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Zhao J, He ZR, Fang SL, Han XK, Jiang LY, Hu YP, Yu H, Zhang LB, Zhou XM. Phylogenomic data resolved the deep relationships of Gymnogynoideae (Selaginellaceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1405253. [PMID: 39081519 PMCID: PMC11287774 DOI: 10.3389/fpls.2024.1405253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/17/2024] [Indexed: 08/02/2024]
Abstract
The unresolved phylogenetic framework within the Selaginellaceae subfamily Gymnogynoideae (ca. 130 species) has hindered our comprehension of the diversification and evolution of Selaginellaceae, one of the most important lineages in land plant evolution. Here, based on plastid and nuclear data extracted from genomic sequencing of more than 90% species of all genera except two in Gymnogynoideae, a phylogenomic study focusing on the contentious relationships among the genera in Gymnogynoideae was conducted. Our major results included the following: (1) Only single-copy region (named NR) and only one ribosomal operon was firstly found in Afroselaginella among vascular plants, the plastome structure of Gymnogynoideae is diverse among the six genera, and the direct repeats (DR) type is inferred as the ancestral state in the subfamily; (2) The first strong evidence was found to support Afroselaginella as a sister to Megaloselaginella. Alternative placements of Ericetorum and Gymnogynum were detected, and their relationships were investigated by analyzing the variation of phylogenetic signals; and (3) The most likely genus-level relationships in Gymnogynoideae might be: ((Bryodesma, Lepidoselaginella), (((Megaloselaginella, Afroselaginella), Ericetorum), Gymnogynum)), which was supported by maximum likelihood phylogeny based on plastid datasets, maximum likelihood, and Bayesian inference based on SCG dataset and concatenated nuclear and plastid datasets and the highest proportion of phylogenetic signals of plastid genes.
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Affiliation(s)
- Jing Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Zhao-Rong He
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Shao-Li Fang
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Xu-Ke Han
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Lu-Yao Jiang
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Yu-Ping Hu
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Hong Yu
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Li-Bing Zhang
- Missouri Botanical Garden, St. Louis, MO, United States
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Xin-Mao Zhou
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
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Jia L, Wang S, Hu J, Miao K, Huang Y, Ji Y. Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the 'woody clade' in Saxifragales. BMC PLANT BIOLOGY 2024; 24:277. [PMID: 38605351 PMCID: PMC11010409 DOI: 10.1186/s12870-024-04917-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/15/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND The "woody clade" in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node in the angiosperm tree of life, as the interfamilial relationships of the WCS remain contentious. Based on a comprehensive sampling of WCS genera, this study aims to recover a robust maternal backbone phylogeny of the WCS by analyzing plastid genome (plastome) sequence data using Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and to explore the possible causes of the phylogenetic recalcitrance with respect to deep relationships within the WCS, in combination with molecular and fossil evidence. RESULTS Although the four WCS families were identically resolved as monophyletic, the MP analysis recovered different tree topologies for the relationships among Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae from the ML and BI phylogenies. The fossil-calibrated plastome phylogeny showed that the WCS underwent a rapid divergence of crown groups in the early Cretaceous (between 104.79 and 100.23 Ma), leading to the origin of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (∼4.56 Ma). Compared with the tree topology recovered in a previous study based on nuclear genome data, cytonuclear discordance regarding the interfamilial relationships of the WCS was detected. CONCLUSIONS Molecular and fossil evidence imply that the early divergence of the WCS might have experienced radiative diversification of crown groups, extensive extinctions at the genus and species levels around the Cretaceous/Paleocene boundary, and ancient hybridization. Such evolutionarily complex events may introduce biases in topological estimations within the WCS due to incomplete lineage sorting, cytonuclear discordance, and long-branch attraction, potentially impacting the accurate reconstruction of deep relationships.
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Affiliation(s)
- Linbo Jia
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shuying Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jinjin Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ke Miao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
| | - Yongjiang Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Chen YP, Turdimatovich TO, Nuraliev MS, Lazarević P, Drew BT, Xiang CL. Phylogeny and biogeography of the northern temperate genus Dracocephalum s.l. (Lamiaceae). Cladistics 2022; 38:429-451. [PMID: 35358338 DOI: 10.1111/cla.12502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/28/2022] Open
Abstract
The northern temperate genus Dracocephalum consists of approximately 70 species mainly distributed in the steppe-desert biomes of Central and West Asia and the alpine region of the Qinghai-Tibetan Plateau (QTP). Previous work has shown that Dracocephalum is not monophyletic and might include Hyssopus and Lallemantia. This study attempts to clarify the phylogenetic relationships, diversification patterns, and the biogeographical history of the three genera (defined as Dracocephalum s.l.). Based on a sampling of 66 taxa comprising more than 80% from extant species of Dracocephalum s.l., morphological, phylogenetic (maximum parsimony, likelihood, and Bayesian inference based on nuclear ITS and ETS, plastid rpl32-trnL, trnL-trnF, ycf1, and ycf1-rps15, and two low-copy nuclear markers AT3G09060 and AT1G09680), molecular dating, diversification, and ancestral range estimation analyses were carried out. Our results demonstrate that both Hyssopus and Lallemantia are embedded within Dracocephalum and nine well-supported clades can be recognized within Dracocephalum s.l. Analyses of divergence times suggest that the genus experienced an early rapid radiation during the middle to late Miocene with major lineages diversifying within a relatively narrow timescale. Ancestral area reconstruction analyses indicate that Dracocephalum s.l. originated in Central and West Asia and southern Siberia, and dispersed from Central and West Asia into the QTP and adjacent areas twice independently during the Pliocene. The aridification of the Asian interior possibly promoted the rapid radiation of Dracocephalum within this region, and the uplift of the QTP appears to have triggered the dispersal and recent rapid diversification of the genus in the QTP and adjacent regions. Combining molecular phylogenetic and morphological evidence, a revised infrageneric classification of Dracocephalum s.l. is proposed, which recognizes nine sections within the genus.
