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Tlou M, Ndou B, Mabona N, Khwathisi A, Ateba C, Madala N, Serepa-Dlamini MH. Next generation sequencing-aided screening, isolation, molecular identification, and antimicrobial potential for bacterial endophytes from the medicinal plant, Elephantorrhiza elephantina. Front Microbiol 2024; 15:1383854. [PMID: 38855763 PMCID: PMC11160484 DOI: 10.3389/fmicb.2024.1383854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/06/2024] [Indexed: 06/11/2024] Open
Abstract
Elephantorrhiza elephantina, a wild plant in southern Africa, is utilized in traditional medicine for various ailments, leading to its endangerment and listing on the Red List of South African Plants. To date, there have been no reports on bacterial endophytes from this plant, their classes of secondary metabolites, and potential medicinal properties. This study presents (i) taxonomic characterization of bacterial endophytes in leaf and root tissues using 16S rRNA, (ii) bacterial isolation, morphological, and phylogenetic characterization, (iii) bacterial growth, metabolite extraction, and LC-MS-based metabolite fingerprinting, and (iv) antimicrobial testing of bacterial crude extracts. Next-generation sequencing yielded 693 and 2,459 DNA read counts for the rhizomes and leaves, respectively, detecting phyla including Proteobacteria, Bacteroidota, Gemmatimonadota, Actinobacteriota, Verrucomicrobiota, Dependentiae, Firmicutes, and Armatimonodata. At the genus level, Novosphingobium, Mesorhizobium, Methylobacterium, and Ralstonia were the most dominant in both leaves and rhizomes. From root tissues, four bacterial isolates were selected, and 16S rRNA-based phylogenetic characterization identified two closely related Pseudomonas sp. (strain BNWU4 and 5), Microbacterium oxydans BNWU2, and Stenotrophomonas maltophilia BNWU1. The ethyl acetate:chloroform (1:1 v/v) organic extract from each isolate exhibited antimicrobial activity against all selected bacterial pathogens. Strain BNWU5 displayed the highest activity, with minimum inhibitory concentrations ranging from 62.5 μg/mL to 250 μg/mL against diarrhoeagenic Escherichia coli, Escherichia coli O157:H7, Salmonella enterica, antibiotic-resistant Vibrio cholerae, Staphylococcus aureus, Bacillus cereus, and Enterococcus durans. LC-MS analysis of the crude extract revealed common antimicrobial metabolites produced by all isolates, including Phenoxomethylpenicilloyl (penicilloyl V), cis-11-Eicosenamide, 3-Hydroxy-3-phenacyloxindole, and 9-Octadecenamide.
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Affiliation(s)
- Matsobane Tlou
- Department of Biochemistry, School of Physical and Chemical Sciences, North-West University, Mmabatho, South Africa
| | - Benedict Ndou
- Department of Biochemistry, School of Physical and Chemical Sciences, North-West University, Mmabatho, South Africa
| | - Nokufa Mabona
- Department of Biochemistry, School of Physical and Chemical Sciences, North-West University, Mmabatho, South Africa
| | - Adivhaho Khwathisi
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Collins Ateba
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, School of Biological Sciences, North-West University, Mmabatho, South Africa
| | - Ntakadzeni Madala
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Mahloro Hope Serepa-Dlamini
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, Johannesburg, South Africa
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2
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Allen A, Magee R, Devaney R, Ardis T, McNally C, McCormick C, Presho E, Doyle M, Ranasinghe P, Johnston P, Kirke R, Harwood R, Farrell D, Kenny K, Smith J, Gordon S, Ford T, Thompson S, Wright L, Jones K, Prodohl P, Skuce R. Whole-Genome sequencing in routine Mycobacterium bovis epidemiology - scoping the potential. Microb Genom 2024; 10:001185. [PMID: 38354031 PMCID: PMC10926703 DOI: 10.1099/mgen.0.001185] [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: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Mycobacterium bovis the main agent of bovine tuberculosis (bTB), presents as a series of spatially-localised micro-epidemics across landscapes. Classical molecular typing methods applied to these micro-epidemics, based on genotyping a few variable loci, have significantly improved our understanding of potential epidemiological links between outbreaks. However, they have limited utility owing to low resolution. Conversely, whole-genome sequencing (WGS) provides the highest resolution data available for molecular epidemiology, producing richer outbreak tracing, insights into phylogeography and epidemic evolutionary history. We illustrate these advantages by focusing on a common single lineage of M. bovis (1.140) from Northern Ireland. Specifically, we investigate the spatial sub-structure of 20 years of herd-level multi locus VNTR analysis (MLVA) surveillance data and WGS data from a down sampled subset of isolates of this MLVA type over the same time frame. We mapped 2108 isolate locations of MLVA type 1.140 over the years 2000-2022. We also mapped the locations of 148 contemporary WGS isolates from this lineage, over a similar geographic range, stratifying by single nucleotide polymorphism (SNP) relatedness cut-offs of 15 SNPs. We determined a putative core range for the 1.140 MLVA type and SNP-defined sequence clusters using a 50 % kernel density estimate, using cattle movement data to inform on likely sources of WGS isolates found outside of core ranges. Finally, we applied Bayesian phylogenetic methods to investigate past population history and reproductive number of the 1.140 M. bovis lineage. We demonstrate that WGS SNP-defined clusters exhibit smaller core ranges than the established MLVA type - facilitating superior disease tracing. We also demonstrate the superior functionality of WGS data in determining how this lineage was disseminated across the landscape, likely via cattle movement and to infer how its effective population size and reproductive number has been in flux since its emergence. These initial findings highlight the potential of WGS data for routine monitoring of bTB outbreaks.
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Affiliation(s)
- Adrian Allen
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Ryan Magee
- Queen’s University Belfast, school of Biological Sciences, UK
| | - Ryan Devaney
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Tara Ardis
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Caitlín McNally
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Carl McCormick
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Eleanor Presho
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Michael Doyle
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Purnika Ranasinghe
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Philip Johnston
- Department of Agriculture, Environment and Rural Affairs for Northern Ireland, Belfast, UK
| | - Raymond Kirke
- Department of Agriculture, Environment and Rural Affairs for Northern Ireland, Belfast, UK
| | - Roland Harwood
- Department of Agriculture, Environment and Rural Affairs for Northern Ireland, Belfast, UK
| | - Damien Farrell
- Central Veterinary Research Laboratory, Kildare, Ireland
- University College Dublin, Dublin, Ireland
| | - Kevin Kenny
- Central Veterinary Research Laboratory, Kildare, Ireland
| | | | | | - Tom Ford
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Suzan Thompson
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Lorraine Wright
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Kerri Jones
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Paulo Prodohl
- Queen’s University Belfast, school of Biological Sciences, UK
| | - Robin Skuce
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
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3
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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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Freyman WA, Johnson MG, Rothfels CJ. homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
| | - Matthew G. Johnson
- Department of Biological Sciences Texas Tech University Lubbock Texas USA
| | - Carl J. Rothfels
- University Herbarium and Department of Integrative Biology University of California Berkeley California USA
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Ray JM, Sánchez-Martínez P, Batista A, Mulcahy DG, Sheehy III CM, Smith EN, Pyron RA, Arteaga A. A new species of Dipsas (Serpentes, Dipsadidae) from central Panama. Zookeys 2023; 1145:131-167. [DOI: 10.3897/zookeys.1145.96616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/03/2023] [Indexed: 02/05/2023] Open
Abstract
A new species of Dipsas Laurenti, 1768, from Central Panama is described based on molecular analyses, hemipenial morphology, and external characters. This is the sixth species of Dipsas to be described for the country; the snake has been suspected to exist since 1977 and has not been thoroughly studied until now. Additionally, morphological comparations including scale counts are done with other species within the genus, and the current geographic distribution of Dipsas temporalis (Werner, 1909), the sister species, is updated. Finally, a key to the species of Dipsas currently known from Middle America is presented.
