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Kapli P, Kotari I, Telford MJ, Goldman N, Yang Z. DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies. Syst Biol 2023; 72:1119-1135. [PMID: 37366056 PMCID: PMC10627555 DOI: 10.1093/sysbio/syad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Indexed: 06/28/2023] Open
Abstract
Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences. Here, we analyze a model of codon evolution under an idealized genetic code and demonstrate that those perceptions may be misconceptions. We conduct a simulation study to assess the utility of protein versus DNA sequences for inferring deep phylogenies, with protein-coding data generated under models of heterogeneous substitution processes across sites in the sequence and among lineages on the tree, and then analyzed using nucleotide, amino acid, and codon models. Analysis of DNA sequences under nucleotide-substitution models (possibly with the third codon positions excluded) recovered the correct tree at least as often as analysis of the corresponding protein sequences under modern amino acid models. We also applied the different data-analysis strategies to an empirical dataset to infer the metazoan phylogeny. Our results from both simulated and real data suggest that DNA sequences may be as useful as proteins for inferring deep phylogenies and should not be excluded from such analyses. Analysis of DNA data under nucleotide models has a major computational advantage over protein-data analysis, potentially making it feasible to use advanced models that account for among-site and among-lineage heterogeneity in the nucleotide-substitution process in inference of deep phylogenies.
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Affiliation(s)
- Paschalia Kapli
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Ioanna Kotari
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, 1210, Austria
| | - Maximilian J Telford
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Nick Goldman
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ziheng Yang
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
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2
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Abstract
The CODEML program in the PAML package has been widely used to analyze protein-coding gene sequences to estimate the synonymous and nonsynonymous rates (dS and dN) and to detect positive Darwinian selection driving protein evolution. For users not familiar with molecular evolutionary analysis, the program is known to have a steep learning curve. Here, we provide a step-by-step protocol to illustrate the commonly used tests available in the program, including the branch models, the site models, and the branch-site models, which can be used to detect positive selection driving adaptive protein evolution affecting particular lineages of the species phylogeny, affecting a subset of amino acid residues in the protein, and affecting a subset of sites along prespecified lineages, respectively. A data set of the myxovirus (Mx) genes from ten mammal and two bird species is used as an example. We discuss a new feature in CODEML that allows users to perform positive selection tests for multiple genes for the same set of taxa, as is common in modern genome-sequencing projects. The PAML package is distributed at https://github.com/abacus-gene/paml under the GNU license, with support provided at its discussion site (https://groups.google.com/g/pamlsoftware). Data files used in this protocol are available at https://github.com/abacus-gene/paml-tutorial.
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Affiliation(s)
- Sandra Álvarez-Carretero
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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3
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Kafimola S, Azimi M, Saberi-Pirooz R, Ilgaz Ç, Kashani GM, Kapli P, Ahmadzadeh F. Diversification in the mountains: Evolutionary history and molecular phylogeny of Anatolian rock lizards. Mol Phylogenet Evol 2023; 180:107675. [PMID: 36528333 DOI: 10.1016/j.ympev.2022.107675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/25/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
Mountains play a key role in forming biodiversity by acting both as barriers to gene flow among populations and as corridors for the migration of populations adapted to the conditions prevailing at high elevations. The Anatolian and the Zagros Mountains are located in the Alpine-Himalayan belt. The formation of these mountains has influenced the distribution and isolation of the animal population since the late Cenozoic. Apathya is a genus of lacertid lizards distributed along these mountains with two species, i.e., Apathya cappadocica and Apathya yassujica. The taxonomy status of lineages within the genus is complicated. In this study, we tried to collect extensive samples from throughout the distribution range, especially within the Zagros Mountains. Also, we used five genetic markers, two mitochondrial (COI and Cyt b) and three nuclear (C-mos, NKTR, and MCIR), to resolve the phylogenetic relationships within the genus and explain several possible scenarios that shaped multiple genetic structures. The combination of results in the current study indicated eight well-support monophyletic lineages that separated to two main groups; group 1 including A. c. cappadocica, A. c. muhtari and A. c. wolteri, group 2 contains four regional clades Turkey, Urmia, Baneh and Ilam, and finally a single clade belonging to the species A. yassujica. In contrast to previous studies, Apathya cappadocica urmiana was divided into four clades and three clades were recognized within Iranian boundaries. The clades have dispersed from Anatolia to adjacent regions in the south of Anatolia and the western Zagros Mountains. According to the evidence generated in this study this clade is paraphyletic. Based on our assumption, orogeny activities and also climate fluctuations in Middle Miocene and Pleistocene have influenced to formation of lineages. In this study we revisit the taxonomy of the genus and demonstrate that the species diversity was substantially underestimated. Our findings suggest that each of the eight clades corresponding to subspecies and distinct geographic regions deserve to be promoted to species level.
