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Graham AM, Lavretsky P, Wilson RE, McCracken KG. High-altitude adaptation is accompanied by strong signatures of purifying selection in the mitochondrial genomes of three Andean waterfowl. PLoS One 2024; 19:e0294842. [PMID: 38170710 PMCID: PMC10763953 DOI: 10.1371/journal.pone.0294842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024] Open
Abstract
Evidence from a variety of organisms points to convergent evolution on the mitochondria associated with a physiological response to oxygen deprivation or temperature stress, including mechanisms for high-altitude adaptation. Here, we examine whether demography and/or selection explains standing mitogenome nucleotide diversity in high-altitude adapted populations of three Andean waterfowl species: yellow-billed pintail (Anas georgica), speckled teal (Anas flavirostris), and cinnamon teal (Spatula cyanoptera). We compared a total of 60 mitogenomes from each of these three duck species (n = 20 per species) across low and high altitudes and tested whether part(s) or all of the mitogenome exhibited expected signatures of purifying selection within the high-altitude populations of these species. Historical effective population sizes (Ne) were inferred to be similar between high- and low-altitude populations of each species, suggesting that selection rather than genetic drift best explains the reduced genetic variation found in mitochondrial genes of high-altitude populations compared to low-altitude populations of the same species. Specifically, we provide evidence that establishment of these three Andean waterfowl species in the high-altitude environment, coincided at least in part with a persistent pattern of negative purifying selection acting on oxidative phosphorylation (OXPHOS) function of the mitochondria. Our results further reveal that the extent of gene-specific purifying selection has been greatest in the speckled teal, the species with the longest history of high-altitude occupancy.
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Affiliation(s)
- Allie M. Graham
- Eccles Institute for Human Genetics, University of Utah, Salt Lake City, UT, United States of America
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States of America
| | - Robert E. Wilson
- School of Natural Resources and Nebraska State Museum, University of Nebraska–Lincoln, Lincoln, NE, United States of America
| | - Kevin G. McCracken
- Department of Biology, University of Miami, Coral Gables, FL, United States of America
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States of America
- Human Genetics and Genomics, University of Miami Miller School of Medicine, Miami, FL, United States of America
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, United States of America
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2
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Patané JSL, Martins J, Setubal JC. A Guide to Phylogenomic Inference. Methods Mol Biol 2024; 2802:267-345. [PMID: 38819564 DOI: 10.1007/978-1-0716-3838-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. Phylogenomics has significant applications in fields such as evolutionary biology, systematics, comparative genomics, and conservation genetics, providing valuable insights into the origins and relationships of species and contributing to our understanding of biological diversity and evolution. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.
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Affiliation(s)
- José S L Patané
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração/Heart Institute Hospital das Clínicas - Faculdade de Medicina da Universidade de São Paulo São Paulo, São Paulo, SP, Brazil
| | - Joaquim Martins
- Integrative Omics group, Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - João Carlos Setubal
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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3
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Carnaccini S, Cáceres CJ, Gay LC, Ferreri LM, Skepner E, Burke DF, Brown IH, Geiger G, Obadan A, Rajao DS, Lewis NS, Perez DR. Antigenic mapping of the hemagglutinin of the H9 subtype influenza A viruses using sera from Japanese quail ( Coturnix c. japonica). J Virol 2023; 97:e0074323. [PMID: 37800947 PMCID: PMC10617583 DOI: 10.1128/jvi.00743-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/18/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Determining the relevant amino acids involved in antigenic drift on the surface protein hemagglutinin (HA) is critical to understand influenza virus evolution and efficient assessment of vaccine strains relative to current circulating strains. We used antigenic cartography to generate an antigenic map of the H9 hemagglutinin (HA) using sera produced in one of the most relevant minor poultry species, Japanese quail. Key antigenic positions were identified and tested to confirm their impact on the antigenic profile. This work provides a better understanding of the antigenic diversity of the H9 HA as it relates to reactivity to quail sera and will facilitate a rational approach for selecting more efficacious vaccines against poultry-origin H9 influenza viruses in minor poultry species.
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Affiliation(s)
- Silvia Carnaccini
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - C. Joaquín Cáceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - L. Claire Gay
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Lucas M. Ferreri
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Eugene Skepner
- Center for Pathogen Evolution, University of Cambridge, Cambridge, United Kingdom
| | - David F. Burke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ian H. Brown
- Animal and Plant Health Agency (APHA), Weybridge, United Kingdom
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Adebimpe Obadan
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Daniela S. Rajao
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Nicola S. Lewis
- World Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
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4
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Commichaux S, Rand H, Javkar K, Molloy EK, Pettengill JB, Pightling A, Hoffmann M, Pop M, Jayeola V, Foley S, Luo Y. Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation. BMC Genomics 2023; 24:165. [PMID: 37016310 PMCID: PMC10074901 DOI: 10.1186/s12864-023-09245-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne outbreak of Salmonella in over a decade. The epidemiological investigation suggested two farms as the likely source of contamination. However, single nucleotide polymorphism (SNP) analysis of the whole genome sequencing data showed that none of the Salmonella isolates collected from the farm regions were linked to the clinical isolates-preventing the use of phylogenetics in source identification. Here, we explored an alternative method for analyzing the whole genome sequencing data driven by the hypothesis that if the outbreak strain had come from the farm regions, then the clinical isolates would disproportionately contain plasmids found in isolates from the farm regions due to horizontal transfer. RESULTS SNP analysis confirmed that the clinical isolates formed a single, nearly-clonal clade with evidence for ancestry in California going back a decade. The clinical clade had a large core genome (4,399 genes) and a large and sparsely distributed accessory genome (2,577 genes, at least 64% on plasmids). At least 20 plasmid types occurred in the clinical clade, more than were found in the literature for Salmonella Newport. A small number of plasmids, 14 from 13 clinical isolates and 17 from 8 farm isolates, were found to be highly similar (> 95% identical)-indicating they might be related by horizontal transfer. Phylogenetic analysis was unable to determine the geographic origin, isolation source, or time of transfer of the plasmids, likely due to their promiscuous and transient nature. However, our resampling analysis suggested that observing a similar number and combination of highly similar plasmids in random samples of environmental Salmonella enterica within the NCBI Pathogen Detection database was unlikely, supporting a connection between the outbreak strain and the farms implicated by the epidemiological investigation. CONCLUSION Horizontally transferred plasmids provided evidence for a connection between clinical isolates and the farms implicated as the source of the outbreak. Our case study suggests that such analyses might add a new dimension to source tracking investigations, but highlights the need for detailed and accurate metadata, more extensive environmental sampling, and a better understanding of plasmid molecular evolution.
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Affiliation(s)
- Seth Commichaux
- Center for Food Safety and Nutrition, Food and Drug Administration, Laurel, MD, USA.
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
- Biological Science Graduate Program, University of Maryland, College Park, MD, USA.
| | - Hugh Rand
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Kiran Javkar
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD, USA
| | - Erin K Molloy
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - James B Pettengill
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Arthur Pightling
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Maria Hoffmann
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Victor Jayeola
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Steven Foley
- Food and Drug Administration, National Center for Toxicological Research, Jefferson, AR, USA
| | - Yan Luo
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
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Roadmap to the study of gene and protein phylogeny and evolution-A practical guide. PLoS One 2023; 18:e0279597. [PMID: 36827278 PMCID: PMC9955684 DOI: 10.1371/journal.pone.0279597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 12/12/2022] [Indexed: 02/25/2023] Open
Abstract
Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies of biodiversity and organismal evolution. This accumulation of data has been paralleled by the creation of numerous public biological databases through which the scientific community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. However, to find the appropriate databases and bioinformatic tools for respective inquiries and aims can be challenging. Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. We provide a protocol for information extraction from biological databases and simple phylogenetic reconstruction using probabilistic and distance methods, facilitating the study of biodiversity and evolution at the molecular level for the broad scientific community.
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6
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Vilani NMJ, Monteiro DALV, Einat H, Jerome B, Fix VD, de Lauro CAM, Oliveira BDM. Melanopsin expression in the retinas of owls with different daily activity patterns. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2022. [DOI: 10.1016/j.jpap.2022.100155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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7
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Sandoval-Padilla I, Zamora-Tavares MDP, Ruiz-Sánchez E, Pérez-Alquicira J, Vargas-Ponce O. Characterization of the plastome of Physaliscordata and comparative analysis of eight species of Physalis sensu stricto. PHYTOKEYS 2022; 210:109-134. [PMID: 36760406 PMCID: PMC9836641 DOI: 10.3897/phytokeys.210.85668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/07/2022] [Indexed: 06/18/2023]
Abstract
In this study, we sequenced, assembled, and annotated the plastome of Physaliscordata Mill. and compared it with seven species of the genus Physalis sensu stricto. Sequencing, annotating, and comparing plastomes allow us to understand the evolutionary mechanisms associated with physiological functions, select possible molecular markers, and identify the types of selection that have acted in different regions of the genome. The plastome of P.cordata is 157,000 bp long and presents the typical quadripartite structure with a large single-copy (LSC) region of 87,267 bp and a small single-copy (SSC) region of 18,501 bp, which are separated by two inverted repeat (IRs) regions of 25,616 bp each. These values are similar to those found in the other species, except for P.angulata L. and P.pruinosa L., which presented an expansion of the LSC region and a contraction of the IR regions. The plastome in all Physalis species studied shows variation in the boundary of the regions with three distinct types, the percentage of the sequence identity between coding and non-coding regions, and the number of repetitive regions and microsatellites. Four genes and 10 intergenic regions show promise as molecular markers and eight genes were under positive selection. The maximum likelihood analysis showed that the plastome is a good source of information for phylogenetic inference in the genus, given the high support values and absence of polytomies. In the Physalis plastomes analyzed here, the differences found, the positive selection of genes, and the phylogenetic relationships do not show trends that correspond to the biological or ecological characteristics of the species studied.