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Storer JM, Walker JA, Baker JN, Hossain S, Roos C, Wheeler TJ, Batzer MA. Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae. Genes (Basel) 2023; 14:249. [PMID: 36833175 PMCID: PMC9956951 DOI: 10.3390/genes14020249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023] Open
Abstract
The history of Alu retroposons has been choreographed by the systematic accumulation of inherited diagnostic nucleotide substitutions to form discrete subfamilies, each having a distinct nucleotide consensus sequence. The oldest subfamily, AluJ, gave rise to AluS after the split between Strepsirrhini and what would become Catarrhini and Platyrrhini. The AluS lineage gave rise to AluY in catarrhines and to AluTa in platyrrhines. Platyrrhine Alu subfamilies Ta7, Ta10, and Ta15 were assigned names based on a standardized nomenclature. However, with the subsequent intensification of whole genome sequencing (WGS), large scale analyses to characterize Alu subfamilies using the program COSEG identified entire lineages of subfamilies simultaneously. The first platyrrhine genome with WGS, the common marmoset (Callithrix jacchus; [caljac3]), resulted in Alu subfamily names sf0 to sf94 in an arbitrary order. Although easily resolved by alignment of the consensus sequences, this naming convention can become increasingly confusing as more genomes are independently analyzed. In this study, we reported Alu subfamily characterization for the platyrrhine three-family clade of Cebidae, Callithrichidae, and Aotidae. We investigated one species/genome from each recognized family of Callithrichidae and Aotidae and of both subfamilies (Cebinae and Saimiriinae) of the family Cebidae. Furthermore, we constructed a comprehensive network of Alu subfamily evolution within the three-family clade of platyrrhines to provide a working framework for future research. Alu expansion in the three-family clade has been dominated by AluTa15 and its derivatives.
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Affiliation(s)
- Jessica M. Storer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA; (J.M.S.); (J.A.W.)
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA; (J.M.S.); (J.A.W.)
| | - Jasmine N. Baker
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Shifat Hossain
- Department of Pharmacy Practice & Science, University of Arizona, Tucson, AZ 85721, USA; (S.H.); (T.J.W.)
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
| | - Travis J. Wheeler
- Department of Pharmacy Practice & Science, University of Arizona, Tucson, AZ 85721, USA; (S.H.); (T.J.W.)
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA; (J.M.S.); (J.A.W.)
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7
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Zhang C, Bzikadze AV, Safonova Y, Mirarab S. A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods. Front Immunol 2022; 13:1014439. [PMID: 36618367 PMCID: PMC9815712 DOI: 10.3389/fimmu.2022.1014439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Affinity maturation (AM) of B cells through somatic hypermutations (SHMs) enables the immune system to evolve to recognize diverse pathogens. The accumulation of SHMs leads to the formation of clonal lineages of antibody-secreting b cells that have evolved from a common naïve B cell. Advances in high-throughput sequencing have enabled deep scans of B cell receptor repertoires, paving the way for reconstructing clonal trees. However, it is not clear if clonal trees, which capture microevolutionary time scales, can be reconstructed using traditional phylogenetic reconstruction methods with adequate accuracy. In fact, several clonal tree reconstruction methods have been developed to fix supposed shortcomings of phylogenetic methods. Nevertheless, no consensus has been reached regarding the relative accuracy of these methods, partially because evaluation is challenging. Benchmarking the performance of existing methods and developing better methods would both benefit from realistic models of clonal lineage evolution specifically designed for emulating B cell evolution. In this paper, we propose a model for modeling B cell clonal lineage evolution and use this model to benchmark several existing clonal tree reconstruction methods. Our model, designed to be extensible, has several features: by evolving the clonal tree and sequences simultaneously, it allows modeling selective pressure due to changes in affinity binding; it enables scalable simulations of large numbers of cells; it enables several rounds of infection by an evolving pathogen; and, it models building of memory. In addition, we also suggest a set of metrics for comparing clonal trees and measuring their properties. Our results show that while maximum likelihood phylogenetic reconstruction methods can fail to capture key features of clonal tree expansion if applied naively, a simple post-processing of their results, where short branches are contracted, leads to inferences that are better than alternative methods.
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Affiliation(s)
- Chao Zhang
- Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, United States
| | - Andrey V. Bzikadze
- Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, United States
| | - Yana Safonova
- Computer Science and Engineering Department, University of California, San Diego, San Diego, CA, United States
| | - Siavash Mirarab
- Electrical and Computer Engineering Department, University of California, San Diego, San Diego, CA, United States,*Correspondence: Siavash Mirarab,
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8
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Lotterhos KE, Fitzpatrick MC, Blackmon H. Simulation Tests of Methods in Evolution, Ecology, and Systematics: Pitfalls, Progress, and Principles. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2022; 53:113-136. [PMID: 38107485 PMCID: PMC10723108 DOI: 10.1146/annurev-ecolsys-102320-093722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Complex statistical methods are continuously developed across the fields of ecology, evolution, and systematics (EES). These fields, however, lack standardized principles for evaluating methods, which has led to high variability in the rigor with which methods are tested, a lack of clarity regarding their limitations, and the potential for misapplication. In this review, we illustrate the common pitfalls of method evaluations in EES, the advantages of testing methods with simulated data, and best practices for method evaluations. We highlight the difference between method evaluation and validation and review how simulations, when appropriately designed, can refine the domain in which a method can be reliably applied. We also discuss the strengths and limitations of different evaluation metrics. The potential for misapplication of methods would be greatly reduced if funding agencies, reviewers, and journals required principled method evaluation.
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Affiliation(s)
- Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA
| | - Matthew C Fitzpatrick
- Appalachian Lab, University of Maryland Center for Environmental Science, Frostburg, Maryland, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas, USA
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9
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Abstract
Phylogenetic models have long assumed that lineages diverge independently. Processes of diversification that are of interest in biogeography, epidemiology, and genome evolution violate this assumption by affecting multiple evolutionary lineages. To relax the assumption of independent divergences and infer patterns of divergences predicted by such processes, we introduce a way of conceptualizing, modeling, and inferring phylogenetic trees. We apply the approach to genomic data from geckos distributed across the Philippines and find support for patterns of shared divergences predicted by repeated fragmentation of the archipelago by interglacial rises in sea level. Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a “super-spreading” event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands’ landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences.
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Pereira EA, Ceron K, Silva HR, Santana DJ. The dispersal between Amazonia and Atlantic Forest during the Early Neogene revealed by the biogeography of the treefrog tribe Sphaenorhynchini (Anura, Hylidae). Ecol Evol 2022; 12:e8754. [PMID: 35386873 PMCID: PMC8975791 DOI: 10.1002/ece3.8754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Elvis Almeida Pereira
- Laboratório de Herpetologia Departamento de Biologia Animal Universidade Federal Rural do Rio de Janeiro Rio de Janeiro Brazil
- Mapinguari ‐ Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis Universidade Federal de Mato Grosso do Sul Campo Grande Brazil
- Laboratório de Genética e Biodiversidade Universidade Federal do Oeste do Pará Santarém Brazil
| | - Karoline Ceron
- Mapinguari ‐ Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis Universidade Federal de Mato Grosso do Sul Campo Grande Brazil
- Departamento de Biologia Animal Universidade Estadual de Campinas (UNICAMP) São Paulo Brazil
| | - Hélio Ricardo Silva
- Laboratório de Herpetologia Departamento de Biologia Animal Universidade Federal Rural do Rio de Janeiro Rio de Janeiro Brazil
| | - Diego José Santana
- Mapinguari ‐ Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis Universidade Federal de Mato Grosso do Sul Campo Grande Brazil
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11
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Huang J, Liu Y, Zhu T, Yang Z. The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics. Syst Biol 2020; 70:774-785. [PMID: 33377913 DOI: 10.1093/sysbio/syaa100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 11/15/2022] Open
Abstract
The phylogenetic bootstrap is the most commonly used method for assessing statistical confidence in estimated phylogenies by non-Bayesian methods such as maximum parsimony and maximum likelihood (ML). It is observed that bootstrap support tends to be high in large genomic data sets whether or not the inferred trees and clades are correct. Here, we study the asymptotic behavior of bootstrap support for the ML tree in large data sets when the competing phylogenetic trees are equally right or equally wrong. We consider phylogenetic reconstruction as a problem of statistical model selection when the compared models are nonnested and misspecified. The bootstrap is found to have qualitatively different dynamics from Bayesian inference and does not exhibit the polarized behavior of posterior model probabilities, consistent with the empirical observation that the bootstrap is more conservative than Bayesian probabilities. Nevertheless, bootstrap support similarly shows fluctuations among large data sets, with no convergence to a point value, when the compared models are equally right or equally wrong. Thus, in large data sets strong support for wrong trees or models is likely to occur. Our analysis provides a partial explanation for the high bootstrap support values for incorrect clades observed in empirical data analysis. [Bootstrap; model selection; star-tree paradox; support value.].
