1
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Janzen T, Etienne RS. Phylogenetic tree statistics: A systematic overview using the new R package 'treestats'. Mol Phylogenet Evol 2024; 200:108168. [PMID: 39117295 DOI: 10.1016/j.ympev.2024.108168] [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: 01/24/2024] [Revised: 07/19/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024]
Abstract
Phylogenetic trees are believed to contain a wealth of information on diversification processes. However, comparing phylogenetic trees is not straightforward due to their high dimensionality. Researchers have therefore defined a wide range of low-dimensional summary statistics. Currently, it remains unexplored to what extent these summary statistics cover the same underlying information and what summary statistics best explain observed variation across phylogenies. Furthermore, a large subset of available summary statistics focusses on measuring the topological features of a phylogenetic tree, but are often only explored at the extreme edge cases of the fully balanced or imbalanced tree and not for trees of intermediate balance. Here, we introduce a new R package called 'treestats', that provides speed optimized code to compute 70 summary statistics. We study correlations between summary statistics on empirical trees and on trees simulated using several diversification models. Furthermore, we introduce an algorithm to create intermediately balanced trees in a well-defined manner, in order to explore variation in summary statistics across a balance gradient. We find that almost all summary statistics are correlated with tree size, and find that it is difficult, if not impossible, to correct for tree size, unless the tree generating model is known. Furthermore, we find that across empirical and simulated trees, at least three large clusters of correlated summary statistics can be found, where statistics group together based on information used (topology or branching times). However, the finer grained correlation structure appears to depend strongly on either the taxonomic group studied (in empirical studies) or the tree generating model (in simulation studies). Amongst statistics describing the (im)balance of a tree, we find that almost all statistics vary non-linearly, and sometimes even non-monotonically, with our generated balance gradient. This indicates that balance is perhaps a more complex property of a tree than previously thought. Furthermore, using our new imbalancing algorithm, we devise a numerical test to identify balance statistics, and identify several statistics as balance statistics that were not previously considered as such. Lastly, our results lead to several recommendations on which statistics to select when analyzing and comparing phylogenetic trees.
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Affiliation(s)
- Thijs Janzen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands.
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
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2
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Gao Y, Feder AF. Detecting branching rate heterogeneity in multifurcating trees with applications in lineage tracing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601073. [PMID: 39005367 PMCID: PMC11244928 DOI: 10.1101/2024.06.27.601073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Understanding cellular birth rate differences is crucial for predicting cancer progression and interpreting tumor-derived genetic data. Lineage tracing experiments enable detailed reconstruction of cellular genealogies, offering new opportunities to measure branching rate heterogeneity. However, the lineage tracing process can introduce complex tree features that complicate this effort. Here, we examine tree characteristics in lineage tracing-derived genealogies and find that editing window placement leads to multifurcations at a tree's root or tips. We propose several ways in which existing tree topology-based metrics can be extended to test for rate heterogeneity on trees even in the presence of lineage-tracing associated distortions. Although these methods vary in power and robustness, a test based on theJ 1 statistic effectively detects branching rate heterogeneity in simulated lineage tracing data. Tests based on other common statistics ( s ^ and the Sackin index) show interior performance toJ 1 . We apply our validated methods to xenograft experimental data and find widespread rate heterogeneity across multiple study systems. Our results demonstrate the potential of tree topology statistics in analyzing lineage tracing data, and highlight the challenges associated with adapting phylogenetic methods to these systems.
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Affiliation(s)
- Yingnan Gao
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alison F Feder
- Department of Genome Sciences, University of Washington, Seattle, WA
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA
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3
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Buigues J, Viñals A, Martínez-Recio R, Monrós JS, Sanjuán R, Cuevas JM. Full-genome sequencing of dozens of new DNA viruses found in Spanish bat feces. Microbiol Spectr 2024; 12:e0067524. [PMID: 38990026 PMCID: PMC11323972 DOI: 10.1128/spectrum.00675-24] [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: 03/13/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024] Open
Abstract
Bats are natural hosts of multiple viruses, many of which have clear zoonotic potential. The search for emerging viruses has been aided by the implementation of metagenomic tools, which have also enabled the detection of unprecedented viral diversity. Currently, this search is mainly focused on RNA viruses, which are largely over-represented in databases. To compensate for this research bias, we analyzed fecal samples from 189 Spanish bats belonging to 22 different species using viral metagenomics. This allowed us to identify 52 complete or near-complete viral genomes belonging to the families Adenoviridae, Circoviridae, Genomoviridae, Papillomaviridae, Parvoviridae, Polyomaviridae and Smacoviridae. Of these, 30 could constitute new species, doubling the number of viruses currently described in Europe. These findings open the door to a more thorough analysis of bat DNA viruses and their zoonotic potential. IMPORTANCE Metagenomics has become a fundamental tool to characterize the global virosphere, allowing us not only to understand the existing viral diversity and its ecological implications but also to identify new and emerging viruses. RNA viruses have a higher zoonotic potential, but this risk is also present for some DNA virus families. In our study, we analyzed the DNA fraction of fecal samples from 22 Spanish bat species, identifying 52 complete or near-complete genomes of different viral families with zoonotic potential. This doubles the number of genomes currently described in Europe. Metagenomic data often produce partial genomes that can be difficult to analyze. Our work, however, has characterized a large number of complete genomes, thus facilitating their taxonomic classification and enabling different analyses to be carried out to evaluate their zoonotic potential. For example, recombination studies are relevant since this phenomenon could play a major role in cross-species transmission.
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Affiliation(s)
- Jaime Buigues
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
| | - Adrià Viñals
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Raquel Martínez-Recio
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
| | - Juan S. Monrós
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
- Department of Genetics, Universitat de València, València, Spain
| | - José M. Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
- Department of Genetics, Universitat de València, València, Spain
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4
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Csordas A, Sipos B, Kurucova T, Volfova A, Zamola F, Tichy B, Hicks DG. Cell Tree Rings: the structure of somatic evolution as a human aging timer. GeroScience 2024; 46:3005-3019. [PMID: 38172489 PMCID: PMC11009167 DOI: 10.1007/s11357-023-01053-4] [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: 04/19/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
Biological age is typically estimated using biomarkers whose states have been observed to correlate with chronological age. A persistent limitation of such aging clocks is that it is difficult to establish how the biomarker states are related to the mechanisms of aging. Somatic mutations could potentially form the basis for a more fundamental aging clock since the mutations are both markers and drivers of aging and have a natural timescale. Cell lineage trees inferred from these mutations reflect the somatic evolutionary process, and thus, it has been conjectured, the aging status of the body. Such a timer has been impractical thus far, however, because detection of somatic variants in single cells presents a significant technological challenge. Here, we show that somatic mutations detected using single-cell RNA sequencing (scRNA-seq) from thousands of cells can be used to construct a cell lineage tree whose structure correlates with chronological age. De novo single-nucleotide variants (SNVs) are detected in human peripheral blood mononuclear cells using a modified protocol. A default model based on penalized multiple regression of chronological age on 31 metrics characterizing the phylogenetic tree gives a Pearson correlation of 0.81 and a median absolute error of ~4 years between predicted and chronological ages. Testing of the model on a public scRNA-seq dataset yields a Pearson correlation of 0.85. In addition, cell tree age predictions are found to be better predictors of certain clinical biomarkers than chronological age alone, for instance glucose, albumin levels, and leukocyte count. The geometry of the cell lineage tree records the structure of somatic evolution in the individual and represents a new modality of aging timer. In addition to providing a numerical estimate of "cell tree age," it unveils a temporal history of the aging process, revealing how clonal structure evolves over life span. Cell Tree Rings complements existing aging clocks and may help reduce the current uncertainty in the assessment of geroprotective trials.
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Affiliation(s)
- Attila Csordas
- AgeCurve Limited, Cambridge, CB2 1SD, UK.
- Doctoral School of Clinical Medicine, University of Szeged, Szeged, H-6720, Hungary.
| | | | - Terezia Kurucova
- CEITEC - Central European Institute of Technology, Masaryk University, 62500, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500, Brno, Czechia
| | - Andrea Volfova
- HealthyLongevity.clinic Inc, 540 University Ave, Palo Alto, CA, 94301, USA
| | - Frantisek Zamola
- HealthyLongevity.clinic Inc, 540 University Ave, Palo Alto, CA, 94301, USA
| | - Boris Tichy
- CEITEC - Central European Institute of Technology, Masaryk University, 62500, Brno, Czechia
| | - Damien G Hicks
- AgeCurve Limited, Cambridge, CB2 1SD, UK
- Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
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5
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Henao-Diaz LF, Pennell M. The Major Features of Macroevolution. Syst Biol 2023; 72:1188-1198. [PMID: 37248967 DOI: 10.1093/sysbio/syad032] [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: 12/23/2021] [Revised: 05/02/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Evolutionary dynamics operating across deep time leave footprints in the shapes of phylogenetic trees. For the last several decades, researchers have used increasingly large and robust phylogenies to study the evolutionary history of individual clades and to investigate the causes of the glaring disparities in diversity among groups. Whereas typically not the focal point of individual clade-level studies, many researchers have remarked on recurrent patterns that have been observed across many different groups and at many different time scales. Whereas previous studies have documented various such regularities in topology and branch length distributions, they have typically focused on a single pattern and used a disparate collection (oftentimes, of quite variable reliability) of trees to assess it. Here we take advantage of modern megaphylogenies and unify previous disparate observations about the shapes embedded in the Tree of Life to create a catalog of the "major features of macroevolution." By characterizing such a large swath of subtrees in a consistent way, we hope to provide a set of phenomena that process-based macroevolutionary models of diversification ought to seek to explain.
