1
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Bowles AMC, Williamson CJ, Williams TA, Donoghue PCJ. Cryogenian Origins of Multicellularity in Archaeplastida. Genome Biol Evol 2024; 16:evae026. [PMID: 38333966 PMCID: PMC10883732 DOI: 10.1093/gbe/evae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution.
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
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2
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Francisco Barbosa F, Mermudes JRM, Russo CAM. Performance of tree-building methods using a morphological dataset and a well-supported Hexapoda phylogeny. PeerJ 2024; 12:e16706. [PMID: 38213769 PMCID: PMC10782957 DOI: 10.7717/peerj.16706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/30/2023] [Indexed: 01/13/2024] Open
Abstract
Recently, many studies have addressed the performance of phylogenetic tree-building methods (maximum parsimony, maximum likelihood, and Bayesian inference), focusing primarily on simulated data. However, for discrete morphological data, there is no consensus yet on which methods recover the phylogeny with better performance. To address this lack of consensus, we investigate the performance of different methods using an empirical dataset for hexapods as a model. As an empirical test of performance, we applied normalized indices to effectively measure accuracy (normalized Robinson-Foulds metric, nRF) and precision, which are measured via resolution, one minus Colless' consensus fork index (1-CFI). Additionally, to further explore phylogenetic accuracy and support measures, we calculated other statistics, such as the true positive rate (statistical power) and the false positive rate (type I error), and constructed receiver operating characteristic plots to visualize the relationship between these statistics. We applied the normalized indices to the reconstructed trees from the reanalyses of an empirical discrete morphological dataset from extant Hexapoda using a well-supported phylogenomic tree as a reference. Maximum likelihood and Bayesian inference applying the k-state Markov (Mk) model (without or with a discrete gamma distribution) performed better, showing higher precision (resolution). Additionally, our results suggest that most available tree topology tests are reliable estimators of the performance measures applied in this study. Thus, we suggest that likelihood-based methods and tree topology tests should be used more often in phylogenetic tree studies based on discrete morphological characters. Our study provides a fair indication that morphological datasets have robust phylogenetic signal.
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Affiliation(s)
| | | | - Claudia A. M. Russo
- Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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3
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Markowski E, Susko E. Performance of Topology Tests under Extreme Selection Bias. Mol Biol Evol 2024; 41:msad280. [PMID: 38142434 PMCID: PMC10773725 DOI: 10.1093/molbev/msad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/13/2023] [Accepted: 12/14/2023] [Indexed: 12/26/2023] Open
Abstract
Tree tests like the Kishino-Hasegawa (KH) test and chi-square test suffer a selection bias that tests like the Shimodaira-Hasegawa (SH) test and approximately unbiased test were intended to correct. We investigate tree-testing performance in the presence of severe selection bias. The SH test is found to be very conservative and, surprisingly, its uncorrected analog, the KH test has low Type I error even in the presence of extreme selection bias, leading to a recommendation that the SH test be abandoned. A chi-square test is found to usually behave well and but to require correction in extreme cases. We show how topology testing procedures can be used to get support values for splits and compare the likelihood-based support values to the approximate likelihood ratio test (aLRT) support values. We find that the aLRT support values are reasonable even in settings with severe selection bias that they were not designed for. We also show how they can be used to construct tests of topologies and, in doing so, point out a multiple comparisons issue that should be considered when looking at support values for splits.
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Affiliation(s)
- Etai Markowski
- Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada
- Apple Incorporated, Cupertino, CA, USA
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada
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4
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Hand SJ, Maugoust J, Beck RMD, Orliac MJ. A 50-million-year-old, three-dimensionally preserved bat skull supports an early origin for modern echolocation. Curr Biol 2023; 33:4624-4640.e21. [PMID: 37858341 DOI: 10.1016/j.cub.2023.09.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 07/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
Bats are among the most recognizable, numerous, and widespread of all mammals. But much of their fossil record is missing, and bat origins remain poorly understood, as do the relationships of early to modern bats. Here, we describe a new early Eocene bat that helps bridge the gap between archaic stem bats and the hyperdiverse modern bat radiation of more than 1,460 living species. Recovered from ∼50 million-year-old cave sediments in the Quercy Phosphorites of southwestern France, Vielasia sigei's remains include a near-complete, three-dimensionally preserved skull-the oldest uncrushed bat cranium yet found. Phylogenetic analyses of a 2,665 craniodental character matrix, with and without 36.8 kb of DNA sequence data, place Vielasia outside modern bats, with total evidence tip-dating placing it sister to the crown clade. Vielasia retains the archaic dentition and skeletal features typical of early Eocene bats, but its inner ear shows specializations found in modern echolocating bats. These features, which include a petrosal only loosely attached to the basicranium, an expanded cochlea representing ∼25% basicranial width, and a long basilar membrane, collectively suggest that the kind of laryngeal echolocation used by most modern bats predates the crown radiation. At least 23 individuals of V. sigei are preserved together in a limestone cave deposit, indicating that cave roosting behavior had evolved in bats by the end of the early Eocene; this period saw the beginning of significant global climate cooling that may have been an evolutionary driver for bats to first congregate in caves.
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Affiliation(s)
- Suzanne J Hand
- ESSRC, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacob Maugoust
- Institut des Sciences de l'Evolution, UMR 5554 CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK.
| | - Maeva J Orliac
- Institut des Sciences de l'Evolution, UMR 5554 CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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5
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Hao X, Lu Q, Zhao H. A molecular phylogeny for all 21 families within Chiroptera (bats). Integr Zool 2023. [PMID: 37853557 DOI: 10.1111/1749-4877.12772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Bats, members of the Chiroptera order, rank as the second most diverse group among mammals. Recent molecular systematic studies on bats have successfully classified 21 families within two suborders: Yinpterochiroptera and Yangochiroptera. Nevertheless, the phylogeny within these 21 families has remained a subject of controversy. In this study, we have employed a balanced approach to establish a robust family-level phylogenetic hypothesis for bats, utilizing a more comprehensive molecular dataset. This dataset includes representative species from all 21 bat families, resulting in a reduced level of missing genetic information. The resulting phylogenetic tree comprises 21 lineages that are strongly supported, each corresponding to one of the bat families. Our findings support to place the Emballonuroidea superfamily as the basal lineage of Yangochiroptera, and that Myzopodidae should be situated as a basal lineage of Emballonuroidea, forming a sister relationship with the clade consisting of Nycteridae and Emballonuridae. Finally, we have conducted dating analyses on this newly resolved phylogenetic tree, providing divergence times for each bat family. Collectively, our study has employed a relatively comprehensive molecular dataset to establish a more robust phylogeny encompassing all 21 bat families. This improved phylogenetic framework will significantly contribute to our understanding of evolutionary processes, ecological roles, disease dynamics, and biodiversity conservation in the realm of bats.
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Affiliation(s)
- Xiangyu Hao
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Qin Lu
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Huabin Zhao
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
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6
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Crichton AI, Beck RMD, Couzens AMC, Worthy TH, Camens AB, Prideaux GJ. A probable koala from the Oligocene of central Australia provides insights into early diprotodontian evolution. Sci Rep 2023; 13:14521. [PMID: 37666885 PMCID: PMC10477348 DOI: 10.1038/s41598-023-41471-0] [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: 06/11/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023] Open
Abstract
Diprotodontians are the morphologically and ecologically most diverse order of marsupials. However, an approximately 30-million-year gap in the Australian terrestrial vertebrate fossil record means that the first half of diprotodontian evolution is unknown. Fossil taxa from immediately either side of this gap are therefore critical for reconstructing the early evolution of the order. Here we report the likely oldest-known koala relatives (Phascolarctidae), from the late Oligocene Pwerte Marnte Marnte Local Fauna (central Australia). These include coeval species of Madakoala and Nimiokoala, as well as a new probable koala (?Phascolarctidae). The new taxon, Lumakoala blackae gen. et sp. nov., was comparable in size to the smallest-known phascolarctids, with body-mass estimates of 2.2-2.6 kg. Its bunoselenodont upper molars retain the primitive metatherian condition of a continuous centrocrista, and distinct stylar cusps B and D which lacked occlusion with the hypoconid. This structural arrangement: (1) suggests a morphocline within Phascolarctidae from bunoselenodonty to selenodonty; and (2) better clarifies the evolutionary transitions between molar morphologies within Vombatomorphia. We hypothesize that the molar form of Lumakoala blackae approximates the ancestral condition of the suborder Vombatiformes. Furthermore, it provides a plausible link between diprotodontians and the putative polydolopimorphians Chulpasia jimthorselli and Thylacotinga bartholomaii from the early Eocene Tingamarra Local Fauna (eastern Australia), which we infer as having molar morphologies consistent with stem diprotodontians.