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Affiliation(s)
- Jun Huang
- Department of Mathematics, Beijing Jiaotong University, Beijing, 100044, China.,Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Yuting Liu
- Department of Mathematics, Beijing Jiaotong University, Beijing, 100044, China
| | - Tianqi Zhu
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures, Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100000, China
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
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12
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Simon C. An Evolving View of Phylogenetic Support. Syst Biol 2020; 71:921-928. [PMID: 32915964 DOI: 10.1093/sysbio/syaa068] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 08/04/2020] [Accepted: 08/15/2020] [Indexed: 01/09/2023] Open
Abstract
If all nucleotide sites evolved at the same rate within molecules and throughout the history of lineages, if all nucleotides were in equal proportion, if any nucleotide or amino acid evolved to any other with equal probability, if all taxa could be sampled, if diversification happened at well-spaced intervals, and if all gene segments had the same history, then tree building would be easy. But of course none of those conditions are true. Hence the need for evaluating the information content and accuracy of phylogenetic trees. The symposium for which this historial essay and presentation were developed focused on the importance of phylogenetic support, specifically branch support for individual clades. Here I present a timeline and review significant events in the history of systematics that set the stage for the development of the sophisticated measures of branch support and examinations of the information content of data highlighted in this symposium.
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Affiliation(s)
- Chris Simon
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Road, University of Connecticut, Storrs, CT
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13
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Zhang C, Dinh VU, Matsen FA. Nonbifurcating Phylogenetic Tree Inference via the Adaptive LASSO. J Am Stat Assoc 2020; 116:858-873. [PMID: 34305211 DOI: 10.1080/01621459.2020.1778481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special features, including sampled ancestors in which we sequence a genotype along with its direct descendants, and polytomies in which multiple descendants arise simultaneously. These features are apparent after identifying zero-length branches in the tree. However, current maximum-likelihood based approaches are not capable of revealing such zero-length branches. In this paper, we find these zero-length branches by introducing adaptive-LASSO-type regularization estimators for the branch lengths of phylogenetic trees, deriving their properties, and showing regularization to be a practically useful approach for phylogenetics.
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Affiliation(s)
- Cheng Zhang
- School of Mathematical Sciences and Center for Statistical Science, Peking University
| | - V U Dinh
- Department of Mathematical Sciences, University of Delaware
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14
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Aguirre-Dugua X, Castellanos-Morales G, Paredes-Torres LM, Hernández-Rosales HS, Barrera-Redondo J, Sánchez-de la Vega G, Tapia-Aguirre F, Ruiz-Mondragón KY, Scheinvar E, Hernández P, Aguirre-Planter E, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Evolutionary Dynamics of Transferred Sequences Between Organellar Genomes in Cucurbita. J Mol Evol 2019; 87:327-342. [PMID: 31701178 DOI: 10.1007/s00239-019-09916-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022]
Abstract
Twenty-nine DNA regions of plastid origin have been previously identified in the mitochondrial genome of Cucurbita pepo (pumpkin; Cucurbitaceae). Four of these regions harbor homolog sequences of rbcL, matK, rpl20-rps12 and trnL-trnF, which are widely used as molecular markers for phylogenetic and phylogeographic studies. We extracted the mitochondrial copies of these regions based on the mitochondrial genome of C. pepo and, along with published sequences for these plastome markers from 13 Cucurbita taxa, we performed phylogenetic molecular analyses to identify inter-organellar transfer events in the Cucurbita phylogeny and changes in their nucleotide substitution rates. Phylogenetic reconstruction and tree selection tests suggest that rpl20 and rbcL mitochondrial paralogs arose before Cucurbita diversification whereas the mitochondrial matK and trnL-trnF paralogs emerged most probably later, in the mesophytic Cucurbita clade. Nucleotide substitution rates increased one order of magnitude in all the mitochondrial paralogs compared to their original plastid sequences. Additionally, mitochondrial trnL-trnF sequences obtained by PCR from nine Cucurbita taxa revealed higher nucleotide diversity in the mitochondrial than in the plastid copies, likely related to the higher nucleotide substitution rates in the mitochondrial region and loss of functional constraints in its tRNA genes.
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Affiliation(s)
- Xitlali Aguirre-Dugua
- Unidad de Biotecnología Y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De Los Barrios 1, Col. Los Reyes Iztacala, 54090, Tlalnepantla, Estado de México, Mexico.
| | - Gabriela Castellanos-Morales
- Departamento de Conservación de La Biodiversidad, El Colegio de La Frontera Sur, Unidad Villahermosa, Carretera Villahermosa-Reforma km. 15.5, Ranchería El Guineo 2a Sección, 86280, Villahermosa, Tabasco, Mexico
| | - Leslie M Paredes-Torres
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Helena S Hernández-Rosales
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Josué Barrera-Redondo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Guillermo Sánchez-de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Fernando Tapia-Aguirre
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Karen Y Ruiz-Mondragón
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Enrique Scheinvar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Paulina Hernández
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas Y Pecuarias (INIFAP), Km 6.5 Carretera Celaya-San Miguel de Allende, 38110, Celaya, Gto., Mexico
| | - Rafael Lira-Saade
- Unidad de Biotecnología Y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De Los Barrios 1, Col. Los Reyes Iztacala, 54090, Tlalnepantla, Estado de México, Mexico.
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico.
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15
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Marin J, Hedges SB. Undersampling Genomes has Biased Time and Rate Estimates Throughout the Tree of Life. Mol Biol Evol 2019; 35:2077-2084. [PMID: 29846659 DOI: 10.1093/molbev/msy103] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Genomic data drive evolutionary research on the relationships and timescale of life but the genomes of most species remain poorly sampled. Phylogenetic trees can be reconstructed reliably using small data sets and the same has been assumed for the estimation of divergence time with molecular clocks. However, we show here that undersampling of molecular data results in a bias expressed as disproportionately shorter branch lengths and underestimated divergence times in the youngest nodes and branches, termed the small sample artifact. In turn, this leads to increasing speciation and diversification rates towards the present. Any evolutionary analyses derived from these biased branch lengths and speciation rates will be similarly biased. The widely used timetrees of the major species-rich studies of amphibians, birds, mammals, and squamate reptiles are all data-poor and show upswings in diversification rate, suggesting that their results were biased by undersampling. Our results show that greater sampling of genomes is needed for accurate time and rate estimation, which are basic data used in ecological and evolutionary research.
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Affiliation(s)
- Julie Marin
- Center for Biodiversity, 502 SERC Building, Temple University, Philadelphia, PA
- Institut de Systématique, Evolution, Biodiversité UMR 7205, Département Systématique et Evolution, Muséum national d'Histoire naturelle, Sorbonne-Universités, Paris Cedex 05 75231, France
| | - S Blair Hedges
- Center for Biodiversity, 502 SERC Building, Temple University, Philadelphia, PA
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16
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DeWitt WS, Mesin L, Victora GD, Minin VN, Matsen FA. Using Genotype Abundance to Improve Phylogenetic Inference. Mol Biol Evol 2019; 35:1253-1265. [PMID: 29474671 PMCID: PMC5913685 DOI: 10.1093/molbev/msy020] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in phylogenetic inference. In this article, we synthesize a stochastic process model with standard sequence-based phylogenetic optimality, and show that tree estimation is substantially improved by doing so. Our method is validated with extensive simulations and an experimental single-cell lineage tracing study of germinal center B cell receptor affinity maturation.