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Affiliation(s)
- Sara Kafimola
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran 1983963113, Iran; Department of Biology, Faculty of Science, University of Zanjan, Zanjan, Iran
| | - Maryam Azimi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran 1983963113, Iran
| | - Reihaneh Saberi-Pirooz
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran 1983963113, Iran
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca- İzmir, Turkey; Research and Application Center for Fauna Flora, Dokuz Eylul University, Buca-İzmir, Turkey
| | | | - Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran 1983963113, Iran.
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4
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Sampaio FL, Day JJ, Mendis Wickramasinghe LJ, Cyriac VP, Papadopoulou A, Brace S, Rajendran A, Simon-Nutbrown C, Flouris T, Kapli P, Ranga Vidanapathirana D, Kotharambath R, Kodandaramaiah U, Gower DJ. A near-complete species-level phylogeny of uropeltid snakes harnessing historical museum collections as a DNA source. Mol Phylogenet Evol 2023; 178:107651. [PMID: 36306995 DOI: 10.1016/j.ympev.2022.107651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Uropeltidae is a clade of small fossorial snakes (ca. 64 extant species) endemic to peninsular India and Sri Lanka. Uropeltid taxonomy has been confusing, and the status of some species has not been revised for over a century. Attempts to revise uropeltid systematics and undertake evolutionary studies have been hampered by incompletely sampled and incompletely resolved phylogenies. To address this issue, we take advantage of historical museum collections, including type specimens, and apply genome-wide shotgun (GWS) sequencing, along with recent field sampling (using Sanger sequencing) to establish a near-complete multilocus species-level phylogeny (ca. 87% complete at species level). This results in a phylogeny that supports the monophyly of all genera (if Brachyophidium is considered a junior synonym of Teretrurus), and provides a firm platform for future taxonomic revision. Sri Lankan uropeltids are probably monophyletic, indicating a single colonisation event of this island from Indian ancestors. However, the position of Rhinophis goweri (endemic to Eastern Ghats, southern India) is unclear and warrants further investigation, and evidence that it may nest within the Sri Lankan radiation indicates a possible recolonisation event. DNA sequence data and morphology suggest that currently recognised uropeltid species diversity is substantially underestimated. Our study highlights the benefits of integrating museum collections in molecular genetic analyses and their role in understanding the systematics and evolutionary history of understudied organismal groups.
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Affiliation(s)
- Filipa L Sampaio
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
| | - Julia J Day
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Vivek P Cyriac
- IISER-TVM Centre for Research and Education in Ecology and Evolution, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695 551, India
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, 2109 Nicosia, Cyprus
| | - Selina Brace
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Albert Rajendran
- Research Department of Zoology, St. John's College, Tirunelveli, Tamil Nadu, India
| | - Cornelia Simon-Nutbrown
- The Lyell Centre for Earth and Marine Science and Technology, Heriot-Watt University, Edinburgh EH14 4BA, UK; Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Tomas Flouris
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Ramachandran Kotharambath
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India
| | - Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695 551, India
| | - David J Gower
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India.
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5
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Flouri T, Huang J, Jiao X, Kapli P, Rannala B, Yang Z. Bayesian phylogenetic inference using relaxed-clocks and the multispecies coalescent. Mol Biol Evol 2022; 39:6652437. [PMID: 35907248 PMCID: PMC9366188 DOI: 10.1093/molbev/msac161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The multispecies coalescent (MSC) model accommodates both species divergences and within-species coalescent and provides a natural framework for phylogenetic analysis of genomic data when the gene trees vary across the genome. The MSC model implemented in the program bpp assumes a molecular clock and the Jukes–Cantor model, and is suitable for analyzing genomic data from closely related species. Here we extend our implementation to more general substitution models and relaxed clocks to allow the rate to vary among species. The MSC-with-relaxed-clock model allows the estimation of species divergence times and ancestral population sizes using genomic sequences sampled from contemporary species when the strict clock assumption is violated, and provides a simulation framework for evaluating species tree estimation methods. We conducted simulations and analyzed two real datasets to evaluate the utility of the new models. We confirm that the clock-JC model is adequate for inference of shallow trees with closely related species, but it is important to account for clock violation for distant species. Our simulation suggests that there is valuable phylogenetic information in the gene-tree branch lengths even if the molecular clock assumption is seriously violated, and the relaxed-clock models implemented in bpp are able to extract such information. Our Markov chain Monte Carlo algorithms suffer from mixing problems when used for species tree estimation under the relaxed clock and we discuss possible improvements. We conclude that the new models are currently most effective for estimating population parameters such as species divergence times when the species tree is fixed.
