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Patané JSL, Martins J, Setubal JC. A Guide to Phylogenomic Inference. Methods Mol Biol 2024; 2802:267-345. [PMID: 38819564 DOI: 10.1007/978-1-0716-3838-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. Phylogenomics has significant applications in fields such as evolutionary biology, systematics, comparative genomics, and conservation genetics, providing valuable insights into the origins and relationships of species and contributing to our understanding of biological diversity and evolution. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.
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Affiliation(s)
- José S L Patané
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração/Heart Institute Hospital das Clínicas - Faculdade de Medicina da Universidade de São Paulo São Paulo, São Paulo, SP, Brazil
| | - Joaquim Martins
- Integrative Omics group, Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - João Carlos Setubal
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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2
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Guo S, Lin X, Song N. Mitochondrial phylogenomics reveals deep relationships of scarab beetles (Coleoptera, Scarabaeidae). PLoS One 2022; 17:e0278820. [PMID: 36512580 PMCID: PMC9746968 DOI: 10.1371/journal.pone.0278820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022] Open
Abstract
In this study, we newly sequenced the complete mitochondrial genomes (mitogenomes) of two phytophagous scarab beetles, and investigated the deep level relationships within Scarabaeidae combined with other published beetle mitogenome sequences. The complete mitogenomes of Dicronocephalus adamsi Pascoe (Cetoniinae) and Amphimallon sp. (Melolonthinae) are 15,563 bp and 17,433 bp in size, respectively. Both mitogenomes have the typical set of 37 genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) and an A+T-rich region, with the same gene arrangement found in the majority of beetles. The secondary structures for ribosomal RNA genes (rrnL and rrnS) were inferred by comparative analysis method. Results from phylogenetic analyses provide support for major lineages and current classification of Scarabaeidae. Amino acid data recovered Scarabaeidae as monophyletic. The Scarabaeidae was split into two clades. One clade contained the subfamilies Scarabaeinae and Aphodiinae. The other major clade contained the subfamilies Dynastinae, Rutelinae, Cetoniinae, Melolonthinae and Sericini. The monophyly of Scarabaeinae, Aphodiinae, Dynastinae, Cetoniinae and Sericini were strongly supported. The Scarabaeinae was the sister group of Aphodiinae. The Cetoniinae was sister to the Dynastinae + Rutelinae clade. The Melolonthinae was a non-monophyletic group. The removal of fast-evolving sites from nucleotide dataset using a pattern sorting method (OV-sorting) supported the family Scarabaeidae as a monophyletic group. At the tribe level, the Onthophagini was non-monophyletic with respect to Oniticellini. Ateuchini was sister to a large clade comprising the tribes Onthophagini, Oniticellini and Onitini. Eurysternini was a sister group of the Phanaeini + Ateuchini clade.
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Affiliation(s)
- Shibao Guo
- Xinyang Agriculture and Forestry University, Xinyang, Henan, China
- * E-mail: (SG); (NS)
| | - Xingyu Lin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
| | - Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
- * E-mail: (SG); (NS)
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Wu H, Yang JB, Liu JX, Li DZ, Ma PF. Organelle Phylogenomics and Extensive Conflicting Phylogenetic Signals in the Monocot Order Poales. FRONTIERS IN PLANT SCIENCE 2022; 12:824672. [PMID: 35173754 PMCID: PMC8841755 DOI: 10.3389/fpls.2021.824672] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
The Poales is one of the largest orders of flowering plants with significant economic and ecological values. Reconstructing the phylogeny of the Poales is important for understanding its evolutionary history that forms the basis for biological studies. However, due to sparse taxon sampling and limited molecular data, previous studies have resulted in a variety of contradictory topologies. In particular, there are three nodes surrounded by incongruence: the phylogenetic ambiguity near the root of the Poales tree, the sister family of Poaceae, and the delimitation of the xyrid clade. We conducted a comprehensive sampling and reconstructed the phylogenetic tree using plastid and mitochondrial genomic data from 91 to 66 taxa, respectively, representing all the 16 families of Poales. Our analyses support the finding of Bromeliaceae and Typhaceae as the earliest diverging groups within the Poales while having phylogenetic relationships with the polytomy. The clade of Ecdeiocoleaceae and Joinvilleaceae is recovered as the sister group of Poaceae. The three families, Mayacaceae, Eriocaulaceae, and Xyridaceae, of the xyrid assembly diverged successively along the backbone of the Poales phylogeny, and thus this assembly is paraphyletic. Surprisingly, we find substantial phylogenetic conflicts within the plastid genomes of the Poales, as well as among the plastid, mitochondrial, and nuclear data. These conflicts suggest that the Poales could have a complicated evolutionary history, such as rapid radiation and polyploidy, particularly allopolyploidy through hybridization. In sum, our study presents a new perspicacity into the complex phylogenetic relationships and the underlying phylogenetic conflicts within the Poales.
