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Morales P, Gajardo F, Valdivieso C, Valladares MA, Di Genova A, Orellana A, Gutiérrez RA, González M, Montecino M, Maass A, Méndez MA, Allende ML. Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes. BMC Genomics 2024; 25:614. [PMID: 38890559 PMCID: PMC11184842 DOI: 10.1186/s12864-024-10416-w] [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: 10/05/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order. RESULTS We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group. CONCLUSIONS The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
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Affiliation(s)
- Pamela Morales
- Millennium Institute Center for Genome Regulation, Santiago, Chile.
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Felipe Gajardo
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Valdivieso
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Moisés A Valladares
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Grupo de Biodiversidad y Cambio Global (GBCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Alex Di Genova
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- DiGenoma-Lab, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
- Centro de Modelamiento Matemático UMI-CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Ariel Orellana
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- ANID Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Mauricio González
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Martin Montecino
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, 837001, Chile
| | - Alejandro Maass
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Modelamiento Matemático IRL 2807 CNRS, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Matemática, Universidad de Chile, Santiago, Chile
| | - Marco A Méndez
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Ecología Aplicada y Sustentabilidad (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Cape Horn International Center (CHIC), Parque Etnobotánico Omora, Universidad de Magallanes, Puerto Williams, Chile
| | - Miguel L Allende
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Cebriá-Mendoza M, Beamud B, Andreu-Moreno I, Arbona C, Larrea L, Díaz W, Sanjuán R, Cuevas JM. Human Anelloviruses: Influence of Demographic Factors, Recombination, and Worldwide Diversity. Microbiol Spectr 2023; 11:e0492822. [PMID: 37199659 PMCID: PMC10269794 DOI: 10.1128/spectrum.04928-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023] Open
Abstract
Anelloviruses represent the major and most diverse component of the healthy human virome, referred to as the anellome. In this study, we determined the anellome of 50 blood donors, forming two sex- and age-matched groups. Anelloviruses were detected in 86% of the donors. The number of detected anelloviruses increased with age and was approximately twice as high in men as in women. A total of 349 complete or nearly complete genomes were classified as belonging to torque teno virus (TTV), torque teno mini virus (TTMV), and torque teno midi virus (TTMDV) anellovirus genera (197, 88, and 64 sequences, respectively). Most donors had intergenus (69.8%) or intragenus (72.1%) coinfections. Despite the limited number of sequences, intradonor recombination analysis showed 6 intragenus recombination events in ORF1. As thousands of anellovirus sequences have been described recently, we finally analyzed the global diversity of human anelloviruses. Species richness and diversity were close to saturation in each anellovirus genus. Recombination was found to be the main factor promoting diversity, although its effect was significantly lower in TTV than in TTMV and TTMDV. Overall, our results suggest that differences in diversity between genera may be caused by variations in the relative contribution of recombination. IMPORTANCE Anelloviruses are the most common human infectious viruses and are considered essentially harmless. Compared to other human viruses, they are characterized by enormous diversity, and recombination is suggested to play an important role in their diversification and evolution. Here, by analyzing the composition of the plasma anellome of 50 blood donors, we find that recombination is also a determinant of viral evolution at the intradonor level. On a larger scale, analysis of anellovirus sequences currently available in databases shows that their diversity is close to saturation and differs among the three human anellovirus genera and that recombination is the main factor explaining this intergenus variability. Global characterization of anellovirus diversity could provide clues about possible associations between certain virus variants and pathologies, as well as facilitate the implementation of unbiased PCR-based detection protocols, which may be relevant for using anelloviruses as endogenous markers of immune status.
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Affiliation(s)
- María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Beatriz Beamud
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- FISABIO-Salud Pública, Generalitat Valenciana, Valencia, Spain
| | - Iván Andreu-Moreno
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Cristina Arbona
- Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | - Luís Larrea
- Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | - Wladimiro Díaz
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- Genomic and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region (FISABIO), Valencia, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- Department of Genetics, Universitat de València, Valencia, Spain
| | - José M. Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
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Al Jewari C, Baldauf SL. Conflict over the eukaryote root resides in strong outliers, mosaics and missing data sensitivity of site-specific (CAT) mixture models. Syst Biol 2022; 72:1-16. [PMID: 35412616 DOI: 10.1093/sysbio/syac029] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/07/2022] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic reconstruction using concatenated loci ("phylogenomics" or "supermatrix phylogeny") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees (SGTs). However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artefacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from a central mean for each individual sequence, while ConWin uses a sliding window to screen for incongruent protein fragments (mosaics). Both methods allow selective masking of individual sequences or sequence fragments in order to minimize missing data, an important consideration for resolving deep splits with limited data. Analyses focused on a set of 76 eukaryotic proteins of bacterial-ancestry previously used in various combinations to assess the branching order among the three major divisions of eukaryotes: Amorphea (mainly animals, fungi and Amoebozoa), Diaphoretickes (most other well-known eukaryotes and nearly all algae) and Excavata, represented here by Discoba (Jakobida, Heterolobosea, and Euglenozoa). ConJak analyses found strong outliers to be concentrated in under-sampled lineages, while ConWin analyses of Discoba, the most under-sampled of the major lineages, detected potentially incongruent fragments scattered throughout. Phylogenetic analyses of the full data using an LG-gamma model support a Discoba sister scenario (neozoan-excavate root), which rises to 99-100% bootstrap support with data masked according to either protocol. However, analyses with two site-specific (CAT) mixture models yielded widely inconsistent results and a striking sensitivity to missing data. The neozoan-excavate root places Amorphea and Diaphoretickes as more closely related to each other than either is to Discoba, a fundamental relationship that should remain unaffected by additional taxa.