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Affiliation(s)
- Tomáš Flouri
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Jun Huang
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK.,School of Biomedical Engineering, Capital Medical University, Beijing, 100069, China
| | - Xiyun Jiao
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK.,Department of Statistics and Data Science, China Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Paschalia Kapli
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ziheng Yang
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
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6
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Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N. SPART: A versatile and standardized data exchange format for species partition information. Mol Ecol Resour 2021; 22:430-438. [PMID: 34288531 DOI: 10.1111/1755-0998.13470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.
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Affiliation(s)
- Aurélien Miralles
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | | | - Sophie Brouillet
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomas Flouri
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomochika Fujisawa
- Center for Data Science Education and Research, Shiga University, Shiga, Japan
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - L Lacey Knowles
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI, USA
| | - Sangeeta Kumari
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jeet Sukumaran
- Biology Department, LS 262, San Diego State University, San Diego, CA, USA
| | - Sarah Lutteropp
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Miguel Vences
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
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7
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Kapli P, Natsidis P, Leite DJ, Fursman M, Jeffrie N, Rahman IA, Philippe H, Copley RR, Telford MJ. Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria. Sci Adv 2021; 7:eabe2741. [PMID: 33741592 PMCID: PMC7978419 DOI: 10.1126/sciadv.abe2741] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/01/2021] [Indexed: 05/05/2023]
Abstract
The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors-inadequate models, short internal branches, faster evolving genes, and unequal branch lengths-coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.
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Affiliation(s)
- Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Paschalis Natsidis
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Daniel J Leite
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Maximilian Fursman
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Nadia Jeffrie
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Imran A Rahman
- Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, UK
| | - Hervé Philippe
- Station d'Ecologie Théorique et Expérimentale, UMR CNRS 5321, Université Paul Sabatier, 09200 Moulis, France
| | - Richard R Copley
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK.
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8
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Natsidis P, Kapli P, Schiffer PH, Telford MJ. Systematic errors in orthology inference and their effects on evolutionary analyses. iScience 2021; 24:102110. [PMID: 33659875 PMCID: PMC7892920 DOI: 10.1016/j.isci.2021.102110] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/03/2021] [Accepted: 01/21/2021] [Indexed: 01/13/2023] Open
Abstract
The availability of complete sets of genes from many organisms makes it possible to identify genes unique to (or lost from) certain clades. This information is used to reconstruct phylogenetic trees; identify genes involved in the evolution of clade specific novelties; and for phylostratigraphy—identifying ages of genes in a given species. These investigations rely on accurately predicted orthologs. Here we use simulation to produce sets of orthologs that experience no gains or losses. We show that errors in identifying orthologs increase with higher rates of evolution. We use the predicted sets of orthologs, with errors, to reconstruct phylogenetic trees; to count gains and losses; and for phylostratigraphy. Our simulated data, containing information only from errors in orthology prediction, closely recapitulate findings from empirical data. We suggest published downstream analyses must be informed to a large extent by errors in orthology prediction that mimic expected patterns of gene evolution. Presence of shared orthologs across species is used for evolutionary analyses We simulated realistic sets of orthologs with no gains or losses Errors predicting shared orthologs correlate with phylogenetic relationships Presence/absence datasets based on errors recapitulate findings from empirical data
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Affiliation(s)
- Paschalis Natsidis
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Ecology, University College London, London WC1E 6BT, UK
| | - Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Ecology, University College London, London WC1E 6BT, UK
| | - Philipp H Schiffer
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Ecology, University College London, London WC1E 6BT, UK
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Ecology, University College London, London WC1E 6BT, UK
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9
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Abstract
The effort to reconstruct the tree of life was revolutionized by the use of sequences of proteins and nucleic acids. Phylogenetic trees are now routinely inferred using hundreds of thousands of amino acid or nucleotide characters. It thus seems surprising that many aspects of the tree of life are still controversial; conflicting results between large scale phylogenomic studies show that errors remain common despite large datasets. These errors often result from systematic biases in the way sequences evolve. While the resulting systematic errors are well understood, it requires careful efforts to reduce their effects.