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Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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5
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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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Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
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Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Water lily ( Nymphaea thermarum) genome reveals variable genomic signatures of ancient vascular cambium losses. Proc Natl Acad Sci U S A 2020; 117:8649-8656. [PMID: 32234787 DOI: 10.1073/pnas.1922873117] [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] [Indexed: 12/31/2022] Open
Abstract
For more than 225 million y, all seed plants were woody trees, shrubs, or vines. Shortly after the origin of angiosperms ∼140 million y ago (MYA), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium, the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem, which are produced by apical meristems and retained in nearly all seed plants. Here, we sequenced and assembled a draft genome of the water lily Nymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compared it to genomes from other cambium-bearing and cambium-less lineages (e.g., monocots and Nelumbo). This revealed lineage-specific patterns of gene loss and divergence. Nymphaea is characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss of REVOLUTA, which influences cambial activity in other angiosperms. We also found the Nymphaea and monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids. Nelumbo displays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent loss of vascular cambium reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent events of trait loss. Our results shed light on the evolution of herbaceousness-one of the key biological innovations associated with the earliest phases of angiosperm evolution.
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Goremykin V. A Novel Test for Absolute Fit of Evolutionary Models Provides a Means to Correctly Identify the Substitution Model and the Model Tree. Genome Biol Evol 2020; 11:2403-2419. [PMID: 31368483 PMCID: PMC6736042 DOI: 10.1093/gbe/evz167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2019] [Indexed: 02/07/2023] Open
Abstract
A novel test is described that visualizes the absolute model-data fit of the substitution and tree components of an evolutionary model. The test utilizes statistics based on counts of character state matches and mismatches in alignments of observed and simulated sequences. This comparison is used to assess model-data fit. In simulations conducted to evaluate the performance of the test, the test estimator was able to identify both the correct tree topology and substitution model under conditions where the Goldman-Cox test-which tests the fit of a substitution model to sequence data and is also based on comparing simulated replicates with observed data-showed high error rates. The novel test was found to identify the correct tree topology within a wide range of DNA substitution model misspecifications, indicating the high discriminatory power of the test. Use of this test provides a practical approach for assessing absolute model-data fit when testing phylogenetic hypotheses.
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Affiliation(s)
- Vadim Goremykin
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trentino, Italy
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9
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Tagliacollo VA, Lanfear R. Estimating Improved Partitioning Schemes for Ultraconserved Elements. Mol Biol Evol 2019; 35:1798-1811. [PMID: 29659989 PMCID: PMC5995204 DOI: 10.1093/molbev/msy069] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ultraconserved (UCEs) are popular markers for phylogenomic studies. They are relatively simple to collect from distantly-related organisms, and contain sufficient information to infer relationships at almost all taxonomic levels. Most studies of UCEs use partitioning to account for variation in rates and patterns of molecular evolution among sites, for example by estimating an independent model of molecular evolution for each UCE. However, rates and patterns of molecular evolution vary substantially within as well as between UCEs, suggesting that there may be opportunities to improve how UCEs are partitioned for phylogenetic inference. We propose and evaluate new partitioning methods for phylogenomic studies of UCEs: Sliding-Window Site Characteristics (SWSC), and UCE Site Position (UCESP). The first method uses site characteristics such as entropy, multinomial likelihood, and GC content to generate partitions that account for heterogeneity in rates and patterns of molecular evolution within each UCE. The second method groups together nucleotides that are found in similar physical locations within the UCEs. We examined the new methods with seven published data sets from a variety of taxa. We demonstrate the UCESP method generates partitions that are worse than other strategies used to partition UCE data sets (e.g., one partition per UCE). The SWSC method, particularly when based on site entropies, generates partitions that account for within-UCE heterogeneity and leads to large increases in the model fit. All of the methods, code, and data used in this study, are available from https://github.com/Tagliacollo/PartitionUCE. Simplified code for implementing the best method, the SWSC-EN, is available from https://github.com/Tagliacollo/PFinderUCE-SWSC-EN.
