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Feng K, Walker JF, Marx HE, Yang Y, Brockington SF, Moore MJ, Rabeler RK, Smith SA. The link between ancient whole-genome duplications and cold adaptations in the Caryophyllaceae. AMERICAN JOURNAL OF BOTANY 2024:e16350. [PMID: 38825760 DOI: 10.1002/ajb2.16350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024]
Abstract
PREMISE The Caryophyllaceae (the carnation family) have undergone multiple transitions into colder climates and convergence on cushion plant adaptation, indicating that they may provide a natural system for cold adaptation research. Previous research has suggested that putative ancient whole-genome duplications (WGDs) are correlated with niche shifts into colder climates across the Caryophyllales. Here, we explored the genomic changes potentially involved in one of these discovered shifts in the Caryophyllaceae. METHODS We constructed a data set combining 26 newly generated transcriptomes with 45 published transcriptomes, including 11 cushion plant species across seven genera. With this data set, we inferred a dated phylogeny for the Caryophyllaceae and mapped ancient WGDs and gene duplications onto the phylogeny. We also examined functional groups enriched for gene duplications related to the climatic shift. RESULTS The ASTRAL topology was mostly congruent with the current consensus of relationships within the family. We inferred 15 putative ancient WGDs in the family, including eight that have not been previously published. The oldest ancient WGD (ca. 64.4-56.7 million years ago), WGD1, was found to be associated with a shift into colder climates by previous research. Gene regions associated with ubiquitination were overrepresented in gene duplications retained after WGD1 and those convergently retained by cushion plants in Colobanthus and Eremogone, along with other functional annotations. CONCLUSIONS Gene family expansions induced by ancient WGDs may have contributed to the shifts to cold climatic niches in the Caryophyllaceae. Transcriptomic data are crucial resources that help unravel heterogeneity in deep-time evolutionary patterns in plants.
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Affiliation(s)
- Keyi Feng
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Joseph F Walker
- Department of Biological Sciences, University of Illinois Chicago, Chicago, 60607, IL, USA
| | - Hannah E Marx
- Department of Biology, University of New Mexico, Albuquerque, 87131, NM, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, 55108, MN, USA
| | | | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, 44074, OH, USA
| | - Richard K Rabeler
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
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2
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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3
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Saul F, Scharmann M, Wakatake T, Rajaraman S, Marques A, Freund M, Bringmann G, Channon L, Becker D, Carroll E, Low YW, Lindqvist C, Gilbert KJ, Renner T, Masuda S, Richter M, Vogg G, Shirasu K, Michael TP, Hedrich R, Albert VA, Fukushima K. Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis. NATURE PLANTS 2023; 9:2000-2015. [PMID: 37996654 DOI: 10.1038/s41477-023-01562-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/09/2023] [Indexed: 11/25/2023]
Abstract
Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.
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Affiliation(s)
- Franziska Saul
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Mathias Scharmann
- Institute for Biochemistry and Biology (IBB), University of Potsdam, Potsdam, Germany
| | - Takanori Wakatake
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Matthias Freund
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Louisa Channon
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Emily Carroll
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | | | - Kadeem J Gilbert
- Department of Plant Biology & W.K. Kellogg Biological Station & Program in Ecology, Evolution, and Behavior, Michigan State University, Hickory Corners, MI, USA
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
| | - Sachiko Masuda
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Michaela Richter
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Gerd Vogg
- Botanical Garden, University of Würzburg, Würzburg, Germany
| | - Ken Shirasu
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany.
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Lan L, Zhao H, Xu S, Kan S, Zhang X, Liu W, Liao X, Tembrock LR, Ren Y, Reeve W, Yang J, Wu Z. A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales. HORTICULTURE RESEARCH 2023; 10:uhad124. [PMID: 37554346 PMCID: PMC10405137 DOI: 10.1093/hr/uhad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/05/2023] [Indexed: 08/10/2023]
Abstract
Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract coloration and breeding. Here, we report a chromosome-level assembly of the giga-genome of Bougainvillea × buttiana 'Mrs Butt', a cultivar thought to be the origin of many other Bougainvillea cultivars. The assembled genome is ~5 Gb with a scaffold N50 of 151 756 278 bp and contains 86 572 genes which have undergone recent whole-genome duplication. We confirmed that multiple rounds of whole-genome multiplication have occurred in the evolutionary history of the Caryophyllales, reconstructed the relationship in the Caryophyllales at whole genome level, and found discordance between species and gene trees as the result of complex introgression events. We investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales species. To explore the potential formation mechanism of diverse bract colors in Bougainvillea, we analyzed the genes involved in betalain and anthocyanin biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars, which may limit anthocyanin biosynthesis. Our findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with bract color, and a higher expression level in the betalain biosynthetic pathway is required for colored bracts. This improved understanding of the correlation between gene expression and bract color allows plant breeding outcomes to be predicted with greater certainty.
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Affiliation(s)
- Lan Lan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- School of Medical, Molecularand Forensic Sciences, Murdoch University, 6150, Western Australia, 90 South Street, Murdoch, Australia
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Huiqi Zhao
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Suxia Xu
- Fujian Key Laboratory of Subtropical Plant Physiology & Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, China
| | - Shenglong Kan
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaoni Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Weichao Liu
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Yonglin Ren
- School of Medical, Molecularand Forensic Sciences, Murdoch University, 6150, Western Australia, 90 South Street, Murdoch, Australia
| | - Wayne Reeve
- School of Medical, Molecularand Forensic Sciences, Murdoch University, 6150, Western Australia, 90 South Street, Murdoch, Australia
| | - Jun Yang
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Baharin A, Ting TY, Goh HH. Omics Approaches in Uncovering Molecular Evolution and Physiology of Botanical Carnivory. PLANTS (BASEL, SWITZERLAND) 2023; 12:408. [PMID: 36679121 PMCID: PMC9867145 DOI: 10.3390/plants12020408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Systems biology has been increasingly applied with multiple omics for a holistic comprehension of complex biological systems beyond the reductionist approach that focuses on individual molecules. Different high-throughput omics approaches, including genomics, transcriptomics, metagenomics, proteomics, and metabolomics have been implemented to study the molecular mechanisms of botanical carnivory. This covers almost all orders of carnivorous plants, namely Caryophyllales, Ericales, Lamiales, and Oxalidales, except Poales. Studies using single-omics or integrated multi-omics elucidate the compositional changes in nucleic acids, proteins, and metabolites. The omics studies on carnivorous plants have led to insights into the carnivory origin and evolution, such as prey capture and digestion as well as the physiological adaptations of trap organ formation. Our understandings of botanical carnivory are further enhanced by the discoveries of digestive enzymes and transporter proteins that aid in efficient nutrient sequestration alongside dynamic molecular responses to prey. Metagenomics studies revealed the mutualistic relationships between microbes and carnivorous plants. Lastly, in silico analysis accelerated the functional characterization of new molecules from carnivorous plants. These studies have provided invaluable molecular data for systems understanding of carnivorous plants. More studies are needed to cover the diverse species with convergent evolution of botanical carnivory.
