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Moreyra LD, Garcia-Jacas N, Roquet C, Ackerfield JR, Arabacı T, Blanco-Gavaldà C, Brochmann C, Calleja JA, Dirmenci T, Fujikawa K, Galbany-Casals M, Gao T, Gizaw A, López-Alvarado J, Mehregan I, Vilatersana R, Yıldız B, Leliaert F, Seregin AP, Susanna A. African Mountain Thistles: Three New Genera in the Carduus-Cirsium Group. PLANTS (BASEL, SWITZERLAND) 2023; 12:3083. [PMID: 37687332 PMCID: PMC10489743 DOI: 10.3390/plants12173083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023]
Abstract
The floras on the highest mountains in tropical eastern Africa are among the most unique floras in the world. Despite the exceptionally high concentration of endemic species, these floras remain understudied from an evolutionary point of view. In this study, we focus on the Carduus-Cirsium group (subtribe Carduinae) to unravel the evolutionary relationships of the species endemic to the tropical Afromontane and Afroalpine floras, aiming to improve the systematics of the group. We applied the Hyb-Seq approach using the Compositae1061 probe set on 190 samples (159 species), encompassing representatives of all genera of Carduinae. We used two recently developed pipelines that enabled the processing of raw sequence reads, identification of paralogous sequences and segregation into orthologous alignments. After the implementation of a missing data filter, we retained sequences from 986 nuclear loci and 177 plastid regions. Phylogenomic analyses were conducted using both concatenated and summary-coalescence methods. The resulting phylogenies were highly resolved and revealed three distinct evolutionary lineages consisting of the African species traditionally referred to as Carduus and Cirsium. Consequently, we propose the three new genera Afrocarduus, Afrocirsium and Nuriaea; the latter did notably not belong to the Carduus-Cirsium group. We detected some incongruences between the phylogenies based on concatenation vs. coalescence and on nuclear vs. plastid datasets, likely attributable to incomplete lineage sorting and/or hybridization.
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Affiliation(s)
- Lucía D. Moreyra
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia, s.n., 08038 Barcelona, Spain; (L.D.M.); (N.G.-J.); (R.V.)
| | - Núria Garcia-Jacas
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia, s.n., 08038 Barcelona, Spain; (L.D.M.); (N.G.-J.); (R.V.)
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC by IBB, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain; (C.R.); (C.B.-G.); (M.G.-C.)
| | | | - Turan Arabacı
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Inönü University, 44280 Malatya, Türkiye;
| | - Carme Blanco-Gavaldà
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC by IBB, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain; (C.R.); (C.B.-G.); (M.G.-C.)
| | - Christian Brochmann
- Natural History Museum, University of Oslo, Blindern, 0318 Oslo, Norway; (C.B.); (A.G.)
| | - Juan Antonio Calleja
- Department of Biology, Autonomous University of Madrid, 28049 Madrid, Spain;
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Tuncay Dirmenci
- Department of Biology, Faculty of Necatibey Education, Balıkesir University, 10145 Balıkesir, Türkiye;
| | - Kazumi Fujikawa
- Kochi Prefectural Makino Botanical Garden, 4200-6, Godaisan, Kochi 781-8125, Japan;
| | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC by IBB, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain; (C.R.); (C.B.-G.); (M.G.-C.)
| | - Tiangang Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Abel Gizaw
- Natural History Museum, University of Oslo, Blindern, 0318 Oslo, Norway; (C.B.); (A.G.)
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa P.O. Box 3434, Ethiopia
| | - Javier López-Alvarado
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC by IBB, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain; (C.R.); (C.B.-G.); (M.G.-C.)
| | - Iraj Mehregan
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran;
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia, s.n., 08038 Barcelona, Spain; (L.D.M.); (N.G.-J.); (R.V.)
| | - Bayram Yıldız
- Ismail Cem Street, No. 35, Yenikale District, 35320 Narlidere Türkiye;
| | | | - Alexey P. Seregin
- Faculty of Biology, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia, s.n., 08038 Barcelona, Spain; (L.D.M.); (N.G.-J.); (R.V.)
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Wang Y, Zhang CF, Ochieng Odago W, Jiang H, Yang JX, Hu GW, Wang QF. Evolution of 101 Apocynaceae plastomes and phylogenetic implications. Mol Phylogenet Evol 2023; 180:107688. [PMID: 36581140 DOI: 10.1016/j.ympev.2022.107688] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 11/21/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
Apocynaceae are one of the ten species-richest angiosperm families. However, the backbone phylogeny of the family is yet less well supported, and the evolution of plastome structure has not been thoroughly studied for the whole family. Herein, a total of 101 complete plastomes including 35 newly sequenced, 24 reassembled from public raw data and the rest from the NCBI GenBank database, representing 26 of 27 tribes of Apocynaceae, were used for comparative plastome analysis. Phylogenetic analyses were conducted using a combined plastid data matrix of 77 protein-coding genes from 162 taxa, encompassing all tribes and 41 of 49 subtribes of Apocynaceae. Plastome lengths ranged from 150,897 bp in Apocynum venetum to 178,616 bp in Hoya exilis. Six types of boundaries between the inverted repeat (IR) regions and single copy (SC) regions were identified. Different sizes of IR expansion were found in three lineages, including Alyxieae, Ceropegieae and Marsdenieae, suggesting multiple expansion events of the IRs over the SC regions in Apocynaceae. The IR regions of Marsdenieae evolved in two ways: expansion towards the large single copy (LSC) region in Lygisma + Stephanotis + Ruehssia + Gymnema (Cosmopolitan clade), and expansion towards both LSC and small single copy (SSC) region in Dischidia-Hoya alliance and Marsdenia (Asia-Pacific clade). Six coding genes and five non-coding regions were identified as highly variable, including accD, ccsA-ndhD, clpP, matK, ndhF, ndhG-ndhI, trnG(GCC)-trnfM(CAU), trnH(GUG)-psbA, trnY(GUA)-trnE(UUC), ycf1, and ycf2. Maximum likelihood and Bayesian phylogenetic analyses resulted in nearly identical tree topologies and produced a well-resolved backbone comprising 15 consecutive dichotomies that subdivided Apocynaceae into 15 clades. The subfamily Periplocoideae were embedded in the Apocynoid grade and were sister to the Echiteae-Odontadenieae-Mesechiteae clade with high support values. Three tribes (Melodineae, Vinceae, and Willughbeieae), the subtribe Amphineuriinae, and four genera (Beaumontia, Ceropegia, Hoya, and Stephanotis) were not resolved as monophyletic. Our work sheds light on the backbone phylogenetic relationships in the family Apocynaceae and offers insights into the evolution of Apocynaceae plastomes using the most densely sampled plastome dataset to date.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Cai-Fei Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Wyclif Ochieng Odago
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Hui Jiang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jia-Xin Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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Xiang R, Wang S, Wan H. The complete chloroplast genome of Holarrhena pubescens and its phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:266-269. [PMID: 36816055 PMCID: PMC9937002 DOI: 10.1080/23802359.2022.2162349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Holarrhena pubescens Wall. ex G. Don, 1837 is an important medicinal plant belonging to the Holarrhena genus in the Apocynaceae family. In this study, the complete chloroplast (cp) genome sequence of H. pubescens was sequenced using the Illumina NovaSeq platform. The cp genome of H. pubescens was 160,108 bp in length with 37.21% overall GC content. The cp genome of H. pubescens containing a large single-copy region (LSC, 88,685 bp), a small single-copy region (SSC, 18,671 bp), and a pair of inverted repeat regions (SSC, 26,376 bp). The cp genome encoded 129 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on complete protein coding genes sequences revealed that H. pubescens was closest to Beaumontia murtonii.
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Affiliation(s)
- Rushuang Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China,College of Pharmaceutical, Dali University, Dali, China
| | - Sijia Wang
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Huihua Wan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China,School of Landscape Architecture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China,CONTACT Huihua Wan Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100070, China
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Murillo-A J, Valencia-D J, Orozco CI, Parra-O C, Neubig KM. Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification. AMERICAN JOURNAL OF BOTANY 2022; 109:1139-1156. [PMID: 35709353 DOI: 10.1002/ajb2.16025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
PREMISE To date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target-enriched nuclear data to improve our understanding of phylogenetic relationships in the family. METHODS We used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species in Brunellia, and several outgroup taxa. We removed loci that indicated biased inference of relationships and applied concatenated and coalescent methods to infer Brunellia phylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage sorting events and assessed their impact on phylogenetic inference. Finally, we performed ancestral-state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections in Brunellia. RESULTS Brunellia comprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses. CONCLUSIONS Phylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene-tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character-state reconstructions. While target enrichment data allows us to broaden our understanding of diversification in Brunellia, the relationships among subclades remain incompletely understood.