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Affiliation(s)
- Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | - Maxim S Nuraliev
- Department of Higher Plants, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Predrag Lazarević
- Institute of Botany and Botanical Garden, Faculty of Biology, University of Belgrade, Belgrade, 11000, Serbia
| | - Bryan T Drew
- Department of Biology, University of Nebraska-Kearney, Kearney, 68849, USA
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Jacob Machado D, Portella de Luna Marques F, Jiménez-Ferbans L, Grant T. An empirical test of the relationship between the bootstrap and likelihood ratio support in maximum likelihood phylogenetic analysis. Cladistics 2021; 38:392-401. [PMID: 34932221 DOI: 10.1111/cla.12496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 11/27/2022] Open
Abstract
In maximum likelihood (ML), the support for a clade can be calculated directly as the likelihood ratio (LR) or log-likelihood difference (S, LLD) of the best trees with and without the clade of interest. However, bootstrap (BS) clade frequencies are more pervasive in ML phylogenetics and are almost universally interpreted as measuring support. In addition to theoretical arguments against that interpretation, BS has several undesirable attributes for a support measure. For example, it does not vary in proportion to optimality or identify clades that are rejected by the evidence and can be overestimated due to missing data. Nevertheless, if BS is a reliable predictor of S, then it might be an efficient indirect method of measuring support-an attractive possibility, given the speed of many BS implementations. To assess the relationship between S and BS, we analyzed 106 empirical datasets retrieved from TreeBASE. Also, to evaluate the degree to which S and BS are affected by the number of replicates during suboptimal tree searches for S and pseudoreplicates during BS estimation, we randomly selected 5 of the 106 datasets and analyzed them using variable numbers of replicates and pseudoreplicates, respectively. The correlation between S and BS was extremely weak in the datasets we analyzed. Increasing the number of replicates during tree search decreased the estimated values of S for most clades, but the magnitude of change was small. In contrast, although increasing pseudoreplicates affected BS values for only approximately 40% of clades, values both increased and decreased, and they did so at much greater magnitudes. Increasing replicates/pseudoreplicates affected the rank order of clades in each tree for both S and BS. Our findings show decisively that BS is not an efficient indirect method of measuring support and suggest that even quite superficial searches to calculate S provide better estimates of support.
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Affiliation(s)
- Denis Jacob Machado
- Programa Inter-unidades de Pós-graduação em Bioinformática, Universidade de São Paulo, Rua do Matão 1010 São Paulo, SP 05508-090, Brazil.,Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC 28223, USA
| | - Fernando Portella de Luna Marques
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Tv. 14, 101 - Butantã, São Paulo, SP, 05508-090, Brazil
| | - Larry Jiménez-Ferbans
- Facultad de Ciencias Básicas, Universidad del Magdalena, Carrera 32 No 22-08, Santa Marta D.T.C.H., Magdalena 470004, Colombia
| | - Taran Grant
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Tv. 14, 101 - Butantã, São Paulo, SP, 05508-090, Brazil
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Goloboff PA, Catalano SA, Torres A. Parsimony analysis of phylogenomic datasets (II): evaluation of PAUP*, MEGA and MPBoot. Cladistics 2021; 38:126-146. [DOI: 10.1111/cla.12476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2021] [Indexed: 12/11/2022] Open
Affiliation(s)
- Pablo A. Goloboff
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 San Miguel de Tucumán Tucumán4000Argentina
- American Museum of Natural History 200 Central Park West New York NY10024USA
| | - Santiago A. Catalano
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 San Miguel de Tucumán Tucumán4000Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo Universidad Nacional de Tucumán Miguel Lillo 205 San Miguel de Tucumán Tucumán4000Argentina
| | - Ambrosio Torres
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 San Miguel de Tucumán Tucumán4000Argentina
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Liu X, Bourgault R, Galli M, Strable J, Chen Z, Feng F, Dong J, Molina I, Gallavotti A. The FUSED LEAVES1-ADHERENT1 regulatory module is required for maize cuticle development and organ separation. THE NEW PHYTOLOGIST 2021; 229:388-402. [PMID: 32738820 PMCID: PMC7754373 DOI: 10.1111/nph.16837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
All aerial epidermal cells in land plants are covered by the cuticle, an extracellular hydrophobic layer that provides protection against abiotic and biotic stresses and prevents organ fusion during development. Genetic and morphological analysis of the classic maize adherent1 (ad1) mutant was combined with genome-wide binding analysis of the maize MYB transcription factor FUSED LEAVES1 (FDL1), coupled with transcriptional profiling of fdl1 mutants. We show that AD1 encodes an epidermally-expressed 3-KETOACYL-CoA SYNTHASE (KCS) belonging to a functionally uncharacterized clade of KCS enzymes involved in cuticular wax biosynthesis. Wax analysis in ad1 mutants indicates that AD1 functions in the formation of very-long-chain wax components. We demonstrate that FDL1 directly binds to CCAACC core motifs present in AD1 regulatory regions to activate its expression. Over 2000 additional target genes of FDL1, including many involved in cuticle formation, drought response and cell wall organization, were also identified. Our results identify a regulatory module of cuticle biosynthesis in maize that is conserved across monocots and eudicots, and highlight previously undescribed factors in lipid metabolism, transport and signaling that coordinate organ development and cuticle formation.
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Affiliation(s)
- Xue Liu
- Waksman Institute of MicrobiologyRutgers UniversityPiscatawayNJ08854‐8020USA
| | - Richard Bourgault
- Department of BiologyAlgoma UniversitySault Ste. MarieONP6A 2G4Canada
| | - Mary Galli
- Waksman Institute of MicrobiologyRutgers UniversityPiscatawayNJ08854‐8020USA
| | - Josh Strable
- School of Integrative Plant SciencePlant Biology SectionCornell UniversityIthacaNY14853USA
| | - Zongliang Chen
- Waksman Institute of MicrobiologyRutgers UniversityPiscatawayNJ08854‐8020USA
| | - Fan Feng
- Waksman Institute of MicrobiologyRutgers UniversityPiscatawayNJ08854‐8020USA
| | - Jiaqiang Dong
- Waksman Institute of MicrobiologyRutgers UniversityPiscatawayNJ08854‐8020USA
| | - Isabel Molina
- Department of BiologyAlgoma UniversitySault Ste. MarieONP6A 2G4Canada
| | - Andrea Gallavotti
- Waksman Institute of MicrobiologyRutgers UniversityPiscatawayNJ08854‐8020USA
- Department of Plant BiologyRutgers UniversityNew BrunswickNJ08901USA
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7
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Liu X, Bourgault R, Galli M, Strable J, Chen Z, Feng F, Dong J, Molina I, Gallavotti A. The FUSED LEAVES1-ADHERENT1 regulatory module is required for maize cuticle development and organ separation. THE NEW PHYTOLOGIST 2021; 229:388-402. [PMID: 32738820 DOI: 10.1101/2020.02.11.943787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/22/2020] [Indexed: 05/27/2023]
Abstract
All aerial epidermal cells in land plants are covered by the cuticle, an extracellular hydrophobic layer that provides protection against abiotic and biotic stresses and prevents organ fusion during development. Genetic and morphological analysis of the classic maize adherent1 (ad1) mutant was combined with genome-wide binding analysis of the maize MYB transcription factor FUSED LEAVES1 (FDL1), coupled with transcriptional profiling of fdl1 mutants. We show that AD1 encodes an epidermally-expressed 3-KETOACYL-CoA SYNTHASE (KCS) belonging to a functionally uncharacterized clade of KCS enzymes involved in cuticular wax biosynthesis. Wax analysis in ad1 mutants indicates that AD1 functions in the formation of very-long-chain wax components. We demonstrate that FDL1 directly binds to CCAACC core motifs present in AD1 regulatory regions to activate its expression. Over 2000 additional target genes of FDL1, including many involved in cuticle formation, drought response and cell wall organization, were also identified. Our results identify a regulatory module of cuticle biosynthesis in maize that is conserved across monocots and eudicots, and highlight previously undescribed factors in lipid metabolism, transport and signaling that coordinate organ development and cuticle formation.