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Affiliation(s)
- Caesar Al Jewari
- Program in Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden 75236
| | - Sandra L Baldauf
- Program in Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden 75236
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Liston A, Weitemier KA, Letelier L, Podani J, Zong Y, Liu L, Dickinson TA. Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization. PeerJ 2021; 9:e12418. [PMID: 34754629 PMCID: PMC8555502 DOI: 10.7717/peerj.12418] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/10/2021] [Indexed: 11/20/2022] Open
Abstract
Background Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups. Methods We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies. Results We obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridization in the evolution of Crataegus. Hybridization between subgenus Americanae and subgenus Sanguineae was documented for the origin of Sanguineae tetraploids, but not for a tetraploid Americanae species. This is also the first application of target capture probes designed with apple genome sequence. We successfully assembled 95% of 257 loci in Crataegus, indicating their potential utility across the genera of the apple tribe.
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Affiliation(s)
- Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Kevin A Weitemier
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America.,Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Lucas Letelier
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - János Podani
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Lorand University, Budapest, Hungary
| | - Yu Zong
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America.,College of Chemistry & Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Lang Liu
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Timothy A Dickinson
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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5
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Ahmadi M, Hemami MR, Kaboli M, Nazarizadeh M, Malekian M, Behrooz R, Geniez P, Alroy J, Zimmermann NE. The legacy of Eastern Mediterranean mountain uplifts: rapid disparity of phylogenetic niche conservatism and divergence in mountain vipers. BMC Ecol Evol 2021; 21:130. [PMID: 34157982 PMCID: PMC8220690 DOI: 10.1186/s12862-021-01863-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/17/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The orogeny of the eastern Mediterranean region has substantially affected ecological speciation patterns, particularly of mountain-dwelling species. Mountain vipers of the genus Montivipera are among the paramount examples of Mediterranean neo-endemism, with restricted ranges in the mountains of Anatolia, the Levant, Caucasus, Alborz, and Zagros. Here we explore the phylogenetic and ecological diversification of Montivipera to reconstruct its ecological niche evolution and biogeographic history. Using 177 sequences of three mitochondrial genes, a dated molecular phylogeny of mountain vipers was reconstructed. Based on 320 occurrence points within the entire range of the genus and six climatic variables, ecological niches were modelled and used to infer ancestral niche occupancy. In addition, the biogeographic history and ancestral states of the species were reconstructed across climate gradients. RESULTS Dated phylogenetic reconstruction revealed that the ancestor of mountain vipers split into two major clades at around 12.18 Mya followed by multiple vicariance events due to rapid orogeny. Montivipera colonised coastal regions from a mountain-dwelling ancestor. We detected a highly complex ecological niche evolution of mountain vipers to temperature seasonality, a variable that also showed a strong phylogenetic signal and high contribution in niche occupation. CONCLUSION Raising mountain belts in the Eastern Mediterranean region and subsequent remarkable changes in temperature seasonality have led to the formation of important centres of diversification and endemism in this biodiversity hotspot. High rates of niche conservatism, low genetic diversity, and segregation of ranges into the endemic distribution negatively influenced the adaptive capacity of mountain vipers. We suggest that these species should be considered as evolutionary significant units and priority species for conservation in Mediterranean mountain ecosystems.
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Affiliation(s)
- Mohsen Ahmadi
- Department of Natural Resources, Isfahan University of Technology, 84156-83111, Isfahan, Iran.
| | - Mahmoud-Reza Hemami
- Department of Natural Resources, Isfahan University of Technology, 84156-83111, Isfahan, Iran
| | - Mohammad Kaboli
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Masoud Nazarizadeh
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre CAS, v.v.i., České Budějovice, Czech Republic
| | - Mansoureh Malekian
- Department of Natural Resources, Isfahan University of Technology, 84156-83111, Isfahan, Iran
| | - Roozbeh Behrooz
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, University of Montpellier, Montpellier, France
| | - Philippe Geniez
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, University of Montpellier, Montpellier, France
| | - John Alroy
- Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW, 2109, Australia
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: cellular, genomic and metabolic complexity. Biol Rev Camb Philos Soc 2020; 95:1198-1232. [PMID: 32301582 PMCID: PMC7539958 DOI: 10.1111/brv.12605] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022]
Abstract
The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental Sciences, Universitat Pompeu Fabra (UPF)Dr. Aiguader 88, 08003BarcelonaSpain
- ICREAPg. Lluís Companys 23, 08010BarcelonaSpain
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Igolkina AA, Bazykin GA, Chizhevskaya EP, Provorov NA, Andronov EE. Matching population diversity of rhizobial nodA and legume NFR5 genes in plant-microbe symbiosis. Ecol Evol 2019; 9:10377-10386. [PMID: 31624556 PMCID: PMC6787799 DOI: 10.1002/ece3.5556] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 07/07/2019] [Accepted: 07/15/2019] [Indexed: 12/31/2022] Open
Abstract
We hypothesized that population diversities of partners in nitrogen-fixing rhizobium-legume symbiosis can be matched for "interplaying" genes. We tested this hypothesis using data on nucleotide polymorphism of symbiotic genes encoding two components of the plant-bacteria signaling system: (a) the rhizobial nodA acyltransferase involved in the fatty acid tail decoration of the Nod factor (signaling molecule); (b) the plant NFR5 receptor required for Nod factor binding. We collected three wild-growing legume species together with soil samples adjacent to the roots from one large 25-year fallow: Vicia sativa, Lathyrus pratensis, and Trifolium hybridum nodulated by one of the two Rhizobium leguminosarum biovars (viciae and trifolii). For each plant species, we prepared three pools for DNA extraction and further sequencing: the plant pool (30 plant indiv.), the nodule pool (90 nodules), and the soil pool (30 samples). We observed the following statistically significant conclusions: (a) a monotonic relationship between the diversity in the plant NFR5 gene pools and the nodule rhizobial nodA gene pools; (b) higher topological similarity of the NFR5 gene tree with the nodA gene tree of the nodule pool, than with the nodA gene tree of the soil pool. Both nonsynonymous diversity and Tajima's D were increased in the nodule pools compared with the soil pools, consistent with relaxation of negative selection and/or admixture of balancing selection. We propose that the observed genetic concordance between NFR5 gene pools and nodule nodA gene pools arises from the selection of particular genotypes of the nodA gene by the host plant.