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Affiliation(s)
- Arthur I Crichton
- College of Science and Engineering, Flinders University, Bedford Park, 5042, Australia.
| | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Salford, England
| | - Aidan M C Couzens
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Trevor H Worthy
- College of Science and Engineering, Flinders University, Bedford Park, 5042, Australia
| | - Aaron B Camens
- College of Science and Engineering, Flinders University, Bedford Park, 5042, Australia
| | - Gavin J Prideaux
- College of Science and Engineering, Flinders University, Bedford Park, 5042, Australia
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7
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Collins AJ, Whitaker RJ. CRISPR Comparison Toolkit: Rapid Identification, Visualization, and Analysis of CRISPR Array Diversity. CRISPR J 2023; 6:386-400. [PMID: 37459160 PMCID: PMC10457644 DOI: 10.1089/crispr.2022.0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 05/23/2023] [Indexed: 08/19/2023] Open
Abstract
CRISPR-Cas systems provide immunity against mobile genetic elements (MGEs) through sequence-specific targeting by spacer sequences encoded in CRISPR arrays. Spacers are highly variable between microbial strains and can be acquired rapidly, making them well suited for use in strain typing of closely related organisms. However, no tools are currently available to automate the process of reconstructing strain histories using CRISPR spacers. We therefore developed the CRISPR Comparison Toolkit (CCTK) to enable analyses of array relationships. The CCTK includes tools to identify arrays, analyze relationships between arrays using CRISPRdiff and CRISPRtree, and predict targets of spacers. CRISPRdiff visualizes arrays and highlights the similarities between them. CRISPRtree infers a phylogenetic tree from array relationships and presents a hypothesis of the evolutionary history of the arrays. The CCTK unifies several CRISPR analysis tools into a single command line application, including the first tool to infer phylogenies from array relationships.
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Affiliation(s)
- Alan J. Collins
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA and University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Rachel J. Whitaker
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA and University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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8
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Basal Anseriformes from the Early Paleogene of North America and Europe. DIVERSITY 2023. [DOI: 10.3390/d15020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
We describe nearly complete skeletons of basal Anseriformes from the Latest Paleocene to the early Eocene of North America and Europe. Collectively, these birds appear to be representative of anseriforms near the divergence of Anhimae and Anseres, but their exact positions relative to these clades remains uncertain. A new family, Anachronornithidae nov. fam., is erected on the basis of one of these, Anachronornis anhimops nov. gen., nov. gen. et sp., to which the others cannot be confidently assigned. The new fossils augment a growing collection of early Pan-Anseriformes, which in their diversity do not paint an unambiguous picture of phylogeny or character state evolution on the path to or within crown-Anseriformes. Anachronornis nov. gen. is similar in some aspects of both cranial and postcranial anatomy to other well-represented early Paleogene Anseriformes and members of Anseres, such as Presbyornis Wetmore, 1926. However, it exhibits a more landfowl-like bill, like that of Anhimae and unlike the spatulate bill of Anseres. Additional specimens of similar basal Anseriformes of uncertain affinities from the early Eocene of North America and Europe further complicate interpretation of character state polarity due to the mosaicism of primitive and derived characters they exhibit.
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9
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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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10
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Wang T, Li TZ, Chen SS, Yang T, Shu JP, Mu YN, Wang KL, Chen JB, Xiang JY, Yan YH. Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:918155. [PMID: 36507421 PMCID: PMC9730426 DOI: 10.3389/fpls.2022.918155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/11/2022] [Indexed: 06/17/2023]
Abstract
Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.
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Affiliation(s)
- Ting Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Ting-Zhang Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Si-Si Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Tuo Yang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jiang-Ping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Yu-Nong Mu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Kang-Lin Wang
- Green Development Institute, Southwest Forestry University, Kunming, China
| | - Jian-Bing Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jian-Ying Xiang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
| | - Yue-Hong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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11
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Hasan NB, Balaban M, Biswas A, Bayzid MS, Mirarab S. Distance-Based Phylogenetic Placement with Statistical Support. BIOLOGY 2022; 11:biology11081212. [PMID: 36009839 PMCID: PMC9404983 DOI: 10.3390/biology11081212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Phylogenetic placement seeks to find the optimal position for a new query species on an existing backbone tree. Fast and accurate distance-based phylogenetic placement methods lack the crucial feature of estimating the support values for various placements of a query sequence. This study presents both parametric and nonparametric methods for measuring the support values of distance-based phylogenetic placements. Abstract Phylogenetic identification of unknown sequences by placing them on a tree is routinely attempted in modern ecological studies. Such placements are often obtained from incomplete and noisy data, making it essential to augment the results with some notion of uncertainty. While the standard likelihood-based methods designed for placement naturally provide such measures of uncertainty, the newer and more scalable distance-based methods lack this crucial feature. Here, we adopt several parametric and nonparametric sampling methods for measuring the support of phylogenetic placements that have been obtained with the use of distances. Comparing the alternative strategies, we conclude that nonparametric bootstrapping is more accurate than the alternatives. We go on to show how bootstrapping can be performed efficiently using a linear algebraic formulation that makes it up to 30 times faster and implement this optimized version as part of the distance-based placement software APPLES. By examining a wide range of applications, we show that the relative accuracy of maximum likelihood (ML) support values as compared to distance-based methods depends on the application and the dataset. ML is advantageous for fragmentary queries, while distance-based support values are more accurate for full-length and multi-gene datasets. With the quantification of uncertainty, our work fills a crucial gap that prevents the broader adoption of distance-based placement tools.
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Affiliation(s)
- Navid Bin Hasan
- Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1205, Bangladesh
| | - Metin Balaban
- Bioinformatics and System Biology Program, UC San Diego, San Diego, CA 92093, USA
| | - Avijit Biswas
- Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1205, Bangladesh
| | - Md. Shamsuzzoha Bayzid
- Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1205, Bangladesh
- Correspondence: (M.S.B.); (S.M.)
| | - Siavash Mirarab
- Electrical and Computer Engineering, UC San Diego, San Diego, CA 92093, USA
- Correspondence: (M.S.B.); (S.M.)
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12
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Mika K, Whittington CM, McAllan BM, Lynch VJ. Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy. eLife 2022; 11:e74297. [PMID: 35770963 PMCID: PMC9275820 DOI: 10.7554/elife.74297] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Structural and physiological changes in the female reproductive system underlie the origins of pregnancy in multiple vertebrate lineages. In mammals, the glandular portion of the lower reproductive tract has transformed into a structure specialized for supporting fetal development. These specializations range from relatively simple maternal nutrient provisioning in egg-laying monotremes to an elaborate suite of traits that support intimate maternal-fetal interactions in Eutherians. Among these traits are the maternal decidua and fetal component of the placenta, but there is considerable uncertainty about how these structures evolved. Previously, we showed that changes in uterine gene expression contributes to several evolutionary innovations during the origins of pregnancy (Mika et al., 2021b). Here, we reconstruct the evolution of entire transcriptomes ('ancestral transcriptome reconstruction') and show that maternal gene expression profiles are correlated with degree of placental invasion. These results indicate that an epitheliochorial-like placenta evolved early in the mammalian stem-lineage and that the ancestor of Eutherians had a hemochorial placenta, and suggest maternal control of placental invasiveness. These data resolve major transitions in the evolution of pregnancy and indicate that ancestral transcriptome reconstruction can be used to study the function of ancestral cell, tissue, and organ systems.