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Affiliation(s)
- José Murillo-A
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 # 45-03, edificio 425, Bogotá, D.C., Colombia
| | - Janice Valencia-D
- School of Biological Sciences, Southern Illinois University Carbondale, 1125 Lincoln Dr., Carbondale, Illinois, 62901-6509, USA
| | - Clara I Orozco
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 # 45-03, edificio 425, Bogotá, D.C., Colombia
| | - Carlos Parra-O
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 # 45-03, edificio 425, Bogotá, D.C., Colombia
| | - Kurt M Neubig
- School of Biological Sciences, Southern Illinois University Carbondale, 1125 Lincoln Dr., Carbondale, Illinois, 62901-6509, USA
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Draper I, Villaverde T, Garilleti R, Burleigh JG, McDaniel SF, Mazimpaka V, Calleja JA, Lara F. An NGS-Based Phylogeny of Orthotricheae (Orthotrichaceae, Bryophyta) With the Proposal of the New Genus Rehubryum From Zealandia. FRONTIERS IN PLANT SCIENCE 2022; 13:882960. [PMID: 35646035 PMCID: PMC9133926 DOI: 10.3389/fpls.2022.882960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Phylogenomic data increase the possibilities of resolving the evolutionary and systematic relationships among taxa. This is especially valuable in groups with few and homoplasious morphological characters, in which systematic and taxonomical delimitations have been traditionally difficult. Such is the case of several lineages within Bryophyta, like Orthotrichaceae, the second most diverse family of mosses. Members of tribe Orthotricheae are common in temperate and cold regions, as well as in high tropical mountains. In extratropical areas, they represent one of the main components of epiphytic communities, both in dry and oceanic or hyperoceanic conditions. The epiphytic environment is considered a hostile one for plant development, mainly due to its low capacity of moisture retention. Thus, the diversification of the Orthotrichaceae in this environment could be seen as striking. Over the last two decades, great taxonomic and systematic progresses have led to a rearrangement at the generic level in this tribe, providing a new framework to link environment to patterns of diversification. Here, we use nuclear loci targeted with the GoFlag 408 enrichment probe set to generate a well-sampled phylogeny with well-supported suprageneric taxa and increasing the phylogenetic resolution within the two recognized subtribes. Specifically, we show that several genera with Ulota-like morphology jointly constitute an independent lineage. Within this lineage, the recently described Atlantichella from Macaronesia and Western Europe appears as the sister group of Ulota bellii from Zealandia. This latter species is here segregated in the new genus Rehubryum. Assessment of the ecological and biogeographical affinities of the species within the phylogenetic framework suggests that niche adaptation (including climate and substrate) may be a key evolutionary driver that shaped the high diversification of Orthotricheae.
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Affiliation(s)
- Isabel Draper
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Tamara Villaverde
- Departamento de Biodiversidad, Ecología y Evolución,Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Ricardo Garilleti
- Departamento de Botánica y Geología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
| | - J. Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Stuart F. McDaniel
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Vicente Mazimpaka
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan A. Calleja
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Francisco Lara
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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Abramson NI, Bodrov SY, Bondareva OV, Genelt-Yanovskiy EA, Petrova TV. A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications. PLoS One 2021; 16:e0248198. [PMID: 34797834 PMCID: PMC8604340 DOI: 10.1371/journal.pone.0248198] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/03/2021] [Indexed: 01/04/2023] Open
Abstract
Arvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.
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Affiliation(s)
- Natalia I. Abramson
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Semyon Yu. Bodrov
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Olga V. Bondareva
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Evgeny A. Genelt-Yanovskiy
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Tatyana V. Petrova
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
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Kolicka M, Dabert M, Olszanowski Z, Dabert J. Sweet or salty? The origin of freshwater gastrotrichs (Gastrotricha, Chaetonotida) revealed by molecular phylogenetic analysis. Cladistics 2021; 36:458-480. [PMID: 34618974 DOI: 10.1111/cla.12424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2020] [Indexed: 11/29/2022] Open
Abstract
Chaetonotidae is the most diverse and widely distributed family of the order Chaetonotida (Gastrotricha) and includes both marine and freshwater species. Although the family is regarded as a sister taxon to the exclusively marine Xenotrichulidae, the type of environment, marine or freshwater, where Chaetonotidae originated is still not known. Here, we reconstructed the phylogeny of the family based on molecular sequence data and mapped both morphological and ecological characters to determine the ancestral environment of the first members of the family. Our results revealed that the freshwater genus Bifidochaetus is the earliest branching lineage in the paraphyletic Chaetonotidae (encompassing Dasydytidae and Neogosseidae). Moreover, we reconstructed Lepidochaetus-Cephalionotus clade as a monophyletic sister group to the remaining chaetonotids, which supports Kisielewski's morphological based hypothesis concerning undifferentiated type of body scales as a most primary character in Chaetonotidae. We also found that reversals to marine habitats occurred independently in different Chaetonotidae lineages, thus marine species in the genera Heterolepidoderma, Halichaetonotus, Aspidiophorus and subgenera Chaetonotus (Schizochaetonotus) or Chaetonotus (Marinochaetus) should be assumed as having secondarily invaded the marine environment. Character mapping revealed a series of synapomorphies that define the clade that includes Chaetonotidae (with Dasydytidae and Neogosseidae), the most important of which may be those linked to reproduction.
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Affiliation(s)
- Małgorzata Kolicka
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Ziemowit Olszanowski
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Jacek Dabert
- Department of Animal Morphology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
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Bitencourt C, Nürk NM, Rapini A, Fishbein M, Simões AO, Middleton DJ, Meve U, Endress ME, Liede-Schumann S. Evolution of Dispersal, Habit, and Pollination in Africa Pushed Apocynaceae Diversification After the Eocene-Oligocene Climate Transition. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.719741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Apocynaceae (the dogbane and milkweed family) is one of the ten largest flowering plant families, with approximately 5,350 species and diverse morphology and ecology, ranging from large trees and lianas that are emblematic of tropical rainforests, to herbs in temperate grasslands, to succulents in dry, open landscapes, and to vines in a wide variety of habitats. Despite a specialized and conservative basic floral architecture, Apocynaceae are hyperdiverse in flower size, corolla shape, and especially derived floral morphological features. These are mainly associated with the development of corolline and/or staminal coronas and a spectrum of integration of floral structures culminating with the formation of a gynostegium and pollinaria—specialized pollen dispersal units. To date, no detailed analysis has been conducted to estimate the origin and diversification of this lineage in space and time. Here, we use the most comprehensive time-calibrated phylogeny of Apocynaceae, which includes approximately 20% of the species covering all major lineages, and information on species number and distributions obtained from the most up-to-date monograph of the family to investigate the biogeographical history of the lineage and its diversification dynamics. South America, Africa, and Southeast Asia (potentially including Oceania), were recovered as the most likely ancestral area of extant Apocynaceae diversity; this tropical climatic belt in the equatorial region retained the oldest extant lineages and these three tropical regions likely represent museums of the family. Africa was confirmed as the cradle of pollinia-bearing lineages and the main source of Apocynaceae intercontinental dispersals. We detected 12 shifts toward accelerated species diversification, of which 11 were in the APSA clade (apocynoids, Periplocoideae, Secamonoideae, and Asclepiadoideae), eight of these in the pollinia-bearing lineages and six within Asclepiadoideae. Wind-dispersed comose seeds, climbing growth form, and pollinia appeared sequentially within the APSA clade and probably work synergistically in the occupation of drier and cooler habitats. Overall, we hypothesize that temporal patterns in diversification of Apocynaceae was mainly shaped by a sequence of morphological innovations that conferred higher capacity to disperse and establish in seasonal, unstable, and open habitats, which have expanded since the Eocene-Oligocene climate transition.
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Yardeni G, Viruel J, Paris M, Hess J, Groot Crego C, de La Harpe M, Rivera N, Barfuss MHJ, Till W, Guzmán-Jacob V, Krömer T, Lexer C, Paun O, Leroy T. Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations. Mol Ecol Resour 2021; 22:927-945. [PMID: 34606683 PMCID: PMC9292372 DOI: 10.1111/1755-0998.13523] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022]
Abstract
Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon‐specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly developed target capture set for Bromeliaceae, a large and ecologically diverse plant family with highly variable diversification rates. The set targets 1776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon‐specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon‐specific set results in higher enrichment success across the entire family; however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, for example the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon‐specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.
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Affiliation(s)
- Gil Yardeni
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Margot Paris
- Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Department of Soil Ecology, Helmholtz Centre for Environmental Research, UFZ, Halle (Saale), Germany
| | - Clara Groot Crego
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Marylaure de La Harpe
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Norma Rivera
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Michael H J Barfuss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Walter Till
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Valeria Guzmán-Jacob
- Biodiversity, Macroecology and Biogeography, University of Goettingen, Göttingen, Germany
| | - Thorsten Krömer
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Xalapa, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Thibault Leroy
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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10
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Wagner ND, Volf M, Hörandl E. Highly Diverse Shrub Willows ( Salix L.) Share Highly Similar Plastomes. FRONTIERS IN PLANT SCIENCE 2021; 12:662715. [PMID: 34539686 PMCID: PMC8448165 DOI: 10.3389/fpls.2021.662715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/23/2021] [Indexed: 05/23/2023]
Abstract
Plastome phylogenomics is used in a broad range of studies where single markers do not bear enough information. Phylogenetic reconstruction in the genus Salix is difficult due to the lack of informative characters and reticulate evolution. Here, we use a genome skimming approach to reconstruct 41 complete plastomes of 32 Eurasian and North American Salix species representing different lineages, different ploidy levels, and separate geographic regions. We combined our plastomes with published data from Genbank to build a comprehensive phylogeny of 61 samples (50 species) using RAxML (Randomized Axelerated Maximum Likelihood). Additionally, haplotype networks for two observed subclades were calculated, and 72 genes were tested to be under selection. The results revealed a highly conserved structure of the observed plastomes. Within the genus, we observed a variation of 1.68%, most of which separated subg. Salix from the subgeneric Chamaetia/Vetrix clade. Our data generally confirm previous plastid phylogenies, however, within Chamaetia/Vetrix phylogenetic results represented neither taxonomical classifications nor geographical regions. Non-coding DNA regions were responsible for most of the observed variation within subclades and 5.6% of the analyzed genes showed signals of diversifying selection. A comparison of nuclear restriction site associated DNA (RAD) sequencing and plastome data on a subset of 10 species showed discrepancies in topology and resolution. We assume that a combination of (i) a very low mutation rate due to efficient mechanisms preventing mutagenesis, (ii) reticulate evolution, including ancient and ongoing hybridization, and (iii) homoplasy has shaped plastome evolution in willows.
