338 results on '"Soltis PS"'
Search Results
2. The Amborella Genome and the Evolution of Flowering Plants
- Author
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Albert, Va, Barbazuk, Wb, Depamphilis, Cw, Der, Jp, Leebens Mack, J, Ma, H, Palmer, Jd, Rounsley, S, Sankoff, D, Schuster, Sc, Soltis, De, Soltis, Ps, Wessler, Sr, Wing, Ra, Ammiraju, Js, Chamala, S, Chanderbali, As, Determann, R, Ralph, P, Talag, J, Tomsho, L, Walts, B, Wanke, S, Chang, Th, Lan, T, Arikit, S, Axtell, Mj, Ayyampalayam, S, Burnette JM 3rd, DE PAOLI, Emanuele, Estill, Jc, Farrell, Np, Harkess, A, Jiao, Y, Liu, K, Mei, W, Meyers, Bc, Shahid, S, Wafula, E, Zhai, J, Zhang, X, Carretero Paulet, L, Lyons, E, Tang, H, Zheng, C, Altman, Ns, Chen, F, Chen, Jq, Chiang, V, De Paoli, E, Fogliani, B, Guo, C, Harholt, J, Job, C, Job, D, Kim, S, Kong, H, Li, G, Li, L, Liu, J, Park, J, Qi, X, Rajjou, L, Burtet Sarramegna, V, Sederoff, R, Sun, Yh, Ulvskov, P, Villegente, M, Xue, Jy, Yeh, Tf, Yu, X, Acosta, Jj, Bruenn, Ra, de Kochko, A, Herrera Estrella LR, Ibarra Laclette, E, Kirst, M, Pissis, Sp, Poncet, V, Tomsho, L., Department of Biological Sciences, University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY)-State University of New York (SUNY), Department of Biology, University of Florida [Gainesville], University of Florida Genetics Institute, Huck Institutes of the Life Sciences [University Park], Intercollege Plant Biology Graduate Program, Pennsylvania State University (Penn State), Penn State System-Penn State System, Center for Comparative Genomics and Bioinformatics, Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA, Université Paris Diderot - Paris 7 (UPD7), Department of Plant Biology [Athens], University of Georgia [USA], Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA, Penn State Univ, Dept Biol, University Pk, PA 16802 USA, Fudan Univ, Sch Life Sci, State Key Lab Genet Engn, Shanghai 200433, Peoples R China, Fudan Univ, Inst Genet, Inst Plant Biol, Ctr Evolutionary Biol,Inst Biomed Sci, Shanghai 200433, Peoples R China, Indiana Univ, Dept Biol, Bloomington, IN 47405 USA, Univ Arizona, Inst Collaborat Res BIO5, Tucson, AZ 85721 USA, Dow AgroSci, Indianapolis, IN 46268 USA, Univ Arizona, Sch Biol Sci, Tucson, AZ 85721 USA, Department of Mathematics and Statistics, University of Ottawa [Ottawa] (uOttawa), Singapore Ctr Environm Life Sci Engn, Singapore, Singapore, Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA, Florida Museum of Natural History, Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UCR), University of California-University of California, Univ Arizona, Arizona Genom Inst, Tucson, AZ 85721 USA, Atlanta Bot Garden, Atlanta, GA 30309 USA, Univ Florida, Dept Biol, Gainesville, FL 32611 USA, Tech Univ Dresden, Inst Bot, D-01062 Dresden, Germany, SUNY Buffalo, Dept Biol Sci, Buffalo, NY 14260 USA, Chongqing Univ Sci & Technol, Dept Biol, Chongqing 4000042, Peoples R China, Univ Delaware, Delaware Biotechnol Inst, Newark, DE 19711 USA, Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA, Univ Udine, Dipartimento Sci Agr & Ambientali, I-33100 Udine, Italy, Penn State Univ, Intercoll Plant Biol Grad Program, University Pk, PA 16802 USA, Univ Arizona, iPlant Collaborat, Tucson, AZ 85721 USA, J Craig Venter Inst, Rockville, MD 20850 USA, Univ Ottawa, Dept Math & Stat, Ottawa, ON K1N 6N5, Canada, Penn State Univ, Dept Stat, University Pk, PA 16802 USA, Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA, Nanjing Univ, Sch Life Sci, Nanjing 210093, Jiangsu, Peoples R China, N Carolina State Univ, Dept Forestry & Environm Resources, Raleigh, NC 27695 USA, Institut Agronomique Néo-Calédonien (IAC), Univ New Caledonia, Lab Insulaire Vivant & Environm, Noumea 98851, New Caledonia, Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China, Univ Copenhagen, Dept Plant & Environm Sci, DK-1871 Frederiksberg C, Denmark, Univ Claude Bernard Lyon, Inst Natl Sci Appl Bayer CropSci Joint Lab UMR524, CNRS, Bayer CropSci, F-69263 Lyon 9, France, Sungshin Womens Univ, Basic Sci Res Inst, Seoul 142732, South Korea, Sungshin Womens Univ, Sch Biol Sci & Chem, Seoul 142732, South Korea, Zhejiang Univ, Coll Life Sci, Lab Systemat & Evolutionary Bot & Biodivers, Hangzhou 310058, Zhejiang, Peoples R China, Zhejiang Univ, Coll Life Sci, Key Lab Conservat Biol Endangered Wildlife, Minist Educ, Hangzhou 310058, Zhejiang, Peoples R China, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Natl Chung Hsing Univ, Dept Forestry, Taichung 40227, Taiwan, Natl Taiwan Univ, Sch Forestry & Resource Conservat, Taipei 10617, Taiwan, Univ Florida, Sch Forest Resources & Conservat, Gainesville, FL 32611 USA, Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Lab Nacl Genom Biodiversidad, Irapuato 36821, Mexico, Univ Florida, Genet Inst, Gainesville, FL 32610 USA, Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA, Heidelberg Inst Theoret Studies, Sci Comp Grp, D-69118 Heidelberg, Germany, NSF Plant Genome Research Program [0922742], NSF, University of Florida [Gainesville] (UF), University of Florida Genetics Institute (UFGI), Center for Comparative Genomics and Bioinformatics (CCBB), Department of Biology [PennState], State Key Laboratory of Genetic Engineering, Fudan University [Shanghai], Institute of Plant Biology [Shanghai], Department of Biology [Bloomington], Indiana University [Bloomington], Indiana University System-Indiana University System, BIO5 - Institute for Collaborative Bioresearch, University of Arizona, Dow AgroSciences LLC, School of Plant Sciences [Tucson], Department of Mathematics and Statistics [Ottawa], University of Ottawa [Ottawa], Singapore Centre for Environmental Life Sciences Engineering [Singapore] (SCELSE), Nanyang Technological University [Singapour], Department of Biochemistry and Molecular Biology [PennState], Arizona Genomics Institute [Tucson], Atlanta Botanical Garden, Department of Biology [Gainesville] (UF|Biology), Institut für Botanik [Dresden], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Department of Biological Sciences [Buffalo], Department of Biology [Chongqing], Chongqing University of Science & Technology, Plant Genome Mapping Laboratory (PGML), Dipartimento di Scienze Agrarie e Ambientali (DiSA), Università degli Studi di Udine - University of Udine [Italie], iPlant Collaborative, J. Craig Venter Institute, Department of Statistics [PennState], Department of Plant Sciences [Knoxville], The University of Tennessee [Knoxville], School of Life Sciences [Nanjing] (SLiS), Nanjing University (NJU), Department of Forestry and Environmental Resources [Raleigh] (FER), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Université de la Nouvelle-Calédonie (UNC), State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany [Beijing] (IB-CAS), Chinese Academy of Sciences [Beijing] (CAS)-Chinese Academy of Sciences [Beijing] (CAS), Department of Plant and Environmental Sciences [Frederiksberg], University of Copenhagen = Københavns Universitet (KU), Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Génomique fonctionnelle des champignons pathogènes des plantes (FungiPath), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Basic Science Research Institute [Seoul], Sungshin Women's University, School of Biological Sciences and Chemistry [Seoul], Laboratory of Systematic & Evolutionary Botany and Biodiversity, Zhejiang University, Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Department of Forestry [Taichung], National Chung Hsing University (NCHU), School of Forestry and Resource Conservation [Taiwan], National Taïwan University (NTU), School of Forest Resources and Conservation [Gainesville] (UF|IFAS|FFGS), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Department of Plant and Microbial Biology [Berkeley], University of California [Berkeley], Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Florida Museum of Natural History [Gainesville], Heidelberg Institute for Theoretical Studies (HITS ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL)
- Subjects
0106 biological sciences ,Most recent common ancestor ,Genetics ,Transposable element ,0303 health sciences ,education.field_of_study ,Multidisciplinary ,Lineage (evolution) ,[SDV]Life Sciences [q-bio] ,Population ,fungi ,food and beverages ,Biology ,01 natural sciences ,Genome ,03 medical and health sciences ,Gene duplication ,Gene family ,education ,Gene ,030304 developmental biology ,010606 plant biology & botany - Abstract
Shaping Plant Evolution Amborella trichopoda is understood to be the most basal extant flowering plant and its genome is anticipated to provide insights into the evolution of plant life on Earth (see the Perspective by Adams ). To validate and assemble the sequence, Chamala et al. (p. 1516 ) combined fluorescent in situ hybridization (FISH), genomic mapping, and next-generation sequencing. The Amborella Genome Project (p. 10.1126/science.1241089 ) was able to infer that a whole-genome duplication event preceded the evolution of this ancestral angiosperm, and Rice et al. (p. 1468 ) found that numerous genes in the mitochondrion were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae.
