369 results on '"Bacon, Christine D."'
Search Results
52. Delimitation of the Segregate Genera of Maytenus s. 1. (Celastraceae) Based on Morphological and Molecular Characters
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McKenna, Miles J., Simmons, Mark P., Bacon, Christine D., and Lombardi, Julio A.
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- 2011
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53. Lanonia (Arecaceae: Palmae), a New Genus from Asia, with a Revision of the Species
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Henderson, Andrew J. and Bacon, Christine D.
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- 2011
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54. Genome scans reveal high levels of gene flow in Hawaiian Pittosporum
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Bacon, Christine D., Allan, Gerard J., Zimmer, Elizabeth A., and Wagner, Warren L.
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- 2011
55. SUPPLEMENTARY INFORMATION from The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard
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Bacon, Christine D., Silvestro, Daniele, Hoorn, Carina, Bogotá-Ángel, Giovanni, Antonelli, Alexandre, and Chazot, Nicolas
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While the latitudinal diversity gradient has received much attention, biodiversity and species richness also vary between continents across similar latitudes. Fossil information can be leveraged to understand the evolutionary mechanisms that generated such variation between continents of similar latitudes. We integrated fossil data into a phylogenetic analysis of the Mauritiinae palms, whose extant diversity is restricted to the Neotropics, but extended across Africa and India during most of the Cenozoic. Mauritiinae diverged from its sister lineage Raphiinae ca 106 Ma. Using ancestral state estimation and a lineage through time analysis, we found that diversity arose globally during the late Cretaceous and Paleocene across South America, Africa and India. The Paleocene–Eocene transition (ca 56 Ma) marked the end of global Mauritiinae expansion, and the beginning of their decline in both Africa and India. Mauritiinae disappeared from the Indian subcontinent and Africa at the end of the Eocene and the Miocene, respectively. By contrast, Neotropical diversity steadily increased over the last 80 Ma. Taken together, our results suggest that the Neotropics functioned as a continental-scale refuge for Mauritiinae palms, where lineages survived and diversified while global climatic changes that drastically reduced rainforests led to their demise on other continents.
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- 2022
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56. Acaulescence promotes speciation and shapes the distribution patterns of palms in Neotropical seasonally dry habitats
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Cássia‐Silva, Cibele, primary, Oliveira, Rafael S., additional, Sales, Lílian P., additional, Freitas, Cíntia G., additional, Jardim, Lucas, additional, Emilio, Thaíse, additional, Bacon, Christine D., additional, and Collevatti, Rosane G., additional
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- 2022
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57. Taxonomy and Conservation: A Case Study from Chamaedorea alternans
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BACON, CHRISTINE D. and BAILEY, C. DONOVAN
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- 2006
58. Incongruent Spatial Distribution of Taxonomic, Phylogenetic, and Functional Diversity in Neotropical Cocosoid Palms
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Freitas, Cintia, primary, Brum, Fernanda T., additional, Cássia-Silva, Cibele, additional, Maracahipes, Leandro, additional, Carlucci, Marcos B., additional, Collevatti, Rosane G., additional, and Bacon, Christine D., additional
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- 2021
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59. The seasonally dry tropical forest species Cavanillesia chicamochae has a middle Quaternary origin
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Bacon, Christine D., primary, Gutiérrez‐Pinto, Natalia, additional, Flantua, Suzette, additional, Castellanos Suárez, Diego, additional, Jaramillo, Carlos, additional, Pennington, R. Toby, additional, and Antonelli, Alexandre, additional
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- 2021
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60. A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics
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G. Ribeiro, Pedro, primary, Torres Jiménez, María Fernanda, additional, Andermann, Tobias, additional, Antonelli, Alexandre, additional, Bacon, Christine D., additional, and Matos‐Maraví, Pável, additional
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- 2021
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61. Fruit colour and range size interact to influence diversification
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Hill, Adrian P., primary, Torres Jiménez, Maria Fernanda, additional, Chazot, Nicolas, additional, Cássia-Silva, Cibele, additional, Faurby, Søren, additional, and Bacon, Christine D., additional
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- 2021
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62. Functional and historical drivers of leaf shape evolution in Palms (Arecaceae)
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Jimenez, Maria Fernanda Torres, primary, Chazot, Nicolas, additional, Emilio, Thaise, additional, Fredin, Johan Uddling, additional, Antonelli, Alexandre, additional, Faurby, Soren, additional, and Bacon, Christine D, additional
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- 2021
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63. Phylogenomics of the Palm Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New Species of Mauritiella
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Jiménez, Maria Fernanda Torres, primary, Prata, Eduardo M. B., additional, Zizka, Alexander, additional, Cohn-Haft, Mario, additional, de Oliveira, Ayslaner V. G., additional, Emilio, Thaise, additional, Chazot, Nicolas, additional, Couvreur, Thomas L. P., additional, Kamga, Suzanne Mogue, additional, Sonké, Bonaventure, additional, Cano, Ángela, additional, Collevatti, Rosane G., additional, Kuhnhäuser, Benedikt G., additional, Baker, William J., additional, Antonelli, Alexandre, additional, and Bacon, Christine D., additional
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- 2021
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64. Biogeographic origins of southern African Silene (Caryophyllaceae)
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Moiloa, Ntwai A., primary, Mesbah, Melilia, additional, Nylinder, Stephan, additional, Manning, John, additional, Forest, Félix, additional, de Boer, Hugo J., additional, Bacon, Christine D., additional, and Oxelman, Bengt, additional
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- 2021
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65. Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses
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Ferreira, Paola de Lima, Batista, Romina, Andermann, Tobias, Groppo, Milton, Bacon, Christine D., and Antonelli, Alexandre
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Data Analysis ,missing data ,High-throughput sequencing ,Genome ,Genetics ,phylogenomics ,Genomics ,Asteraceae ,Molecular Biology ,museomics ,Ecology, Evolution, Behavior and Systematics ,Phylogeny - Abstract
Target sequence capture has emerged as a powerful method to sequence hundreds or thousands of genomic regions in a cost- and time-efficient approach. In most cases, however, targeted regions lack full sequence information for certain samples, due to taxonomic, laboratory, or stochastic factors. Loci lacking molecular data for a large number of samples are commonly excluded from downstream analyses, even though they may still contain valuable information. On the other hand, including data-poor loci may bias phylogenetic analyses. Here we use a target sequence capture dataset of an ecologically and taxonomically diverse group of spiny sunflowers (Asteraceae, or Compositae: Barnadesioideae) to test how the inclusion or exclusion of such data-poor loci affects phylogenetic inference. We investigate the sensitivity of concatenation and coalescent approaches to missing data with matrices of varying taxonomic completeness by filtering loci with different proportions of missing samples prior to data analysis. We find that missing data affect both the topology and branch support of the resulting phylogenies. The matrix containing all loci yielded the overall highest node support values, independently of the amount of missing nucleotides. These results provide empirical support to earlier suggestions based on single genes and data simulations that taxa with high amounts of missing data should not be readily dismissed as they can provide essential information for phylogenomic reconstruction.
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- 2021
66. Genomic and niche divergence in an Amazonian palm species complex
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Bacon, Christine D., Roncal, Julissa, Andermann, Tobias, Barnes, Christopher J., Balslev, Henrik, Gutiérrez-Pinto, Natalia, Morales, Hernán, Núñez-Avelleneda, Luis Alberto, Tunarosa, Natalia, Antonelli, Alexandre, Bacon, Christine D., Roncal, Julissa, Andermann, Tobias, Barnes, Christopher J., Balslev, Henrik, Gutiérrez-Pinto, Natalia, Morales, Hernán, Núñez-Avelleneda, Luis Alberto, Tunarosa, Natalia, and Antonelli, Alexandre
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Environmental heterogeneity across the landscape can cause lineage divergence and speciation. The Geonoma macrostachys (Arecaceae) species complex has been proposed as a candidate case of ecological speciation in Amazonia due to evidence of habitat partitioning and pre-zygotic reproductive barriers between co-occurring morphotypes at a local scale. In this study, we provide a continent-wide perspective of the divergence patterns in G. macrostachys by integrating data from morphological traits, target sequence capture, climate, soil and reproductive biology. A morphometric analysis revealed four morphogroups, defined by traits related to leaf shape. A coalescence-based phylogenetic analysis did not recover the morphogroups as monophyletic, indicating independent evolution of leaf shape across geographical space. We demonstrate scale-dependent habitat differentiation for two of the morphogroups, in which segregation driven mostly by climate was complete at the regional scale but incomplete at the continental scale. Contrary to previous evidence of reproductive isolation in the form of different pollinators and flowering times between sympatric G. macrostachys forms in Peru and Ecuador, these were not found in Colombia, suggesting reproductive barriers have evolved multiple times across its geographical range. Taken together, our findings suggest that ecological divergence and local adaptation is driving diversification in G. macrostachys, and that hyperdiverse regions such as Amazonia are probable arenas for ecological divergence in sympatry.
