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Wood KP, Bonello KE, Plummer ST, Chamberlain RC, Fleming GA, Camitta MGW, Hill KD. Additive value of invasive haemodynamic assessment for predicting post-operative outcomes after Fontan. Cardiol Young 2024:1-6. [PMID: 39188221 DOI: 10.1017/s1047951124025290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Routine pre-Fontan cardiac catheterization remains standard practice at most centres. However, with advances in non-invasive risk assessment, an invasive haemodynamic assessment may not be necessary for all patients.Using retrospective data from patients undergoing Fontan palliation at our institution, we developed a multivariable model to predict the likelihood of a composite adverse post-operative outcome including prolonged length of stay ≥ 30 days, hospital readmission within 6 months, and death and/or transplant within 6 months. Our baseline model included non-invasive risk factors obtained from clinical history and echocardiogram. We then incrementally incorporated invasive haemodynamic data to determine if these variables improved risk prediction.Our baseline model correctly predicted favourable versus adverse post-Fontan outcomes in 118/174 (68%) patients. Covariates associated with adverse outcomes included the presence of a systemic right ventricle (adjusted adds ratio [aOR] 2.9; 95% CI 1.4, 5.8; p = 0.004), earlier surgical era (aOR 3.1 for era 1 vs 2; 95% CI 1.5, 6.5; p = 0.002), and performance of concomitant surgical procedures at the time of Fontan surgery (aOR 2.5; 95% CI 1.1, 5.0; p = 0.026). Incremental addition of invasively acquired haemodynamic data did not improve model performance or percentage of outcomes predicted.Invasively acquired haemodynamic data does not add substantially to non-invasive risk stratification in the majority of patients. Pre-Fontan catheterization may still be beneficial for angiographic evaluation of anatomy, for therapeutic intervention, and in select patients with equivocal risk stratification.
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Affiliation(s)
- Kathleen P Wood
- Department of Pediatrics, Duke Pediatric and Congenital Heart Center, Duke University Medical Center, Durham, NC, USA
| | - Kristin E Bonello
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Sarah T Plummer
- Department of Pediatrics, Division of Pediatric Cardiology, University Hospitals Rainbow Babies and Children's Hospital, Cleveland, OH, USA
| | - Reid C Chamberlain
- Department of Pediatrics, Duke Pediatric and Congenital Heart Center, Duke University Medical Center, Durham, NC, USA
| | - Greg A Fleming
- Department of Pediatrics, Duke Pediatric and Congenital Heart Center, Duke University Medical Center, Durham, NC, USA
| | - Michael G W Camitta
- Department of Pediatrics, Duke Pediatric and Congenital Heart Center, Duke University Medical Center, Durham, NC, USA
| | - Kevin D Hill
- Department of Pediatrics, Duke Pediatric and Congenital Heart Center, Duke University Medical Center, Durham, NC, USA
- Duke Clinical Research Institute, Durham, NC, USA
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2
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Roman I, Fedorenko V, Gromyko O. Phylogenomic analyses of the genus Actinoplanes: description of four novel genera. Int J Syst Evol Microbiol 2024; 74. [PMID: 39046446 DOI: 10.1099/ijsem.0.006464] [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: 07/25/2024] Open
Abstract
The genus Actinoplanes comprises 57 species (in February 2024) that are important components of ecosystems and are widely used in biotechnology, especially pharmaceuticals. Phylogenetic analysis of the family Micromonosporaceae (based on the 16S rRNA gene sequence) allowed us to group members of different genera into separate clades; however, the genus Actinoplanes was divided into three separate clades. Such phylogenetic heterogeneity could be due to the limitations of 16S rRNA gene analysis. In response to this heterogeneity, genomic phylogeny was performed. Phylogenomic reconstruction based on 324 single-copy orthologous genes allowed us to divide the genus Actinoplanes first into four clades and then, based on average nucleotide identity analysis, into five clades. Finally, chemotaxonomic analysis of each clade confirmed each clade's distinctiveness and the necessity to reclassify the genus Actinoplanes. The obtained data allowed us to divide the genus Actinoplanes into five genera: Actinoplanes, Paractinoplanes, Winogradskya, Symbioplanes and Amorphoplanes.
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Affiliation(s)
- Ivan Roman
- Department of Genetics and Biotechnology, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Oleksandr Gromyko
- Department of Genetics and Biotechnology, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
- Microbial Culture Collection of Antibiotic Producers, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
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3
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Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and methods for predicting viral evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585703. [PMID: 38746108 PMCID: PMC11092427 DOI: 10.1101/2024.03.19.585703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the website previr.app .
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Rinne N, Wikman P, Sahari E, Salmi J, Einarsdóttir E, Kere J, Alho K. Developmental dyslexia susceptibility genes DNAAF4, DCDC2, and NRSN1 are associated with brain function in fluently reading adolescents and young adults. Cereb Cortex 2024; 34:bhae144. [PMID: 38610086 PMCID: PMC11014888 DOI: 10.1093/cercor/bhae144] [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: 10/11/2023] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 04/14/2024] Open
Abstract
Reading skills and developmental dyslexia, characterized by difficulties in developing reading skills, have been associated with brain anomalies within the language network. Genetic factors contribute to developmental dyslexia risk, but the mechanisms by which these genes influence reading skills remain unclear. In this preregistered study (https://osf.io/7sehx), we explored if developmental dyslexia susceptibility genes DNAAF4, DCDC2, NRSN1, and KIAA0319 are associated with brain function in fluently reading adolescents and young adults. Functional MRI and task performance data were collected during tasks involving written and spoken sentence processing, and DNA sequence variants of developmental dyslexia susceptibility genes previously associated with brain structure anomalies were genotyped. The results revealed that variation in DNAAF4, DCDC2, and NRSN1 is associated with brain activity in key language regions: the left inferior frontal gyrus, middle temporal gyrus, and intraparietal sulcus. Furthermore, NRSN1 was associated with task performance, but KIAA0319 did not yield any significant associations. Our findings suggest that individuals with a genetic predisposition to developmental dyslexia may partly employ compensatory neural and behavioral mechanisms to maintain typical task performance. Our study highlights the relevance of these developmental dyslexia susceptibility genes in language-related brain function, even in individuals without developmental dyslexia, providing valuable insights into the genetic factors influencing language processing.
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Affiliation(s)
- Nea Rinne
- Department of Psychology and Logopedics, University of Helsinki, Haartmaninkatu 3, 00014 Helsinki, Finland
| | - Patrik Wikman
- Department of Psychology and Logopedics, University of Helsinki, Haartmaninkatu 3, 00014 Helsinki, Finland
| | - Elisa Sahari
- Department of Psychology and Speech-Language Pathology, University of Turku, Assistentinkatu 7, 20500 Turku, Finland
| | - Juha Salmi
- Department of Neuroscience and Biomedical Engineering, Otakaari 3, Aalto University, (AALTO), P.O. BOX 00076, Espoo, Finland
| | - Elisabet Einarsdóttir
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, SE-171 21, Solna, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, H7 Medicin, Huddinge, Sweden
- Folkhälsan Research Center, and Stem Cells and Metabolism Research Program (STEMM), University of Helsinki, PL 63, Haartmaninkatu 8, Helsinki, Finland
| | - Kimmo Alho
- Department of Psychology and Logopedics, University of Helsinki, Haartmaninkatu 3, 00014 Helsinki, Finland
- Advanced Magnetic Imaging Centre, Aalto NeuroImaging, Aalto University, Espoo, Finland
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5
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Kalogianni AI, Bouzalas I, Marka S, Zografaki ME, Mavrikou S, Gelasakis AI. Genetic Characterization of Small Ruminant Lentiviruses Isolated from Dairy Sheep in Greece. Viruses 2024; 16:547. [PMID: 38675890 PMCID: PMC11053789 DOI: 10.3390/v16040547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
The high genetic heterogeneity of small ruminant lentiviruses (SRLV) renders the genetic characterization of the circulating strains crucial for the epidemiological investigation and the designation of effective diagnostic tools. In Greece, research data regarding the genetic diversity of the circulating SRLV strains is scarce, hindering the implementation of efficient surveillance and control programs. The objective of the study was to genetically characterize SRLV strains isolated from intensive dairy sheep farms in Greece and evaluate the variability of the immunodominant regions of the capsid protein. For this reason, a total of 12 SRLV-infected animals from four intensive dairy sheep farms with purebred Chios and Lacaune ewes were used for the amplification and sequencing of an 800 bp gag-pol fragment. The phylogenetic analyses revealed a breed-related circulation of strains; Chios ewes were infected with strains belonging exclusively to a separate group of genotype A, whereas strains belonging to subtype B2 were isolated from Lacaune ewes. Immunodominant epitopes of capsid protein were quite conserved among the strains of the same genotype, except for the Major Homology Region which showed some unique mutations with potential effects on viral evolution. The present study contributes to the extension of the current knowledge regarding the genetic diversity of SRLV strains circulating in sheep in Greece. However, broader genetic characterization studies are warranted for the exploration of possible recombinant events and the more comprehensive classification of the circulating strains.
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Affiliation(s)
- Aphrodite I. Kalogianni
- Laboratory of Anatomy and Physiology of Farm Animals, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens (AUA), Iera Odos 75 Str., 11855 Athens, Greece;
| | - Ilias Bouzalas
- Veterinary Research Institute, Hellenic Agricultural Organization-DEMETER, Campus of Thermi, 57001 Thessaloniki, Greece;
| | - Sofia Marka
- Laboratory of Cell Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens (AUA), EU-CONEXUS European University, 11855 Athens, Greece; (S.M.); (M.-E.Z.); (S.M.)
| | - Maria-Eleftheria Zografaki
- Laboratory of Cell Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens (AUA), EU-CONEXUS European University, 11855 Athens, Greece; (S.M.); (M.-E.Z.); (S.M.)
| | - Sofia Mavrikou
- Laboratory of Cell Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens (AUA), EU-CONEXUS European University, 11855 Athens, Greece; (S.M.); (M.-E.Z.); (S.M.)
| | - Athanasios I. Gelasakis
- Laboratory of Anatomy and Physiology of Farm Animals, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens (AUA), Iera Odos 75 Str., 11855 Athens, Greece;
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6
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Cueva DF, Zug R, Pozo MJ, Molina S, Cisneros R, Bustamante MR, Torres MDL. Evidence of population genetic structure in Ecuadorian Andean bears. Sci Rep 2024; 14:2834. [PMID: 38310153 PMCID: PMC10838292 DOI: 10.1038/s41598-024-53003-5] [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: 03/31/2023] [Accepted: 01/25/2024] [Indexed: 02/05/2024] Open
Abstract
Wildlife conservation in Andean countries is a global priority because of the high levels of biodiversity and endemism. Historically, these countries have had limited resources to monitor wildlife (e.g., through genetic tools) and establish conservation programs. Focusing on the study and emblematic use of a few charismatic species has been a strategic approach to direct efforts for conservation and development planning. Consequently, the Andean bear is a flagship and umbrella species for highly biodiverse Andean countries like Ecuador. The few studies exploring the population genetics of this species have concluded that it has low genetic diversity and few units for conservation as populations appear to be well connected. However, these results might be attributed to ascertainment bias as studies have been performed with heterologous molecular markers. Here, using both mtDNA sequences and species-specific microsatellite markers, we show that Andean bears in Ecuador have population structure. Additionally, we found through the study of three Ecuadorian populations that the species might have a higher genetic diversity than we previously thought. These results could support the revision of research priorities, conservation, and planning strategies to improve connectivity for this species which occurs in crucial biodiversity hotspots.