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- 2013
3. The Amborella genome: an evolutionary reference for plant biology
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Soltis, D, Albert, V, Leebens Mack, J, Palmer, Jd, Wing, Ra, Depamphilis, Cw, Ma, H, Carlson, Je, Altman, N, Kim, S, Kerr Wall, P, Zuccolo, Andrea, and Soltis, Ps
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- 2008
4. Integrating the Study of Polyploidy Across Organisms, Tissues, and Disease.
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Morris JP, Baslan T, Soltis DE, Soltis PS, and Fox DT
- Abstract
Polyploidy is a cellular state containing more than two complete chromosome sets. It has largely been studied as a discrete phenomenon in either organismal, tissue, or disease contexts. Increasingly, however, investigation of polyploidy across disciplines is coalescing around common principles. For example, the recent Polyploidy Across the Tree of Life meeting considered the contribution of polyploidy both in organismal evolution over millions of years and in tumorigenesis across much shorter timescales. Here, we build on this newfound integration with a unified discussion of polyploidy in organisms, cells, and disease. We highlight how common polyploidy is at multiple biological scales, thus eliminating the outdated mindset of its specialization. Additionally, we discuss rules that are likely common to all instances of polyploidy. With increasing appreciation that polyploidy is pervasive in nature and displays fascinating commonalities across diverse contexts, inquiry related to this important topic is rapidly becoming unified.
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- 2024
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5. Phylogenetic evidence clarifies the history of the extrusion of Indochina.
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Li XQ, Peng HW, Xiang KL, Xiang XG, Jabbour F, Ortiz RDC, Soltis PS, Soltis DE, and Wang W
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- Animals, India, Climate, Plants classification, Rivers, Asia, Southeastern, Biological Evolution, Phylogeny
- Abstract
The southeastward extrusion of Indochina along the Ailao Shan-Red River shear zone (ARSZ) is one of two of the most prominent consequences of the India-Asia collision. This plate-scale extrusion has greatly changed Southeast Asian topography and drainage patterns and effected regional climate and biotic evolution. However, little is known about how Indochina was extruded toward the southeast over time. Here, we sampled 42 plant and animal clades (together encompassing 1,721 species) that are distributed across the ARSZ and are not expected to disperse across long distances. We first assess the possible role of climate on driving the phylogenetic separations observed across the ARSZ. We then investigate the temporal dynamics of the extrusion of Indochina through a multitaxon analysis. We show that the lineage divergences across the ARSZ were most likely associated with the Indochinese extrusion rather than climatic events. The lineage divergences began at ~53 Ma and increased sharply ~35 Ma, with two peaks at ~19 Ma and ~7 Ma, and one valley at ~13 Ma. Our results suggest a two-phase model for the extrusion of Indochina, and in each phase, the extrusion was subject to periods of acceleration and decrease, in agreement with the changes of the India-Asia convergence rate and angle from the early Eocene to the late Miocene. This study highlights that a multitaxon analysis can illuminate the timing of subtle historical events that may be difficult for geological data to pinpoint and can be used to explore other tectonic events., Competing Interests: Competing interests statement:The authors declare no competing interest.
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- 2024
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6. Author Correction: Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants.
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Kates HR, O'Meara BC, LaFrance R, Stull GW, James EK, Liu SY, Tian Q, Yi TS, Conde D, Kirst M, Ané JM, Soltis DE, Guralnick RP, Soltis PS, and Folk RA
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- 2024
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7. nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity.
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Gaynor ML, Landis JB, O'Connor TK, Laport RG, Doyle JJ, Soltis DE, Ponciano JM, and Soltis PS
- Abstract
Premise: Traditional methods of ploidal-level estimation are tedious; using DNA sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage sequence data for ploidy inference based on site-based heterozygosity have been developed. However, these approaches may require high-coverage sequence data, use inappropriate probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open-source R package that addresses the main shortcomings of current methods., Methods and Results: nQuack performs model selection for improved ploidy predictions. Here, we implement expectation maximization algorithms with normal, beta, and beta-binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack., Conclusions: Inferring ploidy based on site-based heterozygosity alone is difficult. Even though nQuack is more accurate than similar methods, we suggest caution when relying on any site-based heterozygosity method to infer ploidy., (© 2024 The Author(s). Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
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- 2024
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8. Genome evolution of the ancient hexaploid Platanus × acerifolia (London planetree).
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Yan X, Shi G, Sun M, Shan S, Chen R, Li R, Wu S, Zhou Z, Li Y, Liu Z, Hu Y, Liu Z, Soltis PS, Zhang J, Soltis DE, Ning G, and Bao M
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- Chromosomes, Plant genetics, Gene Duplication, Polyploidy, Genome, Plant, Phylogeny, Evolution, Molecular
- Abstract
Whole-genome duplication (WGD; i.e., polyploidy) and chromosomal rearrangement (i.e., genome shuffling) significantly influence genome structure and organization. Many polyploids show extensive genome shuffling relative to their pre-WGD ancestors. No reference genome is currently available for Platanaceae (Proteales), one of the sister groups to the core eudicots. Moreover, Platanus × acerifolia (London planetree; Platanaceae) is a widely used street tree. Given the pivotal phylogenetic position of Platanus and its 2-y flowering transition, understanding its flowering-time regulatory mechanism has significant evolutionary implications; however, the impact of Platanus genome evolution on flowering-time genes remains unknown. Here, we assembled a high-quality, chromosome-level reference genome for P. × acerifolia using a phylogeny-based subgenome phasing method. Comparative genomic analyses revealed that P . × acerifolia (2 n = 42) is an ancient hexaploid with three subgenomes resulting from two sequential WGD events; Platanus does not seem to share any WGD with other Proteales or with core eudicots. Each P . × acerifolia subgenome is highly similar in structure and content to the reconstructed pre-WGD ancestral eudicot genome without chromosomal rearrangements. The P . × acerifolia genome exhibits karyotypic stasis and gene sub-/neo-functionalization and lacks subgenome dominance. The copy number of flowering-time genes in P. × acerifolia has undergone an expansion compared to other noncore eudicots, mainly via the WGD events. Sub-/neo-functionalization of duplicated genes provided the genetic basis underlying the unique flowering-time regulation in P. × acerifolia . The P . × acerifolia reference genome will greatly expand understanding of the evolution of genome organization, genetic diversity, and flowering-time regulation in angiosperms., Competing Interests: Competing interests statement:The authors declare no competing interest.
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- 2024
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9. Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants.
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Kates HR, O'Meara BC, LaFrance R, Stull GW, James EK, Liu SY, Tian Q, Yi TS, Conde D, Kirst M, Ané JM, Soltis DE, Guralnick RP, Soltis PS, and Folk RA
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- Evolution, Molecular, Biological Evolution, Plant Roots microbiology, Plant Roots genetics, Magnoliopsida genetics, Magnoliopsida microbiology, Symbiosis genetics, Phylogeny, Nitrogen Fixation genetics, Root Nodules, Plant microbiology, Root Nodules, Plant genetics
- Abstract
Root nodule symbiosis (RNS) is a complex trait that enables plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. Pinpointing the evolutionary origins of RNS is critical for understanding its genetic basis, but building this evolutionary context is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.e., the nitrogen-fixing clade (NFC). We developed the most extensive de novo phylogeny for the NFC and an RNS trait database to reconstruct the evolution of RNS. Our analysis identifies evolutionary rate heterogeneity associated with a two-step process: An ancestral precursor state transitioned to a more labile state from which RNS was rapidly gained at multiple points in the NFC. We illustrate how a two-step process could explain multiple independent gains and losses of RNS, contrary to recent hypotheses suggesting one gain and numerous losses, and suggest a broader phylogenetic and genetic scope may be required for genome-phenome mapping., (© 2024. The Author(s).)
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- 2024
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10. Coping with alpine habitats: genomic insights into the adaptation strategies of Triplostegia glandulifera (Caprifoliaceae).