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- 2021
67. Decreased soil moisture due to warming drives phylogenetic diversity and community transitions in the tundra
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Scharn, Ruud, primary, Little, Chelsea J, additional, Bacon, Christine D, additional, Alatalo, Juha M, additional, Antonelli, Alexandre, additional, Björkman, Mats P, additional, Molau, Ulf, additional, Nilsson, R Henrik, additional, and Björk, Robert G, additional
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- 2021
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68. Genomic and niche divergence in an Amazonian palm species complex
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Bacon, Christine D, primary, Roncal, Julissa, additional, Andermann, Tobias, additional, Barnes, Christopher J, additional, Balslev, Henrik, additional, Gutiérrez-Pinto, Natalia, additional, Morales, Hernán, additional, Núñez-Avelleneda, Luis Alberto, additional, Tunarosa, Natalia, additional, and Antonelli, Alexandre, additional
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- 2021
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69. In situradiation explains the frequency of dioecious palms on islands
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Cássia-Silva, Cibele, primary, Freitas, Cíntia G, additional, Jardim, Lucas, additional, Bacon, Christine D, additional, and Collevatti, Rosane G, additional
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- 2021
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70. Unbiased clade age estimation using a Bayesian Brownian Bridge
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Silvestro, Daniele, primary, Bacon, Christine D., additional, Ding, Wenna, additional, Zhang, Qiuyue, additional, Donoghue, Philip C. J., additional, Antonelli, Alexandre, additional, and Xing, Yaowu, additional
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- 2021
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71. Climate and geological change as drivers of Mauritiinae palm biogeography
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Bogotá‐Ángel, Giovanni, primary, Huang, Huasheng, additional, Jardine, Phillip E., additional, Chazot, Nicolas, additional, Salamanca, Sonia, additional, Banks, Hannah, additional, Pardo‐Trujillo, Andres, additional, Plata, Angelo, additional, Dueñas, Hernando, additional, Star, Wim, additional, Langelaan, Rob, additional, Eisawi, Ali, additional, Umeji, Obianuju P., additional, Enuenwemba, Lucky O., additional, Parmar, Shalini, additional, Silveira, Rosemery Rocha, additional, Lim, Jun Ying, additional, Prasad, Vandana, additional, Morley, Robert J., additional, Bacon, Christine D., additional, and Hoorn, Carina, additional
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- 2021
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72. Transitions between biomes are common and directional in Bombacoideae (Malvaceae)
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Zizka, Alexander, Carvalho-Sobrinho, Jefferson, Pennington, Toby R., Queiroz, Luciano, Alcantara, Suzana, Baum, David, Bacon, Christine D., and Antonelli, Alexandre
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Rainforest ,Biome connectivity ,Biome shift ,Diversification ,Seasonally dry biomes ,Tropical biodiversity ,education ,Seasonality ,behavioral disciplines and activities - Abstract
Analysis scripts and required input data to reproduce the analyses of the study. Furthermore, shapefiles containing species distribution ranges as modelled in this study and all analysis scripts as used. The gene alignments can be found in data/phylogeny.
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- 2020
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73. Supplementary Information from Selective extinction against redundant species buffers functional diversity
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Pimiento, Catalina, Bacon, Christine D., Silvestro, Daniele, Hendy, Austin, Jaramillo, Carlos, Zizka, Alexander, Meyer, Xavier, and Antonelli, Alexandre
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The extinction of species can destabilize ecological processes. A way to assess the ecological consequences of species loss is by examining changes in functional diversity. The preservation of functional diversity depends on the range of ecological roles performed by species, or functional richness, and the number of species per role, or functional redundancy. However, current knowledge is based on short timescales and an understanding of how functional diversity responds to long-term biodiversity dynamics has been limited by the availability of deep-time, trait-based data. Here, we compile an exceptional trait dataset of fossil molluscs from a 23-million-year interval in the Caribbean Sea (34 011 records, 4422 species) and develop a novel Bayesian model of multi-trait-dependent diversification to reconstruct mollusc (i) diversity dynamics, (ii) changes in functional diversity, and (iii) extinction selectivity over the last 23 Myr. Our results identify high diversification between 23–5 Mya, leading to increases in both functional richness and redundancy. Conversely, over the last three million years, a period of high extinction rates resulted in the loss of 49% of species but only 3% of functional richness. Extinction rates were significantly higher in small, functionally redundant species suggesting that competition mediated the response of species to environmental change. Taken together, our results identify long-term diversification and selective extinction against redundant species that allowed functional diversity to grow over time, ultimately buffering the ecological functions of biological communities against extinction.
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- 2020
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74. Supplementary Information;Supplementary Dataset from Selective extinction against redundant species buffers functional diversity
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Pimiento, Catalina, Bacon, Christine D., Silvestro, Daniele, Hendy, Austin, Jaramillo, Carlos, Zizka, Alexander, Meyer, Xavier, and Antonelli, Alexandre
- Abstract
The extinction of species can destabilize ecological processes. A way to assess the ecological consequences of species loss is by examining changes in functional diversity. The preservation of functional diversity depends on the range of ecological roles performed by species, or functional richness, and the number of species per role, or functional redundancy. However, current knowledge is based on short timescales and an understanding of how functional diversity responds to long-term biodiversity dynamics has been limited by the availability of deep-time, trait-based data. Here, we compile an exceptional trait dataset of fossil mollusks from a 23-million-year interval in the Caribbean Sea (34 011records, 4422 species) and develop a novel Bayesian model of multi-trait-dependent diversification to reconstruct mollusk (i) diversity dynamics, (ii) changes in functional diversity and (iii) extinction selectivity over the last 23 Myr. Our results identify high diversification between 23–5 Mya, leading to increases in both functional richness and redundancy. Conversely, over the last three million years, a period of high extinction rates resulted in the loss of 49% of species but only 3% of functional richness. Extinction rates were significantly higher in small, functionally redundant species suggesting that competition mediated the response of species to environmental change. Taken together, our results identify long-term diversification and selective extinction against redundant species that allowed functional diversity to grow over time, ultimately buffering the ecological functions of biological communities against extinction.
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- 2020
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75. Selective extinction against redundant species buffers functional diversity
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Pimiento, Catalina; https://orcid.org/0000-0002-5320-7246, Bacon, Christine D; https://orcid.org/0000-0003-2341-2705, Silvestro, Daniele, Hendy, Austin, Jaramillo, Carlos, Zizka, Alexander, Meyer, Xavier, Antonelli, Alexandre, Pimiento, Catalina; https://orcid.org/0000-0002-5320-7246, Bacon, Christine D; https://orcid.org/0000-0003-2341-2705, Silvestro, Daniele, Hendy, Austin, Jaramillo, Carlos, Zizka, Alexander, Meyer, Xavier, and Antonelli, Alexandre
- Abstract
The extinction of species can destabilize ecological processes. A way to assess the ecological consequences of species loss is by examining changes in functional diversity. The preservation of functional diversity depends on the range of ecological roles performed by species, or functional richness, and the number of species per role, or functional redundancy. However, current knowledge is based on short timescales and an understanding of how functional diversity responds to long-term biodiversity dynamics has been limited by the availability of deep-time, trait-based data. Here, we compile an exceptional trait dataset of fossil molluscs from a 23-million-year interval in the Caribbean Sea (34 011 records, 4422 species) and develop a novel Bayesian model of multi-trait-dependent diversification to reconstruct mollusc (i) diversity dynamics, (ii) changes in functional diversity, and (iii) extinction selectivity over the last 23 Myr. Our results identify high diversification between 23–5 Mya, leading to increases in both functional richness and redundancy. Conversely, over the last three million years, a period of high extinction rates resulted in the loss of 49% of species but only 3% of functional richness. Extinction rates were significantly higher in small, functionally redundant species suggesting that competition mediated the response of species to environmental change. Taken together, our results identify long-term diversification and selective extinction against redundant species that allowed functional diversity to grow over time, ultimately buffering the ecological functions of biological communities against extinction.