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Affiliation(s)
- William S DeWitt
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA.,Department of Genome Sciences, University of Washington, Seattle, WA
| | - Luka Mesin
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY
| | | | - Frederick A Matsen
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA
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17
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Schrago CG, Seuánez HN. Large ancestral effective population size explains the difficult phylogenetic placement of owl monkeys. Am J Primatol 2019; 81:e22955. [PMID: 30779198 DOI: 10.1002/ajp.22955] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/05/2018] [Accepted: 12/15/2018] [Indexed: 11/07/2022]
Abstract
The phylogenetic position of owl monkeys, grouped in the genus Aotus, has been a controversial issue for understanding Neotropical primate evolution. Explanations of the difficult phylogenetic assignment of owl monkeys have been elusive, frequently relying on insufficient data (stochastic error) or scenarios of rapid speciation (adaptive radiation) events. Using a coalescent-based approach, we explored the population-level mechanisms likely explaining these topological discrepancies. We examined the topological variance of 2,192 orthologous genes shared between representatives of the three major Cebidae lineages and the outgroup. By employing a methodological framework that allows for reticulated tree topologies, our analysis explicitly tested for non-dichotomous evolutionary processes impacting the finding of the position of owl monkeys in the cebid phylogeny. Our findings indicated that Aotus is a sister lineage of the callitrichines. Most gene trees (>50%) failed to recover the species tree topology, although the distribution of gene trees mismatching the true species topology followed the standard expectation of the multispecies coalescent without reticulation. We showed that the large effective population size of the common ancestor of Aotus and callitrichines was the most likely factor responsible for generating phylogenetic uncertainty. On the other hand, fast speciation scenarios or introgression played minor roles. We propose that the difficult phylogenetic placement of Aotus is explained by population-level processes associated with the large ancestral effective size. These results shed light on the biogeography of the early cebid diversification in the Miocene, highlighting the relevance of evaluating phylogenetic relationships employing population-aware approaches.
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Affiliation(s)
- Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Hector N Seuánez
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Division of Genetics, National Cancer Institute, Rio de Janeiro, Brazil
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18
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Schrago CG, Aguiar BO, Mello B. Comparative evaluation of maximum parsimony and Bayesian phylogenetic reconstruction using empirical morphological data. J Evol Biol 2018; 31:1477-1484. [DOI: 10.1111/jeb.13344] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Carlos G. Schrago
- Department of Genetics; Federal University of Rio de Janeiro; Rio de Janeiro Brazil
| | - Barbara O. Aguiar
- Department of Genetics; Federal University of Rio de Janeiro; Rio de Janeiro Brazil
| | - Beatriz Mello
- Department of Genetics; Federal University of Rio de Janeiro; Rio de Janeiro Brazil
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19
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Hurtado LA, Mateos M, Wang C, Santamaria CA, Jung J, Khalaji-Pirbalouty V, Kim W. Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica. PeerJ 2018; 6:e4337. [PMID: 29576934 PMCID: PMC5853605 DOI: 10.7717/peerj.4337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/17/2018] [Indexed: 11/20/2022] Open
Abstract
The native ranges and invasion histories of many marine species remain elusive due to a dynamic dispersal process via marine vessels. Molecular markers can aid in identification of native ranges and elucidation of the introduction and establishment process. The supralittoral isopod Ligia exotica has a wide tropical and subtropical distribution, frequently found in harbors and ports around the globe. This isopod is hypothesized to have an Old World origin, from where it was unintentionally introduced to other regions via wooden ships and solid ballast. Its native range, however, remains uncertain. Recent molecular studies uncovered the presence of two highly divergent lineages of L. exotica in East Asia, and suggest this region is a source of nonindigenous populations. In this study, we conducted phylogenetic analyses (Maximum Likelihood and Bayesian) of a fragment of the mitochondrial 16S ribosomal (r)DNA gene using a dataset of this isopod that greatly expanded previous representation from Asia and putative nonindigenous populations around the world. For a subset of samples, sequences of 12S rDNA and NaK were also obtained and analyzed together with 16S rDNA. Our results show that L. exotica is comprised of several highly divergent genetic lineages, which probably represent different species. Most of the 16S rDNA genetic diversity (48 haplotypes) was detected in East and Southeast Asia. Only seven haplotypes were observed outside this region (in the Americas, Hawai'i, Africa and India), which were identical or closely related to haplotypes found in East and Southeast Asia. Phylogenetic patterns indicate the L. exotica clade originated and diversified in East and Southeast Asia, and only members of one of the divergent lineages have spread out of this region, recently, suggesting the potential to become invasive is phylogenetically constrained.
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Affiliation(s)
- Luis A. Hurtado
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
| | - Chang Wang
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
- Department of Biology, New York University, New York City, NY, United States of America
| | - Carlos A. Santamaria
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
- Biology Faculty, College of Science and Mathematics, University of South Florida, Sarasota, FL, United States of America
| | - Jongwoo Jung
- Department of Science Education, Ewha Women’s University, Seoul, South Korea
| | | | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul, South Korea
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20
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McManus HA, Fučíková K, Lewis PO, Lewis LA, Karol KG. Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal tree of life. AMERICAN JOURNAL OF BOTANY 2018; 105:315-329. [PMID: 29722901 DOI: 10.1002/ajb2.1066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/19/2017] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY Phylogenomic analyses across the green algae are resolving relationships at the class, order, and family levels and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions. METHODS Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired from representatives of the Hydrodictyaceae using next-generation sequencing methods. Plastomes were characterized, and gene order and content were compared with plastomes spanning the Sphaeropleales. Single-gene and concatenated-gene phylogenetic analyses of plastid and mitochondrial genes were performed. KEY RESULTS The Hydrodictyaceae contain the largest sphaeroplealean plastomes thus far fully sequenced. Conservation of plastome gene order within Hydrodictyaceae is striking compared with more dynamic patterns revealed across Sphaeropleales. Phylogenetic analyses resolve Hydrodictyon sister to a monophyletic Pediastrum, though the morphologically distinct P. angulosum and P. duplex continue to be polyphyletic. Analyses of plastid data supported the neochloridacean genus Chlorotetraëdron as sister to Hydrodictyaceae, while conflicting signal was found in the mitochondrial data. CONCLUSIONS A phylogenomic approach resolved within-family relationships not obtainable with previous phylogenetic analyses. Denser taxon sampling across Sphaeropleales is necessary to capture patterns in plastome evolution, and further taxa and studies are needed to fully resolve the sister lineage to Hydrodictyaceae and polyphyly of Pediastrum angulosum and P. duplex.
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Affiliation(s)
- Hilary A McManus
- Department of Biological and Environmental Sciences, Le Moyne College, 1419 Salt Springs Road, Syracuse, New York, 13066, USA
| | - Karolina Fučíková
- Department of Natural Sciences, Assumption College, 500 Salisbury Street, Worcester, Massachusetts, 01609, USA
| | - Paul O Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269, USA
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269, USA
| | - Kenneth G Karol
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, 2900 Southern Boulevard, Bronx, New York, 10458, USA
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21
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Sayyari E, Mirarab S. Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies. Genes (Basel) 2018; 9:E132. [PMID: 29495636 PMCID: PMC5867853 DOI: 10.3390/genes9030132] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/30/2018] [Accepted: 02/16/2018] [Indexed: 12/23/2022] Open
Abstract
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest.
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Affiliation(s)
- Erfan Sayyari
- Department of Electrical and Computer Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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22
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Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees. Proc Natl Acad Sci U S A 2018; 115:1854-1859. [PMID: 29432193 DOI: 10.1073/pnas.1712673115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Bayesian method is noted to produce spuriously high posterior probabilities for phylogenetic trees in analysis of large datasets, but the precise reasons for this overconfidence are unknown. In general, the performance of Bayesian selection of misspecified models is poorly understood, even though this is of great scientific interest since models are never true in real data analysis. Here we characterize the asymptotic behavior of Bayesian model selection and show that when the competing models are equally wrong, Bayesian model selection exhibits surprising and polarized behaviors in large datasets, supporting one model with full force while rejecting the others. If one model is slightly less wrong than the other, the less wrong model will eventually win when the amount of data increases, but the method may become overconfident before it becomes reliable. We suggest that this extreme behavior may be a major factor for the spuriously high posterior probabilities for evolutionary trees. The philosophical implications of our results to the application of Bayesian model selection to evaluate opposing scientific hypotheses are yet to be explored, as are the behaviors of non-Bayesian methods in similar situations.