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Zhang J, Dong KL, Ren MZ, Wang ZW, Li JH, Sun WJ, Zhao X, Fu XX, Ye JF, Liu B, Zhang DM, Wang MZ, Zeng G, Niu YT, Lu LM, Su JX, Liu ZJ, Soltis PS, Soltis DE, and Chen ZD
- Abstract
How plants find a way to thrive in alpine habitats remains largely unknown. Here we present a chromosome-level genome assembly for an alpine medicinal herb, Triplostegia glandulifera (Caprifoliaceae), and 13 transcriptomes from other species of Dipsacales. We detected a whole-genome duplication event in T. glandulifera that occurred prior to the diversification of Dipsacales. Preferential gene retention after whole-genome duplication was found to contribute to increasing cold-related genes in T. glandulifera . A series of genes putatively associated with alpine adaptation (e.g. CBF s, ERF-VII s, and RAD51C ) exhibited higher expression levels in T. glandulifera than in its low-elevation relative, Lonicera japonica . Comparative genomic analysis among five pairs of high- vs low-elevation species, including a comparison of T. glandulifera and L. japonica , indicated that the gene families related to disease resistance experienced a significantly convergent contraction in alpine plants compared with their lowland relatives. The reduction in gene repertory size was largely concentrated in clades of genes for pathogen recognition (e.g. CNL s, prRLP s, and XII RLK s), while the clades for signal transduction and development remained nearly unchanged. This finding reflects an energy-saving strategy for survival in hostile alpine areas, where there is a tradeoff with less challenge from pathogens and limited resources for growth. We also identified candidate genes for alpine adaptation (e.g. RAD1 , DMC1 , and MSH3 ) that were under convergent positive selection or that exhibited a convergent acceleration in evolutionary rate in the investigated alpine plants. Overall, our study provides novel insights into the high-elevation adaptation strategies of this and other alpine plants., Competing Interests: The authors declare no competing interests., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nanjing Agricultural University.)
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- 2024
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11. Genome-wide DNA methylation dynamics following recent polyploidy in the allotetraploid Tragopogon miscellus (Asteraceae).
- Author
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Shan S, Gitzendanner MA, Boatwright JL, Spoelhof JP, Ethridge CL, Ji L, Liu X, Soltis PS, Schmitz RJ, and Soltis DE
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- DNA Methylation genetics, Polyploidy, Genome, Plant, Tragopogon genetics, Asteraceae genetics
- Abstract
Polyploidy is an important evolutionary force, yet epigenetic mechanisms, such as DNA methylation, that regulate genome-wide expression of duplicated genes remain largely unknown. Here, we use Tragopogon (Asteraceae) as a model system to discover patterns and temporal dynamics of DNA methylation in recently formed polyploids. The naturally occurring allotetraploid Tragopogon miscellus formed in the last 95-100 yr from parental diploids Tragopogon dubius and T. pratensis. We profiled the DNA methylomes of these three species using whole-genome bisulfite sequencing. Genome-wide methylation levels in T. miscellus were intermediate between its diploid parents. However, nonadditive CG and CHG methylation occurred in transposable elements (TEs), with variation among TE types. Most differentially methylated regions (DMRs) showed parental legacy, but some novel DMRs were detected in the polyploid. Differentially methylated genes (DMGs) were also identified and characterized. This study provides the first assessment of both overall and locus-specific patterns of DNA methylation in a recent natural allopolyploid and shows that novel methylation variants can be generated rapidly after polyploid formation. Together, these results demonstrate that mechanisms to regulate duplicate gene expression may arise soon after allopolyploid formation and that these mechanisms vary among genes., (© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation.)
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- 2024
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12. Editorial: Mapping microbial diversity onto the phylogeny of associated plant species.
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Xiang QJ, Kivlin SN, Soltis DE, Yu S, Chu H, Soltis PS, and Zhao Y
- Abstract
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.
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- 2024
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13. Phylogenomics and the rise of the angiosperms.
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Zuntini AR, Carruthers T, Maurin O, Bailey PC, Leempoel K, Brewer GE, Epitawalage N, Françoso E, Gallego-Paramo B, McGinnie C, Negrão R, Roy SR, Simpson L, Toledo Romero E, Barber VMA, Botigué L, Clarkson JJ, Cowan RS, Dodsworth S, Johnson MG, Kim JT, Pokorny L, Wickett NJ, Antar GM, DeBolt L, Gutierrez K, Hendriks KP, Hoewener A, Hu AQ, Joyce EM, Kikuchi IABS, Larridon I, Larson DA, de Lírio EJ, Liu JX, Malakasi P, Przelomska NAS, Shah T, Viruel J, Allnutt TR, Ameka GK, Andrew RL, Appelhans MS, Arista M, Ariza MJ, Arroyo J, Arthan W, Bachelier JB, Bailey CD, Barnes HF, Barrett MD, Barrett RL, Bayer RJ, Bayly MJ, Biffin E, Biggs N, Birch JL, Bogarín D, Borosova R, Bowles AMC, Boyce PC, Bramley GLC, Briggs M, Broadhurst L, Brown GK, Bruhl JJ, Bruneau A, Buerki S, Burns E, Byrne M, Cable S, Calladine A, Callmander MW, Cano Á, Cantrill DJ, Cardinal-McTeague WM, Carlsen MM, Carruthers AJA, de Castro Mateo A, Chase MW, Chatrou LW, Cheek M, Chen S, Christenhusz MJM, Christin PA, Clements MA, Coffey SC, Conran JG, Cornejo X, Couvreur TLP, Cowie ID, Csiba L, Darbyshire I, Davidse G, Davies NMJ, Davis AP, van Dijk KJ, Downie SR, Duretto MF, Duvall MR, Edwards SL, Eggli U, Erkens RHJ, Escudero M, de la Estrella M, Fabriani F, Fay MF, Ferreira PL, Ficinski SZ, Fowler RM, Frisby S, Fu L, Fulcher T, Galbany-Casals M, Gardner EM, German DA, Giaretta A, Gibernau M, Gillespie LJ, González CC, Goyder DJ, Graham SW, Grall A, Green L, Gunn BF, Gutiérrez DG, Hackel J, Haevermans T, Haigh A, Hall JC, Hall T, Harrison MJ, Hatt SA, Hidalgo O, Hodkinson TR, Holmes GD, Hopkins HCF, Jackson CJ, James SA, Jobson RW, Kadereit G, Kahandawala IM, Kainulainen K, Kato M, Kellogg EA, King GJ, Klejevskaja B, Klitgaard BB, Klopper RR, Knapp S, Koch MA, Leebens-Mack JH, Lens F, Leon CJ, Léveillé-Bourret É, Lewis GP, Li DZ, Li L, Liede-Schumann S, Livshultz T, Lorence D, Lu M, Lu-Irving P, Luber J, Lucas EJ, Luján M, Lum M, Macfarlane TD, Magdalena C, Mansano VF, Masters LE, Mayo SJ, McColl K, McDonnell AJ, McDougall AE, McLay TGB, McPherson H, Meneses RI, Merckx VSFT, Michelangeli FA, Mitchell JD, Monro AK, Moore MJ, Mueller TL, Mummenhoff K, Munzinger J, Muriel P, Murphy DJ, Nargar K, Nauheimer L, Nge FJ, Nyffeler R, Orejuela A, Ortiz EM, Palazzesi L, Peixoto AL, Pell SK, Pellicer J, Penneys DS, Perez-Escobar OA, Persson C, Pignal M, Pillon Y, Pirani JR, Plunkett GM, Powell RF, Prance GT, Puglisi C, Qin M, Rabeler RK, Rees PEJ, Renner M, Roalson EH, Rodda M, Rogers ZS, Rokni S, Rutishauser R, de Salas MF, Schaefer H, Schley RJ, Schmidt-Lebuhn A, Shapcott A, Al-Shehbaz I, Shepherd KA, Simmons MP, Simões AO, Simões ARG, Siros M, Smidt EC, Smith JF, Snow N, Soltis DE, Soltis PS, Soreng RJ, Sothers CA, Starr JR, Stevens PF, Straub SCK, Struwe L, Taylor JM, Telford IRH, Thornhill AH, Tooth I, Trias-Blasi A, Udovicic F, Utteridge TMA, Del Valle JC, Verboom GA, Vonow HP, Vorontsova MS, de Vos JM, Al-Wattar N, Waycott M, Welker CAD, White AJ, Wieringa JJ, Williamson LT, Wilson TC, Wong SY, Woods LA, Woods R, Worboys S, Xanthos M, Yang Y, Zhang YX, Zhou MY, Zmarzty S, Zuloaga FO, Antonelli A, Bellot S, Crayn DM, Grace OM, Kersey PJ, Leitch IJ, Sauquet H, Smith SA, Eiserhardt WL, Forest F, and Baker WJ
- Subjects
- Fossils, Nuclear Proteins genetics, Genes, Plant genetics, Genomics, Magnoliopsida genetics, Magnoliopsida classification, Phylogeny, Evolution, Molecular
- Abstract
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods
1,2 . A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4 . Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7 . However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8 . This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade., (© 2024. The Author(s).)- Published
- 2024
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14. Biodiversity and productivity in eastern US forests.
- Author
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Liu Y, Hogan JA, Lichstein JW, Guralnick RP, Soltis DE, Soltis PS, and Scheiner SM
- Subjects
- Biomass, Ecosystem, Phylogeny, United States, Biodiversity, Forests
- Abstract
Despite experimental and observational studies demonstrating that biodiversity enhances primary productivity, the best metric for predicting productivity at broad geographic extents-functional trait diversity, phylogenetic diversity, or species richness-remains unknown. Using >1.8 million tree measurements from across eastern US forests, we quantified relationships among functional trait diversity, phylogenetic diversity, species richness, and productivity. Surprisingly, functional trait and phylogenetic diversity explained little variation in productivity that could not be explained by tree species richness. This result was consistent across the entire eastern United States, within ecoprovinces, and within data subsets that controlled for biomass or stand age. Metrics of functional trait and phylogenetic diversity that were independent of species richness were negatively correlated with productivity. This last result suggests that processes that determine species sorting and packing are likely important for the relationships between productivity and biodiversity. This result also demonstrates the potential confusion that can arise when interdependencies among different diversity metrics are ignored. Our findings show the value of species richness as a predictive tool and highlight gaps in knowledge about linkages between functional diversity and ecosystem functioning., Competing Interests: Competing interests statement:The authors declare no competing interest.