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Affiliation(s)
- L Francisco Henao-Diaz
- Department of Ecology and Evolution, University of Chicago, Chicago, USA
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Matt Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, USA
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6
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Barzilai LP, Schrago CG. Signatures of natural selection in tree topology shape of serially sampled viral phylogenies. Mol Phylogenet Evol 2023; 183:107776. [PMID: 36990305 DOI: 10.1016/j.ympev.2023.107776] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/24/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Tree shape metrics can be computed fast for trees of any size, which makes them promising alternatives to intensive statistical methods and parameter-rich evolutionary models in the era of massive data availability. Previous studies have demonstrated their effectiveness in unveiling important parameters in viral evolutionary dynamics, although the impact of natural selection on the shape of tree topologies has not been thoroughly investigated. We carried out a forward-time and individual-based simulation to investigate whether tree shape metrics of several kinds could predict the selection regime employed to generate the data. To examine the impact of the genetic diversity of the founder viral population, simulations were run under two opposing starting configurations of the genetic diversity of the infecting viral population. We found that four evolutionary regimes, namely, negative, positive, and frequency-dependent selection, as well as neutral evolution, were successfully distinguished by tree topology shape metrics. Two metrics from the Laplacian spectral density profile (principal eigenvalue and peakedness) and the number of cherries were the most informative for indicating selection type. The genetic diversity of the founder population had an impact on differentiating evolutionary scenarios. Tree imbalance, which has been frequently associated with the action of natural selection on intrahost viral diversity, was also characteristic of neutrally evolving serially sampled data. Metrics calculated from empirical analysis of HIV datasets indicated that most tree topologies exhibited shapes closer to the frequency-dependent selection or neutral evolution regimes.
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7
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Sgarbossa D, Lupo U, Bitbol AF. Generative power of a protein language model trained on multiple sequence alignments. eLife 2023; 12:e79854. [PMID: 36734516 PMCID: PMC10038667 DOI: 10.7554/elife.79854] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 02/02/2023] [Indexed: 02/04/2023] Open
Abstract
Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating novel sequences belonging to protein families. Protein language models trained on multiple sequence alignments, such as MSA Transformer, are highly attractive candidates to this end. We propose and test an iterative method that directly employs the masked language modeling objective to generate sequences using MSA Transformer. We demonstrate that the resulting sequences score as well as natural sequences, for homology, coevolution, and structure-based measures. For large protein families, our synthetic sequences have similar or better properties compared to sequences generated by Potts models, including experimentally validated ones. Moreover, for small protein families, our generation method based on MSA Transformer outperforms Potts models. Our method also more accurately reproduces the higher-order statistics and the distribution of sequences in sequence space of natural data than Potts models. MSA Transformer is thus a strong candidate for protein sequence generation and protein design.
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Affiliation(s)
- Damiano Sgarbossa
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- SIB Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Umberto Lupo
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- SIB Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Anne-Florence Bitbol
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- SIB Swiss Institute of BioinformaticsLausanneSwitzerland
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8
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Belluardo F, Jesus Muñoz-Pajares A, Miralles A, Silvestro D, Cocca W, Mihaja Ratsoavina F, Villa A, Roberts SH, Mezzasalma M, Zizka A, Antonelli A, Crottini A. Slow and steady wins the race: Diversification rate is independent from body size and lifestyle in Malagasy skinks (Squamata: Scincidae: Scincinae). Mol Phylogenet Evol 2023; 178:107635. [PMID: 36208694 DOI: 10.1016/j.ympev.2022.107635] [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: 03/23/2022] [Revised: 09/18/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6-4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes - in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression - can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.
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Affiliation(s)
- Francesco Belluardo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.
| | - A Jesus Muñoz-Pajares
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Genética, Universidad de Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
| | - Aurélien Miralles
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Daniele Silvestro
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Ch. du Musée 10, 1700 Fribourg, Switzerland; Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
| | - Walter Cocca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - Fanomezana Mihaja Ratsoavina
- Mention Zoologie et Biodiversité Animale, Domaine Sciences et Technologies, Université d'Antananarivo, B.P. 906, 101 Antananarivo, Madagascar
| | - Andrea Villa
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, 08193 Cerdanyola del Vallès, Spain
| | - Sam Hyde Roberts
- SEED Madagascar, Unit 7, Beethoven Street 1A, W10 4LG London, UK; Oxford Brookes University, Headington Campus, 0X3 0BP Oxford, UK; Operation Wallacea, Wallace House, Old Bolingbroke, PE23 4EX Spilsby, UK
| | - Marcello Mezzasalma
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
| | - Alexander Zizka
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden; Royal Botanic Gardens, Kew, TW9 3AE Richmond, UK; Department of Biology, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
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Esquerré D, Brennan IG, Donnellan S, Keogh JS. Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons. Biol Lett 2022; 18:20220360. [PMID: 36541096 PMCID: PMC9768648 DOI: 10.1098/rsbl.2022.0360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 Mya. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche-filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Stephen Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
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10
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Optimal sequence-based design for multi-antigen HIV-1 vaccines using minimally distant antigens. PLoS Comput Biol 2022; 18:e1010624. [PMID: 36315492 PMCID: PMC9621458 DOI: 10.1371/journal.pcbi.1010624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
The immense global diversity of HIV-1 is a significant obstacle to developing a safe and effective vaccine. We recently showed that infections established with multiple founder variants are associated with the development of neutralization breadth years later. We propose a novel vaccine design strategy that integrates the variability observed in acute HIV-1 infections with multiple founder variants. We developed a probabilistic model to simulate this variability, yielding a set of sequences that present the minimal diversity seen in an infection with multiple founders. We applied this model to a subtype C consensus sequence for the Envelope (Env) (used as input) and showed that the simulated Env sequences mimic the mutational landscape of an infection with multiple founder variants, including diversity at antibody epitopes. The derived set of multi-founder-variant-like, minimally distant antigens is designed to be used as a vaccine cocktail specific to a HIV-1 subtype or circulating recombinant form and is expected to promote the development of broadly neutralizing antibodies. Diverse HIV-1 populations are generally thought to promote neutralizing responses. Current leading HIV-1 vaccine design strategies maximize the distance between antigens to attempt to cover global HIV-1 diversity or serialize immunizations to recapitulate the temporal evolution of HIV-1 during infection. To date, no vaccine has elicited broadly neutralizing antibodies. As we recently demonstrated that infection with multiple HIV-1 founder variants is predictive of neutralization breadth, we propose a novel strategy that endeavors to promote the development of broadly neutralizing antibodies by replicating the diversity of multi-founder variant acute infections. By training an HIV-1 Env consensus sequence on the diversity from acute infections with multiple founders, we derived in silico a set of minimally distant antigens that is representative of the diversity seen in a multi-founder acute infection. As the model is particular to the input sequence, it can produce antigens specific to any HIV-1 subtype or circulating recombinant form (CRF). We applied this to HIV-1 subtype C and obtained a set of minimally distant antigens that can be used as a vaccine cocktail.
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11
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Stockdale JE, Liu P, Colijn C. The potential of genomics for infectious disease forecasting. Nat Microbiol 2022; 7:1736-1743. [PMID: 36266338 DOI: 10.1038/s41564-022-01233-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/18/2022] [Indexed: 11/09/2022]
Abstract
Genomic technologies have led to tremendous gains in understanding how pathogens function, evolve and interact. Pathogen diversity is now measurable at high precision and resolution, in part because over the past decade, sequencing technologies have increased in speed and capacity, at decreased cost. Alongside this, the use of models that can forecast emergence and size of infectious disease outbreaks has risen, highlighted by the coronavirus disease 2019 pandemic but also due to modelling advances that allow for rapid estimates in emerging outbreaks to inform monitoring, coordination and resource deployment. However, genomics studies have remained largely retrospective. While they contain high-resolution views of pathogen diversification and evolution in the context of selection, they are often not aligned with designing interventions. This is a missed opportunity because pathogen diversification is at the core of the most pressing infectious public health challenges, and interventions need to take the mechanisms of virulence and understanding of pathogen diversification into account. In this Perspective, we assess these converging fields, discuss current challenges facing both surveillance specialists and modellers who want to harness genomic data, and propose next steps for integrating longitudinally sampled genomic data with statistical learning and interpretable modelling to make reliable predictions into the future.
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Affiliation(s)
- Jessica E Stockdale
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Pengyu Liu
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada.
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12
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Janzen T, Bokma F, Etienne RS. Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation. Syst Biol 2022; 71:1244-1254. [PMID: 34672354 PMCID: PMC9366449 DOI: 10.1093/sysbio/syab085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/11/2021] [Accepted: 10/16/2021] [Indexed: 11/14/2022] Open
Abstract
Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life. [Molecular clock; phylogenetic reconstruction; speciation; substitution rate variation.].
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Affiliation(s)
- Thijs Janzen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
| | - Folmer Bokma
- Department of BioSciences, Center for Ecological and Evolutionary Synthesis (CEES), University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
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13
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Voznica J, Zhukova A, Boskova V, Saulnier E, Lemoine F, Moslonka-Lefebvre M, Gascuel O. Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks. Nat Commun 2022; 13:3896. [PMID: 35794110 PMCID: PMC9258765 DOI: 10.1038/s41467-022-31511-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Widely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, generally rely on complex mathematical formulae and approximations, and do not scale with dataset size. We develop a likelihood-free, simulation-based approach, which combines deep learning with (1) a large set of summary statistics measured on phylogenies or (2) a complete and compact representation of trees, which avoids potential limitations of summary statistics and applies to any phylodynamics model. Our method enables both model selection and estimation of epidemiological parameters from very large phylogenies. We demonstrate its speed and accuracy on simulated data, where it performs better than the state-of-the-art methods. To illustrate its applicability, we assess the dynamics induced by superspreading individuals in an HIV dataset of men-having-sex-with-men in Zurich. Our tool PhyloDeep is available on github.com/evolbioinfo/phylodeep .
