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Cathcart CA. Multiple evolutionary pressures shape identical consonant avoidance in the world's languages. Proc Natl Acad Sci U S A 2024; 121:e2316677121. [PMID: 38917001 PMCID: PMC11228491 DOI: 10.1073/pnas.2316677121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 05/15/2024] [Indexed: 06/27/2024] Open
Abstract
Languages disfavor word forms containing sequences of similar or identical consonants, due to the biomechanical and cognitive difficulties posed by patterns of this sort. However, the specific evolutionary processes responsible for this phenomenon are not fully understood. Words containing sequences of identical consonants may be more likely to arise than those without; processes of word form mutation may be more likely to remove than create sequences of identical consonants in word forms; finally, words containing identical consonants may die out more frequently than those without. Phylogenetic analyses of the evolution of homologous word forms indicate that words with identical consonants arise less frequently than those without. However, words with identical consonants do not die out more frequently than those without. Further analyses reveal that forms with identical consonants are replaced in basic meaning functions more frequently than words without. Taken together, results suggest that the underrepresentation of sequences of identical consonants is overwhelmingly a by-product of constraints on word form coinage, though processes related to word usage also serve to ensure that such patterns are infrequent in more salient vocabulary items. These findings clarify aspects of processes of lexical evolution and competition that take place during language change, optimizing communicative systems.
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Affiliation(s)
- Chundra A Cathcart
- Department of Comparative Language Science, University of Zurich, Zürich CH-8050, Switzerland
- Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zürich CH-8050, Switzerland
- Deutsche Forschungsgemeinschaft Center "Words, Bones, Genes, Tools", University of Tübingen, Tübingen 72074, Germany
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Askari H, Soleimanian-Zad S, Kadivar M, Shahbazi S. Creating a novel genetic diversity of Trichoderma afroharzianum by γ-radiation for xylanase-cellulase production. Heliyon 2024; 10:e28349. [PMID: 38590889 PMCID: PMC10999882 DOI: 10.1016/j.heliyon.2024.e28349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 02/19/2024] [Accepted: 03/17/2024] [Indexed: 04/10/2024] Open
Abstract
Creating novel sources of a microbial strain using induced mutation can increase enzyme production for industrial use. According to this, we have developed a mutant strain of Trichoderma afroharzianum by Co60 gamma irradiation. Trichoderma mutants were isolated from an optimum dose of 250 Gy. The qualitative and quantitative screening were used for evaluating their enzyme production and the DNA barcoding method was used to identify the best Trichoderma mutant isolates. The highest cellulase (exo-glucanase, endoglucanase, β-glucosidase, and total cellulase) and xylanase activities were observed in superior mutant isolates of Trichoderma afroharzianum NAS107-M44 and Trichoderma afroharzianum NAS107-M82, which is approximately 1.6-2.5 times higher than its parent strain, respectively. The electrophoretic pattern of proteins showed that the exo-glucanase I, endo-glucanase III, and the xylanase I enzymes hydrolyzed the corn bran, synergistically. Overall, gamma irradiation-induced mutation could be an expedient technique to access such superior mutants for the bioconversion of corn bran wastes.
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Affiliation(s)
- Hamed Askari
- Department of Food Science and Technology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Sabihe Soleimanian-Zad
- Department of Food Science and Technology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
- Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Mahdi Kadivar
- Department of Food Science and Technology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Samira Shahbazi
- Nuclear Agriculture School, Nuclear Science and Technology Research Institute (NSTRI), Atomic Energy Organization of Iran (AEOI), Karaj, Iran
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Mohy-Ud-Din W, Chen F, Bashir S, Akhtar MJ, Asghar HN, Farooqi ZUR, Zulfiqar U, Haider FU, Afzal A, Alqahtani MD. Unlocking the potential of glyphosate-resistant bacterial strains in biodegradation and maize growth. Front Microbiol 2023; 14:1285566. [PMID: 38204469 PMCID: PMC10777731 DOI: 10.3389/fmicb.2023.1285566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/27/2023] [Indexed: 01/12/2024] Open
Abstract
Glyphosate [N-(phosphonomethyl)-glycine] is a non-selective herbicide with a broad spectrum activity that is commonly used to control perennial vegetation in agricultural fields. The widespread utilization of glyphosate in agriculture leads to soil, water, and food crop contamination, resulting in human and environmental health consequences. Therefore, it is imperative to devise techniques for enhancing the degradation of glyphosate in soil. Rhizobacteria play a crucial role in degrading organic contaminants. Limited work has been done on exploring the capabilities of indigenously existing glyphosate-degrading rhizobacteria in Pakistani soils. This research attempts to discover whether native bacteria have the glyphosate-degrading ability for a sustainable solution to glyphosate contamination. Therefore, this study explored the potential of 11 native strains isolated from the soil with repeated glyphosate application history and showed resistance against glyphosate at higher concentrations (200 mg kg-1). Five out of eleven strains outperformed in glyphosate degradation and plant growth promotion. High-pressure liquid chromatography showed that, on average, these five strains degraded 98% glyphosate. In addition, these strains promote maize seed germination index and shoot and root fresh biomass up to 73 and 91%, respectively. Furthermore, inoculation gave an average increase of acid phosphatase (57.97%), alkaline phosphatase (1.76-fold), and dehydrogenase activity (1.75-fold) in glyphosate-contaminated soil. The findings indicated the importance of using indigenous rhizobacteria to degrade glyphosate. Therefore, by maintaining soil health, indigenous soil biodiversity can work effectively for the bioremediation of contaminated soils and sustainable crop production in a world facing food security.
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Affiliation(s)
- Waqas Mohy-Ud-Din
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
- Department of Soil and Environmental Sciences, Ghazi University, Dera Ghazi Khan, Pakistan
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
| | - Safdar Bashir
- Department of Soil and Environmental Sciences, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Muhammad Javed Akhtar
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Hafiz Naeem Asghar
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Zia Ur Rahman Farooqi
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Usman Zulfiqar
- Department of Agronomy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Fasih Ullah Haider
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Aneeqa Afzal
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Mashael Daghash Alqahtani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
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Palanisamy A, Marimuthu M, Narayanasamy C, Venkatasamy B, Gandhi K, Lakshmanan P. Invasive flower thrips, Thrips parvispinus (Karny) occurrence, host expansion and genetic diversification in a tropical poly-crop ecosystem. Mol Biol Rep 2023; 50:9909-9923. [PMID: 37874506 DOI: 10.1007/s11033-023-08831-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND Invasive black flower thrips Thrips parvispinus (Karny) has recently emerged as a significant threat to Indian chilli production. Identifying T. parvispinus became difficult due to the complex presence of thrips species in Indian chilli and allied ecosystems. Pest management success depends on assessing invasive pests genetic populations and their distribution in newly habituated areas. METHODS AND RESULTS The current study investigated the genetic diversity and phylogeographic structure of T. parvispinus across major chilli-growing zones representing different agro-climatic conditions in Tamil Nadu. The species-specific chaetotaxy characteristics of T. parvispinus and molecular analysis of the mtCOI gene were used to confirm that the species T. parvispinus has expanded rapidly in three regions (North Western, Western and Cauvery delta), sparsely in one (Southern) and absent from two (hilly and high rainfall). Fifteen allied crops in chilli/capsicum growing tracts served as host plants for T. parvispinus. A shrub species, namely Littleleaf boxwood, Buxus microphylla Siebold & Zucc., is described as a host plant for the first time. On capsicum and chilli, T. parvispinus and Scirtothrips dorsalis coexisted. Thrips palmi, T. tabaci, Frankliniella schultzei, and Microcephalothrips abdominalis co-occurring alongside T. parvispinus on allied crops. CONCLUSION Molecular characterization and haplotype identification help define the genetic composition of T. parvispinus and serve as a foundation for efficient monitoring and creation of Integrated Pest Management (IPM) strategies. As a result, the genetic data presented in this work strongly argues that T. parvispinus as a population is resolving itself towards a fixed state through natural selection that spans its native range globally along with low genetic diversity [Hd: 0.771].
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Affiliation(s)
- Aishwarya Palanisamy
- Department of Agricultural Entomology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India
| | - Murugan Marimuthu
- Department of Agricultural Entomology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India.
| | - Chitra Narayanasamy
- Department of Agricultural Entomology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India
| | - Balasubramani Venkatasamy
- Controller of Examinations, Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India
| | - Karthikeyan Gandhi
- Department of Plant Pathology, Centre for Plant Protection Studies, TNAU, Coimbatore, Tamil Nadu, 641003, India
| | - Pugalendhi Lakshmanan
- Department of Vegetables, Horticultural College & Research Institute, TNAU, Coimbatore, Tamil Nadu, 641003, India
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Miri S, Yeo J, Abubaker S, Hammami R. Neuromicrobiology, an emerging neurometabolic facet of the gut microbiome? Front Microbiol 2023; 14:1098412. [PMID: 36733917 PMCID: PMC9886687 DOI: 10.3389/fmicb.2023.1098412] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
The concept of the gut microbiome is emerging as a metabolic interactome influenced by diet, xenobiotics, genetics, and other environmental factors that affect the host's absorption of nutrients, metabolism, and immune system. Beyond nutrient digestion and production, the gut microbiome also functions as personalized polypharmacy, where bioactive metabolites that our microbes excrete or conjugate may reach systemic circulation and impact all organs, including the brain. Appreciable evidence shows that gut microbiota produce diverse neuroactive metabolites, particularly neurotransmitters (and their precursors), stimulating the local nervous system (i.e., enteric and vagus nerves) and affecting brain function and cognition. Several studies have demonstrated correlations between the gut microbiome and the central nervous system sparking an exciting new research field, neuromicrobiology. Microbiome-targeted interventions are seen as promising adjunctive treatments (pre-, pro-, post-, and synbiotics), but the mechanisms underlying host-microbiome interactions have yet to be established, thus preventing informed evidence-based therapeutic applications. In this paper, we review the current state of knowledge for each of the major classes of microbial neuroactive metabolites, emphasizing their biological effects on the microbiome, gut environment, and brain. Also, we discuss the biosynthesis, absorption, and transport of gut microbiota-derived neuroactive metabolites to the brain and their implication in mental disorders.