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Affiliation(s)
- Dario F Cueva
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador
| | - Rebecca Zug
- Laboratorio de Carnívoros, Universidad San Francisco de Quito USFQ, Diego de Robles y Vía Interoceanica s/n, Quito, 170157, Ecuador
| | - María José Pozo
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador
| | - Santiago Molina
- Laboratorio de Carnívoros, Universidad San Francisco de Quito USFQ, Diego de Robles y Vía Interoceanica s/n, Quito, 170157, Ecuador
- Fundación Zoológica del Ecuador, Pircapamaba s/n y Rumichupa, Guayllabamba, Quito, Ecuador
| | - Rodrigo Cisneros
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto, C/París s/n., 1101608, Loja, Ecuador
| | - Martín R Bustamante
- Fundación Zoológica del Ecuador, Pircapamaba s/n y Rumichupa, Guayllabamba, Quito, Ecuador
| | - María de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador.
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7
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Du X, Liu N, Yan B, Li Y, Liu M, Huang Y. Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron. THE ISME JOURNAL 2024; 18:wrad041. [PMID: 38366066 PMCID: PMC10881299 DOI: 10.1093/ismejo/wrad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/25/2023] [Accepted: 12/26/2024] [Indexed: 02/18/2024]
Abstract
Microorganisms living in soil maintain intricate interactions among themselves, forming the soil microbiota that influences the rhizosphere microbiome and plant growth. However, the mechanisms underlying the soil microbial interactions remain unclear. Streptomyces and Mesorhizobium are commonly found in soil and serve as plant growth-promoting rhizobacteria (PGPR). Here, we identified an unprecedented interaction between the colonies of red-soil-derived Streptomyces sp. FXJ1.4098 and Mesorhizobium sp. BAC0120 and referred to it as "proximity-based defensive mutualism (PBDM)." We found that metabolite-mediated iron competition and sharing between the two microorganisms were responsible for PBDM. Streptomyces sp. FXJ1.4098 produced a highly diffusible siderophore, desferrioxamine, which made iron unavailable to co-cultured Mesorhizobium sp. BAC0120, thereby inhibiting its growth. Streptomyces sp. FXJ1.4098 also released poorly diffusible iron-porphyrin complexes, which could be utilized by Mesorhizobium sp. BAC0120, thereby restoring the growth of nearby Mesorhizobium sp. BAC0120. Furthermore, in ternary interactions, the PBDM strategy contributed to the protection of Mesorhizobium sp. BAC0120 close to Streptomyces sp. FXJ1.4098 from other microbial competitors, resulting in the coexistence of these two PGPR. A scale-up pairwise interaction screening suggested that the PBDM strategy may be common between Mesorhizobium and red-soil-derived Streptomyces. These results demonstrate the key role of iron in complex microbial interactions and provide novel insights into the coexistence of PGPR in soil.
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Affiliation(s)
- Xueyuan Du
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
- College of Life Sciences, University of Chinese Academy of Sciences , Beijing 101408, P. R. China
- National Engineering Laboratory for Site Remediation Technologies, BCEG Environmental Remediation Co., Ltd., Beijing 100015, P. R. China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
| | - Bingfa Yan
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
- College of Life Sciences, University of Chinese Academy of Sciences , Beijing 101408, P. R. China
| | - Yisong Li
- School of Public Health, Qingdao University, Qingdao 266071, P. R. China
| | - Minghao Liu
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
- College of Life Sciences, University of Chinese Academy of Sciences , Beijing 101408, P. R. China
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Kahnt B, Theodorou P, Grimm-Seyfarth A, Onstein RE. When lizards try out a more plant-based lifestyle: The macroevolution of mutualistic lizard-plant-interactions (Squamata: Sauria/Lacertilia). Mol Phylogenet Evol 2023:107839. [PMID: 37290582 DOI: 10.1016/j.ympev.2023.107839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 05/12/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Pollination and seed dispersal of plants by animals are key mutualistic processes for the conservation of plant diversity and ecosystem functioning. Although different animals frequently act as pollinators or seed dispersers, some species can provide both functions, so-called 'double mutualists', suggesting that the evolution of pollination and seed dispersal may be linked. Here, we assess the macroevolution of mutualistic behaviours in lizards (Lacertilia) by applying comparative methods to a phylogeny comprising 2,838 species. We found that both flower visitation (potential pollination) (recorded in 64 species [2.3% of total] across 9 families) and seed dispersal (recorded in 382 species [13,5% of total] across 26 families) have evolved repeatedly in Lacertilia. Furthermore, we found that seed dispersal activity pre-dated flower visitation and that the evolution of seed dispersal activity and flower visitation was correlated, illustrating a potential evolutionary mechanism behind the emergence of double mutualisms. Finally, we provide evidence that lineages with flower visitation or seed dispersal activity have higher diversification rates than lineages lacking these behaviours. Our study illustrates the repeated innovation of (double) mutualisms across Lacertilia and we argue that island settings may provide the ecological conditions under which (double) mutualisms persist over macroevolutionary timescales.
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Affiliation(s)
- Belinda Kahnt
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany.
| | - Panagiotis Theodorou
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
| | - Annegret Grimm-Seyfarth
- Department of Conservation Biology and Social-Ecological Systems, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Naturalis Biodiversity Center, Darwinweg, 2 2333CR Leiden, the Netherlands
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Vandanashree M, Singh AK, Gopal B. Characterization of RNase J. Methods Enzymol 2023; 692:177-215. [PMID: 37925179 DOI: 10.1016/bs.mie.2023.03.020] [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: 11/06/2023]
Abstract
RNase J is involved in RNA maturation as well as degradation of RNA to the level of mononucleotides. This enzyme plays a vital role in maintaining intracellular RNA levels and governs different steps of the cellular metabolism in bacteria. RNase J is the first ribonuclease that was shown to have both endonuclease and 5'-3' exonuclease activity. RNase J enzymes can be identified by their characteristic sequence features and domain architecture. The quaternary structure of RNase J plays a role in regulating enzyme activity. The structure of RNase J has been characterized from several homologs. These reveal extensive overall structural similarity alongside a distinct active site topology that coordinates a metal cofactor. The metal cofactor is essential for catalytic activity. The catalytic activity of RNase J is influenced by oligomerization, the choice and stoichiometry of metal cofactors, and the 5' phosphorylation state of the RNA substrate. Here we describe the sequence and structural features of RNase J alongside phylogenetic analysis and reported functional roles in diverse organisms. We also provide a detailed purification strategy to obtain an RNase J enzyme sample with or without a metal cofactor. Different methods to identify the nature of the bound metal cofactor, the binding affinity and stoichiometry are presented. Finally, we describe enzyme assays to characterize RNase J using radioactive and fluorescence-based strategies with diverse RNA substrates.
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Affiliation(s)
- Muralidharan Vandanashree
- Molecular Biophysics Unit, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Ankur Kumar Singh
- Molecular Biophysics Unit, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Balasubramanian Gopal
- Molecular Biophysics Unit, Division of Biological Sciences, Indian Institute of Science, Bangalore, India.
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de la Fuente R, Díaz-Villanueva W, Arnau V, Moya A. Genomic Signature in Evolutionary Biology: A Review. BIOLOGY 2023; 12:biology12020322. [PMID: 36829597 PMCID: PMC9953303 DOI: 10.3390/biology12020322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023]
Abstract
Organisms are unique physical entities in which information is stored and continuously processed. The digital nature of DNA sequences enables the construction of a dynamic information reservoir. However, the distinction between the hardware and software components in the information flow is crucial to identify the mechanisms generating specific genomic signatures. In this work, we perform a bibliometric analysis to identify the different purposes of looking for particular patterns in DNA sequences associated with a given phenotype. This study has enabled us to make a conceptual breakdown of the genomic signature and differentiate the leading applications. On the one hand, it refers to gene expression profiling associated with a biological function, which may be shared across taxa. This signature is the focus of study in precision medicine. On the other hand, it also refers to characteristic patterns in species-specific DNA sequences. This interpretation plays a key role in comparative genomics, identifying evolutionary relationships. Looking at the relevant studies in our bibliographic database, we highlight the main factors causing heterogeneities in genome composition and how they can be quantified. All these findings lead us to reformulate some questions relevant to evolutionary biology.
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Affiliation(s)
- Rebeca de la Fuente
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Correspondence:
| | - Wladimiro Díaz-Villanueva
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Vicente Arnau
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Andrés Moya
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
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11
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Delfini C, Aliscioni SS, Acosta JM, Pensiero JF, Zuloaga FO. An Update of the Cenchrinae (Poaceae, Panicoideae, Paniceae) and a New Genus for the Subtribe to Clarify the Dubious Position of a Species of Panicum L. PLANTS (BASEL, SWITZERLAND) 2023; 12:749. [PMID: 36840098 PMCID: PMC9966601 DOI: 10.3390/plants12040749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/21/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
Subtribe Cenchrinae, so-called as the "bristle clade", is a monophyletic group of panicoid grasses characterized by having sterile branches or bristles on the inflorescences in most of its species. Within this subtribe is also placed Panicum antidotale Retz., an "incertae sedis" species of Panicum L. which lacks bristles along the inflorescence. In this study, we present an update of the subtribe Cenchrinae based on molecular, morphological, and anatomical evidence to clarify the systematic position of P. antidotale in the Cenchrinae, excluding it from Panicum and establishing it in a new genus (i.e., Janochloa Zuloaga & Delfini); the morphological features distinguishing the new genus from other closely related taxa are properly discussed and an identification key to the 24 genera recognized within Cenchrinae is presented. We also add American Setaria species, not tested before, of subgenera Paurochaetium and Reverchoniae, discussing the position of these taxa in actual phylogeny of the genus as well as defining placements in the tree of Setaria species that were imprecisely located in previous analyses. A comparison with the results from other studies, comments on Stenotaphrum Trin. and a brief discussion on conflicting placements in Cenchrus and related taxa, and of Acritochaete Pilg. are also included.