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Affiliation(s)
- J Voznica
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France.
- Université de Paris, Paris, France.
- Institut de Biologie de l'École Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, Paris, France.
| | - A Zhukova
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France.
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France.
- Institut Pasteur, Université Paris Cité, Epidemiology and Modelling of Antibiotic Evasion, Paris, France.
- Université Paris-Saclay, UVSQ, Inserm, CESP, Villejuif, France.
| | - V Boskova
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - E Saulnier
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
| | - F Lemoine
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - M Moslonka-Lefebvre
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
| | - O Gascuel
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France.
- Institut de Systématique, Evolution, Biodiversité (UMR 7205 - CNRS, Muséum National d'Histoire Naturelle, SU, EPHE, UA), Paris, France.
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14
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A vectorial tree distance measure. Sci Rep 2022; 12:5256. [PMID: 35347186 PMCID: PMC8960910 DOI: 10.1038/s41598-022-08360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/28/2022] [Indexed: 11/08/2022] Open
Abstract
A vectorial distance measure for trees is presented. Given two trees, we define a Tree-Alignment (T-Alignment). We T-align the trees from their centers outwards, starting from the root-branches, to make the next level as similar as possible. The algorithm is recursive; condition on the T-alignment of the root-branches we T-align the sub-branches, thereafter each T-alignment is conditioned on the previous one. We define a minimal T-alignment under a lexicographic order which follows the intuition that the differences between the two trees constitutes a vector. Given such a minimal T-alignment, the difference in the number of branches calculated at any level defines the entry of the distance vector at that level. We compare our algorithm to other well-known tree distance measures in the task of clustering sets of phylogenetic trees. We use the TreeSimGM simulator for generating stochastic phylogenetic trees. The vectorial tree distance (VTD) can successfully separate symmetric from asymmetric trees, and hierarchical from non-hierarchical trees. We also test the algorithm as a classifier of phylogenetic trees extracted from two members of the fungi kingdom, mushrooms and mildews, thus showimg that the algorithm can separate real world phylogenetic trees. The Matlab code can be accessed via: https://gitlab.com/avner.priel/vectorial-tree-distance .
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15
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Abstract
Upon infection, DNA viruses can be sensed by pattern recognition receptors (PRRs), leading to the activation of type I and III interferons to block infection. Therefore, viruses must inhibit these signaling pathways, avoid being detected, or both. Papillomavirus virions are trafficked from early endosomes to the Golgi apparatus and wait for the onset of mitosis to complete nuclear entry. This unique subcellular trafficking strategy avoids detection by cytoplasmic PRRs, a property that may contribute to the establishment of infection. However, as the capsid uncoats within acidic endosomal compartments, the viral DNA may be exposed to detection by Toll-like receptor 9 (TLR9). In this study, we characterized two new papillomaviruses from bats and used molecular archeology to demonstrate that their genomes altered their nucleotide compositions to avoid detection by TLR9, providing evidence that TLR9 acts as a PRR during papillomavirus infection. Furthermore, we showed that TLR9, like other components of the innate immune system, is under evolutionary selection in bats, providing the first direct evidence for coevolution between papillomaviruses and their hosts. Finally, we demonstrated that the cancer-associated human papillomaviruses show a reduction in CpG dinucleotides within a TLR9 recognition complex.
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16
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OUP accepted manuscript. Syst Biol 2022; 71:1378-1390. [DOI: 10.1093/sysbio/syac008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 11/12/2022] Open
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17
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Chindelevitch L, Hayati M, Poon AFY, Colijn C. Network science inspires novel tree shape statistics. PLoS One 2021; 16:e0259877. [PMID: 34941890 PMCID: PMC8699983 DOI: 10.1371/journal.pone.0259877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 10/28/2021] [Indexed: 11/18/2022] Open
Abstract
The shape of phylogenetic trees can be used to gain evolutionary insights. A tree’s shape specifies the connectivity of a tree, while its branch lengths reflect either the time or genetic distance between branching events; well-known measures of tree shape include the Colless and Sackin imbalance, which describe the asymmetry of a tree. In other contexts, network science has become an important paradigm for describing structural features of networks and using them to understand complex systems, ranging from protein interactions to social systems. Network science is thus a potential source of many novel ways to characterize tree shape, as trees are also networks. Here, we tailor tools from network science, including diameter, average path length, and betweenness, closeness, and eigenvector centrality, to summarize phylogenetic tree shapes. We thereby propose tree shape summaries that are complementary to both asymmetry and the frequencies of small configurations. These new statistics can be computed in linear time and scale well to describe the shapes of large trees. We apply these statistics, alongside some conventional tree statistics, to phylogenetic trees from three very different viruses (HIV, dengue fever and measles), from the same virus in different epidemiological scenarios (influenza A and HIV) and from simulation models known to produce trees with different shapes. Using mutual information and supervised learning algorithms, we find that the statistics adapted from network science perform as well as or better than conventional statistics. We describe their distributions and prove some basic results about their extreme values in a tree. We conclude that network science-based tree shape summaries are a promising addition to the toolkit of tree shape features. All our shape summaries, as well as functions to select the most discriminating ones for two sets of trees, are freely available as an R package at http://github.com/Leonardini/treeCentrality.
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Affiliation(s)
- Leonid Chindelevitch
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
- * E-mail:
| | - Maryam Hayati
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Art F. Y. Poon
- Department of Pathology & Laboratory Medicine, University of Western Ontario, London, ON, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
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18
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Lewitus E, Sanders-Buell E, Bose M, O'Sullivan AM, Poltavee K, Li Y, Bai H, Mdluli T, Donofrio G, Slike B, Zhao H, Wong K, Chen L, Miller S, Lee J, Ahani B, Lepore S, Muhammad S, Grande R, Tran U, Dussupt V, Mendez-Rivera L, Nitayaphan S, Kaewkungwal J, Pitisuttithum P, Rerks-Ngarm S, O'Connell RJ, Janes H, Gilbert PB, Gramzinski R, Vasan S, Robb ML, Michael NL, Krebs SJ, Herbeck JT, Edlefsen PT, Mullins JI, Kim JH, Tovanabutra S, Rolland M. RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection. Virus Evol 2021; 7:veab057. [PMID: 34532060 PMCID: PMC8438874 DOI: 10.1093/ve/veab057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 02/01/2023] Open
Abstract
The scale of the HIV-1 epidemic underscores the need for a vaccine. The multitude of circulating HIV-1 strains together with HIV-1’s high evolvability hints that HIV-1 could adapt to a future vaccine. Here, we wanted to investigate the effect of vaccination on the evolution of the virus post-breakthrough infection. We analyzed 2,635 HIV-1 env sequences sampled up to a year post-diagnosis from 110 vaccine and placebo participants who became infected in the RV144 vaccine efficacy trial. We showed that the Env signature sites that were previously identified to distinguish vaccine and placebo participants were maintained over time. In addition, fewer sites were under diversifying selection in the vaccine group than in the placebo group. These results indicate that HIV-1 would possibly adapt to a vaccine upon its roll-out.
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Affiliation(s)
- Eric Lewitus
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | | | - Meera Bose
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | | | - Kultida Poltavee
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Yifan Li
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Hongjun Bai
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Thembi Mdluli
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Gina Donofrio
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Bonnie Slike
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Hong Zhao
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Kim Wong
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Lennie Chen
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Shana Miller
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Jenica Lee
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Bahar Ahani
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Steven Lepore
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Sevan Muhammad
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Rebecca Grande
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Ursula Tran
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Vincent Dussupt
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | | | - Sorachai Nitayaphan
- US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Jaranit Kaewkungwal
- US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | - Robert J O'Connell
- US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Holly Janes
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Peter B Gilbert
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Robert Gramzinski
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Sandhya Vasan
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Merlin L Robb
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Nelson L Michael
- Center for Infectious Disease Research, WRAIR, Silver Spring, MD 20910, USA
| | - Shelly J Krebs
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Paul T Edlefsen
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Jerome H Kim
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | | | - Morgane Rolland
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
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19
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Danesh G, Virlogeux V, Ramière C, Charre C, Cotte L, Alizon S. Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data. PLoS Pathog 2021; 17:e1009916. [PMID: 34520487 PMCID: PMC8462723 DOI: 10.1371/journal.ppat.1009916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 09/24/2021] [Accepted: 08/25/2021] [Indexed: 12/27/2022] Open
Abstract
Opioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having sex with men (MSM) has recently arisen as a significant public health concern. The fact that the virus is transmitting in a heterogeneous population, with different transmission routes, makes prevalence and incidence rates poorly informative. However, additional insights can be gained by analyzing virus phylogenies inferred from dated genetic sequence data. By combining a phylodynamics approach based on Approximate Bayesian Computation (ABC) and an original transmission model, we estimate key epidemiological parameters of an ongoing HCV epidemic among MSMs in Lyon (France). We show that this new epidemic is largely independent of the previously observed non-MSM HCV epidemics and that its doubling time is ten times lower (0.44 years versus 4.37 years). These results have practical implications for HCV control and illustrate the additional information provided by virus genomics in public health.