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Affiliation(s)
- Saba Miri
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - JuDong Yeo
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Sarah Abubaker
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Riadh Hammami
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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Mei N, Postec A, Bartoli M, Vandecasteele C, Wils L, Gil L, Monnin C, Pelletier B, Erauso G, Quéméneur M. Methanobacterium alkalithermotolerans sp. nov., a novel alkaliphilic and hydrogen-utilizing methanogen isolated from an alkaline geothermal spring (La Crouen, New Caledonia). Int J Syst Evol Microbiol 2022; 72. [PMID: 36260502 DOI: 10.1099/ijsem.0.005554] [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: 06/16/2023] Open
Abstract
An anaerobic, hydrogenotrophic methane-producing archaeon was isolated from an alkaline thermal spring (42 °C, pH 9.0) in New Caledonia. This methanogen, designated strain CANT, is alkaliphilic, thermotolerant, with Gram-positive staining non-motile cells. Strain CANT grows autotrophically using hydrogen exclusively as an energy source and carbon dioxide as the sole carbon source (without the requirement of yeast extract or other organic compounds). It grows at 20-45 °C (optimum, 45 °C) and pH 7.3-9.7 (optimum, pH 9.0). NaCl is not required for growth (optimum 0 %) but is tolerated up to 1.5 %. It resists novobiocin, streptomycin and vancomycin but is inhibited by ampicillin and penicillin, among other antibiotics. The genome consists of a circular chromosome (2.2 Mb) containing 2126 predicted protein-encoding genes with a G+C content of 36.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CANT is a member of the genus Methanobacterium, most closely related to the alkaliphilic Methanobacterium alcaliphilum WeN4T with 98.5 % 16S rRNA gene sequence identity. The genomes of strain CANT and M. alcaliphilum DSM 3459, sequenced in this study, share 71.6 % average nucleotide identity and 14.0 % digital DNA-DNA hybridization. Therefore, phylogenetic and physiological results indicate that strain CANT represents a novel species, for which the name Methanobacterium alkalithermotolerans sp. nov. is proposed, and strain CANT (=DSM 102889T= JCM 31304T) is assigned as the type strain.
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Affiliation(s)
- Nan Mei
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
- Present address: School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
| | - Anne Postec
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Manon Bartoli
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Laura Wils
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Lisa Gil
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Christophe Monnin
- GET UMR5563 (CNRS/UPS/IRD/CNES), Géosciences Environnement Toulouse, 14 Avenue Edouard Belin, 31400 Toulouse, France
| | - Bernard Pelletier
- UMR Géoazur, Centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5 - 98848 Nouméa cedex, New Caledonia
| | - Gael Erauso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Marianne Quéméneur
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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Yin YL, Li FL, Wang L. Halomonas salinarum sp. nov., a moderately halophilic bacterium isolated from saline soil in Yingkou, China. Arch Microbiol 2022; 204:466. [PMID: 35802152 PMCID: PMC9266089 DOI: 10.1007/s00203-022-03032-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/28/2022] [Accepted: 06/01/2022] [Indexed: 11/19/2022]
Abstract
Strain G5-11T, a Gram-negative, moderately halotolerant, facultatively aerobic, motile bacterium was isolated from saline soil collected from Yingkou, Liaoning, China. The cells of strain G5-11T grew in the presence of 3–15% (w/v) NaCl (optimum 5%), at between 4 and 35 °C (optimum 30 °C), and at a pH of 6.0–9.0 (optimum 8.0). The major respiratory quinone was Q-9 and the dominant cellular fatty acids were summed feature 8 (C18:1ω7c/C18:1ω6c), C16:0, and summed feature 3 (C16:1ω7c/C16:1ω6c). The major components of the polar lipid profile were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unidentified aminolipid. The G + C content of the strain G5-11T genome was 61.0 mol%. The isolated strain G5-11T showed the highest 16S rRNA gene similarity to Halomonas niordiana LMG 31227T and Halomonas taeanensis DSM 16463T, both reaching 98.3%, followed by Halomonas pacifica NBRC 102220T. The results from phenotypic, chemotaxonomic, and phylogenetic analyses showed that strain G5-11T represented a novel species of the genus Halomonas, for which the name Halomonas salinarum sp. nov. was proposed. The type strain of Halomonas salinarum is G5-11T (= CGMCC 1.12051T = LMG 31677T).
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Affiliation(s)
- Ya-Lin Yin
- MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Fang-Ling Li
- MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lei Wang
- MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.
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Identification, characterization and hydrolase producing performance of thermophilic bacteria: geothermal hot springs in the Eastern and Southeastern Anatolia Regions of Turkey. Antonie van Leeuwenhoek 2022; 115:253-270. [PMID: 35031914 PMCID: PMC8760091 DOI: 10.1007/s10482-021-01678-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 10/18/2021] [Indexed: 10/28/2022]
Abstract
In the last two decades, researchers have increasingly focused on the rich microorganism-based diversity of natural hot spring sources to explore the benefits of thermophiles in industrial and biotechnological fields. Within the scope of this study, a total of 83 thermophilic Bacilli strains were isolated from 7 different geothermal hot springs (at temperatures ranging between 40 and 85 °C) located in the Eastern and Southeastern Anatolia Regions of Turkey. The physiological, morphological, biochemical and molecular properties of the isolates were determined. As a result of the 16S rRNA gene sequence analysis, 5 different species (Bacillus licheniformis, Bacillus sp., Bacillus subtilis, Geobacillus kaustophilus, and Weizmannia coagulans,) were identified. B. licheniformis and B. subtilis were the most frequently encountered species among those obtained from the researched hot spring sources. Phylogenetic analysis was conducted to evaluate the phylogenetic relationships of the isolated species. The results showed that there was no significant difference between the groups and the bacteria in terms of the locations or optimum temperatures of the isolates. The bacterial isolates were screened for amylase, cellulase, lipase and protease hydrolytic enzyme activities. The hydrolytic enzyme production potentials among the isolates were identified in 68 (82%) isolates for amylase, 34 (41%) for cellulase, 69 (83%) for lipase and 73 (88%) for protease. All isolates were found to have at least one or more extracellular enzyme activities. Additionally, it was determined that 27 of the existing isolates (32.8%) were able to produce all of the aforementioned hydrolytic enzymes.
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Field JT, Abrams AJ, Cartee JC, McTavish EJ. Rapid alignment updating with Extensiphy. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jasper Toscani Field
- Quantitative and Systems Biology Program School of Natural Sciences University of California Merced CA USA
| | - A. Jeanine Abrams
- Division of STD Prevention National Centers for HIV/AIDS Viral Hepatitis, STD, and TB Prevention Atlanta GA USA
| | - John C. Cartee
- Division of STD Prevention National Centers for HIV/AIDS Viral Hepatitis, STD, and TB Prevention Atlanta GA USA
| | - Emily Jane McTavish
- Life and Environmental Sciences Department School of Natural Sciences University of California Merced CA USA
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Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia). Microorganisms 2021; 9:microorganisms9071360. [PMID: 34201651 PMCID: PMC8307142 DOI: 10.3390/microorganisms9071360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 01/01/2023] Open
Abstract
(1) Background: The geothermal spring of La Crouen (New Caledonia) discharges warm (42 °C) alkaline water (pH~9) enriched in dissolved nitrogen with traces of methane, but its microbial diversity has not yet been studied. (2) Methods: Cultivation-dependent and -independent methods (e.g., Illumina sequencing and quantitative PCR based on 16S rRNA gene) were used to describe the prokaryotic diversity of this spring. (3) Results: Prokaryotes were mainly represented by Proteobacteria (57% on average), followed by Cyanobacteria, Chlorofexi, and Candidatus Gracilibacteria (GN02/BD1-5) (each > 5%). Both potential aerobes and anaerobes, as well as mesophilic and thermophilic microorganisms, were identified. Some of them had previously been detected in continental hyperalkaline springs found in serpentinizing environments (The Cedars, Samail, Voltri, and Zambales ophiolites). Gammaproteobacteria, Ca. Gracilibacteria and Thermotogae were significantly more abundant in spring water than in sediments. Potential chemolithotrophs mainly included beta- and gammaproteobacterial genera of sulfate-reducers (Ca. Desulfobacillus), methylotrophs (Methyloversatilis), sulfur-oxidizers (Thiofaba, Thiovirga), or hydrogen-oxidizers (Hydrogenophaga). Methanogens (Methanobacteriales and Methanosarcinales) were the dominant Archaea, as found in serpentinization-driven and deep subsurface ecosystems. A novel alkaliphilic hydrogenotrophic methanogen (strain CAN) belonging to the genus Methanobacterium was isolated, suggesting that hydrogenotrophic methanogenesis occurs at La Crouen.