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Affiliation(s)
- Isaac Sandoval-Padilla
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - María del Pilar Zamora-Tavares
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - Eduardo Ruiz-Sánchez
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - Jessica Pérez-Alquicira
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
- Laboratorio Nacional de Identificación y Caracterización Vegetal A(LaniVeg), Consejo Nacional de Ciencia y Tecnología (CONACyT), Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoCONACYTMexico CityMexico
| | - Ofelia Vargas-Ponce
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
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8
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Graham SP, Walker D, Kelehear C, Jensen JB, Dunn K, Guyer C. Georgia Distribution and Characterization of Species within the Eurycea quadridigitata Complex. SOUTHEAST NAT 2022. [DOI: 10.1656/058.021.0207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Sean P. Graham
- Department of Biology, Geology, and Physical Sciences, Sul Ross State University, Alpine, TX 79832
| | - Donald Walker
- Department of Biology, Box 0060, Middle Tennessee State University, Murfreesboro, TN 37132
| | - Crystal Kelehear
- Department of Biology, Geology, and Physical Sciences, Sul Ross State University, Alpine, TX 79832
| | - John B. Jensen
- Conservation Matters, LLC, PO Box 662, Monticello, GA 31064
| | - Khorizon Dunn
- Department of Biological Sciences, Auburn University, Auburn, AL 36849
| | - Craig Guyer
- Department of Biological Sciences, Auburn University, Auburn, AL 36849
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Santander-Jimenez S, Vega-Rodriguez MA, Sousa L. Inter-Algorithm Multiobjective Cooperation for Phylogenetic Reconstruction on Amino Acid Data. IEEE TRANSACTIONS ON CYBERNETICS 2022; 52:3577-3591. [PMID: 32915754 DOI: 10.1109/tcyb.2020.2995464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Inter-algorithm cooperative approaches are increasingly gaining interest as a way to boost the search capabilities of evolutionary algorithms (EAs). However, the growing complexity of real-world optimization problems demands new cooperative designs that implement performance-driven strategies to improve the solution quality. This article explores multiobjective cooperation to address an important problem in bioinformatics: the reconstruction of phylogenetic histories from amino acid data. The proposed method is built using representative algorithms from the three main multiobjective design trends: 1) nondominated sorting genetic algorithm II; 2) indicator-based evolutionary algorithm; and 3) multiobjective evolutionary algorithm based on decomposition. The cooperation is supervised by an Elite island component that, along with managing migrations, retrieves multitrend performance feedback from each approach to run additional instantiations of the most satisfying algorithm in each stage of the execution. Experimentation on five real-world problem instances shows the benefits of the proposal to handle complex optimization tasks, in comparison to stand-alone algorithms, standard island models, and other state-of-the-art methods.
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10
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Di-Nizo CB, Suárez-Villota EY, Silva MJJ. Species limits and recent diversification of Cerradomys (Sigmodontinae: Oryzomyini) during the Pleistocene. PeerJ 2022; 10:e13011. [PMID: 35480563 PMCID: PMC9037131 DOI: 10.7717/peerj.13011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/04/2022] [Indexed: 01/11/2023] Open
Abstract
Cerradomys is a genus of the tribe Oryzomyini with eight species currently recognized, and a controversial taxonomy. These species are mainly distributed in the South America dry diagonal, but some species extend into Atlantic Forest, reaching the coastal sandy plains known as Restingas. This study aimed to address species limits and patterns of diversification of Cerradomys species. For this purpose, we performed cytogenetic and molecular analyses (phylogeny, coalescent species delimitation, barcoding, and divergence times estimation) using multiple mitochondrial and nuclear markers on a comprehensive sampling, representing all nominal taxa reported so far. Chromosomal information was a robust marker recognizing eight Cerradomys species. Reciprocal monophyly was recovered for all the species, except for C. subflavus. These results together with coalescent analyses recovered eight species as the most congruent species delimitation scenario for the genus (mean C tax : 0.72). Divergence time estimates revealed that Cerradomys' diversification occurred about 1.32 million years ago (Mya) during the Pleistocene. Although our results conservatively support the eight Cerradomys species described so far, different lines of evidence suggest that C. langguthi and C. subflavus could potentially be species-complexes. We discussed this scenario in the light of multiple evolutionary processes within and between species and populations, since Cerradomys comprises a species group with recent diversification affected by Pleistocene climatic changes and by the complex biogeographic history of South America dry diagonal. This work supports that the diversity of Cerradomys is underestimated and reiterates that interdisciplinary approaches are mandatory to identify small rodent species properly, and to unhide cryptic species.
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Affiliation(s)
- Camilla B. Di-Nizo
- Laboratório de Ecologia e Evolução, Instituto Butantan, São Paulo, São Paulo, Brazil
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum A. Koenig, Bonn, Germany
| | - Elkin Y. Suárez-Villota
- Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Concepción, Chile
| | - Maria José J. Silva
- Laboratório de Ecologia e Evolução, Instituto Butantan, São Paulo, São Paulo, Brazil
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11
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Padrón PS, Pyrcz TW, Willmott KR. A Contribution Towards Resolving the Systematics of the High-Altitude Tropical Andean Satyrine Genus Altopedaliodes Forster, 1964 (Lepidoptera, Nymphalinae: Satyrinae). NEOTROPICAL ENTOMOLOGY 2021; 50:767-803. [PMID: 34350567 DOI: 10.1007/s13744-021-00897-9] [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: 03/10/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The first phylogenetic hypotheses for the high Andean satyrine butterfly genus Altopedaliodes is proposed based on sequence data from mitochondrial (COI and COII) and nuclear (EF-1α) genes. Four species previously included in the genus were found not to be closely related to the clade containing the type species for Altopedaliodes, and these species are therefore removed and placed in the appropriate genus: Pedaliodes cocytia (C. Felder and R. Felder, 1867) n. comb., Pedaliodes nebris Thieme 1905rev. comb., Neopedaliodes tamaensis (Pyrcz and Viloria 2007) n. comb., and Altopedaliodes similis Henao, Páez and Rodríguez-M., 2017; the last name is here synonymized with Pedaliodes nebris (Thieme 1905) n. syn. A taxonomic revision of the twelve species in Altopedaliodes as newly circumscribed is presented and all the currently recognized taxa are revised. We describe two new species, A. llanganati Padrón, Pyrcz and Willmott n. sp. (Ecuador, Napo) and A. pilimbala Pyrcz and Boyer n. sp. (Colombia, Cauca), and three new subspecies, A. reissi papallacta Padrón, Pyrcz and Willmott n. ssp. (Ecuador, Napo), A. reissi dominica Pyrcz and Padrón n. ssp. (Colombia, Valle del Cauca) and A. halli cagnoni Boyer, Pyrcz and Padrón n. ssp. (Ecuador, Morona-Santiago). A new status is proposed for A. nucea Pyrcz and Viloria 1999, n. stat., we combine Altopedaliodes scydmaena (Hayward, 1968) n. comb. and Altopedaliodes belmira (Pyrcz and Rodríguez, 2004), n. comb., n. stat. into the genus and treat the latter taxon as a species, and we newly treat Altopedaliodes scydmaena kruegeri Pyrcz 1999n. stat. as a subspecies.
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Affiliation(s)
- Pablo Sebastián Padrón
- Laboratorio de Entomologia, Escuela de Biología, Ecología y Gestión, Univ del Azuay, Cuenca, Ecuador.
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Univ of Florida, Gainesville, FL, USA.
| | - Tomasz Wilhelm Pyrcz
- Nature Education Centre, Jagiellonian Univ, Kraków, Poland
- Invertebrate Evolution Dept, Institute of Zoology and Biomedical Research, Jagiellonian Univ, Kraków, Poland
| | - Keith Richard Willmott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Univ of Florida, Gainesville, FL, USA
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12
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Hauzman E, Pierotti MER, Bhattacharyya N, Tashiro JH, Yovanovich CAM, Campos PF, Ventura DF, Chang BSW. Simultaneous expression of UV and violet SWS1 opsins expands the visual palette in a group of freshwater snakes. Mol Biol Evol 2021; 38:5225-5240. [PMID: 34562092 PMCID: PMC8662652 DOI: 10.1093/molbev/msab285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Snakes are known to express a rod visual opsin and two cone opsins, only (SWS1, LWS), a reduced palette resulting from their supposedly fossorial origins. Dipsadid snakes in the genus Helicops are highly visual predators that successfully invaded freshwater habitats from ancestral terrestrial-only habitats. Here, we report the first case of multiple SWS1 visual pigments in a vertebrate, simultaneously expressed in different photoreceptors and conferring both UV and violet sensitivity to Helicops snakes. Molecular analysis and in vitro expression confirmed the presence of two functional SWS1 opsins, likely the result of recent gene duplication. Evolutionary analyses indicate that each sws1 variant has undergone different evolutionary paths with strong purifying selection acting on the UV-sensitive copy and dN/dS ∼1 on the violet-sensitive copy. Site-directed mutagenesis points to the functional role of a single amino acid substitution, Phe86Val, in the large spectral shift between UV and violet opsins. In addition, higher densities of photoreceptors and SWS1 cones in the ventral retina suggest improved acuity in the upper visual field possibly correlated with visually guided behaviors. The expanded visual opsin repertoire and specialized retinal architecture are likely to improve photon uptake in underwater and terrestrial environments, and provide the neural substrate for a gain in chromatic discrimination, potentially conferring unique color vision in the UV–violet range. Our findings highlight the innovative solutions undertaken by a highly specialized lineage to tackle the challenges imposed by the invasion of novel photic environments and the extraordinary diversity of evolutionary trajectories taken by visual opsin-based perception in vertebrates.
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Affiliation(s)
- Einat Hauzman
- Department of Experimental Psychology, Psychology Institute, University of São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Michele E R Pierotti
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Nihar Bhattacharyya
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Juliana H Tashiro
- Department of Experimental Psychology, Psychology Institute, University of São Paulo, São Paulo, Brazil
| | - Carola A M Yovanovich
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Pollyanna F Campos
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Dora F Ventura
- Department of Experimental Psychology, Psychology Institute, University of São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Belinda S W Chang
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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Blue mussels of the Mytilus edulis species complex from South America: The application of species delimitation models to DNA sequence variation. PLoS One 2021; 16:e0256961. [PMID: 34473778 PMCID: PMC8412288 DOI: 10.1371/journal.pone.0256961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Smooth-shelled blue mussels, Mytilus spp., have a worldwide antitropical distribution and are ecologically and economically important. Mussels of the Mytilus edulis species complex have been the focus of numerous taxonomic and biogeographical studies, in particular in the Northern hemisphere, but the taxonomic classification of mussels from South America remains unclear. The present study analysed 348 mussels from 20 sites in Argentina, Chile, Uruguay and the Falkland Islands on the Atlantic and Pacific coasts of South America. We sequenced two mitochondrial locus, Cytochrome c Oxidase subunit I (625 bp) and 16S rDNA (443 bp), and one nuclear gene, ribosomal 18S rDNA (1770 bp). Mitochondrial and nuclear loci were analysed separately and in combination using maximum likelihood and Bayesian inference methods to identify the combination of the most informative dataset and model. Species delimitation using five different models (GMYC single, bGMYC, PTP, bPTP and BPP) revealed that the Mytilus edulis complex in South America is represented by three species: native M. chilensis, M. edulis, and introduced Northern Hemisphere M. galloprovincialis. However, all models failed to delimit the putative species Mytilus platensis. In contrast, however, broad spatial scale genetic structure in South America using Geneland software to analyse COI sequence variation revealed a group of native mussels (putatively M. platensis) in central Argentina and the Falkland Islands. We discuss the scope of species delimitation methods and the use of nuclear and mitochondrial genetic data to the recognition of species within the Mytilus edulis complex at regional and global scales.