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Affiliation(s)
- Gonché Danesh
- MIVEGEC, CNRS, IRD, Université de Montpellier – Montpellier, France
| | - Victor Virlogeux
- Clinical Research Center, Croix-Rousse Hospital, Hospices Civils de Lyon – Lyon, France
| | - Christophe Ramière
- Virology Laboratory, Croix-Rousse Hospital, Hospices Civils de Lyon – Lyon, France
| | - Caroline Charre
- Virology Laboratory, Croix-Rousse Hospital, Hospices Civils de Lyon – Lyon, France
| | - Laurent Cotte
- Infectious Diseases Department, Croix-Rousse Hospital, Hospices Civils de Lyon – Lyon, France
| | - Samuel Alizon
- MIVEGEC, CNRS, IRD, Université de Montpellier – Montpellier, France
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20
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Aduse-Poku K, van Bergen E, Sáfián S, Collins SC, Etienne RS, Herrera-Alsina L, Brakefield PM, Brattström O, Lohman DJ, Wahlberg N. Miocene Climate and Habitat Change Drove Diversification in Bicyclus, Africa's Largest Radiation of Satyrine Butterflies. Syst Biol 2021; 71:570-588. [PMID: 34363477 PMCID: PMC9016770 DOI: 10.1093/sysbio/syab066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/14/2022] Open
Abstract
Compared to other regions, the drivers of diversification in Africa are poorly understood. We studied a radiation of insects with over 100 species occurring in a wide range of habitats across the Afrotropics to investigate the fundamental evolutionary processes and geological events that generate and maintain patterns of species richness on the continent. By investigating the evolutionary history of Bicyclus butterflies within a phylogenetic framework, we inferred the group's origin at the Oligo-Miocene boundary from ancestors in the Congolian rainforests of central Africa. Abrupt climatic fluctuations during the Miocene (ca. 19-17 Ma) likely fragmented ancestral populations, resulting in at least eight early-divergent lineages. Only one of these lineages appears to have diversified during the drastic climate and biome changes of the early Miocene, radiating into the largest group of extant species. The other seven lineages diversified in forest ecosystems during the late Miocene and Pleistocene when climatic conditions were more favourable-warmer and wetter. Our results suggest changing Neogene climate, uplift of eastern African orogens, and biotic interactions might have had different effects on the various subclades of Bicyclus, producing one of the most spectacular butterfly radiations in Africa.
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Affiliation(s)
- Kwaku Aduse-Poku
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK.,Biology Department, University of Richmond, Richmond, 138 UR Drive, USA.,Department of Life and Earth Sciences, Perimeter College, Georgia State University, USA
| | - Erik van Bergen
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK.,Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Szabolcs Sáfián
- Institute of Silviculture and Forest Protection, University of Sopron, Sopron, Hungary
| | - Steve C Collins
- African Butterfly Research Institute, P.O. Box 14308, 0800 Westlands, Nairobi, Kenya
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, 9700 CC Groningen, The Netherlands
| | | | - Paul M Brakefield
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK
| | - Oskar Brattström
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK.,African Butterfly Research Institute, P.O. Box 14308, 0800 Westlands, Nairobi, Kenya.,University of Glasgow, School of Life Sciences, Glasgow, Scotland, UK.,University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Glasgow, Scotland, UK
| | - David J Lohman
- Biology Department, City College of New York, City University of New York, USA.,Ph.D. Program in Biology, Graduate Center, City University of New York, NY, USA.,Entomology Section, National Museum of Natural History, Manila, 1000, Philippines
| | - Niklas Wahlberg
- Department of Biology, Lund University, Sölvegatan35, SE-223, 62 Lund, Sweden
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21
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Barthelemy E, Fortunel C, Jaunatre M, Munoz F. Imprints of Past Habitat Area Reduction on Extant Taxonomic, Functional, and Phylogenetic Composition. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.634413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Past environmental changes have shaped the evolutionary and ecological diversity of extant organisms. Specifically, climatic fluctuations have made environmental conditions alternatively common or rare over time. Accordingly, most taxa have undergone restriction of their distribution to local refugia during habitat contraction, from which they could expand when suitable habitat became more common. Assessing how past restrictions in refugia have shaped species distributions and genetic diversity has motivated much research in evolutionary biology and biogeography. But there is still lack of clear synthesis on whether and how the taxonomic, functional and phylogenetic composition of extant multispecies assemblages retains the imprint of past restriction in refugia. We devised an original eco-evolutionary model to investigate the temporal dynamics of a regional species pool inhabiting a given habitat today, and which have experienced habitat reduction in the past. The model includes three components: (i) a demographic component driving stochastic changes in population sizes and extinctions due to habitat availability, (ii) a mutation and speciation component representing how divergent genotypes emerge and define new species over time, and (iii) a trait evolution component representing how trait values have changed across descendants over time. We used this model to simulate dynamics of multispecies assemblages that occupied a restricted refugia in the past and could expand their distribution subsequently. We characterized the past restriction in refugia in terms of two parameters representing the ending time of past refugia, and the extent of habitat restriction in the refugia. We characterized extant patterns of taxonomic, functional and phylogenetic diversity depending on these parameters. We found that extant relative abundances reflect the lasting influence of more recent refugia on demographic dynamics, while phylogenetic composition reflects the influence of more ancient habitat change. Extant functional diversity depends on the interplay between diversification dynamics and trait evolution, offering new options to jointly infer current trait adaptation and past trait evolution dynamics.
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22
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Richter H. Spectral analysis of transient amplifiers for death-birth updating constructed from regular graphs. J Math Biol 2021; 82:61. [PMID: 33993365 PMCID: PMC8126557 DOI: 10.1007/s00285-021-01609-y] [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: 01/18/2021] [Revised: 03/31/2021] [Accepted: 04/19/2021] [Indexed: 11/24/2022]
Abstract
A central question of evolutionary dynamics on graphs is whether or not a mutation introduced in a population of residents survives and eventually even spreads to the whole population, or becomes extinct. The outcome naturally depends on the fitness of the mutant and the rules by which mutants and residents may propagate on the network, but arguably the most determining factor is the network structure. Some structured networks are transient amplifiers. They increase for a certain fitness range the fixation probability of beneficial mutations as compared to a well-mixed population. We study a perturbation method for identifying transient amplifiers for death–birth updating. The method involves calculating the coalescence times of random walks on graphs and finding the vertex with the largest remeeting time. If the graph is perturbed by removing an edge from this vertex, there is a certain likelihood that the resulting perturbed graph is a transient amplifier. We test all pairwise nonisomorphic regular graphs up to a certain order and thus cover the whole structural range expressible by these graphs. For cubic and quartic regular graphs we find a sufficiently large number of transient amplifiers. For these networks we carry out a spectral analysis and show that the graphs from which transient amplifiers can be constructed share certain structural properties. Identifying spectral and structural properties may promote finding and designing such networks.
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Affiliation(s)
- Hendrik Richter
- HTWK Leipzig University of Applied Sciences, Leipzig, Germany.
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23
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Schrago CG, Barzilai LP. Challenges in estimating virus divergence times in short epidemic timescales with special reference to the evolution of SARS-CoV-2 pandemic. Genet Mol Biol 2021; 44:e20200254. [PMID: 33570080 PMCID: PMC7869796 DOI: 10.1590/1678-4685-gmb-2020-0254] [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: 07/21/2020] [Accepted: 01/18/2021] [Indexed: 11/21/2022] Open
Abstract
The estimation of evolutionary parameters provides essential information for designing public health policies. In short time intervals, however, nucleotide substitutions are ineffective to record all complexities of virus population dynamics. In this sense, the current SARS-CoV-2 pandemic poses a challenge for evolutionary analysis. We used computer simulation to evolve populations in scenarios of varying temporal intervals to evaluate the impact of the age of an epidemic on estimates of time and geography. Before estimating virus timescales, the shape of tree topologies can be used as a proxy to assess the effectiveness of the virus phylogeny in providing accurate estimates of evolutionary parameters. In short timescales, estimates have larger uncertainty. We compared the predictions from simulations with empirical data. The tree shape of SARS-CoV-2 was closer to shorter timescales scenarios, which yielded parametric estimates with larger uncertainty, suggesting that estimates from these datasets should be evaluated cautiously. To increase the accuracy of the estimates of virus transmission times between populations, the uncertainties associated with the age estimates of both the crown and stem nodes should be communicated. We place the age of the common ancestor of the current SARS-CoV-2 pandemic in late September 2019, corroborating an earlier emergence of the virus.