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Sengupta D, Choudhury A, Fortes-Lima C, Aron S, Whitelaw G, Bostoen K, Gunnink H, Chousou-Polydouri N, Delius P, Tollman S, Gómez-Olivé FX, Norris S, Mashinya F, Alberts M, Hazelhurst S, Schlebusch CM, Ramsay M. Genetic substructure and complex demographic history of South African Bantu speakers. Nat Commun 2021; 12:2080. [PMID: 33828095 PMCID: PMC8027885 DOI: 10.1038/s41467-021-22207-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/10/2021] [Indexed: 02/01/2023] Open
Abstract
South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.
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Affiliation(s)
- Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cesar Fortes-Lima
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gavin Whitelaw
- KwaZulu-Natal Museum, Pietermaritzburg, South Africa
- School of Geography, Archaeology & Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa
| | - Koen Bostoen
- UGent Centre for Bantu Studies, Department of Languages and Cultures, Ghent University, Ghent, Belgium
| | - Hilde Gunnink
- UGent Centre for Bantu Studies, Department of Languages and Cultures, Ghent University, Ghent, Belgium
| | - Natalia Chousou-Polydouri
- Department of Comparative Linguistic Science and Center for the Interdisciplinary Study of Language Evolution, University of Zürich, Zürich, Switzerland
| | - Peter Delius
- Department of History, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane Norris
- MRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Felistas Mashinya
- Department of Pathology and Medical Sciences; School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Marianne Alberts
- Department of Pathology and Medical Sciences; School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Carina M Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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12
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Li FL, Zhang YX, Zhang YK, Chen WF, Li WJ, Wang L. Siccirubricoccus phaeus sp. nov., isolated from oil reservoir water and emended description of the genus Siccirubricoccus. Antonie van Leeuwenhoek 2021; 114:355-364. [DOI: 10.1007/s10482-021-01516-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 01/06/2021] [Indexed: 11/28/2022]
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13
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Proposal for a subdivision of the family Psathyrellaceae based on a taxon-rich phylogenetic analysis with iterative multigene guide tree. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01606-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Rama T, Wichmann S. A test of Generalized Bayesian dating: A new linguistic dating method. PLoS One 2020; 15:e0236522. [PMID: 32785236 PMCID: PMC7423060 DOI: 10.1371/journal.pone.0236522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/07/2020] [Indexed: 11/24/2022] Open
Abstract
In current practice, when dating the root of a Bayesian language phylogeny the researcher is required to supply some of the information beforehand, including a distribution of root ages and dates for some nodes serving as calibration points. In addition to the potential subjectivity that this leaves room for, the problem arises that for many of the language families of the world there are no available internal calibration points. Here we address the following questions: Can a new Bayesian framework which overcomes these problems be introduced and how well does it perform? The new framework that we present is generalized in the sense that no family-specific priors or calibration points are needed. We moreover introduce a way to overcome another potential source of subjectivity in Bayesian tree inference as commonly practiced, namely that of manual cognate identification; instead, we apply an automated approach. Dates are obtained by fitting a Gamma regression model to tree lengths and known time depths for 30 phylogenetically independent calibration points. This model is used to predict the time depths of both the root and the internal nodes for 116 language families, producing a total of 1,287 dates for families and subgroups. It turns out that results are similar to those of published Bayesian studies of individual language families. The performance of the method is compared to automated glottochronology, which is an update of the classical method of Swadesh drawing upon automated cognate recognition and a new formula for deriving a time depth from percentages of shared cognates. It is also compared to a third dating method, that of the Automated Similarity Judgment Program (ASJP). In terms of errors and correlations with known dates, ASJP works better than the new method and both work better than automated glottochronology.
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Affiliation(s)
- Taraka Rama
- Department of Linguistics, University of North Texas, Denton, Texas, United States of America
- * E-mail:
| | - Søren Wichmann
- Leiden University Centre for Linguistics, University of Leiden, Leiden, Netherlands
- Laboratory of Quantitative Linguistics, Kazan Federal University, Kazan, Russia
- Beijing Advanced Innovation Center for Language Resources, Beijing Language University, Beijing, China
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15
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Conith AJ, Kidd MR, Kocher TD, Albertson RC. Ecomorphological divergence and habitat lability in the context of robust patterns of modularity in the cichlid feeding apparatus. BMC Evol Biol 2020; 20:95. [PMID: 32736512 PMCID: PMC7393717 DOI: 10.1186/s12862-020-01648-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 07/01/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Adaptive radiations are characterized by extreme and/or iterative phenotypic divergence; however, such variation does not accumulate evenly across an organism. Instead, it is often partitioned into sub-units, or modules, which can differentially respond to selection. While it is recognized that changing the pattern of modularity or the strength of covariation (integration) can influence the range or rate of morphological evolution, the relationship between shape variation and covariation remains unclear. For example, it is possible that rapid phenotypic change requires concomitant changes to the underlying covariance structure. Alternatively, repeated shifts between phenotypic states may be facilitated by a conserved covariance structure. Distinguishing between these scenarios will contribute to a better understanding of the factors that shape biodiversity. Here, we explore these questions using a diverse Lake Malawi cichlid species complex, Tropheops, that appears to partition habitat by depth. RESULTS We construct a phylogeny of Tropheops populations and use 3D geometric morphometrics to assess the shape of four bones involved in feeding (mandible, pharyngeal jaw, maxilla, pre-maxilla) in populations that inhabit deep versus shallow habitats. We next test numerous modularity hypotheses to understand whether fish at different depths are characterized by conserved or divergent patterns of modularity. We further examine rates of morphological evolution and disparity between habitats and among modules. Finally, we raise a single Tropheops species in environments mimicking deep or shallow habitats to discover whether plasticity can replicate the pattern of morphology, disparity, or modularity observed in natural populations. CONCLUSIONS Our data support the hypothesis that conserved patterns of modularity permit the evolution of divergent morphologies and may facilitate the repeated transitions between habitats. In addition, we find the lab-reared populations replicate many trends in the natural populations, which suggests that plasticity may be an important force in initiating depth transitions, priming the feeding apparatus for evolutionary change.
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Affiliation(s)
- Andrew J. Conith
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003 USA
| | - Michael R. Kidd
- Department of Biology & Chemistry, Texas A&M International University, Laredo, TX 78041 USA
| | - Thomas D. Kocher
- Department of Biology, University of Maryland, College Park, MD 20742 USA
| | - R. Craig Albertson
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003 USA
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16
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Stoltz M, Baeumer B, Bouckaert R, Fox C, Hiscott G, Bryant D. Bayesian Inference of Species Trees using Diffusion Models. Syst Biol 2020; 70:145-161. [PMID: 33005955 DOI: 10.1093/sysbio/syaa051] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 11/13/2022] Open
Abstract
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with novel numerical algorithms. The diffusion approach allows for analysis of data sets containing hundreds or thousands of individuals. The method, which we call Snapper, has been implemented as part of the BEAST2 package. We conducted simulation experiments to assess numerical error, computational requirements, and accuracy recovering known model parameters. A reanalysis of soybean SNP data demonstrates that the models implemented in Snapp and Snapper can be difficult to distinguish in practice, a characteristic which we tested with further simulations. We demonstrate the scale of analysis possible using a SNP data set sampled from 399 fresh water turtles in 41 populations. [Bayesian inference; diffusion models; multi-species coalescent; SNP data; species trees; spectral methods.].
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Affiliation(s)
- Marnus Stoltz
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
| | - Boris Baeumer
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
| | - Remco Bouckaert
- Centre for Computational Evolution, University of Auckland, Auckland 1142, New Zealand
| | - Colin Fox
- Department of Physics, University of Otago, Dunedin 9054, New Zealand
| | - Gordon Hiscott
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
| | - David Bryant
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
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17
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Wang XT, Shan JJ, Li XZ, Lin W, Xiu JL, Li DA, Zhang YZ, Wang L. Tepidiphilus olei sp. nov., isolated from the production water of a water-flooded oil reservoir in PR China. Int J Syst Evol Microbiol 2020; 70:4364-4371. [DOI: 10.1099/ijsem.0.004297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, moderately thermophilic, Gram-stain-negative bacterium, designated strain J18T, was isolated from a water-flooded oil reservoir. Cells were aerobic, oxidase- and catalase-positive, with a polar flagellum. Growth occurred at 35–60 °C and at pH 6–8.5. The respiratory quinones were ubiquinone 8 and ubiquinone 9. The dominant cellular fatty acids were C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1
ω7c/C18 : 1
ω6c). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and an unidentified aminophospholipid. The strain showed the highest 16S rRNA gene sequence similarities to
Tepidiphilus margaritifer
DSM 15129T (98.6 %),
Tepidiphilus succinatimandens
DSM 15512T (98.4 %) and
Tepidiphilus thermophilus
DSM 27220T (98.1 %), respectively, and the similarity to other species was lower than 93 %. In the phylogenetic trees, it constituted a unique sub-cluster within the genus
Tepidiphilus
. The DNA G+C content of strain J18T was 64.44 mol%. As compared with the type strains, the genome-to-genome distances of strain J18T were 34.7–40 %. These results confirmed the separate species status of J18T with its close relatives. On the basis of physiological, chemotaxonomic and phylogenetic analyses along with the low levels of identity at the whole-genome level, it can be concluded that strain J18T represents a new species of the genus
Tepidiphilus
, for which the name Tepidiphilus olei sp. nov. is proposed. The type strain of T. olei is J18T (=CGMCC 1.16800T=LMG 31400T).