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Phylogeny and evolution of Cupressaceae: Updates on intergeneric relationships and new insights on ancient intergeneric hybridization. Mol Phylogenet Evol 2022; 177:107606. [PMID: 35952837 DOI: 10.1016/j.ympev.2022.107606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/24/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022]
Abstract
After the merger of the former Taxodiaceae and Cupressaceae s.s., currently the conifer family Cupressaceae (sensu lato) comprises seven subfamilies and 32 genera, most of which are important components of temperate and mountainous forests. With the exception of a recently published genus-level phylogeny of gymnosperms inferred from sequence analysis of 790 orthologs, previous phylogenetic studies of Cupressaceae were based mainly on morphological characters or a few molecular markers, and did not completely resolve the intergeneric relationships. In this study, we reconstructed a robust and well-resolved phylogeny of Cupressaceae represented by all 32 genera, using 1944 genes (Orthogroups) generated from transcriptome sequencing. Reticulate evolution analyses detected a possible ancient hybridization that occurred between ancestors of two subclades of Cupressoideae, including Microbiota-Platycladus-Tetraclinis (MPT) and Juniperus-Cupressus-Hesperocyparis-Callitropsis-Xanthocyparis (JCHCX), although both concatenation and coalescent trees are highly supported. Moreover, divergence time estimation and ancestral area reconstruction indicate that Cupressaceae very likely originated in Asia in the Triassic, and geographic isolation caused by continental separation drove the vicariant evolution of the two subfamilies Cupressoideae and Callitroideae in the northern and southern hemispheres, respectively. Evolutionary analyses of some morphological characters suggest that helically arranged linear-acicular leaves and imbricate bract-scale complexes represent ancestral states, and the shift from linear-acicular leaves to scale-like leaves was associated with the shift from helical to decussate arrangement. Our study sheds new light on phylogeny and evolutionary history of Cupressaceae, and strongly suggests that both dichotomous phylogenetic and reticulate evolution analyses be conducted in phylogenomic studies.
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Effectiveness of Perioperative Comprehensive Evaluation of Hip Fracture in the Elderly. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:4124354. [PMID: 36035830 PMCID: PMC9410974 DOI: 10.1155/2022/4124354] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/13/2022] [Accepted: 07/16/2022] [Indexed: 12/31/2022]
Abstract
Objective The objective is to observe the effect of Comprehensive Geriatric Assessment (CGA) in the perioperative period of hip fracture. Methods From October 2018 to October 2021, 155 patients over the age of 65 diagnosed with hip fracture and treated with surgery at the Department of Trauma Orthopaedics of General Hospital of Ningxia Medical University were randomly divided into two groups using a prospective research method. A total of 70 cases in the CGA group received a perioperative comprehensive assessment of the geriatric, and 85 cases in the control group received routine medical consultation. Results Elderly patients with hip fractures have a high comorbidity index. Patients with abnormal daily activity before injury accounted for 55%, the abnormal rate of nutrition was 58.1%, the abnormal rate of cognition, anxiety, and depression was 81.8%, and 77.3% of the patients were in a weak state. There was no significant difference in age, gender, ASA grade, fracture type, and operation mode between the two groups, but there were significant differences in operation rate at 48 h (χ2 = 22.153; P ≤ 0.001), preoperative waiting time (Z = −6.387; P ≤ 0.001), total hospital stay (Z = −11.756; P ≤ 0.001), and incidence of postoperative delirium (χ2 = 23.897; P ≤ 0.001). Conclusions The implementation of CGA shortened the preoperative waiting time and total hospital stay, increased the 48 h operation rate, and reduced the incidence of postoperative delirium.
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Plastid phylogenomic analyses of the Selaginella sanguinolenta group (Selaginellaceae) reveal conflict signatures resulting from sequence types, outlier genes, and pervasive RNA editing. Mol Phylogenet Evol 2022; 173:107507. [PMID: 35589053 DOI: 10.1016/j.ympev.2022.107507] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 11/23/2022]
Abstract
Different from the generally conserved plastomes (plastid genomes) of most land plants, the Selaginellaceae plastomes exhibit dynamic structure, high GC content and high substitution rates. Previous plastome analyses identified strong conflict on several clades in Selaginella, however the factors causing the conflictions and the impact on the phylogenetic inference have not been sufficiently investigated. Here, we dissect the distribution of phylogenetic signals and conflicts in Selaginella sanguinolenta group, the plastome of which is DR (direct repeats) structure and with genome-wide RNA editing. We analyzed the data sets including 22 plastomes representing all species of the S. sanguinolenta group, covering the entire geographical distribution from the Himalayas to Siberia and the Russian Far East regions. We recovered four different topologies by applying multispecies coalescent (ASTRAL) and concatenation methods (IQ-TREE and RAxML) on four data sets of PC (protein-coding genes), NC (non-coding sequences), PCN (the concatenated PC and NC), and RC (predicted RNA editing sites "C" were corrected by "T"), respectively. Six monophyletic clades, S. nummularifolia clade, S. rossii clade, S. sajanensis clade, S. sanguinolenta I clade, S. sanguinolenta II clade, and S. sanguinolenta III clade, were consistently resolved and supported by the characteristics of GC content, RNA editing frequency, and gene content. However, the relationships among these clades varied across the four topologies. To explore the underlying causes of the uncertainty, we compared the phylogenetic signals of the four topologies. We identified that the sequence types (coding versus non-coding), outlier genes (genes with extremely high |ΔGLS| values), and C-to-U RNA editing frequency in the protein-coding genes were responsible for the unstable phylogenomic relationship. We further revealed a significant positive correlation between the |ΔGLS| values and the variation coefficient of the RNA editing number. Our results demonstrated that the coalescent method performed better than the concatenation method in overcoming the problems caused by outlier genes and extreme RNA editing events. Our study particularly focused on the importance of exploring the plastid phylogenomic conflicts and suggested conducting concatenated analyses cautiously when adopting organelle genome data.
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Pouchon C, Boyer F, Roquet C, Denoeud F, Chave J, Coissac E, Alsos IG, Lavergne S. ORTHOSKIM: in silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications. Mol Ecol Resour 2022; 22:2018-2037. [PMID: 35015377 DOI: 10.1111/1755-0998.13584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/08/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
Abstract
Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in non-model organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: 1) global sequence assembly, 2) mapping against reference sequences, and 3) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and non-coding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g. ultra-conserved elements) or collections of single-copy ortholog genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and 4 RNAseq libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 license and is available at: https://github.com/cpouchon/ORTHOSKIM.
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Affiliation(s)
- Charles Pouchon
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Frédéric Boyer
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Cristina Roquet
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France.,Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057, Evry, France
| | - Jérome Chave
- Laboratoire Évolution et Diversité Biologique (EDB), UMR CNRS-IRD-UPS 5174, 31062, Toulouse Cedex, France
| | - Eric Coissac
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Inger Greve Alsos
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
| | | | | | - Sébastien Lavergne
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
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Stull GW, Qu XJ, Parins-Fukuchi C, Yang YY, Yang JB, Yang ZY, Hu Y, Ma H, Soltis PS, Soltis DE, Li DZ, Smith SA, Yi TS. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. NATURE PLANTS 2021; 7:1015-1025. [PMID: 34282286 DOI: 10.1038/s41477-021-00964-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/10/2021] [Indexed: 05/15/2023]
Abstract
Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the tree of life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here, we examine the relationship of various facets of genomic evolution-including gene and genome duplication, genome size, and chromosome number-with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably, our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants.
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Affiliation(s)
- Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | | | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Yun Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
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11
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Walker JF, Smith SA, Hodel RGJ, Moyroud E. Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets. Syst Biol 2021; 71:943-958. [PMID: 34240209 DOI: 10.1093/sysbio/syab052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/23/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022] Open
Abstract
Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence, and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have greater influence on an inferred relationship, does not assume conflict has arisen from any one source, and does not force the dataset to produce a single bifurcating tree. Using this approach on three empirical datasets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the datasets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic dataset, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic datasets and enrich our inferences of both species' relationships and evolutionary processes.