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Affiliation(s)
- Victor A Tagliacollo
- Programa de Pós-graduação Ciências do Ambiente (CIAMB), Universidade Federal do Tocantins, Palmas, Tocantins, Brazil.,Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Robert Lanfear
- Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
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Song N, Zhang H, Zhao T. Insights into the phylogeny of Hemiptera from increased mitogenomic taxon sampling. Mol Phylogenet Evol 2019; 137:236-249. [PMID: 31121308 DOI: 10.1016/j.ympev.2019.05.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
Abstract
Although reconstruction of the phylogeny of Hemiptera has progressed tremendously over the past two decades, some higher-level relationships remain poorly resolved. Here, we investigated the Hemiptera higher-level relationships using full mitochondrial genome data from 357 ingroup species, representing the most comprehensive sampling yet undertaken for reconstructing the phylogeny of this group. In this study, 92 mitochondrial genomes were newly determined. Various data treatment methods and substitution models were applied to tree reconstructions. Effects of compositional heterogeneity, rate heterogeneity, model adequacy and taxon sampling on support values and topological stability were explored. Phylogenetic analyses (1) confirmed the monophyly of Hemiptera under site-heterogeneous model, (2) placed Sternorrhyncha as sister to all other Hemiptera, (3) recovered Coccoidea as the sister taxon of Aphidoidea, followed successively by Aleyrodoidea and Psylloidea, and (4) indicated that the grouping of Coleorrhyncha and Fulgoromorpha was the result of long-branch attraction effect.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
| | - Hao Zhang
- Henan Vocational and Technological College of Communication, Zhengzhou 450015, China
| | - Te Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
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Plastid phylogenomic insights into the evolution of Caryophyllales. Mol Phylogenet Evol 2019; 134:74-86. [DOI: 10.1016/j.ympev.2018.12.023] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 11/22/2022]
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12
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A Shepherd D, Klaere S. How Well Does Your Phylogenetic Model Fit Your Data? Syst Biol 2018; 68:157-167. [DOI: 10.1093/sysbio/syy066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 10/11/2018] [Indexed: 12/27/2022] Open
Affiliation(s)
- Daisy A Shepherd
- Department of Statistics, The University of Auckland, Auckland, New Zealand
| | - Steffen Klaere
- Department of Statistics, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Near TJ, MacGuigan DJ, Parker E, Struthers CD, Jones CD, Dornburg A. Phylogenetic analysis of Antarctic notothenioids illuminates the utility of RADseq for resolving Cenozoic adaptive radiations. Mol Phylogenet Evol 2018; 129:268-279. [PMID: 30195039 DOI: 10.1016/j.ympev.2018.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/31/2018] [Accepted: 09/01/2018] [Indexed: 10/28/2022]
Abstract
Notothenioids are a clade of ∼120 species of marine fishes distributed in extreme southern hemisphere temperate near-shore habitats and in the Southern Ocean surrounding Antarctica. Over the past 25 years, molecular and morphological approaches have redefined hypotheses of relationships among notothenioid lineages as well as their relationships among major lineages of percomorph teleosts. These phylogenies provide a basis for investigation of mechanisms of evolutionary diversification within the clade and have enhanced our understanding of the notothenioid adaptive radiation. Despite extensive efforts, there remain several questions concerning the phylogeny of notothenioids. In this study, we deploy DNA sequences of ∼100,000 loci obtained using RADseq to investigate the phylogenetic relationships of notothenioids and to assess the utility of RADseq loci for lineages that exhibit divergence times ranging from the Paleogene to the Quaternary. The notothenioid phylogenies inferred from the RADseq loci provide unparalleled resolution and node support for several long-standing problems including, (1) relationships among species of Trematomus, (2) resolution of Indonotothenia cyanobrancha as the sister lineage of Trematomus, (3) the deep paraphyly of Nototheniidae, (4) the paraphyly of Lepidonotothen s.l., (5) paraphyly of Artedidraco, and 6) the monophyly of the Bathydraconidae. Assessment of site rates demonstrates that RADseq loci are similar to mtDNA protein coding genes and exhibit peak phylogenetic informativeness at the time interval during which the major Antarctic notothenioid lineages originated and diversified. In addition to providing a well-resolved phylogenetic hypothesis for notothenioids, our analyses quantify the predicted utility of RADseq loci for Cenozoic phylogenetic inferences.
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Affiliation(s)
- Thomas J Near
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA; Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA.
| | - Daniel J MacGuigan
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Elyse Parker
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Christopher D Jones
- Antarctic Ecosystem Research Division, NOAA Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
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Mongiardino Koch N, Gauthier JA. Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata. PLoS One 2018; 13:e0202729. [PMID: 30133514 PMCID: PMC6105018 DOI: 10.1371/journal.pone.0202729] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/08/2018] [Indexed: 12/23/2022] Open
Abstract
Squamate reptiles are a major component of vertebrate biodiversity whose crown-clade traces its origin to a narrow window of time in the Mesozoic during which the main subclades diverged in rapid succession. Deciphering phylogenetic relationships among these lineages has proven challenging given the conflicting signals provided by genomic and phenomic data. Most notably, the placement of Iguania has routinely differed between data sources, with morphological evidence supporting a sister relationship to the remaining squamates (Scleroglossa hypothesis) and molecular data favoring a highly nested position alongside snakes and anguimorphs (Toxicofera hypothesis). We provide novel insights by generating an expanded morphological dataset and exploring the presence of phylogenetic signal, noise, and biases in molecular data. Our analyses confirm the presence of strong conflicting signals for the position of Iguania between morphological and molecular datasets. However, we also find that molecular data behave highly erratically when inferring the deepest branches of the squamate tree, a consequence of limited phylogenetic signal to resolve this ancient radiation with confidence. This, in turn, seems to result from a rate of evolution that is too high for historical signals to survive to the present. Finally, we detect significant systematic biases, with iguanians and snakes sharing faster rates of molecular evolution and a similarly biased nucleotide composition. A combination of scant phylogenetic signal, high levels of noise, and the presence of systematic biases could result in the misplacement of Iguania. We regard this explanation to be at least as plausible as the complex scenario of convergence and reversals required for morphological data to be misleading. We further evaluate and discuss the utility of morphological data to resolve ancient radiations, as well as its impact in combined-evidence phylogenomic analyses, with results relevant for the assessment of evidence and conflict across the Tree of Life.
