bing, Zheng, Jingming, Enquist, Brian J, and Svenning, Jens-Christian

Subjects
Life on Land, Anthropogenic Effects, Biodiversity, Conservation of Natural Resources, Ecosystem, Humans, Phylogeny, Trees, biodiversity, conservation frameworks, land use, protected areas, tree species
Abstract

Safeguarding Earth's tree diversity is a conservation priority due to the importance of trees for biodiversity and ecosystem functions and services such as carbon sequestration. Here, we improve the foundation for effective conservation of global tree diversity by analyzing a recently developed database of tree species covering 46,752 species. We quantify range protection and anthropogenic pressures for each species and develop conservation priorities across taxonomic, phylogenetic, and functional diversity dimensions. We also assess the effectiveness of several influential proposed conservation prioritization frameworks to protect the top 17% and top 50% of tree priority areas. We find that an average of 50.2% of a tree species' range occurs in 110-km grid cells without any protected areas (PAs), with 6,377 small-range tree species fully unprotected, and that 83% of tree species experience nonnegligible human pressure across their range on average. Protecting high-priority areas for the top 17% and 50% priority thresholds would increase the average protected proportion of each tree species' range to 65.5% and 82.6%, respectively, leaving many fewer species (2,151 and 2,010) completely unprotected. The priority areas identified for trees match well to the Global 200 Ecoregions framework, revealing that priority areas for trees would in large part also optimize protection for terrestrial biodiversity overall. Based on range estimates for >46,000 tree species, our findings show that a large proportion of tree species receive limited protection by current PAs and are under substantial human pressure. Improved protection of biodiversity overall would also strongly benefit global tree diversity.

Published
2022

6. The global abundance of tree palms

Author

Muscarella, Robert, Emilio, Thaise, Phillips, Oliver L, Lewis, Simon L, Slik, Ferry, Baker, William J, Couvreur, Thomas LP, Eiserhardt, Wolf L, Svenning, Jens‐Christian, Affum‐Baffoe, Kofi, Aiba, Shin‐Ichiro, Almeida, Everton C, Almeida, Samuel S, Oliveira, Edmar Almeida, Álvarez‐Dávila, Esteban, Alves, Luciana F, Alvez‐Valles, Carlos Mariano, Carvalho, Fabrício Alvim, Guarin, Fernando Alzate, Andrade, Ana, Aragão, Luis EOC, Murakami, Alejandro Araujo, Arroyo, Luzmila, Ashton, Peter S, Corredor, Gerardo A Aymard, Baker, Timothy R, Camargo, Plinio Barbosa, Barlow, Jos, Bastin, Jean‐François, Bengone, Natacha Nssi, Berenguer, Erika, Berry, Nicholas, Blanc, Lilian, Böhning‐Gaese, Katrin, Bonal, Damien, Bongers, Frans, Bradford, Matt, Brambach, Fabian, Brearley, Francis Q, Brewer, Steven W, Camargo, Jose LC, Campbell, David G, Castilho, Carolina V, Castro, Wendeson, Catchpole, Damien, Martínez, Carlos E Cerón, Chen, Shengbin, Chhang, Phourin, Cho, Percival, Chutipong, Wanlop, Clark, Connie, Collins, Murray, Comiskey, James A, Medina, Massiel Nataly Corrales, Costa, Flávia RC, Culmsee, Heike, David‐Higuita, Heriberto, Davidar, Priya, Aguila‐Pasquel, Jhon, Derroire, Géraldine, Di Fiore, Anthony, Van Do, Tran, Doucet, Jean‐Louis, Dourdain, Aurélie, Drake, Donald R, Ensslin, Andreas, Erwin, Terry, Ewango, Corneille EN, Ewers, Robert M, Fauset, Sophie, Feldpausch, Ted R, Ferreira, Joice, Ferreira, Leandro Valle, Fischer, Markus, Franklin, Janet, Fredriksson, Gabriella M, Gillespie, Thomas W, Gilpin, Martin, Gonmadje, Christelle, Gunatilleke, Arachchige Upali Nimal, Hakeem, Khalid Rehman, Hall, Jefferson S, Hamer, Keith C, Harris, David J, Harrison, Rhett D, Hector, Andrew, Hemp, Andreas, Herault, Bruno, Pizango, Carlos Gabriel Hidalgo, Coronado, Eurídice N Honorio, Hubau, Wannes, Hussain, Mohammad Shah, Ibrahim, Faridah‐Hanum, Imai, Nobuo, Joly, Carlos A, Joseph, Shijo, Anitha, K, Kartawinata, Kuswata, Kassi, Justin, and Killeen, Timothy J