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Affiliation(s)
- Carlos G. Schrago
- Universidade Federal do Rio de Janeiro, Departamento de
Genética, Rio de Janeiro, RJ, Brazil
| | - Lucia P. Barzilai
- Universidade Federal do Rio de Janeiro, Departamento de
Genética, Rio de Janeiro, RJ, Brazil
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24
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Dearlove B, Tovanabutra S, Owen CL, Lewitus E, Li Y, Sanders-Buell E, Bose M, O’Sullivan AM, Kijak G, Miller S, Poltavee K, Lee J, Bonar L, Harbolick E, Ahani B, Pham P, Kibuuka H, Maganga L, Nitayaphan S, Sawe FK, Kim JH, Eller LA, Vasan S, Gramzinski R, Michael NL, Robb ML, Rolland M. Factors influencing estimates of HIV-1 infection timing using BEAST. PLoS Comput Biol 2021; 17:e1008537. [PMID: 33524022 PMCID: PMC7877758 DOI: 10.1371/journal.pcbi.1008537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/11/2021] [Accepted: 11/13/2020] [Indexed: 12/15/2022] Open
Abstract
While large datasets of HIV-1 sequences are increasingly being generated, many studies rely on a single gene or fragment of the genome and few comparative studies across genes have been done. We performed genome-based and gene-specific Bayesian phylogenetic analyses to investigate how certain factors impact estimates of the infection dates in an acute HIV-1 infection cohort, RV217. In this cohort, HIV-1 diagnosis corresponded to the first RNA positive test and occurred a median of four days after the last negative test, allowing us to compare timing estimates using BEAST to a narrow window of infection. We analyzed HIV-1 sequences sampled one week, one month and six months after HIV-1 diagnosis in 39 individuals. We found that shared diversity and temporal signal was limited in acute infection, and insufficient to allow timing inferences in the shortest HIV-1 genes, thus dated phylogenies were primarily analyzed for env, gag, pol and near full-length genomes. There was no one best-fitting model across participants and genes, though relaxed molecular clocks (73% of best-fitting models) and the Bayesian skyline (49%) tended to be favored. For infections with single founders, the infection date was estimated to be around one week pre-diagnosis for env (IQR: 3–9 days) and gag (IQR: 5–9 days), whilst the genome placed it at a median of 10 days (IQR: 4–19). Multiply-founded infections proved problematic to date. Our ability to compare timing inferences to precise estimates of HIV-1 infection (within a week) highlights that molecular dating methods can be applied to within-host datasets from early infection. Nonetheless, our results also suggest caution when using uniform clock and population models or short genes with limited information content. Molecular dating using phylogenetics allows us to estimate the date of an infection from time-stamped within-host sequences alone. There are large datasets of HIV-1 sequences, but genome and gene analyses are not often performed in parallel and rarely with the possibility to compare results against a known narrow window of infection. We showed that all but the longest genes are near-clonal in acute infection, with little information for dating purposes. For infections with single founders, we estimated the eclipse phase—the time between HIV-1 exposure and the first positive diagnostic test—to last between one and two weeks using env, gag, pol and near full-length genomes. This approach could be used to narrow the date of suspected infection in ongoing clinical trials for the prevention of HIV-1 infection.
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Affiliation(s)
- Bethany Dearlove
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Christopher L. Owen
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Eric Lewitus
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Yifan Li
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Meera Bose
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Anne-Marie O’Sullivan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Gustavo Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Shana Miller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Kultida Poltavee
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Jenica Lee
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Lydia Bonar
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Elizabeth Harbolick
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Bahar Ahani
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Phuc Pham
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Lucas Maganga
- National Institute for Medical Research-Mbeya Medical Research Centre, Mbeya, Tanzania
| | | | - Fred K. Sawe
- Kenya Medical Research Institute/U.S. Army Medical Research Directorate-Africa/Kenya-Henry Jackson Foundation MRI, Kericho, Kenya
| | | | - Leigh Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Robert Gramzinski
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Nelson L. Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Merlin L. Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
- * E-mail:
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25
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Abstract
Genealogical tree modeling is essential for estimating evolutionary parameters in population genetics and phylogenetics. Recent mathematical results concerning ranked genealogies without leaf labels unlock opportunities in the analysis of evolutionary trees. In particular, comparisons between ranked genealogies facilitate the study of evolutionary processes of different organisms sampled at multiple time periods. We propose metrics on ranked tree shapes and ranked genealogies for lineages isochronously and heterochronously sampled. Our proposed tree metrics make it possible to conduct statistical analyses of ranked tree shapes and timed ranked tree shapes or ranked genealogies. Such analyses allow us to assess differences in tree distributions, quantify estimation uncertainty, and summarize tree distributions. We show the utility of our metrics via simulations and an application in infectious diseases.
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Affiliation(s)
- Jaehee Kim
- Department of Biology, Stanford University, Stanford, CA 94305
| | | | - Julia A Palacios
- Department of Statistics, Stanford University, Stanford, CA 94305;
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford, CA 94305
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26
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Dearlove B, Lewitus E, Bai H, Li Y, Reeves DB, Joyce MG, Scott PT, Amare MF, Vasan S, Michael NL, Modjarrad K, Rolland M. A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Proc Natl Acad Sci U S A 2020; 117:23652-23662. [PMID: 32868447 PMCID: PMC7519301 DOI: 10.1073/pnas.2008281117] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Many vaccine candidates focus on the Spike protein, as it is targeted by neutralizing antibodies and plays a key role in viral entry. Here we investigate the diversity seen in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences and compare it to the sequence on which most vaccine candidates are based. Using 18,514 sequences, we perform phylogenetic, population genetics, and structural bioinformatics analyses. We find limited diversity across SARS-CoV-2 genomes: Only 11 sites show polymorphisms in >5% of sequences; yet two mutations, including the D614G mutation in Spike, have already become consensus. Because SARS-CoV-2 is being transmitted more rapidly than it evolves, the viral population is becoming more homogeneous, with a median of seven nucleotide substitutions between genomes. There is evidence of purifying selection but little evidence of diversifying selection, with substitution rates comparable across structural versus nonstructural genes. Finally, the Wuhan-Hu-1 reference sequence for the Spike protein, which is the basis for different vaccine candidates, matches optimized vaccine inserts, being identical to an ancestral sequence and one mutation away from the consensus. While the rapid spread of the D614G mutation warrants further study, our results indicate that drift and bottleneck events can explain the minimal diversity found among SARS-CoV-2 sequences. These findings suggest that a single vaccine candidate should be efficacious against currently circulating lineages.
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Affiliation(s)
- Bethany Dearlove
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Eric Lewitus
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Hongjun Bai
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Yifan Li
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Daniel B Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - M Gordon Joyce
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Paul T Scott
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Mihret F Amare
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Sandhya Vasan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Nelson L Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910;
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Morgane Rolland
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910;
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910
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27
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Van Dam MH, Henderson JB, Esposito L, Trautwein M. Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction. Syst Biol 2020; 70:307-321. [PMID: 32750133 PMCID: PMC7875437 DOI: 10.1093/sysbio/syaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022] Open
Abstract
Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]
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Affiliation(s)
- Matthew H Van Dam
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA.,Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA
| | - James B Henderson
- Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA
| | - Lauren Esposito
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA.,Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA
| | - Michelle Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA.,Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA
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28
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Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes. Immunogenetics 2020; 72:279-294. [PMID: 32367185 DOI: 10.1007/s00251-020-01164-8] [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: 02/24/2020] [Accepted: 04/13/2020] [Indexed: 10/24/2022]
Abstract
Protection and neutralization of a vast array of pathogens is accomplished by the tremendous diversity of the B cell receptor (BCR) repertoire. For jawed vertebrates, this diversity is initiated via the somatic recombination of immunoglobulin (Ig) germline elements. While it is clear that the number of these germline segments differs from species to species, the extent of cross-species sequence diversity remains largely uncharacterized. Here we use extensive computational and statistical methods to investigate the sequence diversity and evolutionary relationship between Ig variable (V), diversity (D), and joining (J) germline segments across nine commonly studied species ranging from zebrafish to human. Metrics such as guanine-cytosine (GC) content showed low redundancy across Ig germline genes within a given species. Other comparisons, including amino acid motifs, evolutionary selection, and sequence diversity, revealed species-specific properties. Additionally, we showed that the germline-encoded diversity differs across antibody (recombined V-D-J) repertoires of various B cell subsets. To facilitate future comparative immunogenomics analysis, we created VDJgermlines, an R package that contains the germline sequences from multiple species. Our study informs strategies for the humanization and engineering of therapeutic antibodies.
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29
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Lewitus E, Aristide L, Morlon H. Characterizing and Comparing Phylogenetic Trait Data from Their Normalized Laplacian Spectrum. Syst Biol 2020; 69:234-248. [PMID: 31529071 DOI: 10.1093/sysbio/syz061] [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: 11/24/2018] [Revised: 09/02/2019] [Accepted: 09/10/2019] [Indexed: 11/13/2022] Open
Abstract
The dissection of the mode and tempo of phenotypic evolution is integral to our understanding of global biodiversity. Our ability to infer patterns of phenotypes across phylogenetic clades is essential to how we infer the macroevolutionary processes governing those patterns. Many methods are already available for fitting models of phenotypic evolution to data. However, there is currently no comprehensive nonparametric framework for characterizing and comparing patterns of phenotypic evolution. Here, we build on a recently introduced approach for using the phylogenetic spectral density profile (SDP) to compare and characterize patterns of phylogenetic diversification, in order to provide a framework for nonparametric analysis of phylogenetic trait data. We show how to construct the SDP of trait data on a phylogenetic tree from the normalized graph Laplacian. We demonstrate on simulated data the utility of the SDP to successfully cluster phylogenetic trait data into meaningful groups and to characterize the phenotypic patterning within those groups. We furthermore demonstrate how the SDP is a powerful tool for visualizing phenotypic space across traits and for assessing whether distinct trait evolution models are distinguishable on a given empirical phylogeny. We illustrate the approach in two empirical data sets: a comprehensive data set of traits involved in song, plumage, and resource-use in tanagers, and a high-dimensional data set of endocranial landmarks in New World monkeys. Considering the proliferation of morphometric and molecular data collected across the tree of life, we expect this approach will benefit big data analyses requiring a comprehensive and intuitive framework.