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- 2024
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15. Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance.
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Ma PF, Liu YL, Guo C, Jin G, Guo ZH, Mao L, Yang YZ, Niu LZ, Wang YJ, Clark LG, Kellogg EA, Xu ZC, Ye XY, Liu JX, Zhou MY, Luo Y, Yang Y, Soltis DE, Bennetzen JL, Soltis PS, and Li DZ
- Subjects
- Polyploidy, Genomics, Transcriptome genetics, Genome, Plant genetics, Evolution, Molecular, Tetraploidy, Poaceae genetics
- Abstract
Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time., (© 2024. The Author(s).)
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- 2024
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16. Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data.
- Author
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Patten NN, Gaynor ML, Soltis DE, and Soltis PS
- Abstract
Premise: Digitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs)., Methods and Results: The gatoRs workflow includes functions that streamline downloading records from the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio). We also created functions to clean downloaded specimen records. Unlike previous R packages, gatoRs accounts for differences in download structure between GBIF and iDigBio and allows for user control via interactive cleaning steps., Conclusions: Our pipeline enables the scientific community to process biodiversity data efficiently and is accessible to the R coding novice. We anticipate that gatoRs will be useful for both established and beginning users. Furthermore, we expect our package will facilitate the introduction of biodiversity-related concepts into the classroom via the use of herbarium specimens., (© 2024 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
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- 2024
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17. Water stress modulates terpene biosynthesis and morphophysiology at different ploidal levels in Lippia alba (Mill.) N. E. Brown (Verbenaceae).
- Author
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Lopes JML, Nascimento LSQ, Souza VC, de Matos EM, Fortini EA, Grazul RM, Santos MO, Soltis DE, Soltis PS, Otoni WC, and Viccini LF
- Subjects
- Triploidy, Dehydration, Phylogeny, Lippia genetics, Lippia chemistry, Verbenaceae, Oils, Volatile chemistry, Acyclic Monoterpenes
- Abstract
Monoterpenes are the main component in essential oils of Lippia alba. In this species, the chemical composition of essential oils varies with genome size: citral (geraniol and neral) is dominant in diploids and tetraploids, and linalool in triploids. Because environmental stress impacts various metabolic pathways, we hypothesized that stress responses in L. alba could alter the relationship between genome size and essential oil composition. Water stress affects the flowering, production, and reproduction of plants. Here, we evaluated the effect of water stress on morphophysiology, essential oil production, and the expression of genes related to monoterpene synthesis in diploid, triploid, and tetraploid accessions of L. alba cultivated in vitro for 40 days. First, using transcriptome data, we performed de novo gene assembly and identified orthologous genes using phylogenetic and clustering-based approaches. The expression of candidate genes related to terpene biosynthesis was estimated by real-time quantitative PCR. Next, we assessed the expression of these genes under water stress conditions, whereby 1% PEG-4000 was added to MS medium. Water stress modulated L. alba morphophysiology at all ploidal levels. Gene expression and essential oil production were affected in triploid accessions. Polyploid accessions showed greater growth and metabolic tolerance under stress compared to diploids. These results confirm the complex regulation of metabolic pathways such as the production of essential oils in polyploid genomes. In addition, they highlight aspects of genotype and environment interactions, which may be important for the conservation of tropical biodiversity., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)
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- 2024
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18. Anatomy of a mega-radiation: Biogeography and niche evolution in Astragalus.
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Folk RA, Charboneau JLM, Belitz M, Singh T, Kates HR, Soltis DE, Soltis PS, Guralnick RP, and Siniscalchi CM
- Subjects
- Phylogeny, Phylogeography, Biological Evolution, Ecosystem, Astragalus Plant
- Abstract
Premise: Astragalus (Fabaceae), with more than 3000 species, represents a globally successful radiation of morphologically highly similar species predominant across the northern hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid-adapted clade and what sets it apart from close relatives with far less species richness., Methods: Here, for the first time using extensive phylogenetic sampling, we asked whether (1) Astragalus is uniquely characterized by bursts of radiation or whether diversification instead is uniform and no different from closely related taxa. Then we tested whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats, (3) particular soils, or to (4) chromosome evolution. Finally, we tested (5) whether Astragalus originated in central Asia as proposed and (6) whether niche evolutionary shifts were subsequently associated with the colonization of other continents., Results: Our results point to the importance of heterogeneity in the diversification of Astragalus, with upshifts associated with the earliest divergences but not strongly tied to any abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. Biogeographic shifts have a strong association with the abiotic environment and highlight the importance of central Asia as a biogeographic gateway., Conclusions: Our investigation shows the importance of phylogenetic and evolutionary studies of logistically challenging "mega-radiations." Our findings reject any simple key innovation behind high diversity and underline the often nuanced, multifactorial processes leading to species-rich clades., (© 2024 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
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- 2024
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19. Abundant incongruence in a clade endemic to a biodiversity hotspot: Phylogenetics of the scrub mint clade (Lamiaceae).
- Author
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Naranjo AA, Edwards CE, Gitzendanner MA, Soltis DE, and Soltis PS
- Subjects
- Phylogeny, Sequence Analysis, DNA, Biodiversity, Lamiaceae genetics, Mentha genetics
- Abstract
The Scrub Mint clade(Lamiaceae) provides a unique system for investigating the evolutionary processes driving diversification in the North American Coastal Plain from both a systematic and biogeographic context. The clade comprisesDicerandra, Conradina, Piloblephis, Stachydeoma, and four species of the broadly defined genus Clinopodium(Mentheae; Lamiaceae), almost all of which are endemic to the North American Eastern Coastal Plain. Most species of this clade are threatened or endangered and restricted to sandhill or a mosaic of scrub habitats. We analyzed relationships in this clade to understand the evolution of the group and identify evolutionary mechanisms acting on the clade, with important implications for conservation. We used a target-capture method to sequence and analyze 238 nuclear loci across all species of scrub mints, reconstructed the phylogeny, and calculated gene tree concordance, gene tree estimation error, and reticulation indices for every node in the tree using ML methods. Phylogenetic networks were used to determine reticulation events. Our nuclear phylogenetic estimates were consistent with previous results, while greatly increasing the robustness of taxon sampling. The phylogeny resolved the full relationship between Dicerandra and Conradina and the less-studied members of the clade (Piloblephis, Stachydeoma, Clinopodium spp.). We found hotspots of gene tree discordance and reticulation throughout the tree, especially in perennial Dicerandra. Several instances of reticulation events were uncovered between annual and perennial Dicerandra, and within the Conradina + allies clade. Incomplete lineage sorting also likely contributed to phylogenetic discordance. These results clarify phylogenetic relationships in the clade and provide insight on important evolutionary drivers in the clade, such as hybridization. General relationships in the group were confirmed, while the large amount of gene tree discordance is likely due to reticulation across the phylogeny., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)
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- 2024
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20. Investigation of regulatory divergence between homoeologs in the recently formed allopolyploids, Tragopogon mirus and T. miscellus (Asteraceae).
- Author
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Yoo MJ, Koh J, Boatwright JL, Soltis DE, Soltis PS, Barbazuk WB, and Chen S
- Subjects
- Diploidy, Polyploidy, Evolution, Molecular, Genome, Plant genetics, Tragopogon genetics, Asteraceae genetics
- Abstract
Polyploidy is an important evolutionary process throughout eukaryotes, particularly in flowering plants. Duplicated gene pairs (homoeologs) in allopolyploids provide additional genetic resources for changes in molecular, biochemical, and physiological mechanisms that result in evolutionary novelty. Therefore, understanding how divergent genomes and their regulatory networks reconcile is vital for unraveling the role of polyploidy in plant evolution. Here, we compared the leaf transcriptomes of recently formed natural allotetraploids (Tragopogon mirus and T. miscellus) and their diploid parents (T. porrifolius X T. dubius and T. pratensis X T. dubius, respectively). Analysis of 35 400 expressed loci showed a significantly higher level of transcriptomic additivity compared to old polyploids; only 22% were non-additively expressed in the polyploids, with 5.9% exhibiting transgressive expression (lower or higher expression in the polyploids than in the diploid parents). Among approximately 7400 common orthologous regions (COREs), most loci in both allopolyploids exhibited expression patterns that were vertically inherited from their diploid parents. However, 18% and 20.3% of the loci showed novel expression bias patterns in T. mirus and T. miscellus, respectively. The expression changes of 1500 COREs were explained by cis-regulatory divergence (the condition in which the two parental subgenomes do not interact) between the diploid parents, whereas only about 423 and 461 of the gene expression changes represent trans-effects (the two parental subgenomes interact) in T. mirus and T. miscellus, respectively. The low degree of both non-additivity and trans-effects on gene expression may present the ongoing evolutionary processes of the newly formed Tragopogon polyploids (~80-90 years)., (© 2023 Society for Experimental Biology and John Wiley & Sons Ltd.)