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14
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Berasategui A, Moller AG, Weiss B, Beck CW, Bauchiero C, Read TD, Gerardo NM, Salem H. Symbiont Genomic Features and Localization in the Bean Beetle Callosobruchus maculatus. Appl Environ Microbiol 2021; 87:e0021221. [PMID: 33863703 PMCID: PMC8174668 DOI: 10.1128/aem.00212-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/01/2021] [Indexed: 12/27/2022] Open
Abstract
A pervasive pest of stored leguminous products, the bean beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae) associates with a simple bacterial community during adulthood. Despite its economic importance, little is known about the compositional stability, heritability, localization, and metabolic potential of the bacterial symbionts of C. maculatus. In this study, we applied community profiling using 16S rRNA gene sequencing to reveal a highly conserved bacterial assembly shared between larvae and adults. Dominated by Firmicutes and Proteobacteria, this community is localized extracellularly along the epithelial lining of the bean beetle's digestive tract. Our analysis revealed that only one species, Staphylococcus gallinarum (phylum Firmicutes), is shared across all developmental stages. Isolation and whole-genome sequencing of S. gallinarum from the beetle gut yielded a circular chromosome (2.8 Mb) and one plasmid (45 kb). The strain encodes complete biosynthetic pathways for the production of B vitamins and amino acids, including tyrosine, which is increasingly recognized as an important symbiont-supplemented precursor for cuticle biosynthesis in beetles. A carbohydrate-active enzyme search revealed that the genome codes for a number of digestive enzymes, reflecting the nutritional ecology of C. maculatus. The ontogenic conservation of the gut microbiota in the bean beetle, featuring a "core" community composed of S. gallinarum, may be indicative of an adaptive role for the host. In clarifying symbiont localization and metabolic potential, we further our understanding and study of a costly pest of stored products. IMPORTANCE From supplementing essential nutrients to detoxifying plant secondary metabolites and insecticides, bacterial symbionts are a key source of adaptations for herbivorous insect pests. Despite the pervasiveness and geographical range of the bean beetle Callosobruchus maculatus, the role of microbial symbioses in its natural history remains understudied. Here, we demonstrate that the bean beetle harbors a simple gut bacterial community that is stable throughout development. This community localizes along the insect's digestive tract and is largely dominated by Staphylococcus gallinarum. In elucidating symbiont metabolic potential, we highlight its possible adaptive significance for a widespread agricultural pest.
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Affiliation(s)
| | - Abraham G. Moller
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Benjamin Weiss
- Department of Evolutionary Ecology, Johannes Gutenberg University, Mainz, Germany
| | | | | | - Timothy D. Read
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Hassan Salem
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Mutualisms Research Group, Max Planck Institute for Developmental Biology, Tübingen, Germany
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15
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Ferreira JL, Coleman I, Addison ML, Zachs T, Quigley BL, Wuichet K, Beeby M. The "Jack-of-all-Trades" Flagellum From Salmonella and E. coli Was Horizontally Acquired From an Ancestral β-Proteobacterium. Front Microbiol 2021; 12:643180. [PMID: 33859630 PMCID: PMC8042155 DOI: 10.3389/fmicb.2021.643180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/05/2021] [Indexed: 11/24/2022] Open
Abstract
The γ-proteobacteria are a group of diverse bacteria including pathogenic Escherichia, Salmonella, Vibrio, and Pseudomonas species. The majority swim in liquids with polar, sodium-driven flagella and swarm on surfaces with lateral, non-chemotactic flagella. Notable exceptions are the enteric Enterobacteriaceae such as Salmonella and E. coli. Many of the well-studied Enterobacteriaceae are gut bacteria that both swim and swarm with the same proton-driven peritrichous flagella. How different flagella evolved in closely related lineages, however, has remained unclear. Here, we describe our phylogenetic finding that Enterobacteriaceae flagella are not native polar or lateral γ-proteobacterial flagella but were horizontally acquired from an ancestral β-proteobacterium. Using electron cryo-tomography and subtomogram averaging, we confirmed that Enterobacteriaceae flagellar motors resemble contemporary β-proteobacterial motors and are distinct to the polar and lateral motors of other γ-proteobacteria. Structural comparisons support a model in which γ-proteobacterial motors have specialized, suggesting that acquisition of a β-proteobacterial flagellum may have been beneficial as a general-purpose motor suitable for adjusting to diverse conditions. This acquisition may have played a role in the development of the enteric lifestyle.
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Affiliation(s)
- Josie L Ferreira
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Izaak Coleman
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Max L Addison
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tobias Zachs
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Bonnie L Quigley
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Kristin Wuichet
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
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16
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Baggio JS, Forcelini BB, Wang NY, Ruschel RG, Mertely JC, Peres NA. Outbreak of Leaf Spot and Fruit Rot in Florida Strawberry Caused by Neopestalotiopsis spp. PLANT DISEASE 2021; 105:PDIS06201290RE. [PMID: 32762327 DOI: 10.1094/pdis-06-20-1290-re] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pestalotiopsis-like species have been reported affecting strawberry worldwide. Recently, severe and unprecedented outbreaks have been reported in Florida commercial fields where leaf, fruit, petiole, crown, and root symptoms were observed, and yield was severely affected. The taxonomic status of the fungus is confusing because it has gone through multiple reclassifications over the years. Morphological characteristics, phylogenetic analyses, and pathogenicity tests were evaluated for strawberry isolates recovered from diseased plants in Florida. Phylogenetic analyses derived from the combined internal transcribed spacer, β-tub, and tef1 regions demonstrated that although there was low genetic diversity among the strawberry isolates, there was a clear separation of the isolates in two groups. The first group included isolates recovered over a period of several years, which was identified as Neopestalotiopsis rosae. Most isolates recovered during the recent outbreaks were genetically different and may belong to a new species. On potato dextrose agar, both groups produced white, circular, and cottony colonies. From the bottom, colonies were white to pale yellow for Neopestalotiopsis sp. and pale luteous to orange for N. rosae. Spores for both groups were five-celled with three median versicolored cells. Mycelial growth and spore production were higher for the new Neopestalotiopsis sp. isolates. Isolates from both groups were pathogenic to strawberry roots and crowns. However, the new Neopestalotiopsis sp. proved more aggressive in fruit and leaf inoculation tests, confirming observations from the recent outbreaks in commercial strawberry fields in Florida.
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Affiliation(s)
- Juliana S Baggio
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, U.S.A
| | | | - Nan-Yi Wang
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, U.S.A
| | - Rafaela G Ruschel
- São Paulo State University, College of Agricultural Sciences, Botucatu, São Paulo 18610-034, Brazil
| | - James C Mertely
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, U.S.A
| | - Natalia A Peres
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, U.S.A
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17
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De Santis V, Delmastro GB, Vanetti I, Britton JR, Zaccara S. Species composition of introduced and natural minnow populations of the Phoxinus cryptic complex in the westernmost part of the Po River Basin (north Italy). Biol Invasions 2020. [DOI: 10.1007/s10530-020-02406-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractInvasive alien species are a major driver of biodiversity loss, with their impacts potentially more intense when complexes of cryptic species are involved. In freshwaters, the anthropogenic manipulation of fish communities has resulted in altered fish communities, and in Europe has increased the complexity of Phoxinus species assemblages. Here, we investigated the Phoxinus communities of the westernmost part of the Po river basin, where adjacent freshwater ecosystems (Alpine high-altitude lakes and lowland streams) are representative of different management strategies (i.e. manipulated fish communities via stocking in Alpine lakes vs. natural populations in streams). We tested the genetic composition of the cryptic Phoxinus populations inhabiting these waters, as the species are morphologically indistinct. Sequences of the mitochondrial cytochrome oxidase I (COI) were obtained from 239 specimens, with the results indicating that 17 Alpine high-altitude lakes are now populated by a complex of Phoxinus species, comprising P. septimaniae (native to the Mediterranean area of France), P. csikii (native to the Central Balkans) and P. lumaireul (native to the North Adriatic Sea basins). Their introduction resulted from their use as angling live baits. Minnow populations in lowland streams were primarily comprised of native P. lumaireul, with only a single P. csikii specimen detected. While nuclear sequences of the recombination activating gene 1 (RAG1) marker were not useful for tracking the presence of alien alleles in these stream populations, the COI data emphasised the importance of using molecular tools to investigate cryptic species complexes that have been modified by anthropogenic activities.
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18
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Morris DH, Petrova VN, Rossine FW, Parker E, Grenfell BT, Neher RA, Levin SA, Russell CA. Asynchrony between virus diversity and antibody selection limits influenza virus evolution. eLife 2020; 9:e62105. [PMID: 33174838 PMCID: PMC7748417 DOI: 10.7554/elife.62105] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022] Open
Abstract
Seasonal influenza viruses create a persistent global disease burden by evolving to escape immunity induced by prior infections and vaccinations. New antigenic variants have a substantial selective advantage at the population level, but these variants are rarely selected within-host, even in previously immune individuals. Using a mathematical model, we show that the temporal asynchrony between within-host virus exponential growth and antibody-mediated selection could limit within-host antigenic evolution. If selection for new antigenic variants acts principally at the point of initial virus inoculation, where small virus populations encounter well-matched mucosal antibodies in previously-infected individuals, there can exist protection against reinfection that does not regularly produce observable new antigenic variants within individual infected hosts. Our results provide a theoretical explanation for how virus antigenic evolution can be highly selective at the global level but nearly neutral within-host. They also suggest new avenues for improving influenza control.
