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1,132 results on '"Chase, Mark W."'

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. Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae)

Author

McCarthy, Elizabeth W, Landis, Jacob B, Kurti, Amelda, Lawhorn, Amber J, Chase, Mark W, Knapp, Sandra, Le Comber, Steven C, Leitch, Andrew R, and Litt, Amy

Subjects
Biological Sciences, Evolutionary Biology, Human Genome, Genetics, Stem Cell Research, Biological Evolution, Databases, Genetic, Diploidy, Flowers, Phenotype, Phylogeny, Polyploidy, Solanaceae, Ancestral character state reconstruction, Evolution, Flower color, Flower morphology, Geometric morphometrics, Hybridization, Nicotiana, Microbiology, Plant Biology, Crop and Pasture Production, Plant Biology & Botany, Crop and pasture production, Plant biology
Abstract

BackgroundPolyploidy has played a major role in angiosperm evolution. Previous studies have examined polyploid phenotypes in comparison to their extant progenitors, but not in context of predicted progenitor phenotypes at allopolyploid origin. In addition, differences in the trends of polyploid versus diploid evolution have not been investigated. We use ancestral character-state reconstructions to estimate progenitor phenotype at allopolyploid origin to determine patterns of polyploid evolution leading to morphology of the extant species. We also compare trends in diploid versus allopolyploid evolution to determine if polyploidy modifies floral evolutionary patterns.ResultsPredicting the ancestral phenotype of a nascent allopolyploid from reconstructions of diploid phenotypes at the time of polyploid formation generates different phenotype predictions than when extant diploid phenotypes are used, the outcome of which can alter conclusions about polyploid evolution; however, most analyses yield the same results. Using ancestral reconstructions of diploid floral phenotypes indicate that young polyploids evolve shorter, wider corolla tubes, but older polyploids and diploids do not show any detectable evolutionary trends. Lability of the traits examined (floral shape, corolla tube length, and corolla tube width) differs across young and older polyploids and diploids. Corolla length is more evolutionarily labile in older polyploids and diploids. Polyploids do not display unique suites of floral characters based on both morphological and color traits, but some suites of characters may be evolving together and seem to have arisen multiple times within Nicotiana, perhaps due to the influence of pollinators.ConclusionsYoung polyploids display different trends in floral evolution (shorter, wider corolla tubes, which may result in more generalist pollination) than older polyploids and diploids, suggesting that patterns of divergence are impacted by the early consequences of allopolyploidy, perhaps arising from genomic shock and/or subsequent genome stabilization associated with diploidization. Convergent evolution in floral morphology and color in Nicotiana can be consistent with pollinator preferences, suggesting that pollinators may have shaped floral evolution in Nicotiana.

Published
2019

4. Chromosome number, heterochromatin, and genome size support recent polyploid origin of the Epidendrum nocturnum group and reveal a new species (Laeliinae, Orchidaceae)

Author

Cordeiro, Joel M.P., Chase, Mark W., Hagsater, Eric, Almeida, Erton Mendonça, Costa, Lucas, Souza, Gustavo, Nollet, Felipe, and Felix, Leonardo P.

Subjects
Plant cytotaxonomy, Orchids -- Genetic aspects -- Identification and classification -- Physiological aspects, Botanical research, Biological sciences
Abstract