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Affiliation(s)
- Xue Liu
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Richard Bourgault
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6A 2G4, Canada
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Josh Strable
- School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Fan Feng
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Jiaqiang Dong
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Isabel Molina
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6A 2G4, Canada
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
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8
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Léveillé-Bourret É, Chen BH, Garon-Labrecque MÈ, Ford BA, Starr JR. RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae). Mol Phylogenet Evol 2020; 145:106727. [DOI: 10.1016/j.ympev.2019.106727] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/13/2019] [Accepted: 12/29/2019] [Indexed: 12/15/2022]
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9
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Data, time and money: evaluating the best compromise for inferring molecular phylogenies of non-model animal taxa. Mol Phylogenet Evol 2020; 142:106660. [DOI: 10.1016/j.ympev.2019.106660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022]
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10
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Simmons MP, Sloan DB, Springer MS, Gatesy J. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Mol Phylogenet Evol 2019; 131:80-92. [DOI: 10.1016/j.ympev.2018.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023]
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Canal D, Köster N, Jones KE, Korotkova N, Croat TB, Borsch T. Phylogeny and diversification history of the large Neotropical genus Philodendron (Araceae): Accelerated speciation in a lineage dominated by epiphytes. AMERICAN JOURNAL OF BOTANY 2018; 105:1035-1052. [PMID: 29995336 DOI: 10.1002/ajb2.1111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Philodendron is a large genus of ~560 species and among the most conspicuous epiphytic components of Neotropical forests, yet its phylogenetic relationships, timing of divergence, and diversification history have remained unclear. We present a comprehensive phylogenetic study for Philodendron and investigate its diversification, including divergence-time estimates and diversification rate shift analyses. METHODS We performed the largest phylogenetic reconstruction for Philodendron to date, including 125 taxa with a combined dataset of three plastid regions (petD, rpl16, and trnK/matK). We estimated divergence times using Bayesian evolutionary analysis sampling trees and inferred shifts in diversification rates using Bayesian analysis of macroevolutionary mixtures. KEY RESULTS We found that Philodendron, its three subgenera, and the closely related genus Adelonema are monophyletic. Within Philodendron subgenus Philodendron, 12 statistically well-supported clades are recognized. The genus Philodendron originated ~25 mya and a diversification rate upshift was detected at the origin of subgenus Philodendron ~12 mya. CONCLUSIONS Philodendron is a species-rich Neotropical lineage that diverged from Adelonema during the late Oligocene. Within Philodendron, the three subgenera currently accepted are recovered in two lineages: one contains the subgenera Meconostigma and Pteromischum and the other contains subgenus Philodendron. The lineage containing subgenera Meconostigma and Pteromischum underwent a consistent diversification rate. By contrast, a diversification rate upshift occurred within subgenus Philodendron ~12 mya. This diversification rate upshift is associated with the species radiation of the most speciose subgenus within Philodendron. The sections accepted within subgenus Philodendron are not congruent with the clades recovered. Instead, the clades are geographically defined.
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Affiliation(s)
- Dubán Canal
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
| | - Nils Köster
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
| | - Katy E Jones
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
| | - Nadja Korotkova
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
| | - Thomas B Croat
- Missouri Botanical Garden, Monsanto Research Building, P.O. Box 299, St. Louis, Missouri, 63166, USA
| | - Thomas Borsch
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
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12
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Dobrin BH, Zwickl DJ, Sanderson MJ. The prevalence of terraced treescapes in analyses of phylogenetic data sets. BMC Evol Biol 2018; 18:46. [PMID: 29618314 PMCID: PMC5885316 DOI: 10.1186/s12862-018-1162-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 03/22/2018] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The pattern of data availability in a phylogenetic data set may lead to the formation of terraces, collections of equally optimal trees. Terraces can arise in tree space if trees are scored with parsimony or with partitioned, edge-unlinked maximum likelihood. Theory predicts that terraces can be large, but their prevalence in contemporary data sets has never been surveyed. We selected 26 data sets and phylogenetic trees reported in recent literature and investigated the terraces to which the trees would belong, under a common set of inference assumptions. We examined terrace size as a function of the sampling properties of the data sets, including taxon coverage density (the proportion of taxon-by-gene positions with any data present) and a measure of gene sampling "sufficiency". We evaluated each data set in relation to the theoretical minimum gene sampling depth needed to reduce terrace size to a single tree, and explored the impact of the terraces found in replicate trees in bootstrap methods. RESULTS Terraces were identified in nearly all data sets with taxon coverage densities < 0.90. They were not found, however, in high-coverage-density (i.e., ≥ 0.94) transcriptomic and genomic data sets. The terraces could be very large, and size varied inversely with taxon coverage density and with gene sampling sufficiency. Few data sets achieved a theoretical minimum gene sampling depth needed to reduce terrace size to a single tree. Terraces found during bootstrap resampling reduced overall support. CONCLUSIONS If certain inference assumptions apply, trees estimated from empirical data sets often belong to large terraces of equally optimal trees. Terrace size correlates to data set sampling properties. Data sets seldom include enough genes to reduce terrace size to one tree. When bootstrap replicate trees lie on a terrace, statistical support for phylogenetic hypotheses may be reduced. Although some of the published analyses surveyed were conducted with edge-linked inference models (which do not induce terraces), unlinked models have been used and advocated. The present study describes the potential impact of that inference assumption on phylogenetic inference in the context of the kinds of multigene data sets now widely assembled for large-scale tree construction.