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- 2020
76. Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)
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Eriksson, Jonna Sofia, primary, Bacon, Christine D., additional, Bennett, Dominic J., additional, Pfeil, Bernard E., additional, Oxelman, Bengt, additional, and Antonelli, Alexandre, additional
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- 2021
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77. Landscape configuration of an Amazonian island-like ecosystem drives population structure and genetic diversity of a habitat-specialist bird
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Ritter, Camila D., primary, Ribas, Camila C., additional, Menger, Juliana, additional, Borges, Sergio H., additional, Bacon, Christine D., additional, Metzger, Jean P., additional, Bates, John, additional, and Cornelius, Cintia, additional
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- 2020
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78. Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm
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Melo, Warita A., primary, Vieira, Lucas D., additional, Novaes, Evandro, additional, Bacon, Christine D., additional, and Collevatti, Rosane G., additional
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- 2020
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79. Gender inequality and not female mentors hinder female scientists career outcomes
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Diele-Viegas, Luisa Maria, primary, Almeida, Thamara S, additional, Amati-Martins, Iris, additional, Bacon, Christine D., additional, Silva, Cibele de Cassia, additional, Collevatti, Rosane G., additional, Cordeiro, Tabata E F, additional, Fenker, Jessica, additional, Ferrari, Giuliana, additional, Franco, Ana C S, additional, Gasparetto, Luiza F, additional, Hipolito, Juliana, additional, Hohlenwerger, Camila, additional, Hormanseder, Beatriz, additional, Jesus, Priscila B, additional, Matos, Suzana, additional, Mejia, Daniela P., additional, Murer, Beatriz M, additional, Pavone, Carla B, additional, Pilecco, Flavia B., additional, Queiroz, Caren, additional, Reis, Alice, additional, Santana, Pamela C, additional, Silva, Fernanda, additional, Souza, Lucy, additional, Telles, Mariana P C, additional, Viaggi, Jemilli, additional, and Virginio, Flavia, additional
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- 2020
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80. Two ancient genome duplication events shape diversity in Hibiscus L. (Malvaceae)
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Eriksson, Jonna Sofia, primary, Bacon, Christine D., additional, Bennett, Dominic J., additional, Pfeil, Bernard E., additional, Oxelman, Bengt, additional, and Antonelli, Alexandre, additional
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- 2020
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81. Pollinators drive floral evolution in an Atlantic Forest genus
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Neves, Beatriz, primary, Kessous, Igor M, additional, Moura, Ricardo L, additional, Couto, Dayvid R, additional, Zanella, Camila M, additional, Antonelli, Alexandre, additional, Bacon, Christine D, additional, Salgueiro, Fabiano, additional, and Costa, Andrea F, additional
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- 2020
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82. Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae)
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Helmstetter, Andrew J., primary, Kamga, Suzanne Mogue, additional, Bethune, Kevin, additional, Lautenschläger, Thea, additional, Zizka, Alexander, additional, Bacon, Christine D., additional, Wieringa, Jan J., additional, Stauffer, Fred, additional, Antonelli, Alexandre, additional, Sonké, Bonaventure, additional, and Couvreur, Thomas L. P., additional
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- 2020
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83. Transitions between biomes are common and directional in Bombacoideae (Malvaceae)
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Zizka, Alexander, primary, Carvalho‐Sobrinho, Jefferson G., additional, Pennington, R. Toby, additional, Queiroz, Luciano P., additional, Alcantara, Suzana, additional, Baum, David A., additional, Bacon, Christine D., additional, and Antonelli, Alexandre, additional
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- 2020
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84. A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
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Andermann, Tobias, primary, Torres Jiménez, Maria Fernanda, additional, Matos-Maraví, Pável, additional, Batista, Romina, additional, Blanco-Pastor, José L., additional, Gustafsson, A. Lovisa S., additional, Kistler, Logan, additional, Liberal, Isabel M., additional, Oxelman, Bengt, additional, Bacon, Christine D., additional, and Antonelli, Alexandre, additional
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- 2020
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85. The seasonally dry tropical forest species Cavanillesia chicamochae has a middle Quaternary origin.
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Bacon, Christine D., Gutiérrez‐Pinto, Natalia, Flantua, Suzette, Castellanos Suárez, Diego, Jaramillo, Carlos, Pennington, R. Toby, and Antonelli, Alexandre
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POPULATION differentiation ,ENDANGERED species ,NUCLEOTIDE sequence ,SPECIES ,LANDSCAPE changes ,TROPICAL dry forests - Abstract
Copyright of Biotropica is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2022
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86. Soil fertility and flood regime are correlated with phylogenetic structure of Amazonian palm communities
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Muscarella, Robert, Bacon, Christine D., Faurby, Soren, Antonelli, Alexandre, Kristiansen, Soren Munch, Svenning, Jens-Christian, Balslev, Henrik, Muscarella, Robert, Bacon, Christine D., Faurby, Soren, Antonelli, Alexandre, Kristiansen, Soren Munch, Svenning, Jens-Christian, and Balslev, Henrik
- Abstract