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
| | - Jacques A. Gauthier
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
- Yale Peabody Museum of Natural History, New Haven, Connecticut, United States of America
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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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16
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Rivera-Rivera CJ, Montoya-Burgos JI. Trunk dental tissue evolved independently from underlying dermal bony plates but is associated with surface bones in living odontode-bearing catfish. Proc Biol Sci 2018; 284:rspb.2017.1831. [PMID: 29046381 PMCID: PMC5666107 DOI: 10.1098/rspb.2017.1831] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/15/2017] [Indexed: 11/30/2022] Open
Abstract
Although oral dental tissue is a vertebrate attribute, trunk dental tissue evolved in several extinct vertebrate lineages but is rare among living species. The question of which processes trigger dental-tissue formation in the trunk remains open, and would shed light on odontogenesis evolution. Extra-oral dental structures (odontodes) in the trunk are associated with underlying dermal bony plates, leading us to ask whether the formation of trunk bony plates is necessary for trunk odontodes to emerge. To address this question, we focus on Loricarioidei: an extant, highly diverse group of catfish whose species all have odontodes. We examined the location and cover of odontodes and trunk dermal bony plates for all six loricarioid families and 17 non-loricarioid catfish families for comparison. We inferred the phylogeny of Loricarioidei using a new 10-gene dataset, eight time-calibration points, and noise-reduction techniques. Based on this phylogeny, we reconstructed the ancestral states of odontode and bony plate cover, and find that trunk odontodes emerged before dermal bony plates in Loricarioidei. Yet we discovered that when bony plates are absent, other surface bones are always associated with odontodes, suggesting a link between osteogenic and odontogenic developmental pathways, and indicating a remarkable trunk odontogenic potential in Loricarioidei.
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Affiliation(s)
- Carlos J Rivera-Rivera
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland .,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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17
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Comprehensive phylogeny of acariform mites (Acariformes) provides insights on the origin of the four-legged mites (Eriophyoidea), a long branch. Mol Phylogenet Evol 2018; 119:105-117. [DOI: 10.1016/j.ympev.2017.10.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 10/13/2017] [Accepted: 10/22/2017] [Indexed: 11/19/2022]
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18
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Abstract
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. The abundance of genomic data for an enormous variety of organisms has enabled phylogenomic inference of many groups, and this has motivated the development of many computer programs implementing the associated methods. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.
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Affiliation(s)
- José S L Patané
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil
| | - Joaquim Martins
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil
| | - João C Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil.
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19
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Song N, Cai W, Li H. Insufficient power of mitogenomic data in resolving the auchenorrhynchan monophyly. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx096] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Jinshui District, Zhengzhou, China
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Haidian District, Beijing, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Haidian District, Beijing, China
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20
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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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21
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Dornburg A, Townsend JP, Wang Z. Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. ADVANCES IN GENETICS 2017; 100:1-47. [PMID: 29153398 DOI: 10.1016/bs.adgen.2017.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.
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Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, United States
| | | | - Zheng Wang
- Yale University, New Haven, CT, United States.
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22
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Zhang SD, Jin JJ, Chen SY, Chase MW, Soltis DE, Li HT, Yang JB, Li DZ, Yi TS. Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics. THE NEW PHYTOLOGIST 2017; 214:1355-1367. [PMID: 28186635 DOI: 10.1111/nph.14461] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/26/2016] [Indexed: 05/18/2023]
Abstract
Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.
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Affiliation(s)
- Shu-Dong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Si-Yun Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Mark W Chase
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611-7800, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32608, USA
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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23
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Qu XJ, Jin JJ, Chaw SM, Li DZ, Yi TS. Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae). Sci Rep 2017; 7:41005. [PMID: 28120880 PMCID: PMC5264392 DOI: 10.1038/srep41005] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 12/12/2016] [Indexed: 11/18/2022] Open
Abstract
Long-branch attraction (LBA) is a major obstacle in phylogenetic reconstruction. The phylogenetic relationships among Juniperus (J), Cupressus (C) and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) subclades of Cupressoideae are controversial. Our initial analyses of plastid protein-coding gene matrix revealed both J and C with much longer stem branches than those of HCX, so their sister relationships may be attributed to LBA. We used multiple measures including data filtering and modifying, evolutionary model selection and coalescent phylogenetic reconstruction to alleviate the LBA artifact. Data filtering by strictly removing unreliable aligned regions and removing substitution saturation genes and rapidly evolving sites could significantly reduce branch lengths of subclades J and C and recovered a relationship of J (C, HCX). In addition, using coalescent phylogenetic reconstruction could elucidate the LBA artifact and recovered J (C, HCX). However, some valid methods for other taxa were inefficient in alleviating the LBA artifact in J-C-HCX. Different strategies should be carefully considered and justified to reduce LBA in phylogenetic reconstruction of different groups. Three subclades of J-C-HCX were estimated to have experienced ancient rapid divergence within a short period, which could be another major obstacle in resolving relationships. Furthermore, our plastid phylogenomic analyses fully resolved the intergeneric relationships of Cupressoideae.
