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Zou Y, Zhang Z, Zeng Y, Hu H, Hao Y, Huang S, Li B. Common Methods for Phylogenetic Tree Construction and Their Implementation in R. Bioengineering (Basel) 2024; 11:480. [PMID: 38790347 PMCID: PMC11117635 DOI: 10.3390/bioengineering11050480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing phylogenetic trees, including distance methods, maximum parsimony, maximum likelihood, Bayesian inference, and tree-integration methods (supermatrix and supertree). Here we discuss the advantages, shortcomings, and applications of each method and offer relevant codes to construct phylogenetic trees from molecular data using packages and algorithms in R. This review aims to provide comprehensive guidance and reference for researchers seeking to construct phylogenetic trees while also promoting further development and innovation in this field. By offering a clear and concise overview of the different methods available, we hope to enable researchers to select the most appropriate approach for their specific research questions and datasets.
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Affiliation(s)
- Yue Zou
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Zixuan Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Yujie Zeng
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Hanyue Hu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Sheng Huang
- Animal Nutrition Institute, Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
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Yazaki E, Yabuki A, Imaizumi A, Kume K, Hashimoto T, Inagaki Y. The closest lineage of Archaeplastida is revealed by phylogenomics analyses that include Microheliella maris. Open Biol 2022; 12:210376. [PMID: 35414259 PMCID: PMC9006020 DOI: 10.1098/rsob.210376] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
By clarifying the phylogenetic positions of 'orphan' protists (unicellular micro-eukaryotes with no affinity to extant lineages), we may uncover the novel affiliation between two (or more) major lineages in eukaryotes. Microheliella maris was an orphan protist, which failed to be placed within the previously described lineages by pioneering phylogenetic analyses. In this study, we analysed a 319-gene alignment and demonstrated that M. maris represents a basal lineage of one of the major eukaryotic lineages, Cryptista. We here propose a new clade name 'Pancryptista' for Cryptista plus M. maris. The 319-gene analyses also indicated that M. maris is a key taxon to recover the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista, which is collectively called 'CAM clade' here. Significantly, Cryptophyceae tend to be attracted to Rhodophyta depending on the taxon sampling (ex., in the absence of M. maris and Rhodelphidia) and the particular phylogenetic 'signal' most likely hindered the stable recovery of the monophyly of Archaeplastida in previous studies.
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Affiliation(s)
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
| | - Ayaka Imaizumi
- College of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Keitaro Kume
- Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Tetsuo Hashimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan,Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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3
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Yazaki E, Kume K, Shiratori T, Eglit Y, Tanifuji G, Harada R, Simpson AGB, Ishida KI, Hashimoto T, Inagaki Y. Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP. Proc Biol Sci 2020; 287:20201538. [PMID: 32873198 PMCID: PMC7542792 DOI: 10.1098/rspb.2020.1538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. Barthelona spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one Barthelona strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. We here propose that strain PAP020 is incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected a putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.
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Affiliation(s)
- Euki Yazaki
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Wako, Saitama, Japan
| | - Keitaro Kume
- Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takashi Shiratori
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yana Eglit
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Ibaraki, Japan
| | - Ryo Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ken-Ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tetsuo Hashimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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4
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Brown MW, Heiss AA, Kamikawa R, Inagaki Y, Yabuki A, Tice AK, Shiratori T, Ishida KI, Hashimoto T, Simpson AGB, Roger AJ. Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group. Genome Biol Evol 2018; 10:427-433. [PMID: 29360967 PMCID: PMC5793813 DOI: 10.1093/gbe/evy014] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2018] [Indexed: 01/13/2023] Open
Abstract
Recent phylogenetic analyses position certain “orphan” protist lineages deep in the tree of eukaryotic life, but their exact placements are poorly resolved. We conducted phylogenomic analyses that incorporate deeply sequenced transcriptomes from representatives of collodictyonids (diphylleids), rigifilids, Mantamonas, and ancyromonads (planomonads). Analyses of 351 genes, using site-heterogeneous mixture models, strongly support a novel super-group-level clade that includes collodictyonids, rigifilids, and Mantamonas, which we name “CRuMs”. Further, they robustly place CRuMs as the closest branch to Amorphea (including animals and fungi). Ancyromonads are strongly inferred to be more distantly related to Amorphea than are CRuMs. They emerge either as sister to malawimonads, or as a separate deeper branch. CRuMs and ancyromonads represent two distinct major groups that branch deeply on the lineage that includes animals, near the most commonly inferred root of the eukaryote tree. This makes both groups crucial in examinations of the deepest-level history of extant eukaryotes.