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Affiliation(s)
- Natascha D. Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (With Herbarium), University of Goettingen, Göttingen, Germany
| | - Martin Volf
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (With Herbarium), University of Goettingen, Göttingen, Germany
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11
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Rodda M, Niissalo MA. Plastome evolution and organisation in the Hoya group (Apocynaceae). Sci Rep 2021; 11:14520. [PMID: 34267257 PMCID: PMC8282776 DOI: 10.1038/s41598-021-93890-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/01/2021] [Indexed: 11/12/2022] Open
Abstract
The genus Hoya is highly diverse and many of its species are popular ornamental plants. However, the relationships between Hoya and related genera (the Hoya group) are not fully resolved. In this study, we report 20 newly sequenced plastomes of species in the Hoya group. The complete plastomes vary in length from 175,405 to 178,525 bp while the LSCs vary from 90,248 to 92,364 bp and the complete SSCs vary from 2,285 to 2,304 bp, making the SSC in the Hoya group one of the shortest known in the angiosperms. The plastome structure in the Hoya group is characterised by a massive increase in the size of the inverted repeats as compared to the outgroups. In all ingroup species, the IR/SSC boundary moved from ycf1 to ndhF while this was not observed in outgroup taxa, making it a synapomorphy for the Hoya group. We have also assembled the mitogenome of Hoya lithophytica, which, at 718,734 bp, is the longest reported in the family. The phylogenetic analysis using exons from 42 taxa in the Hoya group and three outgoups confirms that the earliest divergent genus in the Hoya group is Papuahoya, followed by Dischidia. The relationship between Dischidia and the clade which includes all Hoya and Oreosparte taxa, is not fully supported. Oreosparte is nested in Hoya making it paraphyletic unless Clemensiella is recognised as a separate genus.
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Affiliation(s)
- Michele Rodda
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, Singapore, 259569, Singapore.
| | - Matti A Niissalo
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, Singapore, 259569, Singapore
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12
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Pérez-Escobar OA, Dodsworth S, Bogarín D, Bellot S, Balbuena JA, Schley RJ, Kikuchi IA, Morris SK, Epitawalage N, Cowan R, Maurin O, Zuntini A, Arias T, Serna-Sánchez A, Gravendeel B, Torres Jimenez MF, Nargar K, Chomicki G, Chase MW, Leitch IJ, Forest F, Baker WJ. Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. AMERICAN JOURNAL OF BOTANY 2021; 108:1166-1180. [PMID: 34250591 DOI: 10.1002/ajb2.1702] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed. METHODS We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses. RESULTS Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes. CONCLUSIONS Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.
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Affiliation(s)
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2UP, UK
| | - Diego Bogarín
- Lankester Botanic Garden, University of Costa Rica, Cartago, Costa Rica
| | | | | | | | | | | | | | - Robyn Cowan
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
| | | | | | | | | | | | | | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Australia
- National Research Collections, Commonwealth Industrial and Scientific Research Organization, Australia
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mark W Chase
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | | | - Félix Forest
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
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13
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Antonelli A, Clarkson JJ, Kainulainen K, Maurin O, Brewer GE, Davis AP, Epitawalage N, Goyder DJ, Livshultz T, Persson C, Pokorny L, Straub SCK, Struwe L, Zuntini AR, Forest F, Baker WJ. Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes. AMERICAN JOURNAL OF BOTANY 2021; 108:1143-1165. [PMID: 34254285 DOI: 10.1002/ajb2.1697] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. METHODS Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. RESULTS We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). CONCLUSIONS The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.
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Affiliation(s)
- Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | | | - Kent Kainulainen
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22 A, Gothenburg, 413 19, Sweden
| | | | | | | | | | | | - Tatyana Livshultz
- Department of Biodiversity Earth and Environmental Sciences and Academy of Natural Sciences, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, USA
| | - Claes Persson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
| | | | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, 300 Pulteney Street, Geneva, NY, 14456, USA
| | - Lena Struwe
- Department of Ecology, Evolution, and Natural Resources & Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901, USA
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14
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Shah T, Schneider JV, Zizka G, Maurin O, Baker W, Forest F, Brewer GE, Savolainen V, Darbyshire I, Larridon I. Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits. AMERICAN JOURNAL OF BOTANY 2021; 108:1201-1216. [PMID: 34180046 DOI: 10.1002/ajb2.1682] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/23/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. METHODS We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. RESULTS For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. CONCLUSIONS The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.
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Affiliation(s)
- Toral Shah
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | - Julio V Schneider
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - William Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | | | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L., Ledeganckstraat 35, Gent, 9000, Belgium
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15
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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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16
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Mwanzia VM, He DX, Gichira AW, Li Y, Ngarega BK, Karichu MJ, Kamau PW, Li ZZ. The complete plastome sequences of five Aponogeton species (Aponogetonaceae): Insights into the structural organization and mutational hotspots. PLANT DIVERSITY 2020; 42:334-342. [PMID: 33134616 PMCID: PMC7584794 DOI: 10.1016/j.pld.2020.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/26/2020] [Accepted: 02/26/2020] [Indexed: 06/02/2023]
Abstract
Members of the aquatic plant genus Aponogeton are widely used commercially in aquariums because of their variable leaf shape and unique inflorescences. However, due to extensive similarity between species in this genus, morphological characters are generally inadequate for taxonomic classification. Currently, molecular makers available for taxonomic and phylogenetic studies of Aponogeton are limited. One approach to clarifying relationships between species in these complex groups is to use divergence hotspot regions within the genome. Here, we sequenced and analyzed the plastomes of five Aponogeton species collected from China, Zambia, and Kenya, and subsequently screened these plastomes for divergent DNA hotspots. The five plastomes are circular structures with sizes ranging from 154,167 bp to 154,860 bp. The Large and the Small Single Copies are separated by two Inverted Repeats. One hundred and thirteen unique genes were identified including 79 protein-coding, 30 tRNA, and four rRNA genes. We found that the most abundant repeats in all but one species were mononucleotide repeats (A/T) and that there were 23 potential RNA ending sites. Interestingly, a ~3 kb inversion, which includes the accD gene, was detected within the Asian species of Aponogeton. The inversion may be related to more frequent exchanges between this region and the nuclear genome. Furthermore, we detected mutational hotspot sites among the five Aponogeton species. Three of these hotspots are intergenic spacer regions (accD-psaI, rbcL-accD and trnH-GUG-psbA) that might be suitable for use as barcodes to resolve intra-generic relationships. We also identified four highly variable protein-coding genes (ccsA, rpl22, rps16 and ycf1) may be used as barcodes to resolve the higher-level phylogenies. Our study will provide valuable molecular resources for the taxonomic and phylogenomic study of the complex genus Aponogeton.
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Affiliation(s)
- Virginia M. Mwanzia
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ding-Xuan He
- School of Biological and Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Andrew W. Gichira
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yan Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Boniface K. Ngarega
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Mwihaki J. Karichu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | | | - Zhi-Zhong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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17
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Bagley JC, Uribe-Convers S, Carlsen MM, Muchhala N. Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study. Mol Phylogenet Evol 2020; 152:106769. [PMID: 32081762 DOI: 10.1016/j.ympev.2020.106769] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023]
Abstract
Targeted sequence capture is a promising approach for large-scale phylogenomics. However, rapid evolutionary radiations pose significant challenges for phylogenetic inference (e.g. incomplete lineages sorting (ILS), phylogenetic noise), and the ability of targeted nuclear loci to resolve species trees despite such issues remains poorly studied. We test the utility of targeted sequence capture for inferring phylogenetic relationships in rapid, recent angiosperm radiations, focusing on Burmeistera bellflowers (Campanulaceae), which diversified into ~130 species over less than 3 million years. We compared phylogenies estimated from supercontig (exons plus flanking sequences), exon-only, and flanking-only datasets with 506-546 loci (~4.7 million bases) for 46 Burmeistera species/lineages and 10 outgroup taxa. Nuclear loci resolved backbone nodes and many congruent internal relationships with high support in concatenation and coalescent-based species tree analyses, and inferences were largely robust to effects of missing taxa and base composition biases. Nevertheless, species trees were incongruent between datasets, and gene trees exhibited remarkably high levels of conflict (~4-60% congruence, ~40-99% conflict) not simply driven by poor gene tree resolution. Higher gene tree heterogeneity at shorter branches suggests an important role of ILS, as expected for rapid radiations. Phylogenetic informativeness analyses also suggest this incongruence has resulted from low resolving power at short internal branches, consistent with ILS, and homoplasy at deeper nodes, with exons exhibiting much greater risk of incorrect topologies due to homoplasy than other datasets. Our findings suggest that targeted sequence capture is feasible for resolving rapid, recent angiosperm radiations, and that results based on supercontig alignments containing nuclear exons and flanking sequences have higher phylogenetic utility and accuracy than either alone. We use our results to make practical recommendations for future target capture-based studies of Burmeistera and other rapid angiosperm radiations, including that such studies should analyze supercontigs to maximize the phylogenetic information content of loci.