Background and Aims Identifying the processes that generate and maintain biodiversity requires understanding of how evolutionary processes interact with abiotic conditions to structure communities. Edaphic gradients are strongly associated with floristic patterns but, compared with climatic gradients, have received relatively little attention. We asked (1) How does the phylogenetic composition of palm communities vary along edaphic gradients within major habitat types? and (2) To what extent are phylogenetic patterns determined by (a) habitat specialists, (b) small versus large palms, and (c) hyperdiverse genera? Methods We paired data on palm community composition from 501 transects of 0.25 ha located in two main habitat types (non-inundated uplands and seasonally inundated floodplains) in western Amazonian rain forests with information on soil chemistry, climate, phylogeny and metrics of plant size. We focused on exchangeable base concentration (cmol(+) kg(-1)) as a metric of soil fertility and a floristic index of inundation intensity. We used a null model approach to quantify the standard effect size of mean phylogenetic distance for each transect (a metric of phylogenetic community composition) and related this value to edaphic variables using generalized linear mixed models, including a term for spatial autocorrelation. Key Results Overall, we recorded 112 008 individuals belonging to 110 species. Palm communities in non-inundated upland transects (but not floodplain transects) were more phylogenetically clustered in areas of low soil fertility, measured as exchangeable base concentration. In contrast, floodplain transects with more severe flood regimes (as inferred from floristic structure) tended to be phylogenetically clustered. Nearly half of the species recorded (44 %) were upland specialists while 18 % were floodplain specialists. In both habitat types, phylogenetic clustering was largely due to the co-occurrence of small-sized habitat specialists belong
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- 2019
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87. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
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Bravo, Gustavo A., Antonelli, Alexandre, Bacon, Christine D., Bartoszek, Krzysztof, Blom, Mozes P. K., Huynh, Stella, Jones, Graham, Knowles, L. Lacey, Lamichhaney, Sangeet, Marcussen, Thomas, Morlon, Helene, Nakhleh, Luay K., Oxelman, Bengt, Pfeil, Bernard, Schliep, Alexander, Wahlberg, Niklas, Werneck, Fernanda P., Wiedenhoeft, John, Willows-Munro, Sandi, Edwards, Scott V, Bravo, Gustavo A., Antonelli, Alexandre, Bacon, Christine D., Bartoszek, Krzysztof, Blom, Mozes P. K., Huynh, Stella, Jones, Graham, Knowles, L. Lacey, Lamichhaney, Sangeet, Marcussen, Thomas, Morlon, Helene, Nakhleh, Luay K., Oxelman, Bengt, Pfeil, Bernard, Schliep, Alexander, Wahlberg, Niklas, Werneck, Fernanda P., Wiedenhoeft, John, Willows-Munro, Sandi, and Edwards, Scott V
- Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress., Funding Agencies|Chalmers University of Technology; University of Gothenburg; Swedish Research Council; U.S. National Science Foundation; European Research Council under the European Unions Seventh Framework Programme (FP/2007-2013, ERC) [331024]; Swedish Foundation for Strategic Research; Wallenberg Academy Fellowship; Conselho Nacional de Desenvolvimento Cientifico e Tecnologico-CNPq; U.S. National Academy of Sciences; U.S. Agency of International Development-PEER NAS/USAID; LOreal-Unesco For Women in Science Program
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- 2019
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88. Targeted capture of hundreds of nuclear genes unravels phylogenetic relationships of the diverse neotropical palm tribe Geonomateae
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Loiseau, Oriane, Olivares, Ingrid; https://orcid.org/0000-0003-0888-3445, Paris, Margot, de La Harpe, Marylaure, Weigand, Anna, Koubínová, Darina, Rolland, Jonathan, Bacon, Christine D, Balslev, Henrik, Borchsenius, Finn, Cano, Angela, Couvreur, Thomas L P, Delnatte, César, Fardin, Frédérique, Gayot, Marc, Mejía, Fabian, Mota-Machado, Talita, Perret, Mathieu, Roncal, Julissa, Sanin, Maria José, Stauffer, Fred, Lexer, Christian, Kessler, Michael; https://orcid.org/0000-0003-4612-9937, Salamin, Nicolas, Loiseau, Oriane, Olivares, Ingrid; https://orcid.org/0000-0003-0888-3445, Paris, Margot, de La Harpe, Marylaure, Weigand, Anna, Koubínová, Darina, Rolland, Jonathan, Bacon, Christine D, Balslev, Henrik, Borchsenius, Finn, Cano, Angela, Couvreur, Thomas L P, Delnatte, César, Fardin, Frédérique, Gayot, Marc, Mejía, Fabian, Mota-Machado, Talita, Perret, Mathieu, Roncal, Julissa, Sanin, Maria José, Stauffer, Fred, Lexer, Christian, Kessler, Michael; https://orcid.org/0000-0003-4612-9937, and Salamin, Nicolas
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- 2019
89. Make EU trade with Brazil sustainable
- Author
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Kehoe, Laura, Reis, Tiago, Virah-Sawmy, Malika, Balmford, Andrew, Kuemmerle, Tobias, Knohl, Alexander, Antonelli, Alexandre, Hochkirch, Axel, Vira, Bhaskar, Massa, Bruno, Peres, Carlos A., Ammer, Christian, Goerg, Christoph, Schneider, Christoph, Curtis, David, de la Pena, Eduardo, Tello, Enric, Sperfeld, Erik, Corbera, Esteve, Morelli, Federico, Valladares, Fernando, Peterson, Garry, Hide, Geoff, Mace, Georgina, Kallis, Giorgos, Olsson, Gunilla Almered, Brumelis, Guntis, Alexanderson, Helena, Haberl, Helmut, Nuissl, Henning, Kreft, Holger, Ghazoul, Jaboury, Piotrowski, Jan A., Macdiarmid, Jennie, Newig, Jens, Fischer, Joern, Altringham, John, Gledhill, John, Nielsen, Jonas O., Mueller, Joerg, Palmeirim, Jorge, Barlow, Jos, Alonso, Juan C., Presa Asencio, Juan Jose, Steinberger, Julia K., Jones, Julia Patricia Gordon, Cabral, Juliano Sarmento, Dengler, Juergen, Stibral, Karel, Erb, Karlheinz, Rothhaupt, Karl-Otto, Wiegand, Kerstin, Cassar, Louis F., Lens, Luc, Rosalino, Luis Miguel, Wassen, M. J., Stenseke, Marie, Fischer-Kowalski, Marina, Diaz, Mario, Rounsevell, Mark, van Kleunen, Mark, Junginger, Martin, Kaltenpoth, Martin, Zobel, Martin, Weigend, Maximilian, Partel, Meelis, Schilthuizen, Menno, Bastos Araujo, Miguel, Haklay, Muki, Eisenhauer, Nico, Selva, Nuria, Mertz, Ole, Meyfroidt, Patrick, Borges, Paulo A. V., Kovar, Pavel, Smith, Pete, Verburg, Peter, Pysek, Petr, Seppelt, Ralf, Valentini, Riccardo, Whittaker, Robert J., Henrique Faria, Sergio, Ulgiati, Sergio, Loetters, Stefan, Bjorck, Svante, Larson, Sven Ake, Tscharntke, Teja, Domingos, Tiago, Krueger, Tobias, Pascual, Unai, Olsson, Urban, Kati, Vassiliki, Winiwarter, Verena, Reyes-Garcia, Victoria, Vajda, Vivi, Sutherland, William J., de Waroux, Yann le Polain, Buckley, Yvonne, Rammig, Anja, Kasimir, Asa, Crona, Beatrice, Sindicic, Magda, Persson, Martin, Lapka, Miloslav, Di Gregorio, Monica, Hahn, Thomas, Boonstra, Wiebren, Lipsky, Zdenek, Zucaro, A., Roeder, Achim, Lopez