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Affiliation(s)
- Xiao-Tong Wang
- Unovation Bio & EP Technology Company Limited, Beijing, 100029, PR China
| | - Jian-Jie Shan
- Unovation Bio & EP Technology Company Limited, Beijing, 100029, PR China
| | - Xi-Zhe Li
- Research Institute of Petroleum Exploration & Development, PetroChina Company Limited, Langfang, Hebei, 065007, PR China
- Research Institute of Petroleum Exploration & Development, PetroChina Company Limited, Beijing, 10083, PR China
| | - Wei Lin
- Intitute of Porous Flow and Fluid Mechanics, CNPC Key Laboratory of Enhanced Oil Recovery, University of Chinese Academy of Sciences, Langfang, Hebei, 065007, PR China
- Research Institute of Petroleum Exploration & Development, PetroChina Company Limited, Langfang, Hebei, 065007, PR China
| | - Jian-Long Xiu
- Research Institute of Petroleum Exploration & Development, PetroChina Company Limited, Langfang, Hebei, 065007, PR China
| | - Dong-An Li
- Unovation Bio & EP Technology Company Limited, Beijing, 100029, PR China
| | - Yun-Zeng Zhang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-innovation Center for prevention and Control of Important Animal Infectious, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Lei Wang
- State Key Laboratory of Agrobiotechnology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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18
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Li FL, Wang XT, Shan JJ, Li S, Zhang YX, Li XZ, Li DA, Li WJ, Wang L. Oleiliquidispirillum nitrogeniifigens gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from oil reservoir water. Int J Syst Evol Microbiol 2020; 70:3468-3474. [PMID: 32369003 DOI: 10.1099/ijsem.0.004200] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-negative, spiral-shaped bacterium, designated strain 64-1T, was isolated from oil reservoir water collected from Liaohe oilfield, north-eastern China. Growth occurred at 15-55 °C and pH 6.0-10.0. The sole respiratory quinone was Q-10. The predominant cellular fatty acids were summed feature 8 (C18 : 1 ω7c /C18 : 1 ω6c), C16 : 0 and C19 : 0 cyclo ω8c. The polar lipids consisted of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), an unidentified aminophospholipid (UAPL), an unidentified aminolipid (UAL) and two unidentified polar lipids (UPL). The genomic DNA G+C content of strain 64-1T was 64.5 mol%. Strain 64-1T shared the highest 16S rRNA gene sequence similarities with Phaeospirillum chandramohanii JA145T (92.0 %) and Telmatospirillum siberiense 26-4b1T (91.8 %). In the phylogenetic trees, the strain constituted a sub-cluster within the family Rhodospirillaceae. Based on the results of morphological, physiological, biochemical and phylogenetic analysis, strain 64-1T represents a new species of a novel genus within the family Rhodospirillaceae, for which the name Oleiliquidispirillum nitrogeniifigens gen. nov., sp. nov. is proposed. The type strain is 64-1T (=CGMCC 1.16798T=LMG 31399T).
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Affiliation(s)
- Fang-Ling Li
- State Key Laboratory of Agrobiotechnology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xiao-Tong Wang
- Unovation Bio & EP Technology Company Limited, Beijing, 100029, PR China
| | - Jian-Jie Shan
- Unovation Bio & EP Technology Company Limited, Beijing, 100029, PR China
| | - Shuai Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Ya-Xi Zhang
- State Key Laboratory of Agrobiotechnology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xi-Zhe Li
- Research Institute of Petroleum Exploration & Development, PetroChina Company Limited, Langfang, Hebei, 065007, PR China.,Research Institute of Petroleum Exploration & Development, PetroChina Company Limited, Beijing, 10083, PR China
| | - Dong-An Li
- Unovation Bio & EP Technology Company Limited, Beijing, 100029, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Lei Wang
- State Key Laboratory of Agrobiotechnology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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19
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Ding W, Baumdicker F, Neher RA. panX: pan-genome analysis and exploration. Nucleic Acids Res 2019; 46:e5. [PMID: 29077859 PMCID: PMC5758898 DOI: 10.1093/nar/gkx977] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/10/2017] [Indexed: 11/24/2022] Open
Abstract
Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates—the pan-genome—is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome. The visualization consists of connected components that allow rapid filtering and searching of genes and inspection of their evolutionary history. For each gene cluster, panX displays an alignment, a phylogenetic tree, maps mutations within that cluster to the branches of the tree and infers gain and loss of genes on the core-genome phylogeny. PanX is available at pangenome.de. Custom pan-genomes can be visualized either using a web server or by serving panX locally as a browser-based application.
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Affiliation(s)
- Wei Ding
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Franz Baumdicker
- Mathematisches Institut, Albert-Ludwigs University of Freiburg, 79104 Freiburg, Germany
| | - Richard A Neher
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.,Biozentrum and SIB Swiss Institute of Bioinformatics, University of Basel, 4056 Basel, Switzerland
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20
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Pett W, Adamski M, Adamska M, Francis WR, Eitel M, Pisani D, Wörheide G. The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content. Mol Biol Evol 2019; 36:643-649. [PMID: 30690573 DOI: 10.1093/molbev/msz013] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Resolving the relationships of animals (Metazoa) is crucial to our understanding of the origin of key traits such as muscles, guts, and nerves. However, a broadly accepted metazoan consensus phylogeny has yet to emerge. In part, this is because the genomes of deeply diverging and fast-evolving lineages may undergo significant gene turnover, reducing the number of orthologs shared with related phyla. This can limit the usefulness of traditional phylogenetic methods that rely on alignments of orthologous sequences. Phylogenetic analysis of gene content has the potential to circumvent this orthology requirement, with binary presence/absence of homologous gene families representing a source of phylogenetically informative characters. Applying binary substitution models to the gene content of 26 complete animal genomes, we demonstrate that patterns of gene conservation differ markedly depending on whether gene families are defined by orthology or homology, that is, whether paralogs are excluded or included. We conclude that the placement of some deeply diverging lineages may exceed the limit of resolution afforded by the current methods based on comparisons of orthologous protein sequences, and novel approaches are required to fully capture the evolutionary signal from genes within genomes.
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Affiliation(s)
- Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA
| | - Marcin Adamski
- Computational Biology and Bioinformatics Unit, Research School of Biology, The Australian National University, Canberra, Australia
| | - Maja Adamska
- Computational Biology and Bioinformatics Unit, Research School of Biology, The Australian National University, Canberra, Australia
| | - Warren R Francis
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Eitel
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Gert Wörheide
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
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21
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Beaulieu JM, O'Meara BC. Diversity and skepticism are vital for comparative biology: a response to Donoghue and Edwards (2019). AMERICAN JOURNAL OF BOTANY 2019; 106:613-617. [PMID: 31050366 DOI: 10.1002/ajb2.1278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/04/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Brian C O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996-1610, USA
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22
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Tarver JE, Taylor RS, Puttick MN, Lloyd GT, Pett W, Fromm B, Schirrmeister BE, Pisani D, Peterson KJ, Donoghue PCJ. Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss. Genome Biol Evol 2018; 10:1457-1470. [PMID: 29788279 PMCID: PMC6007596 DOI: 10.1093/gbe/evy096] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.
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Affiliation(s)
- James E Tarver
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Richard S Taylor
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Mark N Puttick
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
- Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Graeme T Lloyd
- School of Earth and Environment, University of Leeds, United Kingdom
| | - Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - Bettina E Schirrmeister
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Davide Pisani
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Philip C J Donoghue
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
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23
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Matzke NJ, Irmis RB. Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data. PeerJ 2018; 6:e4553. [PMID: 29637019 PMCID: PMC5890724 DOI: 10.7717/peerj.4553] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 03/08/2018] [Indexed: 12/01/2022] Open
Abstract
Tip-dating, where fossils are included as dated terminal taxa in Bayesian dating inference, is an increasingly popular method. Data for these studies often come from morphological character matrices originally developed for non-dated, and usually parsimony, analyses. In parsimony, only shared derived characters (synapomorphies) provide grouping information, so many character matrices have an ascertainment bias: they omit autapomorphies (unique derived character states), which are considered uninformative. There has been no study of the effect of this ascertainment bias in tip-dating, but autapomorphies can be informative in model-based inference. We expected that excluding autapomorphies would shorten the morphological branchlengths of terminal branches, and thus bias downwards the time branchlengths inferred in tip-dating. We tested for this effect using a matrix for Carboniferous-Permian eureptiles where all autapomorphies had been deliberately coded. Surprisingly, date estimates are virtually unchanged when autapomorphies are excluded, although we find large changes in morphological rate estimates and small effects on topological and dating confidence. We hypothesized that the puzzling lack of effect on dating was caused by the non-clock nature of the eureptile data. We confirm this explanation by simulating strict clock and non-clock datasets, showing that autapomorphy exclusion biases dating only for the clocklike case. A theoretical solution to ascertainment bias is computing the ascertainment bias correction (Mkparsinf), but we explore this correction in detail, and show that it is computationally impractical for typical datasets with many character states and taxa. Therefore we recommend that palaeontologists collect autapomorphies whenever possible when assembling character matrices.