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23
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Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han KL, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL. Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling. Syst Biol 2018; 66:857-879. [PMID: 28369655 DOI: 10.1093/sysbio/syx041] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/22/2017] [Indexed: 01/27/2023] Open
Abstract
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more "biologically-realistic" models is likely to be critical for efforts to reconstruct the tree of life. [Birds; coding exons; GTR model; model fit; Neoaves; non-coding DNA; phylogenomics; taxon sampling.].
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Affiliation(s)
- Sushma Reddy
- Biology Department, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Akanksha Pandey
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Peter A Hosner
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Florida Museum of Natural History, University of Florida, Gainesville, FL 32607, USA
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution-MRC 163, PO Box 37012, Washington, DC 20013-7012, USA
| | - Shannon J Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | | | - Christopher J Huddleston
- Collections Program, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
| | - Sarah Kingston
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution-MRC 163, PO Box 37012, Washington, DC 20013-7012, USA.,Bowdoin College, Department of Biology and Coastal Studies Center, 6500 College Station, Brunwick, ME 04011, USA
| | - Ben D Marks
- Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Kathleen J Miglia
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - William S Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Christopher C Witt
- Department of Biology and Museum of Southwestern Biology, University 15 of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Genetics Institute, University of Florida, Gainesville, FL 32607, USA
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24
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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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25
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Orlando L, Hänni C, Douady CJ. Mammoth and Elephant Phylogenetic Relationships: Mammut Americanum, the Missing Outgroup. Evol Bioinform Online 2017. [DOI: 10.1177/117693430700300019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
At the morphological level, the woolly mammoth has most often been considered as the sister-species of Asian elephants, but at the DNA level, different studies have found support for proximity with African elephants. Recent reports have increased the available sequence data and apparently solved the discrepancy, finding mammoths to be most closely related to Asian elephants. However, we demonstrate here that the three competing topologies have similar likelihood, bayesian and parsimony supports. The analysis further suggests the inadequacy of using Sirenia or Hyracoidea as outgroups. We therefore argue that orthologous sequences from the extinct American mastodon will be required to definitively solve this long-standing question.
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Affiliation(s)
- Ludovic Orlando
- Paleogenetics and Molecular Evolution; IFR 128, Lyon, F-69007, France; Université Lyon 1, Lyon, F-69007, France; CNRS UMR 5242, INRA, Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, Lyon, F-69364 Cédex 07, France
| | - Catherine Hänni
- Paleogenetics and Molecular Evolution; IFR 128, Lyon, F-69007, France; Université Lyon 1, Lyon, F-69007, France; CNRS UMR 5242, INRA, Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, Lyon, F-69364 Cédex 07, France
| | - Christophe J. Douady
- CNRS UMR 5023, Laboratoire d'Ecologie des Hydrosystèmes Fluviaux, Université Claude Bernard Lyon 1, 6 rue R. Dubois, Bat. Darwin-C, F-69622 Villeurbanne Cédex, France
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26
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Piwczyński M, Pape T, Deja-Sikora E, Sikora M, Akbarzadeh K, Szpila K. Molecular phylogeny of Miltogramminae (Diptera: Sarcophagidae): Implications for classification, systematics and evolution of larval feeding strategies. Mol Phylogenet Evol 2017; 116:49-60. [DOI: 10.1016/j.ympev.2017.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/03/2017] [Accepted: 07/05/2017] [Indexed: 11/15/2022]
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27
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Takezaki N, Nishihara H. Support for Lungfish as the Closest Relative of Tetrapods by Using Slowly Evolving Ray-Finned Fish as the Outgroup. Genome Biol Evol 2017; 9:93-101. [PMID: 28082606 PMCID: PMC5381532 DOI: 10.1093/gbe/evw288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2016] [Indexed: 11/14/2022] Open
Abstract
In a previous analysis of the phylogenetic relationships of coelacanths, lungfishes and tetrapods, using cartilaginous fish (CF) as the outgroup, the sister relationship of lungfishes and tetrapods was constructed with high statistical support. However, using as the outgroup ray-finned fish (RF), which are more taxonomically closely related to the three lineages than CF, the sister relationship of coelacanths and tetrapods was most often constructed depending on the methods and the data sets, but the statistical support was generally low except in the cases in which the data set including a small number of species was analyzed. In this study, instead of the fast evolving ray-finned fish, teleost fish (TF), in the previous data sets, by using two slowly evolving RF, gar and bowfin, as the outgroup, we showed that the sister relationship of lungfishes and tetrapods was reconstructed with high statistical support. In our analysis the evolutionary rates of gar and bowfin were similar to each other and one third to one half of TF. The difference of the amino acid frequencies of the two species with other lineages was larger than those of TF. This study provides a strong support for lungfishes as the closest relative of tetrapods and indicates the importance of using an appropriate outgroup with small divergence in phylogenetic construction.
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Affiliation(s)
- Naoko Takezaki
- Life Science Research Center, Kagawa University, Mikicho, Kitagun, Kagawa, Japan
| | - Hidenori Nishihara
- Department of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa Japan
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Santamaria CA, Bluemel JK, Bunbury N, Curran M. Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods. PeerJ 2017; 5:e3894. [PMID: 29018626 PMCID: PMC5633021 DOI: 10.7717/peerj.3894] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 12/02/2022] Open
Abstract
Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently.
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Affiliation(s)
- Carlos A. Santamaria
- Biology Faculty, College of Science and Mathematics, University of South Florida Sarasota-Manatee, Sarasota, FL, United States of America
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, United States of America
| | - Joanna K. Bluemel
- Marine Conservation Society Seychelles, Mahé, Seychelles
- Lowestoft Laboratory, Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, Suffolk, United Kingdom
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29
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Nascimento FF, Reis MD, Yang Z. A biologist's guide to Bayesian phylogenetic analysis. Nat Ecol Evol 2017; 1:1446-1454. [PMID: 28983516 PMCID: PMC5624502 DOI: 10.1038/s41559-017-0280-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/17/2017] [Indexed: 11/09/2022]
Abstract
Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. Here, we summarize the major features of Bayesian phylogenetic inference and discuss Bayesian computation using Markov chain Monte Carlo (MCMC), the diagnosis of an MCMC run, and ways of summarising the MCMC sample. We discuss the specification of the prior, the choice of the substitution model, and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software and provide recommendations as to their use.
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Affiliation(s)
- Fabrícia F Nascimento
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
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30
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Liu B, Alström P, Olsson U, Fjeldså J, Quan Q, Roselaar KCS, Saitoh T, Yao CT, Hao Y, Wang W, Qu Y, Lei F. Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family. Ecol Evol 2017; 7:6346-6357. [PMID: 28861238 PMCID: PMC5574758 DOI: 10.1002/ece3.3136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/01/2017] [Accepted: 05/10/2017] [Indexed: 01/08/2023] Open
Abstract
Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella was present in the Sino‐Himalayan Mountains or these mountains and Central Asia–Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid‐Pliocene to early Pleistocene. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo‐/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacial periods, followed by fragmentation during interglacials—contrary to the usual view that glacial periods resulted mainly in fragmentations.