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Affiliation(s)
- Joseph F Walker
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607 U.S.A
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Edwige Moyroud
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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12
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Shchennikova AV, Beletsky AV, Filyushin MA, Slugina MA, Gruzdev EV, Mardanov AV, Kochieva EZ, Ravin NV. Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs. FRONTIERS IN PLANT SCIENCE 2021; 12:643137. [PMID: 34122470 PMCID: PMC8194089 DOI: 10.3389/fpls.2021.643137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The emergence of the carnivory syndrome and traps in plants is one of the most intriguing questions in evolutionary biology. In the present study, we addressed it by comparative transcriptomics analysis of leaves and leaf-derived pitcher traps from a predatory plant Nepenthes ventricosa × Nepenthes alata. Pitchers were collected at three stages of development and a total of 12 transcriptomes were sequenced and assembled de novo. In comparison with leaves, pitchers at all developmental stages were found to be highly enriched with upregulated genes involved in stress response, specification of shoot apical meristem, biosynthesis of sucrose, wax/cutin, anthocyanins, and alkaloids, genes encoding digestive enzymes (proteases and oligosaccharide hydrolases), and flowering-related MADS-box genes. At the same time, photosynthesis-related genes in pitchers were transcriptionally downregulated. As the MADS-box genes are thought to be associated with the origin of flower organs from leaves, we suggest that Nepenthes species could have employed a similar pathway involving highly conserved MADS-domain transcription factors to develop a novel structure, pitcher-like trap, for capture and digestion of animal prey during the evolutionary transition to carnivory. The data obtained should clarify the molecular mechanisms of trap initiation and development and may contribute to solving the problem of its emergence in plants.
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13
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Introgression is widespread in the radiation of carnivorous Nepenthes pitcher plants. Mol Phylogenet Evol 2021; 163:107214. [PMID: 34052438 DOI: 10.1016/j.ympev.2021.107214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/14/2021] [Accepted: 05/25/2021] [Indexed: 11/23/2022]
Abstract
Introgression and hybridization are important processes in plant evolution, but they are difficult to study from a phylogenetic perspective, because they conflict with the bifurcating evolutionary history typically depicted in phylogenetic models. The role of hybridization in plant evolution is best documented in the form of allo-polyploidizations. In contrast, homoploid hybridization and introgression are less explored, although they may be crucial in adaptive radiations. Here we employ genome-wide data (ddRAD-seq, transcriptomes) to investigate the evolutionary history of Nepenthes, a radiation of c. 160 species of iconic carnivorous plants mainly from tropical Asia. Our data indicates that the main radiation is only c. 5 million years old, and confirms previous bifurcating phylogenies. However, due to a greatly expanded number of loci, we were able test for the first time the long-standing hypotheses of introgression and historical hybridization. The genus presents one very clear case of organellar capture between two distantly related but sympatric groups. Furthermore, all Nepenthes species show introgression signals in their nuclear genomes, as uncovered by a general survey of ABBA-BABA-like statistics. The ancestor of the rapid main radiation shows ancestry from two deeply diverged lineages, as indicated by phylogenetic network analyses. All major clades of the main radiation show further introgression both within and between each other, as suggested by admixture graphs. Our study supports the hypothesis that rapid adaptive radiations are hotspots of introgression in the tree of life, and highlights the need to consider non-treelike processes in evolutionary studies of Nepenthes in particular.
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14
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Abstract
Evolutionary biologists have long been fascinated with the episodes of rapid phenotypic innovation that underlie the emergence of major lineages. Although our understanding of the environmental and ecological contexts of such episodes has steadily increased, it has remained unclear how population processes contribute to emergent macroevolutionary patterns. One insight gleaned from phylogenomics is that gene-tree conflict, frequently caused by population-level processes, is often rampant during the origin of major lineages. With the understanding that phylogenomic conflict is often driven by complex population processes, we hypothesized that there may be a direct correspondence between instances of high conflict and elevated rates of phenotypic innovation if both patterns result from the same processes. We evaluated this hypothesis in six clades spanning vertebrates and plants. We found that the most conflict-rich regions of these six clades also tended to experience the highest rates of phenotypic innovation, suggesting that population processes shaping both phenotypic and genomic evolution may leave signatures at deep timescales. Closer examination of the biological significance of phylogenomic conflict may yield improved connections between micro- and macroevolution and increase our understanding of the processes that shape the origin of major lineages across the Tree of Life.
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15
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Matsumoto H, Mimori T, Fukunaga T. Novel metric for hyperbolic phylogenetic tree embeddings. Biol Methods Protoc 2021; 6:bpab006. [PMID: 33928190 PMCID: PMC8058397 DOI: 10.1093/biomethods/bpab006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 01/09/2023] Open
Abstract
Advances in experimental technologies, such as DNA sequencing, have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of development, differentiation, cancer genomics, and immunogenomics. Thus, the importance of phylogenetic methods is increasingly being recognized, and the development of a novel phylogenetic approach can contribute to several areas of research. Recently, the use of hyperbolic geometry has attracted attention in artificial intelligence research. Hyperbolic space can better represent a hierarchical structure compared to Euclidean space, and can therefore be useful for describing and analyzing a phylogenetic tree. In this study, we developed a novel metric that considers the characteristics of a phylogenetic tree for representation in hyperbolic space. We compared the performance of the proposed hyperbolic embeddings, general hyperbolic embeddings, and Euclidean embeddings, and confirmed that our method could be used to more precisely reconstruct evolutionary distance. We also demonstrate that our approach is useful for predicting the nearest-neighbor node in a partial phylogenetic tree with missing nodes. Furthermore, we proposed a novel approach based on our metric to integrate multiple trees for analyzing tree nodes or imputing missing distances. This study highlights the utility of adopting a geometric approach for further advancing the applications of phylogenetic methods.
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Affiliation(s)
- Hirotaka Matsumoto
- School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan.,Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Saitama, Japan
| | - Takahiro Mimori
- Medical Image Analysis Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Tsukasa Fukunaga
- Department of Computer Science, Graduate School of Information Science and Engineering, The University of Tokyo, Tokyo, Japan
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16
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Harvey MG, Bravo GA, Claramunt S, Cuervo AM, Derryberry GE, Battilana J, Seeholzer GF, McKay JS, O'Meara BC, Faircloth BC, Edwards SV, Pérez-Emán J, Moyle RG, Sheldon FH, Aleixo A, Smith BT, Chesser RT, Silveira LF, Cracraft J, Brumfield RT, Derryberry EP. The evolution of a tropical biodiversity hotspot. Science 2021; 370:1343-1348. [PMID: 33303617 DOI: 10.1126/science.aaz6970] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 05/01/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022]
Abstract
The tropics are the source of most biodiversity yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leveraged samples assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, the suboscine passerines. Our phylogeny, estimated using data from 2389 genomic regions in 1940 individuals of 1283 species, reveals that peak suboscine species diversity in the Neotropics is not associated with high recent speciation rates but rather with the gradual accumulation of species over time. Paradoxically, the highest speciation rates are in lineages from regions with low species diversity, which are generally cold, dry, unstable environments. Our results reveal a model in which species are forming faster in environmental extremes but have accumulated in moderate environments to form tropical biodiversity hotspots.