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Affiliation(s)
- Katelyn Mika
- Department of Human Genetics, University of ChicagoChicagoUnited States
- Department of Organismal Biology and Anatomy, University of ChicagoChicagoUnited States
| | | | | | - Vincent J Lynch
- Department of Biological Sciences, University at Buffalo, State University of New YorkBuffalo,NewyorkUnited States
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13
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Gaunt MW, Pettersson JHO, Kuno G, Gaunt B, de Lamballerie X, Gould EA. Widespread Interspecific Phylogenetic Tree Incongruence Between Mosquito-Borne and Insect-Specific Flaviviruses at Hotspots Originally Identified in Zika Virus. Virus Evol 2022; 8:veac027. [PMID: 35591877 PMCID: PMC9113262 DOI: 10.1093/ve/veac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 10/22/2021] [Accepted: 04/17/2022] [Indexed: 11/16/2022] Open
Abstract
Intraspecies (homologous) phylogenetic incongruence, or ‘tree conflict’ between different loci within the same genome of mosquito-borne flaviviruses (MBFV), was first identified in dengue virus (DENV) and subsequently in Japanese encephalitis virus (JEV), St Louis encephalitis virus, and Zika virus (ZIKV). Recently, the first evidence of phylogenetic incongruence between interspecific members of the MBFV was reported in ZIKV and its close relative, Spondweni virus. Uniquely, these hybrid proteomes were derived from four incongruent trees involving an Aedes-associated DENV node (1 tree) and three different Culex-associated flavivirus nodes (3 trees). This analysis has now been extended across a wider spectrum of viruses within the MBFV lineage targeting the breakpoints between phylogenetic incongruent loci originally identified in ZIKV. Interspecies phylogenetic incongruence at these breakpoints was identified in 10 of 50 viruses within the MBFV lineage, representing emergent Aedes and Culex-associated viruses including JEV, West Nile virus, yellow fever virus, and insect-specific viruses. Thus, interspecies phylogenetic incongruence is widespread amongst the flaviviruses and is robustly associated with the specific breakpoints that coincide with the interspecific phylogenetic incongruence previously identified, inferring they are ‘hotspots’. The incongruence amongst the emergent MBFV group was restricted to viruses within their respective associated epidemiological boundaries. This MBFV group was RY-coded at the third codon position (‘wobble codon’) to remove transition saturation. The resulting ‘wobble codon’ trees presented a single topology for the entire genome that lacked any robust evidence of phylogenetic incongruence between loci. Phylogenetic interspecific incongruence was therefore observed for exactly the same loci between amino acid and the RY-coded ‘wobble codon’ alignments and this incongruence represented either a major part, or the entire genomes. Maximum likelihood codon analysis revealed positive selection for the incongruent lineages. Positive selection could result in the same locus producing two opposing trees. These analyses for the clinically important MBFV suggest that robust interspecific phylogenetic incongruence resulted from amino acid selection. Convergent or parallel evolutions are evolutionary processes that would explain the observation, whilst interspecific recombination is unlikely.
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Affiliation(s)
- Michael W Gaunt
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - John H-O Pettersson
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia
| | - Goro Kuno
- Formerly, Centers for Disease Control, Fort Collins, CO 80521, USA
| | - Bill Gaunt
- Aeon-sys, MBCS Kensington Road, Barnsley S75 2TU, UK
| | - Xavier de Lamballerie
- UMR “Unité des Virus Emergents”, Aix-Marseille Université-IRD 190-Inserm 1207-IHU Méditerranée Infection, Marseille, France
- APHM Public Hospitals of Marseille, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Ernest A Gould
- UMR “Unité des Virus Emergents”, Aix-Marseille Université-IRD 190-Inserm 1207-IHU Méditerranée Infection, Marseille, France
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Muell MR, Chávez G, Prates I, Guillory WX, Kahn TR, Twomey EM, Rodrigues MT, Brown JL. Phylogenomic analysis of evolutionary relationships in Ranitomeya poison frogs (Family Dendrobatidae) using ultraconserved elements. Mol Phylogenet Evol 2022; 168:107389. [PMID: 35026428 DOI: 10.1016/j.ympev.2022.107389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
The use of genome-scale data in phylogenetics has enabled recent strides in determining the relationships between taxa that are taxonomically problematic because of extensive morphological variation. Here, we employ a phylogenomic approach to infer evolutionary relationships within Ranitomeya (Anura: Dendrobatidae), an Amazonian lineage of poison frogs consisting of 16 species with remarkable diversity in color pattern, range size, and parental care behavior. We infer phylogenies with all described species of Ranitomeya from ultraconserved nuclear genomic elements (UCEs) and also estimate divergence times. Our results differ from previous analyses regarding interspecific relationships. Notably, we find that R. toraro and R. defleri are not sister species but rather distantly related, contrary to previous analyses based on smaller genetic datasets. We recover R. uakarii as paraphyletic, designate certain populations formerly assigned to R. fantastica from Peru as R. summersi, and transfer the French Guianan and eastern Brazilian R. amazonica populations to R. variabilis. By clarifying both inter- and intraspecific relationships within Ranitomeya, our study paves the way for future tests of hypotheses on color pattern evolution and historical biogeography.
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Affiliation(s)
- Morgan R Muell
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; Department of Biological Sciences, Auburn University, Auburn, AL, USA.
| | - Germán Chávez
- Instituto Peruano de Herpetología, Lima, Perú; División de Herpetología - CORBIDI, Lima, Perú
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Wilson X Guillory
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; Department of Biological Sciences, Rutgers University Newark, Newark, NJ, USA
| | - Ted R Kahn
- Species Survival Commission (SSC), International Union for Conservation of Nature (IUCN), Gland, Switzerland
| | - Evan M Twomey
- Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | | | - Jason L Brown
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
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15
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Morel B, Barbera P, Czech L, Bettisworth B, Hübner L, Lutteropp S, Serdari D, Kostaki EG, Mamais I, Kozlov AM, Pavlidis P, Paraskevis D, Stamatakis A. Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult. Mol Biol Evol 2021; 38:1777-1791. [PMID: 33316067 PMCID: PMC7798910 DOI: 10.1093/molbev/msaa314] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.
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Affiliation(s)
- Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Pierre Barbera
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Lucas Czech
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Ben Bettisworth
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Lukas Hübner
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sarah Lutteropp
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Dora Serdari
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Mamais
- Department of Health Sciences, European University Cyprus, Nicosia, Cyprus
| | - Alexey M Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Crete, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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16
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Bacus MG, Buenaventura SGC, Mamites AMC, Elizagaque HG, Labrador CC, Delfin FC, Eng MNJ, Lagare AP, Marquez GN, Murao LAE. Genome-based local dynamics of canine rabies virus epidemiology, transmission, and evolution in Davao City, Philippines, 2018-2019. INFECTION GENETICS AND EVOLUTION 2021; 92:104868. [PMID: 33878454 DOI: 10.1016/j.meegid.2021.104868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 11/19/2022]
Abstract
Rabies is a fatal zoonotic and neglected tropical disease caused by the rabies virus (RABV) and is associated with neuronal dysfunction and death, with dogs as the predominant carrier. The Philippines plans to eradicate rabies by 2022, but this is challenged with sub-optimal coverage of vaccination programs coupled with sustained transmission chains, making it unable to eradicate the disease. We investigated the dynamics of canine rabies in the highly urbanized Davao City of the Philippines and its neighboring localities by assessing genetic relationships, transmission patterns, selection pressure, and recombination events using the whole genome sequence of 49 RABV cases from June 2018 to May 2019, majority of which (46%) were from the district of Talomo, Davao City. Although phylogeographic clustering was observed, local variants also exhibited genetic sub-lineages. Phylogenetic and spatial transmission analysis provided evidence for intra- and inter-city transmission predominantly through the Talomo district of Davao City. Around 84% of the cases were owned dogs, but the genetic similiarity of RABVs from stray and owned dogs further alluded to the role of the former as transmission vectors. The high rate of improper vaccination among the affected dogs (80%) was also a likely contributor to transmission. The RABV population under Investigation is generally under strong purifying selection with no evidence of vaccine evasion due to the genetic homogeneity of viruses from vaccinated and improperly vaccinated dogs. However, some homologous recombination (HR) events were identified along the G and L genes, also predominantly associated with viruses from Talomo. The complementary findings on epidemiology, transmission, and recombination for Talomo suggest that high incidence areas can be seeds for virus dispersal and evolution. We recommend further Investigations on the possibility of HR in future large-scale genome studies. Finally, districts associated with these phenomena can be targeted for evidence-based local strategies that can help break RABV transmission chains and prevent emergence of novel strains in Davao City.