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Affiliation(s)
- Baoyan Liu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China.,University of Chinese Academy of Sciences Beijing China
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China.,Department of Animal Ecology Evolutionary Biology Centre Uppsala University Uppsala Sweden.,Swedish Species Information Centre Swedish University of Agricultural Sciences Uppsala Sweden
| | - Urban Olsson
- Systematics and Biodiversity Department of Biology and Environmental Sciences University of Gothenburg Göteborg Sweden
| | - Jon Fjeldså
- Centre for Macroecology, Evolution and Climate Zoological Museum University of Copenhagen Copenhagen Denmark
| | - Qing Quan
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China.,University of Chinese Academy of Sciences Beijing China
| | | | - Takema Saitoh
- Yamashina Institute for Ornithology Abiko Chiba Japan
| | - Cheng-Te Yao
- High-Altitude Experimental Station Endemic Species Research Institute COA Chi-chi Taiwan, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China.,University of Chinese Academy of Sciences Beijing China
| | - Wenjuan Wang
- Center for Watershed Ecology Institute of Life Science and Ministry of Education Key Laboratory of Poyang Lake Environment and Resource Utilization Nanchang University Nanchang China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China.,University of Chinese Academy of Sciences Beijing China
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31
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Gutiérrez-Valencia J, Chomicki G, Renner SS. Recurrent breakdowns of mutualisms with ants in the neotropical ant-plant genus Cecropia (Urticaceae). Mol Phylogenet Evol 2017; 111:196-205. [DOI: 10.1016/j.ympev.2017.04.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/02/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
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Abstract
Molecular evolution can reveal the relationship between sets of homologous sequences and the patterns of change that occur during their evolution. An important aspect of these studies is the inference of a phylogenetic tree, which explicitly describes evolutionary relationships between homologous sequences. This chapter provides an introduction to evolutionary trees and how to infer them from sequence data using some commonly used inferential methodology. It focuses on statistical methods for inferring trees and how to assess the confidence one should have in any resulting tree, with a particular emphasis on the underlying assumptions of the methods and how they might affect the tree estimate. There is also some discussion of the underlying algorithms used to perform tree search and recommendations regarding the performance of different algorithms. Finally, there are a few practical guidelines, including how to combine multiple software packages to improve inference, and a comparison between Bayesian and Maximum likelihood phylogenetics.
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Affiliation(s)
- Simon Whelan
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | - David A Morrison
- Department of Organism Biology, Uppsala University, Uppsala, Sweden
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Hurtado LA, Mateos M, Liu S. Phylogeographic patterns of a lower intertidal isopod in the Gulf of California and the Caribbean and comparison with other intertidal isopods. Ecol Evol 2017; 7:346-357. [PMID: 28070297 PMCID: PMC5214745 DOI: 10.1002/ece3.2599] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/12/2016] [Accepted: 10/19/2016] [Indexed: 11/25/2022] Open
Abstract
A growing body of knowledge on the diversity and evolution of intertidal isopods across different regions worldwide has enhanced our understanding on biological diversification at the poorly studied, yet vast, sea-land interface. High genetic divergences among numerous allopatric lineages have been identified within presumed single broadly distributed species. Excirolana mayana is an intertidal isopod that is commonly found in sandy beaches throughout the Gulf of California. Its distribution in the Pacific extends from this basin to Colombia and in the Atlantic from Florida to Venezuela. Despite its broad distribution and ecological importance, its evolutionary history has been largely neglected. Herein, we examined phylogeographic patterns of E. mayana in the Gulf of California and the Caribbean, based on maximum-likelihood and Bayesian phylogenetic analyses of DNA sequences from four mitochondrial genes (16S rDNA, 12S rDNA, cytochrome oxidase I gene, and cytochrome b gene). We compared the phylogeographic patterns of E. mayana with those of the coastal isopods Ligia and Excirolana braziliensis (Gulf of California and Caribbean) and Tylos (Gulf of California). We found highly divergent lineages in both, the Gulf of California and Caribbean, suggesting the presence of multiple species. We identified two instances of Atlantic-Pacific divergences. Some geographical structuring among the major clades found in the Caribbean is observed. Haplotypes from the Gulf of California form a monophyletic group sister to a lineage found in Venezuela. Phylogeographic patterns of E. mayana in the Gulf of California differ from those observed in Ligia and Tylos in this region. Nonetheless, several clades of E. mayana have similar distributions to clades of these two other isopod taxa. The high levels of cryptic diversity detected in E. mayana also pose challenges for the conservation of this isopod and its fragile environment, the sandy shores.
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Affiliation(s)
- Luis A. Hurtado
- Department of Wildlife and Fisheries SciencesTexas A&M UniversityCollege StationTXUSA
| | - Mariana Mateos
- Department of Wildlife and Fisheries SciencesTexas A&M UniversityCollege StationTXUSA
| | - Shuang Liu
- Department of Wildlife and Fisheries SciencesTexas A&M UniversityCollege StationTXUSA
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34
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Hurtado LA, Mateos M, Mattos G, Liu S, Haye PA, Paiva PC. Multiple transisthmian divergences, extensive cryptic diversity, occasional long-distance dispersal, and biogeographic patterns in a marine coastal isopod with an amphi-American distribution. Ecol Evol 2016; 6:7794-7808. [PMID: 30128130 PMCID: PMC6093162 DOI: 10.1002/ece3.2397] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/21/2016] [Accepted: 08/01/2016] [Indexed: 12/12/2022] Open
Abstract
Excirolana braziliensis is a coastal intertidal isopod with a broad distribution spanning the Atlantic and Pacific tropical and temperate coasts of the American continent. Two separate regional studies (one in Panama and one in Chile) revealed the presence of highly genetically divergent lineages, implying that this taxon constitutes a cryptic species complex. The relationships among the lineages found in these two different regions and in the rest of the distribution, however, remain unknown. To better understand the phylogeographic patterns of E. braziliensis, we conducted phylogenetic analyses of specimens from much of its entire range. We obtained DNA sequences for fragments of four mitochondrial genes (16S rDNA, 12S rDNA, COI, and Cytb) and also used publicly available sequences. We conducted maximum likelihood and Bayesian phylogenetic reconstruction methods. Phylogeographic patterns revealed the following: (1) new highly divergent lineages of E. braziliensis; (2) three instances of Atlantic–Pacific divergences, some of which appear to predate the closure of the Isthmus of Panama; (3) the distributional limit of highly divergent lineages found in Brazil coincides with the boundary between two major marine coastal provinces; (4) evidence of recent long‐distance dispersal in the Caribbean; and (5) populations in the Gulf of California have closer affinities with lineages further south in the Pacific, which contrasts with the closer affinity with the Caribbean reported for other intertidal organisms. The high levels of cryptic diversity detected also bring about challenges for the conservation of this isopod and its fragile environment, the sandy shores. Our findings underscore the importance of comprehensive geographic sampling for phylogeographic and taxonomical studies of broadly distributed putative species harboring extensive cryptic diversity.