The Epidendrum nocturnum Jacq. group comprises about 60 species. Nine species occur in Brazil, predominantly in the Atlantic and Amazon Forests. The group is taxonomically complex because its species are morphologically similar and not easily distinguished. The main objective of this work is to characterize their chromosome evolution and how this has affected species delimitation in Brazilian representatives of the E. nocturnum group. We used chromosome numbers, heterochromatin band patterns, and genome size variation to better understand the chromosome variation, species delimitation, and the relationship among seven representatives of this group. A new species from the Cerrado/Amazon Rainforest ecotone is described based on cytological and morphological characters. The new species, Epidendrum pareciense sp. nov., is a diploid (2n = 40), Epidendrum bahiense Rchb.f., Epidendrum carpophorum Barb.Rodr., Epidendrum micronocturnum Carnevali & G.A.Romero, Epidendrum purpureocaulis Sambin & Essers, and E. nocturnum are tetraploids (2n = 80), and Epidendrum tumuc-humaciense (Veyret) Carnevali & G.A.Romero is hexaploid (2n = 120), the last a new ploidy for the group. Heterochromatin in these species is characterized by guanine-cytosine-rich regions (cromomycin A3 ([CMA.sup.+]) bands) on proximal and terminal regions associated with NORs. Genome size and numbers of CMA terminal bands are directly related to ploidy, suggesting that diploidization has not yet occurred and supporting the hypothesis of a recent polyploid origin for the E. nocturnum group. Key words: chromosome banding, CMA/DAPI, cytotaxonomy, taxonomic complexes, 1C. Le groupe Epidendrum nocturnum Jacq. comprend environ 60 espèces. Neuf espèces sont présentes au Brésil, principalement dans les forêts atlantique et amazonienne. Le groupe est complexe du point de vue taxonomique, car ses espèces sont morphologiquement similaires et ne se distinguent pas facilement. L'objectif principal de ce travail consiste à caractériser leur évolution chromosomique et la façon dont cela a affecté la délimitation des espèces chez les représentants brésiliens du groupe E. nocturnum. Les auteurs ont utilisé le nombre de chromosomes, les patrons des bandes d'hétérochromatine et la variation de la taille du génome pour mieux comprendre la variation chromosomique, la délimitation des espèces et la relation entre sept représentants de ce groupe. Une nouvelle espèce de l'écotone Cerrado/Forêt humide amazonienne est décrite sur la base de caractères cytologiques et morphologiques. La nouvelle espèce, Epidendrum pareciense sp. nov., est diploïde (2n = 40), Epidendrum bahiense Rchb.f., Epidendrum carpophorum Barb.Rodr., Epidendrum micronocturnum Carnevali & G.A.Romero, Epidendrum purpureocaulis Sambin & Essers, et E. nocturnum sont tétraploïdes (2n = 80), et Epidendrum tumuc-humaciense (Veyret) Carnevali & G.A.Romero est hexaploïde (2n = 120), ce dernier représentant une nouvelle ploïdie pour le groupe. L'hétérochromatine de ces espèces est caractérisée par des régions riches en guanine-cytosine (bandes cromomycin A3 ([CMA.sup.+])) sur les régions proximales et terminales associées aux RON. La taille du génome et le nombre de bandes terminales CMA sont directement liés à la ploïdie, suggérant que la diploïdisation n'a pas encore eu lieu et soutenant l'hypothèse d'une origine polyploïde récente pour le groupe E. nocturnum. [Traduit par la Rédaction] Mots-clés : bandes chromosomiques, CMA/DAPI, cytotaxonomie, complexes taxonomiques, 1C., Introduction Epidendrum nocturnum Jacq. is the nomenclatural type of the genus Epidendrum L. (Dressler 1984; Hagsater 1985) and has been considered a highly polymorphic species complex of wide geographic distribution [...]

Published
2022
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6. Recent speciation and adaptation to aridity in the ecologically diverse Pilbara region of Australia enabled the native tobaccos (Nicotiana; Solanaceae) to colonize all Australian deserts.

Author

Cauz‐Santos, Luiz A., Samuel, Rosabelle, Metschina, Dominik, Christenhusz, Maarten J. M., Dodsworth, Steven, Dixon, Kingsley W., Conran, John G., Paun, Ovidiu, and Chase, Mark W.

Subjects
ARID regions, BOTANY, BIOGEOGRAPHY, SOLANACEAE, ECOLOGICAL niche
Abstract

Over the last 6 million years, the arid Australian Eremaean Zone (EZ) has remained as dry as it is today. A widely accepted hypothesis suggests that the flora and fauna of arid regions were more broadly distributed before aridification began. In Australia, this process started around 20 million years ago (Ma), leading to gradual speciation as the climate became increasingly arid. Here, we use genomic data to investigate the biogeography and timing of divergence of native allotetraploid tobaccos, Nicotiana section Suaveolentes (Solanaceae). The original allotetraploid migrants from South America were adapted to mesic areas of Australia and recently radiated in the EZ, including in sandy dune fields (only 1.2 Ma old), after developing drought adaptations. Coalescent and maximum likelihood analyses suggest that Nicotiana section Suaveolentes arrived on the continent around 6 Ma, with the ancestors of the Pilbara (Western Australian) lineages radiating there at the onset of extreme aridity 5 Ma by locally adapting to these various ancient, highly stable habitats. The Pilbara thus served as both a mesic refugium and cradle for adaptations to harsher conditions, due to its high topographical diversity, providing microhabitats with varying moisture levels and its proximity to the ocean, which buffers against extreme aridity. This enabled species like Nicotiana to survive in mesic refugia and subsequently adapt to more arid conditions. These results demonstrate that initially poorly adapted plant groups can develop novel adaptations in situ, permitting extensive and rapid dispersal despite the highly variable and unpredictable extreme conditions of the EZ. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Genetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers.