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Affiliation(s)
- Xiao-Jian Qu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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24
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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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25
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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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26
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Rivera-Rivera CJ, Montoya-Burgos JI. LS³: A Method for Improving Phylogenomic Inferences When Evolutionary Rates Are Heterogeneous among Taxa. Mol Biol Evol 2016; 33:1625-34. [PMID: 26912812 PMCID: PMC4868118 DOI: 10.1093/molbev/msw043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Phylogenetic inference artifacts can occur when sequence evolution deviates from assumptions made by the models used to analyze them. The combination of strong model assumption violations and highly heterogeneous lineage evolutionary rates can become problematic in phylogenetic inference, and lead to the well-described long-branch attraction (LBA) artifact. Here, we define an objective criterion for assessing lineage evolutionary rate heterogeneity among predefined lineages: the result of a likelihood ratio test between a model in which the lineages evolve at the same rate (homogeneous model) and a model in which different lineage rates are allowed (heterogeneous model). We implement this criterion in the algorithm Locus Specific Sequence Subsampling (LS³), aimed at reducing the effects of LBA in multi-gene datasets. For each gene, LS³ sequentially removes the fastest-evolving taxon of the ingroup and tests for lineage rate homogeneity until all lineages have uniform evolutionary rates. The sequences excluded from the homogeneously evolving taxon subset are flagged as potentially problematic. The software implementation provides the user with the possibility to remove the flagged sequences for generating a new concatenated alignment. We tested LS³ with simulations and two real datasets containing LBA artifacts: a nucleotide dataset regarding the position of Glires within mammals and an amino-acid dataset concerning the position of nematodes within bilaterians. The initially incorrect phylogenies were corrected in all cases upon removing data flagged by LS³.
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Affiliation(s)
- Carlos J Rivera-Rivera
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
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27
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Song F, Li H, Jiang P, Zhou X, Liu J, Sun C, Vogler AP, Cai W. Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models. Genome Biol Evol 2016; 8:1411-26. [PMID: 27189999 PMCID: PMC4898802 DOI: 10.1093/gbe/evw086] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2016] [Indexed: 12/15/2022] Open
Abstract
After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.
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Affiliation(s)
- Fan Song
- Department of Entomology, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Pei Jiang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington
| | - Jinpeng Liu
- Markey Cancer Center, University of Kentucky, Lexington
| | - Changhai Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Alfried P Vogler
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
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28
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Lewis PO, Chen MH, Kuo L, Lewis LA, Fučíková K, Neupane S, Wang YB, Shi D. Estimating Bayesian Phylogenetic Information Content. Syst Biol 2016; 65:1009-1023. [PMID: 27155008 PMCID: PMC5066063 DOI: 10.1093/sysbio/syw042] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/15/2016] [Accepted: 05/01/2016] [Indexed: 11/13/2022] Open
Abstract
Measuring the phylogenetic information content of data has a long history in systematics. Here we explore a Bayesian approach to information content estimation. The entropy of the posterior distribution compared with the entropy of the prior distribution provides a natural way to measure information content. If the data have no information relevant to ranking tree topologies beyond the information supplied by the prior, the posterior and prior will be identical. Information in data discourages consideration of some hypotheses allowed by the prior, resulting in a posterior distribution that is more concentrated (has lower entropy) than the prior. We focus on measuring information about tree topology using marginal posterior distributions of tree topologies. We show that both the accuracy and the computational efficiency of topological information content estimation improve with use of the conditional clade distribution, which also allows topological information content to be partitioned by clade. We explore two important applications of our method: providing a compelling definition of saturation and detecting conflict among data partitions that can negatively affect analyses of concatenated data. [Bayesian; concatenation; conditional clade distribution; entropy; information; phylogenetics; saturation.].
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Affiliation(s)
- Paul O Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA;
| | - Ming-Hui Chen
- Department of Statistics, University of Connecticut, 215 Glenbrook Road, Unit 4120, Storrs, CT 06269, USA
| | - Lynn Kuo
- Department of Statistics, University of Connecticut, 215 Glenbrook Road, Unit 4120, Storrs, CT 06269, USA
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Karolina Fučíková
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Suman Neupane
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Yu-Bo Wang
- Department of Statistics, University of Connecticut, 215 Glenbrook Road, Unit 4120, Storrs, CT 06269, USA
| | - Daoyuan Shi
- Department of Statistics, University of Connecticut, 215 Glenbrook Road, Unit 4120, Storrs, CT 06269, USA
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29
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Sun L, Fang L, Zhang Z, Chang X, Penny D, Zhong B. Chloroplast Phylogenomic Inference of Green Algae Relationships. Sci Rep 2016; 6:20528. [PMID: 26846729 PMCID: PMC4742797 DOI: 10.1038/srep20528] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/05/2016] [Indexed: 11/10/2022] Open
Abstract
The green algal phylum Chlorophyta has six diverse classes, but the phylogenetic relationship of the classes within Chlorophyta remains uncertain. In order to better understand the ancient Chlorophyta evolution, we have applied a site pattern sorting method to study compositional heterogeneity and the model fit in the green algal chloroplast genomic data. We show that the fastest-evolving sites are significantly correlated with among-site compositional heterogeneity, and these sites have a much poorer fit to the evolutionary model. Our phylogenomic analyses suggest that the class Chlorophyceae is a monophyletic group, and the classes Ulvophyceae, Trebouxiophyceae and Prasinophyceae are non-monophyletic groups. Our proposed phylogenetic tree of Chlorophyta will offer new insights to investigate ancient green algae evolution, and our analytical framework will provide a useful approach for evaluating and mitigating the potential errors of phylogenomic inferences.