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Affiliation(s)
- Michael G Harvey
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA. .,Biodiversity Collections, The University of Texas at El Paso, El Paso, TX 79968, USA.,Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. .,Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.,Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil
| | - Santiago Claramunt
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S2C6, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada.,Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Andrés M Cuervo
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá 111321, Colombia.,Department of Ecology and Evolutionary Biology, Tulane University, LA 70118, USA
| | - Graham E Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA.,Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jaqueline Battilana
- Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil
| | - Glenn F Seeholzer
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA.,Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jessica Shearer McKay
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Brian C O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Brant C Faircloth
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Jorge Pérez-Emán
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela.,Colección Ornitológica Phelps, Caracas, Venezuela
| | - Robert G Moyle
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Frederick H Sheldon
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, 00014, Helsinki, Finland.,Department of Zoology, Museu Paraense Emílio Goeldi, CP 399, 66040-170 Belém, PA, Brazil
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - R Terry Chesser
- US Geological Survey, Patuxent Wildlife Research Center, Laurel, MD 20708, USA.,National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Luís Fábio Silveira
- Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Robb T Brumfield
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA.,Department of Ecology and Evolutionary Biology, Tulane University, LA 70118, USA
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17
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Carruthers T, Sanderson MJ, Scotland RW. The Implications of Lineage-Specific Rates for Divergence Time Estimation. Syst Biol 2021; 69:660-670. [PMID: 31808929 PMCID: PMC7302051 DOI: 10.1093/sysbio/syz080] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 11/28/2019] [Accepted: 12/01/2019] [Indexed: 11/29/2022] Open
Abstract
Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates—defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior—which has recently been proposed to model rate variation more accurately—does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical data set for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analyzing genomic scale multilocus data sets. [Divergence time estimation; error; rate variation.]
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Affiliation(s)
- Tom Carruthers
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 East Lowell, Tucson, AZ 85721-0088, USA
| | - Robert W Scotland
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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18
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Straub SCK, Boutte J, Fishbein M, Livshultz T. Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb-Seq. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11400. [PMID: 33304663 PMCID: PMC7705337 DOI: 10.1002/aps3.11400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/12/2020] [Indexed: 05/07/2023]
Abstract
PREMISE Apocynaceae is the 10th largest flowering plant family and a focus for study of plant-insect interactions, especially as mediated by secondary metabolites. However, it has few genomic resources relative to its size. Target capture sequencing is a powerful approach for genome reduction that facilitates studies requiring data from the nuclear genome in non-model taxa, such as Apocynaceae. METHODS Transcriptomes were used to design probes for targeted sequencing of putatively single-copy nuclear genes across Apocynaceae. The sequences obtained were used to assess the success of the probe design, the intrageneric and intraspecific variation in the targeted genes, and the utility of the genes for inferring phylogeny. RESULTS From 853 candidate nuclear genes, 835 were consistently recovered in single copy and were variable enough for phylogenomics. The inferred gene trees were useful for coalescent-based species tree analysis, which showed all subfamilies of Apocynaceae as monophyletic, while also resolving relationships among species within the genus Apocynum. Intraspecific comparison of Elytropus chilensis individuals revealed numerous single-nucleotide polymorphisms with potential for use in population-level studies. DISCUSSION Community use of this Hyb-Seq probe set will facilitate and promote progress in the study of Apocynaceae across scales from population genomics to phylogenomics.
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Affiliation(s)
- Shannon C. K. Straub
- Department of BiologyHobart and William Smith Colleges300 Pulteney StreetGenevaNew York14456USA
| | - Julien Boutte
- Department of BiologyHobart and William Smith Colleges300 Pulteney StreetGenevaNew York14456USA
| | - Mark Fishbein
- Department of Plant Biology, Ecology, and EvolutionOklahoma State University301 Physical SciencesStillwaterOklahoma74078USA
| | - Tatyana Livshultz
- Department of Biodiversity, Earth, and Environmental Sciences and the Academy of Natural SciencesDrexel University1900 Benjamin Franklin ParkwayPhiladelphiaPennsylvania19103USA
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19
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Smith SA, Walker-Hale N, Walker JF. Intragenic Conflict in Phylogenomic Data Sets. Mol Biol Evol 2020; 37:3380-3388. [DOI: 10.1093/molbev/msaa170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Abstract
Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to >92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.
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Affiliation(s)
- Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | | | - Joseph F Walker
- The Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, United Kingdom
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20
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Veleba A, Zedek F, Horová L, Veselý P, Srba M, Šmarda P, Bureš P. Is the evolution of carnivory connected with genome size reduction? AMERICAN JOURNAL OF BOTANY 2020; 107:1253-1259. [PMID: 32882073 DOI: 10.1002/ajb2.1526] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/13/2020] [Indexed: 05/24/2023]
Abstract
PREMISE As repeatedly shown, the remarkable variation in the genome size of angiosperms can be shaped by extrinsic selective pressures, including nutrient availability. Carnivory has evolved independently in 10 angiosperm clades, but all carnivorous plants share a common affinity to nutrient-poor habitats. As such, carnivory and genome reduction could be responses to the same environmental pressure. Indeed, the smallest genomes among flowering plants are found in the carnivorous family Lentibulariaceae, where a unique mutation in cytochrome c oxidase (COX) is suspected to promote genome miniaturization. Despite these hypotheses, a phylogenetically informed test of genome size and nutrient availability across carnivorous clades has so far been missing. METHODS Using linear mixed models, we compared genome sizes of 127 carnivorous plants from 7 diverse angiosperm clades with 1072 of their noncarnivorous relatives. We also tested whether genome size in Lentibulariaceae reflects the presence of the COX mutation. RESULTS The genome sizes of carnivorous plants do not differ significantly from those of their noncarnivorous relatives. Based on available data, no significant association between the COX mutation and genome miniaturization could be confirmed, not even when considering polyploidy. CONCLUSIONS Carnivory alone does not seem to significantly affect genome size decrease. Plausibly, it might actually counterbalance the effect of nutrient limitation on genome size evolution. The role of the COX mutation in genome miniaturization needs to be evaluated by analysis of a broader data set because current knowledge of its presence across Lentibulariaceae covers less than 10% of the species diversity in this family.
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Affiliation(s)
- Adam Veleba
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Pavel Veselý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Miroslav Srba
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, CZ, 12844, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
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21
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Yang Q, Bi H, Yang W, Li T, Jiang J, Zhang L, Liu J, Hu Q. The Genome Sequence of Alpine Megacarpaea delavayi Identifies Species-Specific Whole-Genome Duplication. Front Genet 2020; 11:812. [PMID: 32849811 PMCID: PMC7416671 DOI: 10.3389/fgene.2020.00812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/06/2020] [Indexed: 11/18/2022] Open
Abstract
Megacarpaea delavayi (Brassicaceae), a plant found the high mountains of southwest China at high altitudes (3000–4800 m), is used as a vegetable or medicine. Here, we report a draft genome for this species. The assembly genome of M. delavayi is 883 Mb, and 61.59% of the genome is composed of repeat sequences. Annotation of the genome identified a total of 41,114 protein-coding genes. We found that M. delavayi experienced an independent whole-genome duplication (WGD), paralleling those independent WGDs in Iberis, Biscutella, and Anastatica in the early Miocene. Phylogenetic analyses based on the single-copy genes confirmed the position of the genus Megacarpaea within the expanded lineage II of the family and resolved its basal divergence to a subclade consisting of Anastatica, Iberis, and Biscutella. Species-specific and fast-evolving genes in M. delavayi are mainly involved in “DNA repair” and “response to UV-B radiation.” These genetic changes may together help this species survive in high-altitude environments. The reference genome reported here provides a valuable resource for studying adaptation of this and other alpine plants to the high-altitude habitats.