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Affiliation(s)
- Matthew W Brown
- Department of Biological Sciences, Mississippi State University, USA.,Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, USA
| | - Aaron A Heiss
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Graduate School of Global Environmental Studies, Kyoto University, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan.,Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, USA.,Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, USA
| | - Takashi Shiratori
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Ken-Ichiro Ishida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan.,Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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5
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Stadnichuk IN, Tropin IV. Antenna replacement in the evolutionary origin of chloroplasts. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714030163] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Misof B, Meyer B, von Reumont BM, Kück P, Misof K, Meusemann K. Selecting informative subsets of sparse supermatrices increases the chance to find correct trees. BMC Bioinformatics 2013; 14:348. [PMID: 24299043 PMCID: PMC3890606 DOI: 10.1186/1471-2105-14-348] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 09/17/2013] [Indexed: 11/12/2022] Open
Abstract
Background Character matrices with extensive missing data are frequently used in phylogenomics with potentially detrimental effects on the accuracy and robustness of tree inference. Therefore, many investigators select taxa and genes with high data coverage. Drawbacks of these selections are their exclusive reliance on data coverage without consideration of actual signal in the data which might, thus, not deliver optimal data matrices in terms of potential phylogenetic signal. In order to circumvent this problem, we have developed a heuristics implemented in a software called mare which (1) assesses information content of genes in supermatrices using a measure of potential signal combined with data coverage and (2) reduces supermatrices with a simple hill climbing procedure to submatrices with high total information content. We conducted simulation studies using matrices of 50 taxa × 50 genes with heterogeneous phylogenetic signal among genes and data coverage between 10–30%. Results With matrices of 50 taxa × 50 genes with heterogeneous phylogenetic signal among genes and data coverage between 10–30% Maximum Likelihood (ML) tree reconstructions failed to recover correct trees. A selection of a data subset with the herein proposed approach increased the chance to recover correct partial trees more than 10-fold. The selection of data subsets with the herein proposed simple hill climbing procedure performed well either considering the information content or just a simple presence/absence information of genes. We also applied our approach on an empirical data set, addressing questions of vertebrate systematics. With this empirical dataset selecting a data subset with high information content and supporting a tree with high average boostrap support was most successful if information content of genes was considered. Conclusions Our analyses of simulated and empirical data demonstrate that sparse supermatrices can be reduced on a formal basis outperforming the usually used simple selections of taxa and genes with high data coverage.
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Affiliation(s)
- Bernhard Misof
- , Zoologisches Forschungsmuseum Alexander Koenig, zmb, Adenauerallee 160, 53113 Bonn, Germany.
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Coelho SM, Simon N, Ahmed S, Cock JM, Partensky F. Ecological and evolutionary genomics of marine photosynthetic organisms. Mol Ecol 2012; 22:867-907. [PMID: 22989289 DOI: 10.1111/mec.12000] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/10/2012] [Accepted: 07/15/2012] [Indexed: 01/05/2023]
Abstract
Environmental (ecological) genomics aims to understand the genetic basis of relationships between organisms and their abiotic and biotic environments. It is a rapidly progressing field of research largely due to recent advances in the speed and volume of genomic data being produced by next generation sequencing (NGS) technologies. Building on information generated by NGS-based approaches, functional genomic methodologies are being applied to identify and characterize genes and gene systems of both environmental and evolutionary relevance. Marine photosynthetic organisms (MPOs) were poorly represented amongst the early genomic models, but this situation is changing rapidly. Here we provide an overview of the recent advances in the application of ecological genomic approaches to both prokaryotic and eukaryotic MPOs. We describe how these approaches are being used to explore the biology and ecology of marine cyanobacteria and algae, particularly with regard to their functions in a broad range of marine ecosystems. Specifically, we review the ecological and evolutionary insights gained from whole genome and transcriptome sequencing projects applied to MPOs and illustrate how their genomes are yielding information on the specific features of these organisms.
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Affiliation(s)
- Susana M Coelho
- UPMC-Université Paris 06, Station Biologique de Roscoff, Roscoff, France.