Subjects
Life on Land, above-ground biomass, abundance patterns, Arecaceae, local abiotic conditions, Neotropics, pantropical biogeography, tropical rainforest, wood density, Ecology
Abstract

Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location: Tropical and subtropical moist forests. Time period: Current. Major taxa studied: Palms (Arecaceae). Methods: We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co-occurring non-palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results: On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long-term climate stability. Life-form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non-tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above-ground biomass, but the magnitude and direction of the effect require additional work. Conclusions: Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

Published
2020

9. Taxonomy based on science is necessary for global conservation.

Author

Thomson, Scott A, Pyle, Richard L, Ahyong, Shane T, Alonso-Zarazaga, Miguel, Ammirati, Joe, Araya, Juan Francisco, Ascher, John S, Audisio, Tracy Lynn, Azevedo-Santos, Valter M, Bailly, Nicolas, Baker, William J, Balke, Michael, Barclay, Maxwell VL, Barrett, Russell L, Benine, Ricardo C, Bickerstaff, James RM, Bouchard, Patrice, Bour, Roger, Bourgoin, Thierry, Boyko, Christopher B, Breure, Abraham SH, Brothers, Denis J, Byng, James W, Campbell, David, Ceríaco, Luis MP, Cernák, István, Cerretti, Pierfilippo, Chang, Chih-Han, Cho, Soowon, Copus, Joshua M, Costello, Mark J, Cseh, Andras, Csuzdi, Csaba, Culham, Alastair, D'Elía, Guillermo, d'Udekem d'Acoz, Cédric, Daneliya, Mikhail E, Dekker, René, Dickinson, Edward C, Dickinson, Timothy A, van Dijk, Peter Paul, Dijkstra, Klaas-Douwe B, Dima, Bálint, Dmitriev, Dmitry A, Duistermaat, Leni, Dumbacher, John P, Eiserhardt, Wolf L, Ekrem, Torbjørn, Evenhuis, Neal L, Faille, Arnaud, Fernández-Triana, José L, Fiesler, Emile, Fishbein, Mark, Fordham, Barry G, Freitas, André VL, Friol, Natália R, Fritz, Uwe, Frøslev, Tobias, Funk, Vicki A, Gaimari, Stephen D, Garbino, Guilherme ST, Garraffoni, André RS, Geml, József, Gill, Anthony C, Gray, Alan, Grazziotin, Felipe G, Greenslade, Penelope, Gutiérrez, Eliécer E, Harvey, Mark S, Hazevoet, Cornelis J, He, Kai, He, Xiaolan, Helfer, Stephan, Helgen, Kristofer M, van Heteren, Anneke H, Hita Garcia, Francisco, Holstein, Norbert, Horváth, Margit K, Hovenkamp, Peter H, Hwang, Wei Song, Hyvönen, Jaakko, Islam, Melissa B, Iverson, John B, Ivie, Michael A, Jaafar, Zeehan, Jackson, Morgan D, Jayat, J Pablo, Johnson, Norman F, Kaiser, Hinrich, Klitgård, Bente B, Knapp, Dániel G, Kojima, Jun-Ichi, Kõljalg, Urmas, Kontschán, Jenő, Krell, Frank-Thorsten, Krisai-Greilhuber, Irmgard, Kullander, Sven, Latella, Leonardo, Lattke, John E, and Lencioni, Valeria

Subjects
Conservation of Natural Resources, Biodiversity, Biological Sciences, Medical And Health Sciences, Agricultural And Veterinary Sciences, Developmental Biology, Medical and Health Sciences, Agricultural and Veterinary Sciences
Published
2018

13. Global hotspots of plant phylogenetic diversity

Author

Tietje, Melanie, primary, Antonelli, Alexandre, additional, Forest, Félix, additional, Govaerts, Rafaël, additional, Smith, Stephen A., additional, Sun, Miao, additional, Baker, William J., additional, and Eiserhardt, Wolf L., additional

Published
2023
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14. A roadmap for global synthesis of the plant tree of life

Author

Eiserhardt, Wolf L., Antonelli, Alexandre, Bennett, Dominic J., Botigué, Laura R., Burleigh, J. Gordon, Dodsworth, Steven, Enquist, Brian J., Forest, Félix, Kim, Jan T., Kozlov, Alexey M., Leitch, Ilia J., Maitner, Brian S., Mirarab, Siavash, Piel, William H., Pérez-Escobar, Oscar A., Pokorny, Lisa, Rahbek, Carsten, Sandel, Brody, Smith, Stephen A., Stamatakis, Alexandros, Vos, Rutger A., Warnow, Tandy, and Baker, William J.