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Affiliation(s)
- Carolina Delfini
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
| | - Sandra S. Aliscioni
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
- Cátedra de Botánica General, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Juan M. Acosta
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
| | - José F. Pensiero
- Instituto de Ciencias Agropecuarias del Litoral, UNL–CONICET–FCA, Kreder 2805, Esperanza 3080HOF, Santa Fe, Argentina
| | - Fernando O. Zuloaga
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
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12
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Lucas SAM, Graham AM, Presnell JS, Clark NL. Highly Dynamic Gene Family Evolution Suggests Changing Roles for PON Genes Within Metazoa. Genome Biol Evol 2023; 15:evad011. [PMID: 36718542 PMCID: PMC9937041 DOI: 10.1093/gbe/evad011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 10/28/2022] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
Change in gene family size has been shown to facilitate adaptation to different selective pressures. This includes gene duplication to increase dosage or diversification of enzymatic substrates and gene deletion due to relaxed selection. We recently found that the PON1 gene, an enzyme with arylesterase and lactonase activity, was lost repeatedly in different aquatic mammalian lineages, suggesting that the PON gene family is responsive to environmental change. We further investigated if these fluctuations in gene family size were restricted to mammals and approximately when this gene family was expanded within mammals. Using 112 metazoan protein models, we explored the evolutionary history of the PON family to characterize the dynamic evolution of this gene family. We found that there have been multiple, independent expansion events in tardigrades, cephalochordates, and echinoderms. In addition, there have been partial gene loss events in monotremes and sea cucumbers and what appears to be complete loss in arthropods, urochordates, platyhelminths, ctenophores, and placozoans. In addition, we show the mammalian expansion to three PON paralogs occurred in the ancestor of all mammals after the divergence of sauropsida but before the divergence of monotremes from therians. We also provide evidence of a novel PON expansion within the brushtail possum. In the face of repeated expansions and deletions in the context of changing environments, we suggest a range of selective pressures, including pathogen infection and mitigation of oxidative damage, are likely influencing the diversification of this dynamic gene family across metazoa.
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13
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Thin KK, He SW, Ma R, Wang X, Han JG, Zhang XX. Paenibacillus rhizolycopersici sp. nov., an oligotrophic bacterium isolated from a tomato plant in China. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748508 DOI: 10.1099/ijsem.0.005698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A Gram-positive, rod-shaped, motile, endospore-forming strain, DXFW5T, was isolated from the rhizosphere soil of tomato. Strain DXFW5T grew at 20-50 °C (optimum, 25-37 °C), pH 5-8 (optimum, pH 7) and in the presence of 3 % NaCl. It was positive for catalase and oxidase. Phylogenetic analysis using 16S rRNA gene sequences showed this strain was most closely related to Paenibacillus timonensis DSM 16943T (98.0 %) and Paenibacillus barengoltzii DSM 22255T (97.4 %). The DNA G+C content was 52.9 mol%. The digital DNA-DNA hybridization values between strain DXFW5T and P. timonensis DSM 16943T, P. barengoltzii DSM 22255T and P. macerans DSM 24T were 33.1, 24.9 and 21.2 %, respectively. The average nucleotide identity values between strain DXFW5T and P. timonensis DSM 16943T , P. barengoltzii DSM 22255T and P. macerans DSM 24T were 86.93, 81.77 and 75.98 %, respectively. The major fatty acids were anteiso-C15 : 0 (55.1 %), iso-C16 : 0 (13.2 %) and C16 : 0 (10 %). The polar lipids of strain DXFW5T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine two unidentified phospholipids and three unidentified lipids. MK-7 was the major isoprenoid quinone. Based on these results, it was concluded that the isolate represents a novel species of the genus Paenibacillus, for which the name Paenibacillus rhizolycopersici sp. nov. is proposed, with DXFW5T (=ACCC 61751T=JCM 34488T) as the type strain.
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Affiliation(s)
- Kyu Kyu Thin
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Department of Zoology, University of Magway, Magway, 04012, Myanmar
| | - Shan-Wen He
- Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, PR China
| | - Rong Ma
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xing Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ji-Gang Han
- Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, PR China
| | - Xiao-Xia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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14
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Delfini C, Salariato DL, Aliscioni SS, Zuloaga FO. Systematics and Phylogenetic Placement of Panicum L. Species within the Melinidinae Based on Morphological, Anatomical, and Molecular Data (Poaceae, Panicoideae, Paniceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:399. [PMID: 36679111 PMCID: PMC10375907 DOI: 10.3390/plants12020399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Generic boundaries of the African species Panicum deustum Thunb., Panicum trichocladum Hack. ex K. Schum., and Panicum vollesenii Renvoize are analyzed and compared with related genera of the tribe Paniceae and the subtribe Melinidinae. Based on morphological (vegetative and reproductive characters including habit, ligules, inflorescence, spikelets, and ornamentation of the upper anthecium), anatomical (transverse section of leaves), and molecular data (three chloroplast markers), a new genus is proposed for P. deustum, while P. trichocladum and P. vollesenii are transferred to the genus Megathyrsus (Pilg.) B.K. Simon & S.W.L. Jacobs. The phylogenetic position of both taxa within the Melinidinae and their morphological affinities with other genera of the subtribe are also discussed. Additional studies on the Melinidinae will clarify the systematic position of the genera that are still in a doubtful position within the subtribe, such as Eriochloa and Urochloa.
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Affiliation(s)
- Carolina Delfini
- Instituto de Botánica Darwinion (ANCEFN-CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Argentina
| | - Diego L Salariato
- Instituto de Botánica Darwinion (ANCEFN-CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Argentina
| | - Sandra S Aliscioni
- Instituto de Botánica Darwinion (ANCEFN-CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Argentina
- Cátedra de Botánica General, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Fernando O Zuloaga
- Instituto de Botánica Darwinion (ANCEFN-CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Argentina
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15
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Si J, Zhang YZ, Liang JQ, Li HJ. Morphology and phylogeny identify two new species and one new subspecies of Podoscypha from Yunnan Province, Southwest China. Front Microbiol 2023; 14:1151365. [PMID: 36925482 PMCID: PMC10011068 DOI: 10.3389/fmicb.2023.1151365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 03/08/2023] Open
Abstract
In this study, Podoscypha was taxonomically and phylogenetically evaluated. In total, five specimens collected from the tropical areas of Yunnan Province in Southwest China were studied. In combination with morphological observations and phylogenetic analyses based on ITS and LSU loci, two new species and one new subspecies, Podoscypha subinvoluta, P. tropica, and P. petalodes subsp. cystidiata, respectively, were discovered. The illustrated descriptions of the new species and subspecies are provided. Moreover, the main morphological differences between related species are discussed.
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Affiliation(s)
- Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yi-Zhe Zhang
- National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jia-Qi Liang
- National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hai-Jiao Li
- National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
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16
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Sakon JJ, Kiani R. Differences in memory for what, where, and when components of recently formed episodes. J Neurophysiol 2022; 128:310-325. [PMID: 35792500 PMCID: PMC9342146 DOI: 10.1152/jn.00250.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
An integral feature of human memory is the ability to recall past events. What distinguishes such episodic memory from semantic or associative memory is the joint encoding and retrieval of "what," "where," and "when" (WWW) for such events. Surprisingly, little work has addressed whether all three components of WWW are retrieved with equal fidelity when remembering episodes. To study this question, we created a novel task where human participants identified matched or mismatched still images sampled from recently viewed synthetic movies. The mismatch images only probe one of the three WWW components at a time, allowing us to separately test accuracies for each component of the episodes. Crucially, each WWW component in the movies is easily distinguishable in isolation, thereby making any differences in accuracy between components due to how they are joined in memory. We find that memory for "when" has the lowest accuracy, with it being the component most influenced by primacy and recency. Furthermore, the memory of "when" is most susceptible to interference due to changes in task load. These findings suggest that episodes are not stored and retrieved as a coherent whole but instead their components are either stored or retrieved differentially as part of an active reconstruction process. NEW & NOTEWORTHY When we store and subsequently retrieve episodes, does the brain encode them holistically or in separate parts that are later reconstructed? Using a task where participants study abstract episodes and on any given trial are probed on the what, where, and when components, we find mnemonic differences between them. Accuracy for "when" memory is the lowest, as it is most influenced by primacy, recency, and interference, suggesting that episodes are not treated holistically by the brain.
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Affiliation(s)
- John J Sakon
- Center for Neural Science, New York University, New York, New York
| | - Roozbeh Kiani
- Center for Neural Science, New York University, New York, New York.,Neuroscience Institute, NYU Langone Medical Center, New York, New York.,Department of Psychology, New York University, New York, New York
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17
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Phylogenetic relationships in Indian Daphne (Thymelaeaceae) based on nuclear ITS and cpDNAdata. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01125-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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18
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Li G(K, So MKP, Tam KY. Identifying the Big Shots—A Quantile-Matching Way in the Big Data Context. ACM TRANSACTIONS ON MANAGEMENT INFORMATION SYSTEMS 2022. [DOI: 10.1145/3490395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The prevalence of big data has raised significant epistemological concerns in information systems research. This study addresses two of them—the deflated
p
-value problem and the role of explanation and prediction. To address the deflated
p
-value problem, we propose a multivariate effect size method that uses the log-likelihood ratio test. This method measures the joint effect of all variables used to operationalize one factor, thus overcoming the drawback of the traditional effect size method (θ), which can only be applied at the single variable level. However, because factors can be operationalized as different numbers of variables, direct comparison of multivariate effect size is not possible. A quantile-matching method is proposed to address this issue. This method provides consistent comparison results with the classic quantile method. But it is more flexible and can be applied to scenarios where the quantile method fails. Furthermore, an absolute multivariate effect size statistic is developed to facilitate concluding without comparison. We have tested our method using three different datasets and have found that it can effectively differentiate factors with various effect sizes. We have also compared it with prediction analysis and found consistent results: explanatorily influential factors are usually also predictively influential in a large sample scenario.
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Affiliation(s)
- Guangrui (Kayla) Li
- Operations Management and Information Systems, Schulich Business School, York University, Toronto, ON, Canada
| | - Mike K. P. So
- Department of Information Systems, Business Statistics and Operations Management, Business School, Hong Kong University of Science and Technology, Hong Kong
| | - Kar Yan Tam
- Department of Information Systems, Business Statistics and Operations Management, Business School, Hong Kong University of Science and Technology, Hong Kong
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19
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He SW, Ma R, Zhao YY, An L, Huang JH, Zhang Q, Han JG, Zhang XX. Chitinophaga hostae sp. nov., isolated from the rhizosphere soil of Hosta plantaginea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
A Gram-negative, rod-shaped aerobic bacterium designated as strain 2R12T was isolated from the rhizosphere soil of Hosta plantaginea. Phylogenetic analyses based on the 16S rRNA gene revealed that strain 2R12T should be assigned to the genus
Chitinophaga
with the highest sequence similarity to
Chitinophaga arvensicola
DSM 3695T (99.1 %) and
Chitinophaga ginsengisegetis
DSM 18108T (98.6 %). The major fatty acids of strain 2R12T (>10 %) were iso-C15 : 0, C16 :1
ω5c and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids. The predominant respiratory quinone was MK-7. The genomic DNA G+C content was 46.1 mol%. The average nucleotide identity values of strain 2R12T with
C. arvensicola
DSM 3695T and
C. ginsengisegetis
DSM 18108T were 77.9 and 78.8 %, respectively, while in silico DNA–DNA hybridization values for strain 2R12T with these strains were 22.8 and 23.3 %, respectively. Based on comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain 2R12T represents a novel species in the genus
Chitinophaga
, for which the name Chitinophaga hostae sp. nov. is proposed. The type strain is 2R12T (=ACCC 61757T=JCM 34719T).