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Affiliation(s)
- Anna A. Igolkina
- ARRIAM, All‐Russia Research Institute for Agricultural MicrobiologyPushkinRussia
- Peter the Great St. Petersburg Polytechnic UniversitySaint‐PetersburgRussia
| | - Georgii A. Bazykin
- Center for Life SciencesSkolkovo Institute of Science and TechnologyMoscowRussia
- Laboratory for Molecular EvolutionKharkevich Institute of Information Transmission Problems of the Russian Academy of SciencesMoscowRussia
| | | | - Nikolai A. Provorov
- ARRIAM, All‐Russia Research Institute for Agricultural MicrobiologyPushkinRussia
| | - Evgeny E. Andronov
- ARRIAM, All‐Russia Research Institute for Agricultural MicrobiologyPushkinRussia
- Saint‐Petersburg State UniversitySaint‐PetersburgRussia
- Dokuchaev Soil Science InstituteMoscowRussia
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Laumer CE. Inferring Ancient Relationships with Genomic Data: A Commentary on Current Practices. Integr Comp Biol 2019; 58:623-639. [PMID: 29982611 DOI: 10.1093/icb/icy075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Contemporary phylogeneticists enjoy an embarrassment of riches, not only in the volumes of data now available, but also in the diversity of bioinformatic tools for handling these data. Here, I discuss a subset of these tools I consider well-suited to the task of inferring ancient relationships with coding sequence data in particular, encompassing data generation, orthology assignment, alignment and gene tree inference, supermatrix construction, and analysis under the best-fitting models applicable to large-scale datasets. Throughout, I compare and critique methods, considering both their theoretical principles and the details of their implementation, and offering practical tips on usage where appropriate. I also entertain different motivations for analyzing what are almost always originally DNA sequence data as codons, amino acids, and higher-order recodings. Although presented in a linear order, I see value in using the diversity of tools available to us to assess the sensitivity of clades of biological interest to different gene and taxon sets and analytical modes, which can be an indication of the presence of systematic error, of which a few forms remain poorly controlled by even the best available inference methods.
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Affiliation(s)
- Christopher E Laumer
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, EBML-EBI South Building, Hinxton CB10 1SD, UK
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9
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Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 2019; 7:e6399. [PMID: 30783571 PMCID: PMC6378093 DOI: 10.7717/peerj.6399] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022] Open
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alexandre Antonelli
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
| | - Christine D. Bacon
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stella Huynh
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Hélène Morlon
- Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France
| | - Luay K. Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alexander Schliep
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | | | - Fernanda P. Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil
| | - John Wiedenhoeft
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
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10
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Adams RH, Castoe TA. Supergene validation: A model-based protocol for assessing the accuracy of non-model-based supergene methods. MethodsX 2019; 6:2181-2188. [PMID: 31667118 PMCID: PMC6812401 DOI: 10.1016/j.mex.2019.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/19/2019] [Indexed: 11/16/2022] Open
Abstract
Genome-scale species tree inference is largely restricted to heuristic approaches that use estimated gene trees to reconstruct species-level relationships. Central to these heuristic species tree methods is the assumption that the gene trees are estimated without error. To increase the accuracy of input gene trees used to infer species trees, several techniques have recently been developed for constructing longer “supergenes” that represent sets of loci inferred to share the same genealogical history. While these supergene methods are designed to increase the amount of data for gene tree estimation by concatenating several loci into “supergenes” to increase gene tree accuracy, no formal protocols have been proposed to validate this key “supergene” concatenation step. In a recent study, we developed several supergene validation strategies for assessing the accuracy of a popular supergene method: the so-called “statistical binning” pipeline. In this article, we describe a more generalizable and model-based “supergene validation” protocol for assessing the accuracy of supergenes and supergene methods using model-based tests of phylogenetic congruency. Supergenes are validated by adopting model-based tests of topological congruence These model-based procedures out preform non-model based methods for supergene construction The results of this protocol can be used to assess the overall performance of a supergene method across a phylogenomic dataset
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11
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Seo TK, Thorne JL. Information Criteria for Comparing Partition Schemes. Syst Biol 2018; 67:616-632. [PMID: 29309694 DOI: 10.1093/sysbio/syx097] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 12/17/2017] [Indexed: 01/10/2023] Open
Abstract
When inferring phylogenies, one important decision is whether and how nucleotide substitution parameters should be shared across different subsets or partitions of the data. One sort of partitioning error occurs when heterogeneous subsets are mistakenly lumped together and treated as if they share parameter values. The opposite kind of error is mistakenly treating homogeneous subsets as if they result from distinct sets of parameters. Lumping and splitting errors are not equally bad. Lumping errors can yield parameter estimates that do not accurately reflect any of the subsets that were combined whereas splitting errors yield estimates that did not benefit from sharing information across partitions. Phylogenetic partitioning decisions are often made by applying information criteria such as the Akaike information criterion (AIC). As with other information criteria, the AIC evaluates a model or partition scheme by combining the maximum log-likelihood value with a penalty that depends on the number of parameters being estimated. For the purpose of selecting an optimal partitioning scheme, we derive an adjustment to the AIC that we refer to as the AIC$^{(p)}$ and that is motivated by the idea that splitting errors are less serious than lumping errors. We also introduce a similar adjustment to the Bayesian information criterion (BIC) that we refer to as the BIC$^{(p)}$. Via simulation and empirical data analysis, we contrast AIC and BIC behavior to our suggested adjustments. We discuss these results and also emphasize why we expect the probability of lumping errors with the AIC$^{(p)}$ and the BIC$^{(p)}$ to be relatively robust to model parameterization.