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Affiliation(s)
- Michael G Bacus
- Philippine Genome Center Mindanao, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Sheryl Grace C Buenaventura
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Allan Michael C Mamites
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Hannah G Elizagaque
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Christian C Labrador
- Philippine Genome Center Mindanao, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Frederick C Delfin
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Ma Noreen J Eng
- Davao City Veterinary Office, Pichon St., Davao City, Philippines
| | - Arlene P Lagare
- Davao City Veterinary Office, Pichon St., Davao City, Philippines
| | - Gloria N Marquez
- Davao City Veterinary Office, Pichon St., Davao City, Philippines
| | - Lyre Anni E Murao
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines; Philippine Genome Center Mindanao, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines.
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17
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Posada D, Crandall KA. Felsenstein Phylogenetic Likelihood. J Mol Evol 2021; 89:134-145. [PMID: 33438113 PMCID: PMC7803665 DOI: 10.1007/s00239-020-09982-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/07/2020] [Indexed: 01/08/2023]
Abstract
In 1981, the Journal of Molecular Evolution (JME) published an article entitled “Evolutionary trees from DNA sequences: A maximum likelihood approach” by Joseph (Joe) Felsenstein (J Mol Evol 17:368–376, 1981). This groundbreaking work laid the foundation for the emerging field of statistical phylogenetics, providing a tractable way of finding maximum likelihood (ML) estimates of evolutionary trees from DNA sequence data. This paper is the second most cited (more than 9000 citations) in JME after Kimura’s (J Mol Evol 16:111–120, 1980) seminal paper on a model of nucleotide substitution (with nearly 20,000 citations). On the occasion of the 50th anniversary of JME, we elaborate on the significance of Felsenstein’s ML approach to estimating phylogenetic trees.
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Affiliation(s)
- David Posada
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain. .,Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310, Vigo, Spain. .,Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
| | - Keith A Crandall
- Computational Biology Institute and Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA. .,Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA.
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18
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Thompson CEP, Pelletier TA, Carstens BC. Genetic diversity of North American vertebrates in protected areas. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Abstract
Protected areas play a crucial role in the conservation of biodiversity; however, it is unclear if these areas have an influence on genetic diversity. As a first step towards addressing this issue, we compare the genetic diversity inside and outside of protected areas. We tested the null hypothesis that there is no difference between genetic diversity inside compared to outside of protected areas in 44 vertebrate species. By automatically skimming the Global Biodiversity Information Facility (GBIF) and the National Center for Biotechnology Information (NCBI) GenBank we obtained genetic and geographical data to be repurposed and reanalysed. Novel pipelines were used to automate the process of assigning individuals to inside or outside of protected areas and then used to calculate different measures of intraspecific diversity. Forty-eight percent of examined species showed a significant difference in the amount of nucleotide diversity they contained inside compared to outside of protected areas, with similar numbers of species containing more or less genetic diversity inside compared to outside. Although our simulation testing suggests that this result is not an artefact of sampling, it is unclear what factors influence the relative amount of genetic diversity in protected areas across species.
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Affiliation(s)
- Coleen E P Thompson
- Department of Evolution, Ecology, and Organismal Biology & Museum of Biological Diversity, The Ohio State University, Columbus, OH, USA
| | - Tara A Pelletier
- Department of Biology, Center for the Sciences, Box 6931, Radford University, Radford, VA, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology & Museum of Biological Diversity, The Ohio State University, Columbus, OH, USA
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19
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Lato DF, Golding GB. The Location of Substitutions and Bacterial Genome Arrangements. Genome Biol Evol 2020; 13:6035136. [PMID: 33320172 PMCID: PMC7851589 DOI: 10.1093/gbe/evaa260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2020] [Indexed: 01/09/2023] Open
Abstract
Increasing evidence supports the notion that different regions of a genome have unique rates of molecular change. This variation is particularly evident in bacterial genomes where previous studies have reported gene expression and essentiality tend to decrease, whereas substitution rates usually increase with increasing distance from the origin of replication. Genomic reorganization such as rearrangements occur frequently in bacteria and allow for the introduction and restructuring of genetic content, creating gradients of molecular traits along genomes. Here, we explore the interplay of these phenomena by mapping substitutions to the genomes of Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti, quantifying how many substitutions have occurred at each position in the genome. Preceding work indicates that substitution rate significantly increases with distance from the origin. Using a larger sample size and accounting for genome rearrangements through ancestral reconstruction, our analysis demonstrates that the correlation between the number of substitutions and the distance from the origin of replication is significant but small and inconsistent in direction. Some replicons had a significantly decreasing trend (E. coli and the chromosome of S. meliloti), whereas others showed the opposite significant trend (B. subtilis, Streptomyces, pSymA and pSymB in S. meliloti). dN, dS, and ω were examined across all genes and there was no significant correlation between those values and distance from the origin. This study highlights the impact that genomic rearrangements and location have on molecular trends in some bacteria, illustrating the importance of considering spatial trends in molecular evolutionary analysis. Assuming that molecular trends are exclusively in one direction can be problematic.
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Affiliation(s)
- Daniella F Lato
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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20
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Early vertebrate origin of CTCFL, a CTCF paralog, revealed by proximity-guided shark genome scaffolding. Sci Rep 2020; 10:14629. [PMID: 32884037 PMCID: PMC7471279 DOI: 10.1038/s41598-020-71602-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/17/2020] [Indexed: 11/08/2022] Open
Abstract
The nuclear protein CCCTC-binding factor (CTCF) contributes as an insulator to chromatin organization in diverse animals. The gene encoding this protein has a paralog which was first identified to be expressed exclusively in the testis in mammals and designated as CTCFL (also called BORIS). CTCFL orthologs were reported only among amniotes, and thus CTCFL was once thought to have arisen in the amniote lineage. In this study, we identified elasmobranch CTCFL orthologs, and investigated its origin with the aid of a shark genome assembly improved by proximity-guided scaffolding. Our analysis employing evolutionary interpretation of syntenic gene location suggested an earlier timing of the gene duplication between CTCF and CTCFL than previously thought, that is, around the common ancestor of extant vertebrates. Also, our transcriptomic sequencing revealed a biased expression of the catshark CTCFL in the testis, suggesting the origin of the tissue-specific localization in mammals more than 400 million years ago. To understand the historical process of the functional consolidation of the long-standing chromatin regulator CTCF, its additional paralogs remaining in some of the descendant lineages for spatially restricted transcript distribution should be taken into consideration.
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21
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The influence of a priori grouping on inference of genetic clusters: simulation study and literature review of the DAPC method. Heredity (Edinb) 2020; 125:269-280. [PMID: 32753664 PMCID: PMC7553915 DOI: 10.1038/s41437-020-0348-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 11/20/2022] Open
Abstract
Inference of genetic clusters is a key aim of population genetics, sparking development of numerous analytical methods. Within these, there is a conceptual divide between finding de novo structure versus assessment of a priori groups. Recently developed, Discriminant Analysis of Principal Components (DAPC), combines discriminant analysis (DA) with principal component (PC) analysis. When applying DAPC, the groups used in the DA (specified a priori or described de novo) need to be carefully assessed. While DAPC has rapidly become a core technique, the sensitivity of the method to misspecification of groups and how it is being empirically applied, are unknown. To address this, we conducted a simulation study examining the influence of a priori versus de novo group designations, and a literature review of how DAPC is being applied. We found that with a priori groupings, distance between genetic clusters reflected underlying FST. However, when migration rates were high and groups were described de novo there was considerable inaccuracy, both in terms of the number of genetic clusters suggested and placement of individuals into those clusters. Nearly all (90.1%) of 224 studies surveyed used DAPC to find de novo clusters, and for the majority (62.5%) the stated goal matched the results. However, most studies (52.3%) omit key run parameters, preventing repeatability and transparency. Therefore, we present recommendations for standard reporting of parameters used in DAPC analyses. The influence of groupings in genetic clustering is not unique to DAPC, and researchers need to consider their goal and which methods will be most appropriate.