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MESH Headings
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Biological Evolution
- Genetic Variation/genetics
- Humans
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza A virus/genetics
- Influenza A virus/immunology
- Influenza, Human/immunology
- Influenza, Human/transmission
- Influenza, Human/virology
- Models, Statistical
- Selection, Genetic/genetics
- Selection, Genetic/immunology
- Virion/genetics
- Virion/immunology
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Affiliation(s)
- Dylan H Morris
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - Velislava N Petrova
- Department of Human Genetics, Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | - Fernando W Rossine
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - Edyth Parker
- Department of Veterinary Medicine, University of CambridgeCambridgeUnited Kingdom
- Department of Medical Microbiology, Academic Medical Center, University of AmsterdamAmsterdamNetherlands
| | - Bryan T Grenfell
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
- Fogarty International Center, National Institutes of HealthBethesdaUnited States
| | | | - Simon A Levin
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - Colin A Russell
- Department of Medical Microbiology, Academic Medical Center, University of AmsterdamAmsterdamNetherlands
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19
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Genetic and phenotypic displacement of an endemic Barbus complex by invasive European barbel Barbus barbus in central Italy. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02379-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Zaccara S, Patiño J, Convey P, Vanetti I, Cannone N. Multiple colonization and dispersal events hide the early origin and induce a lack of genetic structure of the moss Bryum argenteum in Antarctica. Ecol Evol 2020; 10:8959-8975. [PMID: 32884671 PMCID: PMC7452785 DOI: 10.1002/ece3.6601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 11/16/2022] Open
Abstract
The dispersal routes of taxa with transoceanic disjunctions remain poorly understood, with the potential roles of Antarctica not yet demonstrated. Mosses are suitable organisms to test direct intra-Antarctic dispersal, as major component of the extant Antarctic flora, with the cosmopolitan moss Bryum argenteum as ideal target species. We analyzed the genetic structure of B. argenteum to provide an evolutionary time frame for its radiation and shed light into its historical biogeography in the Antarctic region. We tested two alternative scenarios: (a) intra-Antarctic panmixia and (b) intra-Antarctic genetic differentiation. Furthermore, we tested for evidence of the existence of specific intra-Antarctic dispersal routes. Sixty-seven new samples (40 collected in Antarctica) were sequenced for ITS nrDNA and rps4 cpDNA regions, and phylogenetic trees of B. argenteum were constructed, with a focus on its Southern Hemisphere. Combining our new nrDNA dataset with previously published datasets, we estimated time-calibrated phylogenies based on two different substitution rates (derived from angiosperms and bryophytes) along with ancestral area estimations. Minimum spanning network and pairwise genetic distances were also calculated. B. argenteum was potentially distributed across Africa and Antarctica soon after its origin. Its earliest intra-Antarctic dispersal and diversification occurred during a warming period in the Pliocene. On the same timescale, a radiation took place involving a dispersal event from Antarctica to the sub-Antarctic islands. A more recent event of dispersal and diversification within Antarctica occurred during a warm period in the Pleistocene, creating favorable conditions also for its colonization outside the Antarctic continent worldwide. We provide evidence supporting the hypothesis that contemporary populations of B. argenteum in Antarctica integrate a history of both multiple long-range dispersal events and local persistence combined with in situ diversification. Our data support the hypothesis that B. argenteum has been characterized by strong connectivity within Antarctica, suggesting the existence of intra-Antarctic dispersal routes.
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Affiliation(s)
- Serena Zaccara
- Department of Theoretical and Applied SciencesInsubria UniversityVareseVAItaly
| | - Jairo Patiño
- Plant Conservation and BiogeographyDepartamento de BotánicaEcología y Fisiología VegetalUniversidad de La LagunaLa LagunaSpain
| | - Peter Convey
- British Antarctic SurveyNatural Environment Research CouncilHigh CrossCambridgeUK
| | - Isabella Vanetti
- Department of Theoretical and Applied SciencesInsubria UniversityVareseVAItaly
| | - Nicoletta Cannone
- Department of Science and High TechnologyInsubria UniversityComoCOItaly
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21
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Oliveira RN, Freire CC, Iamarino A, Zanotto PM, Pessoa R, Sanabani SS, Souza SPD, Castilho JG, Batista HBCR, Carnieli P, Macedo CI, Watanabe JT, Brandão PE. Rabies virus diversification in aerial and terrestrial mammals. Genet Mol Biol 2020; 43:e20190370. [PMID: 32745160 PMCID: PMC7416755 DOI: 10.1590/1678-4685-gmb-2019-0370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Rabies is a fatal zoonotic infection of the central nervous system of mammals and has been known to humans for millennia. The etiological agent, is a neurotropic RNA virus in the order Mononegavirales, family Rhabdoviridae, genus Lyssavirus. There are currently accepted to be two cycles for rabies transmission: the urban cycle and the sylvatic cycle. The fact that both cycles originated from a common RABV or lyssavirus ancestor and the adaptive divergence that occurred since then as this ancestor virus adapted to a wide range of fitness landscapes represented by reservoir species in the orders Carnivora and Chiroptera led to the emergence of the diverse RABV lineages currently found in the sylvatic and urban cycles. Here we study full genome phylogenies and the time to the most recent common ancestor (TMRCA) of the RABVs in the sylvatic and urban cycles. Results show that there were differences between the nucleotide substitution rates per site per year for the same RABV genes maintained independently in the urban and sylvatic cycles. The results identify the most suitable gene for phylogenetic analysis, heterotachy among RABV genes and the TMRCA for the two cycles.
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Affiliation(s)
- Rafael N Oliveira
- Instituto Pasteur, Laboratório de Biologia Molecular, São Paulo, SP, Brazil
| | - Caio C Freire
- Universidade de São Paulo, Instituto de Ciências Biomédicas (ICB-II), Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática, São Paulo, SP, Brazil
| | - Atila Iamarino
- Universidade de São Paulo, Instituto de Ciências Biomédicas (ICB-II), Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática, São Paulo, SP, Brazil
| | - Paolo M Zanotto
- Universidade de São Paulo, Instituto de Ciências Biomédicas (ICB-II), Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática, São Paulo, SP, Brazil
| | - Rodrigo Pessoa
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Departamento de Virologia, São Paulo, SP, Brazil
| | - Sabri S Sanabani
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Departamento de Virologia, São Paulo, SP, Brazil
| | | | - Juliana G Castilho
- Instituto Pasteur, Laboratório de Biologia Molecular, São Paulo, SP, Brazil
| | | | - Pedro Carnieli
- Instituto Pasteur, Laboratório de Biologia Molecular, São Paulo, SP, Brazil
| | - Carla I Macedo
- Instituto Pasteur, Laboratório de Biologia Molecular, São Paulo, SP, Brazil
| | - Jaqueline T Watanabe
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Departamento de Virologia, São Paulo, SP, Brazil
| | - Paulo E Brandão
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnica, Departamento de Medicina Veterinária Preventiva e Saúde Animal, São Paulo, SP, Brazil
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22
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Sandkam BA, Campello L, O’Brien C, Nandamuri SP, Gammerdinger WJ, Conte MA, Swaroop A, Carleton KL. Tbx2a Modulates Switching of RH2 and LWS Opsin Gene Expression. Mol Biol Evol 2020; 37:2002-2014. [PMID: 32191319 PMCID: PMC7849988 DOI: 10.1093/molbev/msaa062] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sensory systems are tuned by selection to maximize organismal fitness in particular environments. This tuning has implications for intraspecies communication, the maintenance of species boundaries, and speciation. Tuning of color vision largely depends on the sequence of the expressed opsin proteins. To improve tuning of visual sensitivities to shifts in habitat or foraging ecology over the course of development, many organisms change which opsins are expressed. Changes in this developmental sequence (heterochronic shifts) can create differences in visual sensitivity among closely related species. The genetic mechanisms by which these developmental shifts occur are poorly understood. Here, we use quantitative trait locus analyses, genome sequencing, and gene expression studies in African cichlid fishes to identify a role for the transcription factor Tbx2a in driving a switch between long wavelength sensitive (LWS) and Rhodopsin-like (RH2) opsin expression. We identify binding sites for Tbx2a in the LWS promoter and the highly conserved locus control region of RH2 which concurrently promote LWS expression while repressing RH2 expression. We also present evidence that a single change in Tbx2a regulatory sequence has led to a species difference in visual tuning, providing the first mechanistic model for the evolution of rapid switches in sensory tuning. This difference in visual tuning likely has important roles in evolution as it corresponds to differences in diet, microhabitat choice, and male nuptial coloration.
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Affiliation(s)
| | - Laura Campello
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Conor O’Brien
- Department of Biology, University of Maryland, College Park, MD
| | | | | | - Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD
| | - Anand Swaroop
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD
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23
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Salem H, Kirsch R, Pauchet Y, Berasategui A, Fukumori K, Moriyama M, Cripps M, Windsor D, Fukatsu T, Gerardo NM. Symbiont Digestive Range Reflects Host Plant Breadth in Herbivorous Beetles. Curr Biol 2020; 30:2875-2886.e4. [PMID: 32502409 DOI: 10.1016/j.cub.2020.05.043] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/05/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
Numerous adaptations are gained in light of a symbiotic lifestyle. Here, we investigated the obligate partnership between tortoise leaf beetles (Chrysomelidae: Cassidinae) and their pectinolytic Stammera symbionts to detail how changes to the bacterium's streamlined metabolic range can shape the digestive physiology and ecological opportunity of its herbivorous host. Comparative genomics of 13 Stammera strains revealed high functional conservation, highlighted by the universal presence of polygalacturonase, a primary pectinase targeting nature's most abundant pectic class, homogalacturonan (HG). Despite this conservation, we unexpectedly discovered a disparate distribution for rhamnogalacturonan lyase, a secondary pectinase hydrolyzing the pectic heteropolymer, rhamnogalacturonan I (RG-I). Consistent with the annotation of rhamnogalacturonan lyase in Stammera, cassidines are able to depolymerize RG-I relative to beetles whose symbionts lack the gene. Given the omnipresence of HG and RG-I in foliage, Stammera that encode pectinases targeting both substrates allow their hosts to overcome a greater diversity of plant cell wall polysaccharides and maximize access to the nutritionally rich cytosol. Possibly facilitated by their symbionts' expanded digestive range, cassidines additionally endowed with rhamnogalacturonan lyase appear to utilize a broader diversity of angiosperms than those beetles whose symbionts solely supplement polygalacturonase. Our findings highlight how symbiont metabolic diversity, in concert with host adaptations, may serve as a potential source of evolutionary innovations for herbivorous lineages.
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Affiliation(s)
- Hassan Salem
- Department of Biology, Emory University, Atlanta, GA 30322, USA; National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Mutualisms Research Group, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
| | - Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | | | - Kayoko Fukumori
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Minoru Moriyama
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Michael Cripps
- AgResearch, Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Donald Windsor
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Takema Fukatsu
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
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24
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Jermiin LS, Catullo RA, Holland BR. A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics. NAR Genom Bioinform 2020; 2:lqaa041. [PMID: 33575594 PMCID: PMC7671319 DOI: 10.1093/nargab/lqaa041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.