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Affiliation(s)
- Tae-Kun Seo
- Department of Biological Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Jeffrey L Thorne
- Bioinformatics Research Center, Box 7566, North Carolina State University, Raleigh NC 27695-7566, USA
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12
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Pagán I. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view. INFECTION GENETICS AND EVOLUTION 2018; 65:187-199. [PMID: 30055330 DOI: 10.1016/j.meegid.2018.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
During the past four decades, the scientific community has seen an exponential advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of plant virus populations. Predating these advances, the field of Phylogenetics has significantly contributed to understand important aspects of plant virus evolution. This review aims at summarizing the impact of Phylogenetics in the current knowledge on three major aspects of plant virus evolution that have benefited from the development of phylogenetic inference: (1) The identification and classification of plant virus diversity. (2) The mechanisms and forces shaping the evolution of plant virus populations. (3) The understanding of the interaction between plant virus evolution, epidemiology and ecology. The work discussed here highlights the important role of phylogenetic approaches in the study of the dynamics of plant virus populations.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28223, Spain.
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13
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Accetto T, Janež N. The lytic Myoviridae of Enterobacteriaceae form tight recombining assemblages separated by discontinuities in genome average nucleotide identity and lateral gene flow. Microb Genom 2018; 4. [PMID: 29583117 PMCID: PMC5885020 DOI: 10.1099/mgen.0.000169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In Bacteria, a working consensus of species circumscription may have been reached and one of the most prominent criteria is high average nucleotide identity (ANI). ANI in effect groups strains that may recombine more or less frequently, depending on their biology, as opposed to rare interspecies gene transfer. For bacteriophages, which show various lifestyles, the nature of the fundamental natural unit, if it exists in a biological sense, is not well understood and defined. The approaches based on dot-plots are useful to group similar bacteriophages, yet are not quantitative and use arbitrarily set cut-offs. Here, we focus on lytic Myoviridae and test the ANI metric for group delineation. We show that ANI-based groups are in agreement with the International Committee on Taxonomy of Viruses (ICTV) classification and already established dot-plot groups, which are occasionally further refined owing to higher resolution of ANI analysis. Furthermore, these groups are separated among themselves by clear ANI discontinuities. Their members readily exchange core genes with each other while they do not with bacteriophages of other ANI groups, not even with the most similar. Thus, ANI-delineated groups may represent the natural units in lytic Myoviridae evolution with features that resemble those encountered in bacterial species.
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Affiliation(s)
- Tomaž Accetto
- 1Biotechnical Faculty, Animal Science Department, University of Ljubljana, Domžale, Slovenia
| | - Nika Janež
- 2Center of Excellence for Biosensors Instrumentation and Process Control, Center for Biotechnology, Tovarniška 26, 5270 Ajdovščina, Slovenia
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14
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Da Cunha V, Gaia M, Gadelle D, Nasir A, Forterre P. Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. PLoS Genet 2017; 13:e1006810. [PMID: 28604769 PMCID: PMC5484517 DOI: 10.1371/journal.pgen.1006810] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 06/26/2017] [Accepted: 05/09/2017] [Indexed: 11/22/2022] Open
Abstract
The eocyte hypothesis, in which Eukarya emerged from within Archaea, has been boosted by the description of a new candidate archaeal phylum, "Lokiarchaeota", from metagenomic data. Eukarya branch within Lokiarchaeota in a tree reconstructed from the concatenation of 36 universal proteins. However, individual phylogenies revealed that lokiarchaeal proteins sequences have different evolutionary histories. The individual markers phylogenies revealed at least two subsets of proteins, either supporting the Woese or the Eocyte tree of life. Strikingly, removal of a single protein, the elongation factor EF2, is sufficient to break the Eukaryotes-Lokiarchaea affiliation. Our analysis suggests that the three lokiarchaeal EF2 proteins have a chimeric organization that could be due to contamination and/or homologous recombination with patches of eukaryotic sequences. A robust phylogenetic analysis of RNA polymerases with a new dataset indicates that Lokiarchaeota and related phyla of the Asgard superphylum are sister group to Euryarchaeota, not to Eukarya, and supports the monophyly of Archaea with their rooting in the branch leading to Thaumarchaeota.
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Affiliation(s)
- Violette Da Cunha
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie Paris, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Morgan Gaia
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie Paris, France
| | - Daniele Gadelle
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Arshan Nasir
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Patrick Forterre
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie Paris, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
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15
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Kates HR, Soltis PS, Soltis DE. Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci. Mol Phylogenet Evol 2017; 111:98-109. [PMID: 28288944 DOI: 10.1016/j.ympev.2017.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 11/28/2022]
Abstract
Phylogenetics can facilitate the study of plant domestication by resolving sister relationships between crops and their wild relatives, thereby identifying the ancestors of cultivated plants. Previous phylogenetic studies of the six Cucurbita crop lineages (pumpkins and squashes) and their wild relatives suggest histories of deep coalescence that complicate uncovering the genetic origins of the six crop taxa. We investigated the evolution of wild and domesticated Cucurbita using the most comprehensive and robust molecular-based phylogeny for Cucurbita to date based on 44 loci derived from introns of single-copy nuclear genes. We discovered novel relationships among Cucurbita species and recovered the first Cucurbita tree with well-supported resolution within species. Cucurbita comprises a clade of mesophytic annual species that includes all six crop taxa and a grade of xerophytic perennial species that represent the ancestral xerophytic habit of the genus. Based on phylogenetic resolution within-species we hypothesize that the magnitude of domestication bottlenecks varies among Cucurbita crop lineages. Our phylogeny clarifies how wild Cucurbita species are related to the domesticated taxa. We find close relationships between two wild species and crop lineages not previously identified. Expanded geographic sampling of key wild species is needed for improved understanding of the evolution of domesticated Cucurbita.