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Affiliation(s)
- Qiao Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hao Bi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenjie Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ting Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiebei Jiang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China.,State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Quanjun Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
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22
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Martín-Rodríguez I, Vargas P, Ojeda F, Fernández-Mazuecos M. An enigmatic carnivorous plant: ancient divergence of Drosophyllaceae but recent differentiation of Drosophyllum lusitanicum across the Strait of Gibraltar. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1771467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Irene Martín-Rodríguez
- Departamento de Biología-IVAGRO, Universidad de Cádiz, Campus Río San Pedro, Puerto Real, E-11510, Spain
- Departamento de Biología, Geología, Física y Química Inorgánica, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Calle Tulipán s/n, Móstoles, E-28933, Spain
| | - Pablo Vargas
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, Madrid, E-28014, Spain
| | - Fernando Ojeda
- Departamento de Biología-IVAGRO, Universidad de Cádiz, Campus Río San Pedro, Puerto Real, E-11510, Spain
| | - Mario Fernández-Mazuecos
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, Madrid, E-28014, Spain
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23
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Deschamps-Francoeur G, Simoneau J, Scott MS. Handling multi-mapped reads in RNA-seq. Comput Struct Biotechnol J 2020; 18:1569-1576. [PMID: 32637053 PMCID: PMC7330433 DOI: 10.1016/j.csbj.2020.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/06/2020] [Accepted: 06/07/2020] [Indexed: 11/07/2022] Open
Abstract
Many eukaryotic genomes harbour large numbers of duplicated sequences, of diverse biotypes, resulting from several mechanisms including recombination, whole genome duplication and retro-transposition. Such repeated sequences complicate gene/transcript quantification during RNA-seq analysis due to reads mapping to more than one locus, sometimes involving genes embedded in other genes. Genes of different biotypes have dissimilar levels of sequence duplication, with long-noncoding RNAs and messenger RNAs sharing less sequence similarity to other genes than biotypes encoding shorter RNAs. Many strategies have been elaborated to handle these multi-mapped reads, resulting in increased accuracy in gene/transcript quantification, although separate tools are typically used to estimate the abundance of short and long genes due to their dissimilar characteristics. This review discusses the mechanisms leading to sequence duplication, the biotypes affected, the computational strategies employed to deal with multi-mapped reads and the challenges that still remain to be overcome.
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Affiliation(s)
- Gabrielle Deschamps-Francoeur
- Département de Biochimie et Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Joël Simoneau
- Département de Biochimie et Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Michelle S Scott
- Département de Biochimie et Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
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Larson DA, Walker JF, Vargas OM, Smith SA. A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales. AMERICAN JOURNAL OF BOTANY 2020; 107:773-789. [PMID: 32350864 DOI: 10.1002/ajb2.1469] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/12/2020] [Indexed: 05/27/2023]
Abstract
PREMISE Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications. METHODS We used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods, and is summarized in a consensus framework. RESULTS Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole-genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications. CONCLUSIONS We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.
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Affiliation(s)
- Drew A Larson
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joseph F Walker
- Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, CB2 1LR, UK
| | - Oscar M Vargas
- Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, CA, 95060, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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25
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Murphy B, Forest F, Barraclough T, Rosindell J, Bellot S, Cowan R, Golos M, Jebb M, Cheek M. A phylogenomic analysis of Nepenthes (Nepenthaceae). Mol Phylogenet Evol 2020; 144:106668. [DOI: 10.1016/j.ympev.2019.106668] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
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26
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Scharmann M, Grafe TU, Metali F, Widmer A. Sex is determined by XY chromosomes across the radiation of dioecious Nepenthes pitcher plants. Evol Lett 2019; 3:586-597. [PMID: 31867120 PMCID: PMC6906984 DOI: 10.1002/evl3.142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 08/23/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022] Open
Abstract
Species with separate sexes (dioecy) are a minority among flowering plants, but dioecy has evolved multiple times independently in their history. The sex-determination system and sex-linked genomic regions are currently identified in a limited number of dioecious plants only. Here, we study the sex-determination system in a genus of dioecious plants that lack heteromorphic sex chromosomes and are not amenable to controlled breeding: Nepenthes pitcher plants. We genotyped wild populations of flowering males and females of three Nepenthes taxa using ddRAD-seq and sequenced a male inflorescence transcriptome. We developed a statistical tool (privacy rarefaction) to distinguish true sex specificity from stochastic noise in read coverage of sequencing data from wild populations and identified male-specific loci and XY-patterned single nucleotide polymorphsims (SNPs) in all three Nepenthes taxa, suggesting the presence of homomorphic XY sex chromosomes. The male-specific region of the Y chromosome showed little conservation among the three taxa, except for the essential pollen development gene DYT1 that was confirmed as male specific by PCR in additional Nepenthes taxa. Hence, dioecy and part of the male-specific region of the Nepenthes Y-chromosomes likely have a single evolutionary origin.
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Affiliation(s)
- Mathias Scharmann
- Institute of Integrative BiologyETH ZurichZürich8092Switzerland
- Department of Ecology and EvolutionUniversity of LausanneLausanne1015Switzerland
| | - T. Ulmar Grafe
- Faculty of ScienceUniversiti Brunei DarussalamGadongBE 1410Brunei Darussalam
| | - Faizah Metali
- Faculty of ScienceUniversiti Brunei DarussalamGadongBE 1410Brunei Darussalam
| | - Alex Widmer
- Institute of Integrative BiologyETH ZurichZürich8092Switzerland
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27
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Smith SA, Walker-Hale N, Walker JF, Brown JW. Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants. Syst Biol 2019; 69:579-592. [DOI: 10.1093/sysbio/syz078] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 10/16/2019] [Accepted: 11/18/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a data set in order to resolve recalcitrant relationships and, importantly, identify what the data set is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant data set. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested conflicts limited the ability of data filtering methods to fully ameliorate conflicting signal amongst gene trees. These analyses confirmed that the underlying conflicting signal does not support broad concatenation of genes. Our approach provides a means of dissecting a specific data set to address deep phylogenetic relationships while also identifying the inferential boundaries of the data set. [Angiosperms; coalescent; gene-tree conflict; genomics; phylogenetics; phylogenomics.]
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Affiliation(s)
- Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA
| | - Nathanael Walker-Hale
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, Cambridge, UK
| | - Joseph F Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA
- Sainsbury Laboratory (SLCU), University of Cambrige, Bateman St, Cambridge CB2 1LR, Cambridge, UK
| | - Joseph W Brown
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, Sheffield, UK
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28
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Walker JF, Walker-Hale N, Vargas OM, Larson DA, Stull GW. Characterizing gene tree conflict in plastome-inferred phylogenies. PeerJ 2019; 7:e7747. [PMID: 31579615 PMCID: PMC6764362 DOI: 10.7717/peerj.7747] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/25/2019] [Indexed: 11/20/2022] Open
Abstract
Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes.
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Affiliation(s)
- Joseph F. Walker
- Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, United Kingdom
| | - Nathanael Walker-Hale
- Department of Plant Sciences, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Oscar M. Vargas
- University of California, Santa Cruz, Santa Cruz, United States of America
| | - Drew A. Larson
- University of Michigan—Ann Arbor, Ann Arbor, MI, United States of America
| | - Gregory W. Stull
- Department of Botany, Smithsonian Institution, Washington, United States of America
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29
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Wang N, Yang Y, Moore MJ, Brockington SF, Walker JF, Brown JW, Liang B, Feng T, Edwards C, Mikenas J, Olivieri J, Hutchison V, Timoneda A, Stoughton T, Puente R, Majure LC, Eggli U, Smith SA. Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments. Mol Biol Evol 2019; 36:112-126. [PMID: 30371871 DOI: 10.1093/molbev/msy200] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we present detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and proposed a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche but did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and whereas these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.