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Affiliation(s)
- Lars S Jermiin
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Biology & Environment Science, University College Dublin, Belfield, Dublin 4, Ireland
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Renee A Catullo
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Science and Health & Hawkesbury Institute of the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
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Walker DM, Hill AJ, Albecker MA, McCoy MW, Grisnik M, Romer A, Grajal-Puche A, Camp C, Kelehear C, Wooten J, Rheubert J, Graham SP. Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity. MICROBIAL ECOLOGY 2020; 79:985-997. [PMID: 31802185 DOI: 10.1007/s00248-019-01456-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.
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Affiliation(s)
- Donald M Walker
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA.
| | - Aubree J Hill
- Department of Biology, Tennessee Technological University, 1100 N. Dixie Ave, Cookeville, TN, 38505, USA
| | - Molly A Albecker
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Michael W McCoy
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Matthew Grisnik
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA
| | - Alexander Romer
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA
| | - Alejandro Grajal-Puche
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA
| | - Carlos Camp
- Department of Biology, Piedmont College, 1021 Central Avenue, Demorest, GA, 30535, USA
| | - Crystal Kelehear
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Ancon, Panama, Republic of Panama
- Department of Biology, Geology and Physical Sciences, Sul Ross State University, Alpine, TX, 79832, USA
| | - Jessica Wooten
- Department of Biology, Piedmont College, 1021 Central Avenue, Demorest, GA, 30535, USA
| | - Justin Rheubert
- Department of Natural Sciences, The University of Findlay, 1000 N. Main St, Findlay, OH, 45840, USA
| | - Sean P Graham
- Department of Biology, Geology and Physical Sciences, Sul Ross State University, Alpine, TX, 79832, USA
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Jensen AR, Jenkins Shaw J, Żyła D, Solodovnikov A. A total-evidence approach resolves phylogenetic placement of ‘Cafius’ gigas, a unique recently extinct rove beetle from Lord Howe Island. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Cafius gigas Lea, 1929 (Coleoptera: Staphylinidae) was a large rove beetle endemic to Lord Howe Island (LHI) resembling Cafius and the LHI flightless endemic Hesperus dolichoderes (Lea, 1925). Like several other LHI endemics, C. gigas became extinct due to human-introduced rats. It is a legacy species valuable for understanding the LHI biota in terms of evolutionary biology and historical biogeography. Whether C. gigas was a member of Cafius Curtis, 1829, restricted to oceanic shores and prone to trans-oceanic dispersal, or related to H. dolichoderes, would have different implications. We subjected C. gigas to a total-evidence phylogenetic analyses of morphological and molecular data using model-based and parsimony methods. As a result, it is transferred to Hesperus Fauvel, 1874 with the new combination Hesperus gigas (Lea, 1929) comb. nov. Our analysis indicates that the montane leaf litter inhabitant H. gigas evolved neither in situ nor from a seashore Cafius-ancestor, or from an ancestor shared by two other LHI endemic congeners, Hesperus pacificus Olliff, 1887 and H. dolichoderes. It also suggests that all three Hesperus species that currently occur on LHI could have evolved on various seamounts at various times before reaching LHI.
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Affiliation(s)
- Arn Rytter Jensen
- Natural History Museum of Denmark, Universitetsparken, Copenhagen, Denmark
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome Italy
| | - Josh Jenkins Shaw
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dagmara Żyła
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Osborn Dr, Ames, IA, USA
- Department of Invertebrate Zoology and Parasitology, University of Gdańsk, Wita Stwosza, Gdańsk, Poland
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Bacillus subtilis EA-CB0575 genome reveals clues for plant growth promotion and potential for sustainable agriculture. Funct Integr Genomics 2020; 20:575-589. [PMID: 32198678 DOI: 10.1007/s10142-020-00736-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/17/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022]
Abstract
Bacillus subtilis is a remarkably diverse bacterial species that displays many ecological functions. Given its genomic diversity, the strain Bacillus subtilis EA-CB0575, isolated from the rhizosphere of a banana plant, was sequenced and assembled to determine the genomic potential associated with its plant growth promotion potential. The genome was sequenced by Illumina technology and assembled using Velvet 1.2.10, resulting in a whole genome of 4.09 Mb with 4332 genes. Genes involved in the production of indoles, siderophores, lipopeptides, volatile compounds, phytase, bacilibactin, and nitrogenase were predicted by gene annotation or by metabolic pathway prediction by RAST. These potential traits were determined using in vitro biochemical tests, finding that B. subtilis EA-CB0575 produces two families of lipopeptides (surfactin and fengycin), solubilizes phosphate, fixes nitrogen, and produces indole and siderophores compounds. Finally, strain EA-CB0575 increased 34.60% the total dry weight (TDW) of tomato plants with respect to non-inoculated plants at greenhouse level. These results suggest that the identification of strain-specific genes and predicted metabolic pathways might explain the strain potential to promote plant growth by several mechanisms of action, accelerating the development of plant biostimulants for sustainable agricultural.
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Sato T, Abramov AV, Raichev EG, Kosintsev PA, Väinölä R, Murakami T, Kaneko Y, Masuda R. Phylogeography and population history of the least weasel ( Mustela nivalis) in the Palearctic based on multilocus analysis. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takuma Sato
- Department of Natural History Sciences, Graduate School of Science Hokkaido University Sapporo Japan
| | - Alexei V. Abramov
- Zoological Institute Russian Academy of Sciences St. Petersburg Russia
| | | | - Pavel A. Kosintsev
- Institute of Plant and Animal Ecology Ural Branch, Russian Academy of Sciences Ekaterinburg Russia
- Ural Federal University Ekaterinburg Russia
| | - Risto Väinölä
- Finnish Museum of Natural History University of Helsinki Helsinki Finland
| | | | - Yayoi Kaneko
- Faculty of Agriculture Tokyo University of Agriculture and Technology Fuchu Japan
| | - Ryuichi Masuda
- Department of Natural History Sciences, Graduate School of Science Hokkaido University Sapporo Japan
- Department of Biological Sciences, Faculty of Science Hokkaido University Sapporo Japan
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Paul GR, Leber A, Nemastil CJ, Novak KJ, Brady M, Stack-Simone S, Greninger AL, Antonara S. Identification of Mycobacterium porcinum in patients with cystic Fibrosis: Pathogen or contaminant? J Cyst Fibros 2020; 19:580-586. [PMID: 31982335 DOI: 10.1016/j.jcf.2020.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 01/03/2020] [Accepted: 01/13/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Mycobacterium porcinum is a non-tuberculous mycobacterium (NTM) identified in potable water. The identification and clinical impact of M. porcinum in patients with cystic fibrosis (CF) has not been described. In our institution, M. porcinum was isolated exclusively during hospitalization in a cluster of patients with CF. METHODS Patients with CF who were hospitalized between September 2016 and September 2018 and could expectorate sputum were included, and samples were processed per institutional guidelines. Post-hospitalization and one-year clinical outcomes on those who isolated M. porcinum in respiratory cultures were reviewed. Whole genome sequencing was performed on M. porcinum isolates obtained from patients and environmental sources to identify source of acquisition. RESULTS Review of 14 CF patients with 16 M. porcinum isolates revealed rapid time to culture positivity within 0.8 (0.04-8.0) days after admission. M. porcinum was isolated in teenagers and adults irrespective of baseline pulmonary function, body mass index, or CF genotype. Whole genome sequencing suggested all isolates belong to the same M. porcinum strain and confirmed the source of acquisition to the ice machine. Review of patients' clinical course, including three patients who underwent lung transplantation, suggested a pseudo-outbreak with minimal clinical impact. CONCLUSIONS NTM, including M. porcinum, are ubiquitous in potable water and institutional water reservoirs. Our findings suggest M. porcinum is a transient colonizer rather than a pathogen. Challenges exist in discerning the role of NTM as a contributor of pulmonary morbidity in patients with CF, and adherence to established guidelines regarding NTM related pulmonary disease remains important.
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Affiliation(s)
- Grace R Paul
- Division of Pulmonary Medicine, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205 USA.
| | - Amy Leber
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
| | - Christopher J Nemastil
- Division of Pulmonary Medicine, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205 USA.
| | - Kimberly J Novak
- Division of Pulmonary Medicine, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205 USA.
| | - Michael Brady
- Division of Infectious disease, Nationwide Children's Hospital, Columbus, OH, USA.
| | | | | | - Stella Antonara
- Department of Laboratory Services, OhioHealth, Columbus, OH, USA.
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Hsu HC, Chou WC, Kuo YF. 3D revelation of phenotypic variation, evolutionary allometry, and ancestral states of corolla shape: a case study of clade Corytholoma (subtribe Ligeriinae, family Gesneriaceae). Gigascience 2020; 9:giz155. [PMID: 31967295 PMCID: PMC6974915 DOI: 10.1093/gigascience/giz155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/22/2019] [Accepted: 12/08/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Quantification of corolla shape variations helps biologists to investigate plant diversity and evolution. 3D images capture the genuine structure and provide comprehensive spatial information. RESULTS This study applied X-ray micro-computed tomography (µCT) to acquire 3D structures of the corollas of clade Corytholoma and extracted a set of 415 3D landmarks from each specimen. By applying the geometric morphometrics (GM) to the landmarks, the first 4 principal components (PCs) in the 3D shape and 3D form analyses, respectively, accounted for 87.86% and 96.34% of the total variance. The centroid sizes of the corollas only accounted for 5.46% of the corolla shape variation, suggesting that the evolutionary allometry was weak. The 4 morphological traits corresponding to the 4 shape PCs were defined as tube curvature, lobe area, tube dilation, and lobe recurvation. Tube curvature and tube dilation were strongly associated with the pollination type and contained phylogenetic signals in clade Corytholoma. The landmarks were further used to reconstruct corolla shapes at the ancestral states. CONCLUSIONS With the integration of µCT imaging into GM, the proposed approach boosted the precision in quantifying corolla traits and improved the understanding of the morphological traits corresponding to the pollination type, impact of size on shape variation, and evolution of corolla shape in clade Corytholoma.
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Affiliation(s)
- Hao-Chun Hsu
- Department of Biomechatronics Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
| | - Wen-Chieh Chou
- Department of Biomechatronics Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
| | - Yan-Fu Kuo
- Department of Biomechatronics Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
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Naser-Khdour S, Minh BQ, Zhang W, Stone EA, Lanfear R. The Prevalence and Impact of Model Violations in Phylogenetic Analysis. Genome Biol Evol 2019; 11:3341-3352. [PMID: 31536115 PMCID: PMC6893154 DOI: 10.1093/gbe/evz193] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2019] [Indexed: 12/24/2022] Open
Abstract
In phylogenetic inference, we commonly use models of substitution which assume that sequence evolution is stationary, reversible, and homogeneous (SRH). Although the use of such models is often criticized, the extent of SRH violations and their effects on phylogenetic inference of tree topologies and edge lengths are not well understood. Here, we introduce and apply the maximal matched-pairs tests of homogeneity to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic data sets. We show that roughly one-quarter of all the partitions we analyzed (23.5%) reject the SRH assumptions, and that for 25% of data sets, tree topologies inferred from all partitions differ significantly from topologies inferred using the subset of partitions that do not reject the SRH assumptions. This proportion increases when comparing trees inferred using the subset of partitions that rejects the SRH assumptions, to those inferred from partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. Our results also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in https://github.com/roblanf/SRHtests, and the new tests we describe are available as a new option in IQ-TREE (http://www.iqtree.org).