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- 2024
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21. Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales.
- Author
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Tian Q, Stull GW, Kellermann J, Medan D, Nge FJ, Liu SY, Kates HR, Soltis DE, Soltis PS, Guralnick RP, Folk RA, Onstein RE, and Yi TS
- Subjects
- Ecosystem, Phylogeny, Biodiversity, Genetic Speciation, Biological Evolution, Rhamnaceae
- Abstract
The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales., (© 2024 The Authors New Phytologist © 2024 New Phytologist Foundation.)
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- 2024
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22. Draft genome assemblies for two species of Escallonia (Escalloniales).
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Chanderbali AS, Dervinis C, Anghel IG, Soltis DE, Soltis PS, and Zapata F
- Subjects
- Phylogeny, Genome, Transcriptome, Genomics, Magnoliopsida genetics
- Abstract
Objectives: Escallonia (Escalloniaceae) belongs to the Escalloniales, a diverse clade of flowering plants with unclear placement in the tree of life. Escallonia species show impressive morphological and ecological diversity and are widely distributed across three hotspots of biodiversity in the Neotropics. To shed light on the genomic substrate of this radiation and the phylogenetic placement of Escalloniales as well as to generate useful data for comparative evolutionary genomics across flowering plants, we produced and annotated draft genomes for two species of Escallonia., Data Description: Genomic DNA from E. rubra and E. herrerae was sequenced with Oxford Nanopore sequencing chemistry, generating 3.4 and 12 million sequence reads with an average read length of 9.4 and 9.1 Kb (approximately 31 and 111 Gb of sequence data), respectively. In addition, we generated Illumina 100-bp paired-end short read data for E. rubra (approximately 75 Gb of sequence data). The Escallonia rubra genome was 566 Mb, with 3,233 contigs and an N50 of 285 Kb. The assembled genome for E. herrerae was 994 Mp, with 5,760 contigs and an N50 of 317 Kb. The genome sequences were annotated with 31,038 (E. rubra) and 47,905 (E. herrerea) protein-coding gene models supported by transcriptome/protein evidence and/or Pfam domain content. BUSCO assessments indicated completeness levels of approximately 98% for the genome assemblies and 88% for the genome annotations., (© 2023. The Author(s).)
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- 2024
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23. The panzootic potential of SARS-CoV-2.
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Mabry ME, Fanelli A, Mavian C, Lorusso A, Manes C, Soltis PS, and Capua I
- Abstract
Each year, SARS-CoV-2 is infecting an increasingly unprecedented number of species. In the present article, we combine mammalian phylogeny with the genetic characteristics of isolates found in mammals to elaborate on the host-range potential of SARS-CoV-2. Infections in nonhuman mammals mirror those of contemporary viral strains circulating in humans, although, in certain species, extensive viral circulation has led to unique genetic signatures. As in other recent studies, we found that the conservation of the ACE2 receptor cannot be considered the sole major determinant of susceptibility. However, we are able to identify major clades and families as candidates for increased surveillance. On the basis of our findings, we argue that the use of the term panzootic could be a more appropriate term than pandemic to describe the ongoing scenario. This term better captures the magnitude of the SARS-CoV-2 host range and would hopefully inspire inclusive policy actions, including systematic screenings, that could better support the management of this worldwide event., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Institute of Biological Sciences.)
- Published
- 2023
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24. Foliar endophyte diversity in Eastern Asian-Eastern North American disjunct tree species - influences of host identity, environment, phylogeny, and geographic isolation.
- Author
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Zhou W, Shi W, Soltis PS, Soltis DE, and Xiang QJ
- Abstract
Introduction: The well-known eastern Asian (EA) and eastern North American (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or lineages isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these lineages. Here we compared foliar endophytic fungi and bacteria-archaea (FEF and FEB) in 17 EA-ENA disjunct species or clade pairs from genera representing conifers and 10 orders of five major groups of angiosperms and 23 species of Cornus from EA and North America., Methods: Metagenomic sequencing of fungal ITS and bacterial-archaeal 16S rDNA was used to capture the foliar endophytic communities. Alpha and beta diversity of fungi and bacteria were compared at multiple scales and dimensions to gain insights into the relative roles of historical geographic isolation, host identity, phylogeny, and environment from samples at different sites in shaping endophytic diversity patterns., Results: We found that beta diversity of endophytes varied greatly among plant individuals within species and between species among genera at the same sampling site, and among three sampling sites, but little variation between region-of-origin of all plant species (EA vs ENA) and between EA-ENA disjunct counterparts within genera. Various numbers of indicator fungal species differing in abundance were identified for each plant genus and Cornus species. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance of plants was detected among the disjunct genera but not among species of Cornus . However, significant correlations between beta diversities at different taxonomic scales of endophytes and phylogenetic distances of Cornus species were observed., Discussion: Our results suggest important roles of host identity and environment (sampling sites), and a likely minor role of phylogenetic divergence and historical biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera and Cornus . The results lead to a hypothesis that the sister taxa in EA and ENA likely differ in FEF and FEB when growing in native habitats due to differences in local environments, which may potentially drive allopatric divergence of the functional features of species., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2023 Zhou, Shi, Soltis, Soltis and Xiang.)
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- 2023
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25. Chromosome-scale genome assembly of the 'Munstead' cultivar of Lavandula angustifolia.
- Author
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Hamilton JP, Vaillancourt B, Wood JC, Wang H, Jiang J, Soltis DE, Buell CR, and Soltis PS
- Subjects
- Genome, Genomics, Chromosomes, Open Reading Frames, Lavandula genetics
- Abstract
Objectives: Lavandula angustifolia (English lavender) is commercially important not only as an ornamental species but also as a major source of fragrances. To better understand the genomic basis of chemical diversity in lavender, we sequenced, assembled, and annotated the 'Munstead' cultivar of L. angustifolia., Data Description: A total of 80 Gb of Oxford Nanopore Technologies reads was used to assemble the 'Munstead' genome using the Canu genome assembler software. Following multiple rounds of error correction and scaffolding using Hi-C data, the final chromosome-scale assembly represents 795,075,733 bp across 25 chromosomes with an N50 scaffold length of 31,371,815 bp. Benchmarking Universal Single Copy Orthologs analysis revealed 98.0% complete orthologs, indicative of a high-quality assembly representative of genic space. Annotation of protein-coding sequences revealed 58,702 high-confidence genes encoding 88,528 gene models. Access to the 'Munstead' genome will permit comparative analyses within and among lavender accessions and provides a pivotal species for comparative analyses within Lamiaceae., (© 2023. The Author(s).)
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- 2023
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26. Quantifying error in occurrence data: Comparing the data quality of iNaturalist and digitized herbarium specimen data in flowering plant families of the southeastern United States.
- Author
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White E, Soltis PS, Soltis DE, and Guralnick R
- Subjects
- Data Accuracy, North Carolina, South Carolina, Virginia, Magnoliopsida
- Abstract
iNaturalist has the potential to be an extremely rich source of organismal occurrence data. Launched in 2008, it now contains over 150 million uploaded observations as of May 2023. Based on the findings of a limited number of past studies assessing the taxonomic accuracy of participatory science-driven sources of occurrence data such as iNaturalist, there has been concern that some portion of these records might be misidentified in certain taxonomic groups. In this case study, we compare Research Grade iNaturalist observations with digitized herbarium specimens, both of which are currently available for combined download from large data aggregators and are therefore the primary sources of occurrence data for large-scale biodiversity/biogeography studies. Our comparisons were confined regionally to the southeastern United States (Florida, Georgia, North Carolina, South Carolina, Texas, Tennessee, Kentucky, and Virginia). Occurrence records from ten plant families (Gentianaceae, Ericaceae, Melanthiaceae, Ulmaceae, Fabaceae, Asteraceae, Fagaceae, Cyperaceae, Juglandaceae, Apocynaceae) were downloaded and scored on taxonomic accuracy. We found a comparable and relatively low rate of misidentification among both digitized herbarium specimens and Research Grade iNaturalist observations within the study area. This finding illustrates the utility and high quality of iNaturalist data for future research in the region, but also points to key differences between data types, giving each a respective advantage, depending on applications of the data., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 White et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2023
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27. Angiosperm phylogenetic diversity is lower in Africa than South America.
- Author
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Qian H, Kessler M, Zhang J, Jin Y, Soltis DE, Qian S, Zhou Y, and Soltis PS
- Subjects
- Phylogeny, South America, Africa, Tropical Climate, Biodiversity, Magnoliopsida genetics
- Abstract
Although originating from a common Gondwanan flora, the diversity and composition of the floras of Africa and South America have greatly diverged since continental breakup of Africa from South America now having much higher plant species richness. However, the phylogenetic diversity of the floras and what this tells us about their evolution remained unexplored. We show that for a given species richness and considering land surface area, topography, and present-day climate, angiosperm phylogenetic diversity in South America is higher than in Africa. This relationship holds regardless of whether all climatically matched areas or only matched areas in tropical climates are considered. Phylogenetic diversity is high relative to species richness in refugial areas in Africa and in northwestern South America, once the gateway for immigration from the north. While species richness is strongly influenced by massive plant radiations in South America, we detect a pervasive influence of historical processes on the phylogenetic diversity of both the South American and African floras.