Author

Wimalarathna, Nilni A., Wickramasuriya, Anushka M., Metschina, Dominik, Cauz-Santos, Luiz A., Bandupriya, Dharshani, Ariyawansa, Kahandawa G. S. U., Gopallawa, Bhathiya, Chase, Mark W., Samuel, Rosabelle, and Silva, Tara D.

Subjects
GENETIC variation, BLACK pepper (Plant), GENOME-wide association studies, PEPPER growing, SINGLE nucleotide polymorphisms, POPULATION genetics, NUCLEOTIDE sequencing
Abstract

Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from eight main black pepper growing regions in Sri Lanka. The sequencing effort resulted in 1,976 million raw reads, averaging 11.3 million reads per accession, revealing 150,356 high-quality single nucleotide polymorphisms (SNPs) distributed across 26 chromosomes. Population structure analysis revealed two subpopulations (K = 2): a dominant group consisting of 152 accessions sourced from both home gardens and large-scale cultivations, and a smaller group comprising 23 accessions exclusively from native collections in home gardens. This clustering was further supported by principal component analysis, with the first two principal components explaining 35.2 and 12.1% of the total variation. Genetic diversity analysis indicated substantial gene flow (Nm = 342.21) and a low fixation index (FST = 0.00073) between the two subpopulations, with no clear genetic differentiation among accessions from different agro-climatic regions. These findings demonstrate that most current black pepper genotypes grown in Sri Lanka share a common genetic background, emphasizing the necessity to broaden the genetic base to enhance resilience to biotic and abiotic stresses. This study represents the first attempt at analyzing black pepper genetic diversity using high-resolution SNP markers, laying the foundation for future genome-wide association studies for SNP-based gene discovery and breeding. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Author Correction: Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Author

Serna-Sánchez, Maria Alejandra, Pérez-Escobar, Oscar A., Bogarín, Diego, Torres-Jimenez, María Fernanda, Alvarez-Yela, Astrid Catalina, Arcila-Galvis, Juliana E., Hall, Climbie F., de Barros, Fábio, Pinheiro, Fábio, Dodsworth, Steven, Chase, Mark W., Antonelli, Alexandre, and Arias, Tatiana

Published
2021
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12. Plastid phylogenomic insights into relationships of all flowering plant families

Author

Li, Hong-Tao, Luo, Yang, Gan, Lu, Ma, Peng-Fei, Gao, Lian-Ming, Yang, Jun-Bo, Cai, Jie, Gitzendanner, Matthew A., Fritsch, Peter W., Zhang, Ting, Jin, Jian-Jun, Zeng, Chun-Xia, Wang, Hong, Yu, Wen-Bin, Zhang, Rong, van der Bank, Michelle, Olmstead, Richard G., Hollingsworth, Peter M., Chase, Mark W., Soltis, Douglas E., Soltis, Pamela S., Yi, Ting-Shuang, and Li, De-Zhu

Published
2021
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15. Origin of angiosperms and the puzzle of the Jurassic gap

Author

Li, Hong-Tao, Yi, Ting-Shuang, Gao, Lian-Ming, Ma, Peng-Fei, Zhang, Ting, Yang, Jun-Bo, Gitzendanner, Matthew A., Fritsch, Peter W., Cai, Jie, Luo, Yang, Wang, Hong, van der Bank, Michelle, Zhang, Shu-Dong, Wang, Qing-Feng, Wang, Jian, Zhang, Zhi-Rong, Fu, Chao-Nan, Yang, Jing, Hollingsworth, Peter M., Chase, Mark W., Soltis, Douglas E., Soltis, Pamela S., and Li, De-Zhu

Published
2019
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46. Angiosperm Phylogeny Based on matK Sequence Information

Author

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

Published
2003

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