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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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Mavrodiev EV, Madorsky A. On Pattern-Cladistic Analyses Based on Complete Plastid Genome Sequences. Acta Biotheor 2023; 71:22. [PMID: 37922001 DOI: 10.1007/s10441-023-09475-5] [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] [Received: 02/18/2023] [Accepted: 10/26/2023] [Indexed: 11/05/2023]
Abstract
The fundamental Hennigian principle, grouping solely on synapomorphy, is seldom used in modern phylogenetics. In the submitted paper, we apply this principle in reanalyzing five datasets comprising 197 complete plastid genomes (plastomes). We focused on the latter because plastome-based DNA sequence data gained dramatic popularity in molecular systematics during the last decade. We show that pattern-cladistic analyses based on complete plastid genome sequences can successfully resolve affinities between plant taxa, simultaneously simplifying both the genomic and analytical frameworks of phylogenetic studies. We developed "Matrix to Newick" (M2N), a program to represent the standard molecular alignment of plastid genomes in the form of trees or relationships directly. Thus, massive plastome-based DNA sequence data can be successfully represented in a relational form rather than as a standard molecular alignment. Application of methods of median supertree construction (the Average Consensus method has been used as an example in this study) or Maximum Parsimony analysis to relational representations of plastome sequence data may help systematist to avoid the complicated assumption-based frameworks of Maximum Likelihood or Bayesian phylogenetics that are most used today in massive plastid sequence data analyses. We also found that significant amounts of pure genomic information that typically accommodate the majority of current plastid phylogenomic studies can be effectively dropped by systematists if they focus on the pattern-cladistics or relational analyses of plastome-based molecular data. The proposed pattern-cladistic approach is a powerful and straightforward heuristic alternative to modern plastome-based phylogenetics.
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Affiliation(s)
- Evgeny V Mavrodiev
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
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Smith SS, Chu D, Qu T, Aggleton JA, Schneider RA. Species-specific sensitivity to TGFβ signaling and changes to the Mmp13 promoter underlie avian jaw development and evolution. eLife 2022; 11:e66005. [PMID: 35666955 PMCID: PMC9246370 DOI: 10.7554/elife.66005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/03/2022] [Indexed: 12/02/2022] Open
Abstract
Precise developmental control of jaw length is critical for survival, but underlying molecular mechanisms remain poorly understood. The jaw skeleton arises from neural crest mesenchyme (NCM), and we previously demonstrated that these progenitor cells express more bone-resorbing enzymes including Matrix metalloproteinase 13 (Mmp13) when they generate shorter jaws in quail embryos versus longer jaws in duck. Moreover, if we inhibit bone resorption or Mmp13, we can increase jaw length. In the current study, we uncover mechanisms establishing species-specific levels of Mmp13 and bone resorption. Quail show greater activation of and sensitivity to transforming growth factor beta (TGFβ) signaling than duck; where intracellular mediators like SMADs and targets like Runt-related transcription factor 2 (Runx2), which bind Mmp13, become elevated. Inhibiting TGFβ signaling decreases bone resorption, and overexpressing Mmp13 in NCM shortens the duck lower jaw. To elucidate the basis for this differential regulation, we examine the Mmp13 promoter. We discover a SMAD-binding element and single nucleotide polymorphisms (SNPs) near a RUNX2-binding element that distinguish quail from duck. Altering the SMAD site and switching the SNPs abolish TGFβ sensitivity in the quail Mmp13 promoter but make the duck promoter responsive. Thus, differential regulation of TGFβ signaling and Mmp13 promoter structure underlie avian jaw development and evolution.