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Affiliation(s)
- Nicholas J Matzke
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Randall B Irmis
- Department of Geology & Geophysics, University of Utah, Salt Lake City, UT, United States of America.,Natural History Museum of Utah, Salt Lake City, UT, United States of America
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24
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Methodological evaluation of DNA-based molecular keys to identify categories of mislabelling in commercial products from genus Merluccius spp. Food Chem 2018; 239:640-648. [DOI: 10.1016/j.foodchem.2017.06.138] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/06/2017] [Accepted: 06/26/2017] [Indexed: 11/19/2022]
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25
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Nies F, Wörner S, Wunsch N, Armant O, Sharma V, Hesselschwerdt A, Falk F, Weber N, Weiß J, Trautmann A, Posten C, Prakash T, Lamparter T. Characterization of Phormidium lacuna strains from the North Sea and the Mediterranean Sea for biotechnological applications. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Melo MMA, Daniele-Silva A, Teixeira DG, Estrela AB, Melo KRT, Oliveira VS, Rocha HAO, Ferreira LDS, Pontes DL, Lima JPMS, Silva-Júnior AA, Barbosa EG, Carvalho E, Fernandes-Pedrosa MF. Structure and in vitro activities of a Copper II-chelating anionic peptide from the venom of the scorpion Tityus stigmurus. Peptides 2017; 94:91-98. [PMID: 28552408 DOI: 10.1016/j.peptides.2017.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/09/2023]
Abstract
Anionic Peptides are molecules rich in aspartic acid (Asp) and/or glutamic acid (Glu) residues in the primary structure. This work presents, for the first time, structural characterization and biological activity assays of an anionic peptide from the venom of the scorpion Tityus stigmurus, named TanP. The three-dimensional structure of TanP was obtained by computational modeling and refined by molecular dynamic (MD) simulations. Furthermore, we have performed circular dichroism (CD) analysis to predict TanP secondary structure, and UV-vis spectroscopy to evaluate its chelating activity. CD indicated predominance of random coil conformation in aqueous medium, as well as changes in structure depending on pH and temperature. TanP has chelating activity on copper ions, which modified the peptide's secondary structure. These results were corroborated by MD data. The molar ratio of binding (TanP:copper) depends on the concentration of peptide: at lower TanP concentration, the molar ratio was 1:5 (TanP:Cu2+), whereas in concentrated TanP solution, the molar ratio was 1:3 (TanP:Cu2+). TanP was not cytotoxic to non-neoplastic or cancer cell lines, and showed an ability to inhibit the in vitro release of nitric oxide by LPS-stimulated macrophages. Altogether, the results suggest TanP is a promising peptide for therapeutic application as a chelating agent.
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Affiliation(s)
- Menilla M A Melo
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil
| | - Alessandra Daniele-Silva
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | - Diego G Teixeira
- Laboratório de Sistemas Metabólicos, Centro de Biociências, UFRN, Natal, RN, Brazil
| | - Andréia B Estrela
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | - Karolline R T Melo
- Laboratório de Biotecnologia de Polímeros Naturais, UFRN, Natal, RN, Brazil
| | | | - Hugo A O Rocha
- Laboratório de Biotecnologia de Polímeros Naturais, UFRN, Natal, RN, Brazil
| | | | - Daniel L Pontes
- Laboratório de Química de Coordenação e Polímeros, UFRN, Natal, RN, Brazil
| | - João P M S Lima
- Laboratório de Sistemas Metabólicos, Centro de Biociências, UFRN, Natal, RN, Brazil
| | - Arnóbio A Silva-Júnior
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil
| | - Euzebio G Barbosa
- Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil; Laboratório de Química Farmacêutica, UFRN, Natal, RN, Brazil
| | - Eneas Carvalho
- Centro de Biotecnologia, Instituto Butantan, São Paulo, SP, Brazil
| | - Matheus F Fernandes-Pedrosa
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil.
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Radtkey RR. ADAPTIVE RADIATION OF DAY-GECKOS (PHELSUMA) IN THE SEYCHELLES ARCHIPELAGO: A PHYLOGENETIC ANALYSIS. Evolution 2017; 50:604-623. [PMID: 28568942 DOI: 10.1111/j.1558-5646.1996.tb03872.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/1994] [Accepted: 04/18/1995] [Indexed: 11/26/2022]
Abstract
A phylogenetic analysis using characters derived from mitochondrial DNA was used to show that the species of Phelsuma in the Seychelles Islands represent a single, monophyletic lineage that has diversified as a result of both historical and ecological factors. In the distant past, the Seychelles archipelago was physically invaded by a single species of Phesluma. Separate eustatic sea level changes likely led first to allopatric speciation and then to the secondary contact of these sister species. Differences in the relative timing of the secondary contact between island groups resulted in P. sundbergi evolving an intermediate body size in the group of islands associated with Mahé and a large body size, while sympatric with P. astriata, in the group of islands associated with Praslin. Ecological information was used to support the conclusion that the actual evolutionary mechanism for the body size shift was a response to frequency dependent natural selection of P. sundbergi in single-species and two-species competitive regimes.
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Affiliation(s)
- Ray R Radtkey
- Department of Zoology, University of Texas at Austin, Austin, Texas, 78712
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28
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Remita MA, Halioui A, Malick Diouara AA, Daigle B, Kiani G, Diallo AB. A machine learning approach for viral genome classification. BMC Bioinformatics 2017; 18:208. [PMID: 28399797 PMCID: PMC5387389 DOI: 10.1186/s12859-017-1602-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/15/2017] [Indexed: 01/18/2023] Open
Abstract
Background Advances in cloning and sequencing technology are yielding a massive number of viral genomes. The classification and annotation of these genomes constitute important assets in the discovery of genomic variability, taxonomic characteristics and disease mechanisms. Existing classification methods are often designed for specific well-studied family of viruses. Thus, the viral comparative genomic studies could benefit from more generic, fast and accurate tools for classifying and typing newly sequenced strains of diverse virus families. Results Here, we introduce a virus classification platform, CASTOR, based on machine learning methods. CASTOR is inspired by a well-known technique in molecular biology: restriction fragment length polymorphism (RFLP). It simulates, in silico, the restriction digestion of genomic material by different enzymes into fragments. It uses two metrics to construct feature vectors for machine learning algorithms in the classification step. We benchmark CASTOR for the classification of distinct datasets of human papillomaviruses (HPV), hepatitis B viruses (HBV) and human immunodeficiency viruses type 1 (HIV-1). Results reveal true positive rates of 99%, 99% and 98% for HPV Alpha species, HBV genotyping and HIV-1 M subtyping, respectively. Furthermore, CASTOR shows a competitive performance compared to well-known HIV-1 specific classifiers (REGA and COMET) on whole genomes and pol fragments. Conclusion The performance of CASTOR, its genericity and robustness could permit to perform novel and accurate large scale virus studies. The CASTOR web platform provides an open access, collaborative and reproducible machine learning classifiers. CASTOR can be accessed at http://castor.bioinfo.uqam.ca. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1602-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohamed Amine Remita
- Laboratoire de bioinformatique, département d'informatique, Université du Québec à Montréal, Montreal, P.O. Box 8888 Downtown Station, H3C 3P8, Qc, Canada.,Pharmaqam Center, Université du Québec à Montréal (Québec), Montréal (Quebec), PO BOX 8888 Downtown Station, H3C 3P8, Canada
| | - Ahmed Halioui
- Laboratoire de bioinformatique, département d'informatique, Université du Québec à Montréal, Montreal, P.O. Box 8888 Downtown Station, H3C 3P8, Qc, Canada.,Pharmaqam Center, Université du Québec à Montréal (Québec), Montréal (Quebec), PO BOX 8888 Downtown Station, H3C 3P8, Canada
| | - Abou Abdallah Malick Diouara
- Laboratoire de bioinformatique, département d'informatique, Université du Québec à Montréal, Montreal, P.O. Box 8888 Downtown Station, H3C 3P8, Qc, Canada.,Pharmaqam Center, Université du Québec à Montréal (Québec), Montréal (Quebec), PO BOX 8888 Downtown Station, H3C 3P8, Canada
| | - Bruno Daigle
- Laboratoire de bioinformatique, département d'informatique, Université du Québec à Montréal, Montreal, P.O. Box 8888 Downtown Station, H3C 3P8, Qc, Canada.,Pharmaqam Center, Université du Québec à Montréal (Québec), Montréal (Quebec), PO BOX 8888 Downtown Station, H3C 3P8, Canada
| | - Golrokh Kiani
- Laboratoire de bioinformatique, département d'informatique, Université du Québec à Montréal, Montreal, P.O. Box 8888 Downtown Station, H3C 3P8, Qc, Canada.,Pharmaqam Center, Université du Québec à Montréal (Québec), Montréal (Quebec), PO BOX 8888 Downtown Station, H3C 3P8, Canada
| | - Abdoulaye Baniré Diallo
- Laboratoire de bioinformatique, département d'informatique, Université du Québec à Montréal, Montreal, P.O. Box 8888 Downtown Station, H3C 3P8, Qc, Canada. .,Pharmaqam Center, Université du Québec à Montréal (Québec), Montréal (Quebec), PO BOX 8888 Downtown Station, H3C 3P8, Canada.
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29
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Ata AETM, Abd El-Twab MH, Helmey RK, Dahy H. Phylogenetic relationships among Egyptian species of Anthemideae (Asteraceae) using ITS markers. CHROMOSOME BOTANY 2017; 12:1-6. [DOI: 10.3199/iscb.12.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Affiliation(s)
| | | | - Rasha Kamal Helmey
- Department of Botany and Microbiology, Faculty of Science, Minia University, Egypt
| | - Hadeer Dahy
- Department of Botany and Microbiology, Faculty of Science, Minia University, Egypt
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30
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Estimation of Gene Insertion/Deletion Rates with Missing Data. Genetics 2016; 204:513-529. [PMID: 27565162 DOI: 10.1534/genetics.116.191973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/17/2016] [Indexed: 11/18/2022] Open
Abstract
Lateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modeled in a maximum-likelihood framework with the additional flexibility of modeling potential missing data. The performance of the models is illustrated using simulations and a data set on gene family phyletic patterns from Gardnerella vaginalis that includes an ancient taxon. A novel application involving pseudogenization/genome reduction magnitudes is also illustrated, using gene family data from Mycobacterium spp. Finally, an R package called indelmiss is available from the Comprehensive R Archive Network at https://cran.r-project.org/package=indelmiss, with support documentation and examples.