Published
2018

16. Global shortfalls in threat assessments for endemic flora by country

Author

Gallagher, Rachael V., primary, Allen, Stuart P., additional, Govaerts, Rafaël, additional, Rivers, Malin C., additional, Allen, Andrew P., additional, Keith, David A., additional, Merow, Cory, additional, Maitner, Brian, additional, Butt, Nathalie, additional, Auld, Tony D., additional, Enquist, Brian J., additional, Eiserhardt, Wolf L., additional, Wright, Ian J., additional, Mifsud, Jonathon C. O., additional, Espinosa‐Ruiz, Sylvia, additional, Possingham, Hugh, additional, and Adams, Vanessa M., additional

Published
2023
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17. A global assessment of the Raunkiæran shortfall in plants: geographic biases in our knowledge of plant traits.

Author

Maitner, Brian, Gallagher, Rachael, Svenning, Jens‐Christian, Tietje, Melanie, Wenk, Elizabeth H., and Eiserhardt, Wolf L.

Subjects
PLANT diversity, PHYTOGEOGRAPHY
Abstract

This article is part of the Special Collection 'Global plant diversity and distribution'. See https://www.newphytologist.org/global-plant-diversity for more details. [ABSTRACT FROM AUTHOR]

Published
2023
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19. A species‐level phylogenetic framework and infrageneric classification for the genus Maesa (Primulaceae).

Author

Sumanon, Pirada, Balslev, Henrik, Utteridge, Timothy M.A., and Eiserhardt, Wolf L.

Subjects
PRIMULACEAE, BOTANICAL specimens, POPULATION genetics, PHYLOGEOGRAPHY, BIOGEOGRAPHY, TAXONOMISTS, CLASSIFICATION
Abstract

The systematization of Maesa, a genus of almost 200 species, has haunted taxonomists for more than a century due to its lack of distinct qualitative characters or discontinuities in quantitative characters for species delimitation. The clarification of phylogenetic relationships in such a problematic genus like Maesa is essential to aid infrageneric classification and species delimitation. Here, a species‐level phylogenetic tree of Maesa is reconstructed. Leaf materials were sampled mainly from herbarium specimens which cover 60% of the species across the entire distribution range of the genus. Targeted sequence capture with the Angiosperms353 probe set was used to acquire sequences for downstream bioinformatic analyses. We obtained a species tree inferred from 310 gene trees that divides Maesa into an African clade and an Asian‐Pacific clade. The African clade is further divided into two subclades, while the Asian‐Pacific clade is divided into three subclades; all subclades are well supported. Hence, we propose five subgenera of Maesa, namely M. subg. Maesa, subg. Indicae, subg. Monotaxis, subg. Papuanae and subg. Ramentaceae. In addition, we scrutinize some species complexes within the genus; however, with the lack of phylogenetic signal at shallow levels, we are unable to conclusively resolve all species boundaries in these complexes. This study provides the phylogenomic framework to untangle taxonomic problems in the genus Maesa and lays the foundation for further detailed studies in biogeography, trait evolution and population genetics. [ABSTRACT FROM AUTHOR]

Published
2023
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40. Six new species of Maesa (Primulaceae) from Papua New Guinea

Author

Sumanon, Pirada, Eiserhardt, Wolf L., Balslev, Henrik, and Utteridge, Timothy M.A.

Subjects
Papua New Guinea, Papuasia, Tracheophyta, Magnoliopsida, Myrsinaceae, Biodiversity, Malesia, Plantae, Taxonomy, Ericales, Primulaceae
Abstract

Six new species of Maesa (Primulaceae-Maesoideae) from Papua New Guinea, namely M. angustibracteolata, M. aurulenta, M. brassii, M. oblanceolatifolia, M. pusilliflora and M. prolatifructa are described and illustrated based on observations from herbarium specimens; the taxonomic affinities of each species are also discussed.