Baucells, Adria, Danet, Alain, Franco, Aldina, Nieto Roman, Alejandra, Lehikoinen, Aleksi, Collalti, Alessio, Keller, Alexander, Strugariu, Alexandru, Perrigo, Allison, Fernandez-Llamazares, Alvaro, Salaseviciene, Alvija, Hinsley, Amy, Santos, Ana M. C., Novoa, Ana, Rodrigues, Ana, Mascarenhas, Andre, Martins, Andrea Damacena, Holzschuh, Andrea, Meseguer, Andrea S., Hadjichambis, Andreas, Mayer, Andreas, Hacket-Pain, Andrew, Ringsmuth, Andrew, de Frutos, Angel, Stein, Anke, Heikkinen, Anna, Smith, Annabel, Bjoersne, Anna-Karin, Bagneres, Anne-Genevieve, Machordom, Annie, Kristin, Anton, Ghoddousi, Arash, Staal, Arie, Martin, Arnaud, Taylor, Astrid, Borrell, Asuncion, Marescaux, Audrey, Torres, Aurora, Helm, Aveliina, Bauer, Barbara, Smetschka, Barbara, Rodriguez-Labajos, Beatriz, Peco, Begona, Gambin, Belinda, Celine, Bellard, Phalan, Ben, Cotta, Benedetta, Rugani, Benedetto, Jarcuska, Benjamin, Leroy, Boris, Nikolov, Boris Petrov, Milchev, Boyan Petrov, Brown, Calum, Ritter, Camila Duarte, Gomes, Carmen Bessa, Meyer, Carsten, Munteanu, Catalina, Penone, Caterina, Friis, Cecilie, Teplitsky, Celine, Roemer, Charlotte, Orland, Chloe, Voigt, Christian C., Levers, Christian, Zang, Christian, Bacon, Christine D., Meyer, Christoph, Wordley, Claire, Grilo, Clara, Cattaneo, Claudio, Battisti, Corrado, Banks-Leite, Cristina, Zurell, Damaris, Challender, Dan, Mueller, Daniel, Matenaar, Daniela, Silvestro, Daniele, McKay, David Armstrong, Buckley, David, Frantz, David, Gremillet, David, Mateos, David Moreno, Sanchez-Fernandez, David, Vieites, David, Ascoli, Davide, Arlt, Debora, Louis, Deharveng, Zemp, Delphine Clara, Strubbe, Diederik, Gil, Diego, Llusia, Diego, Bennett, Dominic J., Chobanov, Dragan Petrov, Aguilera, Eduardo, Oliveira, Eduardo, Pynegar, Edwin L., Granda, Elena, Grieco, Elisa, Conrad, Elisabeth, Revilla, Eloy, Lindkvist, Emilie, Caprio, Enrico, zu Ermgassen, Erasmus, Berenguer, Erika, Ochu, Erinma, Polaina, Ester, Nuernberger, Fabian, Esculier, Fabien, de Castro, Fabio, Albanito, Fabrizio, Langerwisch, Fanny, Batsleer, Femke, Ascensao, Fernando, Moyano, Fernando Esteban, Sayol, Ferran, Buzzetti, Filippo Maria, Eiro, Flavio, Volaire, Florence, Gollnow, Florian, Menzel, Florian, Pilo, Francesca, Moreira, Francisco, Briens, Francois, Essl, Franz, Vlahos, George, Billen, Gilles, Vacchiano, Giorgio, Wong, Grace, Gruychev, Gradimir Valentinov, Fandos, Guillermo, Petter, Gunnar, Sinare, Hanna, Mumby, Hannah S., Cottyn, Hanne, Seebens, Hanno, Bjorklund, Heidi, Schroeder, Heike, Lopez Hernandez, Heriberto D., Rebelo, Hugo, Chenet, Hugues, De la Riva, Ignacio, Torre, Ignasi, Aalders, Inge, Grass, Ingo, Chuine, Isabelle, Goepel, Jan, Wieringa, Jan J., Engler, Jan O., Pergl, Jan, Schnitzler, Jan, Vavra, Jan, Medvedovic, Jasna, Cabello, Javier, Martin, Jean-Louis, Mutke, Jens, Lewis, Jerome, da Silva, Jessica Fonseca, Marull, Joan, Carvalho, Joana, Carnicer, Jofre, Enqvist, Johan, Simaika, John P., Noguera, Jose C., Blanco Moreno, Jose M., Bruna, Josef, Garnier, Josette, Fargallo, Juan A., Rocha, Juan Carlos, Carrillo, Juan D., Infante-Amate, Juan, Traba Diaz, Juan, Schleicher, Judith, Simon, Judy, Noe, Julia Le, Gerlach, Justin, Eriksson, K. Martin, Prince, Karine, Ostapowicz, Katarzyna, Stajerova, Katerina, Farrell, Katharine N., Snell, Katherine, Yates, Katherine, Fleischer, Katrin, Darras, Kevin, Schumacher, Kim, Orach, Kirill, Thonicke, Kirsten, Riede, Klaus, Heller, Klaus-Gerhard, Wang-Erlandsson, Lan, Pereira, Laura, Riggi, Laura, Florez, Laura V., Emperaire, Laure, Durieux, Laurent, Tatin, Laurent, Rozylowicz, Laurentiu, Latella, Leonardo, Andresen, Louise C., Cahen-Fourot, Louison, de Agua, Luis Borda, Boto, Luis, Lassaletta, Luis, Amo, Luisa, Sekerka, Lukas, Morales, Manuel B., Macia, Manuel J., Suarez, Manuela Gonzalez, Cabeza, Mar, Londo, Marc, Pollet, Marc, Schwieder, Marcel, Peters, Marcell K., D'Amico, Marcello, Casazza, Marco, Florencio, Margarita, Felipe-Lucia, Maria, Gebara, Maria Fernanda, Johansson, Maria, Garcia, Maria Mancilla, Piquer-Rodriguez, Maria, Tengo, Maria, Elias, Marianne, Leve, Marine, Conde, Marta, Winter, Marten, Koster, Martijn, Mayer, Martin, Salek, Martin, Schlerf, Martin, Sullivan, Martin, Baumann, Matthias, Pichler, Melanie, Marselle, Melissa, Oddie, Melissa, Razanajatovo, Mialy, Borregaard, Michael Krabbe, Theurl, Michaela C., Hernandez, Miguel, Krofel, Miha, Kechev, Mihail Ognianov, Clark, Mike, Rands, Mike, Antal, Miklos, Pucetaite, Milda, Islar, Mine, Truong, Minh-Xuan A., Vighi, Morgana, Johanisova, Nadia, Prat, Narcis, Escobar, Neus, Deguines, Nicolas, Rust, Niki, Zafra-Calvo, Noelia, Maurel, Noelie, Wagner, Norman, Fitton, Nuala, Ostermann, Ole, Panferov, Oleg, Ange, Olivia, Canals, Oriol, Englund, Oskar, De Smedt, Pallieter, Petridis, Panos, Heikkurinen, Pasi, Weigelt, Patrick, Henriksson, Patrik J. G., de Castro, Paula Drummond, Matos-Maravi, Pavel, Duran, Paz, Aragon, Pedro, Cardoso, Pedro, Leitao, Pedro J., Hosner, Peter A., Biedermann, Peter, Keil, Petr, Petrik, Petr, Martin, Philip, Bocquillon, Pierre, Renaud, Pierre-Cyril, Addison, Prue, Antwis, Rachael, Carmenta, Rachel, Barrientos, Rafael, Smith, Rebecca, Rocha, Ricardo, Fuchs, Richard, Felix, Rob, Kanka, Robert, Aguilee, Robin, Padro Caminal, Roc, Libbrecht, Romain, Lorrilliere, Romain, van der Ent, Ruud J., Henders, Sabine, Pueyo, Salvador, Roturier, Samuel, Jacobs, Sander, Lavorel, Sandra, Leonhardt, Sara Diana, Fraixedas, Sara, Villen-Perez, Sara, Cornell, Sarah, Redlich, Sarah, De Smedt, Sebastian, van der Linden, Sebastian, Perez-Ortega, Sergio, Petrovan, Silviu, Cesarz, Simone, Sjoberg, Sissel, Caillon, Sophie, Schindler, Stefan, Trogisch, Stefan, Taiti, Stefano, Oppel, Steffen, Lutter, Stephan, Garnett, Tara, Guedes, Thais, Wanger, Thomas Cherico, Kastner, Thomas, Worthington, Thomas, Daw, Tim, Schmoll, Tim, McPhearson, Timon, Engl, Tobias, Rutting, Tobias, Vaclavik, Tomas, Jucker, Tommaso, Robillard, Tony, Krause, Torsten, Ljubomirov, Toshko, Aavik, Tsipe, Richardson, Vanessa A., Masterson, Vanessa Anne, Seufert, Verena, Cathy, Vet Gibault, Colino Rabanal, Victor, Montade, Vincent, Thieu, Vincent, Sober, Virve, Morin, Xavier, Mehrabi, Zia, Gonzalez, Adriana Trompetero, Sanz-Cobena, Alberto, Christie, Alec Philip, Romero-Munoz, Alfredo, Dauriach, Alice, Queiroz, Allan Souza, Golland, Ami, Evans, Amy Louise, Cordero, Ana Maria Araujo, Dara, Andrey, Rilovic, Andro, Pedersen, Anna Frohn, Csergo, Anna Maria, Lewerentz, Anne, Monserand, Antoine, Valdecasas, Antonio G., Doherty, Anya, Semper-Pascual, Asuncion, Bleyhl, Benjamin, Rutschmann, Benjamin, Bongalov, Boris, Hankerson, Brett, Heylen, Brigitte, Alonso-Alvarez, Carlos, Comandulli, Carolina, Frossard, Carolina