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Affiliation(s)
- Shan-Wen He
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, PR China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai 200232, PR China
- National Innovation Alliance of National Forestry and Grassland Administration on Afforestation and Landscaping of Challenging Urban Sites, Shanghai 200232, PR China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Rong Ma
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ying-Ying Zhao
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai 200232, PR China
- National Innovation Alliance of National Forestry and Grassland Administration on Afforestation and Landscaping of Challenging Urban Sites, Shanghai 200232, PR China
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, PR China
| | - Lei An
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai 200232, PR China
- National Innovation Alliance of National Forestry and Grassland Administration on Afforestation and Landscaping of Challenging Urban Sites, Shanghai 200232, PR China
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, PR China
| | - Jun-Hua Huang
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai 200232, PR China
- National Innovation Alliance of National Forestry and Grassland Administration on Afforestation and Landscaping of Challenging Urban Sites, Shanghai 200232, PR China
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, PR China
| | - Qi Zhang
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai 200232, PR China
- National Innovation Alliance of National Forestry and Grassland Administration on Afforestation and Landscaping of Challenging Urban Sites, Shanghai 200232, PR China
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, PR China
| | - Ji-Gang Han
- National Innovation Alliance of National Forestry and Grassland Administration on Afforestation and Landscaping of Challenging Urban Sites, Shanghai 200232, PR China
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, PR China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai 200232, PR China
| | - Xiao-Xia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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20
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Proença CEB, Tuler AC, Lucas EJ, Vasconcelos TNDC, de Faria JEQ, Staggemeier VG, de-Carvalho PS, Forni-Martins ER, Inglis PW, da Mata LR, da Costa IR. Diversity, phylogeny and evolution of the rapidly evolving genus Psidium L. (Myrtaceae, Myrteae). ANNALS OF BOTANY 2022; 129:367-388. [PMID: 35034117 PMCID: PMC8944734 DOI: 10.1093/aob/mcac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Psidium is the fourthth largest genus of Myrtaceae in the Neotropics. Psidium guajava is widely cultivated in the tropics for its edible fruit. It is commercially under threat due to the disease guava decline. Psidium cattleyanum is one of the 100 most invasive organisms in the world. Knowledge of the phylogenetic relationships within Psidium is poor. We aim to provide a review of the biology, morphology and ecology of Psidium, a phylogenetic tree, an infrageneric classification and a list of species. METHODS Morphological and geographic data were obtained by studying Psidium in herbaria and in the field between 1988 and 2020. Forty-six herbaria were visited personally. A database of approx. 6000 specimens was constructed, and the literature was reviewed. Thirty species (about a third of the species in the genus) were sampled for molecular phylogenetic inference. Two chloroplast (psbA-trnH and ndhF) and two nuclear (external transcribed spacer and internal transcribed spacer) regions were targeted. Phylogenetic trees were constructed using maximum likelihood (ML; RaxML) and Bayesian inference (BI; MrBayes). KEY RESULTS Psidium is a monophyletic genus with four major clades recognized as sections. Section Psidium (ten species), to which P. guajava belongs, is sister to the rest of the genus; it is widespread across the Neotropics. Section Obversifolia (six species; restricted to the Brazilian Atlantic Forest), which includes P. cattleyanum, is sister to the innermost clade composed of sister sections Apertiflora (31 species; widespread but most diverse in the Brazilian Atlantic Forest) + Mitranthes (26 species; widespread in dry forests and probably diverse in the Caribbean). Characters associated with diversification within Psidium are discussed. CONCLUSIONS Research on pre-foliation, colleters, leaf anatomy, leaf physiology, staminal development, placentation and germination associated with the anatomy of the opercular plug is desirable. Studies are biased towards sections Psidium and Obversifolia, with other sections poorly known.
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Affiliation(s)
| | - Amélia Carlos Tuler
- Instituto Nacional da Mata Atlântica, Av. José Ruschi 4, Santa Teresa, ES, CEP, Brazil
| | | | | | | | - Vanessa Graziele Staggemeier
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, R. das Biociências, Lagoa Nova, Natal, RN, CEP, Brazil
| | | | | | | | - Lorena Ramos da Mata
- Empresa Brasileira de Pesquisa Agropecuária, Recursos Genéticos e Biotecnologia (EMBRAPA CENARGEN)
, SAIN Parque Rural, W5, Asa Norte, Brasília, DF, Brazil
| | - Itayguara Ribeiro da Costa
- Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici Bloco 906, Fortaleza, CE, Brazil
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21
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Hızlı H, Takma Ç, Yazgan E. Comparison of different models for estimation of direct and maternal genetic parameters on body weights in Awassi sheep. Arch Anim Breed 2022; 65:121-128. [PMID: 35350593 PMCID: PMC8949804 DOI: 10.5194/aab-65-121-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 02/07/2022] [Indexed: 11/20/2022] Open
Abstract
The present study was conducted to estimate the (co)variance
components for birth and weaning weight (BW and WW) in 8142 Awassi sheep
between 2015 and 2017. Estimates were calculated with single-trait
analysis by the average information restricted maximum likelihood (AI-REML)
method, using a derivative-free algorithm by fitting six different
univariate animal models. The negative of the log-likelihood function
(LogL), Akaike information criterion (AIC), and Bayesian information
criterion (BIC) tests were used for selecting the best fitted model. In
addition, the goodness of fit between the two models was compared with the
likelihood ratio test (LRT). Depending on the models, ha2 and
hm2 ranged from 0.230 to 0.240 and 0.015 to 0.033 for BW, and 0.108
to 0.168 and 0.024 to 0.081 for WW, respectively. Model 3 for BW and Model
2 for WW were chosen as the best models by LogL comparison criteria.
According to the LRT ratio test Model 2, Model 3, and Model 4 for BW and
Model 2, Model 3, Model 4, Model 5, and Model 6 for WW were significant (p<0.05). Including maternal genetic or maternal permanent
environmental effects in these models was found to be significant in terms
of parameter estimates.
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Affiliation(s)
- Hatice Hızlı
- Department of Animal Breeding, Eastern Mediterranean Agricultural Research Institute, Adana, Turkey
| | - Çiğdem Takma
- Department of Animal Science, Faculty of Agriculture, Ege University, Izmir, Turkey
| | - Ertan Yazgan
- Department of Animal Breeding, Eastern Mediterranean Agricultural Research Institute, Adana, Turkey
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22
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Wang H, Gu Y, Zhao D, Qiao Z, Zheng J, Gao J, Ren C, Xu Y. Caproicibacterium lactatifermentans sp. nov., isolated from pit clay used for the production of Chinese strong aroma-type liquor. Int J Syst Evol Microbiol 2022; 72. [PMID: 35085065 DOI: 10.1099/ijsem.0.005206] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two recently reported bacterial strains that were identified as the dominant caproate-producing bacteria in pit clay, were further characterized to determine their phylogeny and taxonomy. The two strains, designated as LBM19010T and JNU-WLY1368, were short rod-shaped, Gram-stain-positive, non-motile and strictly anaerobic. Analysis of the 16S rRNA gene sequences revealed that strains LBM19010T and JNU-WLY1368 shared a 16S rRNA gene sequence similarity of 99.93 % and belonged to a recent proposed genus Caproicibacterium in the family Oscillospiraceae. The proposed type strain, LBM19010T, showed the highest 16S rRNA gene sequence similarity to Caproicibacterium amylolyticum LBM18003T (96.34%), followed by Caproiciproducens galactitolivorans JCM 30532T (94.14 %). The pairwise average nucleotide identity and average amino acid identity values between strains LBM19010T and LBM18003T were 74.84 and 76.18 %, respectively. Growth of strain LBM19010T occurred at pH 4.5-7.5 (optimum, pH 5.0-5.5), 20-40 °C (optimum, 35 °C) and with 0-1 % (w/v) NaCl (optimum, 0 %). Strains LBM19010T and JNU-WLY1368 were both able to ferment several hexoses, disaccharides, starch and lactate but not pentoses. Caproate and butyrate were the major end-products from glucose. The predominant cellular fatty acids (>10 %) of strain LBM19010T were C16 : 0 (56.3 %), C14 : 0 DMA (19.5 %) and C14 : 0 (14.9 %). The identified polar lipids of strain LBM19010T were diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and nine unidentified glycolipids. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strains LBM19010T and JNU-WLY1368 belong to a novel species of the genus Caproicibacterium, for which the name Caproicibacterium lactatifermentans sp. nov. is proposed. The type strain is LBM19010T (=GDMCC 1.1627T=JCM 33782T).
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Affiliation(s)
- Huilin Wang
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Yang Gu
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Dong Zhao
- China Light Industry Key Laboratory of Solid-state Fermentation for Strong Aroma-type Liquor, Yibin 644007, PR China
| | - Zongwei Qiao
- China Light Industry Key Laboratory of Solid-state Fermentation for Strong Aroma-type Liquor, Yibin 644007, PR China
| | - Jia Zheng
- China Light Industry Key Laboratory of Solid-state Fermentation for Strong Aroma-type Liquor, Yibin 644007, PR China
| | - Jiangjing Gao
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Cong Ren
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, PR China
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23
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Ai X, Qiu B, Zhou Y, Li S, Li Q, Huan J, Li J, Hu N, Chen N, Liu F, Wang D, Chu C, Wang B, Chen L, Jiang H, Huang S, Huang X, Bi N, Liu H. Comparison and quantification of different concurrent chemotherapy regimens with radiotherapy in locally advanced non-small cell lung cancer: Clinical outcomes and theoretical results from an extended LQ and TCP model. Radiother Oncol 2021; 167:34-41. [PMID: 34890734 DOI: 10.1016/j.radonc.2021.11.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 11/13/2021] [Accepted: 11/29/2021] [Indexed: 12/25/2022]
Abstract
PURPOSE To develop a new radiobiological model and compare the efficacy of four concurrent chemotherapy regimens administered with radiotherapy in locally advanced non-small-cell lung cancer (LANSCLC) by in-field locoregional progression-free survival (LPFS). MATERIALS AND METHODS 151 LANSCLC patients were reviewed and divided into 5 groups according to their concurrent chemotherapy regimens, including 24 patients treated with radiotherapy alone, 30 treated with concurrent 4-week etoposide-cisplatin (EP), 26 with 3-week pemetrexed-cisplatin (AP), 37 with weekly paclitaxel-cisplatin (TP) and 34 with weekly docetaxel-cisplatin (DP). In-field LPFS and toxicities were compared among groups. A novel tumor control probability (TCP) model, LQRGC, incorporating four "R"s of radiobiology, Gompertzian tumor growth and chemotherapeutic effect, was related to in-field LPFS. Chemo-induced biologically effective doses (BEDs) in LQRGC/TCP model were used to quantify the concurrent chemotherapeutic efficacy. RESULTS The median follow-up time was 54.5 months. The weekly DP and 4-week EP groups had favorable median in-field LPFS (EP:46.2 months, AP:30.3 months, TP:12.2 months, DP: not reached, radiotherapy alone: 12.2 months, p = 0.001). The 4-week EP group had a higher incidence of ≥grade 3 leukopenia (EP:76.7%, AP:15.4%, TP:24.3%, DP:14.7%, radiotherapy alone: 12.5%, p < 0.001) than the other four. The LQRGC/TCP model fitted well with the in-field LPFS with the average absolute and relative fitting errors of 6.36% and 12.12%. The chemo-induced BEDs of EP, AP, TP and DP were 5.17, 0.63, 1.89 and 2.52 Gy, respectively. CONCLUSION The LQRGC/TCP model achieved promising fitting accuracy for in-field LPFS. As quantified by the model, the 4-week EP and weekly DP showed higher chemo-induced BEDs when concurrently administered with radiotherapy in LANSCLC.