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31
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Kjer KM, Simon C, Yavorskaya M, Beutel RG. Progress, pitfalls and parallel universes: a history of insect phylogenetics. J R Soc Interface 2016; 13:20160363. [PMID: 27558853 PMCID: PMC5014063 DOI: 10.1098/rsif.2016.0363] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/19/2016] [Indexed: 11/12/2022] Open
Abstract
The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.
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Affiliation(s)
- Karl M Kjer
- Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Margarita Yavorskaya
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
| | - Rolf G Beutel
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
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32
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33
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Pisani D, Pett W, Dohrmann M, Feuda R, Rota-Stabelli O, Philippe H, Lartillot N, Wörheide G. Genomic data do not support comb jellies as the sister group to all other animals. Proc Natl Acad Sci U S A 2015; 112:15402-7. [PMID: 26621703 PMCID: PMC4687580 DOI: 10.1073/pnas.1518127112] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the "Ctenophora-sister" hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.
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Affiliation(s)
- Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom; School of Biological Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom;
| | - Walker Pett
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France
| | - Martin Dohrmann
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany
| | - Roberto Feuda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige 38010, Italy
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d'Ecologie Expérimentale du CNRS, Moulis 09200, France; Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montreal, QC, Canada H3C 3J7
| | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France
| | - Gert Wörheide
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany; Bayerische Staatssammlung für Paläontologie und Geologie, Munich 80333, Germany
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Leaché AD, Banbury BL, Felsenstein J, de Oca ANM, Stamatakis A. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies. Syst Biol 2015; 64:1032-47. [PMID: 26227865 PMCID: PMC4604835 DOI: 10.1093/sysbio/syv053] [Citation(s) in RCA: 210] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 07/24/2015] [Indexed: 01/01/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths.
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Affiliation(s)
- Adam D Leaché
- Department of Biology, University of Washington, Seattle, WA 98195, USA; Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA;
| | - Barbara L Banbury
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Joseph Felsenstein
- Department of Biology, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Adrián Nieto-Montes de Oca
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, México 04510, Distrito Federal, México
| | - Alexandros Stamatakis
- Exelixis Laboratory, Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany; and Department of Informatics, Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
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35
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Wright AM, Hillis DM. Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data. PLoS One 2014; 9:e109210. [PMID: 25279853 PMCID: PMC4184849 DOI: 10.1371/journal.pone.0109210] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/03/2014] [Indexed: 11/19/2022] Open
Abstract
Despite the introduction of likelihood-based methods for estimating phylogenetic trees from phenotypic data, parsimony remains the most widely-used optimality criterion for building trees from discrete morphological data. However, it has been known for decades that there are regions of solution space in which parsimony is a poor estimator of tree topology. Numerous software implementations of likelihood-based models for the estimation of phylogeny from discrete morphological data exist, especially for the Mk model of discrete character evolution. Here we explore the efficacy of Bayesian estimation of phylogeny, using the Mk model, under conditions that are commonly encountered in paleontological studies. Using simulated data, we describe the relative performances of parsimony and the Mk model under a range of realistic conditions that include common scenarios of missing data and rate heterogeneity.
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Affiliation(s)
- April M. Wright
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - David M. Hillis
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
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36
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Kim T, Hao W. DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood. BMC Bioinformatics 2014; 15:320. [PMID: 25260628 PMCID: PMC4261585 DOI: 10.1186/1471-2105-15-320] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 09/25/2014] [Indexed: 11/17/2022] Open
Abstract
Background The study of discrete characters is crucial for the understanding of evolutionary processes. Even though great advances have been made in the analysis of nucleotide sequences, computer programs for non-DNA discrete characters are often dedicated to specific analyses and lack flexibility. Discrete characters often have different transition rate matrices, variable rates among sites and sometimes contain unobservable states. To obtain the ability to accurately estimate a variety of discrete characters, programs with sophisticated methodologies and flexible settings are desired. Results DiscML performs maximum likelihood estimation for evolutionary rates of discrete characters on a provided phylogeny with the options that correct for unobservable data, rate variations, and unknown prior root probabilities from the empirical data. It gives users options to customize the instantaneous transition rate matrices, or to choose pre-determined matrices from models such as birth-and-death (BD), birth-death-and-innovation (BDI), equal rates (ER), symmetric (SYM), general time-reversible (GTR) and all rates different (ARD). Moreover, we show application examples of DiscML on gene family data and on intron presence/absence data. Conclusion DiscML was developed as a unified R program for estimating evolutionary rates of discrete characters with no restriction on the number of character states, and with flexibility to use different transition models. DiscML is ideal for the analyses of binary (1s/0s) patterns, multi-gene families, and multistate discrete morphological characteristics. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-320) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, 48202 Detroit, USA.
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37
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Ames RM, Money D, Lovell SC. Inferring gene family histories in yeast identifies lineage specific expansions. PLoS One 2014; 9:e99480. [PMID: 24921666 PMCID: PMC4055711 DOI: 10.1371/journal.pone.0099480] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 05/15/2014] [Indexed: 11/24/2022] Open
Abstract
The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We show that the rates of gene family evolution vary both between gene families and between species. We are also able to identify those families that have experienced rapid lineage specific expansion/contraction and show that these families are enriched for specific functions. Moreover, we find that families with specific functions are repeatedly expanded in multiple species, suggesting the presence of common adaptations and that these family expansions/contractions are not random. Additionally, we identify potential specialisations, unique to specific species, in the functions of lineage specific expanded families. These results suggest that an important mechanism in the evolution of genome content is the presence of lineage-specific gene family changes.
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Affiliation(s)
- Ryan M. Ames
- Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
| | - Daniel Money
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Simon C. Lovell
- Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
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Nguyen VX, Detcharoen M, Tuntiprapas P, Soe-Htun U, Sidik JB, Harah MZ, Prathep A, Papenbrock J. Genetic species identification and population structure of Halophila (Hydrocharitaceae) from the Western Pacific to the Eastern Indian Ocean. BMC Evol Biol 2014; 14:92. [PMID: 24886000 PMCID: PMC4026155 DOI: 10.1186/1471-2148-14-92] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 04/25/2014] [Indexed: 11/10/2022] Open
Abstract
Background The Indo-Pacific region has the largest number of seagrass species worldwide and this region is considered as the origin of the Hydrocharitaceae. Halophila ovalis and its closely-related species belonging to the Hydrocharitaceae are well-known as a complex taxonomic challenge mainly due to their high morphological plasticity. The relationship of genetic differentiation and geographic barriers of H. ovalis radiation was not much studied in this region. Are there misidentifications between H. ovalis and its closely related species? Does any taxonomic uncertainty among different populations of H. ovalis persist? Is there any genetic differentiation among populations in the Western Pacific and the Eastern Indian Ocean, which are separated by the Thai-Malay peninsula? Genetic markers can be used to characterize and identify individuals or species and will be used to answer these questions. Results Phylogenetic analyses of the nuclear ribosomal internal transcribed spacer region based on materials collected from 17 populations in the Western Pacific and the Eastern Indian Ocean showed that some specimens identified as H. ovalis belonged to the H. major clade, also supported by morphological data. Evolutionary divergence between the two clades is between 0.033 and 0.038, much higher than the evolutionary divergence among H. ovalis populations. Eight haplotypes were found; none of the haplotypes from the Western Pacific is found in India and vice versa. Analysis of genetic diversity based on microsatellite analysis revealed that the genetic diversity in the Western Pacific is higher than in the Eastern Indian Ocean. The unrooted neighbor-joining tree among 14 populations from the Western Pacific and the Eastern Indian Ocean showed six groups. The Mantel test results revealed a significant correlation between genetic and geographic distances among populations. Results from band-based and allele frequency-based approaches from Amplified Fragment Length Polymorphism showed that all samples collected from both sides of the Thai-Malay peninsula were clustered into two clades: Gulf of Thailand and Andaman Sea. Conclusions Our study documented the new records of H. major for Malaysia and Myanmar. The study also revealed that the Thai-Malay peninsula is a geographic barrier between H. ovalis populations in the Western Pacific and the Eastern Indian Ocean.
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Affiliation(s)
| | | | | | | | | | | | | | - Jutta Papenbrock
- Institute of Botany, Leibniz University Hannover, Herrenhäuserstr, 2, D-30419 Hannover, Germany.
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Hipp AL, Eaton DAR, Cavender-Bares J, Fitzek E, Nipper R, Manos PS. A framework phylogeny of the American oak clade based on sequenced RAD data. PLoS One 2014; 9:e93975. [PMID: 24705617 PMCID: PMC3976371 DOI: 10.1371/journal.pone.0093975] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 03/05/2014] [Indexed: 11/19/2022] Open
Abstract
Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23-33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters. RAD-Seq data were readily combined across runs, with no difference in phylogenetic placement between technical replicates, which overlapped by only 43-64% in locus coverage. 17% (4,715) of the loci we analyzed could be mapped with high confidence to one or more expressed sequence tags in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as equal-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. We introduce a partitioned RAD visualization method (implemented in the R package RADami; http://cran.r-project.org/web/packages/RADami) to investigate the possibility that suboptimal topologies supported by large numbers of loci--due, for example, to reticulate evolution or lineage sorting--are masked by the globally optimal tree. We find no evidence for strongly-supported alternative topologies in our study, suggesting that the phylogeny we recover is a robust estimate of large-scale phylogenetic patterns in the American oak clade. Our study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23-33 million year-old clade.