M., Mckeon, Caroline, Godde, Cecile, Palm, Celinda, Singh, Chandrakant, Sieger, Charlotte Sophie, Ohrling, Christian, Paitan, Claudia Parra, Cooper, Conor, Edler, Daniel, Roessler, Daniela C., Kessner-Beierlein, Daniela, Garcia del Amo, David, Lopez Bosch, David, Gueldner, Dino, Noll, Domink, Motivans, Elena, Canteri, Elisabetta, Garnett, Emma, Malecore, Eva, Brambach, Fabian, Ruedenauer, Fabian, Yin, Fang, Hurtado, Fernando, Mempel, Finn, de Freitas, Flavio Luiz Mazzaro, Pendrill, Florence, Leijten, Floris, Somma, Francesca, Schug, Franz, De Knijf, Geert, Peterson, Gustaf, Pe'er, Guy, Booth, Hollie, Rhee, Howon, Staude, Ingmar, Gherghel, Iulian, Vila Traver, Jaime, Kerner, Janika, Hinton, Jennifer, Hortal, Joaquin, Persson, Joel, Uddling, Johan, Coenen, Johanna, Geldmann, Jonas, Geschke, Jonas, Juergensen, Jonathan, Lobo, Jorge M., Skejo, Josip, Heinen, Julia Helena, Schuenzel, Julia, Daniel-Ferreira, Juliana, Christophe Piquet, Julien, Murtough, Katie L., Prevel, Leonie, Hissa, Leticia B. V., af Segerstad, Louise Hard, Willemse, Luc, Benavides, Lucia, Sovova, Lucie, Figueiredo, Ludmilla, Leidinger, Ludwig, Piemontese, Luigi, da Fonte, Luis Fernando Marin, Moreta, Lys Sanz, Bhan, Manan, Toledo-Hernandez, Manuel, Engert, Manuela, Davoli, Marco, Mas Navarro, Maria, Voigt, Maria, Zirion, Maria, Wandl, Marie-Theres, Kipson, Marina, Johnson, Mark D., Lukic, Marko, Goula, Marta, Jung, Martin, Nunes, Matheus Henrique, Alvarez, Matheus Rodriguez, van den Burg, Matthijs P., Guerrero, Mayra Daniela Pena, Greenfield, Michael, Lobmann, Michael, Nygren, Michelle, Guth, Miriam Karen, Koh, Niak, Stanek, Nicola, Roux, Nicolas, Karagouni, Niki, Tiralla, Nina, Mairota, Paola, Savaget, Paulo, von Doehren, Peer, Benyei, Petra, Lena, Philippe, Rufin, Philippe, Janke, Rebekka, Santagata, Remo, Motta, Renzo, Battiston, Roberto, Oyanedel, Rodrigo, Bernardo-Madrid, Ruben, Vasconcelos, Sasha, Henriques, Sergio, Bager, Simon L., Qin, Siyu, Ivkovic, Slobodan, Cooke, Sophia, Ernst, Stefan, Schmelzer, Stefan, da Silva, Sven, Faberova, Tamara, Enseroth, Tanja, De Marzo, Teresa, Pienkowski, Thomas, Engel, Thore, Boehnert, Tim, Swinfield, Tom, Kurdikova, Vendula, Chvatalova, Veronika, Lopez-Marquez, Violeta, Arlidge, William, Zhang, Zhijie, Kehoe, Laura, Reis, Tiago, Virah-Sawmy, Malika, Balmford, Andrew, Kuemmerle, Tobias, Knohl, Alexander, Antonelli, Alexandre, Hochkirch, Axel, Vira, Bhaskar, Massa, Bruno, Peres, Carlos A., Ammer, Christian, Goerg, Christoph, Schneider, Christoph, Curtis, David, de la Pena, Eduardo, Tello, Enric, Sperfeld, Erik, Corbera, Esteve, Morelli, Federico, Valladares, Fernando, Peterson, Garry, Hide, Geoff, Mace, Georgina, Kallis, Giorgos, Olsson, Gunilla Almered, Brumelis, Guntis, Alexanderson, Helena, Haberl, Helmut, Nuissl, Henning, Kreft, Holger, Ghazoul, Jaboury, Piotrowski, Jan A., Macdiarmid, Jennie, Newig, Jens, Fischer, Joern, Altringham, John, Gledhill, John, Nielsen, Jonas O., Mueller, Joerg, Palmeirim, Jorge, Barlow, Jos, Alonso, Juan C., Presa Asencio, Juan Jose, Steinberger, Julia K., Jones, Julia Patricia Gordon, Cabral, Juliano Sarmento, Dengler, Juergen, Stibral, Karel, Erb, Karlheinz, Rothhaupt, Karl-Otto, Wiegand, Kerstin, Cassar, Louis F., Lens, Luc, Rosalino, Luis Miguel, Wassen, M. J., Stenseke, Marie, Fischer-Kowalski, Marina, Diaz, Mario, Rounsevell, Mark, van Kleunen, Mark, Junginger, Martin, Kaltenpoth, Martin, Zobel, Martin, Weigend, Maximilian, Partel, Meelis, Schilthuizen, Menno, Bastos Araujo, Miguel, Haklay, Muki, Eisenhauer, Nico, Selva, Nuria, Mertz, Ole, Meyfroidt, Patrick, Borges, Paulo A. V., Kovar, Pavel, Smith, Pete, Verburg, Peter, Pysek, Petr, Seppelt, Ralf, Valentini, Riccardo, Whittaker, Robert J., Henrique Faria, Sergio, Ulgiati, Sergio, Loetters, Stefan, Bjorck, Svante, Larson, Sven Ake, Tscharntke, Teja, Domingos, Tiago, Krueger, Tobias, Pascual, Unai, Olsson, Urban, Kati, Vassiliki, Winiwarter, Verena, Reyes-Garcia, Victoria, Vajda, Vivi, Sutherland, William J., de Waroux, Yann le Polain, Buckley, Yvonne, Rammig, Anja, Kasimir, Asa, Crona, Beatrice, Sindicic, Magda, Persson, Martin, Lapka, Miloslav, Di Gregorio, Monica, Hahn, Thomas, Boonstra, Wiebren, Lipsky, Zdenek, Zucaro, A., Roeder, Achim, Lopez Baucells, Adria, Danet, Alain, Franco, Aldina, Nieto Roman, Alejandra, Lehikoinen, Aleksi, Collalti, Alessio, Keller, Alexander, Strugariu, Alexandru, Perrigo, Allison, Fernandez-Llamazares, Alvaro, Salaseviciene, Alvija, Hinsley, Amy, Santos, Ana M. C., Novoa, Ana, Rodrigues, Ana, Mascarenhas, Andre, Martins, Andrea Damacena, Holzschuh, Andrea, Meseguer, Andrea S., Hadjichambis, Andreas, Mayer, Andreas, Hacket-Pain, Andrew, Ringsmuth, Andrew, de Frutos, Angel, Stein, Anke, Heikkinen, Anna, Smith, Annabel, Bjoersne, Anna-Karin, Bagneres, Anne-Genevieve, Machordom, Annie, Kristin, Anton, Ghoddousi, Arash, Staal, Arie, Martin, Arnaud, Taylor, Astrid, Borrell, Asuncion, Marescaux, Audrey, Torres, Aurora, Helm, Aveliina, Bauer, Barbara, Smetschka, Barbara, Rodriguez-Labajos, Beatriz, Peco, Begona, Gambin, Belinda, Celine, Bellard, Phalan, Ben, Cotta, Benedetta, Rugani, Benedetto, Jarcuska, Benjamin, Leroy, Boris, Nikolov, Boris Petrov, Milchev, Boyan Petrov, Brown, Calum, Ritter, Camila Duarte, Gomes, Carmen Bessa, Meyer, Carsten, Munteanu, Catalina, Penone, Caterina, Friis, Cecilie, Teplitsky, Celine, Roemer, Charlotte, Orland, Chloe, Voigt, Christian C., Levers, Christian, Zang, Christian, Bacon, Christine D., Meyer, Christoph, Wordley, Claire, Grilo, Clara, Cattaneo, Claudio, Battisti, Corrado, Banks-Leite, Cristina, Zurell, Damaris, Challender, Dan, Mueller, Daniel, Matenaar, Daniela, Silvestro, Daniele, McKay, David Armstrong, Buckley, David, Frantz, David, Gremillet, David, Mateos, David Moreno, Sanchez-Fernandez, David, Vieites, David, Ascoli, Davide, Arlt, Debora, Louis, Deharveng, Zemp, Delphine Clara, Strubbe, Diederik, Gil, Diego, Llusia, Diego, Bennett, Dominic J., Chobanov, Dragan Petrov, Aguilera, Eduardo, Oliveira, Eduardo, Pynegar, Edwin L., Granda, Elena, Grieco, Elisa, Conrad, Elisabeth, Revilla, Eloy, Lindkvist, Emilie, Caprio, Enrico, zu Ermgassen, Erasmus, Berenguer, Erika, Ochu, Erinma, Polaina, Ester, Nuernberger, Fabian, Esculier, Fabien, de Castro, Fabio, Albanito, Fabrizio, Langerwisch, Fanny, Batsleer, Femke, Ascensao, Fernando, Moyano, Fernando Esteban, Sayol, Ferran, Buzzetti, Filippo Maria, Eiro, Flavio, Volaire, Florence, Gollnow, Florian, Menzel, Florian, Pilo, Francesca, Moreira, Francisco, Briens, Francois, Essl, Franz, Vlahos, George, Billen, Gilles, Vacchiano, Giorgio, Wong, Grace, Gruychev, Gradimir