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22
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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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23
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Neves JMM, Almeida JPFA, Sturaro MJ, FabrÉ NN, Pereira RJ, Mott T. Deep genetic divergence and paraphyly in cryptic species of Mugil fishes (Actinopterygii: Mugilidae). SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1729892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Jessika M. M. Neves
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - JoÃo P. F. A. Almeida
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Marcelo J. Sturaro
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Nidia N. FabrÉ
- Laboratório de Ecologia, Peixes e Pesca, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Ricardo J. Pereira
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - TamÍ Mott
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
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24
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Choi JY, Lye ZN, Groen SC, Dai X, Rughani P, Zaaijer S, Harrington ED, Juul S, Purugganan MD. Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice. Genome Biol 2020; 21:21. [PMID: 32019604 PMCID: PMC7001208 DOI: 10.1186/s13059-020-1938-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/17/2020] [Indexed: 01/23/2023] Open
Abstract
Background The circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group’s evolutionary history is not fully resolved. To address these gaps, we use long-read nanopore sequencing and assemble the genomes of two circum-basmati rice varieties. Results We generate two high-quality, chromosome-level reference genomes that represent the 12 chromosomes of Oryza. The assemblies show a contig N50 of 6.32 Mb and 10.53 Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies, we characterize structural variations segregating across circum-basmati genomes. We discover repeat expansions not observed in japonica—the rice group most closely related to circum-basmati—as well as the presence and absence variants of over 20 Mb, one of which is a circum-basmati-specific deletion of a gene regulating awn length. We further detect strong evidence of admixture between the circum-basmati and circum-aus groups. This gene flow has its greatest effect on chromosome 10, causing both structural variation and single-nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties shows three major geographically structured genetic groups: Bhutan/Nepal, India/Bangladesh/Myanmar, and Iran/Pakistan. Conclusion The availability of high-quality reference genomes allows functional and evolutionary genomic analyses providing genome-wide evidence for gene flow between circum-aus and circum-basmati, describes the nature of circum-basmati structural variation, and reveals the presence/absence variation in this important and iconic rice variety group.
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Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.
| | - Zoe N Lye
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Simon C Groen
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | | | | | | | | | - Sissel Juul
- Oxford Nanopore Technologies, New York, NY, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA. .,Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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25
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de la Haba RR, López-Hermoso C, Sánchez-Porro C, Konstantinidis KT, Ventosa A. Comparative Genomics and Phylogenomic Analysis of the Genus Salinivibrio. Front Microbiol 2019; 10:2104. [PMID: 31572321 PMCID: PMC6749099 DOI: 10.3389/fmicb.2019.02104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/27/2019] [Indexed: 12/02/2022] Open
Abstract
In the genomic era phylogenetic relationship among prokaryotes can be inferred from the core orthologous genes (OGs) or proteins in order to elucidate their evolutionary history and current taxonomy should benefits of that. The genus Salinivibrio belongs to the family Vibrionaceae and currently includes only five halophilic species, in spite the fact that new strains are very frequently isolated from hypersaline environments. Species belonging to this genus have undergone several reclassifications and, moreover, there are many strains of Salinivibrio with available genomes which have not been affiliated to the existing species or have been wrongly designated. Therefore, a phylogenetic study using the available genomic information is necessary to clarify the relationships of existing strains within this genus and to review their taxonomic affiliation. For that purpose, we have also sequenced the first complete genome of a Salinivibrio species, Salinivibrio kushneri AL184T, which was employed as a reference to order the contigs of the draft genomes of the type strains of the current species of this genus, as well as to perform a comparative analysis with all the other available Salinivibrio sp. genomes. The genome of S. kushneri AL184T was assembled in two circular chromosomes (with sizes of 2.84 Mb and 0.60 Mb, respectively), as typically occurs in members of the family Vibrionaceae, with nine complete ribosomal operons, which might explain the fast growing rate of salinivibrios cultured under laboratory conditions. Synteny analysis among the type strains of the genus revealed a high level of genomic conservation in both chromosomes, which allow us to hypothesize a slow speciation process or homogenization events taking place in this group of microorganisms to be tested experimentally in the future. Phylogenomic and orthologous average nucleotide identity (OrthoANI)/average amino acid identity (AAI) analyses also evidenced the elevated level of genetic relatedness within members of this genus and allowed to group all the Salinivibrio strains with available genomes in seven separated species. Genome-scale attribute study of the salinivibrios identified traits related to polar flagellum, facultatively anaerobic growth and osmotic response, in accordance to the phenotypic features described for species of this genus.
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Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Clara López-Hermoso
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | | | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
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26
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Godini R, Fallahi H. A brief overview of the concepts, methods and computational tools used in phylogenetic tree construction and gene prediction. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100586] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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27
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Brian JI, Davy SK, Wilkinson SP. Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts. PeerJ 2019; 7:e7178. [PMID: 31289699 PMCID: PMC6598746 DOI: 10.7717/peerj.7178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/22/2019] [Indexed: 12/23/2022] Open
Abstract
Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.
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Affiliation(s)
- Joshua I Brian
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Shaun P Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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28
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Abstract
Addressing the origin of axial-patterning machinery is essential for understanding the evolution of animal form. Historically, sponges, a lineage that branched off early in animal evolution, were thought to lack Hox and ParaHox genes, suggesting that these critical axial-patterning genes arose after sponges diverged. However, a recent study has challenged this long-held doctrine by claiming to identify ParaHox genes (Cdx family) in two calcareous sponge species, Sycon ciliatum and Leucosolenia complicata. We reanalyzed the main data sets in this paper and analyzed an additional data set that expanded the number of bilaterians represented and removed outgroup homeodomains. As in the previous study, our Neighbor-Joining analyses of the original data sets recovered a clade that included sponge and Cdx genes, whereas Bayesian analyses placed these sponge genes within the NKL subclass of homeodomains. Unlike the original study, only one of our two maximum-likelihood analyses was congruent with Cdx genes in sponges. Our analyses of our additional data set led to the sponge genes consistently being placed within the NKL subclass of homeodomains regardless of method or model. Our results show more support for these sponge genes belonging to the NKL subclass, and therefore imply that Hox and ParaHox genes arose after Porifera diverged from the rest of animals.
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Affiliation(s)
- Claudia C Pastrana
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine.,Department of Biology, University of Miami
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine.,Department of Biology, University of Florida
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine.,Department of Biology, University of Florida
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29
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Marjanović D, Laurin M. Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix. PeerJ 2019; 6:e5565. [PMID: 30631641 PMCID: PMC6322490 DOI: 10.7717/peerj.5565] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 08/12/2018] [Indexed: 01/23/2023] Open
Abstract
The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69-122) recovered, for example, Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the "temnospondyl hypothesis" on the origin of Lissamphibia (TH) to be more parsimonious than the "lepospondyl hypothesis" (LH)-though only, as we show, by one step. We report 4,200 misscored cells, over half of them due to typographic and similar accidental errors. Further, some characters were duplicated; some had only one described state; for one, most taxa were scored after presumed relatives. Even potentially continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved-we document and justify all changes to the matrix-but no characters are added, we find (Analysis R1) much longer trees with, for example, monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; and Anthracosauria either crownward or rootward of Temnospondyli. The LH is nine steps shorter than the TH (R2; constrained) and 12 steps shorter than the "polyphyly hypothesis" (PH-R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, a large clade that includes the adelogyrinids, urocordylid "nectrideans" and aïstopods occupies that position. As expected from the taxon/character ratio, most bootstrap values are low. Adding 56 terminal taxa to the original 102 increases the resolution (and decreases most bootstrap values). The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4; unconstrained) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires several more regains of lost bones than the LH. Casineria, in which we tentatively identify a postbranchial lamina, emerges rather far from amniote origins in a gephyrostegid-chroniosuchian grade. Bayesian inference (Analysis EB, settings as in R4) mostly agrees with R4. High posterior probabilities are found for Lissamphibia (1.00) and the LH (0.92); however, many branches remain weakly supported, and most are short, as expected from the small character sample. We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian inference vs. equally weighted vs. reweighted parsimony), some character complexes (e.g. preaxial/postaxial polarity in limb development), and prospects for further improvement of this matrix. Even in its revised state, the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates. Sufficient improvement will be laborious-but not difficult.