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Affiliation(s)
- Luis A Hurtado
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Gustavo Mattos
- Programa de Pós-Graduação em Ecologia Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Shuang Liu
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Pilar A Haye
- Departamento de Biología Marina Universidad Católica del Norte Coquimbo Chile.,Centro de Estudios Avanzados en Zonas Áridas (CEAZA) Coquimbo Chile.,Interdisciplinary Center for Aquaculture Research (INCAR) Universidad de Concepción Casilla 160-C Concepción Chile
| | - Paulo C Paiva
- Programa de Pós-Graduação em Ecologia Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil.,Departamento de Zoologia Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
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35
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Suh A. The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. ZOOL SCR 2016. [DOI: 10.1111/zsc.12213] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Alexander Suh
- Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University SE ‐ 752 36 Uppsala Sweden
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36
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Zhou X, Frandsen PB, Holzenthal RW, Beet CR, Bennett KR, Blahnik RJ, Bonada N, Cartwright D, Chuluunbat S, Cocks GV, Collins GE, deWaard J, Dean J, Flint OS, Hausmann A, Hendrich L, Hess M, Hogg ID, Kondratieff BC, Malicky H, Milton MA, Morinière J, Morse JC, Mwangi FN, Pauls SU, Gonzalez MR, Rinne A, Robinson JL, Salokannel J, Shackleton M, Smith B, Stamatakis A, StClair R, Thomas JA, Zamora-Muñoz C, Ziesmann T, Kjer KM. The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life. Philos Trans R Soc Lond B Biol Sci 2016; 371:20160025. [PMID: 27481793 PMCID: PMC4971193 DOI: 10.1098/rstb.2016.0025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2016] [Indexed: 12/15/2022] Open
Abstract
DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and 'species' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, People's Republic of China College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
| | - Paul B Frandsen
- Office of Research Information Services, Office of the Chief Information Officer, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Ralph W Holzenthal
- Department of Entomology, University of Minnesota, 1980 Folwell Avenue, St Paul, MN 55108, USA
| | - Clare R Beet
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Kristi R Bennett
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Roger J Blahnik
- Department of Entomology, University of Minnesota, 1980 Folwell Avenue, St Paul, MN 55108, USA
| | - Núria Bonada
- Grup de Recerca Freshwater Ecology and Management (FEM), Departament d'Ecologia, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal, 643, 08028 Barcelona, Catalonia, Spain
| | | | - Suvdtsetseg Chuluunbat
- Department of Biology, Mongolian National University of Education, 3rd Palace, Beijing Street, Ulaanbaatar 14191, Mongolia
| | - Graeme V Cocks
- 44 Marks Street, Hermit Park, Queensland 4812, Australia
| | - Gemma E Collins
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Jeremy deWaard
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - John Dean
- Environment Protection Authority Victoria, Ernest Jones Drive, Macleod 3085, Australia
| | - Oliver S Flint
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Axel Hausmann
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - Lars Hendrich
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - Monika Hess
- Büro H2-Ökologische Gutachten, Hess+Heckes GbR, Rumfordstraße 42, 80469 München, Germany
| | - Ian D Hogg
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Boris C Kondratieff
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO 80523, USA
| | - Hans Malicky
- Biologische Station Lunz, Austrian Academy of Sciences, A-3293 Lunz am see, Austria
| | - Megan A Milton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Jérôme Morinière
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - John C Morse
- Department of Plant and Environmental Sciences, Clemson University, PO Box 340310, Clemson, SC 29634-0310, USA
| | | | - Steffen U Pauls
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - María Razo Gonzalez
- Unidad Multidisciplinaria de Docencia e Investigación, Universidad Nacional Autónoma de Mexcio, Facultad de Ciencias, Campus Juriquilla, Querétaro, 76230, México
| | - Aki Rinne
- Finnish Environment Institute, Merikasarminkatu 8 D, 00160 Helsinki, Finland
| | - Jason L Robinson
- Illinois Natural History Survey, Prairie Research Institute at the University of Illinois at Urbana-Champaign, 1816 S. Oak Street, MC 652, Champaign, IL 61820, USA
| | - Juha Salokannel
- Aquatic Insects Expert Group of Finland, Siikinkatu 13, 33710, Tampere, Finland
| | - Michael Shackleton
- Murray-Darling Freshwater Research Centre, La Trobe University, 133 McKoy Street, Wodonga, Victoria 3691, Australia
| | - Brian Smith
- National Institute of Water and Atmospheric Research, PO Box, 11115, Hamilton 3240, New Zealand
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, 35 D-69118 Heidelberg, Germany
| | - Ros StClair
- Environment Protection Authority Victoria, Ernest Jones Drive, Macleod 3085, Australia
| | - Jessica A Thomas
- BioArch, Environment Building, Department of Biology, University of York, York, YO10 5DD, UK
| | - Carmen Zamora-Muñoz
- Department of Zoology, Faculty of Sciences, University of Granada, C/Severo Ochoa s/n, 18071 Granada, Spain
| | - Tanja Ziesmann
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fu¨r Molekulare Biodiversitätsforschung (ZMB), Bonn 5 76131 Karlsruhe, Germany
| | - Karl M Kjer
- Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA
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Jonathan Shaw A, Devos N, Liu Y, Cox CJ, Goffinet B, Flatberg KI, Shaw B. Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss). ANNALS OF BOTANY 2016; 118:185-96. [PMID: 27268484 PMCID: PMC4970357 DOI: 10.1093/aob/mcw086] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/11/2016] [Accepted: 03/28/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided. METHODS We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium KEY RESULTS Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made, in the genera Eosphagnum and Flatbergium CONCLUSIONS Newly resolved relationships now permit phylogenetic analyses of morphological, biochemical and ecological traits among Sphagnum species. The results clarify long-standing disagreements about subgeneric relationships and intrageneric classification.
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Affiliation(s)
- A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Nicolas Devos
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Yang Liu
- Department of Ecology and Evolutionary Biology, 75 North Eagleville Road, Storrs, CT 06269, USA
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, Edif. 7, 8005-139 Faro, Portugal
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, 75 North Eagleville Road, Storrs, CT 06269, USA
| | - Kjell Ivar Flatberg
- NTNU University Museum, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Blanka Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA
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38
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Palacios M, Voelker G, Arias Rodriguez L, Mateos M, Tobler M. Phylogenetic analyses of the subgenus Mollienesia (Poecilia, Poeciliidae, Teleostei) reveal taxonomic inconsistencies, cryptic biodiversity, and spatio-temporal aspects of diversification in Middle America. Mol Phylogenet Evol 2016; 103:230-244. [PMID: 27472959 DOI: 10.1016/j.ympev.2016.07.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 07/16/2016] [Accepted: 07/22/2016] [Indexed: 01/19/2023]
Abstract
The subgenus Mollienesia is a diverse group of freshwater fishes, including species that have served as important models across multiple biological disciplines. Nonetheless, the taxonomic history of this group has been conflictive and convoluted, in part because the evolutionary relationships have not been rigorously resolved. We conducted a comprehensive molecular phylogenetic analysis of the subgenus Mollienesia to identify taxonomic discrepancies and potentially identify undescribed species, estimate ancestral areas of origin and estimate dates of divergence, as well as explore biogeographical patterns. Our findings confirm the presence of three main clades composed of the P. latipinna, P. sphenops, and P. mexicana species complexes. Unlike previously hypothesized morphology-based analyses, species found on the Caribbean Islands are not part of Mollienesia, but are more closely related to species of the subgenus Limia. Our study also revealed several taxonomic inconsistencies and distinct lineages in the P. mexicana species complex that may represent undescribed species. The diversity in the subgenus Mollienesia is a result of dynamic geologic activity leading to vicariant events, dispersal across geologic blocks, and ecological speciation.
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Affiliation(s)
- Maura Palacios
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 2258 TAMU, College Station, TX 77843, USA.
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 2258 TAMU, College Station, TX 77843, USA
| | - Lenin Arias Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), C.P. 86150 Villahermosa, Tabasco, Mexico
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 2258 TAMU, College Station, TX 77843, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
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Abdala CS, Baldo D, Juárez RA, Espinoza RE. The First Parthenogenetic Pleurodont Iguanian: A New All-femaleLiolaemus(Squamata: Liolaemidae) from Western Argentina. COPEIA 2016. [DOI: 10.1643/ch-15-381] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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40
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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: 27] [Impact Index Per Article: 3.4] [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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Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent. PLoS Genet 2016; 12:e1006006. [PMID: 27144273 PMCID: PMC4856265 DOI: 10.1371/journal.pgen.1006006] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 04/04/2016] [Indexed: 11/19/2022] Open
Abstract
The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation. Trees have long formed in biology the basic structure with which to represent and understand evolutionary relationships. Mathematical models, computational methods, and software tools for inferring phylogenetic trees and studying their mathematical properties are currently the norm in biology. The availability of genomic data from closely related species, as well as from multiple individuals within species, have brought the two fields of phylogenetics and population genetics closer than ever. In particular, the last two decades have witnessed a great flourish in the development and implementation of phylogenetic methods based on the multispecies coalescent model to capture the intricate relationship between gene and genome evolution. However, when reticulation processes such as hybridization occur, the phylogenetic history is best represented by a network. In this work, we demonstrate how the multispecies coalescent model can be adapted to reticulate evolutionary histories and report on a Bayesian method for inference of such histories under this extended model. As networks subsume trees, the model and method provide a principled and unified statistical framework for inferring treelike and non-treelike evolutionary relationships.