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Affiliation(s)
- Heather R Kates
- Univ Florida, Genet Inst, Gainesville, FL 32611, USA; Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611, USA.
| | - Pamela S Soltis
- Univ Florida, Genet Inst, Gainesville, FL 32611, USA; Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611, USA
| | - Douglas E Soltis
- Univ Florida, Genet Inst, Gainesville, FL 32611, USA; Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611, USA; Univ Florida, Dept Biol, Gainesville, FL 32611, USA
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16
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Naranjo-Ortíz MA, Brock M, Brunke S, Hube B, Marcet-Houben M, Gabaldón T. Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes. Front Microbiol 2016; 7:2001. [PMID: 28066338 PMCID: PMC5169069 DOI: 10.3389/fmicb.2016.02001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/29/2016] [Indexed: 01/22/2023] Open
Abstract
Analysis of the growing number of available fully-sequenced genomes has shown that Horizontal Gene Transfer (HGT) in eukaryotes is more common than previously thought. It has been proposed that genes with certain functions may be more prone to HGT than others, but we still have a very poor understanding of the selective forces driving eukaryotic HGT. Recent work uncovered that d-amino acid racemases have been commonly transferred from bacteria to fungi, but their role in the receiving organisms is currently unknown. Here, we set out to assess whether d-amino acid racemases are commonly transferred to and between eukaryotic groups. For this we performed a global survey that used a novel automated phylogeny-based HGT-detection algorithm (Abaccus). Our results revealed that at least 7.0% of the total eukaryotic racemase repertoire is the result of inter- or intra-domain HGT. These transfers are significantly enriched in plant-associated fungi. For these, we hypothesize a possible role for the acquired racemases allowing to exploit minoritary nitrogen sources in plant biomass, a nitrogen-poor environment. Finally, we performed experiments on a transferred aspartate-glutamate racemase in the fungal human pathogen Candida glabrata, which however revealed no obvious biological role.
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Affiliation(s)
- Miguel A Naranjo-Ortíz
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Matthias Brock
- Fungal Genetics and Biology Group, School of Life Sciences, University of Nottingham Nottingham, UK
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Hans Knoell Institute Jena Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Hans Knoell Institute JenaJena, Germany; Friedrich Schiller UniversityJena, Germany; Center for Sepsis Control and Care, University HospitalJena, Germany
| | - Marina Marcet-Houben
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA)Barcelona, Spain
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17
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Minton RL, Cruz MAM, Farman ML, Perez KE. Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). Zookeys 2016:137-154. [PMID: 27833437 PMCID: PMC5096375 DOI: 10.3897/zookeys.626.9633] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/16/2016] [Indexed: 01/03/2023] Open
Abstract
Helicoidea is a diverse group of land snails with a global distribution. While much is known regarding the relationships of helicoid taxa, comparatively little is known about the evolution of the mitochondrial genome in the superfamily. We sequenced two complete mitochondrial genomes from Praticolellamexicana Perez, 2011 representing the first such data from the helicoid family Polygyridae, and used them in an evolutionary analysis of mitogenomic gene order. We found the mitochondrial genome of Praticolellamexicana to be 14,008 bp in size, possessing the typical 37 metazoan genes. Multiple alternate stop codons are used, as are incomplete stop codons. Mitogenome size and nucleotide content is consistent with other helicoid species. Our analysis of gene order suggested that Helicoidea has undergone four mitochondrial rearrangements in the past. Two rearrangements were limited to tRNA genes only, and two involved protein coding genes.
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Affiliation(s)
- Russell L Minton
- School of Science and Computer Engineering, University of Houston Clear Lake, 2700 Bay Area Boulevard MC 39, Houston, Texas 77058 USA
| | - Marco A Martinez Cruz
- Department of Biology, University of Texas Rio Grande Valley, 1201 West University Drive, Edinburg, Texas 78539 USA
| | - Mark L Farman
- UK Healthcare Genomics, 225 Plant Science Building, 1405 Veteran's Drive, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Kathryn E Perez
- Department of Biology, University of Texas Rio Grande Valley, 1201 West University Drive, Edinburg, Texas 78539 USA
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18
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Planet PJ, Narechania A, Chen L, Mathema B, Boundy S, Archer G, Kreiswirth B. Architecture of a Species: Phylogenomics of Staphylococcus aureus. Trends Microbiol 2016; 25:153-166. [PMID: 27751626 DOI: 10.1016/j.tim.2016.09.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/07/2016] [Accepted: 09/22/2016] [Indexed: 12/11/2022]
Abstract
A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the 'core' genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement.
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Affiliation(s)
- Paul J Planet
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA; Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia & University of Pennsylvania, Philadelphia, PA, USA.