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Affiliation(s)
- Barbara H. Dobrin
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St, Tucson, AZ 85721 USA
| | - Derrick J. Zwickl
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St, Tucson, AZ 85721 USA
| | - Michael J. Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St, Tucson, AZ 85721 USA
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Léveillé-Bourret É, Starr JR, Ford BA. Why are there so many sedges? Sumatroscirpeae, a missing piece in the evolutionary puzzle of the giant genus Carex (Cyperaceae). Mol Phylogenet Evol 2017; 119:93-104. [PMID: 29113924 DOI: 10.1016/j.ympev.2017.10.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 10/18/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
For over a century, the origins and mechanisms underlying the diversification of the enormous temperate genus Carex (>2100 species; Cariceae, Cyperaceae) have remained largely speculative. Characteristics such as its diverse ecology, varied biogeography, and intriguing cytology have made Carex a powerful model for studying plant evolution, but its uncertain sister-group relationships hinder its use in studies that depend on accurate ancestral state estimates and biogeographic inferences. To identify the sister to Carex, we estimated the phylogeny of all genera in the Cariceae-Dulichieae-Scirpeae clade (CDS) using three plastid and two nuclear ribosomal markers. Ancestral state reconstructions of key characters were made, and a time-calibrated tree estimated. Carex is strongly supported as sister to the rare East Asian Sumatroscirpus, sole genus of a new tribe, Sumatroscirpeae trib. nov. Believed to be unique to Carex, the perigynium (prophyllar bract enclosing a flower) is in fact a synapomorphy shared with this small tribe (∼4 species) that appeared 36 Mya. We thus suggest the initial key innovation in the remarkable diversification of Carex is not the perigynium, but could be the release of mechanical constraints on perigynia through spikelet truncation, resulting in novel adaptive morphologies. Monoecy, chromosomal change, and rapid inflorescence development enabling phenological isolation may also be involved. The tiny tribe Sumatroscirpeae will provide unprecedented insights into the inflorescence homology, evolution, diversification, and biogeographic history of its sister-group Carex, one of the world's most diverse plant lineages.
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Affiliation(s)
| | - Julian R Starr
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Bruce A Ford
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Kück P, Wilkinson M, Groß C, Foster PG, Wägele JW. Can quartet analyses combining maximum likelihood estimation and Hennigian logic overcome long branch attraction in phylogenomic sequence data? PLoS One 2017; 12:e0183393. [PMID: 28841676 PMCID: PMC5571918 DOI: 10.1371/journal.pone.0183393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/03/2017] [Indexed: 12/28/2022] Open
Abstract
Systematic biases such as long branch attraction can mislead commonly relied upon model-based (i.e. maximum likelihood and Bayesian) phylogenetic methods when, as is usually the case with empirical data, there is model misspecification. We present PhyQuart, a new method for evaluating the three possible binary trees for any quartet of taxa. PhyQuart was developed through a process of reciprocal illumination between a priori considerations and the results of extensive simulations. It is based on identification of site-patterns that can be considered to support a particular quartet tree taking into account the Hennigian distinction between apomorphic and plesiomorphic similarity, and employing corrections to the raw observed frequencies of site-patterns that exploit expectations from maximum likelihood estimation. We demonstrate through extensive simulation experiments that, whereas maximum likeilihood estimation performs well in many cases, it can be outperformed by PhyQuart in cases where it fails due to extreme branch length asymmetries producing long-branch attraction artefacts where there is only very minor model misspecification.
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Affiliation(s)
- Patrick Kück
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, 53113, Germany
- The Natural History Museum, London, SW7 5BD, United Kingdom
| | - Mark Wilkinson
- The Natural History Museum, London, SW7 5BD, United Kingdom
| | - Christian Groß
- The Natural History Museum, London, SW7 5BD, United Kingdom
- Delft University of Technology, Delft, 2628 CD, The Netherlands
| | | | - Johann W. Wägele
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, 53113, Germany
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15
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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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16
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Simmons MP. Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella
is supported as sister and Observed Variability is biased. Cladistics 2016; 33:488-512. [DOI: 10.1111/cla.12177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2016] [Indexed: 01/16/2023] Open
Affiliation(s)
- Mark P. Simmons
- Department of Biology; Colorado State University; Fort Collins CO 80523-1878 USA
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17
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Gatesy J, Meredith RW, Janecka JE, Simmons MP, Murphy WJ, Springer MS. Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia. Cladistics 2016; 33:295-332. [DOI: 10.1111/cla.12170] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 12/14/2022] Open
Affiliation(s)
- John Gatesy
- Department of Biology University of California Riverside CA 92521 USA
| | - Robert W. Meredith
- Department of Biology and Molecular Biology Montclair State University Montclair NJ 07043 USA
| | - Jan E. Janecka
- Department of Biological Sciences Duquesne University Pittsburgh PA 15282 USA
| | - Mark P. Simmons
- Department of Biology Colorado State University Fort Collins CO 80523 USA
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA
| | - Mark S. Springer
- Department of Biology University of California Riverside CA 92521 USA
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18
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Simmons MP, Gatesy J. Biases of tree-independent-character-subsampling methods. Mol Phylogenet Evol 2016; 100:424-443. [DOI: 10.1016/j.ympev.2016.04.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 04/15/2016] [Indexed: 12/21/2022]
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19
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Warren JM, Simmons MP, Wu Z, Sloan DB. Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes. Genome Biol Evol 2016; 8:364-74. [PMID: 26759362 PMCID: PMC4779610 DOI: 10.1093/gbe/evw003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2016] [Indexed: 12/20/2022] Open
Abstract
The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses.
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Affiliation(s)
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins
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Simmons MP, Gatesy J. Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms. Mol Phylogenet Evol 2015; 91:98-122. [DOI: 10.1016/j.ympev.2015.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/01/2015] [Accepted: 05/14/2015] [Indexed: 11/24/2022]
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Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar. Mol Phylogenet Evol 2015; 94:365-82. [PMID: 26432393 DOI: 10.1016/j.ympev.2015.09.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/11/2015] [Accepted: 09/15/2015] [Indexed: 01/05/2023]
Abstract
Of the 97 currently recognized genera of Celastraceae, 19 are native to Madagascar, including six endemics. In this study we conducted the most thorough phylogenetic analysis of Celastraceae yet completed with respect to both character and taxon sampling, and include representatives of five new endemic genera. Fifty-one new accessions, together with 328 previously used accessions of Celastrales, were sampled for morphological characters, two rDNA gene regions, and two plastid gene regions. The endemic Malagasy genera are resolved in two separate lineages-Xenodrys by itself and all other endemic genera in a clade that also includes four lineages inferred to have dispersed from Madagascar: Brexia madagascariensis (Mascarene Islands, coastal Africa), Elaeodendron (West Indies, Africa to New Caledonia), and Pleurostylia (Africa to New Caledonia). Of the 12 extant Malagasy Celastraceae lineages identified, eight are clearly of African origin. The origins of the remaining four lineages are less clear, but reasonable possibilities include America, Eurasia, Africa, southern India, Malesia, and Australia. Based on 95% credible age intervals from fossil-calibrated molecular dating, all 12 extant Malagasy Celastraceae lineages appear to have arisen following dispersal after the separation of Madagascar from other landmasses within the last 70 million years.