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Affiliation(s)
- Eric Lewitus
- Ecole Normale Superieure Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'Ecole Normale Superieure (IBENS) CNRS UMR 8197 INSERM U1024 46rue d'Ulm,F-75005, Paris, France.,Henry M. Jackson Foundation in support of the US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Leandro Aristide
- Ecole Normale Superieure Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'Ecole Normale Superieure (IBENS) CNRS UMR 8197 INSERM U1024 46rue d'Ulm,F-75005, Paris, France
| | - Hélène Morlon
- Ecole Normale Superieure Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'Ecole Normale Superieure (IBENS) CNRS UMR 8197 INSERM U1024 46rue d'Ulm,F-75005, Paris, France
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30
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Rolland M, Tovanabutra S, Dearlove B, Li Y, Owen CL, Lewitus E, Sanders-Buell E, Bose M, O’Sullivan A, Rossenkhan R, Labuschagne JPL, Edlefsen PT, Reeves DB, Kijak G, Miller S, Poltavee K, Lee J, Bonar L, Harbolick E, Ahani B, Pham P, Kibuuka H, Maganga L, Nitayaphan S, Sawe FK, Eller LA, Gramzinski R, Kim JH, Michael NL, Robb ML. Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand. PLoS Pathog 2020; 16:e1008179. [PMID: 32027734 PMCID: PMC7004303 DOI: 10.1371/journal.ppat.1008179] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/01/2019] [Indexed: 01/21/2023] Open
Abstract
Most HIV-1 infected individuals do not know their infection dates. Precise infection timing is crucial information for studies that document transmission networks or drug levels at infection. To improve infection timing, we used the prospective RV217 cohort where the window when plasma viremia becomes detectable is narrow: the last negative visit occurred a median of four days before the first detectable HIV-1 viremia with an RNA test, referred below as diagnosis. We sequenced 1,280 HIV-1 genomes from 39 participants at a median of 4, 32 and 170 days post-diagnosis. HIV-1 infections were dated by using sequence-based methods and a viral load regression method. Bayesian coalescent and viral load regression estimated that infections occurred a median of 6 days prior to diagnosis (IQR: 9–3 and 11–4 days prior, respectively). Poisson-Fitter, which analyzes the distribution of hamming distances among sequences, estimated a median of 7 days prior to diagnosis (IQR: 15–4 days) based on sequences sampled 4 days post-diagnosis, but it did not yield plausible results using sequences sampled at 32 days. Fourteen participants reported a high-risk exposure event at a median of 8 days prior to diagnosis (IQR: 12 to 6 days prior). These different methods concurred that HIV-1 infection occurred about a week before detectable viremia, corresponding to 20 days (IQR: 34–15 days) before peak viral load. Together, our methods comparison helps define a framework for future dating studies in early HIV-1 infection. HIV-1 infected individuals rarely know when they became infected but knowing when an infection occurred provides critical information regarding HIV-1 pathogenesis and epidemiology. Using a unique cohort in which infection was known to have occurred in a narrow interval, we investigated methods to estimate the timing of infections. Several methods suggested that HIV-1 infection typically occurs a median of one week before the infection can be detected by HIV-1 RNA testing. Going forward, we provide a strategy that can be used to elucidate the origin of an acute/early infection.
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Affiliation(s)
- Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
- * E-mail:
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Bethany Dearlove
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Yifan Li
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Christopher L. Owen
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Eric Lewitus
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Meera Bose
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - AnneMarie O’Sullivan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Raabya Rossenkhan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | | | - Paul T. Edlefsen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Daniel B. Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Gustavo Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Shana Miller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Kultida Poltavee
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Jenica Lee
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Lydia Bonar
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Elizabeth Harbolick
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Bahar Ahani
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Phuc Pham
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Lucas Maganga
- National Institute for Medical Research-Mbeya Medical Research Center, Mbeya, Tanzania
| | | | - Fred K. Sawe
- Kenya Medical Research Institute/U.S. Army Medical Research Directorate-Africa/Kenya-Henry Jackson Foundation MRI, Kericho, Kenya
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Robert Gramzinski
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | | | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | - Merlin L. Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
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31
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Lewitus E, Rolland M. A non-parametric analytic framework for within-host viral phylogenies and a test for HIV-1 founder multiplicity. Virus Evol 2019; 5:vez044. [PMID: 31700680 PMCID: PMC6826062 DOI: 10.1093/ve/vez044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Phylogenetics is a powerful tool for understanding the diversification dynamics of viral pathogens. Here we present an extension of the spectral density profile of the modified graph Laplacian, which facilitates the characterization of within-host molecular evolution of viruses and the direct comparison of diversification dynamics between hosts. This approach is non-parametric and therefore fast and model-free. We used simulations of within-host evolutionary scenarios to evaluate the efficiency of our approach and to demonstrate the significance of interpreting a viral phylogeny by its spectral density profile in terms of diversification dynamics. The key features that are captured by the profile are positive selection on the viral gene (or genome), temporal changes in substitution rates, mutational fitness, and time between sampling. Using sequences from individuals infected with HIV-1, we showed the utility of this approach for characterizing within-host diversification dynamics, for comparing dynamics between hosts, and for charting disease progression in infected individuals sampled over multiple years. We furthermore propose a heuristic test for assessing founder heterogeneity, which allows us to classify infections with single and multiple HIV-1 founder viruses. This non-parametric approach can be a valuable complement to existing parametric approaches.
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Affiliation(s)
- Eric Lewitus
- U.S. Military HIV Research Program (MHRP), WRAIR, 503 Robert Grant Avenue, Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr, Bethesda, MD, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program (MHRP), WRAIR, 503 Robert Grant Avenue, Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr, Bethesda, MD, USA
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32
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Morales AE, Ruedi M, Field K, Carstens BC. Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats,
Myotis
*. Evolution 2019; 73:2263-2280. [DOI: 10.1111/evo.13849] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Ariadna E. Morales
- Department of Evolution, Ecology and Organismal Biology Ohio State University Columbus Ohio 43210
- Department of Mammalogy and Herpetology, Division of Vertebrate Zoology American Museum of Natural History New York New York 10024
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology Natural History Museum of Geneva Geneva 1208 Switzerland
| | - Kathryn Field
- Department of Evolution, Ecology and Organismal Biology Ohio State University Columbus Ohio 43210
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology Ohio State University Columbus Ohio 43210
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33
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Avino M, Ng GT, He Y, Renaud MS, Jones BR, Poon AFY. Tree shape-based approaches for the comparative study of cophylogeny. Ecol Evol 2019; 9:6756-6771. [PMID: 31312429 PMCID: PMC6618157 DOI: 10.1002/ece3.5185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/21/2019] [Accepted: 03/29/2019] [Indexed: 12/17/2022] Open
Abstract
Cophylogeny is the congruence of phylogenetic relationships between two different groups of organisms due to their long-term interaction. We investigated the use of tree shape distance measures to quantify the degree of cophylogeny. We implemented a reverse-time simulation model of pathogen phylogenies within a fixed host tree, given cospeciation probability, host switching, and pathogen speciation rates. We used this model to evaluate 18 distance measures between host and pathogen trees including two kernel distances that we developed for labeled and unlabeled trees, which use branch lengths and accommodate different size trees. Finally, we used these measures to revisit published cophylogenetic studies, where authors described the observed associations as representing a high or low degree of cophylogeny. Our simulations demonstrated that some measures are more informative than others with respect to specific coevolution parameters especially when these did not assume extreme values. For real datasets, trees' associations projection revealed clustering of high concordance studies suggesting that investigators are describing it in a consistent way. Our results support the hypothesis that measures can be useful for quantifying cophylogeny. This motivates their usage in the field of coevolution and supports the development of simulation-based methods, i.e., approximate Bayesian computation, to estimate the underlying coevolutionary parameters.