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- 2023
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28. Doubling down on polyploidy.
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Spoelhof JP, Soltis PS, and Soltis DE
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- 2023
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29. Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method.
- Author
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Folk RA, Gaynor ML, Engle-Wrye NJ, O'Meara BC, Soltis PS, Soltis DE, Guralnick RP, Smith SA, Grady CJ, and Okuyama Y
- Subjects
- Phylogeny, Phylogeography, Bayes Theorem, Hybridization, Genetic
- Abstract
Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit. [Ancestral niche reconstruction; hybridization; paleoclimate; pleistocene.]., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Society of Systematic Biologists.)
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- 2023
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30. Evolutionary history of the Arctic flora.
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Zhang J, Li XQ, Peng HW, Hai L, Erst AS, Jabbour F, Ortiz RDC, Xia FC, Soltis PS, Soltis DE, and Wang W
- Subjects
- Arctic Regions, Biological Evolution, Climate Change, Ecosystem, Tundra
- Abstract
The Arctic tundra is a relatively young and new type of biome and is especially sensitive to the impacts of global warming. However, little is known about how the Arctic flora was shaped over time. Here we investigate the origin and evolutionary dynamics of the Arctic flora by sampling 32 angiosperm clades that together encompass 3626 species. We show that dispersal into the Arctic and in situ diversification within the Arctic have similar trends through time, initiating at approximately 10-9 Ma, increasing sharply around 2.6 Ma, and peaking around 1.0-0.7 Ma. Additionally, we discover the existence of a long-term dispersal corridor between the Arctic and western North America. Our results suggest that the initiation and diversification of the Arctic flora might have been jointly driven by progressive landscape and climate changes and sea-level fluctuations since the early Late Miocene. These findings have important conservation implications given rapidly changing climate conditions in the Arctic., (© 2023. The Author(s).)
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- 2023
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31. Phenotypic trait variation in the North American Tragopogon allopolyploid complex.
- Author
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Jordon-Thaden IE, Spoelhof JP, Viccini LF, Combs J, Gomez F Jr, Walker I, Soltis DE, and Soltis PS
- Subjects
- Diploidy, Polyploidy, North America, Genome, Plant, Tragopogon genetics
- Abstract
Premise: Recently formed allopolyploids Tragopogon mirus and T. miscellus and their diploid parental species, T. dubius, T. porrifolius, and T. pratensis, offer a rare opportunity to study the earliest stages of allopolyploidy. The allopolyploid species have also been resynthesized, allowing comparisons between the youngest possible allopolyploid lineages and their natural, established counterparts. For the first time, we compared phenotypic traits on a large scale in Tragopogon diploids, natural allopolyploids, and three generations of synthetic allopolyploids., Methods: Our large common-garden experiment measured traits in growth, development, physiology, and reproductive fitness. We analyzed trait differences between allopolyploids and their parental species, and between synthetic and natural allopolyploids., Results: As in many polyploids, the allopolyploid species had some larger physical traits and a higher capacity for photosynthesis than diploid species. Reproductive fitness traits were variable and inconsistent. Allopolyploids had intermediate phenotypes compared to their diploid parents in several traits, but patterns of variation often varied between allopolyploid complexes. Resynthesized and natural allopolyploid lines generally showed minor to nonexistent trait differences., Conclusions: In Tragopogon, allopolyploidy results in some typical phenotypic changes, including gigas effects and increased photosynthetic capacity. Being polyploid did not produce a significant reproductive advantage. Comparisons between natural and synthetic T. mirus and T. miscellus are consistent with very limited, idiosyncratic phenotypic evolution following allopolyploidization., (© 2023 Botanical Society of America.)
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- 2023
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32. High-molecular-weight DNA extraction for long-read sequencing of plant genomes: An optimization of standard methods.
- Author
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Kang M, Chanderbali A, Lee S, Soltis DE, Soltis PS, and Kim S
- Abstract
Premise: Developing an effective and easy-to-use high-molecular-weight (HMW) DNA extraction method is essential for genomic research, especially in the era of third-generation sequencing. To efficiently use technologies capable of generating long-read sequences, it is important to maximize both the length and purity of the extracted DNA; however, this is frequently difficult to achieve with plant samples., Methods and Results: We present a HMW DNA extraction method that combines (1) a nuclei extraction method followed by (2) a traditional cetyltrimethylammonium bromide (CTAB) DNA extraction method for plants with optimized extraction conditions that influence HMW DNA recovery. Our protocol produced DNA fragments (percentage of fragments >20 kbp) that were, on average, ca. five times longer than those obtained using a commercial kit, and contaminants were removed more effectively., Conclusions: This effective HMW DNA extraction protocol can be used as a standard protocol for a diverse array of taxa, which will enhance plant genomic research., (© 2023 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
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- 2023
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33. Plant and fungal species interactions differ between aboveground and belowground habitats in mountain forests of eastern China.
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Yang T, Tedersoo L, Soltis PS, Soltis DE, Sun M, Ma Y, Ni Y, Liu X, Fu X, Shi Y, Lin HY, Zhao YP, Fu C, Dai CC, Gilbert JA, and Chu H
- Subjects
- Humans, Biodiversity, Forests, Plants microbiology, Soil, Soil Microbiology, Ecosystem, Fungi genetics
- Abstract
Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody plant species across more than 2,000-km span of mountain forests in eastern China. The relative contributions of plant, climate, soil and space to the variation of fungal communities were assessed, and the plant-fungus network topologies were inferred. Plant phylogeny was the strongest predictor for fungal community composition in leaves, accounting for 19.1% of the variation. In soils, plant phylogeny, climatic factors and soil properties explained 9.2%, 9.0% and 8.7% of the variation in soil fungal community, respectively. The plant-fungus networks in leaves exhibited significantly higher specialization, modularity and robustness (resistance to node loss), but less complicated topology (e.g., significantly lower linkage density and mean number of links) than those in soils. In addition, host/fungus preference combinations and key species, such as hubs and connectors, in bipartite networks differed strikingly between aboveground and belowground samples. The findings provide novel insights into cross-kingdom (plant-fungus) species co-occurrence at large spatial scales. The data further suggest that community shifts of trees due to climate change or human activities will impair aboveground and belowground forest fungal diversity in different ways., (© 2022. Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature.)
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- 2023
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34. The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data.
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Larson DA, Chanderbali AS, Maurin O, Gonçalves DJP, Dick CW, Soltis DE, Soltis PS, Fritsch PW, Clarkson JJ, Grall A, Davies NMJ, Larridon I, Kikuchi IABS, Forest F, Baker WJ, Smith SA, and Utteridge TMA
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- Phylogeny, Base Sequence, Sequence Analysis, DNA, DNA, Plant genetics, Primulaceae genetics
- Abstract
The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has obstructed the identification of major morphological and biogeographic transitions within the clade. We used target capture sequencing with the Angiosperms353 probes, taxon-sampling encompassing nearly all genera of the family, tree-based sequence curation, and multiple phylogenetic approaches to investigate the major clades of Primulaceae and their relationship to other Ericales. We generated dated phylogenetic trees and conducted broad-scale biogeographic analyses as well as stochastic character mapping of growth habit. We show that Ardisia, a pantropical genus and the largest in the family, is not monophyletic, with at least 19 smaller genera nested within it. Neotropical members of Ardisia and several smaller genera form a clade, an ancestor of which arrived in the Neotropics and began diversifying about 20 Ma. This Neotropical clade is most closely related to Elingamita and Tapeinosperma, which are most diverse on islands of the Pacific. Both Androsace and Primula are non-monophyletic by the inclusion of smaller genera. Ancestral state reconstructions revealed that there have either been parallel transitions to an herbaceous habit in Primuloideae, Samolus, and at least three lineages of Myrsinoideae, or a common ancestor of nearly all Primulaceae was herbaceous. Our results provide a robust estimate of phylogenetic relationships across Primulaceae and show that a revised classification of Myrsinoideae and several other clades within the family is necessary to render all genera monophyletic., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2023
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35. Deep reticulation: the long legacy of hybridization in vascular plant evolution.
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Stull GW, Pham KK, Soltis PS, and Soltis DE
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- Phylogeny, Genomics, Genome, Plants genetics, Hybridization, Genetic, Magnoliopsida genetics
- Abstract
Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community., (© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)
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- 2023
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36. Towards a global perspective for Salvia L.: Phylogeny, diversification and floral evolution.