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Affiliation(s)
- Ning Wang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, MN
| | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Joseph F Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Joseph W Brown
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Bin Liang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Tao Feng
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Caroline Edwards
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Jessica Mikenas
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Julia Olivieri
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Vera Hutchison
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Alfonso Timoneda
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Tommy Stoughton
- Center for the Environment, MSC 63, Plymouth State University, Plymouth, NH
| | - Raúl Puente
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ.,Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - Urs Eggli
- Sukkulenten-Sammlung Zürich, Zürich, Switzerland
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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30
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Ciezarek AG, Osborne OG, Shipley ON, Brooks EJ, Tracey SR, McAllister JD, Gardner LD, Sternberg MJE, Block B, Savolainen V. Phylotranscriptomic Insights into the Diversification of Endothermic Thunnus Tunas. Mol Biol Evol 2019; 36:84-96. [PMID: 30364966 PMCID: PMC6340463 DOI: 10.1093/molbev/msy198] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Birds, mammals, and certain fishes, including tunas, opahs and lamnid sharks, are endothermic, conserving internally generated, metabolic heat to maintain body or tissue temperatures above that of the environment. Bluefin tunas are commercially important fishes worldwide, and some populations are threatened. They are renowned for their endothermy, maintaining elevated temperatures of the oxidative locomotor muscle, viscera, brain and eyes, and occupying cold, productive high-latitude waters. Less cold-tolerant tunas, such as yellowfin tuna, by contrast, remain in warm-temperate to tropical waters year-round, reproducing more rapidly than most temperate bluefin tuna populations, providing resiliency in the face of large-scale industrial fisheries. Despite the importance of these traits to not only fisheries but also habitat utilization and responses to climate change, little is known of the genetic processes underlying the diversification of tunas. In collecting and analyzing sequence data across 29,556 genes, we found that parallel selection on standing genetic variation is associated with the evolution of endothermy in bluefin tunas. This includes two shared substitutions in genes encoding glycerol-3 phosphate dehydrogenase, an enzyme that contributes to thermogenesis in bumblebees and mammals, as well as four genes involved in the Krebs cycle, oxidative phosphorylation, β-oxidation, and superoxide removal. Using phylogenetic techniques, we further illustrate that the eight Thunnus species are genetically distinct, but found evidence of mitochondrial genome introgression across two species. Phylogeny-based metrics highlight conservation needs for some of these species.
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Affiliation(s)
- Adam G Ciezarek
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
| | - Owen G Osborne
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
| | - Oliver N Shipley
- Shark Research and Conservation Program, The Cape Eleuthera Institute, Rock Sound, Eleuthera, The Bahamas
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY
| | - Edward J Brooks
- Shark Research and Conservation Program, The Cape Eleuthera Institute, Rock Sound, Eleuthera, The Bahamas
| | - Sean R Tracey
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Jaime D McAllister
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Luke D Gardner
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA
| | - Michael J E Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, Kensington, London, United Kingdom
| | - Barbara Block
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA
| | - Vincent Savolainen
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
- Corresponding author: E-mail:
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31
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Plastid phylogenomic insights into the evolution of Caryophyllales. Mol Phylogenet Evol 2019; 134:74-86. [DOI: 10.1016/j.ympev.2018.12.023] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 11/22/2022]
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32
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Nikolov LA, Shushkov P, Nevado B, Gan X, Al-Shehbaz IA, Filatov D, Bailey CD, Tsiantis M. Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity. THE NEW PHYTOLOGIST 2019; 222:1638-1651. [PMID: 30735246 DOI: 10.1111/nph.15732] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/10/2019] [Indexed: 05/03/2023]
Abstract
The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, the relationships among major lineages in the family remain unresolved, hampering comparative research. Here, we inferred a Brassicaceae phylogeny using newly generated targeted enrichment sequence data of 1827 exons (> 940 000 bases) representing 63 species, as well as sequenced genome data of 16 species, together representing 50 of the 52 currently recognized Brassicaceae tribes. A third of the samples were derived from herbarium material, facilitating broad taxonomic coverage of the family. Six major clades formed successive sister groups to the rest of Brassicaceae. We also recovered strong support for novel relationships among tribes, and resolved the position of 16 taxa previously not assigned to a tribe. The broad utility of these phylogenetic results is illustrated through a comparative investigation of genome-wide expression signatures that distinguish simple from complex leaves in Brassicaceae. Our study provides an easily extendable dataset for further advances in Brassicaceae systematics and a timely higher-level phylogenetic framework for a wide range of comparative studies of multiple traits in an intensively investigated group of plants.
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Affiliation(s)
- Lachezar A Nikolov
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Philip Shushkov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Xiangchao Gan
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Ihsan A Al-Shehbaz
- Missouri Botanical Garden, 4344 Shaw Boulevard, St Louis, MO, 63110, USA
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
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33
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Liu Y, Johnson MG, Cox CJ, Medina R, Devos N, Vanderpoorten A, Hedenäs L, Bell NE, Shevock JR, Aguero B, Quandt D, Wickett NJ, Shaw AJ, Goffinet B. Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nat Commun 2019; 10:1485. [PMID: 30940807 PMCID: PMC6445109 DOI: 10.1038/s41467-019-09454-w] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 03/07/2019] [Indexed: 11/21/2022] Open
Abstract
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30 moss orders reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes are much higher in mosses than in seed plants, consistent with the emerging concept of evolutionary dynamism in mosses. Our results highlight the evolutionary significance of taxa with reduced morphologies, shed light on the relative tempo and mechanisms underlying major cladogenic events, and suggest hypotheses for the relationships and delineation of moss orders.
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Affiliation(s)
- Yang Liu
- Fairy Lake Botanical Garden & Chinese Academy of Sciences, Shenzhen, 518004, China
- BGI-Shenzhen, Shenzhen, 518120, China
| | | | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319, Faro, Portugal
| | - Rafael Medina
- Department of Biology, Augustana College, Rock Island, IL, 61201, USA
| | - Nicolas Devos
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | | | - Lars Hedenäs
- Department of Botany, Swedish Museum of Natural History, Stockholm, Box 50007, 10405, Sweden
| | - Neil E Bell
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - James R Shevock
- California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, 53115, Germany
| | | | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA.
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34
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Walker JF, Walker-Hale N, Vargas OM, Larson DA, Stull GW. Characterizing gene tree conflict in plastome-inferred phylogenies. PeerJ 2019. [PMID: 31579615 DOI: 10.1101/512079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes.