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Affiliation(s)
- Mariano Avino
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
| | - Garway T Ng
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
| | - Yiying He
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
| | - Mathias S Renaud
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
| | - Bradley R Jones
- BC Centre for Excellence in HIV/AIDS Vancouver British Columbia Canada
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada.,Department of Applied Mathematics Western University London Ontario Canada
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34
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Burbrink FT, Ruane S, Kuhn A, Rabibisoa N, Randriamahatantsoa B, Raselimanana AP, Andrianarimalala MSM, Cadle JE, Lemmon AR, Lemmon EM, Nussbaum RA, Jones LN, Pearson R, Raxworthy CJ. The Origins and Diversification of the Exceptionally Rich Gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar. Syst Biol 2019; 68:918-936. [DOI: 10.1093/sysbio/syz026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Processes leading to spectacular diversity of both form and species on islands have been well-documented under island biogeography theory, where distance from source and island size are key factors determining immigration and extinction resistance. But far less understood are the processes governing in situ diversification on the world’s mega islands, where large and isolated land masses produced morphologically distinct radiations from related taxa on continental regions. Madagascar has long been recognized as a natural laboratory due to its isolation, lack of influence from adjacent continents, and diversification of spectacular vertebrate radiations. However, only a handful of studies have examined rate shifts of in situ diversification for this island. Here, we examine rates of diversification in the Malagasy snakes of the family Pseudoxyrhophiinae (gemsnakes) to understand if rates of speciation were initially high, enhanced by diversification into distinct biomes, and associated with key dentition traits. Using a genomic sequence-capture data set for 366 samples, we determine that all previously described and newly discovered species are delimitable and therefore useful candidates for understanding diversification trajectories through time. Our analysis detected no shifts in diversification rate between clades or changes in biome or dentition type. Remarkably, we demonstrate that rates of diversification of the gemsnake radiation, which originated in Madagascar during the early Miocene, remained steady throughout the Neogene. However, we do detect a significant slowdown in diversification during the Pleistocene. We also comment on the apparent paradox where most living species originated in the Pleistocene, despite diversification rates being substantially higher during the earlier 15 myr.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
| | - Sara Ruane
- Department of Biological Sciences, 206 Boyden Hall, Rutgers University-Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Arianna Kuhn
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
- Department of Biology, The Graduate School and University Center, The City University of New York, 365 Fifth Ave., New York, NY 10016, USA
| | - Nirhy Rabibisoa
- Mention Sciences de la Vie et de l’Environnement, Faculté des Sciences, de Technologies et de l’Environnement, Université de Mahajanga, Campus Universitaire d’Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Bernard Randriamahatantsoa
- Mention Sciences de la Vie et de l’Environnement, Faculté des Sciences, de Technologies et de l’Environnement, Université de Mahajanga, Campus Universitaire d’Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Achille P Raselimanana
- Mention: Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, BP 906, Antananarivo 101, Madagascar
| | - Mamy S M Andrianarimalala
- Mention: Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, BP 906, Antananarivo 101, Madagascar
| | - John E Cadle
- Department of Biology, East Georgia State College, Swainsboro, GA 30401, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Ronald A Nussbaum
- Division of Reptiles and Amphibians, Museum of Zoology, Research Museums Center, 3600 Varsity Drive, University of Michigan, Ann Arbor, MI 48108, USA
| | - Leonard N Jones
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Richard Pearson
- Centre for Biodiversity & Environment Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Christopher J Raxworthy
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
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35
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Lewitus E, Bittner L, Malviya S, Bowler C, Morlon H. Clade-specific diversification dynamics of marine diatoms since the Jurassic. Nat Ecol Evol 2018; 2:1715-1723. [PMID: 30349092 PMCID: PMC6217985 DOI: 10.1038/s41559-018-0691-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023]
Abstract
Diatoms are one of the most abundant and diverse groups of phytoplankton and play a major role in marine ecosystems and the Earth's biogeochemical cycles. Here we combine DNA metabarcoding data from the Tara Oceans expedition with palaeoenvironmental data and phylogenetic models of diversification to analyse the diversity dynamics of marine diatoms. We reveal a primary effect of variation in carbon dioxide partial pressure (pCO2) on early diatom diversification, followed by a major burst of diversification in the late Eocene epoch, after which diversification is chiefly affected by sea level, an influx of silica availability and competition with other planktonic groups. Our results demonstrate a remarkable heterogeneity of diversification dynamics across diatoms and suggest that a changing climate will favour some clades at the expense of others.
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Affiliation(s)
- Eric Lewitus
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, Université PSL, Paris, France.
- US Military HIV Research Program, WRAIR, Silver Spring, MD, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
| | - Lucie Bittner
- Sorbonne Université, Université des Antilles, CNRS, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Paris, France
| | - Shruti Malviya
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, Université PSL, Paris, France
- Tata Institute of Fundamental Research, Bangalore, India
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, Université PSL, Paris, France
| | - Hélène Morlon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, Université PSL, Paris, France
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36
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Topological assessment of metabolic networks reveals evolutionary information. Sci Rep 2018; 8:15918. [PMID: 30374088 PMCID: PMC6206017 DOI: 10.1038/s41598-018-34163-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 10/07/2018] [Indexed: 12/03/2022] Open
Abstract
Evolutionary information was inferred from the topology of metabolic networks corresponding to 17 plant species belonging to major plant lineages Chlorophytes, Bryophytes, Lycophytes and Angiosperms. The plant metabolic networks were built using the substrate-product network modeling based on the metabolic reactions available on the PlantCyc database (version 9.5), from which their local topological properties such as degree, in-degree, out-degree, clustering coefficient, hub-score, authority-score, local efficiency, betweenness and eigencentrality were measured. The topological measurements corresponding to each metabolite within the networks were considered as a set of metabolic characters to compound a feature vector representing each plant. Our results revealed that some local topological characters are able to discern among plant kinships, since similar phylogenies were found when comparing dendrograms obtained by topological metrics to the one obtained by DNA sequences of chloroplast genes. Furthermore, we also found that even a smaller number of metabolic characters is able to separate among major clades with high bootstrap support (BS > 95), while for some suborders a bigger content has been required.
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37
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Yermanos AD, Dounas AK, Stadler T, Oxenius A, Reddy ST. Tracing Antibody Repertoire Evolution by Systems Phylogeny. Front Immunol 2018; 9:2149. [PMID: 30333820 PMCID: PMC6176079 DOI: 10.3389/fimmu.2018.02149] [Citation(s) in RCA: 16] [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: 05/22/2018] [Accepted: 08/30/2018] [Indexed: 01/03/2023] Open
Abstract
Antibody evolution studies have been traditionally limited to either tracing a single clonal lineage (B cells derived from a single V-(D)-J recombination) over time or examining bulk functionality changes (e.g., tracing serum polyclonal antibody proteins). Studying a single B cell disregards the majority of the humoral immune response, whereas bulk functional studies lack the necessary resolution to analyze the co-existing clonal diversity. Recent advances in high-throughput sequencing (HTS) technologies and bioinformatics have made it possible to examine multiple co-evolving antibody monoclonal lineages within the context of a single repertoire. A plethora of accompanying methods and tools have been introduced in hopes of better understanding how pathogen presence dictates the global evolution of the antibody repertoire. Here, we provide a comprehensive summary of the tremendous progress of this newly emerging field of systems phylogeny of antibody responses. We present an overview encompassing the historical developments of repertoire phylogenetics, state-of-the-art tools, and an outlook on the future directions of this fast-advancing and promising field.
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Affiliation(s)
- Alexander Dimitri Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Andreas Kevin Dounas
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Annette Oxenius
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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38
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Eberle J, Dimitrov D, Valdez-Mondragón A, Huber BA. Microhabitat change drives diversification in pholcid spiders. BMC Evol Biol 2018; 18:141. [PMID: 30231864 PMCID: PMC6145181 DOI: 10.1186/s12862-018-1244-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/16/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Microhabitat changes are thought to be among the main drivers of diversification. However, this conclusion is mostly based on studies on vertebrates. Here, we investigate the influence of microhabitat on diversification rates in pholcid spiders (Araneae, Pholcidae). Diversification analyses were conducted in the framework of the largest molecular phylogeny of pholcid spiders to date based on three nuclear and three mitochondrial loci from 600 species representing more than 85% of the currently described pholcid genera. RESULTS Assessments of ancestral microhabitat revealed frequent evolutionary change. In particular, within the largest subfamily Pholcinae, numerous changes from near-ground habitats towards leaves and back were found. In general, taxa occupying leaves and large sheltered spaces had higher diversification rates than ground-dwelling taxa. Shifts in speciation rate were found in leaf- and space-dwelling taxa. CONCLUSIONS Our analyses result in one of the most comprehensive phylogenies available for a major spider family and provide a framework for any subsequent studies of pholcid spider biology. Diversification analyses strongly suggest that microhabitat is an important factor influencing diversification patterns in pholcid spiders.
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Affiliation(s)
- Jonas Eberle
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
| | - Dimitar Dimitrov
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway
- Department of Natural History, University Museum of Bergen, University of Bergen, PO Box 7800, NO-5020 Bergen, Norway
| | - Alejandro Valdez-Mondragón
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
- Instituto de Biologia UNAM, sede Tlaxcala. Contiguo FES-Zaragoza Campus III, Ex Fábrica San Manuel de Morcom s/n, San Miguel Contla, Municipio de Santa Cruz Tlaxcala, C.P, 90640 Tlaxcala, Mexico
| | - Bernhard A. Huber
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
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Rabosky DL. BAMM at the court of false equivalency: A response to Meyer and Wiens. Evolution 2018; 72:2246-2256. [DOI: 10.1111/evo.13566] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/14/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Daniel L. Rabosky
- Museum of ZoologyUniversity of Michigan Ann Arbor MI 48109‐1079
- Department of Ecology and Evolutionary BiologyUniversity of Michigan Ann Arbor MI 48109‐1079
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40
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Navaud O, Barbacci A, Taylor A, Clarkson JP, Raffaele S. Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens. Mol Ecol 2018; 27:1309-1323. [PMID: 29421852 PMCID: PMC5900718 DOI: 10.1111/mec.14523] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 01/07/2023]
Abstract
The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite cophylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events and the highest proportion of broad host range species. Our findings suggest that the emergence of broad host range fungal pathogens results largely from host jumps, as previously reported for oomycete parasites, probably combined with low speciation rates. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.
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Affiliation(s)
- Olivier Navaud
- LIPM, Université de Toulouse, INRA, CNRSCastanet‐TolosanFrance
| | - Adelin Barbacci
- LIPM, Université de Toulouse, INRA, CNRSCastanet‐TolosanFrance
| | - Andrew Taylor
- Warwick Crop CentreSchool of Life SciencesUniversity of WarwickCoventryUK
| | - John P. Clarkson
- Warwick Crop CentreSchool of Life SciencesUniversity of WarwickCoventryUK
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41
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Knowles LL, Huang H, Sukumaran J, Smith SA. A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories. AMERICAN JOURNAL OF BOTANY 2018; 105:376-384. [PMID: 29710372 DOI: 10.1002/ajb2.1064] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/30/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Discordant gene trees are commonly encountered when sequences from thousands of loci are applied to estimate phylogenetic relationships. Several processes contribute to this discord. Yet, we have no methods that jointly model different sources of conflict when estimating phylogenies. An alternative to analyzing entire genomes or all the sequenced loci is to identify a subset of loci for phylogenetic analysis. If we can identify data partitions that are most likely to reflect descent from a common ancestor (i.e., discordant loci that indeed reflect incomplete lineage sorting [ILS], as opposed to some other process, such as lateral gene transfer [LGT]), we can analyze this subset using powerful coalescent-based species-tree approaches. METHODS Test data sets were simulated where discord among loci could arise from ILS and LGT. Data sets where analyzed using the newly developed program CLASSIPHY (Huang et al., ) to assess whether our ability to distinguish the cause of discord among loci varied when ILS and LGT occurred in the recent versus deep past and whether the accuracy of these inferences were affected by the mutational process. KEY RESULTS We show that accuracy of probabilistic classification of individual loci by the cause of discord differed when ILS and LGT events occurred more recently compared with the distant past and that the signal-to-noise ratio arising from the mutational process contributes to difficulties in inferring LGT data partitions. CONCLUSIONS We discuss our findings in terms of the promise and limitations of identifying subsets of loci for species-tree inference that will not violate the underlying coalescent model (i.e., data partitions in which ILS, and not LGT, contributes to discord). We also discuss the empirical implications of our work given the many recalcitrant nodes in the tree of life (e.g., origins of angiosperms, amniotes, or Neoaves), and recent arguments for concatenating loci.