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Affiliation(s)
- XinLei Ai
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Bo Qiu
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Lung Cancer Institute of Sun Yat-sen University, Guangzhou, PR China; Guangdong Association Study of Thoracic Oncology, Guangzhou, PR China
| | - Yin Zhou
- Evidance Medical Technologies Inc., Suzhou, PR China
| | - Su Li
- Clinical Research, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - QiWen Li
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Lung Cancer Institute of Sun Yat-sen University, Guangzhou, PR China; Guangdong Association Study of Thoracic Oncology, Guangzhou, PR China
| | - Jian Huan
- Department of Radiation Oncology, The Affiliated Suzhou Science & Technology Town Hospital of Nanjing Medical University, Suzhou, PR China
| | - JiBin Li
- Clinical Research, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Nan Hu
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - NaiBin Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - FangJie Liu
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - DaQuan Wang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Chu Chu
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Bin Wang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Li Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - HaiHang Jiang
- Homology Medical Technologies Inc., Ningbo, PR China
| | - ShiYu Huang
- Department of Radiation Oncology, Chengdu Western Hospital, Chengdu, PR China
| | - XiaoYan Huang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Nan Bi
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China.
| | - Hui Liu
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China; Lung Cancer Institute of Sun Yat-sen University, Guangzhou, PR China; Guangdong Association Study of Thoracic Oncology, Guangzhou, PR China.
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Moen DS. Improving inference and avoiding overinterpretation of hidden-state diversification models: Specialized plant breeding has no effect on diversification in frogs. Evolution 2021; 76:373-384. [PMID: 34854483 DOI: 10.1111/evo.14406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 11/30/2022]
Abstract
The hidden-state speciation and extinction (HiSSE) model helps avoid spurious results when testing whether a character affects diversification rates. However, care must be taken to optimally analyze models and interpret results. Recently, Tonini et al. (TEA hereafter) studied anuran (frog and toad) diversification with HiSSE methods. They concluded that their focal state, breeding in phytotelmata, increases net diversification rates. Yet this conclusion is counterintuitive, because the state that purportedly increases net diversification rates is 14 times rarer among species than the alternative. Herein, I revisit TEA's analyses and demonstrate problems with inferring model likelihoods, conducting post hoc tests, and interpreting results. I also reevaluate their top models and find that diverse strategies are necessary to reach the parameter values that maximize each model's likelihood. In contrast to TEA, I find no support for an effect of phytotelm breeding on net diversification rates in Neotropical anurans. In particular, even though the most highly supported models include the focal character, averaging parameter estimates over hidden states shows that the focal character does not influence diversification rates. Finally, I suggest ways to better analyze and interpret complex diversification models-both state-dependent and beyond-for future studies in other organisms.
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Affiliation(s)
- Daniel S Moen
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
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25
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Fitzhugh K. Phylogenetic Inference and the Misplaced Premise of Substitution Rates. Acta Biotheor 2021; 69:799-819. [PMID: 33956263 DOI: 10.1007/s10441-021-09412-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 04/13/2021] [Indexed: 11/24/2022]
Abstract
Three competing 'methods' have been endorsed for inferring phylogenetic hypotheses: parsimony, likelihood, and Bayesianism. The latter two have been claimed superior because they take into account rates of sequence substitution. Can rates of substitution be justified on its own accord in inferences of explanatory hypotheses? Answering this question requires addressing four issues: (1) the aim of scientific inquiry, (2) the nature of why-questions, (3) explanatory hypotheses as answers to why-questions, and (4) acknowledging that neither parsimony, likelihood, nor Bayesianism are inferential actions leading to explanatory hypotheses. The aim of scientific inquiry is to acquire causal understanding of effects. Observation statements of organismal characters lead to implicit or explicit why-questions. Those questions, conveyed in data matrices, assume the truth of observation statements, which is contrary to subsequently invoking substitution rates within inferences to phylogenetic hypotheses. Inferences of explanatory hypotheses are abductive in form, such that some version of an evolutionary theory(ies) is/are included or implied. If rates of sequence evolution are to be considered, it must be done prior to, rather than within abduction, which requires renaming those putatively-shared nucleotides subject to substitution rates. There are, however, no epistemic grounds for renaming characters to accommodate rates, calling into question the legitimacy of causally accounting for sequence data.
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Affiliation(s)
- Kirk Fitzhugh
- Natural History Museum of Los Angeles County, 900 Exposition Blvd, Los Angeles, CA, 90007, USA.
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26
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Lampri PN, Bouranta C, Radea C, Parmakelis A. Hidden diversity revealed in the freshwater snails, Bythinella and Pseudamnicola, in the Island of Crete. Integr Zool 2021; 17:804-824. [PMID: 34599771 DOI: 10.1111/1749-4877.12594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Crete with its complex geomorphological history is the island with the highest number of endemism observed in animal and plant taxa throughout the Aegean archipelago. While other groups of organisms within Crete are well-studied, the freshwater gastropod fauna still remains poorly investigated. Bythinella and Pseudamnicola, are 2 genera of freshwater springsnails, both present on the island, inhabiting springs and other freshwater habitats. Here, we conduct a comprehensive study on the distribution of the different genetic lineages of the 2 gastropod genera in order to assess the mode of their differentiation on the island and infer the actual number of species present in the island. Towards these aims, sequence data from the mitochondrial gene were used and analyzed within a phylogenetic framework. For Bythinella, our results strongly support at least 5 delineated Bythinella spp. inhabiting Crete, which correspond to the already described species from previous studies with the addition of a new one. Bythinella analyses reveal an old time-frame of differentiation with vicariant phenomena being more likely the main drivers shaping the present-day distribution of the genus' genetic lineages. For Pseudamnicola, our data indicate the presence of at least 2 delineated Pseudamnicola spp. with a differentiation more consistent to an isolation-by-distance pattern of a relatively recent origin. Dispersion processes followed by isolation of the populations and/or recent speciation, seem to be the underlying process for the current distribution of Pseudamnicola lineages.
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Affiliation(s)
- Paraskevi Niki Lampri
- Section of Ecology and Taxonomy, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece.,Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research, Anavyssos Attica, Greece
| | - Christina Bouranta
- Section of Ecology and Taxonomy, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Canella Radea
- Section of Ecology and Taxonomy, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Aristeidis Parmakelis
- Section of Ecology and Taxonomy, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
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Mortimer K, Fitzhugh K, dos Brasil AC, Lana P. Who's who in Magelona: phylogenetic hypotheses under Magelonidae Cunningham & Ramage, 1888 (Annelida: Polychaeta). PeerJ 2021; 9:e11993. [PMID: 35070516 PMCID: PMC8759375 DOI: 10.7717/peerj.11993] [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: 05/20/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022] Open
Abstract
Known as shovel head worms, members of Magelonidae comprise a group of polychaetes readily recognised by the uniquely shaped, dorso-ventrally flattened prostomium and paired ventro-laterally inserted papillated palps. The present study is the first published account of inferences of phylogenetic hypotheses within Magelonidae. Members of 72 species of Magelona and two species of Octomagelona were included, with outgroups including members of one species of Chaetopteridae and four of Spionidae. The phylogenetic inferences were performed to causally account for 176 characters distributed among 79 subjects, and produced 2,417,600 cladograms, each with 404 steps. A formal definition of Magelonidae is provided, represented by a composite phylogenetic hypothesis explaining seven synapomorphies: shovel-shaped prostomium, prostomial ridges, absence of nuchal organs, ventral insertion of palps and their papillation, presence of a burrowing organ, and unique body regionation. Octomagelona is synonymised with Magelona due to the latter being paraphyletic relative to the former. The consequence is that Magelonidae is monotypic, such that Magelona cannot be formally defined as associated with any phylogenetic hypotheses. As such, the latter name is an empirically empty placeholder, but because of the binomial name requirement mandated by the International Code of Zoological Nomenclature, the definition is identical to that of Magelonidae. Several key features for future descriptions are suggested: prostomial dimensions, presence/absence of prostomial horns, morphology of anterior lamellae, presence/absence of specialised chaetae, and lateral abdominal pouches. Additionally, great care must be taken to fully describe and illustrate all thoracic chaetigers in descriptions.
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Affiliation(s)
- Kate Mortimer
- Natural Sciences, Amgueddfa Cymru–National Museum Wales, Cardiff, Wales, United Kingdom
| | - Kirk Fitzhugh
- Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Ana Claudia dos Brasil
- Departamento de Biologia Animal, Instituto de Ciências Biológicas e da Saúde, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Paulo Lana
- Centro de Estudos do Mar, Universidade Federal do Paraná, Pontal do Sul, Paraná, Brazil
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Viñuela Rodríguez N, Šanda R, Zogaris S, Vukić J. Evolutionary history of the Pelasgus minnows (Teleostei: Leuciscidae), an ancient endemic genus from the Balkan Peninsula. Mol Phylogenet Evol 2021; 164:107274. [PMID: 34333114 DOI: 10.1016/j.ympev.2021.107274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 10/20/2022]
Abstract
The Balkans are one of the European biodiversity hotspots, hosting outstandingly rich, yet threatened, flora and fauna. This region hosts one of the richest endemic freshwater ichthyofauna in Europe, including several genera occurring exclusively here. One of these is the genus of the primary freshwater minnows Pelasgus, which was designated only in 2007. The genus is one of the most ancient genera of the family Leuciscidae and comprises seven small-bodied species, inhabiting slower, well-vegetated courses of rivers. This work is the first molecular multilocus phylogeny of the genus, based on one mitochondrial and three nuclear markers. In total, 305 individuals across almost entire distribution range of the genus were analysed. We inferred the evolutionary history of the species by comparing the results of our calibrated multilocus coalescent species-tree to palaeogeological events. The diversification of the genus started in the early Miocene and continued through to the beginning of Pleistocene. We identified the regions of the oldest colonization by Pelasgus, the drainages of the ancient lakes Ohrid and Prespa, and the southernmost part of the Peloponnese, hosting Pelasgus minutus, P. prespensis and P. laconicus, respectively. We showed that P. prespensis is not endemic to Lake Prespa, as previously thought; it occurs also in the Albanian River Devoll. This corroborates the emerging opinion that the endemic taxa of ancient lakes evolved within larger-scale historic drainages and not only within the lakes. Our results showed that the species with the most recent common ancestor of the early Pliocene origin, P. thesproticus, P. epiroticus, P. stymphalicus and P. marathonicus, have neighbouring distribution ranges. Pelasgus epiroticus is especially interesting, not only for its pronounced genetic diversity with a geographic pattern, but also for being found at three localities within the native distribution range of P. stymphalicus as a result of a translocation. At two of these localities, we identified hybrids between the two species, and at one of them, the genetically pure native species was not found at all. This points to a threat of the loss of the native ichthyofauna due to unintentional translocations.
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Affiliation(s)
- Nuria Viñuela Rodríguez
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic
| | - Radek Šanda
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic; Department of Zoology, National Museum, Václavské nám. 68, Prague 1, 11000, Czech Republic
| | - Stamatis Zogaris
- Hellenic Centre for Marine Research, Institute of Marine Biological Sciences and Inland Waters, Athinon-Souniou Ave., Anavissos, Attica, 19013, Greece
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic.