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Affiliation(s)
- Justin C Bagley
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Simon Uribe-Convers
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - Mónica M Carlsen
- Research Department, Science and Conservation Division, Missouri Botanical Garden, St. Louis, MO 63110, USA
| | - Nathan Muchhala
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA
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18
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Jones KE, Fér T, Schmickl RE, Dikow RB, Funk VA, Herrando‐Moraira S, Johnston PR, Kilian N, Siniscalchi CM, Susanna A, Slovák M, Thapa R, Watson LE, Mandel JR. An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11295. [PMID: 31667023 PMCID: PMC6814182 DOI: 10.1002/aps3.11295] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/05/2019] [Indexed: 05/23/2023]
Abstract
PREMISE Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. METHODS Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. RESULTS Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DISCUSSION The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.
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Affiliation(s)
- Katy E. Jones
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinKönigin‐Luise‐Str. 6–814195BerlinGermany
| | - Tomáš Fér
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
| | - Roswitha E. Schmickl
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
- Institute of BotanyThe Czech Academy of SciencesZámek 1CZ 25243PrůhoniceCzech Republic
| | - Rebecca B. Dikow
- Data Science LabOffice of the Chief Information OfficerSmithsonian InstitutionWashingtonD.C.20013‐7012USA
| | - Vicki A. Funk
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonD.C.20013‐7012USA
| | | | - Paul R. Johnston
- Freie Universität BerlinEvolutionary BiologyBerlinGermany
- Berlin Center for Genomics in Biodiversity ResearchBerlinGermany
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB)BerlinGermany
| | - Norbert Kilian
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinKönigin‐Luise‐Str. 6–814195BerlinGermany
| | - Carolina M. Siniscalchi
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB‐CSIC‐ICUB)Pg. del Migdia s.n.ES 08038BarcelonaSpain
| | - Marek Slovák
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
- Plant Science and Biodiversity CentreSlovak Academy of SciencesSK‐84523BratislavaSlovakia
| | - Ramhari Thapa
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
| | - Linda E. Watson
- Department of Plant Biology, Ecology, and EvolutionOklahoma State UniversityStillwaterOklahoma74078USA
| | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
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Stepanek JG, Patrick Kociolek J. Molecular phylogeny of the diatom genera Amphora and Halamphora (Bacillariophyta) with a focus on morphological and ecological evolution. JOURNAL OF PHYCOLOGY 2019; 55:442-456. [PMID: 30659609 DOI: 10.1111/jpy.12836] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/01/2019] [Indexed: 06/09/2023]
Abstract
The taxonomic history of the diatom genus Amphora is one of a broad early morphological concept resulting in the inclusion of a diversity of taxa, followed by an extended period of revision and refinement. The introduction of molecular systematics has increased the pace of revision and has largely resolved the relationships between the major lineages, indicating homoplasy in the evolution of amphoroid symmetry. Within the two largest monophyletic lineages, the genus Halamphora and the now taxonomically refined genus Amphora, the intrageneric morphological and ecological relationships have yet to be explored within a phylogenetic framework. Critical among this is whether the range of morphological features exhibited within these diverse genera are reflective of evolutionary groupings or, as with many previously studied amphoroid features, are nonhomologous when examined phylogenetically. Presented here is a four-marker molecular phylogeny that includes 31 taxa from the genus Amphora and 77 taxa from the genus Halamphora collected from fresh, brackish, and salt waters from coastal and inland habitats of the United States and Japan. These phylogenies illustrate complex patterns in the evolution of frustule morphology and ecology within the genera and the implications of this on the taxonomy, classification, and organization of the genera are discussed.
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Affiliation(s)
- Joshua G Stepanek
- Department of Biology, Colorado Mountain College Vail Valley, Edwards, Colorado, 81632, USA
| | - J Patrick Kociolek
- Museum of Natural History and Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, 80309, USA
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20
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Ollerton J, Liede-Schumann S, Endress ME, Meve U, Rech AR, Shuttleworth A, Keller HA, Fishbein M, Alvarado-Cárdenas LO, Amorim FW, Bernhardt P, Celep F, Chirango Y, Chiriboga-Arroyo F, Civeyrel L, Cocucci A, Cranmer L, da Silva-Batista IC, de Jager L, Deprá MS, Domingos-Melo A, Dvorsky C, Agostini K, Freitas L, Gaglianone MC, Galetto L, Gilbert M, González-Ramírez I, Gorostiague P, Goyder D, Hachuy-Filho L, Heiduk A, Howard A, Ionta G, Islas-Hernández SC, Johnson SD, Joubert L, Kaiser-Bunbury CN, Kephart S, Kidyoo A, Koptur S, Koschnitzke C, Lamborn E, Livshultz T, Machado IC, Marino S, Mema L, Mochizuki K, Morellato LPC, Mrisha CK, Muiruri EW, Nakahama N, Nascimento VT, Nuttman C, Oliveira PE, Peter CI, Punekar S, Rafferty N, Rapini A, Ren ZX, Rodríguez-Flores CI, Rosero L, Sakai S, Sazima M, Steenhuisen SL, Tan CW, Torres C, Trøjelsgaard K, Ushimaru A, Vieira MF, Wiemer AP, Yamashiro T, Nadia T, Queiroz J, Quirino Z. The diversity and evolution of pollination systems in large plant clades: Apocynaceae as a case study. ANNALS OF BOTANY 2019; 123:311-325. [PMID: 30099492 PMCID: PMC6344220 DOI: 10.1093/aob/mcy127] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/10/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Large clades of angiosperms are often characterized by diverse interactions with pollinators, but how these pollination systems are structured phylogenetically and biogeographically is still uncertain for most families. Apocynaceae is a clade of >5300 species with a worldwide distribution. A database representing >10 % of species in the family was used to explore the diversity of pollinators and evolutionary shifts in pollination systems across major clades and regions. METHODS The database was compiled from published and unpublished reports. Plants were categorized into broad pollination systems and then subdivided to include bimodal systems. These were mapped against the five major divisions of the family, and against the smaller clades. Finally, pollination systems were mapped onto a phylogenetic reconstruction that included those species for which sequence data are available, and transition rates between pollination systems were calculated. KEY RESULTS Most Apocynaceae are insect pollinated with few records of bird pollination. Almost three-quarters of species are pollinated by a single higher taxon (e.g. flies or moths); 7 % have bimodal pollination systems, whilst the remaining approx. 20 % are insect generalists. The less phenotypically specialized flowers of the Rauvolfioids are pollinated by a more restricted set of pollinators than are more complex flowers within the Apocynoids + Periplocoideae + Secamonoideae + Asclepiadoideae (APSA) clade. Certain combinations of bimodal pollination systems are more common than others. Some pollination systems are missing from particular regions, whilst others are over-represented. CONCLUSIONS Within Apocynaceae, interactions with pollinators are highly structured both phylogenetically and biogeographically. Variation in transition rates between pollination systems suggest constraints on their evolution, whereas regional differences point to environmental effects such as filtering of certain pollinators from habitats. This is the most extensive analysis of its type so far attempted and gives important insights into the diversity and evolution of pollination systems in large clades.