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Affiliation(s)
- Andrew L. Hipp
- The Morton Arboretum, Lisle, Illinois, United States of America
- The Field Museum, Department of Botany, Chicago, Illinois, United States of America
- * E-mail:
| | - Deren A. R. Eaton
- The Field Museum, Department of Botany, Chicago, Illinois, United States of America
- University of Chicago, Committee on Evolutionary Biology, Chicago, Illinois, United States of America
| | - Jeannine Cavender-Bares
- University of Minnesota, College of Biological Sciences, Saint Paul, Minnesota, United States of America
| | | | - Rick Nipper
- Floragenex, Inc., Eugene, Oregon, United States of America
| | - Paul S. Manos
- Duke University, Department of Biology, Durham, North Carolina, United States of America
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40
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Cohen O, Ashkenazy H, Levy Karin E, Burstein D, Pupko T. CoPAP: Coevolution of presence-absence patterns. Nucleic Acids Res 2013; 41:W232-7. [PMID: 23748951 PMCID: PMC3692100 DOI: 10.1093/nar/gkt471] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Evolutionary analysis of phyletic patterns (phylogenetic profiles) is widely used in biology, representing presence or absence of characters such as genes, restriction sites, introns, indels and methylation sites. The phyletic pattern observed in extant genomes is the result of ancestral gain and loss events along the phylogenetic tree. Here we present CoPAP (coevolution of presence–absence patterns), a user-friendly web server, which performs accurate inference of coevolving characters as manifested by co-occurring gains and losses. CoPAP uses state-of-the-art probabilistic methodologies to infer coevolution and allows for advanced network analysis and visualization. We developed a platform for comparing different algorithms that detect coevolution, which includes simulated data with pairs of coevolving sites and independent sites. Using these simulated data we demonstrate that CoPAP performance is higher than alternative methods. We exemplify CoPAP utility by analyzing coevolution among thousands of bacterial genes across 681 genomes. Clusters of coevolving genes that were detected using our method largely coincide with known biosynthesis pathways and cellular modules, thus exhibiting the capability of CoPAP to infer biologically meaningful interactions. CoPAP is freely available for use at http://copap.tau.ac.il/.
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Affiliation(s)
- Ofir Cohen
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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41
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Chalkiadakis E, Dufourcq R, Schmitt S, Brandily C, Kervarec N, Coatanea D, Amir H, Loubersac L, Chanteau S, Guezennec J, Dupont-Rouzeyrol M, Simon-Colin C. Partial characterization of an exopolysaccharide secreted by a marine bacterium, Vibrio neocaledonicus sp. nov., from New Caledonia. J Appl Microbiol 2013; 114:1702-12. [PMID: 23480553 DOI: 10.1111/jam.12184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 02/24/2013] [Accepted: 03/04/2013] [Indexed: 12/01/2022]
Abstract
AIMS Exopolysaccharides (EPS) are industrially valuable molecules with numerous useful properties. This study describes the techniques used for the identification of a novel Vibrio bacterium and preliminary characterization of its EPS. METHODS AND RESULTS Bioprospection in marine intertidal areas of New Caledonia followed by screening for EPS producing brought to selection of the isolate NC470. Phylogenetic analysis (biochemical tests, gene sequencing and DNA-DNA relatedness) permitted to identify NC470 as a new member of the Vibrio genus. The EPS was produced in batch fermentation, purified using the ultrafiltration process and analysed by colorimetry, Fourier Transform Infrared spectroscopy, gas chromatography, Nuclear Magnetic Resonance and HPLC-size exclusion chromatography. This EPS exhibits a high N-acetyl-hexosamines and uronic acid content with a low amount of neutral sugar. The molecular mass was 672 × 10(3) Da. These data are relevant for possible technological exploitation. CONCLUSIONS We propose the name Vibrio neocaledonicus sp. nov for this isolate NC470, producing an EPS with an unusual sugar composition. Comparison with other known polymers permitted to select applications for this polymer. SIGNIFICANCE AND IMPACT OF THE STUDY This study contributes to evaluate the marine biodiversity of New Caledonia. It also highlights the biotechnological potential of New Caledonia marine bacteria.
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42
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Yuri T, Kimball RT, Harshman J, Bowie RCK, Braun MJ, Chojnowski JL, Han KL, Hackett SJ, Huddleston CJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Witt CC, Braun EL. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. BIOLOGY 2013; 2:419-44. [PMID: 24832669 PMCID: PMC4009869 DOI: 10.3390/biology2010419] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 11/19/2022]
Abstract
Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.
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Affiliation(s)
- Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - John Harshman
- 4869 Pepperwood Way, San Jose, CA 95124, USA; E-Mail:
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; E-Mail:
| | - Michael J. Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD 20742, USA
| | - Jena L. Chojnowski
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Shannon J. Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA; E-Mail:
| | - Christopher J. Huddleston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
| | - William S. Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA; E-Mail:
| | - Sushma Reddy
- Biology Department, Loyola University Chicago, Chicago, IL 60660, USA; E-Mail:
| | - Frederick H. Sheldon
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA; E-Mail:
| | - David W. Steadman
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; E-Mail:
| | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA; E-Mail:
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
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Abstract
Single-nucleotide polymorphism (SNP) data are routinely obtained by sequencing a region of interest in a small panel, constructing a chip with probes specific to sites found to vary in the panel, and using the chip to assay subsequent samples. The size of the chip is often reduced by removing low-frequency alleles from the set of SNPs. Using coalescent estimation of the scaled population size parameter, Θ, as a test case, we demonstrate the loss of information inherent in this procedure and develop corrections for coalescent analysis of SNPs obtained via a panel. We show that more accurate Θ-estimates can be recovered if the panel size is known, but at considerable computational cost as the panel individuals must be explicitly modeled in the analysis. We extend this technique to apply to the case where rare alleles have been omitted from the SNP panel. We find that when appropriate corrections for panel ascertainment and rare-allele omission are used, the biases introduced by ascertainment are largely correctable, but recovered estimates are less accurate than would be obtained with fully sequenced data. This method is then applied to recombinant multiple population data to investigate the effects of recombination and migration on the estimate of Θ.
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44
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Koch JM, Holder MT. An Algorithm for Calculating the Probability of Classes of Data Patterns on a Genealogy. PLOS CURRENTS 2012; 4:e4fd1286980c08. [PMID: 23868168 PMCID: PMC3712476 DOI: 10.1371/4fd1286980c08] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Felsenstein's pruning algorithm allows one to calculate the probability of any particular data pattern arising on a phylogeny given a model of character evolution. Here we present a similar dynamic programming algorithm. Our algorithm treats the tree and model as known. The algorithm makes it feasible to calculate the probability that a randomly selected character will be a member of a particular class of character patterns. Specifically, we are interested in binning patterns by the number of parsimony steps and the set of states observed at the tips of the tree. This algorithm was developed to expand the range of data set sizes that can be used with Waddell et al.'s marginal testing approach for assessing the adequacy of a model. The algorithms introduced can also be used in likelihood calculations which correct for ascertainment biases. For example, Lewis introduced an Mkv model which corrects for the lack of constant sites. The probability of a constant pattern arising can be calculated using the algorithm that we present, or by enumerating all possible constant patterns and calculating the probability of each one. Because the number of constant data patterns is small, both methods are efficient. However, elaborations of the Mkv model (such as those in Nylander et al) require calculating the probability of parsimony-uninformative patterns arising. For large trees and characters with many possible character states, the number of possible parismony-uninformative patterns is immense. In these cases, the algorithms introduced here will be more efficient. The algorithm has been implemented in open source software written in C++.
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Affiliation(s)
| | - Mark T Holder
- Department of Ecology and Evolutionary Biology, University of Kansas
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45
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Mavrodiev EV, Laktionov AP, Cellinese N. A maximum likelihood approach to generate hypotheses on the evolution and historical biogeography in the Lower Volga Valley regions (southwest Russia). Ecol Evol 2012; 2:1765-79. [PMID: 22957179 PMCID: PMC3434936 DOI: 10.1002/ece3.282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 04/23/2012] [Accepted: 04/27/2012] [Indexed: 11/21/2022] Open
Abstract
The evolution of the diverse flora in the Lower Volga Valley (LVV) (southwest Russia) is complex due to the composite geomorphology and tectonic history of the Caspian Sea and adjacent areas. In the absence of phylogenetic studies and temporal information, we implemented a maximum likelihood (ML) approach and stochastic character mapping reconstruction aiming at recovering historical signals from species occurrence data. A taxon-area matrix of 13 floristic areas and 1018 extant species was constructed and analyzed with RAxML and Mesquite. Additionally, we simulated scenarios with numbers of hypothetical extinct taxa from an unknown palaeoflora that occupied the areas before the dramatic transgression and regression events that have occurred from the Pleistocene to the present day. The flora occurring strictly along the river valley and delta appear to be younger than that of adjacent steppes and desert-like regions, regardless of the chronology of transgression and regression events that led to the geomorphological formation of the LVV. This result is also supported when hypothetical extinct taxa are included in the analyses. The history of each species was inferred by using a stochastic character mapping reconstruction method as implemented in Mesquite. Individual histories appear to be independent from one another and have been shaped by repeated dispersal and extinction events. These reconstructions provide testable hypotheses for more in-depth investigations of their population structure and dynamics.