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Affiliation(s)
- Suha Naser-Khdour
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Bui Quang Minh
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- Research School of Computer Science, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Wenqi Zhang
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eric A Stone
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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32
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Craig JM, Kim LY, Tagliacollo VA, Albert JS. Phylogenetic revision of Gymnotidae (Teleostei: Gymnotiformes), with descriptions of six subgenera. PLoS One 2019; 14:e0224599. [PMID: 31697735 PMCID: PMC6837465 DOI: 10.1371/journal.pone.0224599] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 10/18/2019] [Indexed: 12/01/2022] Open
Abstract
The diversity of gymnotid electric fishes has been intensely studied over the past 25 years, with 35 species named since 1994, compared to 11 species in the previous 236 years. Substantial effort has also been applied in recent years to documenting gymnotid interrelationships, with seven systematic studies published using morphological and molecular datasets. Nevertheless, until now, all gymnotids have been assigned to one of just two supraspecific taxa, the subfamily Electrophorinae with one genus Electrophorus and three valid species and the subfamily Gymnotine also with one genus Gymnotus and 43 valid species. This simple classification has obscured the substantial phenotypic and lineage diversity within the subfamily Gymnotine and hampered ecological and evolutionary studies of gymnotid biology. Here we present the most well-resolved and taxon-complete phylogeny of the Gymnotidae to date, including materials from all but one of the valid species. This phylogeny was constructed using a five-gene molecular dataset and a 115-character morphological dataset, enabling the inclusion of several species for which molecular data are still lacking. This phylogeny was time-calibrated using biogeographical priors in the absence of a fossil record. The tree topology is similar to those of previous studies, recovering all the major clades previously recognized with informal names. We propose a new gymnotid classification including two subfamilies (Electrophorinae and Gymnotinae) and six subgenera within the genus Gymnotus. Each subgenus exhibits a distinctive biogeographic distribution, within which most species have allopatric distributions and the subgenera are diverged from one another by an estimated 5–35 million years. We further provide robust taxonomic diagnoses, descriptions and identification keys to all gymnotid subgenera and all but four species. This new taxonomy more equitably partitions species diversity among supra-specific taxa, employing the previously vacant subgenus and subfamily ranks. This new taxonomy renders known gymnotid diversity more accessible to study by highlighting the deep divergences (chronological, geographical, genetic and morphological) among its several clades.
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Affiliation(s)
- Jack M. Craig
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States of America
- * E-mail:
| | - Lesley Y. Kim
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States of America
| | | | - James S. Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States of America
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Dimitrov KM, Abolnik C, Afonso CL, Albina E, Bahl J, Berg M, Briand FX, Brown IH, Choi KS, Chvala I, Diel DG, Durr PA, Ferreira HL, Fusaro A, Gil P, Goujgoulova GV, Grund C, Hicks JT, Joannis TM, Torchetti MK, Kolosov S, Lambrecht B, Lewis NS, Liu H, Liu H, McCullough S, Miller PJ, Monne I, Muller CP, Munir M, Reischak D, Sabra M, Samal SK, Servan de Almeida R, Shittu I, Snoeck CJ, Suarez DL, Van Borm S, Wang Z, Wong FYK. Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 74:103917. [PMID: 31200111 PMCID: PMC6876278 DOI: 10.1016/j.meegid.2019.103917] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 02/07/2023]
Abstract
Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world.
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Affiliation(s)
- Kiril M Dimitrov
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA.
| | - Celia Abolnik
- Department of Production Studies, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, Pretoria 0110, South Africa
| | - Claudio L Afonso
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA.
| | - Emmanuel Albina
- CIRAD, UMR ASTRE, F-97170 Petit-Bourg, Guadeloupe, France; ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France
| | - Justin Bahl
- Center for Ecology of Infectious Disease, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden
| | - Francois-Xavier Briand
- ANSES, Avian and Rabbit Virology Immunology and Parasitology Unit, National reference laboratory for avian Influenza and Newcastle disease, BP 53, 22440 Ploufragan, France
| | - Ian H Brown
- OIE/FAO International Reference Laboratory for Newcastle Disease, Animal and Plant Health Agency (APHA -Weybridge), Addlestone KT15 3NB, UK
| | - Kang-Seuk Choi
- Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs (MAFRA), 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea
| | - Ilya Chvala
- Federal Governmental Budgetary Institution, Federal Centre for Animal Health, FGI ARRIAH, Vladimir 600901, Russia
| | - Diego G Diel
- Department of Veterinary and Biomedical Sciences, Animal Disease, Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD, USA
| | - Peter A Durr
- CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia
| | - Helena L Ferreira
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA; University of Sao Paulo, ZMV, FZEA, Pirassununga 13635900, Brazil
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, Legnaro 35020, Italy
| | - Patricia Gil
- ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France; CIRAD, UMR ASTRE, F-34398 Montpellier, France
| | - Gabriela V Goujgoulova
- National Diagnostic and Research Veterinary Medical Institute, 15 Pencho Slaveikov blvd., Sofia 1606, Bulgaria
| | - Christian Grund
- Friedrich-Loeffler-Institut, 17493 Greifswald, Insel Riems, Germany
| | - Joseph T Hicks
- Center for Ecology of Infectious Disease, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Tony M Joannis
- Regional Laboratory for Animal Influenzas and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Mia Kim Torchetti
- National Veterinary Services Laboratories, Diagnostics and Biologics, Veterinary Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, 1920 Dayton Ave, Ames, IA 50010, USA
| | - Sergey Kolosov
- Federal Governmental Budgetary Institution, Federal Centre for Animal Health, FGI ARRIAH, Vladimir 600901, Russia
| | - Bénédicte Lambrecht
- Infectious Diseases in Animals, SCIENSANO, Groeselenberg 99, 1180, Ukkel, Brussels, Belgium
| | - Nicola S Lewis
- OIE/FAO International Reference Laboratory for Newcastle Disease, Animal and Plant Health Agency (APHA -Weybridge), Addlestone KT15 3NB, UK; Royal Veterinary College, University of London, 4 Royal College Street, London NW1 0TU, UK
| | - Haijin Liu
- College of Veterinary Medicine, Northwest A & F University, Yangling, Shaanxi 712100, PR China
| | - Hualei Liu
- China Animal Health and Epidemiology Center (CAHEC), 369 Nanjing Road, Qingdao 266032, China
| | - Sam McCullough
- CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia
| | - Patti J Miller
- Department of Population Health, College of Veterinary Medicine, University of Georgia, 953 College Station Road, Athens, GA 30602, USA
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, Legnaro 35020, Italy
| | - Claude P Muller
- Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Dilmara Reischak
- Ministério da Agricultura, Pecuária e Abastecimento, Laboratório Federal de Defesa Agropecuário, Campinas, SP 13100-105, Brazil
| | - Mahmoud Sabra
- Department of Poultry Diseases, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Siba K Samal
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Renata Servan de Almeida
- ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France; CIRAD, UMR ASTRE, F-34398 Montpellier, France
| | - Ismaila Shittu
- Regional Laboratory for Animal Influenzas and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Chantal J Snoeck
- Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - David L Suarez
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA
| | - Steven Van Borm
- Infectious Diseases in Animals, SCIENSANO, Groeselenberg 99, 1180, Ukkel, Brussels, Belgium
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center (CAHEC), 369 Nanjing Road, Qingdao 266032, China
| | - Frank Y K Wong
- CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia
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Martin P, Sonet G, Smitz N, Backeljau T. Phylogenetic analysis of the Baikalodrilus species flock (Annelida: Clitellata: Naididae), an endemic genus to Lake Baikal (Russia). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Lake Baikal is populated by an endemic genus of oligochaetes (Baikalodrilus), which currently comprises 24 morphospecies. The genus can be considered as a ‘species flock’. However, the validity of many species is questionable: the great similarity in their description and the lack of unequivocal diagnostic characters often lead species identification to an impasse. In order to clarify the systematics of this genus, we analysed two nuclear and two mitochondrial DNA markers of 40 Baikalodrilus specimens. DNA and morphological approaches are mostly congruent in suggesting ten candidate species, although two additional species are suspected. A reassessment of the taxonomic value of the morphological characteristics of Baikalodrilus suggests that there are few that can be used as distinctive, specific criteria in the genus. The association between candidate and nominal species remains problematic, except for three species identified prior to molecular analyses. Baikalodrilus trituberculum sp. nov. is described. Phylogenetic inferences suggests that the earliest split in Baikalodrilus and the time of divergence of most lineages corresponding to species are consistent with the hypothesis of a general rearrangement of the Baikal fauna, following major environmental changes due to a general cooling in the Early Pleistocene.
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Affiliation(s)
- Patrick Martin
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy and Phylogeny, Belgium
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy and Phylogeny, Belgium
| | - Nathalie Smitz
- Royal Museum of Central Africa, Department of Biology (BopCo), Belgium
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy and Phylogeny, Belgium
- University of Antwerp, Evolutionary Ecology Group, Belgium
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Zaccara S, Quadroni S, De Santis V, Vanetti I, Carosi A, Britton R, Lorenzoni M. Genetic and morphological analyses reveal a complex biogeographic pattern in the endemic barbel populations of the southern Italian peninsula. Ecol Evol 2019; 9:10185-10197. [PMID: 31624544 PMCID: PMC6787835 DOI: 10.1002/ece3.5521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 11/12/2022] Open
Abstract
The Italian peninsula is a biodiversity hotspot, with its freshwater fish fauna characterized by high levels of local endemism. Two endemic fluvio-lacustrine fishes of the genus Barbus (barbel, family Cyprinidae) have allopatric distributions in the Tyrrhenian and Adriatic basins of Italy. Barbus plebejus inhabits the mid- to northern Adriatic basins, while B. tyberinus is widespread in all central-northern basins draining into the Tyrrhenian Sea. For basins in Southern Italy draining into the southern parts of these seas, there remains a knowledge gap on their barbel populations due to no previous genetic and morphological studies, despite their apparent biogeographic isolation. Correspondingly, this study quantified the presence and distribution of barbels in the Adriatic and Tyrrhenian basins of Southern Italy through genetic and morphological analyses of 197 fish sampled across eight populations. Testing of how local isolation has influenced the evolution and persistence of these populations was completed by examining sequence variation at two mitochondrial loci (cytochrome b and D-loop) and performing geometric morphometric analyses of body shape, plus measuring 11 morphometric and meristic characters. Phylogenetic and morphological analyses revealed the presence of two genetically distinct lineages that differed significantly from adjacent B. tyberinus and B. plebejus populations. These two new taxa, here described as SI1 and SI2 Barbus lineages, are highly structured and reflect a complex mosaic biogeographic pattern that is strongly associated with the underlying hydrographical scenarios of the basins. The geographic isolation of these basins thus has high evolutionary importance that has to be considered for maintaining endemism.