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Affiliation(s)
- Joseph F Walker
- Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, United Kingdom
| | - Nathanael Walker-Hale
- Department of Plant Sciences, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Oscar M Vargas
- University of California, Santa Cruz, Santa Cruz, United States of America
| | - Drew A Larson
- University of Michigan-Ann Arbor, Ann Arbor, MI, United States of America
| | - Gregory W Stull
- Department of Botany, Smithsonian Institution, Washington, United States of America
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Davis AL, Babb MH, Lowe MC, Yeh AT, Lee BT, Martin CH. Testing Darwin's Hypothesis about the Wonderful Venus Flytrap: Marginal Spikes Form a "Horrid Prison" for Moderate-Sized Insect Prey. Am Nat 2018; 193:309-317. [PMID: 30720364 DOI: 10.1086/701433] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Botanical carnivory is a novel feeding strategy associated with numerous physiological and morphological adaptations. However, the benefits of these novel carnivorous traits are rarely tested. We used field observations, lab experiments, and a seminatural experiment to test prey capture function of the marginal spikes on snap traps of the Venus flytrap (Dionaea muscipula). Our field and laboratory results suggested inefficient capture success: fewer than one in four prey encounters led to prey capture. Removing the marginal spikes decreased the rate of prey capture success for moderate-sized cricket prey by 90%, but this effect disappeared for larger prey. The nonlinear benefit of spikes suggests that they provide a better cage for capturing more abundant insects of moderate and small sizes, but they may also provide a foothold for rare large prey to escape. Our observations support Darwin's hypothesis that the marginal spikes form a "horrid prison" that increases prey capture success for moderate-sized prey, but the decreasing benefit for larger prey is unexpected and previously undocumented. Thus, we find surprising complexity in the adaptive landscape for one of the most wonderful evolutionary innovations among all plants. These findings enrich understanding of the evolution and diversification of novel trap morphology in carnivorous plants.
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Walker JF, Brown JW, Smith SA. Analyzing Contentious Relationships and Outlier Genes in Phylogenomics. Syst Biol 2018; 67:916-924. [PMID: 29893968 DOI: 10.1093/sysbio/syy043] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/02/2018] [Indexed: 01/19/2023] Open
Abstract
Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, and that less than one percent of genes may ultimately drive species tree inference in supermatrix analyses. Herein, we examined two data sets where supermatrix and coalescent-based species trees conflict. We identified two highly influential "outlier" genes in each data set. When removed from each data set, the inferred supermatrix trees matched the topologies obtained from coalescent analyses. We also demonstrate that, while the outlier genes in the vertebrate data set have been shown in a previous study to be the result of errors in orthology detection, the outlier genes from a plant data set did not exhibit any obvious systematic error, and therefore, may be the result of some biological process yet to be determined. While topological comparisons among a small set of alternate topologies can be helpful in discovering outlier genes, they can be limited in several ways, such as assuming all genes share the same topology. Coalescent species tree methods relax this assumption but do not explicitly facilitate the examination of specific edges. Coalescent methods often also assume that conflict is the result of incomplete lineage sorting. Herein, we explored a framework that allows for quickly examining alternative edges and support for large phylogenomic data sets that does not assume a single topology for all genes. For both data sets, these analyses provided detailed results confirming the support for coalescent-based topologies. This framework suggests that we can improve our understanding of the underlying signal in phylogenomic data sets by asking more targeted edge-based questions.
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Affiliation(s)
- Joseph F Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph W Brown
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Clark JW, Donoghue PCJ. Whole-Genome Duplication and Plant Macroevolution. TRENDS IN PLANT SCIENCE 2018; 23:933-945. [PMID: 30122372 DOI: 10.1016/j.tplants.2018.07.006] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/29/2018] [Accepted: 07/12/2018] [Indexed: 05/18/2023]
Abstract
Whole-genome duplication (WGD) is characteristic of almost all fundamental lineages of land plants. Unfortunately, the timings of WGD events are loosely constrained and hypotheses of evolutionary consequence are poorly formulated, making them difficult to test. Using examples from across the plant kingdom, we show that estimates of timing can be improved through the application of molecular clock methodology to multigene datasets. Further, we show that phenotypic change can be quantified in morphospaces and that relative phenotypic disparity can be compared in the light of WGD. Together, these approaches facilitate tests of hypotheses on the role of WGD in plant evolution, underscoring the potential of plants as a model system for investigating the role WGD in macroevolution.
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Affiliation(s)
- James W Clark
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TH, UK.
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TH, UK.
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Henarejos-Escudero P, Guadarrama-Flores B, García-Carmona F, Gandía-Herrero F. Digestive glands extraction and precise pigment analysis support the exclusion of the carnivorous plant Dionaea muscipula Ellis from the Caryophyllales order. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:342-348. [PMID: 30080622 DOI: 10.1016/j.plantsci.2018.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 06/08/2023]
Abstract
In the order Caryophyllales, plants synthesize betalains instead of anthocyanins, with only two exceptions, the Caryophyllaceae and Molluginaceae. Dionaea muscipula Ellis was included in the Caryophyllales order but recent research based on genetic studies proposed the consideration of the Droseraceae family into the Nepenthales order. In this work we face the dilemma of the phylogenetic classification of Dionaea from a phytochemical point of view. Dionaea's pigments were analyzed by using techniques of structural analysis. Extracts from the leaves, mature stem and flowers of different specimens of Dionaea were analyzed, to find possible differences in the types of pigments or in their proportion in different parts of the plant. These extracts were analyzed by spectrophotometry, HPLC co-elution and ESI-MS/MS. In addition, digestive glands were extracted from the snap trap with minor sample manipulation and by reducing the non-pigmented plant tissue. Considering only the digestive glands instead of whole snap traps, the analyses allowed to quantitate and elucidate the structure of the compounds responsible for the red coloration: delphinidin-3-O-glucoside (myrtillin), cyanidin-3-O-glucoside (kuromanin) and a third compound, the aglycone cyanidin, detected in the species for the first time. The unambiguous results of the present work support the exclusion of Dionaea from the Caryophyllales.
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Affiliation(s)
- Paula Henarejos-Escudero
- Departamento de Bioquímica y Biología Molecular A, Unidad Docente de Biología, Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum″, Universidad de Murcia, 30100, Murcia, Spain
| | - Berenice Guadarrama-Flores
- Departamento de Bioquímica y Biología Molecular A, Unidad Docente de Biología, Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum″, Universidad de Murcia, 30100, Murcia, Spain
| | - Francisco García-Carmona
- Departamento de Bioquímica y Biología Molecular A, Unidad Docente de Biología, Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum″, Universidad de Murcia, 30100, Murcia, Spain
| | - Fernando Gandía-Herrero
- Departamento de Bioquímica y Biología Molecular A, Unidad Docente de Biología, Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum″, Universidad de Murcia, 30100, Murcia, Spain.
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So many genes, so little time: A practical approach to divergence-time estimation in the genomic era. PLoS One 2018; 13:e0197433. [PMID: 29772020 PMCID: PMC5957400 DOI: 10.1371/journal.pone.0197433] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/02/2018] [Indexed: 11/24/2022] Open
Abstract
Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. “Gene shopping”, wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated lognormal (UCLN) models. However, this overlap was often due to imprecise estimates from the UCLN model. We find that “gene shopping” can be an efficient approach to divergence-time inference for phylogenomic datasets that may otherwise be characterized by extensive gene tree heterogeneity.
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Walker JF, Yang Y, Feng T, Timoneda A, Mikenas J, Hutchison V, Edwards C, Wang N, Ahluwalia S, Olivieri J, Walker-Hale N, Majure LC, Puente R, Kadereit G, Lauterbach M, Eggli U, Flores-Olvera H, Ochoterena H, Brockington SF, Moore MJ, Smith SA. From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales. AMERICAN JOURNAL OF BOTANY 2018; 105:446-462. [PMID: 29738076 DOI: 10.1002/ajb2.1069] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/04/2018] [Indexed: 05/27/2023]
Abstract
PREMISE OF THE STUDY The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. METHODS We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene-tree conflict analyses. KEY RESULTS Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is not only a common feature of phylogenomic studies, but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling. CONCLUSIONS Transcriptomes are useful both for species-tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species-tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large data sets.