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8
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Wu CS, Wang YN, Hsu CY, Lin CP, Chaw SM. Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny. Genome Biol Evol 2011; 3:1284-95. [PMID: 21933779 PMCID: PMC3219958 DOI: 10.1093/gbe/evr095] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2011] [Indexed: 12/13/2022] Open
Abstract
The relationships among the extant five gymnosperm groups--gnetophytes, Pinaceae, non-Pinaceae conifers (cupressophytes), Ginkgo, and cycads--remain equivocal. To clarify this issue, we sequenced the chloroplast genomes (cpDNAs) from two cupressophytes, Cephalotaxus wilsoniana and Taiwania cryptomerioides, and 53 common chloroplast protein-coding genes from another three cupressophytes, Agathis dammara, Nageia nagi, and Sciadopitys verticillata, and a non-Cycadaceae cycad, Bowenia serrulata. Comparative analyses of 11 conifer cpDNAs revealed that Pinaceae and cupressophytes each lost a different copy of inverted repeats (IRs), which contrasts with the view that the same IR has been lost in all conifers. Based on our structural finding, the character of an IR loss no longer conflicts with the "gnepines" hypothesis (gnetophytes sister to Pinaceae). Chloroplast phylogenomic analyses of amino acid sequences recovered incongruent topologies using different tree-building methods; however, we demonstrated that high heterotachous genes (genes that have highly different rates in different lineages) contributed to the long-branch attraction (LBA) artifact, resulting in incongruence of phylogenomic estimates. Additionally, amino acid compositions appear more heterogeneous in high than low heterotachous genes among the five gymnosperm groups. Removal of high heterotachous genes alleviated the LBA artifact and yielded congruent and robust tree topologies in which gnetophytes and Pinaceae formed a sister clade to cupressophytes (the gnepines hypothesis) and Ginkgo clustered with cycads. Adding more cupressophyte taxa could not improve the accuracy of chloroplast phylogenomics for the five gymnosperm groups. In contrast, removal of high heterotachous genes from data sets is simple and can increase confidence in evaluating the phylogeny of gymnosperms.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ya-Nan Wang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Chi-Yao Hsu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ching-Ping Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Regier JC, Zwick A. Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of arthropods. PLoS One 2011; 6:e23408. [PMID: 21829732 PMCID: PMC3150433 DOI: 10.1371/journal.pone.0023408] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 07/15/2011] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND This study aims to investigate the strength of various sources of phylogenetic information that led to recent seemingly robust conclusions about higher-level arthropod phylogeny and to assess the role of excluding or downweighting synonymous change for arriving at those conclusions. METHODOLOGY/PRINCIPAL FINDINGS The current study analyzes DNA sequences from 68 gene segments of 62 distinct protein-coding nuclear genes for 80 species. Gene segments analyzed individually support numerous nodes recovered in combined-gene analyses, but few of the higher-level nodes of greatest current interest. However, neither is there support for conflicting alternatives to these higher-level nodes. Gene segments with higher rates of nonsynonymous change tend to be more informative overall, but those with lower rates tend to provide stronger support for deeper nodes. Higher-level nodes with bootstrap values in the 80% - 99% range for the complete data matrix are markedly more sensitive to substantial drops in their bootstrap percentages after character subsampling than those with 100% bootstrap, suggesting that these nodes are likely not to have been strongly supported with many fewer data than in the full matrix. Data set partitioning of total data by (mostly) synonymous and (mostly) nonsynonymous change improves overall node support, but the result remains much inferior to analysis of (unpartitioned) nonsynonymous change alone. Clusters of genes with similar nonsynonymous rate properties (e.g., faster vs. slower) show some distinct patterns of node support but few conflicts. Synonymous change is shown to contribute little, if any, phylogenetic signal to the support of higher-level nodes, but it does contribute nonphylogenetic signal, probably through its underlying heterogeneous nucleotide composition. Analysis of seemingly conservative indels does not prove useful. CONCLUSIONS Generating a robust molecular higher-level phylogeny of Arthropoda is currently possible with large amounts of data and an exclusive reliance on nonsynonymous change.
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Affiliation(s)
- Jerome C. Regier
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland, United States of America
| | - Andreas Zwick
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland, United States of America
- Entomology, State Museum of Natural History, Stuttgart, Germany
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10
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Dorrell RG, Smith AG. Do red and green make brown?: perspectives on plastid acquisitions within chromalveolates. EUKARYOTIC CELL 2011; 10:856-68. [PMID: 21622904 PMCID: PMC3147421 DOI: 10.1128/ec.00326-10] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The chromalveolate "supergroup" is of key interest in contemporary phycology, as it contains the overwhelming majority of extant algal species, including several phyla of key importance to oceanic net primary productivity such as diatoms, kelps, and dinoflagellates. There is also intense current interest in the exploitation of these algae for industrial purposes, such as biodiesel production. However, the evolution of the constituent species, and in particular the origin and radiation of the chloroplast genomes, remains poorly understood. In this review, we discuss current theories of the origins of the extant red alga-derived chloroplast lineages in the chromalveolates and the potential ramifications of the recent discovery of large numbers of green algal genes in chromalveolate genomes. We consider that the best explanation for this is that chromalveolates historically possessed a cryptic green algal endosymbiont that was subsequently replaced by a red algal chloroplast. We consider how changing selective pressures acting on ancient chromalveolate lineages may have selectively favored the serial endosymbioses of green and red algae and whether a complex endosymbiotic history facilitated the rise of chromalveolates to their current position of ecological prominence.