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Affiliation(s)
- Serena Zaccara
- Department of Theoretical and Applied SciencesUniversity of InsubriaVareseItaly
| | - Silvia Quadroni
- Department of Theoretical and Applied SciencesUniversity of InsubriaVareseItaly
| | - Vanessa De Santis
- Department of Theoretical and Applied SciencesUniversity of InsubriaVareseItaly
| | - Isabella Vanetti
- Department of Theoretical and Applied SciencesUniversity of InsubriaVareseItaly
| | - Antonella Carosi
- Department of Chemistry, Biology and BiotechnologyUniversity of PerugiaPerugiaItaly
| | - Robert Britton
- Department of Life and Environmental SciencesFaculty of Science and TechnologyBournemouth UniversityPooleUK
| | - Massimo Lorenzoni
- Department of Chemistry, Biology and BiotechnologyUniversity of PerugiaPerugiaItaly
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Hauzman E, Kalava V, Bonci DMO, Ventura DF. Characterization of the melanopsin gene (Opn4x) of diurnal and nocturnal snakes. BMC Evol Biol 2019; 19:174. [PMID: 31462236 PMCID: PMC6714106 DOI: 10.1186/s12862-019-1500-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 08/22/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND A number of non-visual responses to light in vertebrates, such as circadian rhythm control and pupillary light reflex, are mediated by melanopsins, G-protein coupled membrane receptors, conjugated to a retinal chromophore. In non-mammalian vertebrates, melanopsin expression is variable within the retina and extra-ocular tissues. Two paralog melanopsin genes were classified in vertebrates, Opn4x and Opn4m. Snakes are highly diversified vertebrates with a wide range of daily activity patterns, which raises questions about differences in structure, function and expression pattern of their melanopsin genes. In this study, we analyzed the melanopsin genes expressed in the retinas of 18 snake species from three families (Viperidae, Elapidae, and Colubridae), and also investigated extra-retinal tissue expression. RESULTS Phylogenetic analysis revealed that the amplified gene belongs to the Opn4x group, and no expression of the Opn4m was found. The same paralog is expressed in the iris, but no extra-ocular expression was detected. Molecular evolutionary analysis indicated that melanopsins are evolving primarily under strong purifying selection, although lower evolutionary constraint was detected in snake lineages (ω = 0.2), compared to non-snake Opn4x and Opn4m (ω = 0.1). Statistical analysis of selective constraint suggests that snake phylogenetic relationships have driven stronger effects on melanopsin evolution, than the species activity pattern. In situ hybridization revealed the presence of melanopsin within cells in the outer and inner nuclear layers, in the ganglion cell layer, and intense labeling in the optic nerve. CONCLUSIONS The loss of the Opn4m gene and extra-ocular photosensitive tissues in snakes may be associated with a prolonged nocturnal/mesopic bottleneck in the early history of snake evolution. The presence of melanopsin-containing cells in all retinal nuclear layers indicates a globally photosensitive retina, and the expression in classic photoreceptor cells suggest a regionalized co-expression of melanopsin and visual opsins.
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Affiliation(s)
- Einat Hauzman
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, Av. Professor Mello Moraes, 1721, Bloco A - Sala D9. Butantã, São Paulo, SP, 05508-030, Brazil. .,Instituto Israelita de Ensino e Pesquisa Albert Einstein, São Paulo, Brazil.
| | | | - Daniela Maria Oliveira Bonci
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, Av. Professor Mello Moraes, 1721, Bloco A - Sala D9. Butantã, São Paulo, SP, 05508-030, Brazil.,Instituto Israelita de Ensino e Pesquisa Albert Einstein, São Paulo, Brazil
| | - Dora Fix Ventura
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, Av. Professor Mello Moraes, 1721, Bloco A - Sala D9. Butantã, São Paulo, SP, 05508-030, Brazil.,Instituto Israelita de Ensino e Pesquisa Albert Einstein, São Paulo, Brazil
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Garcia AK, Kaçar B. How to resurrect ancestral proteins as proxies for ancient biogeochemistry. Free Radic Biol Med 2019; 140:260-269. [PMID: 30951835 DOI: 10.1016/j.freeradbiomed.2019.03.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/11/2019] [Accepted: 03/26/2019] [Indexed: 10/27/2022]
Abstract
Throughout the history of life, enzymes have served as the primary molecular mediators of biogeochemical cycles by catalyzing the metabolic pathways that interact with geochemical substrates. The byproducts of enzymatic activities have been preserved as chemical and isotopic signatures in the geologic record. However, interpretations of these signatures are limited by the assumption that such enzymes have remained functionally conserved over billions of years of molecular evolution. By reconstructing ancient genetic sequences in conjunction with laboratory enzyme resurrection, preserved biogeochemical signatures can instead be related to experimentally constrained, ancestral enzymatic properties. We may thereby investigate instances within molecular evolutionary trajectories potentially tied to significant biogeochemical transitions evidenced in the geologic record. Here, we survey recent enzyme resurrection studies to provide a reasoned assessment of areas of success and common pitfalls relevant to ancient biogeochemical applications. We conclude by considering the Great Oxidation Event, which provides a constructive example of a significant biogeochemical transition that warrants investigation with ancestral enzyme resurrection. This event also serves to highlight the pitfalls of facile interpretation of paleophenotype models and data, as applied to two examples of enzymes that likely both influenced and were influenced by the rise of atmospheric oxygen - RuBisCO and nitrogenase.
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Affiliation(s)
- Amanda K Garcia
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Betül Kaçar
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Astronomy and Steward Observatory, University of Arizona, Tucson, AZ, 85721, USA.
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Santander-Jiménez S, Vega-Rodríguez MA, Sousa L. A multiobjective adaptive approach for the inference of evolutionary relationships in protein-based scenarios. Inf Sci (N Y) 2019. [DOI: 10.1016/j.ins.2019.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Zaccara S, Quadroni S, Vanetti I, Carosi A, La Porta G, Crosa G, Britton R, Lorenzoni M. Morphologic and genetic variability in the Barbus fishes (Teleostei, Cyprinidae) of Central Italy. ZOOL SCR 2019. [DOI: 10.1111/zsc.12341] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Serena Zaccara
- Department of Theoretical and Applied Sciences University of Insubria Varese VA Italy
| | - Silvia Quadroni
- Department of Theoretical and Applied Sciences University of Insubria Varese VA Italy
| | - Isabella Vanetti
- Department of Theoretical and Applied Sciences University of Insubria Varese VA Italy
| | - Antonella Carosi
- Department of Chemistry, Biology and Biotechnology University of Perugia Perugia PG Italy
| | - Gianandrea La Porta
- Department of Chemistry, Biology and Biotechnology University of Perugia Perugia PG Italy
| | - Giuseppe Crosa
- Department of Theoretical and Applied Sciences University of Insubria Varese VA Italy
| | - Robert Britton
- Centre for Conservation Ecology and Environmental Change Bournemouth University Poole Dorset UK
| | - Massimo Lorenzoni
- Department of Chemistry, Biology and Biotechnology University of Perugia Perugia PG Italy
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40
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Goldberg DL, Landy JA, Travis J, Springer MS, Reznick DN. In love and war: The morphometric and phylogenetic basis of ornamentation, and the evolution of male display behavior, in the livebearer genus
Poecilia. Evolution 2019; 73:360-377. [DOI: 10.1111/evo.13671] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 12/06/2018] [Accepted: 12/09/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel L. Goldberg
- Behavior, Ecology, Evolution, and Systematics Section, School of Biological Sciences Illinois State University Normal Illinois 61761
- Department of Biology University of California Riverside California 92521
| | - Joseph A. Landy
- Department of Biological Science Florida State University Tallahassee Florida 32306
| | - Joseph Travis
- Department of Biological Science Florida State University Tallahassee Florida 32306
| | - Mark S. Springer
- Department of Biology University of California Riverside California 92521
| | - David N. Reznick
- Department of Biology University of California Riverside California 92521
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41
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Maheepala DC, Emerling CA, Rajewski A, Macon J, Strahl M, Pabón-Mora N, Litt A. Evolution and Diversification of FRUITFULL Genes in Solanaceae. FRONTIERS IN PLANT SCIENCE 2019; 10:43. [PMID: 30846991 PMCID: PMC6394111 DOI: 10.3389/fpls.2019.00043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 01/11/2019] [Indexed: 05/12/2023]
Abstract
Ecologically and economically important fleshy edible fruits have evolved from dry fruit numerous times during angiosperm diversification. However, the molecular mechanisms that underlie these shifts are unknown. In the Solanaceae there has been a major shift to fleshy fruits in the subfamily Solanoideae. Evidence suggests that an ortholog of FRUITFULL (FUL), a transcription factor that regulates cell proliferation and limits the dehiscence zone in the silique of Arabidopsis, plays a similar role in dry-fruited Solanaceae. However, studies have shown that FUL orthologs have taken on new functions in fleshy fruit development, including regulating elements of tomato ripening such as pigment accumulation. FUL belongs to the core eudicot euFUL clade of the angiosperm AP1/FUL gene lineage. The euFUL genes fall into two paralogous clades, euFULI and euFULII. While most core eudicots have one gene in each clade, Solanaceae have two: FUL1 and FUL2 in the former, and MBP10 and MBP20 in the latter. We characterized the evolution of the euFUL genes to identify changes that might be correlated with the origin of fleshy fruit in Solanaceae. Our analyses revealed that the Solanaceae FUL1 and FUL2 clades probably originated through an early whole genome multiplication event. By contrast, the data suggest that the MBP10 and MBP20 clades are the result of a later tandem duplication event. MBP10 is expressed at weak to moderate levels, and its atypical short first intron lacks putative transcription factor binding sites, indicating possible pseudogenization. Consistent with this, our analyses show that MBP10 is evolving at a faster rate compared to MBP20. Our analyses found that Solanaceae euFUL gene duplications, evolutionary rates, and changes in protein residues and expression patterns are not correlated with the shift in fruit type. This suggests deeper analyses are needed to identify the mechanism underlying the change in FUL ortholog function.