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Affiliation(s)
- Jeff Ollerton
- Faculty of Arts, Science and Technology, University of Northampton, Northampton, UK
- For correspondence. E-mail:
| | | | - Mary E Endress
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Ulrich Meve
- Lehrstuhl für Pflanzensystematik, Universität Bayreuth, Bayreuth, Germany
| | - André Rodrigo Rech
- Universidade Federal dos Vales do Jequitinhonha e Mucuri (UFVJM), Curso de Licenciatura em Educação do Campo - LEC, Campus JK - Diamantina, Minas Gerais, Brazil
| | - Adam Shuttleworth
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Héctor A Keller
- Instituto de Botánica del Nordeste, UNNE-CONICET, Corrientes, Argentina
| | - Mark Fishbein
- Department of Plant Biology, Ecology, and Evolution, Stillwater, OK, USA
| | | | - Felipe W Amorim
- Laboratório de Ecologia da Polinização e Interações – LEPI, Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista “Júlio de Mesquita Filho”- Unesp, Botucatu - SP, Brazil
| | - Peter Bernhardt
- Saint Louis University, Department of Biology, St. Louis, MO, USA
| | - Ferhat Celep
- Mehmet Akif Ersoy Mah. 269. Cad. Urankent Prestij Konutları, Demetevler, Ankara, Turkey
| | - Yolanda Chirango
- Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa
| | | | - Laure Civeyrel
- EDB, UMR 5174, Université de Toulouse, UPS, Toulouse cedex, France
| | - Andrea Cocucci
- Laboratorio de Ecología Evolutiva - Biología Floral, IMBIV (UNC-CONICET), Argentina
| | - Louise Cranmer
- Faculty of Arts, Science and Technology, University of Northampton, Northampton, UK
| | - Inara Carolina da Silva-Batista
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, Rio de Janiero, RJ, Brazil
| | - Linde de Jager
- Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Mariana Scaramussa Deprá
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes-RJ, Brazil
| | - Arthur Domingos-Melo
- Departamento de Botânica - CB, Laboratório de Biologia Floral e Reprodutiva - POLINIZAR, Universidade Federal de Pernambuco, Recife - PE, Brazil
| | - Courtney Dvorsky
- Saint Louis University, Department of Biology, St. Louis, MO, USA
| | - Kayna Agostini
- Universidade Federal de São Carlos - UFSCar, Centro de Ciências Agrárias, Depto. Ciências da Natureza, Matemática e Educação, Araras, SP, Brazil
| | - Leandro Freitas
- Jardim Botânico do Rio de Janeiro, Rio de Janeiro - RJ, Brazil
| | - Maria Cristina Gaglianone
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes-RJ, Brazil
| | - Leo Galetto
- Facultad de Ciencias Exactas, Fisicas y Naturales, Universidad Nacional de Córdoba (UNC) and IMBIV (CONICET-UNC). CP, Córdoba, Argentina
| | - Mike Gilbert
- Herbarium - Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Ixchel González-Ramírez
- Laboratorio de Plantas Vasculares, Departamento de Biología Comparada, Facultad de Ciencias, UNAM, Mexico
| | - Pablo Gorostiague
- Laboratorio de Investigaciones Botánicas (LABIBO), Facultad de Ciencias Naturales, Universidad Nacional de Salta-CONICET. Salta, Argentina
| | - David Goyder
- Herbarium - Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Leandro Hachuy-Filho
- Laboratório de Ecologia da Polinização e Interações – LEPI, Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista “Júlio de Mesquita Filho”- Unesp, Botucatu - SP, Brazil
| | - Annemarie Heiduk
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Aaron Howard
- Biology Department, Franklin and Marshall College, Lancaster, PA, USA
| | - Gretchen Ionta
- Natural History Museum, Georgia College, Milledgeville, GA, USA
| | - Sofia C Islas-Hernández
- Laboratorio de Plantas Vasculares, Departamento de Biología Comparada, Facultad de Ciencias, UNAM, Mexico
| | - Steven D Johnson
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Lize Joubert
- Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | | | - Susan Kephart
- Department of Biology, Willamette University Salem, OR, USA
| | - Aroonrat Kidyoo
- Department of Botany, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Suzanne Koptur
- Natural History Museum, Georgia College, Milledgeville, GA, USA
| | - Cristiana Koschnitzke
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, Rio de Janiero, RJ, Brazil
| | - Ellen Lamborn
- Faculty of Arts, Science and Technology, University of Northampton, Northampton, UK
| | - Tatyana Livshultz
- Department of Biodiversity Earth and Environmental Sciences and Academy of Natural Sciences, Drexel University, Philadephia, PA, USA
| | - Isabel Cristina Machado
- Departamento de Botânica - CB, Laboratório de Biologia Floral e Reprodutiva - POLINIZAR, Universidade Federal de Pernambuco, Recife - PE, Brazil
| | - Salvador Marino
- Laboratorio de Ecología Evolutiva - Biología Floral, IMBIV (UNC-CONICET), Argentina
| | - Lumi Mema
- Department of Biodiversity Earth and Environmental Sciences and Academy of Natural Sciences, Drexel University, Philadephia, PA, USA
| | - Ko Mochizuki
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Leonor Patrícia Cerdeira Morellato
- Universidade Estadual Paulista UNESP, Instituto de Biociências, Departamento de Botânica, Laboratório de Fenologia, Rio Claro, SP, Brazil
| | | | - Evalyne W Muiruri
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Naoyuki Nakahama
- Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | | | | | | | - Craig I Peter
- Department of Botany, Rhodes University, Grahamstown, South Africa
| | - Sachin Punekar
- Biospheres, Eshwari, Nanasaheb Peshva Marg, Near Ramna Ganpati, Lakshminagar, Parvati, Pune, Maharashtra, India
| | - Nicole Rafferty
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Alessandro Rapini
- Departamento de Biologia, Universidade Estadual de Feira de Santana, Novo Horizonte, Feira de Santana, Bahia, Brazil
| | - Zong-Xin Ren
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, PR China
| | - Claudia I Rodríguez-Flores
- Laboratorio de Ecología, UBIPRO, FES-Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Estado de México, México
| | - Liliana Rosero
- Escuela de Ciencias Biológicas, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Shoko Sakai
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Marlies Sazima
- Departamento de Biologia Vegetal, Instituto de Biologia, Caixa, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Sandy-Lynn Steenhuisen
- Department of Plant Sciences, Natural and Agricultural Sciences, University of the Free State, Qwaqwa campus, Phuthaditjhaba, Republic of South Africa
| | | | - Carolina Torres
- Facultad de Ciencias Exactas, Fisicas y Naturales, Universidad Nacional de Córdoba (UNC) and IMBIV (CONICET-UNC). CP, Córdoba, Argentina
| | - Kristian Trøjelsgaard
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej, Aalborg, Denmark
| | - Atushi Ushimaru
- Graduate School of Human Development and Environment, Kobe University, Tsurukabuto, Kobe City, Japan
| | - Milene Faria Vieira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV), Viçosa, Minas Gerais, Brazil
| | - Ana Pía Wiemer
- Museo Botánico Córdoba y Cátedra de Morfología Vegetal (IMBIV-UNC-CONICET), Córdoba, Argentina
| | - Tadashi Yamashiro
- Graduate School of Technology, Industrial and Social Science, Tokushima University, Minamijyosanjima, Tokushima, Japan
| | - Tarcila Nadia
- Centro Acadêmico de Vitória, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Joel Queiroz
- Departamento de Educação, Universidade Federal da Paraiba, Mamnguape, Paraiba, Brazil
| | - Zelma Quirino
- Departamento de Engenharia e Meio Ambiente, Universidade Federal da Paraiba, Rio Tinto, Paraíba, Brazil
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Rao H, Song ZH, Cui RP, Li QE, Zou JB. Characterization of the complete chloroplast genome of Periploca sepium Bunge (Apocynaceae: Periplocoideae: Periploca), a traditional Chinese medicinal plant. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1544044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Hua Rao
- College of Life Sciences, Shaanxi Normal University, Chang’an, Xi’an, People’s Republic of China
| | - Zhan-Hui Song
- Shihezi University, Shihezi, Xinjiang, People’s Republic of China
| | - Ru-Peng Cui
- Shihezi University, Shihezi, Xinjiang, People’s Republic of China
| | - Qi-En Li
- Tibetan Medicine Research Center of Qinghai University, Qinghai University Tibetan Medical College, Xining, Qinghai, People’s Republic of China
| | - Jia-Bin Zou
- College of Life Sciences, Shaanxi Normal University, Chang’an, Xi’an, People’s Republic of China
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Herrando-Moraira S. Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae). Mol Phylogenet Evol 2018; 128:69-87. [PMID: 30036700 DOI: 10.1016/j.ympev.2018.07.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/17/2022]
Abstract
Target enrichment is a cost-effective sequencing technique that holds promise for elucidating evolutionary relationships in fast-evolving lineages. However, potential biases and impact of bioinformatic sequence treatments in phylogenetic inference have not been thoroughly explored yet. Here, we investigate this issue with an ultimate goal to shed light into a highly diversified group of Compositae (Asteraceae) constituted by four main genera: Arctium, Cousinia, Saussurea, and Jurinea. Specifically, we compared sequence data extraction methods implemented in two easy-to-use workflows, PHYLUCE and HybPiper, and assessed the impact of two filtering practices intended to reduce phylogenetic noise. In addition, we compared two phylogenetic inference methods: (1) the concatenation approach, in which all loci were concatenated in a supermatrix; and (2) the coalescence approach, in which gene trees were produced independently and then used to construct a species tree under coalescence assumptions. Here we confirm the usefulness of the set of 1061 COS targets (a nuclear conserved orthology loci set developed for the Compositae) across a variety of taxonomic levels. Intergeneric relationships were completely resolved: there are two sister groups, Arctium-Cousinia and Saussurea-Jurinea, which are in agreement with a morphological hypothesis. Intrageneric relationships among species of Arctium, Cousinia, and Saussurea are also well defined. Conversely, conflicting species relationships remain for Jurinea. Methodological choices significantly affected phylogenies in terms of topology, branch length, and support. Across all analyses, the phylogeny obtained using HybPiper and the strictest scheme of removing fast-evolving sites was estimated as the optimal. Regarding methodological choices, we conclude that: (1) trees obtained under the coalescence approach are topologically more congruent between them than those inferred using the concatenation approach; (2) refining treatments only improved support values under the concatenation approach; and (3) branch support values are maximized when fast-evolving sites are removed in the concatenation approach, and when a higher number of loci is analyzed in the coalescence approach.
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Affiliation(s)
- Sonia Herrando-Moraira
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s.n., 08038 Barcelona, Spain.
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Fonseca LHM, Lohmann LG. Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the “Adenocalymma-Neojobertia” clade (Bignonieae, Bignoniaceae). Mol Phylogenet Evol 2018; 123:1-15. [DOI: 10.1016/j.ympev.2018.01.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 01/25/2018] [Accepted: 01/31/2018] [Indexed: 10/18/2022]
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Foster CSP, Henwood MJ, Ho SYW. Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea). Mol Phylogenet Evol 2018; 127:156-167. [PMID: 29803950 DOI: 10.1016/j.ympev.2018.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 04/17/2018] [Accepted: 05/17/2018] [Indexed: 10/16/2022]
Abstract
Data sets comprising small numbers of genetic markers are not always able to resolve phylogenetic relationships. This has frequently been the case in molecular systematic studies of plants, with many analyses being based on sequence data from only two or three chloroplast genes. An example of this comes from the riceflowers Pimelea Banks & Sol. ex Gaertn. (Thymelaeaceae), a large genus of flowering plants predominantly distributed in Australia. Despite the considerable morphological variation in the genus, low sequence divergence in chloroplast markers has led to the phylogeny of Pimelea remaining largely uncertain. In this study, we resolve the backbone of the phylogeny of Pimelea in comprehensive Bayesian and maximum-likelihood analyses of plastome sequences from 41 taxa. However, some relationships received only moderate to poor support, and the Pimelea clade contained extremely short internal branches. By using topology-clustering analyses, we demonstrate that conflicting phylogenetic signals can be found across the trees estimated from individual chloroplast protein-coding genes. A relaxed-clock dating analysis reveals that Pimelea arose in the mid-Miocene, with most divergences within the genus occurring during a subsequent rapid diversification. Our new phylogenetic estimate offers better resolution and is more strongly supported than previous estimates, providing a platform for future taxonomic revisions of both Pimelea and the broader subfamily. Our study has demonstrated the substantial improvements in phylogenetic resolution that can be achieved using plastome-scale data sets in plant molecular systematics.