Valentinov, Fandos, Guillermo, Petter, Gunnar, Sinare, Hanna, Mumby, Hannah S., Cottyn, Hanne, Seebens, Hanno, Bjorklund, Heidi, Schroeder, Heike, Lopez Hernandez, Heriberto D., Rebelo, Hugo, Chenet, Hugues, De la Riva, Ignacio, Torre, Ignasi, Aalders, Inge, Grass, Ingo, Chuine, Isabelle, Goepel, Jan, Wieringa, Jan J., Engler, Jan O., Pergl, Jan, Schnitzler, Jan, Vavra, Jan, Medvedovic, Jasna, Cabello, Javier, Martin, Jean-Louis, Mutke, Jens, Lewis, Jerome, da Silva, Jessica Fonseca, Marull, Joan, Carvalho, Joana, Carnicer, Jofre, Enqvist, Johan, Simaika, John P., Noguera, Jose C., Blanco Moreno, Jose M., Bruna, Josef, Garnier, Josette, Fargallo, Juan A., Rocha, Juan Carlos, Carrillo, Juan D., Infante-Amate, Juan, Traba Diaz, Juan, Schleicher, Judith, Simon, Judy, Noe, Julia Le, Gerlach, Justin, Eriksson, K. Martin, Prince, Karine, Ostapowicz, Katarzyna, Stajerova, Katerina, Farrell, Katharine N., Snell, Katherine, Yates, Katherine, Fleischer, Katrin, Darras, Kevin, Schumacher, Kim, Orach, Kirill, Thonicke, Kirsten, Riede, Klaus, Heller, Klaus-Gerhard, Wang-Erlandsson, Lan, Pereira, Laura, Riggi, Laura, Florez, Laura V., Emperaire, Laure, Durieux, Laurent, Tatin, Laurent, Rozylowicz, Laurentiu, Latella, Leonardo, Andresen, Louise C., Cahen-Fourot, Louison, de Agua, Luis Borda, Boto, Luis, Lassaletta, Luis, Amo, Luisa, Sekerka, Lukas, Morales, Manuel B., Macia, Manuel J., Suarez, Manuela Gonzalez, Cabeza, Mar, Londo, Marc, Pollet, Marc, Schwieder, Marcel, Peters, Marcell K., D'Amico, Marcello, Casazza, Marco, Florencio, Margarita, Felipe-Lucia, Maria, Gebara, Maria Fernanda, Johansson, Maria, Garcia, Maria Mancilla, Piquer-Rodriguez, Maria, Tengo, Maria, Elias, Marianne, Leve, Marine, Conde, Marta, Winter, Marten, Koster, Martijn, Mayer, Martin, Salek, Martin, Schlerf, Martin, Sullivan, Martin, Baumann, Matthias, Pichler, Melanie, Marselle, Melissa, Oddie, Melissa, Razanajatovo, Mialy, Borregaard, Michael Krabbe, Theurl, Michaela C., Hernandez, Miguel, Krofel, Miha, Kechev, Mihail Ognianov, Clark, Mike, Rands, Mike, Antal, Miklos, Pucetaite, Milda, Islar, Mine, Truong, Minh-Xuan A., Vighi, Morgana, Johanisova, Nadia, Prat, Narcis, Escobar, Neus, Deguines, Nicolas, Rust, Niki, Zafra-Calvo, Noelia, Maurel, Noelie, Wagner, Norman, Fitton, Nuala, Ostermann, Ole, Panferov, Oleg, Ange, Olivia, Canals, Oriol, Englund, Oskar, De Smedt, Pallieter, Petridis, Panos, Heikkurinen, Pasi, Weigelt, Patrick, Henriksson, Patrik J. G., de Castro, Paula Drummond, Matos-Maravi, Pavel, Duran, Paz, Aragon, Pedro, Cardoso, Pedro, Leitao, Pedro J., Hosner, Peter A., Biedermann, Peter, Keil, Petr, Petrik, Petr, Martin, Philip, Bocquillon, Pierre, Renaud, Pierre-Cyril, Addison, Prue, Antwis, Rachael, Carmenta, Rachel, Barrientos, Rafael, Smith, Rebecca, Rocha, Ricardo, Fuchs, Richard, Felix, Rob, Kanka, Robert, Aguilee, Robin, Padro Caminal, Roc, Libbrecht, Romain, Lorrilliere, Romain, van der Ent, Ruud J., Henders, Sabine, Pueyo, Salvador, Roturier, Samuel, Jacobs, Sander, Lavorel, Sandra, Leonhardt, Sara Diana, Fraixedas, Sara, Villen-Perez, Sara, Cornell, Sarah, Redlich, Sarah, De Smedt, Sebastian, van der Linden, Sebastian, Perez-Ortega, Sergio, Petrovan, Silviu, Cesarz, Simone, Sjoberg, Sissel, Caillon, Sophie, Schindler, Stefan, Trogisch, Stefan, Taiti, Stefano, Oppel, Steffen, Lutter, Stephan, Garnett, Tara, Guedes, Thais, Wanger, Thomas Cherico, Kastner, Thomas, Worthington, Thomas, Daw, Tim, Schmoll, Tim, McPhearson, Timon, Engl, Tobias, Rutting, Tobias, Vaclavik, Tomas, Jucker, Tommaso, Robillard, Tony, Krause, Torsten, Ljubomirov, Toshko, Aavik, Tsipe, Richardson, Vanessa A., Masterson, Vanessa Anne, Seufert, Verena, Cathy, Vet Gibault, Colino Rabanal, Victor, Montade, Vincent, Thieu, Vincent, Sober, Virve, Morin, Xavier, Mehrabi, Zia, Gonzalez, Adriana Trompetero, Sanz-Cobena, Alberto, Christie, Alec Philip, Romero-Munoz, Alfredo, Dauriach, Alice, Queiroz, Allan Souza, Golland, Ami, Evans, Amy Louise, Cordero, Ana Maria Araujo, Dara, Andrey, Rilovic, Andro, Pedersen, Anna Frohn, Csergo, Anna Maria, Lewerentz, Anne, Monserand, Antoine, Valdecasas, Antonio G., Doherty, Anya, Semper-Pascual, Asuncion, Bleyhl, Benjamin, Rutschmann, Benjamin, Bongalov, Boris, Hankerson, Brett, Heylen, Brigitte, Alonso-Alvarez, Carlos, Comandulli, Carolina, Frossard, Carolina M., Mckeon, Caroline, Godde, Cecile, Palm, Celinda, Singh, Chandrakant, Sieger, Charlotte Sophie, Ohrling, Christian, Paitan, Claudia Parra, Cooper, Conor, Edler, Daniel, Roessler, Daniela C., Kessner-Beierlein, Daniela, Garcia del Amo, David, Lopez Bosch, David, Gueldner, Dino, Noll, Domink, Motivans, Elena, Canteri, Elisabetta, Garnett, Emma, Malecore, Eva, Brambach, Fabian, Ruedenauer, Fabian, Yin, Fang, Hurtado, Fernando, Mempel, Finn, de Freitas, Flavio Luiz Mazzaro, Pendrill, Florence, Leijten, Floris, Somma, Francesca, Schug, Franz, De Knijf, Geert, Peterson, Gustaf, Pe'er, Guy, Booth, Hollie, Rhee, Howon, Staude, Ingmar, Gherghel, Iulian, Vila Traver, Jaime, Kerner, Janika, Hinton, Jennifer, Hortal, Joaquin, Persson, Joel, Uddling, Johan, Coenen, Johanna, Geldmann, Jonas, Geschke, Jonas, Juergensen, Jonathan, Lobo, Jorge M., Skejo, Josip, Heinen, Julia Helena, Schuenzel, Julia, Daniel-Ferreira, Juliana, Christophe Piquet, Julien, Murtough, Katie L., Prevel, Leonie, Hissa, Leticia B. V., af Segerstad, Louise Hard, Willemse, Luc, Benavides, Lucia, Sovova, Lucie, Figueiredo, Ludmilla, Leidinger, Ludwig, Piemontese, Luigi, da Fonte, Luis Fernando Marin, Moreta, Lys Sanz, Bhan, Manan, Toledo-Hernandez, Manuel, Engert, Manuela, Davoli, Marco, Mas Navarro, Maria, Voigt, Maria, Zirion, Maria, Wandl, Marie-Theres, Kipson, Marina, Johnson, Mark D., Lukic, Marko, Goula, Marta, Jung, Martin, Nunes, Matheus Henrique, Alvarez, Matheus Rodriguez, van den Burg, Matthijs P., Guerrero, Mayra Daniela Pena, Greenfield, Michael, Lobmann, Michael, Nygren, Michelle, Guth, Miriam Karen, Koh, Niak, Stanek, Nicola, Roux, Nicolas, Karagouni, Niki, Tiralla, Nina, Mairota, Paola, Savaget, Paulo, von Doehren, Peer, Benyei, Petra, Lena, Philippe, Rufin, Philippe, Janke, Rebekka, Santagata, Remo, Motta, Renzo, Battiston, Roberto, Oyanedel, Rodrigo, Bernardo-Madrid, Ruben, Vasconcelos, Sasha, Henriques, Sergio, Bager, Simon L., Qin, Siyu, Ivkovic, Slobodan, Cooke, Sophia, Ernst, Stefan, Schmelzer, Stefan, da Silva, Sven, Faberova, Tamara, Enseroth, Tanja, De Marzo, Teresa, Pienkowski, Thomas, Engel, Thore, Boehnert, Tim, Swinfield, Tom, Kurdikova, Vendula, Chvatalova, Veronika, Lopez-Marquez, Violeta, Arlidge, William, and Zhang, Zhijie