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Affiliation(s)
- Richard G Dorrell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom.
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11
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Maruyama S, Suzaki T, Weber APM, Archibald JM, Nozaki H. Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids. BMC Evol Biol 2011; 11:105. [PMID: 21501489 PMCID: PMC3101172 DOI: 10.1186/1471-2148-11-105] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 04/18/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Euglenophytes are a group of photosynthetic flagellates possessing a plastid derived from a green algal endosymbiont, which was incorporated into an ancestral host cell via secondary endosymbiosis. However, the impact of endosymbiosis on the euglenophyte nuclear genome is not fully understood due to its complex nature as a 'hybrid' of a non-photosynthetic host cell and a secondary endosymbiont. RESULTS We analyzed an EST dataset of the model euglenophyte Euglena gracilis using a gene mining program designed to detect laterally transferred genes. We found E. gracilis genes showing affinity not only with green algae, from which the secondary plastid in euglenophytes evolved, but also red algae and/or secondary algae containing red algal-derived plastids. Phylogenetic analyses of these 'red lineage' genes suggest that E. gracilis acquired at least 14 genes via eukaryote-to-eukaryote lateral gene transfer from algal sources other than the green algal endosymbiont that gave rise to its current plastid. We constructed an EST library of the aplastidic euglenid Peranema trichophorum, which is a eukaryovorous relative of euglenophytes, and also identified 'red lineage' genes in its genome. CONCLUSIONS Our data show genome mosaicism in E. gracilis and P. trichophorum. One possible explanation for the presence of these genes in these organisms is that some or all of them were independently acquired by lateral gene transfer and contributed to the successful integration and functioning of the green algal endosymbiont as a secondary plastid. Alternative hypotheses include the presence of a phagocytosed alga as the single source of those genes, or a cryptic tertiary endosymbiont harboring secondary plastid of red algal origin, which the eukaryovorous ancestor of euglenophytes had acquired prior to the secondary endosymbiosis of a green alga.
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Affiliation(s)
- Shinichiro Maruyama
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo, Japan.
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12
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Green BR. After the primary endosymbiosis: an update on the chromalveolate hypothesis and the origins of algae with Chl c. PHOTOSYNTHESIS RESEARCH 2011; 107:103-15. [PMID: 20676772 DOI: 10.1007/s11120-010-9584-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 07/07/2010] [Indexed: 05/24/2023]
Abstract
The chromalveolate hypothesis proposed by Cavalier-Smith (J Euk Microbiol 46:347-366, 1999) suggested that all the algae with chlorophyll c (heterokonts, haptophytes, cryptophytes, and dinoflagellates), as well as the ciliates, apicomplexans, oomycetes, and other non-photosynthetic relatives, shared a common ancestor that acquired a chloroplast by secondary endosymbiosis of a red alga. Much of the evidence from plastid and nuclear genomes supports a red algal origin for plastids of the photosynthetic lineages, but the number of secondary endosymbioses and the number of plastid losses have not been resolved. The issue is complicated by the fact that nuclear genomes are mosaics of genes acquired over a very long time period, not only by vertical descent but also by endosymbiotic and horizontal gene transfer. Phylogenomic analysis of the available whole-genome data has suggested major alterations to our view of eukaryotic evolution, and given rise to alternative models. The next few years may see even more changes once a more representative collection of sequenced genomes becomes available.
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Affiliation(s)
- Beverley R Green
- Botany Department, University of British Columbia, Vancouver, B.C, V6T 1Z4, Canada.