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Affiliation(s)
- Dinusha C. Maheepala
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Christopher A. Emerling
- Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, École Pratique des Hautes Études, Montpellier, France
| | - Alex Rajewski
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Jenna Macon
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Maya Strahl
- The New York Botanical Garden, Bronx, NY, United States
| | | | - Amy Litt
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Amy Litt,
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Suárez-Villota EY, Quercia CA, Díaz LM, Vera-Sovier V, Nuñez JJ. Speciation in a biodiversity hotspot: Phylogenetic relationships, species delimitation, and divergence times of Patagonian ground frogs from the Eupsophus roseus group (Alsodidae). PLoS One 2018; 13:e0204968. [PMID: 30543633 PMCID: PMC6292574 DOI: 10.1371/journal.pone.0204968] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/27/2018] [Indexed: 11/19/2022] Open
Abstract
The alsodid ground frogs of the Eupsophus genus are divided into two groups, the roseus (2n = 30) and vertebralis (2n = 28), which are distributed throughout the temperate Nothofagus forests of South America. Currently, the roseus group is composed by four species, while the vertebralis group consists of two. Phylogenetic relationships and species delimitation within each group are controversial. In fact, previous analyses considered that the roseus group was composed of between four to nine species. In this work, we evaluated phylogenetic relationships, diversification times, and species delimitation within the roseus group using a multi-locus dataset. For this purpose, mitochondrial (D-loop, Cyt b, and COI) and nuclear (POMC and CRYBA1) partial sequences from 164 individuals were amplified, representing all species. Maximum Likelihood (ML) and Bayesian approaches were used to reconstruct phylogenetic relationships. Species tree was estimated using BEAST and singular value decomposition scores for species quartets (SVDquartets). Species limits were evaluated with six coalescent approaches. Diversification times were estimated using mitochondrial and nuclear rates with LogNormal relaxed clock in BEAST. Nine well-supported monophyletic lineages were recovered in Bayesian, ML, and SVDquartets, including eight named species and a lineage composed by specimens from the Villarrica population (Bootstrap:>70, PP:> 0.99). Single-locus species delimitation analyses overestimated the species number in E. migueli, E. calcaratus, and E. roseus lineages, while multi-locus analyses recovered as species the nine lineages observed in phylogenetic analyses (Ctax = 0.69). It is hypothesized that Eupsophus diversification occurred during Mid-Pleistocene (0.42-0.14 Mya), with most species having originated after the Last Southern Patagonian Glaciation (0.18 Mya). Our results revitalize the hypothesis that the E. roseus group is composed of eight species and support the Villarrica lineage as a new putative species.
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Affiliation(s)
| | - Camila A. Quercia
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Leila M. Díaz
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Victoria Vera-Sovier
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - José J. Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
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43
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Neiber MT, Glaubrecht M. Unparalleled disjunction or unexpected relationships? Molecular phylogeny and biogeography of Melanopsidae (Caenogastropoda: Cerithioidea), with the description of a new family and a new genus from the ancient continent Zealandia. Cladistics 2018; 35:401-425. [DOI: 10.1111/cla.12361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2018] [Indexed: 11/27/2022] Open
Affiliation(s)
- Marco T. Neiber
- Department of Animal Diversity Center of Natural History (CeNak) Zoological Museum Universität Hamburg Martin‐Luther‐King‐Platz 3 D‐20146 Hamburg Germany
| | - Matthias Glaubrecht
- Department of Animal Diversity Center of Natural History (CeNak) Zoological Museum Universität Hamburg Martin‐Luther‐King‐Platz 3 D‐20146 Hamburg Germany
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44
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Pérez-Losada M, Arenas M, Castro-Nallar E. Microbial sequence typing in the genomic era. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 63:346-359. [PMID: 28943406 PMCID: PMC5908768 DOI: 10.1016/j.meegid.2017.09.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/18/2022]
Abstract
Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal; Children's National Medical Center, Washington, DC 20010, USA.
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago 8370146, Chile
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45
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Suárez-Villota EY, Quercia CA, Nuñez JJ, Gallardo MH, Himes CM, Kenagy GJ. Monotypic status of the South American relictual marsupial Dromiciops gliroides (Microbiotheria). J Mammal 2018. [DOI: 10.1093/jmammal/gyy073] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Elkin Y Suárez-Villota
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla, Valdivia, Chile
| | - Camila A Quercia
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla, Valdivia, Chile
| | - José J Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla, Valdivia, Chile
| | - Milton H Gallardo
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla, Valdivia, Chile
| | - Christopher M Himes
- Burke Museum and Department of Biology, University of Washington, Seattle, WA, USA
| | - G J Kenagy
- Burke Museum and Department of Biology, University of Washington, Seattle, WA, USA
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46
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Suárez-Villota EY, Quercia CA, Nuñez JJ. Mitochondrial genomes of the South American frogs Eupsophus vertebralis and E. emiliopugini (Neobatrachia: Alsodidae) and their phylogenetic relationships. J Genomics 2018; 6:98-102. [PMID: 29973959 PMCID: PMC6030769 DOI: 10.7150/jgen.26122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 05/25/2018] [Indexed: 11/05/2022] Open
Abstract
We report the sequencing and compare the mitochondrial genomes of the South American ground frogs Eupsophus vertebralis and E. emiliopugini and reconstruct phylogenetic relationships among Eupsophus species. These genomes consist of 16,156 and 16,711 bp in length, respectively and contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes (tRNA), and partial non-coding D-loop region. Both genomes share 94.5% identity with 879 variable sites. A phylogenetic analysis with other available mitogenomes recovered both species as the sister clade of Alsodes gargola. Sequences from D-loop, CO1, and Cyt b, amplified and sequenced with primers developed from the mitochondrial genomes, allowed us to reconstruct phylogenetic relationships among Eupsophus species. Since our report represents the first mitogenomes for the genus Eupsophus, we expect these data will be valuable for further studies on conservation genetics and on the evolution of Patagonian amphibians.
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Affiliation(s)
- Elkin Y. Suárez-Villota
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
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Smith ML, Ruffley M, Rankin AM, Espíndola A, Tank DC, Sullivan J, Carstens BC. Testing for the presence of cryptic diversity in tail-dropper slugs (Prophysaon) using molecular data. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Megan L Smith
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Aronoff Labs, Columbus, OH, USA
| | - Megan Ruffley
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Andrew M Rankin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Anahí Espíndola
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Aronoff Labs, Columbus, OH, USA
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Abstract
Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 Rhizopus strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopus consists of three major clades, with R. microsporus as the basal species and the sister lineage to R. stolonifer and two closely related species R. arrhizus and R. delemar A comparative analysis of the mating type locus across Rhizopus reveals that its structure is flexible even between different species in the same genus, but shows similarities between Rhizopus and other mucoralean fungi. The topology of single-gene phylogenies built for two genes involved in mating is similar to the phylogenomic tree. Comparison of the total length of the genome assemblies showed that genome size varies by as much as threefold within a species and is driven by changes in transposable element copy numbers and genome duplications.
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49
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Kutralam-Muniasamy G, Corona-Hernandez J, Narayanasamy RK, Marsch R, Pérez-Guevara F. Phylogenetic diversification and developmental implications of poly-(R)-3-hydroxyalkanoate gene cluster assembly in prokaryotes. FEMS Microbiol Lett 2018; 364:3888817. [PMID: 28655209 DOI: 10.1093/femsle/fnx135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/23/2017] [Indexed: 11/13/2022] Open
Abstract
Many polyhydroxyalkanoates (PHAs) system genes, such as phaC, phaA, phaB, phaR, phaP and phaZ, are often found to be organised in the form of operon-like clusters. In this study, a genome survey was performed to identify such clustered PHA systems among 256 prokaryotic organisms. These data were then used to generate a comprehensive 16S rRNA species tree depicting the phylogenetic distribution of the observed clusters with diverse gene arrangements. In addition, the gene occurrences and physical linkages between PHA system genes were quantitatively estimated. From this, we identified a centrally connected hub gene, i.e. the phaC gene of PHA. Furthermore, a comparative investigation was performed between the clusters of PHA and glycogen, which decoded the role of the hub gene in the cluster organisation of both systems. Together, these findings suggest that the highly connected hub gene might contribute substantively towards the organisation and maintenance of the gene network connectivity in the clusters, particularly in the storage reserve systems.
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Affiliation(s)
- Gurusamy Kutralam-Muniasamy
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Juan Corona-Hernandez
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Ravi-Kumar Narayanasamy
- Department of Infectomics y Molecular Pathogenesis, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Rodolfo Marsch
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Fermín Pérez-Guevara
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México.,Nanoscience and Nanotechnology Program, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
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Onuț-Brännström I, Benjamin M, Scofield DG, Heiðmarsson S, Andersson MGI, Lindström ES, Johannesson H. Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing. Sci Rep 2018. [PMID: 29535321 PMCID: PMC5849601 DOI: 10.1038/s41598-018-22470-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In this study, we explored the diversity of green algal symbionts (photobionts) in sympatric populations of the cosmopolitan lichen-forming fungi Thamnolia and Cetraria. We sequenced with both Sanger and Ion Torrent High-Throughput Sequencing technologies the photobiont ITS-region of 30 lichen thalli from two islands: Iceland and Öland. While Sanger recovered just one photobiont genotype from each thallus, the Ion Torrent data recovered 10-18 OTUs for each pool of 5 lichen thalli, suggesting that individual lichens can contain heterogeneous photobiont populations. Both methods showed evidence for photobiont sharing between Thamnolia and Cetraria on Iceland. In contrast, our data suggest that on Öland the two mycobionts associate with distinct photobiont communities, with few shared OTUs revealed by Ion Torrent sequencing. Furthermore, by comparing our sequences with public data, we identified closely related photobionts from geographically distant localities. Taken together, we suggest that the photobiont composition in Thamnolia and Cetraria results from both photobiont-mycobiont codispersal and local acquisition during mycobiont establishment and/or lichen growth. We hypothesize that this is a successful strategy for lichens to be flexible in the use of the most adapted photobiont for the environment.
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Affiliation(s)
- Ioana Onuț-Brännström
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mitchell Benjamin
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Douglas G Scofield
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX), Uppsala University, Uppsala, Sweden
| | - Starri Heiðmarsson
- Icelandic Institute of Natural History, Akureyri Division, Borgir Nordurslod, Iceland
| | - Martin G I Andersson
- Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Eva S Lindström
- Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
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