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Affiliation(s)
- Linhua Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ling Fang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenhua Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xin Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - David Penny
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Bojian Zhong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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30
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Simmons MP, Sloan DB, Gatesy J. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Mol Phylogenet Evol 2016; 97:76-89. [PMID: 26768112 DOI: 10.1016/j.ympev.2015.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/03/2015] [Accepted: 12/20/2015] [Indexed: 10/22/2022]
Abstract
Gene-tree-estimation error is a major concern for coalescent methods of phylogenetic inference. We sampled eight empirical studies of ancient lineages with diverse numbers of taxa and genes for which the original authors applied one or more coalescent methods. We found that the average pairwise congruence among gene trees varied greatly both between studies and also often within a study. We recommend that presenting plots of pairwise congruence among gene trees in a dataset be treated as a standard practice for empirical coalescent studies so that readers can readily assess the extent and distribution of incongruence among gene trees. ASTRAL-based coalescent analyses generally outperformed MP-EST and STAR with respect to both internal consistency (congruence between analyses of subsamples of genes with the complete dataset of all genes) and congruence with the concatenation-based topology. We evaluated the approach of subsampling gene trees that are, on average, more congruent with other gene trees as a method to reduce artifacts caused by gene-tree-estimation errors on coalescent analyses. We suggest that this method is well suited to testing whether gene-tree-estimation error is a primary cause of incongruence between concatenation- and coalescent-based results, to reconciling conflicting phylogenetic results based on different coalescent methods, and to identifying genes affected by artifacts that may then be targeted for reciprocal illumination. We provide scripts that automate the process of calculating pairwise gene-tree incongruence and subsampling trees while accounting for differential taxon sampling among genes. Finally, we assert that multiple tree-search replicates should be implemented as a standard practice for empirical coalescent studies that apply MP-EST.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA
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31
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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. Mol Phylogenet Evol 2016; 94:447-62. [DOI: 10.1016/j.ympev.2015.10.027] [Citation(s) in RCA: 265] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Song N, Li H, Cai W, Yan F, Wang J, Song F. Phylogenetic relationships of Hemiptera inferred from mitochondrial and nuclear genes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4380-4389. [PMID: 26478175 DOI: 10.3109/19401736.2015.1089538] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Here, we reconstructed the Hemiptera phylogeny based on the expanded mitochondrial protein-coding genes and the nuclear 18S rRNA gene, separately. The differential rates of change across lineages may associate with long-branch attraction (LBA) effect and result in conflicting estimates of phylogeny from different types of data. To reduce the potential effects of systematic biases on inferences of topology, various data coding schemes, site removal method, and different algorithms were utilized in phylogenetic reconstruction. We show that the outgroups Phthiraptera, Thysanoptera, and the ingroup Sternorrhyncha share similar base composition, and exhibit "long branches" relative to other hemipterans. Thus, the long-branch attraction between these groups is suspected to cause the failure of recovering Hemiptera under the homogeneous model. In contrast, a monophyletic Hemiptera is supported when heterogeneous model is utilized in the analysis. Although higher level phylogenetic relationships within Hemiptera remain to be answered, consensus between analyses is beginning to converge on a stable phylogeny.
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Affiliation(s)
- Nan Song
- a College of Plant Protection, Henan Agricultural University , Zhengzhou , People's Republic of China and
| | - Hu Li
- b Department of Entomology , China Agricultural University , Beijing , People's Republic of China
| | - Wanzhi Cai
- b Department of Entomology , China Agricultural University , Beijing , People's Republic of China
| | - Fengming Yan
- a College of Plant Protection, Henan Agricultural University , Zhengzhou , People's Republic of China and
| | - Jianyun Wang
- b Department of Entomology , China Agricultural University , Beijing , People's Republic of China
| | - Fan Song
- b Department of Entomology , China Agricultural University , Beijing , People's Republic of China
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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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Zhong B, Sun L, Penny D. The Origin of Land Plants: A Phylogenomic Perspective. Evol Bioinform Online 2015; 11:137-41. [PMID: 26244002 PMCID: PMC4498653 DOI: 10.4137/ebo.s29089] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/04/2015] [Accepted: 06/08/2015] [Indexed: 11/16/2022] Open
Abstract
Land plants are a natural group, and Charophyte algae are the closest lineages of land plants and have six morphologically diverged groups. The conjugating green algae (Zygnematales) are now suggested to be the extant sister group to land plants, providing the novel understanding for character evolution and early multicellular innovations in land plants. We review recent molecular phylogenetic work on the origin of land plants and discuss some future directions in phylogenomic analyses.