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Affiliation(s)
- Charles S P Foster
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Murray J Henwood
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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25
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Jabaily RS, Shepherd KA, Michener PS, Bush CJ, Rivero R, Gardner AG, Sessa EB. Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l. (Goodeniaceae). Mol Phylogenet Evol 2018; 127:502-512. [PMID: 29758275 DOI: 10.1016/j.ympev.2018.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/22/2018] [Accepted: 05/07/2018] [Indexed: 11/30/2022]
Abstract
Goodeniaceae is a primarily Australian flowering plant family with a complex taxonomy and evolutionary history. Previous phylogenetic analyses have successfully resolved the backbone topology of the largest clade in the family, Goodenia s.l., but have failed to clarify relationships within the species-rich and enigmatic Goodenia clade C, a prerequisite for taxonomic revision of the group. We used genome skimming to retrieve sequences for chloroplast, mitochondrial, and nuclear markers for 24 taxa representing Goodenia s.l., with a particular focus on Goodenia clade C. We performed extensive hypothesis tests to explore incongruence in clade C and evaluate statistical support for clades within this group, using datasets from all three genomic compartments. The mitochondrial dataset is comparable to the chloroplast dataset in providing resolution within Goodenia clade C, though backbone support values within this clade remain low. The hypothesis tests provided an additional, complementary means of evaluating support for clades. We propose that the major subclades of Goodenia clade C (C1-C3 + Verreauxia) are the result of a rapid radiation, and each represents a distinct lineage.
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Affiliation(s)
- Rachel S Jabaily
- Department of Organismal Biology & Ecology, Colorado College, Colorado Springs, CO 80903, USA; Department of Biology, Rhodes College, Memphis, TN 38112, USA.
| | - Kelly A Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Kensington, WA 6151, Australia.
| | | | - Caroline J Bush
- Department of Biology, Rhodes College, Memphis, TN 38112, USA.
| | - Rodrigo Rivero
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Department of Natural Resources and Environmental Management, University of Hawaii- Mānoa, Honolulu, HI 96822, USA.
| | - Andrew G Gardner
- Department of Biological Sciences, California State University, Stanislaus, One University Circle, Turlock, CA 95382, USA.
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Genetics Institute, University of Florida, Gainesville, FL 32607, USA.
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Dillenberger MS, Wei N, Tennessen JA, Ashman TL, Liston A. Plastid genomes reveal recurrent formation of allopolyploid Fragaria. AMERICAN JOURNAL OF BOTANY 2018; 105:862-874. [PMID: 29797560 DOI: 10.1002/ajb2.1085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/07/2018] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Recurrent formation of polyploid taxa is a common observation in many plant groups. Haploid, cytoplasmic genomes like the plastid genome can be used to overcome the problem of homeologous genes and recombination in polyploid taxa. Fragaria (Rosaceae) contains several octo- and decaploid species. We use plastome sequences to infer the plastid ancestry of these taxa with special focus on the decaploid Fragaria cascadensis. METHODS We used genome skimming of 96 polyploid Fragaria samples on a single Illumina HiSeq 3000 lane to obtain whole plastome sequences. These sequences were used for phylogenetic reconstructions and dating analyses. Ploidy of all samples was inferred with flow cytometry, and plastid inheritance was examined in a controlled cross of F. cascadensis. KEY RESULTS The plastid genome phylogeny shows that only the octoploid F. chiloensis is monophyletic, all other polyploid taxa were supported to be para- or polyphyletic. The decaploid Fragaria cascadensis has biparental plastid inheritance and four different plastid donors. Diversification of the F. cascadensis clades occurred in the last 230,000 years. The southern part of its distribution range harbors considerably higher genetic diversity, suggestive of a potential refugium. CONCLUSIONS Fragaria cascadensis had at least four independent origins from parents with different plastomes. In contrast, para- and polyphyletic taxa of the octoploid Fragaria species are best explained by incomplete lineage sorting and/or hybridization. Biogeographic patterns in F. cascadensis are probably a result of range shift during the last glacial maximum.
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Affiliation(s)
- Markus S Dillenberger
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Na Wei
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jacob A Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
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Livshultz T, Kaltenegger E, Straub SCK, Weitemier K, Hirsch E, Koval K, Mema L, Liston A. Evolution of pyrrolizidine alkaloid biosynthesis in Apocynaceae: revisiting the defence de-escalation hypothesis. THE NEW PHYTOLOGIST 2018; 218:762-773. [PMID: 29479722 PMCID: PMC5873419 DOI: 10.1111/nph.15061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/10/2018] [Indexed: 05/23/2023]
Abstract
Plants produce specialized metabolites for their defence. However, specialist herbivores adapt to these compounds and use them for their own benefit. Plants attacked predominantly by specialists may be under selection to reduce or eliminate production of co-opted chemicals: the defence de-escalation hypothesis. We studied the evolution of pyrrolizidine alkaloids (PAs) in Apocynaceae, larval host plants for PA-adapted butterflies (Danainae, milkweed and clearwing butterflies), to test if the evolutionary pattern is consistent with de-escalation. We used the first PA biosynthesis specific enzyme (homospermidine synthase, HSS) as tool for reconstructing PA evolution. We found hss orthologues in diverse Apocynaceae species, not all of them known to produce PAs. The phylogenetic analysis showed a monophyletic origin of the putative hss sequences early in the evolution of one Apocynaceae lineage (the APSA clade). We found an hss pseudogene in Asclepias syriaca, a species known to produce cardiac glycosides but no PAs, and four losses of an HSS amino acid motif. APSA clade species are significantly more likely to be Danainae larval host plants than expected if all Apocynaceae species were equally likely to be exploited. Our findings are consistent with PA de-escalation as an adaptive response to specialist attack.
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Affiliation(s)
- Tatyana Livshultz
- Department of Biodiversity, Earth, and Environmental SciencesAcademy of Natural Sciences of Drexel University1900 Benjamin Franklin ParkwayPhiladelphiaPA19103USA
| | - Elisabeth Kaltenegger
- Biochemical Ecology and Molecular EvolutionBotanical InstituteChristian‐Albrechts University KielOlshausenstrasse 4024098KielGermany
| | | | - Kevin Weitemier
- Department of Botany & Plant PathologyOregon State University2082 Cordley HallCorvallisOR97331USA
| | - Elliot Hirsch
- Department of Biodiversity, Earth, and Environmental SciencesAcademy of Natural Sciences of Drexel University1900 Benjamin Franklin ParkwayPhiladelphiaPA19103USA
| | - Khrystyna Koval
- Department of Biodiversity, Earth, and Environmental SciencesAcademy of Natural Sciences of Drexel University1900 Benjamin Franklin ParkwayPhiladelphiaPA19103USA
| | - Lumi Mema
- Department of Biodiversity, Earth, and Environmental SciencesAcademy of Natural Sciences of Drexel University1900 Benjamin Franklin ParkwayPhiladelphiaPA19103USA
| | - Aaron Liston
- Department of Botany & Plant PathologyOregon State University2082 Cordley HallCorvallisOR97331USA
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Fishbein M, Livshultz T, Straub SCK, Simões AO, Boutte J, McDonnell A, Foote A. Evolution on the backbone: Apocynaceae phylogenomics and new perspectives on growth forms, flowers, and fruits. AMERICAN JOURNAL OF BOTANY 2018; 105:495-513. [PMID: 29733432 DOI: 10.1002/ajb2.1067] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 02/20/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY We provide the largest phylogenetic analyses to date of Apocynaceae in terms of taxa and molecular data as a framework for analyzing the evolution of vegetative and reproductive traits. METHODS We produced maximum-likelihood phylogenies of Apocynaceae using 21 plastid loci sampled from 1045 species (nearly 25% of the family) and complete plastomes from 73 species. We reconstructed ancestral states and used model comparisons in a likelihood framework to analyze character evolution across Apocynaceae. KEY RESULTS We obtained a well-supported phylogeny of Apocynaceae, resolving poorly understood tribal and subtribal relationships (e.g., among Amsonieae and Hunterieae, within Asclepiadeae), rejecting monophyly of Melodineae and Odontadenieae, and placing previously unsampled and enigmatic taxa (e.g., Pycnobotrya). We provide new insights into the evolution of Apocynaceae, including frequent shifts between herbaceousness and woodiness, reversibility of twining, integrated evolution of the corolla and gynostegium, and ancestral baccate fruits. CONCLUSIONS Increased sampling and selection of best-fitting models of evolution provide more resolved and robust estimates of phylogeny and character evolution than obtained in previous studies. Evolutionary inferences are sensitive to choice of phylogenetic frameworks and models.
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Affiliation(s)
- Mark Fishbein
- Department of Plant Biology, Ecology& Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Tatyana Livshultz
- Department of Biodiversity, Earth & Environmental Sciences & Academy of Natural Sciences of Drexel University, Philadelphia, PA, 19103, USA
| | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, 14456, USA
| | - André O Simões
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas - UNICAMP, CP. 6109, 13083-970, Campinas São Paulo, Brazil
| | - Julien Boutte
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, 14456, USA
| | - Angela McDonnell
- Department of Plant Biology, Ecology& Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
- Department of Biology, Bucknell University, Lewisburg, PA, 17837, USA
| | - Abbey Foote
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, 14456, USA
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A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae). Mol Phylogenet Evol 2017; 117:124-134. [DOI: 10.1016/j.ympev.2017.02.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/06/2017] [Accepted: 02/06/2017] [Indexed: 11/18/2022]
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Berger BA, Han J, Sessa EB, Gardner AG, Shepherd KA, Ricigliano VA, Jabaily RS, Howarth DG. The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1700042. [PMID: 29109919 PMCID: PMC5664964 DOI: 10.3732/apps.1700042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/07/2017] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. METHODS Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes. RESULTS Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions. DISCUSSION Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.