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Affiliation(s)
- L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI, 48109-1079, USA
| | - Huateng Huang
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI, 48109-1079, USA
| | - Jeet Sukumaran
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI, 48109-1079, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI, 48109-1079, USA
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Miho E, Yermanos A, Weber CR, Berger CT, Reddy ST, Greiff V. Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires. Front Immunol 2018; 9:224. [PMID: 29515569 PMCID: PMC5826328 DOI: 10.3389/fimmu.2018.00224] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/26/2018] [Indexed: 12/21/2022] Open
Abstract
The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires, thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity and to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic, and (iv) machine learning methods applied to dissect, quantify, and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology toward coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.
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Affiliation(s)
- Enkelejda Miho
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- aiNET GmbH, ETH Zürich, Basel, Switzerland
| | - Alexander Yermanos
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Cédric R. Weber
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christoph T. Berger
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
- Department of Internal Medicine, Clinical Immunology, University Hospital Basel, Basel, Switzerland
| | - Sai T. Reddy
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Victor Greiff
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Department of Immunology, University of Oslo, Oslo, Norway
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43
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Colijn C, Plazzotta G. A Metric on Phylogenetic Tree Shapes. Syst Biol 2018; 67:113-126. [PMID: 28472435 PMCID: PMC5790134 DOI: 10.1093/sysbio/syx046] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 04/11/2017] [Indexed: 11/15/2022] Open
Abstract
The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterization to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical versus USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We describe several metrics based on the same core characterization, and illustrate how to extend the metric to incorporate trees’ branch lengths or other features such as overall imbalance. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average tree shapes.
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Affiliation(s)
- C Colijn
- Department of Mathematics, Imperial College, 180 Queen's Gate, London SW7 2AZ, UK
| | - G Plazzotta
- Department of Mathematics, Imperial College, 180 Queen's Gate, London SW7 2AZ, UK
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Rabosky DL, Mitchell JS, Chang J. Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models. Syst Biol 2017; 66:477-498. [PMID: 28334223 PMCID: PMC5790138 DOI: 10.1093/sysbio/syx037] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 11/13/2022] Open
Abstract
Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore et al. (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (i) BAMM's likelihood function is incorrect, because it does not account for unobserved rate shifts; (ii) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (iii) diversification rate estimates from BAMM are unreliable. Here, we show that these and other conclusions from MEA are generally incorrect or unjustified. We first demonstrate that MEA's numerical assessment of the BAMM likelihood is compromised by their use of an invalid likelihood function. We then show that "unobserved rate shifts" appear to be irrelevant for biologically plausible parameterizations of the diversification process. We find that the purportedly extreme prior sensitivity reported by MEA cannot be replicated with standard usage of BAMM v2.5, or with any other version when conventional Bayesian model selection is performed. Finally, we demonstrate that BAMM performs very well at estimating diversification rate variation across the ${\sim}$20% of simulated trees in MEA's data set for which it is theoretically possible to infer rate shifts with confidence. Due to ascertainment bias, the remaining 80% of their purportedly variable-rate phylogenies are statistically indistinguishable from those produced by a constant-rate birth-death process and were thus poorly suited for the summary statistics used in their performance assessment. We demonstrate that inferences about diversification rates have been accurate and consistent across all major previous releases of the BAMM software. We recognize an acute need to address the theoretical foundations of rate-shift models for phylogenetic trees, and we expect BAMM and other modeling frameworks to improve in response to mathematical and computational innovations. However, we remain optimistic that that the imperfect tools currently available to comparative biologists have provided and will continue to provide important insights into the diversification of life on Earth.
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Affiliation(s)
- Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jonathan S. Mitchell
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jonathan Chang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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Lewitus É, Morlon H. [The rules of biodiversity in deep time]. Med Sci (Paris) 2017; 33:123-126. [PMID: 28240199 DOI: 10.1051/medsci/20173302003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Éric Lewitus
- Institut de Biologie, École Normale Supérieure, 46, rue d'Ulm, 75005 Paris, France
| | - Hélène Morlon
- Institut de Biologie, École Normale Supérieure, 46, rue d'Ulm, 75005 Paris, France
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Affiliation(s)
- Pablo A. Goloboff
- Unidad Ejecutora Lillo; Fundación Miguel Lillo; CONICET; Miguel Lillo 251 4000 San Miguel de Tucumán Argentina
| | - Joan S. Arias
- Unidad Ejecutora Lillo; Fundación Miguel Lillo; CONICET; Miguel Lillo 251 4000 San Miguel de Tucumán Argentina
- Facultad de Ciencias Naturales; Universidad Nacional de Tucumán; Miguel Lillo 205 4000 San Miguel de Tucumán Argentina
| | - Claudia A. Szumik
- Unidad Ejecutora Lillo; Fundación Miguel Lillo; CONICET; Miguel Lillo 251 4000 San Miguel de Tucumán Argentina
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Abstract
Identifying modes of species diversification is fundamental to our understanding of how biodiversity changes over evolutionary time. Diversification modes are captured in species phylogenies, but characterizing the landscape of diversification has been limited by the analytical tools available for directly comparing phylogenetic trees of groups of organisms. Here, we use a novel, non-parametric approach and 214 family-level phylogenies of vertebrates representing over 500 million years of evolution to identify major diversification modes, to characterize phylogenetic space, and to evaluate the bounds and central tendencies of species diversification. We identify five principal patterns of diversification to which all vertebrate families hold. These patterns, mapped onto multidimensional space, constitute a phylogenetic space with distinct properties. Firstly, phylogenetic space occupies only a portion of all possible tree space, showing family-level phylogenies to be constrained to a limited range of diversification patterns. Secondly, the geometry of phylogenetic space is delimited by quantifiable trade-offs in tree size and the heterogeneity and stem-to-tip distribution of branching events. These trade-offs are indicative of the instability of certain diversification patterns and effectively bound speciation rates (for successful clades) within upper and lower limits. Finally, both the constrained range and geometry of phylogenetic space are established by the differential effects of macroevolutionary processes on patterns of diversification. Given these properties, we show that the average path through phylogenetic space over evolutionary time traverses several diversification stages, each of which is defined by a different principal pattern of diversification and directed by a different macroevolutionary process. The identification of universal patterns and natural constraints to diversification provides a foundation for understanding the deep-time evolution of biodiversity. A meta-analysis of 214 family-level vertebrate trees containing more than 12,000 species and spanning 500 million years of evolution reveals general patterns of species diversification and the constraints acting on them. Are there universal laws in the evolution of biodiversity? Why do some clades go extinct and others flourish? These questions are fundamental to our understanding of present-day biodiversity. In a meta-analysis of nearly 12,000 species spanning ~500 million years of evolution, we find that there are five principal patterns of diversification to which all vertebrate families hold, and that these patterns can be mapped into a multidimensional phylogenetic space. Importantly, because certain diversification patterns invariably lead to extinction, clades do not explore all possible phylogenetic space, and thus the evolution of biodiversity is constrained by a set of loose but inviolable rules. We characterize the biotic and abiotic factors precipitating those rules with important implications for our knowledge of the emergence and maintenance of the diversity of life around us.
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Affiliation(s)
- Eric Lewitus
- Institut de Biologie, École Normale Supérieure, Paris, France
- * E-mail:
| | - Hélène Morlon
- Institut de Biologie, École Normale Supérieure, Paris, France
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Morlon H, Lewitus E, Condamine FL, Manceau M, Clavel J, Drury J. RPANDA
: an R package for macroevolutionary analyses on phylogenetic trees. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12526] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hélène Morlon
- CNRS UMR 8197 Institut de Biologie Ecole Normale Supérieure 46 rue d'Ulm 75005 Paris France
| | - Eric Lewitus
- CNRS UMR 8197 Institut de Biologie Ecole Normale Supérieure 46 rue d'Ulm 75005 Paris France
| | - Fabien L. Condamine
- CNRS UMR 5554 Institut des Sciences de l'Evolution Place Eugène Bataillon 34000 Montpellier France
| | - Marc Manceau
- CNRS UMR 8197 Institut de Biologie Ecole Normale Supérieure 46 rue d'Ulm 75005 Paris France
| | - Julien Clavel
- CNRS UMR 8197 Institut de Biologie Ecole Normale Supérieure 46 rue d'Ulm 75005 Paris France
| | - Jonathan Drury
- CNRS UMR 8197 Institut de Biologie Ecole Normale Supérieure 46 rue d'Ulm 75005 Paris France
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