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Yokoi KJ, Tsutsui S, Arakawa GY, Takaba M, Fujii K, Kaneko S. Molecular and biochemical characteristics of inulosucrase InuBK from Alkalihalobacillus krulwichiae JCM 11691. Biosci Biotechnol Biochem 2021; 85:1830-1838. [PMID: 34021568 DOI: 10.1093/bbb/zbab094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/13/2021] [Indexed: 12/16/2022]
Abstract
Information about the inulosucrase of nonlactic acid bacteria is scarce. We found a gene encoding inulosucrase (inuBK) in the genome of the Gram-positive bacterium Alkalihalobacillus krulwichiae JCM 11691. The inuBK open reading frame encoded a protein comprising 456 amino acids. We expressed His-tagged InuBK in culture medium using a Brevibacillus system. The optimal pH and temperature of purified InuBK were 7.0-9.0 and 50-55 °C, respectively. The findings of high-performance anion-exchange chromatography, nuclear magnetic resonance spectroscopy, and high-performance size-exclusion chromatography with multiangle laser light scattering showed that the polysaccharide produced by InuBK was an inulin with a molecular weight of 3806, a polydispersity index (PI) of 1.047, and fructosyl chain lengths with 3-27 degrees of polymerization. The size of InuBK was smaller than commercial inulins, and the PI of the inulin that it produced was lower.
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Affiliation(s)
- Ken-Ji Yokoi
- Toyama Prefectural Food Research Institute, Toyama, Japan
| | - Sosyu Tsutsui
- Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Gen-Ya Arakawa
- Toyama Prefectural Food Research Institute, Toyama, Japan
| | | | | | - Satoshi Kaneko
- Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
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Complete chloroplast genome of novel Adrinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis. Sci Rep 2021; 11:11731. [PMID: 34083611 PMCID: PMC8175739 DOI: 10.1038/s41598-021-91071-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
Adrinandra megaphylla Hu is a medicinal plant belonging to the Adrinandra genus, which is well-known for its potential health benefits due to its bioactive compounds. This study aimed to assemble and annotate the chloroplast genome of A. megaphylla as well as compare it with previously published cp genomes within the Adrinandra genus. The chloroplast genome was reconstructed using de novo and reference-based assembly of paired-end reads generated by long-read sequencing of total genomic DNA. The size of the chloroplast genome was 156,298 bp, comprised a large single-copy (LSC) region of 85,688 bp, a small single-copy (SSC) region of 18,424 bp, and a pair of inverted repeats (IRa and IRb) of 26,093 bp each; and a total of 51 SSRs and 48 repeat structures were detected. The chloroplast genome includes a total of 131 functional genes, containing 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The A. megaphylla chloroplast genome indicated that gene content and structure are highly conserved. The phylogenetic reconstruction using complete cp sequences, matK and trnL genes from Pentaphylacaceae species exhibited a genetic relationship. Among them, matK sequence is a better candidate for phylogenetic resolution. This study is the first report for the chloroplast genome of the A. megaphylla.
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Thi Nguyen T, Lama S, Kumar Ainala S, Sankaranarayanan M, Singh Chauhan A, Rae Kim J, Park S. Development of Pseudomonas asiatica as a host for the production of 3-hydroxypropionic acid from glycerol. BIORESOURCE TECHNOLOGY 2021; 329:124867. [PMID: 33640696 DOI: 10.1016/j.biortech.2021.124867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
Pseudomonas asiatica C1, which could grow on glucose and aerobically synthesize coenzyme B12, was isolated and developed as a microbial cell factory for the production of 3-hydroxypropionic acid (3-HP) from glycerol. Three heterologous enzymes, glycerol dehydratase (GDHt), GDHt reactivase (GdrAB) and aldehyde dehydrogenase (ALDH), constituting the 3-HP synthesis pathway, were introduced, and three putative dehydrogenases, responsible for 3-HP degradation, were disrupted. In addition, the transcriptional repressor glpR and the glycerol kinase glpK were removed to increase glycerol import while eliminating the catabolic use of glycerol. Furthermore, the global regulatory protein encoded by crc and several putative oxidoreductases (PDORs) were disrupted. One resulting strain, when grown on glucose, could produce 3-HP at ~ 700 mM in 48 h in a fed-batch bioreactor experiment, with the molar yield > 0.99 on glycerol without much by-products. This study demonstrates that P. asiatica C1 is a promising host for production of 3-HP from glycerol.
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Affiliation(s)
- Trinh Thi Nguyen
- School of Energy and Chemical Engineering, UNIST, Ulsan 44919, Republic of Korea; School of Chemical and Biomolecular Engineering, Pusan National University, Geumjeong-gu, Busan 46241, Republic of Korea
| | - Suman Lama
- School of Energy and Chemical Engineering, UNIST, Ulsan 44919, Republic of Korea
| | - Satish Kumar Ainala
- NOROO Bio R&D Center, NOROO Holdings Co., Ltd, Gyeonggi-do 16229, Republic of Korea
| | - Mugesh Sankaranarayanan
- School of Chemical and Biomolecular Engineering, Pusan National University, Geumjeong-gu, Busan 46241, Republic of Korea; Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Chennai 600062, India
| | - Ashish Singh Chauhan
- School of Chemical and Biomolecular Engineering, Pusan National University, Geumjeong-gu, Busan 46241, Republic of Korea
| | - Jung Rae Kim
- School of Chemical and Biomolecular Engineering, Pusan National University, Geumjeong-gu, Busan 46241, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, UNIST, Ulsan 44919, Republic of Korea; School of Chemical and Biomolecular Engineering, Pusan National University, Geumjeong-gu, Busan 46241, Republic of Korea.
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Katz J, Holzer PH, Kliman HJ. Genetics, not the uterine environment, drive the formation of trophoblast inclusions: Insights from a twin study. Placenta 2021; 114:133-138. [PMID: 33941390 DOI: 10.1016/j.placenta.2021.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Trophoblast inclusions (TIs) are associated with aneuploidy and pregnancy loss and have thus been considered to be a marker of genetic abnormality. However, to date, no study has specifically explored whether TIs are a manifestation of fetal genetics or, rather, the result of the intrauterine environment. The goal of this study was to compare the frequency of TIs in the placentas of monozygotic (MZ) and dizygotic (DZ) twin pairs in order to determine whether the formation of TIs is genetically driven or not. METHODS We performed a retrospective case series of placentas from 48 twin pairs. The placentas were grouped based on zygosity: MZ, DZ, or unknown (UZ). The average number of total TIs per slide was calculated for each twin individual and the mean absolute difference in the total TIs per slide between the twin pairs was calculated for each zygosity group and compared. RESULTS The mean difference in the total TIs per slide for DZ twins was significantly greater than the mean difference in the total TIs per slide for MZ twins (p = 0.003). The mean difference in the total TIs per slide for the UZ group was also significantly greater than the mean difference in total TIs per slide between MZ twin pairs (p = 0.028). DISCUSSION Our finding that MZ twins were significantly more concordant than DZ twins for the average number of TIs per slide supports the conclusion that TIs are intrinsic to the genetics of the fetus, not the uterine environment.
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Affiliation(s)
- Julia Katz
- Yale College, Yale University, New Haven, CT, USA
| | - Parker H Holzer
- Department of Statistics & Data Science, Yale University, New Haven, CT, USA
| | - Harvey J Kliman
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA.
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Abadi S, Avram O, Rosset S, Pupko T, Mayrose I. ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning. Mol Biol Evol 2021; 37:3338-3352. [PMID: 32585030 DOI: 10.1093/molbev/msaa154] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they are not always feasible, and sometimes depend on preliminary assumptions which do not hold for sequence data. Moreover, although these methods are dedicated to revealing the processes that underlie the sequence data, they do not always produce the most accurate trees. Notably, phylogeny reconstruction consists of two related tasks, topology reconstruction and branch-length estimation. It was previously shown that in many cases the most complex model, GTR+I+G, leads to topologies that are as accurate as using existing model selection criteria, but overestimates branch lengths. Here, we present ModelTeller, a computational methodology for phylogenetic model selection, devised within the machine-learning framework, optimized to predict the most accurate nucleotide substitution model for branch-length estimation. We demonstrate that ModelTeller leads to more accurate branch-length inference than current model selection criteria on data sets simulated under realistic processes. ModelTeller relies on a readily implemented machine-learning model and thus the prediction according to features extracted from the sequence data results in a substantial decrease in running time compared with existing strategies. By harnessing the machine-learning framework, we distinguish between features that mostly contribute to branch-length optimization, concerning the extent of sequence divergence, and features that are related to estimates of the model parameters that are important for the selection made by current criteria.
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Affiliation(s)
- Shiran Abadi
- School of Plant Sciences and Food security, Tel-Aviv University, Tel-Aviv, Israel
| | - Oren Avram
- School of Molecular Cell Biology & Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Saharon Rosset
- Department of Statistics and Operations Research, School of Mathematical Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Tal Pupko
- School of Molecular Cell Biology & Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Itay Mayrose
- School of Plant Sciences and Food security, Tel-Aviv University, Tel-Aviv, Israel
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Abstract
In 1981, the Journal of Molecular Evolution (JME) published an article entitled "Evolutionary trees from DNA sequences: A maximum likelihood approach" by Joseph (Joe) Felsenstein (J Mol Evol 17:368-376, 1981). This groundbreaking work laid the foundation for the emerging field of statistical phylogenetics, providing a tractable way of finding maximum likelihood (ML) estimates of evolutionary trees from DNA sequence data. This paper is the second most cited (more than 9000 citations) in JME after Kimura's (J Mol Evol 16:111-120, 1980) seminal paper on a model of nucleotide substitution (with nearly 20,000 citations). On the occasion of the 50th anniversary of JME, we elaborate on the significance of Felsenstein's ML approach to estimating phylogenetic trees.
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Affiliation(s)
- David Posada
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain.
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310, Vigo, Spain.
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
| | - Keith A Crandall
- Computational Biology Institute and Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA.
- Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA.
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Othman SN, Putri ET, Messenger KR, Bae Y, Yang Y, Bova T, Reed T, Amin H, Chuang MF, Jang Y, Borzée A. Impact of the Miocene orogenesis on Kaloula spp. radiation and implication of local refugia on genetic diversification. Integr Zool 2021; 17:261-284. [PMID: 33734569 DOI: 10.1111/1749-4877.12538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The phylogeography of the Kaloula genus in East Asia is still poorly understood. One of the difficulties is the absence of fossils to corroborate molecular dating estimates. Here, we examined the mitochondrial structure of Kaloula spp. in East Asia and focused on the impact of glaciations on the northernmost species: Kaloula borealis. We determined the phylogenetic relationships, molecular dating, and genetic connectivity assessments within the genus from 1211 bp of concatenated mitochondrial 12S and 16S. The relaxed clock analyses reveal the emergence of Kaloula spp. common ancestor in East and Southeast Asia between the Eocene and Oligocene, c. 38.47 Ma (24.69-53.65). The genetic diversification of lineages then increased on the East Asian Mainland during the Lower Miocene, c. 20.10 (8.73-30.65), most likely originating from the vicariance and radiation triggered by the orogeny of the Qinghai-Tibetan Plateau. Later, the dispersal towards the North East Asian Mainland during the Upper Miocene drove the population diversification of K. borealis c. 9.01 Ma (3.66-15.29). Finally, the central mainland population became isolated following orogenesis events and diverged into K. rugifera during the Pliocene, c. 3.06 Ma (0.02-10.90). The combination of population genetic and barrier analyses revealed a significant genetic isolation between populations of Kaloula spp. matching with the massive Qinling-Daba Mountain chain located in south-central China. Finally, we highlight a young divergence within the Eastern Mainland population of K. borealis, possibly attributed to refugia in south eastern China from which populations later expanded.