- Published
- 2019
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- View/download PDF
90. In situ radiation explains the frequency of dioecious palms on islands.
- Author
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Cássia-Silva, Cibele, Freitas, Cíntia G, Jardim, Lucas, Bacon, Christine D, and Collevatti, Rosane G
- Subjects
PALMS ,ISLANDS ,ARCHIPELAGOES ,POLYGAMY ,RADIATION ,COMPARATIVE method - Abstract
Background and Aims Dioecy has evolved up to 5000 times in angiosperms, despite the potentially high intrinsic costs to unisexuality. Dioecy prevents inbreeding, which is especially relevant on isolated islands when gene pools are small. Dioecy is also associated with certain dispersal traits, such as fruit size and type. However, the influence of dioecy on other life history traits and island distribution remains poorly understood. Here, we test the effect of dioecy on palm (Arecaceae) speciation rates, fruit size and frequency on islands. Methods We used phylogenetic comparative methods to estimate the ancestral state of the sexual system and its impact on speciation rates and fruit size. Frequency of sexual systems, effect of insularity on the probability of being dioecious, and phylogenetic clustering of island dioecious vs. mainland species were inferred. Lastly, we determined the interplay of insularity and sexual system on speciation rates. Key Results Palms repeatedly evolved different sexual systems (dioecy, monoecy and polygamy) from a hermaphrodite origin. Differences in speciation rates and fruit size among the different sexual systems were not identified. An effect of islands on the probability of the palms being dioecious was also not found. However, we found a high frequency and phylogenetic clustering of dioecious palms on islands, which were not correlated with higher speciation rates. Conclusions The high frequency and phylogenetic clustering may be the result of in situ radiation and suggest an 'island effect' for dioecious palms, which was not explained by differential speciation rates. This island effect also cannot be attributed to long-distance dispersal due to the lack of fruit size difference among sexual systems, and particularly because palm dispersal to islands is highly constrained by the interaction between the sizes of fruit and frugivores. Taken together, we suggest that trait flexibility in sexual system evolution and the in situ radiation of dioecious lineages are the underlying causes of the outstanding distribution of palms on islands. [ABSTRACT FROM AUTHOR]
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- 2021
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91. Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia)
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Bacon Christine D, McKenna Miles J, Simmons Mark P, and Wagner Warren L
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Hawaii ,Hybridization ,Lineage sorting ,Microsatellite ,Pritchardia ,Radiation ,Evolution ,QH359-425 - Abstract
Abstract Background Robust species delimitations are fundamental for conservation, evolutionary, and systematic studies, but they can be difficult to estimate, particularly in rapid and recent radiations. The consensus that species concepts aim to identify evolutionarily distinct lineages is clear, but the criteria used to distinguish evolutionary lineages differ based on the perceived importance of the various characteristics of evolving populations. We examined three different species-delimitation criteria (monophyly, absence of genetic intermediates, and diagnosability) to determine whether currently recognized species of Hawaiian Pritchardia are distinct lineages. Results Data from plastid and nuclear genes, microsatellite loci, and morphological characters resulted in various levels of lineage subdivision that were likely caused by differing evolutionary rates between data sources. Additionally, taxonomic entities may be confounded because of the effects of incomplete lineage sorting and/or gene flow. A coalescent species tree was largely congruent with the simultaneous analysis, consistent with the idea that incomplete lineage sorting did not mislead our results. Furthermore, gene flow among populations of sympatric lineages likely explains the admixture and lack of resolution between those groups. Conclusions Delimiting Hawaiian Pritchardia species remains difficult but the ability to understand the influence of the evolutionary processes of incomplete lineage sorting and hybridization allow for mechanisms driving species diversity to be inferred. These processes likely extend to speciation in other Hawaiian angiosperm groups and the biota in general and must be explicitly accounted for in species delimitation.
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- 2012
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92. Drivers of bromeliad leaf and floral bract variation across a latitudinal gradient in the Atlantic Forest
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Neves, Beatriz, primary, Zanella, Camila M., additional, Kessous, Igor M., additional, Uribbe, Fernando P., additional, Salgueiro, Fabiano, additional, Bered, Fernanda, additional, Antonelli, Alexandre, additional, Bacon, Christine D., additional, and Costa, Andrea F., additional
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- 2019
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93. A guide to carrying out a phylogenomic target sequence capture project
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Andermann, Tobias, primary, Torres Jimenez, Maria Fernanda, additional, Matos-Maraví, Pável, additional, Batista, Romina, additional, Blanco-Pastor, José L, additional, Gustafsson, A. Lovisa S, additional, Kistler, Logan, additional, Liberal, Isabel M, additional, Oxelman, Bengt, additional, Bacon, Christine D, additional, and Antonelli, Alexandre, additional
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- 2019
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94. Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae
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Loiseau, Oriane, primary, Olivares, Ingrid, additional, Paris, Margot, additional, de La Harpe, Marylaure, additional, Weigand, Anna, additional, Koubínová, Darina, additional, Rolland, Jonathan, additional, Bacon, Christine D., additional, Balslev, Henrik, additional, Borchsenius, Finn, additional, Cano, Angela, additional, Couvreur, Thomas L. P., additional, Delnatte, César, additional, Fardin, Frédérique, additional, Gayot, Marc, additional, Mejía, Fabian, additional, Mota-Machado, Talita, additional, Perret, Mathieu, additional, Roncal, Julissa, additional, Sanin, Maria José, additional, Stauffer, Fred, additional, Lexer, Christian, additional, Kessler, Michael, additional, and Salamin, Nicolas, additional
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- 2019
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95. Travel for two
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Bacon, Christine D., primary
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- 2019
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96. Phylogenomics, biogeography and evolution in the American genus Brahea (Arecaceae)
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Barrett, Craig F, primary, Sinn, Brandon T, additional, King, Loren T, additional, Medina, Jesus C, additional, Bacon, Christine D, additional, Lahmeyer, Sean C, additional, and Hodel, Donald R, additional
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- 2019
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97. Could coastal plants in western Amazonia be relicts of past marine incursions?
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Bernal, Rodrigo, primary, Bacon, Christine D., additional, Balslev, Henrik, additional, Hoorn, Carina, additional, Bourlat, Sarah J., additional, Tuomisto, Hanna, additional, Salamanca, Sonia, additional, van Manen, Milan Teunissen, additional, Romero, Ingrid, additional, Sepulchre, Pierre, additional, and Antonelli, Alexandre, additional
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- 2019
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98. Ancient Polyploidy and Genome Evolution in Palms
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Barrett, Craig F, primary, McKain, Michael R, additional, Sinn, Brandon T, additional, Ge, Xue-Jun, additional, Zhang, Yuqu, additional, Antonelli, Alexandre, additional, and Bacon, Christine D, additional
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- 2019
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99. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
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Bravo, Gustavo A., primary, Antonelli, Alexandre, additional, Bacon, Christine D., additional, Bartoszek, Krzysztof, additional, Blom, Mozes P. K., additional, Huynh, Stella, additional, Jones, Graham, additional, Knowles, L. Lacey, additional, Lamichhaney, Sangeet, additional, Marcussen, Thomas, additional, Morlon, Hélène, additional, Nakhleh, Luay K., additional, Oxelman, Bengt, additional, Pfeil, Bernard, additional, Schliep, Alexander, additional, Wahlberg, Niklas, additional, Werneck, Fernanda P., additional, Wiedenhoeft, John, additional, Willows-Munro, Sandi, additional, and Edwards, Scott V., additional
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- 2019
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100. Niche conservatism drives a global discrepancy in palm species richness between seasonally dry and moist habitats
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Cássia‐Silva, Cibele, primary, Freitas, Cíntia G., additional, Alves, Davi M. C. C., additional, Bacon, Christine D., additional, and Collevatti, Rosane G., additional
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- 2019
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