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Affiliation(s)
- Evgeny V Mavrodiev
- Florida Museum of Natural History, University of FloridaGainesville, Florida 32611–7800, USA
| | - Alexy P Laktionov
- Department of Biology, Astrakhan State UniversityAstrakhan 414056, Russian Federation
| | - Nico Cellinese
- Florida Museum of Natural History, University of FloridaGainesville, Florida 32611–7800, USA
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46
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Sawaya SM, Lennon D, Buschiazzo E, Gemmell N, Minin VN. Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model. Genome Biol Evol 2012; 4:636-47. [PMID: 22593552 PMCID: PMC3516246 DOI: 10.1093/gbe/evs050] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microsatellites make up ∼3% of the human genome, and there is increasing evidence that some microsatellites can have important functions and can be conserved by selection. To investigate this conservation, we performed a genome-wide analysis of human microsatellites and measured their conservation using a binary character birth--death model on a mammalian phylogeny. Using a maximum likelihood method to estimate birth and death rates for different types of microsatellites, we show that the rates at which microsatellites are gained and lost in mammals depend on their sequence composition, length, and position in the genome. Additionally, we use a mixture model to account for unequal death rates among microsatellites across the human genome. We use this model to assign a probability-based conservation score to each microsatellite. We found that microsatellites near the transcription start sites of genes are often highly conserved, and that distance from a microsatellite to the nearest transcription start site is a good predictor of the microsatellite conservation score. An analysis of gene ontology terms for genes that contain microsatellites near their transcription start site reveals that regulatory genes involved in growth and development are highly enriched with conserved microsatellites.
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Affiliation(s)
- Sterling M Sawaya
- Centre for Reproduction and Genomics, Department of Anatomy and Structural Biology, University of Otago, Dunedin, New Zealand
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47
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Cohen O, Pupko T. Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony--a simulation study. Genome Biol Evol 2011; 3:1265-75. [PMID: 21971516 PMCID: PMC3215202 DOI: 10.1093/gbe/evr101] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2011] [Indexed: 12/26/2022] Open
Abstract
Bacterial evolution is characterized by frequent gain and loss events of gene families. These events can be inferred from phyletic pattern data-a compact representation of gene family repertoire across multiple genomes. The maximum parsimony paradigm is a classical and prevalent approach for the detection of gene family gains and losses mapped on specific branches. We and others have previously developed probabilistic models that aim to account for the gain and loss stochastic dynamics. These models are a critical component of a methodology termed stochastic mapping, in which probabilities and expectations of gain and loss events are estimated for each branch of an underlying phylogenetic tree. In this work, we present a phyletic pattern simulator in which the gain and loss dynamics are assumed to follow a continuous-time Markov chain along the tree. Various models and options are implemented to make the simulation software useful for a large number of studies in which binary (presence/absence) data are analyzed. Using this simulation software, we compared the ability of the maximum parsimony and the stochastic mapping approaches to accurately detect gain and loss events along the tree. Our simulations cover a large array of evolutionary scenarios in terms of the propensities for gene family gains and losses and the variability of these propensities among gene families. Although in all simulation schemes, both methods obtain relatively low levels of false positive rates, stochastic mapping outperforms maximum parsimony in terms of true positive rates. We further studied the factors that influence the performance of both methods. We find, for example, that the accuracy of maximum parsimony inference is substantially reduced when the goal is to map gain and loss events along internal branches of the phylogenetic tree. Furthermore, the accuracy of stochastic mapping is reduced with smaller data sets (limited number of gene families) due to unreliable estimation of branch lengths. Our simulator and simulation results are additionally relevant for the analysis of other types of binary-coded data, such as the existence of homologues restriction sites, gaps, and introns, to name a few. Both the simulation software and the inference methodology are freely available at a user-friendly server: http://gloome.tau.ac.il/.
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Affiliation(s)
- Ofir Cohen
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- National Evolutionary Synthesis Center, Durham, North Carolina
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48
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Vanderpoorten A, Gradstein SR, Carine MA, Devos N. The ghosts of Gondwana and Laurasia in modern liverwort distributions. Biol Rev Camb Philos Soc 2010; 85:471-87. [PMID: 20015315 DOI: 10.1111/j.1469-185x.2009.00111.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent advances in phylogenetics and, in particular, molecular dating, indicate that transoceanic dispersal has played an important role in shaping plant and animal distributions, obscuring any effect of tectonic history. Taxonomic sampling in biogeographic studies is, however, systematically biased towards vertebrates and higher plants and the possibility remains that a much stronger signature of ancient vicariance might be evident among other organisms, particularly among basal land plants. Here, an explicit Bayesian model-based approach was used to investigate global-scale biogeographic patterns among liverwort genera and to determine whether the patterns identified are consistent with the expectations of vicariance or dispersal scenarios. The distribution of each genus was mapped onto the phylograms describing the floristic affinities among areas in order to define the synapomorphic transitions supporting the observed groupings. The probabilities of change in a branch were calculated by implementing the Markov model of BayesTraits. The consistent ambiguity in ancestral state reconstructions returned by the unconstrained, two-rate model indicated that the overall signal in the data was weak, leading us to test the performance of competing, explicit models. The analyses resolved clades of geographic areas that are mostly consistent with the kingdoms traditionally identified for plants and animals, but with strikingly lower rates of endemism. The major split observed in the phylograms is into almost entirely Laurasian and Gondwanan clades. Other patterns recovered by the analyses, including Wallace's line and the South Atlantic Disjunction, have also traditionally been interpreted in terms of vicariance. These observations contrast with the idea that, in spore-dispersed organisms like bryophytes and pteridophytes, dispersal obscures evidence of vicariance. However, some discrepancies between the liverwort trees and expectations from a continental drift scenario were observed, such as the sister-group relationship of the Australian and New Zealand floras, which is supported by the co-occurrence of many genera, often endemic to these two areas. Together with an interpretation of the results within a phylogenetic context, our analyses suggest that patterns, which are at first sight consistent with an ancient vicariance hypothesis, may, in fact, conceal a complex mixture of relictual distributions and more recent, asymmetrical dispersal events. Our results provide a framework for testing specific evolutionary hypotheses concerning the extremely low levels of endemism in bryophytes and in particular, the significance of dispersal and cryptic diversification.
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Affiliation(s)
- Alain Vanderpoorten
- Institute of Botany, University of Liège, B22 Sart Tilman, 4000 Liège, Belgium.
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49
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Fink S, Fischer MC, Excoffier L, Heckel G. Genomic scans support repetitive continental colonization events during the rapid radiation of voles (Rodentia: Microtus): the utility of AFLPs versus mitochondrial and nuclear sequence markers. Syst Biol 2010; 59:548-72. [PMID: 20834011 DOI: 10.1093/sysbio/syq042] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single locus studies might not resolve phylogenetic relationships and the evolutionary history of taxa. The analysis of multiple markers promises higher resolution, and congruence among loci may indicate that the phylogenies represent the underlying species history. Here, we examine the utility of a genome-wide approach based on amplified fragment length polymorphisms (AFLP) and several DNA sequence markers in resolving phylogenetic signals in the rapidly radiating rodent genus Microtus which produced about 70 vole species within the last 1.2-2 myr. The current Holarctic distribution of Microtus is assumed to have resulted from three independent colonization events out of Asia to North America, Europe, and northern Asia without subsequent colonization, which would have led to deep splits between species from different continents. We investigated this hypothesis of three single colonization events by reconstructing the phylogenetic relationships among species from all three continents based on data from the first exon of the nuclear arginine vasopressin receptor 1a gene (EXON1), an adjacent noncoding region and the mitochondrial cytochrome b gene. The phylogenetic patterns obtained from these sequence markers are contrasted to genome-wide data on more than 1800 amplified fragment length polymorphisms (AFLP) analyzed for the same samples. Our results show that the single sequence markers partially resolve the phylogenetic relationships within Microtus, but with some incongruence mostly between EXON1 and the other loci. However, deeper nodes of the radiation are only weakly supported and neither the combination of the markers nor additional nuclear sequences improved the resolution significantly. AFLPs provided much stronger support for major continent-specific clades, and show also that reciprocal monophyly of American and European voles is incomplete. Our results demonstrate that Microtus voles colonized the American and European continents each repeatedly in several independent events on similar colonization routes during their radiation. More generally, this study supports the suitability of AFLPs as an alternative to sequence markers to resolve the evolutionary history of rapidly radiating taxa.
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Affiliation(s)
- Sabine Fink
- Department of Biology, Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
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50
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Abstract
Bacterial gene content variation during the course of evolution has been widely acknowledged and its pattern has been actively modeled in recent years. Gene truncation or gene pseudogenization also plays an important role in shaping bacterial genome content. Truncated genes could also arise from small-scale lateral gene transfer events. Unfortunately, the information of truncated genes has not been considered in any existing mathematical models on gene content variation. In this study, we developed a model to incorporate truncated genes. Maximum-likelihood estimates (MLEs) of the new model reveal fast rates of gene insertions/deletions on recent branches, suggesting a fast turnover of many recently transferred genes. The estimates also suggest that many truncated genes are in the process of being eliminated from the genome. Furthermore, we demonstrate that the ignorance of truncated genes in the estimation does not lead to a systematic bias but rather has a more complicated effect. Analysis using the new model not only provides more accurate estimates on gene gains/losses (or insertions/deletions), but also reduces any concern of a systematic bias from applying simplified models to bacterial genome evolution. Although not a primary purpose, the model incorporating truncated genes could be potentially used for phylogeny reconstruction using gene family content.
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