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Moein F, Jamzad Z, Rahiminejad M, Landis JB, Mirtadzadini M, Soltis DE, and Soltis PS
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- Phylogeny, Iran, Flowers, Biological Evolution, Salvia genetics
- Abstract
Salvia is the most species-rich genus in Lamiaceae, encompassing approximately 1000 species distributed all over the world. We sought a new evolutionary perspective for Salvia by employing macroevolutionary analyses to address the tempo and mode of diversification. To study the association of floral traits with speciation and extinction, we modelled and explored the evolution of corolla length and the lever-mechanism pollination system across our Salvia phylogeny. We reconstructed a multigene phylogeny for 366 species of Salvia in the broad sense including all major recognized lineages and 50 species from Iran, a region previously overlooked in studies of the genus. Our comprehensive sampling of Iranian species of Salvia provides higher phylogenetic resolution for southwestern Asian species than obtained in previous studies. Our phylogenetic data in combination with divergence time estimates were used to examine the evolution of corolla length, woody versus herbaceous habit, and presence versus absence of a lever mechanism. We investigated the timing and dependence of Salvia diversification related to corolla length evolution through a disparity test and BAMM analysis. A HiSSE model was used to evaluate the dependency of diversification on the lever-mechanism pollination system in Salvia. A medium corolla length (15-18 mm) was reconstructed as the ancestral state for Salvia with multiple shifts to shorter and longer corollas. Macroevolutionary model analyses indicate that corolla length disparity is high throughout Salvia evolution, significantly different from expectations under a Brownian motion model during the last 28 million years of evolution. Our analyses show evidence of a higher diversification rate of corolla length for some Andean species of Salvia compared to other members of the genus. Based on our tests of diversification models, we reject the hypothesis of a direct effect of the lever mechanism on Salvia diversification. Therefore, we suggest caution in considering the lever-mechanism pollination system as one of the main drivers of speciation in Salvia., (© 2023 European Society for Evolutionary Biology.)
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- 2023
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37. Rethinking the Ph.D. dissertation in botany: Widening the circle.
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Soltis DE, Smocovitis VB, Pham KK, Cortez MBS, Smith AL, and Soltis PS
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- 2023
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38. An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data.
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Du ZY, Jenny Xiang QY, Cheng J, Zhou W, Wang QF, Soltis DE, and Soltis PS
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- Phylogeny, Biological Evolution, Genomics, Africa, Phylogeography, Cornaceae
- Abstract
Premise: A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s.l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group., Methods: We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis., Results: A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene, whereas dispersal into South America likely occurred during the Neogene. Diversification within the northern hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following rules of the PhyloCode., Conclusions: Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names., (© 2022 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
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- 2023
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39. Developing a CRISPR System in Nongenetic Model Polyploids.
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Shan S, Yang B, Hauser BA, Soltis PS, and Soltis DE
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- Acclimatization, Biological Assay, Polyploidy, Clustered Regularly Interspaced Short Palindromic Repeats, Asteraceae
- Abstract
The genetic consequences following polyploidy (i.e., whole-genome duplication; WGD) vary greatly across organisms and through time since polyploidization. At the gene level in allopolyploids, changes include loss/retention of both parental gene copies, function/expression divergence between the two parental copies, and silencing of one parental copy. Functional studies of genes with different retention patterns contribute to a better understanding of the genetic factors underlying the success of polyploids. Most research on gene functions to date focuses on a few well-established genetic models or crops. However, many species that best exemplify the polyploidy process are nongenetic models; the lack of an efficient genome editing system hinders functional studies in these systems. In this chapter, we discuss the considerations of developing CRISPR, a robust and efficient genome editing system, in polyploid plants that are not genetic models. We use diploid and polyploid Tragopogon (Asteraceae) as examples of a well-studied evolutionary model system for which abundant genetic and genomic resources are lacking. Using this system, we provide our protocols for sgRNA design, plasmid construction, a useful protoplast transient assay, and a plant transformation method we developed for this system. We also provide suggestions for possible modifications to these protocols to help promote successful application to other non-models. With the rapid applications of CRISPR in plant sciences, the broad adaptation of CRISPR in studies of the evolutionary significance of WGD holds enormous potential. We hope our studies and methods developed for polyploid Tragopogon will provide a guideline for establishing a CRISPR system in other nongenetic model polyploids of evolutionary or other interest., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
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- 2023
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40. Phylogenetic diversity of eastern Asia-eastern North America disjunct plants is mainly associated with divergence time.
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Lin HY, Sun M, Hao YJ, Li D, Gitzendanner MA, Fu CX, Soltis DE, Soltis PS, and Zhao YP
- Abstract
The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution. However, the patterns of phylogenetic diversity (PD) and phylogenetic beta diversity (PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America (EA-ENA disjuncts) and their associated factors remain unknown. Here we investigated the standardized effect size of PD (SES-PD), PBD, and potentially associated factors in 11 natural mixed forest sites (five in EA and six in ENA) where abundant EA-ENA disjuncts occur. We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale (1.96 vs -1.12), even though the number of disjunct species in ENA is much lower than in EA (128 vs 263). SES-PD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites. The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites. Based on the unweighted unique fraction metric (UniFrac) distance and the phylogenetic community dissimilarity, PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites. Based on the standardized effect size of mean pairwise distances (SES-MPD), nine of eleven studied sites showed a neutral community structure (-1.96 ≤ SES-MPD ≤ 1.96). Both Pearson's r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time. Moreover, SES-PD of the EA-ENA disjuncts was positively correlated with temperature-related climatic factors, although negatively correlated with mean diversification rate and community structure. By applying approaches from phylogenetics and community ecology, our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.)
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- 2022
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41. Hindcast-validated species distribution models reveal future vulnerabilities of mangroves and salt marsh species.
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Hodel RGJ, Soltis DE, and Soltis PS
- Abstract
Rapid climate change is threatening biodiversity via habitat loss, range shifts, increases in invasive species, novel species interactions, and other unforeseen changes. Coastal and estuarine species are especially vulnerable to the impacts of climate change due to sea level rise and may be severely impacted in the next several decades. Species distribution modeling can project the potential future distributions of species under scenarios of climate change using bioclimatic data and georeferenced occurrence data. However, models projecting suitable habitat into the future are impossible to ground truth. One solution is to develop species distribution models for the present and project them to periods in the recent past where distributions are known to test model performance before making projections into the future. Here, we develop models using abiotic environmental variables to quantify the current suitable habitat available to eight Neotropical coastal species: four mangrove species and four salt marsh species. Using a novel model validation approach that leverages newly available monthly climatic data from 1960 to 2018, we project these niche models into two time periods in the recent past (i.e., within the past half century) when either mangrove or salt marsh dominance was documented via other data sources. Models were hindcast-validated and then used to project the suitable habitat of all species at four time periods in the future under a model of climate change. For all future time periods, the projected suitable habitat of mangrove species decreased, and suitable habitat declined more severely in salt marsh species., Competing Interests: The authors declare no conflict of interest., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)
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- 2022
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42. Dynamic genome evolution in a model fern.
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Marchant DB, Chen G, Cai S, Chen F, Schafran P, Jenkins J, Shu S, Plott C, Webber J, Lovell JT, He G, Sandor L, Williams M, Rajasekar S, Healey A, Barry K, Zhang Y, Sessa E, Dhakal RR, Wolf PG, Harkess A, Li FW, Rössner C, Becker A, Gramzow L, Xue D, Wu Y, Tong T, Wang Y, Dai F, Hua S, Wang H, Xu S, Xu F, Duan H, Theißen G, McKain MR, Li Z, McKibben MTW, Barker MS, Schmitz RJ, Stevenson DW, Zumajo-Cardona C, Ambrose BA, Leebens-Mack JH, Grimwood J, Schmutz J, Soltis PS, Soltis DE, and Chen ZH
- Subjects
- DNA Transposable Elements, Evolution, Molecular, Genome, Plant, Plants genetics, Ferns genetics
- Abstract
The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology., (© 2022. The Author(s).)
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- 2022
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43. Biotic colonization of subtropical East Asian caves through time.
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Li XQ, Xiang XG, Jabbour F, Hagen O, Ortiz RDC, Soltis PS, Soltis DE, and Wang W
- Subjects
- Animals, Asia, Eastern, Phylogeny, Biodiversity, Caves, Forests
- Abstract
Caves are home to unique and fragile biotas with high levels of endemism. However, little is known about how the biotic colonization of caves has developed over time, especially in caves from middle and low latitudes. Subtropical East Asia holds the world's largest karst landform with numerous ancient caves, which harbor a high diversity of cave-dwelling organisms and are regarded as a biodiversity hotspot. Here, we assess the temporal dynamics of biotic colonization of subtropical East Asian caves through a multi-taxon analysis with representatives of green plants, animals, and fungi. We then investigate the consequences of paleonviromental changes on the colonization dynamics of these caves in combination with reconstructions of vegetation, temperature, and precipitation. We discover that 88% of cave colonization events occurred after the Oligocene-Miocene boundary, and organisms from the surrounding forest were a major source for subtropical East Asian cave biodiversity. Biotic colonization of subtropical East Asian caves during the Neogene was subject to periods of acceleration and decrease, in conjunction with large-scale, seasonal climatic changes and evolution of local forests. This study highlights the long-term evolutionary interaction between surface and cave biotas; our climate-vegetation-relict model proposed for the subtropical East Asian cave biota may help explain the evolutionary origins of other mid-latitude subterranean biotas.