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Affiliation(s)
- David Marjanović
- Science Programme “Evolution and Geoprocesses”, Museum für Naturkunde—Leibniz Institute for Evolutionary and Biodiversity Research, Berlin, Germany
| | - Michel Laurin
- Centre de Recherches sur la Paléobiologie et les Paléoenvironnements (CR2P), Centre national de la Recherche scientifique (CNRS)/Muséum national d’Histoire naturelle (MNHN)/Sorbonne Université, Paris, France
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30
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Betancur-R R, Arcila D, Vari RP, Hughes LC, Oliveira C, Sabaj MH, Ortí G. Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes. Evolution 2018; 73:329-345. [PMID: 30426469 DOI: 10.1111/evo.13649] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 11/30/2022]
Abstract
Phylogenomic studies using genome-wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than 1000 exons, 500 ultraconserved element (UCE) loci, and transcriptomic sequences that support incongruent hypotheses. The contentious non-monophyly of the order Characiformes proposed by two studies is shown to be a spurious outcome induced by sample contamination in the transcriptomic dataset and an ambiguous result due to poor taxonomic sampling in the UCE dataset. By exploring the effects of number of taxa and loci used for analysis, we show that the power of GGI to discriminate among competing hypotheses is diminished by limited taxonomic sampling, but not equally sensitive to gene sampling. Taken together, our results reinforce the notion that merely increasing the number of genetic loci for a few representative taxa is not a robust strategy to advance phylogenetic knowledge of recalcitrant groups. We leverage the expanded exon capture dataset generated here for Characiformes (206 species in 23 out of 24 families) to produce a comprehensive phylogeny and a revised classification of the order.
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Affiliation(s)
- Ricardo Betancur-R
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico, 00931.,Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013
| | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, Oklahoma, 73019
| | - Richard P Vari
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, Oklahoma, 73019
| | - Lily C Hughes
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Department of Biological Sciences, The George Washington University, Washington, DC, 20052
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Mark H Sabaj
- Department of Ichthyology, The Academy of Natural Sciences of Drexel University, Philadelphia, Pennsylvania, 19103
| | - Guillermo Ortí
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Department of Biological Sciences, The George Washington University, Washington, DC, 20052
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31
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Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. Proc Natl Acad Sci U S A 2018; 115:11030-11035. [PMID: 30297402 DOI: 10.1073/pnas.1806268115] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Secondary metabolites are key in how organisms from all domains of life interact with their environment and each other. The iron-binding molecule pulcherrimin was described a century ago, but the genes responsible for its production in budding yeasts have remained uncharacterized. Here, we used phylogenomic footprinting on 90 genomes across the budding yeast subphylum Saccharomycotina to identify the gene cluster associated with pulcherrimin production. Using targeted gene replacements in Kluyveromyces lactis, we characterized the four genes that make up the cluster, which likely encode two pulcherriminic acid biosynthesis enzymes, a pulcherrimin transporter, and a transcription factor involved in both biosynthesis and transport. The requirement of a functional putative transporter to utilize extracellular pulcherrimin-complexed iron demonstrates that pulcherriminic acid is a siderophore, a chelator that binds iron outside the cell for subsequent uptake. Surprisingly, we identified homologs of the putative transporter and transcription factor genes in multiple yeast genera that lacked the biosynthesis genes and could not make pulcherrimin, including the model yeast Saccharomyces cerevisiae We deleted these previously uncharacterized genes and showed they are also required for pulcherrimin utilization in S. cerevisiae, raising the possibility that other genes of unknown function are linked to secondary metabolism. Phylogenetic analyses of this gene cluster suggest that pulcherrimin biosynthesis and utilization were ancestral to budding yeasts, but the biosynthesis genes and, subsequently, the utilization genes, were lost in many lineages, mirroring other microbial public goods systems that lead to the rise of cheater organisms.
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32
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Boreotropical range expansion and long-distance dispersal explain two amphi-Pacific tropical disjunctions in Sabiaceae. Mol Phylogenet Evol 2018; 124:181-191. [DOI: 10.1016/j.ympev.2018.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 11/15/2022]
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33
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de Sampaio WB, de Oliveira FSS, de Carvalho Filho AO, Silva AC, de Paiva AC, Gattass M. Classification of breast tissues into mass and non-mass by means of the micro-genetic algorithm, phylogenetic trees, LBP and SVM. COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING: IMAGING & VISUALIZATION 2018. [DOI: 10.1080/21681163.2016.1240630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Wener Borges de Sampaio
- Applied Computing Group – NCA, Federal University of Maranhão UFMA, Campus do Bacanga, São Lus, Brazil
| | | | | | - Aristófanes Corrêa Silva
- Applied Computing Group – NCA, Federal University of Maranhão UFMA, Campus do Bacanga, São Lus, Brazil
| | - Anselmo Cardoso de Paiva
- Applied Computing Group – NCA, Federal University of Maranhão UFMA, Campus do Bacanga, São Lus, Brazil
| | - Marcelo Gattass
- Computer Science Department, Pontifical Catholic University of Rio de Janeiro – PUC-Rio, Rio de Janeiro, Brazil
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34
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Shi LX, Zhang C, Wang YP, Tang QY, Danley PD, Liu HZ. Evolutionary relationships of two balitorids (Cypriniformes, Balitoridae) revealed by comparative mitogenomics. ZOOL SCR 2018. [DOI: 10.1111/zsc.12282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Li-Xia Shi
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Chen Zhang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Yin-Ping Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Qiong-Ying Tang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- College of Life Sciences; Huzhou University; Huzhou, Zhejiang China
| | | | - Huan-Zhang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
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35
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Puttick MN, Morris JL, Williams TA, Cox CJ, Edwards D, Kenrick P, Pressel S, Wellman CH, Schneider H, Pisani D, Donoghue PCJ. The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte. Curr Biol 2018; 28:733-745.e2. [PMID: 29456145 DOI: 10.1016/j.cub.2018.01.063] [Citation(s) in RCA: 240] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/15/2018] [Accepted: 01/22/2018] [Indexed: 11/28/2022]
Abstract
The evolutionary emergence of land plant body plans transformed the planet. However, our understanding of this formative episode is mired in the uncertainty associated with the phylogenetic relationships among bryophytes (hornworts, liverworts, and mosses) and tracheophytes (vascular plants). Here we attempt to clarify this problem by analyzing a large transcriptomic dataset with models that allow for compositional heterogeneity between sites. Zygnematophyceae is resolved as sister to land plants, but we obtain several distinct relationships between bryophytes and tracheophytes. Concatenated sequence analyses that can explicitly accommodate site-specific compositional heterogeneity give more support for a mosses-liverworts clade, "Setaphyta," as the sister to all other land plants, and weak support for hornworts as the sister to all other land plants. Bryophyte monophyly is supported by gene concatenation analyses using models explicitly accommodating lineage-specific compositional heterogeneity and analyses of gene trees. Both maximum-likelihood analyses that compare the fit of each gene tree to proposed species trees and Bayesian supertree estimation based on gene trees support bryophyte monophyly. Of the 15 distinct rooted relationships for embryophytes, we reject all but three hypotheses, which differ only in the position of hornworts. Our results imply that the ancestral embryophyte was more complex than has been envisaged based on topologies recognizing liverworts as the sister lineage to all other embryophytes. This requires many phenotypic character losses and transformations in the liverwort lineage, diminishes inconsistency between phylogeny and the fossil record, and prompts re-evaluation of the phylogenetic affinity of early land plant fossils, the majority of which are considered stem tracheophytes.
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Affiliation(s)
- Mark N Puttick
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Jennifer L Morris
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal
| | - Dianne Edwards
- School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Silvia Pressel
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Charles H Wellman
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Harald Schneider
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China.
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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36
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Jelić D, Jelić M, Žutinić P, Šimunović I, Zupančič P, Naseka AM. Distribution of endangered Italian gudgeon Romanogobio benacensis (Cypriniformes, Cyprinidae, Gobioninae) with remarks on distinguishing morphological characters. Zookeys 2018:103-127. [PMID: 29430207 PMCID: PMC5806454 DOI: 10.3897/zookeys.729.20615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 10/20/2017] [Indexed: 11/20/2022] Open
Abstract
Distribution data on many freshwater fish species in Croatia are scarce and species
identifications are difficult, requiring further detailed studies. This paper presents a
report of the Italian gudgeon Romanogobiobenacensis from the Mirna River in
the Istra Peninsula in Croatia, in the south-east from its previously known distribution
range. The identification of R.benacensis in Croatia was supported
by a morphological comparison with R.benacensis from Italy and Slovenia,
the common gudgeon Gobiogobio, and the Danubian gudgeon
Gobioobtusirostris from geographically
close locations. A combination of character states (number of scales between anus and
anal-fin origin, branched pectoral-fin rays, lateral-line scales, total, abdominal, and
caudal vertebrae, and the size and number of lateral blotches) distinguishes
R.benacensis from both
G.gobio and
G.obtusirostris. The phylogenetic
analyses using mitochondrial sequences of cytochrome b gene confirmed that specimens from
the Mirna River belong to R.benacensis. Also, Reka River system
(Adriatic Sea basin) in Slovenia is inhabited by a possibly introduced Danubian gudgeon,
G.obtusirostris, and not by
R.benacensis.