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Takezaki N, Nishihara H. Resolving the Phylogenetic Position of Coelacanth: The Closest Relative Is Not Always the Most Appropriate Outgroup. Genome Biol Evol 2016; 8:1208-21. [PMID: 27026053 PMCID: PMC4860700 DOI: 10.1093/gbe/evw071] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Determining the phylogenetic relationship of two extant lineages of lobe-finned fish, coelacanths and lungfishes, and tetrapods is important for understanding the origin of tetrapods. We analyzed data sets from two previous studies along with a newly collected data set, each of which had varying numbers of species and genes and varying extent of missing sites. We found that in all the data sets the sister relationship of lungfish and tetrapods was constructed with the use of cartilaginous fish as the outgroup with a high degree of statistical support. In contrast, when ray-finned fish were used as the outgroup, which is taxonomically an immediate outgroup of lobe-finned fish and tetrapods, the sister relationship of coelacanth and tetrapods was supported most strongly, although the statistical support was weaker. Even though it is generally accepted that the closest relative is an appropriate outgroup, our analysis suggested that the large divergence of the ray-finned fish as indicated by their long branch lengths and different amino acid frequencies made them less suitable as an outgroup than cartilaginous fish.
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Affiliation(s)
- Naoko Takezaki
- Life Science Research Center, Kagawa University, Mikicho, Kitagun, Kagawa, Japan
| | - Hidenori Nishihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-Cho, Midori-Ku, Yokohama, Kanagawa, Japan
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Frost SDW, Murrell B, Hossain ASMM, Silverman GJ, Pond SLK. Assigning and visualizing germline genes in antibody repertoires. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0240. [PMID: 26194754 PMCID: PMC4528417 DOI: 10.1098/rstb.2014.0240] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Identifying the germline genes involved in immunoglobulin rearrangements is an essential first step in the analysis of antibody repertoires. Based on our prior work in analysing diverse recombinant viruses, we present IgSCUEAL (Immunoglobulin Subtype Classification Using Evolutionary ALgorithms), a phylogenetic approach to assign V and J regions of immunoglobulin sequences to their corresponding germline alleles, with D regions assigned using a simple pairwise alignment algorithm. We also develop an interactive web application for viewing the results, allowing the user to explore the frequency distribution of sequence assignments and CDR3 region length statistics, which is useful for summarizing repertoires, as well as a detailed viewer of rearrangements and region alignments for individual query sequences. We demonstrate the accuracy and utility of our method compared with sequence similarity-based approaches and other non-phylogenetic model-based approaches, using both simulated data and a set of evaluation datasets of human immunoglobulin heavy chain sequences. IgSCUEAL demonstrates the highest accuracy of V and J assignment amongst existing approaches, even when the reassorted sequence is highly mutated, and can successfully cluster sequences on the basis of shared V/J germline alleles.
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Affiliation(s)
- Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - A S Md Mukarram Hossain
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK
| | - Gregg J Silverman
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
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Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH. Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae). Mol Phylogenet Evol 2016; 97:32-42. [DOI: 10.1016/j.ympev.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/04/2015] [Accepted: 12/23/2015] [Indexed: 02/02/2023]
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45
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Phylogenic analysis of adhesion related genes Mad1 revealed a positive selection for the evolution of trapping devices of nematode-trapping fungi. Sci Rep 2016; 6:22609. [PMID: 26941065 PMCID: PMC4778117 DOI: 10.1038/srep22609] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/17/2016] [Indexed: 12/27/2022] Open
Abstract
Adhesions, the major components of the extracellular fibrillar polymers which accumulate on the outer surface of adhesive traps of nematode-trapping fungi, are thought to have played important roles during the evolution of trapping devices. Phylogenetic analyses based on the genes related to adhesive materials can be of great importance for understanding the evolution of trapping devices. Recently, AoMad1, one homologous gene of the entomopathogenic fungus Metarhizium anisopliae cell wall protein MAD1, has been functionally characterized as involved in the production of adhesions in the nematode-trapping fungus Arthrobotrys oligospora. In this study, we cloned Mad1 homologous genes from nematode-trapping fungi with various trapping devices. Phylogenetic analyses suggested that species which formed nonadhesive constricting ring (CR) traps more basally placed and species with adhesive traps evolved along two lineages. Likelihood ratio tests (LRT) revealed that significant positive selective pressure likely acted on the ancestral trapping devices including both adhesive and mechanical traps, indicating that the Mad1 genes likely played important roles during the evolution of nematode-trapping fungi. Our study provides new insights into the evolution of trapping devices of nematode-trapping fungi and also contributes to understanding the importance of adhesions during the evolution of nematode-trapping fungi.
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Zhang C, Stadler T, Klopfstein S, Heath TA, Ronquist F. Total-Evidence Dating under the Fossilized Birth-Death Process. Syst Biol 2016; 65:228-49. [PMID: 26493827 PMCID: PMC4748749 DOI: 10.1093/sysbio/syv080] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 10/12/2015] [Indexed: 11/16/2022] Open
Abstract
Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth-death (FBD) process, which has been used to model speciation, extinction, and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of data sets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants, and bees). Previous total-evidence dating analyses of this data set were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push toward more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.
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Affiliation(s)
- Chi Zhang
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, 4053 Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), Switzerland
| | - Seraina Klopfstein
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden; Department of Invertebrates, Natural History Museum Bern, CH-3005 Bern, Switzerland
| | - Tracy A Heath
- Department of Integrative Biology, University of California, Berkeley, CA 94720 USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA; Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden;
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Koralewski TE, Mateos M, Krutovsky KV. Conflicting genomic signals affect phylogenetic inference in four species of North American pines. AOB PLANTS 2016; 8:plw019. [PMID: 27060161 PMCID: PMC4866652 DOI: 10.1093/aobpla/plw019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 03/19/2016] [Indexed: 05/14/2023]
Abstract
Adaptive evolutionary processes in plants may be accompanied by episodes of introgression, parallel evolution and incomplete lineage sorting that pose challenges in untangling species evolutionary history. Genus Pinus (pines) is one of the most abundant and most studied groups among gymnosperms, and a good example of a lineage where these phenomena have been observed. Pines are among the most ecologically and economically important plant species. Some, such as the pines of the southeastern USA (southern pines in subsection Australes), are subjects of intensive breeding programmes. Despite numerous published studies, the evolutionary history of Australes remains ambiguous and often controversial. We studied the phylogeny of four major southern pine species: shortleaf (Pinus echinata), slash (P. elliottii), longleaf (P. palustris) and loblolly (P. taeda), using sequences from 11 nuclear loci and maximum likelihood and Bayesian methods. Our analysis encountered resolution difficulties similar to earlier published studies. Although incomplete lineage sorting and introgression are two phenomena presumptively underlying our results, the phylogenetic inferences seem to be also influenced by the genes examined, with certain topologies supported by sets of genes sharing common putative functionalities. For example, genes involved in wood formation supported the clade echinata-taeda, genes linked to plant defence supported the clade echinata-elliottii and genes linked to water management properties supported the clade echinata-palustris The support for these clades was very high and consistent across methods. We discuss the potential factors that could underlie these observations, including incomplete lineage sorting, hybridization and parallel or adaptive evolution. Our results likely reflect the relatively short evolutionary history of the subsection that is thought to have begun during the middle Miocene and has been influenced by climate fluctuations.
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Affiliation(s)
- Tomasz E Koralewski
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, USA
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 2258 TAMU, College Station, TX 77843-2258, USA
| | - Konstantin V Krutovsky
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, USA Department of Forest Genetics and Forest Tree Breeding, Büsgen-Institute, Georg-August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia
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Noda M, Oshida T, Abramov AV, Baranova G, Baryshinikov G, Ichikawa H, Masuda R. Phylogeography of the Eurasian red squirrel (Sciurus vulgaris orientis) on the boreal island of Hokkaido, Japan. J NAT HIST 2015. [DOI: 10.1080/00222933.2015.1083056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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49
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Kim JI, Linton EW, Shin W. Taxon-rich multigene phylogeny of the photosynthetic euglenoids (Euglenophyceae). Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00098] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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50
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Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. Mol Phylogenet Evol 2015; 89:28-36. [DOI: 10.1016/j.ympev.2015.03.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 03/10/2015] [Accepted: 03/13/2015] [Indexed: 11/20/2022]
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