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Affiliation(s)
- Siti N Othman
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Eggy Triana Putri
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea.,Department of Biology, Faculty of Mathematics and Natural Science, Andalas University, Indonesia
| | - Kevin R Messenger
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yoonhyuk Bae
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Yi Yang
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Timothy Bova
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Thomas Reed
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Hina Amin
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Ming-Feng Chuang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
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Tamburus AF, Mantelatto FL. A molecular perspective on the systematics of the spider crab genus Libinia Leach, 1815 (Majoidea:Epialtidae). INVERTEBR SYST 2021. [DOI: 10.1071/is20085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Libinia, a genus of spider crabs, encompasses 10 valid species, three from the eastern Pacific and seven from the western Atlantic. Previous phylogenetic hypotheses based on molecular and larval morphological data suggested an uncertain position of the genus Libinia within the family Epialtidae. Therefore, we investigated the evolutionary relationships among the species of Libinia, and also suggested a position for this genus within the family. Phylogenetic trees were obtained from concatenated mtDNA sequences of 16S and COI fragments. Molecular dating methods were used to estimate the relative timing of origin and diversification within Libinia. Eighteen new primers were designed, and PCR conditions were standardised to amplify the COI fragments of older or poorly preserved pinned specimens, generating ~550 base pair sequences. Phylogenetic hypotheses supported the monophyly of the genus. Species that occur in the eastern Pacific and the ones found in the western Atlantic do not form monophyletic clades related to this geographical separation. In the eastern Pacific, there is low phylogenetic proximity between Libinia mexicana and L. setosa; and since we did not sample L. peruana, we inferred that it should cluster with L. setosa or L. mexicana due to morphological similarity. Libinia spinosa is separate from the other species, L. mexicana was a sister group of L. cavirostris, and L. ferreirae was closely related to L. dubia and L. rhomboidea, which occur in the Gulf of Mexico and in the Caribbean, respectively. In the Gulf of Mexico, L. dubia and L. emarginata are closely related. Although L. erinacea was not sampled, we suggest, from previous studies, that it should group with L. dubia due to morphological similarities. The phylogenetic hypothesis suggests the monophyly of Libinia, with its origins at the late Eocene. Finally, the recovered clades based on two molecular markers agreed with a parallel, linked morphological study that is still in progress.
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Goh CBS, Wong LW, Parimannan S, Rajandas H, Loke S, Croft L, Yule CM, Pasbakhsh P, Lee SM, Tan JBL. Chitinophaga extrema sp. nov., isolated from subsurface soil and leaf litter in a tropical peat swamp forest. Int J Syst Evol Microbiol 2020; 70:6355-6363. [PMID: 33146596 DOI: 10.1099/ijsem.0.004539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
A Gram-negative, filamentous aerobic bacterium designated as strain Mgbs1T was isolated on 12 April 2017 from the subsurface soil and leaf litter substrate at the base of a Koompassia malaccensis tree in a tropical peat swamp forest in the northern regions of the state of Selangor, Malaysia (3° 39' 04.7' N 101° 17' 43.7'' E). Phylogenetic analyses based on the full 16S rRNA sequence revealed that strain Mgbs1T belongs to the genus Chitinophaga with the greatest sequence similarity to Chitinophaga terrae KP01T (97.65 %), Chitinophaga jiangningensis DSM27406T (97.58 %), and Chitinophaga dinghuensis DHOC24T (97.17 %). The major fatty acids of strain Mgbs1T (>10 %) are iso-C15 : 0, C16 : 1 ω5c and iso-C17 : 0 3-OH while the predominant respiratory quinone is menaquinone-7. Strain Mgbs1T has a complete genome size of 8.03 Mb, with a G+C content of 48.5 mol%. The DNA-DNA hybridization (DDH) score between strain Mgbs1T and C. jiangningensis DSM27406T was 15.9 %, while in silico DDH values of strain Mgbs1T against C. dinghuensis DHOC24T and C. terrae KP01T were 20.0 and 19.10% respectively. Concurrently, Average Nucleotide Identity (ANI) scores between strain Mgbs1T against all three reference strains are 73.2 %. Based on the phenotypic, chemotaxonomic, and phylogenetic consensus, strain Mgbs1T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga extrema sp. nov. is proposed (=DSM 108835T=JCM 33276T).
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Affiliation(s)
- Calvin Bok Sun Goh
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Li Wen Wong
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, 08100 Bedong, Kedah, Malaysia
- Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, 08100 Bedong, Kedah, Malaysia
- Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Stella Loke
- Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Lawrence Croft
- Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Catherine Mary Yule
- School of Science and Engineering, University of the Sunshine Coast, Queensland 4556, Australia
| | - Pooria Pasbakhsh
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Sui Mae Lee
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Joash Ban Lee Tan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
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Mayrose I, Lysak MA. The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches. Genome Biol Evol 2020; 13:5923296. [PMID: 33566095 PMCID: PMC7875004 DOI: 10.1093/gbe/evaa220] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.
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Affiliation(s)
- Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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Methane, arsenic, selenium and the origins of the DMSO reductase family. Sci Rep 2020; 10:10946. [PMID: 32616801 PMCID: PMC7331816 DOI: 10.1038/s41598-020-67892-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/16/2020] [Indexed: 11/16/2022] Open
Abstract
Mononuclear molybdoenzymes of the dimethyl sulfoxide reductase (DMSOR) family catalyze a number of reactions essential to the carbon, nitrogen, sulfur, arsenic, and selenium biogeochemical cycles. These enzymes are also ancient, with many lineages likely predating the divergence of the last universal common ancestor into the Bacteria and Archaea domains. We have constructed rooted phylogenies for over 1,550 representatives of the DMSOR family using maximum likelihood methods to investigate the evolution of the arsenic biogeochemical cycle. The phylogenetic analysis provides compelling evidence that formylmethanofuran dehydrogenase B subunits, which catalyze the reduction of CO2 to formate during hydrogenotrophic methanogenesis, constitutes the most ancient lineage. Our analysis also provides robust support for selenocysteine as the ancestral ligand for the Mo/W atom. Finally, we demonstrate that anaerobic arsenite oxidase and respiratory arsenate reductase catalytic subunits represent a more ancient lineage of DMSORs compared to aerobic arsenite oxidase catalytic subunits, which evolved from the assimilatory nitrate reductase lineage. This provides substantial support for an active arsenic biogeochemical cycle on the anoxic Archean Earth. Our work emphasizes that the use of chalcophilic elements as substrates as well as the Mo/W ligand in DMSORs has indelibly shaped the diversification of these enzymes through deep time.
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Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22. 3 Biotech 2020; 10:160. [PMID: 32206494 DOI: 10.1007/s13205-020-2148-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/16/2020] [Indexed: 12/12/2022] Open
Abstract
In this study, a bacterial strain CP22 with ability to produce cellulase, xylanase and mannanase was isolated from the oil palm compost. Based on the 16S rRNA gene analysis, the strain was affiliated to genus Micromonospora. To further investigate genes that are related to cellulose and hemicellulose degradation, the genome of strain CP22 was sequenced, annotated and analyzed. The de novo assembled genome of strain CP22 featured a size of 5,856,203 bp with G + C content of 70.84%. Detailed genome analysis on lignocellulose degradation revealed a total of 60 genes consisting of 47 glycoside hydrolase domains and 16 carbohydrate esterase domains predicted to be involved in cellulolytic and hemicellulolytic deconstruction. Particularly, 20 genes encode for cellulases (8 endoglucanases, 3 exoglucanases and 9 β-glucosidases) and 40 genes encode for hemicellulases (15 endo-1,4-β-xylanase, 3 β-xylosidase, 3 α-arabinofuranosidase, 10 acetyl xylan esterase, 6 polysaccharide deacetylase, 1 β-mannanase, 1 β-mannosidase and 1 α-galactosidase). Thirty-two genes encoding carbohydrate-binding modules (CBM) from six different families (CBM2, CBM4, CBM6, CBM9, CBM13 and CBM22) were present in the genome of strain CP22. These CBMs were found in 27 cellulolytic and hemicellulolytic genes, indicating their potential role in enhancing the substrate-binding capability of the enzymes. CBM2 and CBM13 are the major CBMs present in cellulases and hemicellulases (xylanases and mannanases), respectively. Moreover, a GH10 xylanase was found to contain 3 CBMs (1 CBM9 and 2 CBM22) and these CBMs were reported to bind specifically to xylan. This genome-based analysis could facilitate the exploration of this strain for lignocellulosic biomass degradation.
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Šmíd J, Mazuch T, Nováková L, Modrý D, Malonza PK, Abdirahman Elmi HS, Carranza S, Moravec J. Phylogeny and Systematic Revision of the Gecko Genus Hemidactylus from the Horn of Africa (Squamata: Gekkonidae). HERPETOLOGICAL MONOGRAPHS 2020. [DOI: 10.1655/herpmonographs-d-19-00010.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Jiří Šmíd
- Department of Zoology, National Museum, Cirkusová 1740, 19300, Prague, Czech Republic
| | | | - Lucie Nováková
- Department of Zoology, National Museum, Cirkusová 1740, 19300, Prague, Czech Republic
| | - David Modrý
- Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1/3, Brno 62142, Czech Republic
| | - Patrick K. Malonza
- Section of Herpetology, National Museums of Kenya, P.O. Box 40658-00100, Museum Hill Road, Nairobi, Kenya
| | | | - Salvador Carranza
- Institute of Evolutionary Biology (CSICut i-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37–49, Barcelona, Spain
| | - Jiří Moravec
- Department of Zoology, National Museum, Cirkusová 1740, 19300, Prague, Czech Republic
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Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020; 18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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43
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Miller JB, McKinnon LM, Whiting MF, Ridge PG. Codon use and aversion is largely phylogenetically conserved across the tree of life. Mol Phylogenet Evol 2019; 144:106697. [PMID: 31805345 DOI: 10.1016/j.ympev.2019.106697] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 04/10/2019] [Accepted: 11/29/2019] [Indexed: 01/11/2023]
Abstract
Using parsimony, we analyzed codon usages across 12,337 species and 25,727 orthologous genes to rank specific genes and codons according to their phylogenetic signal. We examined each codon within each ortholog to determine the codon usage for each species. In total, 890,814 codons were parsimony informative. Next, we compared species that used a codon with species that did not use the codon. We assessed each codon's congruence with species relationships provided in the Open Tree of Life (OTL) and determined the statistical probability of observing these results by random chance. We determined that 25,771 codons had no parallelisms or reversals when mapped to the OTL. Codon usages from orthologous genes spanning many species were 1109× more likely to be congruent with species relationships in the OTL than would be expected by random chance. Using the OTL as a reference, we show that codon usage is phylogenetically conserved within orthologous genes in archaea, bacteria, plants, mammals, and other vertebrates. We also show how to use our provided framework to test different tree hypotheses by confirming the placement of turtles as sister taxa to archosaurs.