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Affiliation(s)
- Dušan Jelić
- Croatian Institute for Biodiversity, Maksimirska cesta 129/5, HR-10000 Zagreb, Croatia.,BIOTA j.d.o.o./Ltd, Braće Radića 128A, HR-43290 Grubišno Polje, Croatia
| | - Mišel Jelić
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Petar Žutinić
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Ivana Šimunović
- Croatian Institute for Biodiversity, Maksimirska cesta 129/5, HR-10000 Zagreb, Croatia
| | - Primož Zupančič
- Dinaric Research Institute, Dolsko 14, SI-1262 Dol pri Ljubljani, Slovenia
| | - Alexander M Naseka
- Dinaric Research Institute, Dolsko 14, SI-1262 Dol pri Ljubljani, Slovenia.,Faculty for Biology and Soil, Saint Petersburg State University, Universitetskaya Emb. 7/9, Saint Petersburg 199034, Russia
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37
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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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38
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Roig FJ, González-Candelas F, Sanjuán E, Fouz B, Feil EJ, Llorens C, Baker-Austin C, Oliver JD, Danin-Poleg Y, Gibas CJ, Kashi Y, Gulig PA, Morrison SS, Amaro C. Phylogeny of Vibrio vulnificus from the Analysis of the Core-Genome: Implications for Intra-Species Taxonomy. Front Microbiol 2018; 8:2613. [PMID: 29358930 PMCID: PMC5765525 DOI: 10.3389/fmicb.2017.02613] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/14/2017] [Indexed: 01/22/2023] Open
Abstract
Vibrio vulnificus (Vv) is a multi-host pathogenic species currently subdivided into three biotypes (Bts). The three Bts are human-pathogens, but only Bt2 is also a fish-pathogen, an ability that is conferred by a transferable virulence-plasmid (pVvbt2). Here we present a phylogenomic analysis from the core genome of 80 Vv strains belonging to the three Bts recovered from a wide range of geographical and ecological sources. We have identified five well-supported phylogenetic groups or lineages (L). L1 comprises a mixture of clinical and environmental Bt1 strains, most of them involved in human clinical cases related to raw seafood ingestion. L2 is formed by a mixture of Bt1 and Bt2 strains from various sources, including diseased fish, and is related to the aquaculture industry. L3 is also linked to the aquaculture industry and includes Bt3 strains exclusively, mostly related to wound infections or secondary septicemia after farmed-fish handling. Lastly, L4 and L5 include a few strains of Bt1 associated with specific geographical areas. The phylogenetic trees for ChrI and II are not congruent to one another, which suggests that inter- and/or intra-chromosomal rearrangements have been produced along Vv evolution. Further, the phylogenetic trees for each chromosome and the virulence plasmid were also not congruent, which also suggests that pVvbt2 has been acquired independently by different clones, probably in fish farms. From all these clones, the one with zoonotic capabilities (Bt2-Serovar E) has successfully spread worldwide. Based on these results, we propose a new updated classification of the species based on phylogenetic lineages rather than on Bts, as well as the inclusion of all Bt2 strains in a pathovar with the particular ability to cause fish vibriosis, for which we suggest the name "piscis."
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Affiliation(s)
- Francisco J Roig
- Estructura de Investigación Interdisciplinar en Biotecnología y Biomedicina BIOTECMED, University of Valencia, Valencia, Spain.,Departmento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain.,Biotechvana, Parc Cientific, Universitat de Valencia, Valencia, Spain
| | - Fernando González-Candelas
- Joint Research Unit on Infection and Public Health FISABIO-Salud Pública and Universitat de Valencia-I2SysBio, Valencia, Spain.,CIBEResp, National Network Center for Research on Epidemiology and Public Health, Instituto de Salud Carlos III, Valencia, Spain
| | - Eva Sanjuán
- Estructura de Investigación Interdisciplinar en Biotecnología y Biomedicina BIOTECMED, University of Valencia, Valencia, Spain.,Departmento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain
| | - Belén Fouz
- Estructura de Investigación Interdisciplinar en Biotecnología y Biomedicina BIOTECMED, University of Valencia, Valencia, Spain.,Departmento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain
| | - Edward J Feil
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Carlos Llorens
- Biotechvana, Parc Cientific, Universitat de Valencia, Valencia, Spain
| | - Craig Baker-Austin
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
| | - James D Oliver
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States.,Duke University Marine Lab, Beaufort, NC, United States
| | - Yael Danin-Poleg
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Cynthia J Gibas
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Yechezkel Kashi
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Paul A Gulig
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, United States
| | - Shatavia S Morrison
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Carmen Amaro
- Estructura de Investigación Interdisciplinar en Biotecnología y Biomedicina BIOTECMED, University of Valencia, Valencia, Spain.,Departmento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain
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39
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Jain A, Roustan V, Weckwerth W, Ebersberger I. Studying AMPK in an Evolutionary Context. Methods Mol Biol 2018; 1732:111-142. [PMID: 29480472 DOI: 10.1007/978-1-4939-7598-3_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The AMPK protein kinase forms the heart of a complex network controlling the metabolic activities in a eukaryotic cell. Unraveling the steps by which this pathway evolved from its primordial roots in the last eukaryotic common ancestor to its present status in contemporary species has the potential to shed light on the evolution of eukaryotes. A homolog search for the proteins interacting in this pathway is considerably straightforward. However, interpreting the results, when reconstructing the evolutionary history of the pathway over larger evolutionary distances, bears a number of pitfalls. With this in mind, we present a protocol to trace a metabolic pathway across contemporary species and backward in evolutionary time. Alongside the individual analysis steps, we provide guidelines for data interpretation generalizing beyond the analysis of AMPK.
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Affiliation(s)
- Arpit Jain
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Valentin Roustan
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany. .,Senckenberg Biodiversity and Climate Research Centre (BIK-F), Frankfurt, Germany.
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40
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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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41
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Susko E. Using Minimum Bootstrap support for Splits to Construct Confidence Regions for Trees. Evol Bioinform Online 2017. [DOI: 10.1177/117693430600200030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Many of the estimated topologies in phylogenetic studies are presented with the bootstrap support for each of the splits in the topology indicated. If phylogenetic estimation is unbiased, high bootstrap support for a split suggests that there is a good deal of certainty that the split actually is present in the tree and low bootstrap support suggests that one or more of the taxa on one side of the estimated split might in reality be located with taxa on the other side. In the latter case the follow-up questions about how many and which of the taxa could reasonably be incorrectly placed as well as where they might alternatively be placed are not addressed through the presented bootstrap support. We present here an algorithm that finds the set of all trees with minimum bootstrap support for their splits greater than some given value. The output is a ranked list of trees, ranked according to the minimum bootstrap supports for splits in the trees. The number of such trees and their topologies provides useful supplementary information in bootstrap analyses about the reasons for low bootstrap support for splits. We also present ways of quantifying low bootstrap support by considering the set of all topologies with minimum bootstrap greater than some quantity as providing a confidence region of topologies. Using a double bootstrap we are able to choose a cutoff so that the set of topologies with minimum bootstrap support for a split greater than that cutoff gives an approximate 95% confidence region. As with bootstrap support one advantage of the methods is that they are generally applicable to the wide variety of phylogenetic estimation methods.