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Affiliation(s)
- Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Tomáš Flouri
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
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10
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Kapli P, Telford MJ. Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha. Sci Adv 2020; 6:eabc5162. [PMID: 33310849 PMCID: PMC7732190 DOI: 10.1126/sciadv.abc5162] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/27/2020] [Indexed: 05/21/2023]
Abstract
The evolutionary relationships of two animal phyla, Ctenophora and Xenacoelomorpha, have proved highly contentious. Ctenophora have been proposed as the most distant relatives of all other animals (Ctenophora-first rather than the traditional Porifera-first). Xenacoelomorpha may be primitively simple relatives of all other bilaterally symmetrical animals (Nephrozoa) or simplified relatives of echinoderms and hemichordates (Xenambulacraria). In both cases, one of the alternative topologies must be a result of errors in tree reconstruction. Here, using empirical data and simulations, we show that the Ctenophora-first and Nephrozoa topologies (but not Porifera-first and Ambulacraria topologies) are strongly supported by analyses affected by systematic errors. Accommodating this finding suggests that empirical studies supporting Ctenophora-first and Nephrozoa trees are likely to be explained by systematic error. This would imply that the alternative Porifera-first and Xenambulacraria topologies, which are supported by analyses designed to minimize systematic error, are the most credible current alternatives.
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Affiliation(s)
- Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
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11
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Vasilikopoulos A, Misof B, Meusemann K, Lieberz D, Flouri T, Beutel RG, Niehuis O, Wappler T, Rust J, Peters RS, Donath A, Podsiadlowski L, Mayer C, Bartel D, Böhm A, Liu S, Kapli P, Greve C, Jepson JE, Liu X, Zhou X, Aspöck H, Aspöck U. Correction to: An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola). BMC Evol Biol 2020; 20:133. [PMID: 33059595 PMCID: PMC7558605 DOI: 10.1186/s12862-020-01695-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Alexandros Vasilikopoulos
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Bernhard Misof
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Karen Meusemann
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.,Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany.,Australian National Insect Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2601, Australia
| | - Doria Lieberz
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743, Jena, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Torsten Wappler
- Natural History Department, Hessisches Landesmuseum Darmstadt, 64283, Darmstadt, Germany
| | - Jes Rust
- Steinmann-Institut für Geologie, Mineralogie und Paläontologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115, Bonn, Germany
| | - Ralph S Peters
- Centre for Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Daniela Bartel
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Alexander Böhm
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), 60325, Frankfurt, Germany
| | - James E Jepson
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, T23 N73K, Cork, Ireland
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine, Medical Parasitology, Medical University of Vienna (MUW), 1090, Vienna, Austria
| | - Ulrike Aspöck
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria.,Zoological Department II, Natural History Museum of Vienna, 1010, Vienna, Austria
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12
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Vasilikopoulos A, Misof B, Meusemann K, Lieberz D, Flouri T, Beutel RG, Niehuis O, Wappler T, Rust J, Peters RS, Donath A, Podsiadlowski L, Mayer C, Bartel D, Böhm A, Liu S, Kapli P, Greve C, Jepson JE, Liu X, Zhou X, Aspöck H, Aspöck U. An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola). BMC Evol Biol 2020; 20:64. [PMID: 32493355 PMCID: PMC7268685 DOI: 10.1186/s12862-020-01631-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The latest advancements in DNA sequencing technologies have facilitated the resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain unresolved. The phylogeny of Neuropterida has been extensively studied, but no strong consensus exists concerning the phylogenetic relationships within the order Neuroptera. Here, we assembled a novel transcriptomic dataset to address previously unresolved issues in the phylogeny of Neuropterida and to infer divergence times within the group. We tested the robustness of our phylogenetic estimates by comparing summary coalescent and concatenation-based phylogenetic approaches and by employing different quartet-based measures of phylogenomic incongruence, combined with data permutations. RESULTS Our results suggest that the order Raphidioptera is sister to Neuroptera + Megaloptera. Coniopterygidae is inferred as sister to all remaining neuropteran families suggesting that larval cryptonephry could be a ground plan feature of Neuroptera. A clade that includes Nevrorthidae, Osmylidae, and Sisyridae (i.e. Osmyloidea) is inferred as sister to all other Neuroptera except Coniopterygidae, and Dilaridae is placed as sister to all remaining neuropteran families. Ithonidae is inferred as the sister group of monophyletic Myrmeleontiformia. The phylogenetic affinities of Chrysopidae and Hemerobiidae were dependent on the data type analyzed, and quartet-based analyses showed only weak support for the placement of Hemerobiidae as sister to Ithonidae + Myrmeleontiformia. Our molecular dating analyses suggest that most families of Neuropterida started to diversify in the Jurassic and our ancestral character state reconstructions suggest a primarily terrestrial environment of the larvae of Neuropterida and Neuroptera. CONCLUSION Our extensive phylogenomic analyses consolidate several key aspects in the backbone phylogeny of Neuropterida, such as the basal placement of Coniopterygidae within Neuroptera and the monophyly of Osmyloidea. Furthermore, they provide new insights into the timing of diversification of Neuropterida. Despite the vast amount of analyzed molecular data, we found that certain nodes in the tree of Neuroptera are not robustly resolved. Therefore, we emphasize the importance of integrating the results of morphological analyses with those of sequence-based phylogenomics. We also suggest that comparative analyses of genomic meta-characters should be incorporated into future phylogenomic studies of Neuropterida.