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Affiliation(s)
- Spenser S Smith
- Department of Orthopaedic Surgery, University of California, San FranciscoSan FranciscoUnited States
| | - Daniel Chu
- Department of Orthopaedic Surgery, University of California, San FranciscoSan FranciscoUnited States
| | - Tiange Qu
- Department of Orthopaedic Surgery, University of California, San FranciscoSan FranciscoUnited States
| | - Jessye A Aggleton
- Department of Orthopaedic Surgery, University of California, San FranciscoSan FranciscoUnited States
| | - Richard A Schneider
- Department of Orthopaedic Surgery, University of California, San FranciscoSan FranciscoUnited States
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Synapomorphies Behind Shared Derived Characters: Examples from the Great Apes' Genomic Data. Acta Biotheor 2020; 68:357-365. [PMID: 31583559 DOI: 10.1007/s10441-019-09368-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
Abstract
Phylogenetic systematics (e.g., cladistics) is one of the most important analytical frameworks of modern Biology. It seems to be common knowledge that within phylogenetics, 'groups' must be defined based solely on the synapomorphies or on the "derived" characters that unite two or more taxa in a clade or monophyletic group. Thus, the idea of synapomorphy seems to be of fundamental influence and importance. Here I will show that the most common and straightforward understanding of synapomorphy as a shared derived character is not sufficient and eventually must be rejected in favor of Nelson's relational interpretation of such term. Arguing for this point and using three examples from previously published Apes' genomic matrices, I explicitly demonstrate that the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon, may be successfully recovered by three-taxon statement analysis (3TA) and three-taxon statement average consensus analysis (3TS-ACA) even if all of the evident standard shared derived molecular characters of the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon, have been excluded from the molecular alignments. Neither conventional Maximum Parsimony nor Maximum Likelihood or Bayesian Inference can do this in such situation. Thus, our results show that the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon has appeared, in some way, behind standard shared derived characters: the last ones could be excluded, but the relationship remains the same.
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How to Study Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Systematics Association Special Volumes. Cladistics 2020. [DOI: 10.1017/9781139047678.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Relationship Diagrams. Cladistics 2020. [DOI: 10.1017/9781139047678.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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The Separation of Classification and Phylogenetics. Cladistics 2020. [DOI: 10.1017/9781139047678.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Beyond Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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The Interrelationships of Organisms. Cladistics 2020. [DOI: 10.1017/9781139047678.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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How to Study Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Modern Artificial Methods and Raw Data. Cladistics 2020. [DOI: 10.1017/9781139047678.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Further Myths and More Misunderstandings. Cladistics 2020. [DOI: 10.1017/9781139047678.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Afterword. Cladistics 2020. [DOI: 10.1017/9781139047678.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Systematics: Exposing Myths. Cladistics 2020. [DOI: 10.1017/9781139047678.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Essentialism and Typology. Cladistics 2020. [DOI: 10.1017/9781139047678.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Beyond Classification: How to Study Phylogeny. Cladistics 2020. [DOI: 10.1017/9781139047678.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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How to Study Classification: ‘Total Evidence’ vs. ‘Consensus’, Character Congruence vs. Taxonomic Congruence, Simultaneous Analysis vs. Partitioned Data. Cladistics 2020. [DOI: 10.1017/9781139047678.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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What This Book Is About. Cladistics 2020. [DOI: 10.1017/9781139047678.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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How to Study Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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The Cladistic Programme. Cladistics 2020. [DOI: 10.1017/9781139047678.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Index. Cladistics 2020. [DOI: 10.1017/9781139047678.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Parameters of Classification: Ordo Ab Chao. Cladistics 2020. [DOI: 10.1017/9781139047678.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Monothetic and Polythetic Taxa. Cladistics 2020. [DOI: 10.1017/9781139047678.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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How to Study Classification: Consensus Techniques and General Classifications. Cladistics 2020. [DOI: 10.1017/9781139047678.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Non-taxa or the Absence of –Phyly: Paraphyly and Aphyly. Cladistics 2020. [DOI: 10.1017/9781139047678.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Introduction: Carving Nature at Its Joints, or Why Birds Are Not Dinosaurs and Men Are Not Apes. Cladistics 2020. [DOI: 10.1017/9781139047678.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Preface. Cladistics 2020. [DOI: 10.1017/9781139047678.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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