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Affiliation(s)
- Brent A. Berger
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Jiahong Han
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Emily B. Sessa
- Department of Biology, University of Florida, Box 118525, Gainesville, Florida 32611 USA
| | - Andrew G. Gardner
- Department of Biological Sciences, California State University, Stanislaus, One University Circle, Turlock, California 95382 USA
| | - Kelly A. Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington 6151, Western Australia, Australia
| | - Vincent A. Ricigliano
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Road, Tucson, Arizona 85719 USA
| | - Rachel S. Jabaily
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee 38112 USA
| | - Dianella G. Howarth
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
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Abstract
PREMISE OF THE STUDY Rapid radiations are difficult to reconstruct when organismal diversification and biogeographic movement outpace the evolution of genes typically used in phylogenetic analyses. The 125 kb of unique sequence from complete plastid genomes (= plastomes) largely solves the molecular sampling problem, and taxon sampling that triangulates the base of each major subclade largely solves the long-branch attraction problem. This combination of molecular and phylogenetic sampling is used to reconstruct the cosmopolitan radiation of lobeliads, with special focus on the origin of the giant lobelias. METHODS An alignment of 18 previously generated and 61 new plastomes was analyzed to produce the phylogenetic estimate upon which the biogeographic reconstruction was based. KEY RESULTS Originating in southern Africa, the Lobeliaceae underwent a spectacular cosmopolitan radiation about 20 million years ago. One lineage colonized Madagascar and eastern Asia, which was the source area for the evolution of the giant lobelias. A second lineage colonized the Mediterranean and North America, in quick succession. South America and Australia were also colonized from South Africa, most likely as independent events, but detailed biogeographic reconstruction is limited by inferred extinction events. The south Pacific segregate genera Apetahia and Sclerotheca are inferred to have Hawaiian ancestry. The East African radiation independently reached Ethiopia, West Africa, and Brazil. CONCLUSIONS With adequate molecular and taxon sampling, many details of rapid radiations can be accurately inferred. However, not all lineages survived, and analyses of extant species cannot recover details that have been lost due to extinction.
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Affiliation(s)
- Eric B Knox
- Department of Biology, Indiana University, Bloomington, Indiana 47405 USA
| | - Chunjiao Li
- Department of Biology, Indiana University, Bloomington, Indiana 47405 USA
- School of Life Sciences, Northeast Normal University, Changchun 130024 China
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Léveillé-Bourret É, Starr JR, Ford BA, Moriarty Lemmon E, Lemmon AR. Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics. Syst Biol 2017; 67:94-112. [DOI: 10.1093/sysbio/syx050] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/28/2017] [Indexed: 11/13/2022] Open
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Vining KJ, Johnson SR, Ahkami A, Lange I, Parrish AN, Trapp SC, Croteau RB, Straub SCK, Pandelova I, Lange BM. Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement. MOLECULAR PLANT 2017; 10:323-339. [PMID: 27867107 DOI: 10.1016/j.molp.2016.10.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 10/28/2016] [Accepted: 10/29/2016] [Indexed: 05/08/2023]
Abstract
The genus Mentha encompasses mint species cultivated for their essential oils, which are formulated into a vast array of consumer products. Desirable oil characteristics and resistance to the fungal disease Verticillium wilt are top priorities for the mint industry. However, cultivated mints have complex polyploid genomes and are sterile. Breeding efforts, therefore, require the development of genomic resources for fertile mint species. Here, we present draft de novo genome and plastome assemblies for a wilt-resistant South African accession of Mentha longifolia (L.) Huds., a diploid species ancestral to cultivated peppermint and spearmint. The 353 Mb genome contains 35 597 predicted protein-coding genes, including 292 disease resistance gene homologs, and nine genes determining essential oil characteristics. A genetic linkage map ordered 1397 genome scaffolds on 12 pseudochromosomes. More than two million simple sequence repeats were identified, which will facilitate molecular marker development. The M. longifolia genome is a valuable resource for both metabolic engineering and molecular breeding. This is exemplified by employing the genome sequence to clone and functionally characterize the promoters in a peppermint cultivar, and demonstrating the utility of a glandular trichome-specific promoter to increase expression of a biosynthetic gene, thereby modulating essential oil composition.
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Affiliation(s)
- Kelly J Vining
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA.
| | - Sean R Johnson
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Amirhossein Ahkami
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Iris Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Amber N Parrish
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Susan C Trapp
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Rodney B Croteau
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY 14456, USA
| | - Iovanna Pandelova
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - B Markus Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA.
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Jo S, Kim HW, Kim YK, Cheon SH, Kim KJ. The complete plastome sequence of Carissa macrocarpa (Eckl.) A. DC. (Apocynaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:26-28. [PMID: 33473704 PMCID: PMC7800814 DOI: 10.1080/23802359.2016.1233468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this study, we determined the complete plastome sequence of Carissa macrocarpa (Eckl.) A. DC. (Apocynaceae) (NCBI acc. no. KX364402). The gene order and structure of the C. macrocarpa plastome are similar to those of a typical angiosperm. The complete plastome is 155,297 bp in length, and consists of a large single-copy region of 85,586 bp and a small single-copy region of 18,131 bp, which are separated by two inverted repeats of 25,792 bp. The plastome contains 113 genes, of which 79 are protein-coding genes, 30 are tRNA genes and 4 are rRNA genes. Sixteen genes contained one intron and two genes have two introns. The average A–T content of the plastome is 62.0%. A total of 31 simple sequence repeat loci were identified within the genome. Phylogenetic analysis revealed that C. macrocarpa is a member of the paraphyletic subfamily Rauvolfioideae of Apocynaceae. The sister group relationship of C. macrocarpa to the Apocynoideae–Asclepiadoideae clade is supported by 100% bootstrap values.
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Affiliation(s)
- Sangjin Jo
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Hoe-Won Kim
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Young-Kee Kim
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Se-Hwan Cheon
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Ki-Joong Kim
- Division of Life Sciences, Korea University, Seoul, Korea
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Reginato M, Neubig KM, Majure LC, Michelangeli FA. The first complete plastid genomes of Melastomataceae are highly structurally conserved. PeerJ 2016; 4:e2715. [PMID: 27917315 PMCID: PMC5131623 DOI: 10.7717/peerj.2715] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/24/2016] [Indexed: 11/20/2022] Open
Abstract
Background In the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics. Methods Genome skimming was performed for 16 species spread across the Melastomataceae. Plastomes were assembled, annotated and compared to eight sequenced plastids in the Myrtales. Phylogenetic inference was performed using Maximum Likelihood on six different data sets, where putative biases were taken into account. Summary statistics were generated for all introns and intergenic spacers with suitable size for polymerase chain reaction (PCR) amplification and used to rank the markers by phylogenetic information. Results The majority of the plastomes sampled are conserved in gene content and order, as well as in sequence length and GC content within plastid regions and sequence classes. Departures include the putative presence of rps16 and rpl2 pseudogenes in some plastomes. Phylogenetic analyses of the majority of the schemes analyzed resulted in the same topology with high values of bootstrap support. Although there is still uncertainty in some relationships, in the highest supported topologies only two nodes received bootstrap values lower than 95%. Discussion Melastomataceae plastomes are no exception for the general patterns observed in the genomic structure of land plant chloroplasts, being highly conserved and structurally similar to most other Myrtales. Despite the fact that the full plastome phylogeny shares most of the clades with the previously widely used and reduced data set, some changes are still observed and bootstrap support is higher. The plastome data set presented here is a step towards phylogenomic analyses in the Melastomataceae and will be a useful resource for future studies.
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Affiliation(s)
- Marcelo Reginato
- Institute of Systematic Botany, The New York Botanical Garden , Bronx, New York , United States
| | - Kurt M Neubig
- Department of Plant Biology, Southern Illinois University of Carbondale , Carbondale, Illinois , United States
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden , Phoenix, Arizona , United States
| | - Fabian A Michelangeli
- Institute of Systematic Botany, The New York Botanical Garden , Bronx, New York , United States
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Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 2016; 17:134. [PMID: 27339192 PMCID: PMC4918201 DOI: 10.1186/s13059-016-1004-2] [Citation(s) in RCA: 716] [Impact Index Per Article: 89.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.
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Affiliation(s)
- Henry Daniell
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA.