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Affiliation(s)
- Joseph F Walker
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Tao Feng
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Alfonso Timoneda
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Jessica Mikenas
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Vera Hutchison
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Caroline Edwards
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Ning Wang
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Sonia Ahluwalia
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Julia Olivieri
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
- Institute of Computational and Mathematical Engineering (ICME), Stanford University, 475 Via Ortega, Suite B060, Stanford, CA, 94305-4042, USA
| | - Nathanael Walker-Hale
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Kelburn, Wellington, 6012, New Zealand
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden, 1201 N. Galvin Pkwy, Phoenix, AZ, 85008, USA
| | - Raúl Puente
- Department of Research, Conservation and Collections, Desert Botanical Garden, 1201 N. Galvin Pkwy, Phoenix, AZ, 85008, USA
| | - Gudrun Kadereit
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
- Institut für Molekulare und Organismische Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
| | - Maximilian Lauterbach
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
- Institut für Molekulare und Organismische Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
| | - Urs Eggli
- Sukkulenten-Sammlung Zürich / Grün Stadt Zürich, Mythenquai 88, CH-8002, Zürich, Switzerland
| | - Hilda Flores-Olvera
- Departamento de Botánica, Universidad Nacional Autónoma de México, Apartado, Postal 70-367, 04510, Mexico City, Mexico
| | - Helga Ochoterena
- Departamento de Botánica, Universidad Nacional Autónoma de México, Apartado, Postal 70-367, 04510, Mexico City, Mexico
| | | | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
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Smith SA, Brown JW. Constructing a broadly inclusive seed plant phylogeny. AMERICAN JOURNAL OF BOTANY 2018; 105:302-314. [PMID: 29746720 DOI: 10.1002/ajb2.1019] [Citation(s) in RCA: 349] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/19/2017] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY Large phylogenies can help shed light on macroevolutionary patterns that inform our understanding of fundamental processes that shape the tree of life. These phylogenies also serve as tools that facilitate other systematic, evolutionary, and ecological analyses. Here we combine genetic data from public repositories (GenBank) with phylogenetic data (Open Tree of Life project) to construct a dated phylogeny for seed plants. METHODS We conducted a hierarchical clustering analysis of publicly available molecular data for major clades within the Spermatophyta. We constructed phylogenies of major clades, estimated divergence times, and incorporated data from the Open Tree of Life project, resulting in a seed plant phylogeny. We estimated diversification rates, excluding those taxa without molecular data. We also summarized topological uncertainty and data overlap for each major clade. KEY RESULTS The trees constructed for Spermatophyta consisted of 79,881 and 353,185 terminal taxa; the latter included the Open Tree of Life taxa for which we could not include molecular data from GenBank. The diversification analyses demonstrated nested patterns of rate shifts throughout the phylogeny. Data overlap and inference uncertainty show significant variation throughout and demonstrate the continued need for data collection across seed plants. CONCLUSIONS This study demonstrates a means for combining available resources to construct a dated phylogeny for plants. However, this approach is an early step and more developments are needed to add data, better incorporating underlying uncertainty, and improve resolution. The methods discussed here can also be applied to other major clades in the tree of life.
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Affiliation(s)
- Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Joseph W Brown
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
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42
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Pease JB, Brown JW, Walker JF, Hinchliff CE, Smith SA. Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life. AMERICAN JOURNAL OF BOTANY 2018; 105:385-403. [PMID: 29746719 DOI: 10.1002/ajb2.1016] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/05/2017] [Indexed: 05/21/2023]
Abstract
PREMISE OF THE STUDY Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As data sets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative. METHODS We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in large-sparse and genome-wide data sets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We tested QS with simulations and recent plant phylogenies inferred from variously sized data sets. KEY RESULTS QS scores demonstrated convergence with increasing replicates and were not strongly affected by branch depth. Patterns of QS support from different phylogenies led to a coherent understanding of ancestral branches defining key disagreements, including the relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to liverworts. The relationships of ANA-grade angiosperms (Amborella, Nymphaeales, Austrobaileyales), major monocot groups, bryophytes, and fern families are likely highly discordant in their evolutionary histories, rather than poorly informed. QS can also detect discordance due to introgression in phylogenomic data. CONCLUSIONS Quartet Sampling is an efficient synthesis of phylogenetic tests that offers more comprehensive and specific information on branch support than conventional measures. The QS method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted when reconstructing complex evolutionary histories, in particular those surrounding ANA-grade, monocots, and nonvascular plants.
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Affiliation(s)
- James B Pease
- Department of Biology, Wake Forest University, 455 Vine Street, Winston-Salem, North Carolina, 27101, USA
| | - Joseph W Brown
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, Michigan, 48109, USA
| | - Joseph F Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, Michigan, 48109, USA
| | - Cody E Hinchliff
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho, 83844, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, Michigan, 48109, USA
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Smith SA, Brown JW, Yang Y, Bruenn R, Drummond CP, Brockington SF, Walker JF, Last N, Douglas NA, Moore MJ. Disparity, diversity, and duplications in the Caryophyllales. THE NEW PHYTOLOGIST 2018; 217:836-854. [PMID: 28892163 DOI: 10.1111/nph.14772] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/28/2017] [Indexed: 05/27/2023]
Abstract
The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species. We phylogenetically mapped putative WGDs as identified from analyses on transcriptomic and genomic data and analyzed these in conjunction with shifts in climatic occupancy and lineage diversification rate. Thirteen putative WGDs and 27 diversification shifts could be mapped onto the phylogeny. Of these, four WGDs were concurrent with diversification shifts, with other diversification shifts occurring at more recent nodes than WGDs. Five WGDs were associated with shifts to colder climatic occupancy. While we find that many diversification shifts occur after WGDs, it is difficult to consider diversification and duplication to be tightly correlated. Our findings suggest that duplications may often occur along with shifts in either diversification rate, climatic occupancy, or rate of evolution.
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Affiliation(s)
- Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48103, USA
| | - Joseph W Brown
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48103, USA
| | - Ya Yang
- Department of Plant Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St Paul, MN, 55108, USA
| | - Riva Bruenn
- Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH, 44074-1097, USA
| | - Chloe P Drummond
- Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH, 44074-1097, USA
| | | | - Joseph F Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48103, USA
| | - Noah Last
- Department of Plant Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St Paul, MN, 55108, USA
| | - Norman A Douglas
- Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH, 44074-1097, USA
| | - Michael J Moore
- Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH, 44074-1097, USA
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Yang Y, Moore MJ, Brockington SF, Mikenas J, Olivieri J, Walker JF, Smith SA. Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. THE NEW PHYTOLOGIST 2018; 217:855-870. [PMID: 28944472 DOI: 10.1111/nph.14812] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/09/2017] [Indexed: 05/14/2023]
Abstract
Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. We assembled a data set of transcriptomes and genomes from 168 species in Caryophyllales, of which 43 transcriptomes were newly generated for this study, representing one of the most densely sampled genomic-scale data sets available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped the phylogenetic distribution of polyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for allopolyploidy. We identified 26 ancient and more recent polyploidy events distributed throughout Caryophyllales. Two of these events were inferred to be allopolyploidy. Through dense phylogenomic sampling, we show the propensity of polyploidy throughout the evolutionary history of Caryophyllales. We also provide a framework for utilizing transcriptome data to detect allopolyploidy, which is important as it may have different macroevolutionary implications compared with autopolyploidy.
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Affiliation(s)
- Ya Yang
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Michael J Moore
- Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH, 44074-1097, USA
| | | | - Jessica Mikenas
- Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH, 44074-1097, USA
| | - Julia Olivieri
- Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH, 44074-1097, USA
| | - Joseph F Walker
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
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