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Affiliation(s)
- Edward Susko
- Genome Atlantic, Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
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42
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Ribeiro JRI, Ohba SY, Pluot-Sigwalt D, Stefanello F, Bu W, Meyin-A-Ebong SE, Guilbert E. Phylogenetic analysis and revision of subfamily classification of Belostomatidae genera (Insecta: Heteroptera: Nepomorpha). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx041] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- JosÉ Ricardo I Ribeiro
- Universidade Federal do Pampa, Campus São Gabriel, Avenida Antônio Trilha, Centro, Brasil
| | - Shin-Ya Ohba
- Biological Laboratory, Faculty of Education, Nagasaki University, Nagasaki, Japan
| | | | - Fabiano Stefanello
- Laboratório de Biologia Comparada e Abelhas, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, São Paulo, Brazil
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | | | - Eric Guilbert
- Muséum national d’Histoire naturelle, MECADEV - UMR 7179 MNHN/CNRS, Paris, France
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43
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Nuclear and mitochondrial phylogeny of Rossella (Hexactinellida: Lyssacinosida, Rossellidae): a species and a species flock in the Southern Ocean. Polar Biol 2017. [DOI: 10.1007/s00300-017-2155-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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44
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Selvatti AP, Galvão A, Pereira AG, Pedreira Gonzaga L, Russo CADM. An African Origin of the Eurylaimides (Passeriformes) and the Successful Diversification of the Ground-Foraging Pittas (Pittidae). Mol Biol Evol 2017; 34:483-499. [PMID: 28069777 DOI: 10.1093/molbev/msw250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The Eurylaimides is one of the few passerine groups with a pantropical distribution. In this study, we generated a multi-calibrated tree with 83% of eurylaimid species diversity based on 30 molecular loci. Particular attention was given to the monotypic Sapayoidae to reconstruct the biogeography of this radiation. We conducted several topological tests including nonoverlapping subsampling of the concatenated alignment and coalescent species tree reconstruction. These tests firmly placed the South American Sapayoidae as the sister group to all other Eurylaimides families (split at ∼28 Ma), with increasing branch support as highly variable sites were removed. This topology is consistent with the breakup of the insular connection between Africa and South America (Atlantogea) that took place between the middle Eocene and the early Oligocene. We recovered Africa as the cradle of the core Eurylaimides, and this result is supported by all African lineages corresponding to the oldest splits within each family in this group. Our timescale suggests that desertification and the uplift of the Tibetan Plateau caused a parallel divergence between African and Asian lineages in all major clades in the core Eurylaimides at 22-9 Ma. We also propose that the ground-foraging behavior in the Pittidae ancestor allowed the pitta lineage to thrive and coexist with the older arboreal lineages of the core Eurylaimides. In contrast, the diversification of pittas in Australia was likely hindered by direct competition with the endemic ground-foraging oscines that had been well established in that continent since the Eocene.
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Affiliation(s)
- Alexandre Pedro Selvatti
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Instituto de Biologia, Rio de Janeiro, RJ, Brazil
| | - Ana Galvão
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Anieli Guirro Pereira
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Instituto de Biologia, Rio de Janeiro, RJ, Brazil
| | - Luiz Pedreira Gonzaga
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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45
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Vicente Dos Santos V, Tixier MS. Which molecular markers for assessing which taxonomic level? The case study of the mite family Phytoseiidae (Acari: Mesostigmata). Cladistics 2017; 33:251-267. [PMID: 34715727 DOI: 10.1111/cla.12166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2016] [Indexed: 11/29/2022] Open
Abstract
The use of molecular markers for resolving systematics issues has improved our knowledge of life history. However, for the taxa studied herein-the predatory mite family Phytoseiidae-molecular phylogeny is impeded by a lack of suitable markers for deeper taxonomic levels. This study aims (i) to establish DNA amplification protocols for molecular markers known to resolve supraspecific nodes in other taxa, (ii) to determine their individual performance in assessing the clustering of species, genera, tribes and subfamilies, and (iii) to characterize the additional information provided when markers are concatenated. A new phylogenetic index is proposed based on ecological concepts, considering trees as a community of nodes. New and efficient protocols for DNA amplification of six molecular markers are provided. The concatenated tree globally provides more robust and reliable information, especially for deeper nodes. However, for assessing species identification and within-genera phylogenies, the combined use of six markers does not seem necessary, underlining the need to resize experiments depending on their taxonomic objectives. Finally, this study lays the methodological foundations with which to test the present Phytoseiidae classification as the first phylogeny obtained shows incongruence with the present morphological classification.
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Affiliation(s)
- Victor Vicente Dos Santos
- Montpellier SupAgro, Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations (INRA/IRD/CIRAD/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, Montferrier-sur-Lez Cedex, 34988, France
| | - Marie-Stephane Tixier
- Montpellier SupAgro, Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations (INRA/IRD/CIRAD/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, Montferrier-sur-Lez Cedex, 34988, France
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46
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Anderson FE, Williams BW, Horn KM, Erséus C, Halanych KM, Santos SR, James SW. Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms. BMC Evol Biol 2017; 17:123. [PMID: 28558722 PMCID: PMC5450073 DOI: 10.1186/s12862-017-0973-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 05/18/2017] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved. METHODS In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families and a representative of Moniligastridae, another terrestrial annelid group thought to be closely related to Crassiclitellata. We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion. RESULTS AND DISCUSSION We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea. CONCLUSIONS These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships.
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Affiliation(s)
- Frank E Anderson
- Department of Zoology, Southern Illinois University, Carbondale, IL, 62901, USA.
| | - Bronwyn W Williams
- Department of Zoology, Southern Illinois University, Carbondale, IL, 62901, USA
- North Carolina Museum of Natural Sciences, Research Laboratory, Raleigh, North Carolina, 27699, USA
| | - Kevin M Horn
- Department of Zoology, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Christer Erséus
- Department of Biological and Environmental Sciences, University of Gothenburg, 405 30, Göteborg, SE, Sweden
| | - Kenneth M Halanych
- Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Scott R Santos
- Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Samuel W James
- Department of Biology, University of Iowa, Iowa City, Iowa, 52242, USA
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47
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van Hooff JJE, Snel B, Kops GJPL. Unique Phylogenetic Distributions of the Ska and Dam1 Complexes Support Functional Analogy and Suggest Multiple Parallel Displacements of Ska by Dam1. Genome Biol Evol 2017; 9:1295-1303. [PMID: 28472331 PMCID: PMC5439489 DOI: 10.1093/gbe/evx088] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 12/27/2022] Open
Abstract
Faithful chromosome segregation relies on kinetochores, the large protein complexes that connect chromatin to spindle microtubules. Although human and yeast kinetochores are largely homologous, they track microtubules with the unrelated protein complexes Ska (Ska-C, human) and Dam1 (Dam1-C, yeast). We here uncovered that Ska-C and Dam1-C are both widespread among eukaryotes, but in an exceptionally inverse manner, supporting their functional analogy. Within the complexes, all Ska-C and various Dam1-C subunits are ancient paralogs, showing that gene duplication shaped these complexes. We examined various evolutionary scenarios to explain the nearly mutually exclusive patterns of Ska-C and Dam1-C in present-day species. We propose that Ska-C was present in the last eukaryotic common ancestor, that subsequently Dam1-C displaced Ska-C in an early fungus and was horizontally transferred to diverse non-fungal lineages, displacing Ska-C in these lineages too.
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Affiliation(s)
- Jolien J. E. van Hooff
- Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, The Netherlands
- Molecular Cancer Research, University Medical Center Utrecht, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, The Netherlands
| | - Geert J. P. L. Kops
- Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- Molecular Cancer Research, University Medical Center Utrecht, The Netherlands
- Cancer Genomics Netherlands, University Medical Center Utrecht, The Netherlands
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48
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Castlebury LA, Rossman AY, Jaklitsch WJ, Vasilyeva LN. A preliminary overview of the Diaporthales based on large subunit nuclear ribosomal DNA sequences. Mycologia 2017. [DOI: 10.1080/15572536.2003.11833157] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Amy Y. Rossman
- Systematic Botany and Mycology Laboratory, USDA-ARS, 10300 Baltimore Ave., Beltsville, Maryland, USA 20705
| | | | - Larissa N. Vasilyeva
- Institute of Biology & Soil Science, Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
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49
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Kropp BR, Matheny PB. Basidiospore homoplasy and variation in theInocybe chelanensisgroup in North America. Mycologia 2017. [DOI: 10.1080/15572536.2005.11832979] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - P. Brandon Matheny
- Department of Biology, Box 351330, University of Washington, Seattle, Washington 98195-5325
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50
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Peever T, Barve M, Stone L, Kaiser W. Evolutionary relationships among Ascochyta species infecting wild and cultivated hosts in the legume tribes Cicereae and Vicieae. Mycologia 2017. [DOI: 10.1080/15572536.2007.11832601] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | - L.J. Stone
- Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430
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