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Sanderson MJ, McMahon MM, Stamatakis A, Zwickl DJ, Steel M. Impacts of Terraces on Phylogenetic Inference. Syst Biol 2015; 64:709-26. [DOI: 10.1093/sysbio/syv024] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 04/15/2015] [Indexed: 11/14/2022] Open
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23
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Petersen G, Seberg O, Cuenca A, Stevenson DW, Thadeo M, Davis JI, Graham S, Ross TG. Phylogeny of the Alismatales (Monocotyledons) and the relationship ofAcorus(Acorales?). Cladistics 2015; 32:141-159. [DOI: 10.1111/cla.12120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2015] [Indexed: 11/28/2022] Open
Affiliation(s)
- Gitte Petersen
- Natural History Museum of Denmark; University of Copenhagen; Sølvgade 83 Opg. S DK-1307 Copenhagen Denmark
| | - Ole Seberg
- Natural History Museum of Denmark; University of Copenhagen; Sølvgade 83 Opg. S DK-1307 Copenhagen Denmark
| | - Argelia Cuenca
- Natural History Museum of Denmark; University of Copenhagen; Sølvgade 83 Opg. S DK-1307 Copenhagen Denmark
| | | | | | - Jerrold I. Davis
- L. H. Bailey Hortorium and Section of Plant Biology; Cornell University; Ithaca NY 14853 USA
| | - Sean Graham
- Department of Botany; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - T. Gregory Ross
- Department of Botany; University of British Columbia; Vancouver BC V6T 1Z4 Canada
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Mugrabi de Kuppler AL, Fagúndez J, Bellstedt DU, Oliver EGH, Léon J, Pirie MD. Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae). Mol Phylogenet Evol 2015; 88:121-31. [PMID: 25888972 DOI: 10.1016/j.ympev.2015.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 04/02/2015] [Accepted: 04/06/2015] [Indexed: 10/23/2022]
Abstract
Whilst most of the immense species richness of heathers (Calluna, Daboecia and Erica: Ericeae; Ericaceae) is endemic to Africa, particularly the Cape Floristic Region, the oldest lineages are found in the Northern Hemisphere. We present phylogenetic hypotheses for the major clades of Ericeae represented by multiple accessions of all northern Erica species and placeholder taxa for the large nested African/Madagascan clade. We identified consistent, strongly supported conflict between gene trees inferred from ITS and chloroplast DNA sequences with regard to the position of Erica lusitanica. We used coalescent simulations to test whether this conflict could be explained by coalescent stochasticity, as opposed to reticulation (e.g. hybridisation), given estimates of clade ages, generation time and effective population sizes (Ne). A standard approach, comparing overall differences between real and simulated trees, could not clearly reject coalescence. However, additional simulations showed that at the (higher) Ne necessary to explain conflict in E. lusitanica, further topological conflict would also be expected. Ancient hybridisation between ancestors of northern species is therefore a plausible scenario to explain the origin of E. lusitanica, and its morphological similarities to E. arborea. Assuming either process influences the results of species tree and further evolutionary inference. The coalescence scenario is equivocal with regard the standing hypothesis of stepping stone dispersal of Erica from Europe into Africa; whereas reticulate evolution in E. lusitanica would imply that the colonisation of Tropical East Africa by E. arborea instead occurred independently of dispersals within the rest of the African/Madagascan clade.
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Affiliation(s)
- A L Mugrabi de Kuppler
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität Bonn, Katzenburgweg 5, 53115 Bonn, Germany
| | - J Fagúndez
- Department of Plant and Animal Biology and Ecology, University of A Coruña, Faculty of Science, 15001 A Coruña, Spain
| | - D U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - E G H Oliver
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - J Léon
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität Bonn, Katzenburgweg 5, 53115 Bonn, Germany
| | - M D Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa; Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099 Mainz, Germany.
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25
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Freudenstein JV, Chase MW. Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification. ANNALS OF BOTANY 2015; 115:665-81. [PMID: 25578379 PMCID: PMC4343289 DOI: 10.1093/aob/mcu253] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/05/2014] [Accepted: 11/25/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The largest subfamily of orchids, Epidendroideae, represents one of the most significant diversifications among flowering plants in terms of pollination strategy, vegetative adaptation and number of species. Although many groups in the subfamily have been resolved, significant relationships in the tree remain unclear, limiting conclusions about diversification and creating uncertainty in the classification. This study brings together DNA sequences from nuclear, plastid and mitochrondrial genomes in order to clarify relationships, to test associations of key characters with diversification and to improve the classification. METHODS Sequences from seven loci were concatenated in a supermatrix analysis for 312 genera representing most of epidendroid diversity. Maximum-likelihood and parsimony analyses were performed on this matrix and on subsets of the data to generate trees and to investigate the effect of missing values. Statistical character-associated diversification analyses were performed. KEY RESULTS Likelihood and parsimony analyses yielded highly resolved trees that are in strong agreement and show significant support for many key clades. Many previously proposed relationships among tribes and subtribes are supported, and some new relationships are revealed. Analyses of subsets of the data suggest that the relatively high number of missing data for the full analysis is not problematic. Diversification analyses show that epiphytism is most strongly associated with diversification among epidendroids, followed by expansion into the New World and anther characters that are involved with pollinator specificity, namely early anther inflexion, cellular pollinium stalks and the superposed pollinium arrangement. CONCLUSIONS All tested characters show significant association with speciation in Epidendroideae, suggesting that no single character accounts for the success of this group. Rather, it appears that a succession of key features appeared that have contributed to diversification, sometimes in parallel.