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Liang Chen
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA
| | - Barun Mathema
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sam Boundy
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Gordon Archer
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Barry Kreiswirth
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA
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19
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Making sense of genomes of parasitic worms: Tackling bioinformatic challenges. Biotechnol Adv 2016; 34:663-686. [DOI: 10.1016/j.biotechadv.2016.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/25/2016] [Accepted: 03/01/2016] [Indexed: 01/25/2023]
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20
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Gupta RS. Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification. FEMS Microbiol Rev 2016; 40:520-53. [PMID: 27279642 DOI: 10.1093/femsre/fuw011] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2016] [Indexed: 12/24/2022] Open
Abstract
Analyses of genome sequences, by some approaches, suggest that the widespread occurrence of horizontal gene transfers (HGTs) in prokaryotes disguises their evolutionary relationships and have led to questioning of the Darwinian model of evolution for prokaryotes. These inferences are critically examined in the light of comparative genome analysis, characteristic synapomorphies, phylogenetic trees and Darwin's views on examining evolutionary relationships. Genome sequences are enabling discovery of numerous molecular markers (synapomorphies) such as conserved signature indels (CSIs) and conserved signature proteins (CSPs), which are distinctive characteristics of different prokaryotic taxa. Based on these molecular markers, exhibiting high degree of specificity and predictive ability, numerous prokaryotic taxa of different ranks, currently identified based on the 16S rRNA gene trees, can now be reliably demarcated in molecular terms. Within all studied groups, multiple CSIs and CSPs have been identified for successive nested clades providing reliable information regarding their hierarchical relationships and these inferences are not affected by HGTs. These results strongly support Darwin's views on evolution and classification and supplement the current phylogenetic framework based on 16S rRNA in important respects. The identified molecular markers provide important means for developing novel diagnostics, therapeutics and for functional studies providing important insights regarding prokaryotic taxa.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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21
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Abstract
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent-due to events such as incomplete lineage sorting or horizontal gene transfer-it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modeling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such "process-agnostic" approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance and clustering methods; their comparative performance in the context of tree incongruence is largely unknown. Furthermore, because standard model selection criteria such as AIC cannot be applied to problems with a variable number of topologies, the issue of inferring the optimal number of clusters is poorly understood. Here, we perform a large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history. We observe that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward's method. We also introduce two statistical tests to infer the optimal number of clusters and show that they strongly outperform the silhouette criterion, a general-purpose heuristic. We illustrate the usefulness of the approach by 1) identifying errors in a previous phylogenetic analysis of yeast species and 2) identifying topological incongruence among newly sequenced loci of the globeflower fly genus Chiastocheta We release treeCl, a new program to cluster genes of common evolutionary history (http://git.io/treeCl).
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Affiliation(s)
- Kevin Gori
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Campus, Hinxton, United Kingdom
| | - Tomasz Suchan
- Department of Ecology and Evolution, Biophore Building, UNIL-Sorge, University of Lausanne, Lausanne, Switzerland
| | - Nadir Alvarez
- Department of Ecology and Evolution, Biophore Building, UNIL-Sorge, University of Lausanne, Lausanne, Switzerland
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Campus, Hinxton, United Kingdom
| | - Christophe Dessimoz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Campus, Hinxton, United Kingdom Department of Ecology and Evolution, Biophore Building, UNIL-Sorge, University of Lausanne, Lausanne, Switzerland Department of Genetics, Evolution & Environment, University College London, London, United Kingdom Department of Computer Science, University College London, London, United Kingdom Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Biophore, Lausanne, Switzerland
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22
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Simmons MP, Sloan DB, Gatesy J. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Mol Phylogenet Evol 2016; 97:76-89. [PMID: 26768112 DOI: 10.1016/j.ympev.2015.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/03/2015] [Accepted: 12/20/2015] [Indexed: 10/22/2022]
Abstract
Gene-tree-estimation error is a major concern for coalescent methods of phylogenetic inference. We sampled eight empirical studies of ancient lineages with diverse numbers of taxa and genes for which the original authors applied one or more coalescent methods. We found that the average pairwise congruence among gene trees varied greatly both between studies and also often within a study. We recommend that presenting plots of pairwise congruence among gene trees in a dataset be treated as a standard practice for empirical coalescent studies so that readers can readily assess the extent and distribution of incongruence among gene trees. ASTRAL-based coalescent analyses generally outperformed MP-EST and STAR with respect to both internal consistency (congruence between analyses of subsamples of genes with the complete dataset of all genes) and congruence with the concatenation-based topology. We evaluated the approach of subsampling gene trees that are, on average, more congruent with other gene trees as a method to reduce artifacts caused by gene-tree-estimation errors on coalescent analyses. We suggest that this method is well suited to testing whether gene-tree-estimation error is a primary cause of incongruence between concatenation- and coalescent-based results, to reconciling conflicting phylogenetic results based on different coalescent methods, and to identifying genes affected by artifacts that may then be targeted for reciprocal illumination. We provide scripts that automate the process of calculating pairwise gene-tree incongruence and subsampling trees while accounting for differential taxon sampling among genes. Finally, we assert that multiple tree-search replicates should be implemented as a standard practice for empirical coalescent studies that apply MP-EST.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA
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23
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Re-evaluating the phylogeny of allopolyploid Gossypium L. Mol Phylogenet Evol 2015; 92:45-52. [DOI: 10.1016/j.ympev.2015.05.023] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/19/2015] [Accepted: 05/29/2015] [Indexed: 01/06/2023]
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24
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Pillonel T, Bertelli C, Salamin N, Greub G. Taxogenomics of the order Chlamydiales. Int J Syst Evol Microbiol 2015; 65:1381-1393. [PMID: 25634949 DOI: 10.1099/ijs.0.000090] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial classification is a long-standing problem for taxonomists and species definition itself is constantly debated among specialists. The classification of strict intracellular bacteria such as members of the order Chlamydiales mainly relies on DNA- or protein-based phylogenetic reconstructions because these organisms exhibit few phenotypic differences and are difficult to culture. The availability of full genome sequences allows the comparison of the performance of conserved protein sequences to reconstruct Chlamydiales phylogeny. This approach permits the identification of markers that maximize the phylogenetic signal and the robustness of the inferred tree. In this study, a set of 424 core proteins was identified and concatenated to reconstruct a reference species tree. Although individual protein trees present variable topologies, we detected only few cases of incongruence with the reference species tree, which were due to horizontal gene transfers. Detailed analysis of the phylogenetic information of individual protein sequences (i) showed that phylogenies based on single randomly chosen core proteins are not reliable and (ii) led to the identification of twenty taxonomically highly reliable proteins, allowing the reconstruction of a robust tree close to the reference species tree. We recommend using these protein sequences to precisely classify newly discovered isolates at the family, genus and species levels.