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- 2022
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44. Bridging the Research Gap between Live Collections in Zoos and Preserved Collections in Natural History Museums.
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Poo S, Whitfield SM, Shepack A, Watkins-Colwell GJ, Nelson G, Goodwin J, Bogisich A, Brennan PLR, D'Agostino J, Koo MS, Mendelson JR 3rd, Snyder R, Wilson S, Aronsen GP, Bentley AC, Blackburn DC, Borths MR, Campbell ML, Conde DA, Cook JA, Daza JD, Dembiec DP, Dunnum JL, Early CM, Ferguson AW, Greene A, Guralnick R, Janney C, Johnson D, Knightly F, Poulin S, Rocha L, Soltis PS, Thiers B, and Chakrabarty P
- Abstract
Zoos and natural history museums are both collections-based institutions with important missions in biodiversity research and education. Animals in zoos are a repository and living record of the world's biodiversity, whereas natural history museums are a permanent historical record of snapshots of biodiversity in time. Surprisingly, despite significant overlap in institutional missions, formal partnerships between these institution types are infrequent. Life history information, pedigrees, and medical records maintained at zoos should be seen as complementary to historical records of morphology, genetics, and distribution kept at museums. Through examining both institution types, we synthesize the benefits and challenges of cross-institutional exchanges and propose actions to increase the dialog between zoos and museums. With a growing recognition of the importance of collections to the advancement of scientific research and discovery, a transformational impact could be made with long-term investments in connecting the institutions that are caretakers of living and preserved animals., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Institute of Biological Sciences.)
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- 2022
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45. The Cycas genome and the early evolution of seed plants.
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Liu Y, Wang S, Li L, Yang T, Dong S, Wei T, Wu S, Liu Y, Gong Y, Feng X, Ma J, Chang G, Huang J, Yang Y, Wang H, Liu M, Xu Y, Liang H, Yu J, Cai Y, Zhang Z, Fan Y, Mu W, Sahu SK, Liu S, Lang X, Yang L, Li N, Habib S, Yang Y, Lindstrom AJ, Liang P, Goffinet B, Zaman S, Wegrzyn JL, Li D, Liu J, Cui J, Sonnenschein EC, Wang X, Ruan J, Xue JY, Shao ZQ, Song C, Fan G, Li Z, Zhang L, Liu J, Liu ZJ, Jiao Y, Wang XQ, Wu H, Wang E, Lisby M, Yang H, Wang J, Liu X, Xu X, Li N, Soltis PS, Van de Peer Y, Soltis DE, Gong X, Liu H, and Zhang S
- Subjects
- Cycadopsida genetics, Genes, Plant, Ginkgo biloba genetics, Phylogeny, Seeds genetics, Cycas genetics
- Abstract
Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists., (© 2022. The Author(s).)
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- 2022
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46. Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication.
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Zhang Q, Zhao L, Folk RA, Zhao JL, Zamora NA, Yang SX, Soltis DE, Soltis PS, Gao LM, Peng H, and Yu XQ
- Subjects
- Gene Duplication, Hybridization, Genetic, Phylogeny, Plastids genetics, Ericales, Theaceae genetics
- Abstract
Background and Aims: Theaceae, with three tribes, nine genera and more than 200 species, are of great economic and ecological importance. Recent phylogenetic analyses based on plastomic data resolved the relationships among the three tribes and the intergeneric relationships within two of those tribes. However, generic-level relationships within the largest tribe, Theeae, were not fully resolved. The role of putative whole-genome duplication (WGD) events in the family and possible hybridization events among genera within Theeae also remain to be tested further., Methods: Transcriptomes or low-depth whole-genome sequencing of 57 species of Theaceae, as well as additional plastome sequence data, were generated. Using a dataset of low-copy nuclear genes, we reconstructed phylogenetic relationships using concatenated, species tree and phylogenetic network approaches. We further conducted molecular dating analyses and inferred possible WGD events by examining the distribution of the number of synonymous substitutions per synonymous site (Ks) for paralogues in each species. For plastid protein-coding sequences , phylogenies were reconstructed for comparison with the results obtained from analysis of the nuclear dataset., Results: Based on the 610 low-copy nuclear genes (858 606 bp in length) investigated, Stewartieae was resolved as sister to the other two tribes. Within Theeae, the Apterosperma-Laplacea clade grouped with Pyrenaria, leaving Camellia and Polyspora as sister. The estimated ages within Theaceae were largely consistent with previous studies based mainly on plastome data. Two reticulation events within Camellia and one between the common ancestor of Gordonia and Schima were found. All members of the tea family shared two WGD events, an older At-γ and a recent Ad-β; both events were also shared with the outgroups (Diapensiaceae, Pentaphylacaceae, Styracaceae and Symplocaceae)., Conclusions: Our analyses using low-copy nuclear genes improved understanding of phylogenetic relationships at the tribal and generic levels previously proposed based on plastome data, but the phylogenetic position of the Apterosperma-Laplacea clade needs more attention. There is no evidence for extensive intergeneric hybridization within Theeae or for a Theaceae-specific WGD event. Land bridges (e.g. the Bering land bridge) during the Late Oligocene may have permitted the intercontinental plant movements that facilitated the putative ancient introgression between the common ancestor of Gordonia and Schima., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
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- 2022
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47. Buxus and Tetracentron genomes help resolve eudicot genome history.
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Chanderbali AS, Jin L, Xu Q, Zhang Y, Zhang J, Jian S, Carroll E, Sankoff D, Albert VA, Howarth DG, Soltis DE, and Soltis PS
- Subjects
- Buxus classification, Evolution, Molecular, Genomics, Hybridization, Genetic, Phylogeny, Sequence Analysis, DNA, Buxus genetics, Genome, Plant, Magnoliopsida genetics
- Abstract
Ancient whole-genome duplications (WGDs) characterize many large angiosperm lineages, including angiosperms themselves. Prominently, the core eudicot lineage accommodates 70% of all angiosperms and shares ancestral hexaploidy, termed gamma. Gamma arose via two WGDs that occurred early in eudicot history; however, the relative timing of these is unclear, largely due to the lack of high-quality genomes among early-diverging eudicots. Here, we provide complete genomes for Buxus sinica (Buxales) and Tetracentron sinense (Trochodendrales), representing the lineages most closely related to core eudicots. We show that Buxus and Tetracentron are both characterized by independent WGDs, resolve relationships among early-diverging eudicots and their respective genomes, and use the RACCROCHE pipeline to reconstruct ancestral genome structure at three key phylogenetic nodes of eudicot diversification. Our reconstructions indicate genome structure remained relatively stable during early eudicot diversification, and reject hypotheses of gamma arising via inter-lineage hybridization between ancestral eudicot lineages, involving, instead, only stem lineage core eudicot ancestors., (© 2022. The Author(s).)
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- 2022
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48. Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation.
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Hu H, Scheben A, Verpaalen B, Tirnaz S, Bayer PE, Hodel RGJ, Batley J, Soltis DE, Soltis PS, and Edwards D
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- Stress, Physiological genetics, Genome, Plant, Magnoliopsida genetics
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- 2022
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49. Why sequence all eukaryotes?
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Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK, Kress WJ, Kuraku S, Lawniczak MKN, Lindblad-Toh K, Lopez JV, Moran NA, Robinson GE, Ryder OA, Shapiro B, Soltis PS, Warnow T, Zhang G, and Lewin HA
- Subjects
- Animals, Biodiversity, Biological Evolution, Ecology, Ecosystem, Genome, Genomics methods, Humans, Phylogeny, Base Sequence genetics, Eukaryota genetics, Genomics ethics
- Abstract
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine., Competing Interests: The authors declare no competing interest., (Copyright © 2022 the Author(s). Published by PNAS.)
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- 2022
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50. Standards recommendations for the Earth BioGenome Project.
- Author
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Lawniczak MKN, Durbin R, Flicek P, Lindblad-Toh K, Wei X, Archibald JM, Baker WJ, Belov K, Blaxter ML, Marques Bonet T, Childers AK, Coddington JA, Crandall KA, Crawford AJ, Davey RP, Di Palma F, Fang Q, Haerty W, Hall N, Hoff KJ, Howe K, Jarvis ED, Johnson WE, Johnson RN, Kersey PJ, Liu X, Lopez JV, Myers EW, Pettersson OV, Phillippy AM, Poelchau MF, Pruitt KD, Rhie A, Castilla-Rubio JC, Sahu SK, Salmon NA, Soltis PS, Swarbreck D, Thibaud-Nissen F, Wang S, Wegrzyn JL, Zhang G, Zhang H, Lewin HA, and Richards S
- Subjects
- Animals, Biodiversity, Genomics methods, Humans, Reference Standards, Reference Values, Sequence Analysis, DNA methods, Sequence Analysis, DNA standards, Base Sequence genetics, Eukaryota genetics, Genomics standards
- Abstract
A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met., Competing Interests: Competing interest statement: P.F. is a member of the scientific advisory boards of Fabric Genomics, Inc. and Eagle Genomics, Ltd., (Copyright © 2022 the Author(s). Published by PNAS.)
- Published
- 2022
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