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Affiliation(s)
- John V Freudenstein
- Herbarium, Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA, Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AE, UK and School of Plant Biology, The University of Western Australia, Crawley, WA 600, Australia
| | - Mark W Chase
- Herbarium, Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA, Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AE, UK and School of Plant Biology, The University of Western Australia, Crawley, WA 600, Australia Herbarium, Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA, Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AE, UK and School of Plant Biology, The University of Western Australia, Crawley, WA 600, Australia
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A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses. Mol Phylogenet Evol 2014; 80:267-80. [DOI: 10.1016/j.ympev.2014.08.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/16/2014] [Accepted: 08/20/2014] [Indexed: 12/27/2022]
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Simmons MP, Randle CP. Disparate parametric branch-support values from ambiguous characters. Mol Phylogenet Evol 2014; 78:66-86. [DOI: 10.1016/j.ympev.2014.04.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 04/23/2014] [Accepted: 04/29/2014] [Indexed: 11/25/2022]
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28
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Dubious resolution and support from published sparse supermatrices: The importance of thorough tree searches. Mol Phylogenet Evol 2014; 78:334-48. [DOI: 10.1016/j.ympev.2014.06.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/30/2014] [Accepted: 06/01/2014] [Indexed: 11/17/2022]
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Goloboff PA, Simmons MP. Bias in Tree Searches and its Consequences for Measuring Group Supports. Syst Biol 2014; 63:851-61. [DOI: 10.1093/sysbio/syu051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Pablo A. Goloboff
- CONICET, INSUE, Fundación Miguel Lillo, Miguel Lillo 251, 4000 S.M. de Tucumán, Argentina; and 2Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Mark P. Simmons
- CONICET, INSUE, Fundación Miguel Lillo, Miguel Lillo 251, 4000 S.M. de Tucumán, Argentina; and 2Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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Simmons MP. Limitations of locally sampled characters in phylogenetic analyses of sparse supermatrices. Mol Phylogenet Evol 2014; 74:1-14. [DOI: 10.1016/j.ympev.2014.01.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 01/30/2014] [Accepted: 01/30/2014] [Indexed: 11/16/2022]
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Struck TH, Wey-Fabrizius AR, Golombek A, Hering L, Weigert A, Bleidorn C, Klebow S, Iakovenko N, Hausdorf B, Petersen M, Kück P, Herlyn H, Hankeln T. Platyzoan paraphyly based on phylogenomic data supports a noncoelomate ancestry of spiralia. Mol Biol Evol 2014; 31:1833-49. [PMID: 24748651 DOI: 10.1093/molbev/msu143] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Based on molecular data three major clades have been recognized within Bilateria: Deuterostomia, Ecdysozoa, and Spiralia. Within Spiralia, small-sized and simply organized animals such as flatworms, gastrotrichs, and gnathostomulids have recently been grouped together as Platyzoa. However, the representation of putative platyzoans was low in the respective molecular phylogenetic studies, in terms of both, taxon number and sequence data. Furthermore, increased substitution rates in platyzoan taxa raised the possibility that monophyletic Platyzoa represents an artifact due to long-branch attraction. In order to overcome such problems, we employed a phylogenomic approach, thereby substantially increasing 1) the number of sampled species within Platyzoa and 2) species-specific sequence coverage in data sets of up to 82,162 amino acid positions. Using established and new measures (long-branch score), we disentangled phylogenetic signal from misleading effects such as long-branch attraction. In doing so, our phylogenomic analyses did not recover a monophyletic origin of platyzoan taxa that, instead, appeared paraphyletic with respect to the other spiralians. Platyhelminthes and Gastrotricha formed a monophylum, which we name Rouphozoa. To the exclusion of Gnathifera, Rouphozoa and all other spiralians represent a monophyletic group, which we name Platytrochozoa. Platyzoan paraphyly suggests that the last common ancestor of Spiralia was a simple-bodied organism lacking coelomic cavities, segmentation, and complex brain structures, and that more complex animals such as annelids evolved from such a simply organized ancestor. This conclusion contradicts alternative evolutionary scenarios proposing an annelid-like ancestor of Bilateria and Spiralia and several independent events of secondary reduction.
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Affiliation(s)
- Torsten H Struck
- Zoological Research Museum Alexander Koenig, Bonn, GermanyUniversity of Osnabrück, FB05 Biology/Chemistry, AG Zoology, Osnabrück, Germany
| | - Alexandra R Wey-Fabrizius
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
| | - Anja Golombek
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Lars Hering
- Animal Evolution and Development, Institute of Biology II, University of Leipzig, Leipzig, Germany
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Christoph Bleidorn
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Sabrina Klebow
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
| | - Nataliia Iakovenko
- Department of Biology and Ecology, Ostravian University in Ostrava, Ostrava, Czech RepublicDepartment of Invertebrate Fauna and Systematics, Schmalhausen Institute of Zoology NAS of Ukraine, Kyiv, Ukraine
| | | | - Malte Petersen
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Patrick Kück
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Holger Herlyn
- Institute of Anthropology, Johannes Gutenberg University, Mainz, Germany
| | - Thomas Hankeln
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
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Simmons MP, Norton AP. Divergent maximum-likelihood-branch-support values for polytomies. Mol Phylogenet Evol 2014; 73:87-96. [DOI: 10.1016/j.ympev.2014.01.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 01/09/2014] [Accepted: 01/21/2014] [Indexed: 10/25/2022]
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33
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Barrett CF, Specht CD, Leebens-Mack J, Stevenson DW, Zomlefer WB, Davis JI. Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)? ANNALS OF BOTANY 2014; 113:119-33. [PMID: 24280362 PMCID: PMC3864734 DOI: 10.1093/aob/mct264] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 09/16/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Zingiberales comprise a clade of eight tropical monocot families including approx. 2500 species and are hypothesized to have undergone an ancient, rapid radiation during the Cretaceous. Zingiberales display substantial variation in floral morphology, and several members are ecologically and economically important. Deep phylogenetic relationships among primary lineages of Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot tree of life. METHODS Next-generation sequencing was used to construct complete plastid gene sets for nine taxa of Zingiberales, which were added to five previously sequenced sets in an attempt to resolve deep relationships among families in the order. Variation in taxon sampling, process partition inclusion and partition model parameters were examined to assess their effects on topology and support. KEY RESULTS Codon-based likelihood analysis identified a strongly supported clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)), sister to (Musaceae, (Lowiaceae, Strelitziaceae)), collectively sister to Heliconiaceae. However, the deepest divergences in this phylogenetic analysis comprised short branches with weak support. Additionally, manipulation of matrices resulted in differing deep topologies in an unpredictable fashion. Alternative topology testing allowed statistical rejection of some of the topologies. Saturation fails to explain observed topological uncertainty and low support at the base of Zingiberales. Evidence for conflict among the plastid data was based on a support metric that accounts for conflicting resampled topologies. CONCLUSIONS Many relationships were resolved with robust support, but the paucity of character information supporting the deepest nodes and the existence of conflict suggest that plastid coding regions are insufficient to resolve and support the earliest divergences among families of Zingiberales. Whole plastomes will continue to be highly useful in plant phylogenetics, but the current study adds to a growing body of literature suggesting that they may not provide enough character information for resolving ancient, rapid radiations.