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Affiliation(s)
- Alexandros Vasilikopoulos
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Bernhard Misof
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Karen Meusemann
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
- Australian National Insect Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2601, Australia
| | - Doria Lieberz
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743, Jena, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Torsten Wappler
- Natural History Department, Hessisches Landesmuseum Darmstadt, 64283, Darmstadt, Germany
| | - Jes Rust
- Steinmann-Institut für Geologie, Mineralogie und Paläontologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115, Bonn, Germany
| | - Ralph S Peters
- Centre for Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Daniela Bartel
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Alexander Böhm
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), 60325, Frankfurt, Germany
| | - James E Jepson
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, T23 N73K, Cork, Ireland
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine, Medical Parasitology, Medical University of Vienna (MUW), 1090, Vienna, Austria
| | - Ulrike Aspöck
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
- Zoological Department II, Natural History Museum of Vienna, 1010, Vienna, Austria
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13
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Serdari D, Kostaki EG, Paraskevis D, Stamatakis A, Kapli P. Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV. PeerJ 2019; 7:e7754. [PMID: 31667012 PMCID: PMC6816385 DOI: 10.7717/peerj.7754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/26/2019] [Indexed: 12/15/2022] Open
Abstract
Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.
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Affiliation(s)
- Dora Serdari
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandros Stamatakis
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics Evolution and Environment, University College London, University of London, London, United Kingdom
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14
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Wipfler B, Letsch H, Frandsen PB, Kapli P, Mayer C, Bartel D, Buckley TR, Donath A, Edgerly-Rooks JS, Fujita M, Liu S, Machida R, Mashimo Y, Misof B, Niehuis O, Peters RS, Petersen M, Podsiadlowski L, Schütte K, Shimizu S, Uchifune T, Wilbrandt J, Yan E, Zhou X, Simon S. Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects. Proc Natl Acad Sci U S A 2019; 116:3024-3029. [PMID: 30642969 PMCID: PMC6386694 DOI: 10.1073/pnas.1817794116] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyneoptera represents one of the major lineages of winged insects, comprising around 40,000 extant species in 10 traditional orders, including grasshoppers, roaches, and stoneflies. Many important aspects of polyneopteran evolution, such as their phylogenetic relationships, changes in their external appearance, their habitat preferences, and social behavior, are unresolved and are a major enigma in entomology. These ambiguities also have direct consequences for our understanding of the evolution of winged insects in general; for example, with respect to the ancestral habitats of adults and juveniles. We addressed these issues with a large-scale phylogenomic analysis and used the reconstructed phylogenetic relationships to trace the evolution of 112 characters associated with the external appearance and the lifestyle of winged insects. Our inferences suggest that the last common ancestors of Polyneoptera and of the winged insects were terrestrial throughout their lives, implying that wings did not evolve in an aquatic environment. The appearance of the first polyneopteran insect was mainly characterized by ancestral traits such as long segmented abdominal appendages and biting mouthparts held below the head capsule. This ancestor lived in association with the ground, which led to various specializations including hardened forewings and unique tarsal attachment structures. However, within Polyneoptera, several groups switched separately to a life on plants. In contrast to a previous hypothesis, we found that social behavior was not part of the polyneopteran ground plan. In other traits, such as the biting mouthparts, Polyneoptera shows a high degree of evolutionary conservatism unique among the major lineages of winged insects.