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Affiliation(s)
- Justin B Miller
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Lauren M McKinnon
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT 84602, USA; M.L. Bean Museum, Brigham Young University, Provo, UT 84602, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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Johnston MA. Phylogenetic revision of the psammophilic Trogloderus LeConte (Coleoptera: Tenebrionidae), with biogeographic implications for the Intermountain Region. PeerJ 2019; 7:e8039. [PMID: 31741795 PMCID: PMC6858821 DOI: 10.7717/peerj.8039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/15/2019] [Indexed: 11/20/2022] Open
Abstract
The genus Trogloderus LeConte, 1879, which is restricted to dunes and sandy habitats in the western United States, is revised using morphological and molecular information. Six new species are described from desert regions: Trogloderus arcanus New Species (Lahontan Trough); Trogloderus kandai New Species (Owens Valley); Trogloderus major New Species (Mohave Desert); Trogloderus skillmani New Species (eastern Great Basin and Mohave Desert); Trogloderus verpus New Species (eastern Colorado Plateau); and Trogloderus warneri New Species (western Colorado Plateau). A molecular phylogeny is presented for the genus and used to infer its historical biogeography. The most recent common ancestor of Trogloderus is dated to 5.2 mya and is inferred to have inhabited the Colorado Plateau. Current species most likely arose during the mid-Pleistocene where the geographic features of the Lahontan Trough, Bouse Embayment and Kaibab Plateau were significant factors driving speciation.
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Affiliation(s)
- M Andrew Johnston
- Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, USA
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45
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Huang GD, Liu XM, Huang TL, Xia LC. The statistical power of k-mer based aggregative statistics for alignment-free detection of horizontal gene transfer. Synth Syst Biotechnol 2019; 4:150-156. [PMID: 31508512 PMCID: PMC6723412 DOI: 10.1016/j.synbio.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/14/2019] [Accepted: 08/05/2019] [Indexed: 12/21/2022] Open
Abstract
Alignment-based database search and sequence comparison are commonly used to detect horizontal gene transfer (HGT). However, with the rapid increase of sequencing depth, hundreds of thousands of contigs are routinely assembled from metagenomics studies, which challenges alignment-based HGT analysis by overwhelming the known reference sequences. Detecting HGT by k-mer statistics thus becomes an attractive alternative. These alignment-free statistics have been demonstrated in high performance and efficiency in whole-genome and transcriptome comparisons. To adapt k-mer statistics for HGT detection, we developed two aggregative statistics TsumS and Tsum*, which subsample metagenome contigs by their representative regions, and summarize the regional D2S and D2* metrics by their upper bounds. We systematically studied the aggregative statistics’ power at different k-mer size using simulations. Our analysis showed that, in general, the power of TsumS and Tsum* increases with sequencing coverage, and reaches a maximum power >80% at k = 6, with 5% Type-I error and the coverage ratio >0.2x. The statistical power of TsumS and Tsum* was evaluated with realistic simulations of HGT mechanism, sequencing depth, read length, and base error. We expect these statistics to be useful distance metrics for identifying HGT in metagenomic studies.
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Affiliation(s)
- Guan-Da Huang
- School of Physics and Optoelectronics, South China University of Technology, Guangzhou, 510640, China
| | - Xue-Mei Liu
- School of Physics and Optoelectronics, South China University of Technology, Guangzhou, 510640, China
| | - Tian-Lai Huang
- School of Physics and Optoelectronics, South China University of Technology, Guangzhou, 510640, China
| | - Li-C Xia
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
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Martínez-Marín GJ, García-Ruiz A, Vásquez-Peláez CG, Román-Ponce SI, Ruiz-López FJ. Effect of calving age on genetic evaluation of milk yield in Holstein cattle. Trop Anim Health Prod 2019; 52:365-371. [PMID: 31359354 DOI: 10.1007/s11250-019-02023-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 07/22/2019] [Indexed: 11/27/2022]
Abstract
The aim of this study was to evaluate the effect of including calving age (CA) on genetic evaluation models for Holstein cattle. The evaluated models included the permanent environment, the sire-herd interactions, and the animals and residual effects as random. The fixed effects included the average production of milk, fat, and protein and the herd-year-season effect. The analyzed data included 603,521 records of milk production (in kg) corresponding to 438,098 animals from 527 herds. Additionally, there were 179,122 records of fat and protein components, corresponding to 148,930 animals from 137 herds. The records were classified by first lactation only (FL) and all available lactations (AL) for validation test (VT). The FL records corresponded to 275,487 milk production records with a mean of 10,874.1 ± 2773.9 kg at a mean CA of 25.6 ± 4.2 months. For FL, the milk components consisted of 78,955 records with a mean fat production of 392.86 ± 89.9 kg, a mean protein production of 362.8 ± 74.9 kg and a mean CA of 25.2 ± 4.1 months. For AL, the number of records was 603,521 for milk production with a mean of 10,802.8 ± 2905.9 kg and a mean CA of 35.6 ± 11.5 months. For the milk components, there were 179,122 records with a mean of 36.1 ± 9.5 months for CA and 388.3 ± 98.4 kg and 356.7 ± 82.6 kg for fat and protein, respectively. Three models were compared: the base model (M0) described above, and two alternative models that included CA in a linear and quadratic form (M1 and M2, respectively). Estimations of the variance components (VC) and breeding value (BV) were obtained using a repeatability animal model, with the same phenotypic and pedigree information used for all models. To select the best fit model for the data, a likelihood ratio test (LRtest) was used. A validation test (VT) was also applied to each model to evaluate the consistency of the genetic trends for females with information on AL and FL. The inclusion of CA in its linear form (M1) was the model that achieved the best results in the LRtest and an acceptable value for the VT. These results show that CA improves the model fit for BV prediction and reliability.
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Affiliation(s)
- G J Martínez-Marín
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Ajuchitlán, 76280, Querétaro, Mexico
| | - A García-Ruiz
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Ajuchitlán, 76280, Querétaro, Mexico
| | - C G Vásquez-Peláez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Av. Universidad, 3000, Mexico City, Mexico
| | - S I Román-Ponce
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Ajuchitlán, 76280, Querétaro, Mexico
| | - F J Ruiz-López
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Ajuchitlán, 76280, Querétaro, Mexico.
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Hu Z, Sackton TB, Edwards SV, Liu JS. Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees. Mol Biol Evol 2019; 36:1086-1100. [PMID: 30851112 PMCID: PMC6501877 DOI: 10.1093/molbev/msz049] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Conservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved nonexonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.
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Affiliation(s)
- Zhirui Hu
- Department of Statistics, Harvard University, Cambridge, MA
| | | | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA
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O'Donnell K, Lutzoni FM, Ward TJ, Benny GL. Evolutionary relationships among mucoralean fungi (Zygomycota): Evidence for family polyphyly on a large scale. Mycologia 2019. [DOI: 10.1080/00275514.2001.12063160] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Kerry O'Donnell
- Microbial Properties Research Unit, National Center for Agricultural Utilization Research, U.S. Department of Agriculture, Agricultural Research Service, 1815 North University Street, Peoria, Illinois, USA 61604-3999
| | - François M. Lutzoni
- Department of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois, USA 60605-2496
| | - Todd J. Ward
- Microbial Properties Research Unit, National Center for Agricultural Utilization Research, U.S. Department of Agriculture, Agricultural Research Service, 1815 North University Street, Peoria, Illinois, USA 61604-3999
| | - Gerald L. Benny
- Department of Plant Pathology, 1453 Fifield Hall, University of Florida, Gainesville, Florida, USA 32611-0680
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Ancient diversification, biogeography, and the role of climatic niche evolution in the Old World cat snakes (Colubridae, Telescopus). Mol Phylogenet Evol 2019; 134:35-49. [PMID: 30703516 DOI: 10.1016/j.ympev.2019.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 01/25/2023]
Abstract
The process of species diversification is often associated with niche shifts in the newly arising lineages so that interspecific competition is minimized. However, an opposing force known as niche conservatism causes that related species tend to resemble each other in their niche requirements. Due to the inherent multidimensionality of niche space, some niche components may be subject to divergent evolution while others remain conserved in the process of speciation. One such possible component is the species' climatic niche. Here, we test the role of climatic niche evolution on the diversification of the Old World cat snakes of the genus Telescopus. These slender, nocturnal snakes are distributed in arid and semiarid areas throughout Africa, southwest Asia and adjoining parts of Europe. Because phylogenetic relationships among the Telescopus species are virtually unknown, we generated sequence data for eight genetic markers from ten of the 14 described species and reconstructed a time-calibrated phylogeny of the genus. Phylogenetic analysesindicate that the genus is of considerably old origin that dates back to the Eocene/Oligocene boundary. Biogeographical analyses place the ancestor of the genus in Africa, where it diversified into the species observed today and from where it colonized Arabia and the Levant twice independently. The colonization of Arabia occurred in the Miocene, that of the Levant either in the Late Oligocene or Early Miocene. We then identified temperature and precipitation niche space and breadth of the species included in the phylogeny and examined whether there is phylogenetic signal in these climatic niche characteristics. Despite the vast range of the genus and its complex biogeographic history, most Telescopus species have similar environmental requirements with preference for arid to semiarid conditions. One may thus expect that the genus' climatic niche will be conserved. However, our results suggest that most of the climatic niche axes examined show no phylogenetic signal, being indicative of no evolutionary constraints on the climatic niche position and niche breadth in Telescopus. The only two variables with positive phylogenetic signal (temperature niche position and precipitation niche breadth) evolved under the Brownian motion model, also indicating no directional selection on these traits. As a result, climatic niche evolution does not seem to be the major driver for the diversification in Telescopus.
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An Empirical Study on the Key Factors of Intelligent Upgrade of Small and Medium-sized Enterprises in China. SUSTAINABILITY 2019. [DOI: 10.3390/su11030619] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Promoting the intelligent upgrades of small and medium-sized enterprises is one of the important tasks of implementing “Made in China 2025” in China. As a front runner of nation-level reform, Zhejiang Province has provided much room for innovation and development, along with the emergence of a new type of ecology, accelerated formation of two ecosystems and international cooperation, and a supportive policy environment. Therefore, this paper uses 173 Small and Medium-sized Enterprises (SMEs) from Zhejiang Province as the research objects, builds a binary selection model, and analyzes the dynamic and constraining mechanism of intelligent upgrades of SMEs with regard to employee qualification, technology, capital, policy environment, and so on. The study finds that: First, among three main industries, manufacturing is the major industry for the intelligent upgrades of SMEs and there are significant demonstration effects and industry heterogeneity. Secondly, the willingness to upgrade intelligently for SMEs is relatively strong. More than half of SMEs that have not intelligently upgraded show willingness to implement intelligent upgrades. Thirdly, factors such as corporate profitability, human capital quality, and industry intelligence level have significantly promoted the intelligent upgrades of SMEs, while the impact of labor cost, capital structure, government subsidies, and other variables are not significant. This conclusion still works after a number of robustness tests. Last but not least, based on the above conclusions, this paper proposes corresponding policy recommendations which are practically beneficial to the development of SMEs in China.
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