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming Yu
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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Endress PK. Development and evolution of extreme synorganization in angiosperm flowers and diversity: a comparison of Apocynaceae and Orchidaceae. ANNALS OF BOTANY 2016; 117:749-67. [PMID: 26292994 PMCID: PMC4845794 DOI: 10.1093/aob/mcv119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/22/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Apocynaceae and Orchidaceae are two angiosperm families with extreme flower synorganization. They are unrelated, the former in eudicots, the latter in monocots, but they converge in the formation of pollinia and pollinaria, which do not occur in any other angiosperm family, and for which extreme synorganization of floral organs is a precondition. In each family extensive studies on flower development and evolution have been performed; however, newer comparative studies focusing on flower synorganization and involving both families together are lacking. SCOPE For this study an extensive search through the morphological literature has been conducted. Based on this and my own studies on flowers in various Apocynaceae and Orchidaceae and complex flowers in other angiosperms with scanning electron microscopy and with microtome section series, a review on convergent floral traits in flower development and architecture in the two families is presented. KEY FINDINGS There is a tendency of protracted development of synorganized parts in Apocynaceae and Orchidaceae (development of synorganization of two or more organs begins earlier the more accentuated it is at anthesis). Synorganization (or complexity) also paves the way for novel structures. One of the most conspicuous such novel structures in Apocynaceae is the corona, which is not the product of synorganization of existing organs; however, it is probably enhanced by synorganization of other, existing, floral parts. In contrast to synorganized parts, the corona appears developmentally late. CONCLUSIONS Synorganization of floral organs may lead to a large number of convergences in clades that are only very distantly related. The convergences that have been highlighted in this comparative study should be developmentally investigated directly in parallel in future studies.
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Affiliation(s)
- Peter K Endress
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
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Leaché AD, Banbury BL, Linkem CW, de Oca ANM. Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)? BMC Evol Biol 2016; 16:63. [PMID: 27000803 PMCID: PMC4802581 DOI: 10.1186/s12862-016-0628-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/29/2016] [Indexed: 01/25/2023] Open
Abstract
Background Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution. Results The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20–25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997). Conclusions Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0628-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam D Leaché
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA. .,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98195, USA.
| | - Barbara L Banbury
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA.,Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail Stop M4-B402, Seattle, 98109, Washington, USA
| | - Charles W Linkem
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
| | - Adrián Nieto-Montes de Oca
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, México
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Gardner AG, Sessa EB, Michener P, Johnson E, Shepherd KA, Howarth DG, Jabaily RS. Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies. Mol Phylogenet Evol 2015; 94:605-617. [PMID: 26463342 DOI: 10.1016/j.ympev.2015.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 09/18/2015] [Accepted: 10/02/2015] [Indexed: 12/25/2022]
Abstract
Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia+Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A+Goodenia B) (Velleia+Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.
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Affiliation(s)
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Genetics Institute, University of Florida, Gainesville, FL 32607, USA
| | - Pryce Michener
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - Eden Johnson
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - Kelly A Shepherd
- Western Australian Herbarium, Department of Parks and Wildlife, Kensington, WA 6151, Australia
| | - Dianella G Howarth
- Department of Biological Sciences, St. John's University, Queens, NY 11439, USA
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Su Z, Townsend JP. Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects. BMC Evol Biol 2015; 15:86. [PMID: 25968460 PMCID: PMC4429678 DOI: 10.1186/s12862-015-0364-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 04/29/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The detection and avoidance of "long-branch effects" in phylogenetic inference represents a longstanding challenge for molecular phylogenetic investigations. A consequence of parallelism and convergence, long-branch effects arise in phylogenetic inference when there is unequal molecular divergence among lineages, and they can positively mislead inference based on parsimony especially, but also inference based on maximum likelihood and Bayesian approaches. Long-branch effects have been exhaustively examined by simulation studies that have compared the performance of different inference methods in specific model trees and branch length spaces. RESULTS In this paper, by generalizing the phylogenetic signal and noise analysis to quartets with uneven subtending branches, we quantify the utility of molecular characters for resolution of quartet phylogenies via parsimony. Our quantification incorporates contributions toward the correct tree from either signal or homoplasy (i.e. "the right result for either the right reason or the wrong reason"). We also characterize a highly conservative lower bound of utility that incorporates contributions to the correct tree only when they correspond to true, unobscured parsimony-informative sites (i.e. "the right result for the right reason"). We apply the generalized signal and noise analysis to classic quartet phylogenies in which long-branch effects can arise due to unequal rates of evolution or an asymmetrical topology. Application of the analysis leads to identification of branch length conditions in which inference will be inconsistent and reveals insights regarding how to improve sampling of molecular loci and taxa in order to correctly resolve phylogenies in which long-branch effects are hypothesized to exist. CONCLUSIONS The generalized signal and noise analysis provides analytical prediction of utility of characters evolving at diverse rates of evolution to resolve quartet phylogenies with unequal branch lengths. The analysis can be applied to identifying characters evolving at appropriate rates to resolve phylogenies in which long-branch effects are hypothesized to occur.
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Affiliation(s)
- Zhuo Su
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
| | - Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
- Department of Biostatistics, Yale University, New Haven, CT, 06520, USA.
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
- Department of Biostatistics, Yale School of Public Health, 135 College St #222., New Haven, CT, 06511, United States of America.
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Whelan NV, Kocot KM, Halanych KM. Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians. Integr Comp Biol 2015; 55:1084-95. [PMID: 25972566 DOI: 10.1093/icb/icv037] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite an explosion in the amount of sequence data, phylogenomics has failed to settle controversy regarding some critical nodes on the animal tree of life. Understanding relationships among Bilateria, Ctenophora, Cnidaria, Placozoa, and Porifera is essential for studying how complex traits such as neurons, muscles, and gastrulation have evolved. Recent studies have cast doubt on the historical viewpoint that sponges are sister to all other animal lineages with recent studies recovering ctenophores as sister. However, the ctenophore-sister hypothesis has been criticized as unrealistic and caused by systematic error. We review past phylogenomic studies and potential causes of systematic error in an effort to identify areas that can be improved in future studies. Increased sampling of taxa, less missing data, and a priori removal of sequences and taxa that may cause systematic error in phylogenomic inference will likely be the most fruitful areas of focus when assembling future datasets. Ultimately, we foresee metazoan relationships being resolved with higher support in the near future, and we caution against dismissing novel hypotheses merely because they conflict with historical viewpoints of animal evolution.
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Affiliation(s)
- Nathan V Whelan
- *Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA;
| | - Kevin M Kocot
- School of Biological Sciences, The University of Queensland, 325 Goddard Building, St Lucia, QLD 4101, Australia
| | - Kenneth M Halanych
- *Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA
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Alfonso-Morales A, Rios L, Martínez-Pérez O, Dolz R, Valle R, Perera CL, Bertran K, Frías MT, Ganges L, Díaz de Arce H, Majó N, Núñez JI, Pérez LJ. Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent. PLoS One 2015; 10:e0125853. [PMID: 25946336 PMCID: PMC4422720 DOI: 10.1371/journal.pone.0125853] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/26/2015] [Indexed: 11/19/2022] Open
Abstract
Background Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. Methodology/Principal Findings Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population. Conclusions/Significance This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for molecular epidemiology studies.
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Affiliation(s)
| | - Liliam Rios
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba
| | | | - Roser Dolz
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Rosa Valle
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Carmen L. Perera
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba
| | - Kateri Bertran
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Maria T. Frías
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba
| | - Llilianne Ganges
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Heidy Díaz de Arce
- Hospital Italiano de Buenos Aires, Juan D. Perón 4190, C1181ACH Buenos Aires, Argentina
| | - Natàlia Majó
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - José I. Núñez
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Lester J. Pérez
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba
- * E-mail:
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Abstract
Elucidating relationships among early animal lineages has been difficult, and recent phylogenomic analyses place Ctenophora sister to all other extant animals, contrary to the traditional view of Porifera as the earliest-branching animal lineage. To date, phylogenetic support for either ctenophores or sponges as sister to other animals has been limited and inconsistent among studies. Lack of agreement among phylogenomic analyses using different data and methods obscures how complex traits, such as epithelia, neurons, and muscles evolved. A consensus view of animal evolution will not be accepted until datasets and methods converge on a single hypothesis of early metazoan relationships and putative sources of systematic error (e.g., long-branch attraction, compositional bias, poor model choice) are assessed. Here, we investigate possible causes of systematic error by expanding taxon sampling with eight novel transcriptomes, strictly enforcing orthology inference criteria, and progressively examining potential causes of systematic error while using both maximum-likelihood with robust data partitioning and Bayesian inference with a site-heterogeneous model. We identified ribosomal protein genes as possessing a conflicting signal compared with other genes, which caused some past studies to infer ctenophores and cnidarians as sister. Importantly, biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out. Placement of ctenophores as sister to all other animals, and sponge monophyly, are strongly supported under multiple analyses, herein.
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New sources of lycopsamine-type pyrrolizidine alkaloids and their distribution in Apocynaceae. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Tropical Refuges with Exceptionally High Phylogenetic Diversity Reveal Contrasting Phylogenetic Structures. ACTA ACUST UNITED AC 2015. [DOI: 10.1155/2015/758019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Loss of phylogenetic diversity (PD) has gained increasing attention in conservation biology. However, PD is not equally distributed in a phylogeny and can be better assessed when species relatedness (phylogenetic structure: PS) is also considered. Here, we investigate PD and PS in two refuges of biodiversity in northeastern Brazil: the Bahia Costal Forest (BCF) in the Atlantic Forest domain and Chapada Diamantina (CD) in the Caatinga domain. We used geographic data of 205 species at two spatial scales and a chronogram of Apocynaceae based on matK sequences to estimate PD and PS. Our results show an exceptionally high PD in both refuges, overdispersed in BCF and clustered in CD, although this difference is less evident or absent for recent relationships, especially at a smaller spatial scale. Overall, PS suggests long-term competitive exclusion under climatic stability, currently balanced by habitat filtering, in BCF, and biome conservatism and limited dispersal leading to in situ diversification and high density of microendemics in CD. The phylogenetically clustered flora in CD, also threatened by climate changes, are naturally more vulnerable than BCF. Therefore, while in situ conservation may ensure protection of biodiversity in BCF, emergency ex situ conservation is strongly recommended in CD.
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