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Abstract
The integrated functioning of two photosystems (I and II) whether in cyanobacteria or in chloroplasts is the outstanding sign of a common ancestral origin. Many variations on the basic theme are currently evident in oxygenic photosynthetic organisms whether they are prokaryotes, unicellular, or multicellular. By conservative estimates, oxygenic photosynthesis has been around for at least ca. 2.2-2.7 billions years, consistent with cyanobacteria-type microfossils, biomarkers, and an atmospheric rise in oxygen to less than 1.0% of the present concentration. The presumptions of chloroplast formation by the cyanobacterial uptake into a eukaryote prior to 1.6 BYa ago are confounded by assumptions of host type(s) and potential tolerance of oxygen toxicity. The attempted dating and interrelationships of particular chloroplasts in various plant or animal lineages has relied heavily on phylogenomic analysis and evaluations that have been difficult to confirm separately. Many variations occur in algal groups, involving the type and number of accessory pigments, and the number(s) of membranes (2-4) enclosing a chloroplast, which can both help and complicate inferences made about early or late origins of chloroplasts. Integration of updated phylogenomics with physiological and cytological observations remains a special challenge, but could lead to more accurate assumptions of initial and extant endosymbiotic event(s) leading toward stable chloroplast associations.
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Affiliation(s)
- Elisabeth Gantt
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
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14
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Palpitomonas bilix gen. et sp. nov.: A Novel Deep-branching Heterotroph Possibly Related to Archaeplastida or Hacrobia. Protist 2010; 161:523-38. [DOI: 10.1016/j.protis.2010.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 01/31/2010] [Indexed: 11/19/2022]
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15
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del Campo EM, del Hoyo A, Royo C, Casano LM, Alvarez R, Barreno E. A single primer pair gives a specific ortholog amplicon in a wide range of Cyanobacteria and plastid-bearing organisms: applicability in inventory of reference material from collections and phylogenetic analysis. Mol Phylogenet Evol 2010; 57:1323-8. [PMID: 20875864 DOI: 10.1016/j.ympev.2010.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 09/13/2010] [Accepted: 09/17/2010] [Indexed: 10/19/2022]
Abstract
The scarcity of universally applied molecular markers for algae has resulted in the development of multiple, independent and not easily comparable systems. The goal of this work is to increase the number of available molecular markers and to generate easily comparable systems. Thereby, we have designed a primer pair capable of amplifying a broad range of organisms: Cyanobacteria, Chlorophyta, Chlorarachniophyta, Cryptophyta, Euglenida, Glaucophyta, Rhodophyta, Stramenopiles and Streptophyta including plants. This primer pair can amplify a portion of the 23S rRNA gene with sufficient variability to identify reference material form collections across a broad range of taxa and perform phylogenetic studies alongside other available markers.
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Affiliation(s)
- E M del Campo
- Department of Plant Biology, University of Alcalá, 28871-Alcalá de Henares, Madrid, Spain.
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Whelan S, Blackburne BP, Spencer M. Phylogenetic substitution models for detecting heterotachy during plastid evolution. Mol Biol Evol 2010; 28:449-58. [PMID: 20724379 DOI: 10.1093/molbev/msq215] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is widespread evidence of lineage-specific rate variation, known as heterotachy, during protein evolution. Changes in the structural and functional constraints acting on a protein can lead to heterotachy, and it is plausible that such changes, known as covarion shifts, may affect many amino acids at once. Several previous attempts to model heterotachy have used covarion models, where the sequence undergoes covarion drift, whereby each site may switch independently among a set of discrete classes having different substitution rates. However, such independent switching may not capture biologically important events where the selective forces acting on a protein affect many sites at once. We describe a new class of models that allow the rates of substitution and switching to vary among branches of a phylogenetic tree. Such models are better able to handle covarion shifts. We apply these models to a set of genes occurring in nonphotosynthetic bacteria, cyanobacteria, and the plastids of green and red algae. We find that 4/5 genes show evidence of some form of rate switching and that 3/5 genes show evidence that the relative switching rate differs among taxonomic groups. We conclude that covarion shifts may be frequent during the deep evolution of plastid genes and that our methodology may provide a powerful new tool for investigating such shifts in other systems.
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Affiliation(s)
- Simon Whelan
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
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Mitsui H, Arisue N, Sakihama N, Inagaki Y, Horii T, Hasegawa M, Tanabe K, Hashimoto T. Phylogeny of Asian primate malaria parasites inferred from apicoplast genome-encoded genes with special emphasis on the positions of Plasmodium vivax and P. fragile. Gene 2010; 450:32-8. [DOI: 10.1016/j.gene.2009.10.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 08/20/2009] [Accepted: 10/01/2009] [Indexed: 11/25/2022]
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Deschamps P, Moreira D. Signal Conflicts in the Phylogeny of the Primary Photosynthetic Eukaryotes. Mol Biol Evol 2009; 26:2745-53. [DOI: 10.1093/molbev/msp189] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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