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Affiliation(s)
- Craig F. Barrett
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Chelsea D. Specht
- Departments of Plant and Microbial Biology and Integrative Biology, The University and Jepson Herbaria, University of California, Berkeley CA 94720, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | | | - Wendy B. Zomlefer
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Jerrold I. Davis
- Department of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NY 14853, USA
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Kück P, Struck TH. BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions. Mol Phylogenet Evol 2014; 70:94-8. [DOI: 10.1016/j.ympev.2013.09.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/12/2013] [Accepted: 09/14/2013] [Indexed: 10/26/2022]
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Dell’Ampio E, Meusemann K, Szucsich NU, Peters RS, Meyer B, Borner J, Petersen M, Aberer AJ, Stamatakis A, Walzl MG, Minh BQ, von Haeseler A, Ebersberger I, Pass G, Misof B. Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects. Mol Biol Evol 2014; 31:239-49. [PMID: 24140757 PMCID: PMC3879454 DOI: 10.1093/molbev/mst196] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. To get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies by using an extended transcriptome data set. Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive data sets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we used Four-cluster Likelihood Mapping (FcLM) to measure the degree of congruence among genes of a data set, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated neither with functional class assignment of these genes nor with model misspecification due to unpartitioned analyses. The herein analyzed data set is the currently largest data set covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. Although this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artifacts.
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Affiliation(s)
| | - Karen Meusemann
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany
- CSIRO Ecosystem Sciences, Australian National Insect Collection, Acton, ACT, Australia
| | | | - Ralph S. Peters
- Zoologisches Forschungsmuseum Alexander Koenig, Abteilung Arthropoda, Bonn, Germany
| | - Benjamin Meyer
- Institut für Systemische Neurowissenschaften, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Janus Borner
- Biozentrum Grindel & Zoologisches Museum, Universität Hamburg, Hamburg, Germany
| | - Malte Petersen
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany
| | - Andre J. Aberer
- Heidelberg Institute for Theoretical Studies (HITS), Scientific Computing Group, Heidelberg, Germany
| | - Alexandros Stamatakis
- Heidelberg Institute for Theoretical Studies (HITS), Scientific Computing Group, Heidelberg, Germany
- Karlsruher Institut für Technologie, Fakultät für Informatik, Karlsruhe, Germany
| | - Manfred G. Walzl
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Ingo Ebersberger
- Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Günther Pass
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany
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Amelia Chemisquy M, Prevosti FJ. Evaluating the clade size effect in alternative measures of branch support. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- María Amelia Chemisquy
- División Mastozoología; Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Buenos Aires Argentina - CONICET
| | - Francisco J. Prevosti
- División Mastozoología; Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Buenos Aires Argentina - CONICET
- Departamento de Ciencias Básicas; Universidad Nacional de Luján; Buenos Aires Argentina
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Jungfer KH, Faivovich J, Padial JM, Castroviejo-Fisher S, Lyra MM, V. M. Berneck B, Iglesias PP, Kok PJR, MacCulloch RD, Rodrigues MT, Verdade VK, Torres Gastello CP, Chaparro JC, Valdujo PH, Reichle S, Moravec J, Gvoždík V, Gagliardi-Urrutia G, Ernst R, De la Riva I, Means DB, Lima AP, Señaris JC, Wheeler WC, F. B. Haddad C. Systematics of spiny-backed treefrogs (Hylidae:Osteocephalus): an Amazonian puzzle. ZOOL SCR 2013. [DOI: 10.1111/zsc.12015] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Karl-Heinz Jungfer
- División Herpetología; Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’-CONICET; Angel Gallardo 470; C1405DJR; Buenos Aires; Argentina
| | | | - José M. Padial
- Section of Amphibians and Reptiles; Carnegie Museum of Natural History; 4400 Forbes Avenue; Pittsburgh; PA; 15213-4080; USA
| | | | - Mariana M. Lyra
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; Av. 24A 1515; CEP 13506-900; Rio Claro; São Paulo; Brazil
| | - Bianca V. M. Berneck
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; Av. 24A 1515; CEP 13506-900; Rio Claro; São Paulo; Brazil
| | - Patricia P. Iglesias
- Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Instituto de Ecología, Genética y Evolución de Buenos Aires; IEGEBA-CONICET; Universidad de Buenos Aires; Ciudad Universitaria Pab. II; C1428EHA; Buenos Aires; Argentina
| | | | - Ross D. MacCulloch
- Department of Natural History; Royal Ontario Museum; 100 Queens Park; Toronto; ON; M5S 2C6; Canada
| | - Miguel T. Rodrigues
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Caixa Postal 11461; CEP 05508-090; São Paulo; Brazil
| | - Vanessa K. Verdade
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; Av. dos Estados; 5001; CEP 09210-971; Santo André; São Paulo; Brazil
| | - Claudia P. Torres Gastello
- Departamento de Herpetología; Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos; Av. Arenales 1256; Apto. 14-0434; Lima 14; Peru
| | - Juan Carlos Chaparro
- Museo de Historia Natural; Universidad Nacional de San Antonio Abad del Cusco; Cusco; Peru
| | - Paula H. Valdujo
- Departamento de Ecologia; Instituto de Biociências; Universidade de São Paulo; Rua do Matão, travessa 14; 05508-900; São Paulo; SP; Brazil
| | - Steffen Reichle
- Fundación para la Conservación del Bosque Chiquitano; Av. Ejército Nacional No 160; Santa Cruz de la Sierra; Bolivia
| | - Jiří Moravec
- Department of Zoology; National Museum; Prague 9; Czech Republic
| | - Václav Gvoždík
- Department of Zoology; National Museum; Prague 9; Czech Republic
| | - Giussepe Gagliardi-Urrutia
- Programa de Investigación en Biodiversidad Amazónica del Instituto de Investigaciones de la Amazonia Peruana; Av. Quiñonez Km 2.5; Iquitos; Perú
| | - Raffael Ernst
- Museum für Tierkunde; Senckenberg Natural History Collections Dresden; Königsbrücker Landstr. 159; D-01109; Dresden; Germany
| | - Ignacio De la Riva
- Department of Biodiversity and Evolutionary Biology; Museo Nacional de Ciencias Naturales-CSIC; C/José Gutiérrez Abascal 2; 28006; Madrid; Spain
| | - Donald Bruce Means
- Coastal Plains Institute and Land Conservancy; 1313 Milton Street; Tallahassee; FL; 32303; USA
| | - Albertina P. Lima
- Instituto Nacional de Pesquisas da Amazônia; Caixa Postal 478; CEP 69011-970; Manaus; Amazonas; Brazil
| | - J. Celsa Señaris