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Affiliation(s)
- Trestan Pillonel
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
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Li J, Wong CF, Wong MT, Huang H, Leung FC. Modularized evolution in archaeal methanogens phylogenetic forest. Genome Biol Evol 2014; 6:3344-59. [PMID: 25502908 PMCID: PMC4986457 DOI: 10.1093/gbe/evu259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2014] [Indexed: 11/13/2022] Open
Abstract
Methanogens are methane-producing archaea that plays a key role in the global carbon cycle. To date, the evolutionary history of methanogens and closely related nonmethanogen species remains unresolved among studies conducted upon different genetic markers, attributing to horizontal gene transfers (HGTs). With an effort to decipher both congruent and conflicting evolutionary events, reconstruction of coevolved gene clusters and hierarchical structure in the archaeal methanogen phylogenetic forest, comprehensive evolution, and network analyses were performed upon 3,694 gene families from 41 methanogens and 33 closely related archaea. Our results show that 1) greater than 50% of genes are in topological dissonance with others; 2) the prevalent interorder HGTs, even for core genes, in methanogen genomes led to their scrambled phylogenetic relationships; 3) most methanogenesis-related genes have experienced at least one HGT; 4) greater than 20% of the genes in methanogen genomes were transferred horizontally from other archaea, with genes involved in cell-wall synthesis and defense system having been transferred most frequently; 5) the coevolution network contains seven statistically robust modules, wherein the central module has the highest average node strength and comprises a majority of the core genes; 6) different coevolutionary module genes boomed in different time and evolutionary lineage, constructing diversified pan-genome structures; 7) the modularized evolution is also closely related to the vertical evolution signals and the HGT rate of the genes. Overall, this study presented a modularized phylogenetic forest that describes a combination of complicated vertical and nonvertical evolutionary processes for methanogenic archaeal species.
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Affiliation(s)
- Jun Li
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, China
| | - Chi-Fat Wong
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, China School of Biological Sciences, Faculty of Science, The University of Hong Kong, China
| | - Mabel Ting Wong
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, China Present address: Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - He Huang
- Center for Marine Environmental Studies, Ehime University, Japan
| | - Frederick C Leung
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, China Bioinformatics Center, Nanjing Agricultural University, People's Republic of China
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McInerney J, Cummins C, Haggerty L. Goods-thinking vs. tree-thinking: Finding a place for mobile genetic elements. Mob Genet Elements 2014; 1:304-308. [PMID: 22545244 PMCID: PMC3337142 DOI: 10.4161/mge.19153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
While it has become increasingly clear that the Tree of Life hypothesis has limitations in its ability to describe the evolution of all evolving entities on the planet, there has been a marked reluctance to move away from the tree-based language. Ironically, while modifying the idea of the Tree of Life to the extent that it is only very distantly related to its original descriptions, there has been a very careful attempt to retain the language of tree-thinking. The recent movement away from a tree-thinking language toward a goods-thinking language and perspective is a significant improvement. In this commentary, we describe how goods-thinking can provide better descriptions of evolution, can integrate evolution with environment more closely and can offer an equal place for Mobile Genetic Elements and chromosomal elements in discussions of evolutionary history.
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Affiliation(s)
- James McInerney
- Bioinformatics and Molecular Evolution Unit; Department of Biology; National University of Ireland Maynooth, Co.; Kildare, Ireland
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O'Malley MA. When integration fails: Prokaryote phylogeny and the tree of life. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:551-62. [PMID: 23137776 DOI: 10.1016/j.shpsc.2012.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today's literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history (often called 'universal phylogeny'). Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a 'meta-heuristic' in the normative commitments guiding scientific practice.
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Affiliation(s)
- Maureen A O'Malley
- Department of Philosophy, University of Sydney, Quadrangle A14, NSW 2006, Australia.