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Affiliation(s)
- Bojian Zhong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Linhua Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - David Penny
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Goremykin VV, Nikiforova SV, Cavalieri D, Pindo M, Lockhart P. The Root of Flowering Plants and Total Evidence. Syst Biol 2015; 64:879-91. [DOI: 10.1093/sysbio/syv028] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
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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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Abstract
The large phylogenetic distance separating eukaryotic genes and their archaeal orthologs has prevented identification of the position of the eukaryotic root in phylogenomic studies. Recently, an innovative approach has been proposed to circumvent this issue: the use as phylogenetic markers of proteins that have been transferred from bacterial donor sources to eukaryotes, after their emergence from Archaea. Using this approach, two recent independent studies have built phylogenomic datasets based on bacterial sequences, leading to different predictions of the eukaryotic root. Taking advantage of additional genome sequences from the jakobid Andalucia godoyi and the two known malawimonad species (Malawimonas jakobiformis and Malawimonas californiana), we reanalyzed these two phylogenomic datasets. We show that both datasets pinpoint the same phylogenetic position of the eukaryotic root that is between "Unikonta" and "Bikonta," with malawimonad and collodictyonid lineages on the Unikonta side of the root. Our results firmly indicate that (i) the supergroup Excavata is not monophyletic and (ii) the last common ancestor of eukaryotes was a biflagellate organism. Based on our results, we propose to rename the two major eukaryotic groups Unikonta and Bikonta as Opimoda and Diphoda, respectively.
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Sun M, Soltis DE, Soltis PS, Zhu X, Burleigh JG, Chen Z. Deep phylogenetic incongruence in the angiosperm clade Rosidae. Mol Phylogenet Evol 2015; 83:156-66. [DOI: 10.1016/j.ympev.2014.11.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 11/01/2014] [Accepted: 11/05/2014] [Indexed: 10/24/2022]
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The phylogenetic utility of acetyltransferase (ARD1) and glutaminyl tRNA synthetase (QtRNA) for reconstructing Cenozoic relationships as exemplified by the large Australian cicada Pauropsalta generic complex. Mol Phylogenet Evol 2015; 83:258-77. [DOI: 10.1016/j.ympev.2014.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 06/25/2014] [Accepted: 07/14/2014] [Indexed: 11/19/2022]
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Meiklejohn KA, Danielson MJ, Faircloth BC, Glenn TC, Braun EL, Kimball RT. Incongruence among different mitochondrial regions: A case study using complete mitogenomes. Mol Phylogenet Evol 2014; 78:314-23. [DOI: 10.1016/j.ympev.2014.06.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/31/2014] [Accepted: 06/02/2014] [Indexed: 01/22/2023]
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41
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Cooper ED. Overly simplistic substitution models obscure green plant phylogeny. TRENDS IN PLANT SCIENCE 2014; 19:576-582. [PMID: 25023343 DOI: 10.1016/j.tplants.2014.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/25/2014] [Accepted: 06/05/2014] [Indexed: 06/03/2023]
Abstract
Phylogenetic analysis is an increasingly common and valuable component of plant science. Knowledge of the phylogenetic relationships between plant groups is a prerequisite for understanding the origin and evolution of important plant features, and phylogenetic analysis of individual genes and gene families provides fundamental insights into how those genes and their functions evolved. However, despite an active research community exploring and improving phylogenetic methods, the analytical methods commonly used, and the phylogenetic results they produce, are accorded far more confidence than they warrant. In this opinion article, I emphasise that important parts of the green plant phylogeny are inconsistently resolved and I argue that the lack of consistency arises due to inadequate modelling of changes in the substitution process.
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Affiliation(s)
- Endymion D Cooper
- CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA.
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Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae. Mol Phylogenet Evol 2014; 80:169-85. [PMID: 25109653 DOI: 10.1016/j.ympev.2014.07.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 07/18/2014] [Accepted: 07/21/2014] [Indexed: 11/21/2022]
Abstract
Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 taxa of Apocynaceae, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira-Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia+the Asian clade, Baisseeae+milkweeds, and Periplocoideae+the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the basis for study of convergent floral morphologies and their adaptive value.
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Xi Z, Liu L, Rest JS, Davis CC. Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies. Syst Biol 2014; 63:919-32. [DOI: 10.1093/sysbio/syu055] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; 2Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; 3Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Liang Liu
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; 2Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; 3Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Joshua S. Rest
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; 2Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; 3Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; 2Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; 3Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
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44
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Liu Y, Cox CJ, Wang W, Goffinet B. Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias. Syst Biol 2014; 63:862-78. [PMID: 25070972 DOI: 10.1093/sysbio/syu049] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea for resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here, we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum-likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino acid data provide implicit support for their respective optimal topologies, and clearly reject the hypotheses that bryophytes are monophyletic, liverworts and mosses share a unique common ancestor, or hornworts are sister to the remaining land plants. We determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a nonstationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoid the effects of synonymous substitutions that underlie codon-usage bias, again recovered liverworts being sister to the remaining land plants but without support. These analyses indicate that the inference of an early-branching moss lineage based on the nucleotide data is caused by convergent compositional biases. Accommodating among-site amino acid compositional heterogeneity (CAT-model) yields no support for the optimal resolution of liverwort as sister to the rest of land plants, suggesting that the robust inference of the liverwort position in homogeneous analyses may be due in part to compositional biases among sites. All analyses support a paraphyletic bryophytes with hornworts composing the sister-group to tracheophytes. We conclude that while genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein-coding gene data and their amino acid translations by evaluating the impact of substitutional saturation, synonymous substitutions, and compositional biases through data deletion strategies and by analyzing the data using heterogeneous composition models. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even when analyzing large-scale data sets, no matter how well-supported, without fully exploring the effects of substitution models.