Published
2021

44. Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation.

Author

Carruthers, Tom, Sun, Miao, Baker, William J, Smith, Stephen A, Vos, Jurriaan M de, and Eiserhardt, Wolf L

Subjects
TIME perception, HORIZONTAL gene transfer, SPECIES, FOSSILS
Abstract

Phylogenetic analyses are increasingly being performed with data sets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from the erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analyzing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with the species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation. [Divergence time estimation; gene trees; species tree; topological incongruence.] [ABSTRACT FROM AUTHOR]

Published
2022
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45. Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication

Author

Pérez-Escobar, Oscar A, primary, Bellot, Sidonie, additional, Przelomska, Natalia A S, additional, Flowers, Jonathan M, additional, Nesbitt, Mark, additional, Ryan, Philippa, additional, Gutaker, Rafal M, additional, Gros-Balthazard, Muriel, additional, Wells, Tom, additional, Kuhnhäuser, Benedikt G, additional, Schley, Rowan, additional, Bogarín, Diego, additional, Dodsworth, Steven, additional, Diaz, Rudy, additional, Lehmann, Manuela, additional, Petoe, Peter, additional, Eiserhardt, Wolf L, additional, Preick, Michaela, additional, Hofreiter, Michael, additional, Hajdas, Irka, additional, Purugganan, Michael, additional, Antonelli, Alexandre, additional, Gravendeel, Barbara, additional, Leitch, Ilia J, additional, Jimenez, Maria Fernanda Torres, additional, Papadopulos, Alexander S T, additional, Chomicki, Guillaume, additional, Renner, Susanne S, additional, and Baker, William J, additional

Published
2021
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47. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

Author

Baker, William J, primary, Bailey, Paul, additional, Barber, Vanessa, additional, Barker, Abigail, additional, Bellot, Sidonie, additional, Bishop, David, additional, Botigué, Laura R, additional, Brewer, Grace, additional, Carruthers, Tom, additional, Clarkson, James J, additional, Cook, Jeffrey, additional, Cowan, Robyn S, additional, Dodsworth, Steven, additional, Epitawalage, Niroshini, additional, Françoso, Elaine, additional, Gallego, Berta, additional, Johnson, Matthew G, additional, Kim, Jan T, additional, Leempoel, Kevin, additional, Maurin, Olivier, additional, Mcginnie, Catherine, additional, Pokorny, Lisa, additional, Roy, Shyamali, additional, Stone, Malcolm, additional, Toledo, Eduardo, additional, Wickett, Norman J, additional, Zuntini, Alexandre R, additional, Eiserhardt, Wolf L, additional, Kersey, Paul J, additional, Leitch, Ilia J, additional, and Forest, Félix, additional

Published
2021
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48. A robust phylogenomic framework for the calamoid palms

Author

Kuhnhäuser, Benedikt G., primary, Bellot, Sidonie, additional, Couvreur, Thomas L.P., additional, Dransfield, John, additional, Henderson, Andrew, additional, Schley, Rowan, additional, Chomicki, Guillaume, additional, Eiserhardt, Wolf L., additional, Hiscock, Simon J., additional, and Baker, William J., additional

Published
2021
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50. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

Author

Baker, William J., primary, Bailey, Paul, additional, Barber, Vanessa, additional, Barker, Abigail, additional, Bellot, Sidonie, additional, Bishop, David, additional, Botigué, Laura R., additional, Brewer, Grace, additional, Carruthers, Tom, additional, Clarkson, James J., additional, Cook, Jeffrey, additional, Cowan, Robyn S., additional, Dodsworth, Steven, additional, Epitawalage, Niroshini, additional, Françoso, Elaine, additional, Gallego, Berta, additional, Johnson, Matthew G., additional, Kim, Jan T., additional, Leempoel, Kevin, additional, Maurin, Olivier, additional, McGinnie, Catherine, additional, Pokorny, Lisa, additional, Roy, Shyamali, additional, Stone, Malcolm, additional, Toledo, Eduardo, additional, Wickett, Norman J., additional, Zuntini, Alexandre R., additional, Eiserhardt, Wolf L., additional, Kersey, Paul J., additional, Leitch, Ilia J., additional, and Forest, Félix, additional

Published
2021
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