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Lasek-Nesselquist E, Gogarten JP. The effects of model choice and mitigating bias on the ribosomal tree of life. Mol Phylogenet Evol 2013; 69:17-38. [PMID: 23707703 DOI: 10.1016/j.ympev.2013.05.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/26/2013] [Accepted: 05/08/2013] [Indexed: 01/03/2023]
Abstract
Deep-level relationships within Bacteria, Archaea, and Eukarya as well as the relationships of these three domains to each other require resolution. The ribosomal machinery, universal to all cellular life, represents a protein repertoire resistant to horizontal gene transfer, which provides a largely congruent signal necessary for reconstructing a tree suitable as a backbone for life's reticulate history. Here, we generate a ribosomal tree of life from a robust taxonomic sampling of Bacteria, Archaea, and Eukarya to elucidate deep-level intra-domain and inter-domain relationships. Lack of phylogenetic information and systematic errors caused by inadequate models (that cannot account for substitution rate or compositional heterogeneities) or improper model selection compound conflicting phylogenetic signals from HGT and/or paralogy. Thus, we tested several models of varying sophistication on three different datasets, performed removal of fast-evolving or long-branched Archaea and Eukarya, and employed three different strategies to remove compositional heterogeneity to examine their effects on the topological outcome. Our results support a two-domain topology for the tree of life, where Eukarya emerges from within Archaea as sister to a Korarchaeota/Thaumarchaeota (KT) or Crenarchaeota/KT clade for all models under all or at least one of the strategies employed. Taxonomic manipulation allows single-matrix and certain mixture models to vacillate between two-domain and three-domain phylogenies. We find that models vary in their ability to resolve different areas of the tree of life, which does not necessarily correlate with model complexity. For example, both single-matrix and some mixture models recover monophyletic Crenarchaeota and Euryarchaeota archaeal phyla. In contrast, the most sophisticated model recovers a paraphyletic Euryarchaeota but detects two large clades that comprise the Bacteria, which were recovered separately but never together in the other models. Overall, models recovered consistent topologies despite dataset modifications due to the removal of compositional bias, which reflects either ineffective bias reduction or robust datasets that allow models to overcome reconstruction artifacts. We recommend a comparative approach for evolutionary models to identify model weaknesses as well as consensus relationships.
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Schuster TM, Setaro SD, Kron KA. Age estimates for the buckwheat family Polygonaceae based on sequence data calibrated by fossils and with a focus on the amphi-Pacific Muehlenbeckia. PLoS One 2013; 8:e61261. [PMID: 23585884 PMCID: PMC3621405 DOI: 10.1371/journal.pone.0061261] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 03/11/2013] [Indexed: 11/19/2022] Open
Abstract
The buckwheat family Polygonaceae is a diverse group of plants and is a good model for investigating biogeography, breeding systems, coevolution with symbionts such as ants and fungi, functional trait evolution, hybridization, invasiveness, morphological plasticity, pollen morphology and wood anatomy. The main goal of this study was to obtain age estimates for Polygonaceae by calibrating a Bayesian phylogenetic analysis, using a relaxed molecular clock with fossil data. Based on the age estimates, we also develop hypotheses about the historical biogeography of the Southern Hemisphere group Muehlenbeckia. We are interested in addressing whether vicariance or dispersal could account for the diversification of Muehlenbeckia, which has a "Gondwanan" distribution. Eighty-one species of Polygonaceae were analysed with MrBayes to infer species relationships. One nuclear (nrITS) and three chloroplast markers (the trnL-trnF spacer region, matK and ndhF genes) were used. The molecular data were also analysed with Beast to estimate divergence times. Seven calibration points including fossil pollen and a leaf fossil of Muehlenbeckia were used to infer node ages. Results of the Beast analyses indicate an age of 110.9 (exponential/lognormal priors)/118.7 (uniform priors) million years (Myr) with an uncertainty interval of (90.7-125.0) Myr for the stem age of Polygonaceae. This age is older than previously thought (Maastrichtian, approximately 65.5-70.6 Myr). The estimated divergence time for Muehlenbeckia is 41.0/41.6 (39.6-47.8) Myr and its crown clade is 20.5/22.3 (14.2-33.5) Myr old. Because the breakup of Gondwana occurred from 95-30 Myr ago, diversification of Muehlenbeckia is best explained by oceanic long-distance and maybe stepping-stone dispersal rather than vicariance. This study is the first to give age estimates for clades of Polygonaceae and functions as a jumping-off point for future studies on the historical biogeography of the family.
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Affiliation(s)
- Tanja M Schuster
- Department of Biology, Wake Forest University, Winston-Salem, NC, USA.
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A scalable and flexible approach for investigating the genomic landscapes of phylogenetic incongruence. Mol Phylogenet Evol 2013; 66:1067-74. [DOI: 10.1016/j.ympev.2012.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 11/16/2012] [Accepted: 11/25/2012] [Indexed: 11/19/2022]
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Wu CS, Chaw SM, Huang YY. Chloroplast phylogenomics indicates that Ginkgo biloba is sister to cycads. Genome Biol Evol 2013; 5:243-54. [PMID: 23315384 PMCID: PMC3595029 DOI: 10.1093/gbe/evt001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2013] [Indexed: 12/23/2022] Open
Abstract
Molecular phylogenetic studies have not yet reached a consensus on the placement of Ginkgoales, which is represented by the only living species, Ginkgo biloba (common name: ginkgo). At least six discrepant placements of ginkgo have been proposed. This study aimed to use the chloroplast phylogenomic approach to examine possible factors that lead to such disagreeing placements. We found the sequence types used in the analyses as the most critical factor in the conflicting placements of ginkgo. In addition, the placement of ginkgo varied in the trees inferred from nucleotide (NU) sequences, which notably depended on breadth of taxon sampling, tree-building methods, codon positions, positions of Gnetopsida (common name: gnetophytes), and including or excluding gnetophytes in data sets. In contrast, the trees inferred from amino acid (AA) sequences congruently supported the monophyly of a ginkgo and Cycadales (common name: cycads) clade, regardless of which factors were examined. Our site-stripping analysis further revealed that the high substitution saturation of NU sequences mainly derived from the third codon positions and contributed to the variable placements of ginkgo. In summary, the factors we surveyed did not affect results inferred from analyses of AA sequences. Congruent topologies in our AA trees give more confidence in supporting the ginkgo-cycad sister-group hypothesis.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ya-Yi Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Lapierre P, Lasek-Nesselquist E, Gogarten JP. The impact of HGT on phylogenomic reconstruction methods. Brief Bioinform 2012; 15:79-90. [DOI: 10.1093/bib/bbs050] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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