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Affiliation(s)
- Yang Liu
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Cymon J Cox
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wei Wang
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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45
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Wofford AM, Finch K, Bigott A, Willyard A. A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae). APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1400002. [PMID: 25202625 PMCID: PMC4103111 DOI: 10.3732/apps.1400002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/27/2014] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Recently released Pinus plastome sequences support characterization of 15 plastid simple sequence repeat (cpSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. • METHODS Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compared interspecific variation between cpSSRs and nucleotide sequences of ycf1 and tested intraspecific variation for cpSSRs using 911 samples in the P. ponderosa species complex. • RESULTS The cpSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions, and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. • DISCUSSION The protocol allows efficient genotyping of many samples. The cpSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for cpSSR loci in a plastome alignment for the target group.
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Affiliation(s)
- Austin M. Wofford
- Department of Biology, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032 USA
| | - Kristen Finch
- Department of Biology, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032 USA
| | - Adam Bigott
- Department of Biology, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032 USA
| | - Ann Willyard
- Department of Biology, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032 USA
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46
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Zhong B, Fong R, Collins LJ, McLenachan PA, Penny D. Two new fern chloroplasts and decelerated evolution linked to the long generation time in tree ferns. Genome Biol Evol 2014; 6:1166-73. [PMID: 24787621 PMCID: PMC4040995 DOI: 10.1093/gbe/evu087] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We report the chloroplast genomes of a tree fern (Dicksonia squarrosa) and a "fern ally" (Tmesipteris elongata), and show that the phylogeny of early land plants is basically as expected, and the estimates of divergence time are largely unaffected after removing the fastest evolving sites. The tree fern shows the major reduction in the rate of evolution, and there has been a major slowdown in the rate of mutation in both families of tree ferns. We suggest that this is related to a generation time effect; if there is a long time period between generations, then this is probably incompatible with a high mutation rate because otherwise nearly every propagule would probably have several lethal mutations. This effect will be especially strong in organisms that have large numbers of cell divisions between generations. This shows the necessity of going beyond phylogeny and integrating its study with other properties of organisms.
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Affiliation(s)
- Bojian Zhong
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Richard Fong
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Lesley J Collins
- Faculty of Health Sciences, Universal College of Learning, Palmerston North, New Zealand
| | | | - David Penny
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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47
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Drew BT, Ruhfel BR, Smith SA, Moore MJ, Briggs BG, Gitzendanner MA, Soltis PS, Soltis DE. Another Look at the Root of the Angiosperms Reveals a Familiar Tale. Syst Biol 2014; 63:368-82. [DOI: 10.1093/sysbio/syt108] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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48
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Lemmon EM, Lemmon AR. High-Throughput Genomic Data in Systematics and Phylogenetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135822] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, Florida 32306;
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, Florida 32306;
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Xi Z, Rest JS, Davis CC. Phylogenomics and coalescent analyses resolve extant seed plant relationships. PLoS One 2013; 8:e80870. [PMID: 24278335 PMCID: PMC3836751 DOI: 10.1371/journal.pone.0080870] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 10/15/2013] [Indexed: 12/29/2022] Open
Abstract
The extant seed plants include more than 260,000 species that belong to five main lineages: angiosperms, conifers, cycads, Ginkgo, and gnetophytes. Despite tremendous effort using molecular data, phylogenetic relationships among these five lineages remain uncertain. Here, we provide the first broad coalescent-based species tree estimation of seed plants using genome-scale nuclear and plastid data By incorporating 305 nuclear genes and 47 plastid genes from 14 species, we identify that i) extant gymnosperms (i.e., conifers, cycads, Ginkgo, and gnetophytes) are monophyletic, ii) gnetophytes exhibit discordant placements within conifers between their nuclear and plastid genomes, and iii) cycads plus Ginkgo form a clade that is sister to all remaining extant gymnosperms. We additionally observe that the placement of Ginkgo inferred from coalescent analyses is congruent across different nucleotide rate partitions. In contrast, the standard concatenation method produces strongly supported, but incongruent placements of Ginkgo between slow- and fast-evolving sites. Specifically, fast-evolving sites yield relationships in conflict with coalescent analyses. We hypothesize that this incongruence may be related to the way in which concatenation methods treat sites with elevated nucleotide substitution rates. More empirical and simulation investigations are needed to understand this potential weakness of concatenation methods.
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Affiliation(s)
- Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Joshua S. Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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50
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Zhong B, Xi Z, Goremykin VV, Fong R, Mclenachan PA, Novis PM, Davis CC, Penny D. Streptophyte Algae and the Origin of Land Plants Revisited Using Heterogeneous Models with Three New Algal Chloroplast Genomes. Mol Biol Evol 2013; 31:177-83. [DOI: 10.1093/molbev/mst200] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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