- Laboratorio de Ecología y Genética de Poblaciones; Centro de Ecología; Instituto Venezolano de Investigaciones Científicas; Apartado 21827; Caracas; 1020-A; Venezuela
| | - Ward C. Wheeler
- Division of Invertebrate Zoology; American Museum of Natural History; Central Park West at 79th Street; New York; NY; 10024-5192; USA
| | - Célio F. B. Haddad
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; Av. 24A 1515; CEP 13506-900; Rio Claro; São Paulo; Brazil
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Phylogeny of the Asian Hedyotis–Oldenlandia complex (Spermacoceae, Rubiaceae): Evidence for high levels of polyphyly and the parallel evolution of diplophragmous capsules. Mol Phylogenet Evol 2013; 67:110-22. [DOI: 10.1016/j.ympev.2013.01.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 12/05/2012] [Accepted: 01/08/2013] [Indexed: 11/23/2022]
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Simmons MP, Norton AP. Quantification and relative severity of inflated branch-support values generated by alternative methods: An empirical example. Mol Phylogenet Evol 2013; 67:277-96. [DOI: 10.1016/j.ympev.2013.01.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/18/2013] [Accepted: 01/31/2013] [Indexed: 10/27/2022]
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Petersen G, Seberg O, Davis JI. Phylogeny of the Liliales (Monocotyledons) with special emphasis on data partition congruence and RNA editing. Cladistics 2012; 29:274-295. [DOI: 10.1111/j.1096-0031.2012.00427.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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41
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Barrett CF, Davis JI, Leebens-Mack J, Conran JG, Stevenson DW. Plastid genomes and deep relationships among the commelinid monocot angiosperms. Cladistics 2012; 29:65-87. [DOI: 10.1111/j.1096-0031.2012.00418.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Seberg O, Petersen G, Davis JI, Pires JC, Stevenson DW, Chase MW, Fay MF, Devey DS, Jørgensen T, Sytsma KJ, Pillon Y. Phylogeny of the Asparagales based on three plastid and two mitochondrial genes. AMERICAN JOURNAL OF BOTANY 2012; 99:875-889. [PMID: 22539521 DOI: 10.3732/ajb.1100468] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized families, their circumscription, and relationships are somewhat controversial. METHODS Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequency-within-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated. KEY RESULTS The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent. CONCLUSIONS Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.
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Affiliation(s)
- Ole Seberg
- Botanical Garden, Natural History Museum of Denmark, Sølvgade 83, Copenhagen K, Denmark.
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Simmons MP. Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data. Mol Phylogenet Evol 2011; 62:472-84. [PMID: 22067131 DOI: 10.1016/j.ympev.2011.10.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 10/10/2011] [Accepted: 10/23/2011] [Indexed: 10/16/2022]
Abstract
Non-random distributions of missing data are a general problem for likelihood-based statistical analyses, including those in a phylogenetic context. Extensive non-randomly distributed missing data are particularly problematic in supermatrix analyses that include many terminals and/or loci. It has been widely reported that missing data can lead to loss of resolution, but only very rarely create misleading or otherwise unsupported results in a parsimony context. Yet this does not hold for all parametric-based analyses because of their assumption of homogeneity across characters and lineages, which can lead to both long-branch attraction and long-branch repulsion. Contrived examples were used to demonstrate that non-random distributions of missing data, even without rate heterogeneity among characters and a well fitting model, can provide misleading likelihood-based topologies and branch-support values that are radically unstable based on slight modifications to character sampling. The same can occur despite complete absence of parsimony-informative characters. Otherwise unsupported resolution and high branch support for these clades were found to occur frequently in 22 empirical examples derived from a published supermatrix. Partitioning characters based on the distribution of missing data helped to decrease, but did not eliminate, these artifacts. These artifacts were exacerbated by low quality tree searches, particularly when holding only a single optimal tree that must be fully resolved.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA.
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44
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Simmons MP. Misleading results of likelihood-based phylogenetic analyses in the presence of missing data. Cladistics 2011; 28:208-222. [DOI: 10.1111/j.1096-0031.2011.00375.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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45
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Simmons MP, McKenna MJ, Bacon CD, Yakobson K, Cappa JJ, Archer RH, Ford AJ. Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes. Mol Phylogenet Evol 2011; 62:9-20. [PMID: 22001302 DOI: 10.1016/j.ympev.2011.08.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 08/10/2011] [Accepted: 08/20/2011] [Indexed: 11/17/2022]
Abstract
The phylogeny of Celastraceae tribe Euonymeae (≈ 230 species in eight genera in both the Old and New Worlds) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. Tribe Euonymeae has been defined as those genera of Celastraceae with generally opposite leaves, isomerous carpels, loculicidally dehiscent capsules, and arillate seeds (except Microtropis). Euonymus is the most diverse (129 species) and widely cultivated genus in the tribe. We infer that tribe Euonymeae consists of at least six separate lineages within Celastraceae and that a revised natural classification of the family is needed. Microtropis and Quetzalia are inferred to be distinct sister groups that together are sister to Zinowiewia. The endangered Monimopetalum chinense is an isolated and early derived lineage of Celastraceae that represents an important component of phylogenetic diversity within the family. Hedraianthera is sister to Brassiantha, and we describe a second species (Brassiantha hedraiantheroides A.J. Ford) that represents the first reported occurrence of this genus in Australia. Euonymus globularis, from eastern Australia, is sister to Menepetalum, which is endemic to New Caledonia, and we erect a new genus (Dinghoua R.H. Archer) for it. The Madagascan species of Euonymus are sister to Pleurostylia and recognized as a distinct genus (Astrocassine ined.). Glyptopetalum, Torralbasia, and Xylonymus are all closely related to Euonymus sensu stricto and are questionably distinct from it. Current intrageneric classifications of Euonymus are not completely natural and require revision.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA.
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