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Affiliation(s)
- Benjamin Wipfler
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-University Jena, 07743 Jena, Germany;
- Center of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Harald Letsch
- Department für Botanik und Biodiversitätsforschung, Universität Wien, 1030 Vienna, Austria
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84604
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20002
| | - Paschalia Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Daniela Bartel
- Department of Integrative Zoology, Universität Wien, 1090 Vienna, Austria
| | - Thomas R Buckley
- New Zealand Arthropod Collection, Manaaki Whenua - Landcare Research, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Janice S Edgerly-Rooks
- Department of Biology, College of Arts and Sciences, Santa Clara University, Santa Clara, CA 95053
| | - Mari Fujita
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen 518083, China
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Yuta Mashimo
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Oliver Niehuis
- Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, 79104 Freiburg, Germany
| | - Ralph S Peters
- Center of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Kai Schütte
- Tierökologie und Naturschutz, Universität Hamburg, 20146 Hamburg, Germany
| | - Shota Shimizu
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Toshiki Uchifune
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
- Yokosuka City Museum, Fukadadai, Kanagawa 238-0016, Japan
| | - Jeanne Wilbrandt
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Evgeny Yan
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-University Jena, 07743 Jena, Germany
- Borissiak Palaeontological Institute, Russian Academy of Sciences, 123 Moscow, Russia
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100083, China
| | - Sabrina Simon
- Biosystematics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
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15
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Ahmadzadeh F, Lymberakis P, Pirouz RS, Kapli P. The evolutionary history of two lizards (Squamata: Lacertidae) is linked to the geological development of Iran. ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Šmíd J, Moravec J, Gvoždík V, Štundl J, Frynta D, Lymberakis P, Kapli P, Wilms T, Schmitz A, Shobrak M, Yousefkhani SH, Rastegar-Pouyani E, Castilla AM, Els J, Mayer W. Cutting the Gordian Knot: Phylogenetic and ecological diversification of theMesalina brevirostrisspecies complex (Squamata, Lacertidae). ZOOL SCR 2017. [DOI: 10.1111/zsc.12254] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiří Šmíd
- Department of Zoology; National Museum; Prague Czech Republic
- South African National Biodiversity Institute; Claremont Cape Town South Africa
| | - Jiří Moravec
- Department of Zoology; National Museum; Prague Czech Republic
| | - Václav Gvoždík
- Department of Zoology; National Museum; Prague Czech Republic
| | - Jan Štundl
- Department of Zoology; National Museum; Prague Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - Daniel Frynta
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - Petros Lymberakis
- Natural History Museum of Crete - University of Crete; Herakleio Greece
| | - Paschalia Kapli
- The Exelixis Lab; Scientific Computing Group; Heidelberg Institute for Theoretical Studies; Heidelberg Germany
| | | | - Andreas Schmitz
- Department of Herpetology and Ichthyology; Natural History Museum of Geneva; Geneva Switzerland
| | - Mohammed Shobrak
- Biology Department; Faculty of Science; Taif University; Taif Saudi Arabia
| | | | | | - Aurora M. Castilla
- Qatar Environment and Energy Research Institute; Hamad Bin Khalifa University (Qatar Foundation); Doha Qatar
| | - Johannes Els
- Breeding Centre for Endangered Arabian Wildlife, Environment and Protected Areas Authority; Sharjah United Arab Emirates
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Grímsson F, Kapli P, Hofmann CC, Zetter R, Grimm GW. Eocene Loranthaceae pollen pushes back divergence ages for major splits in the family. PeerJ 2017; 5:e3373. [PMID: 28607837 PMCID: PMC5466002 DOI: 10.7717/peerj.3373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/04/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND We revisit the palaeopalynological record of Loranthaceae, using pollen ornamentation to discriminate lineages and to test molecular dating estimates for the diversification of major lineages. METHODS Fossil Loranthaceae pollen from the Eocene and Oligocene are analysed and documented using scanning-electron microscopy. These fossils were associated with molecular-defined clades and used as minimum age constraints for Bayesian node dating using different topological scenarios. RESULTS The fossil Loranthaceae pollen document the presence of at least one extant root-parasitic lineage (Nuytsieae) and two currently aerial parasitic lineages (Psittacanthinae and Loranthinae) by the end of the Eocene in the Northern Hemisphere. Phases of increased lineage diversification (late Eocene, middle Miocene) coincide with global warm phases. DISCUSSION With the generation of molecular data becoming easier and less expensive every day, neontological research should re-focus on conserved morphologies that can be traced through the fossil record. The pollen, representing the male gametophytic generation of plants and often a taxonomic indicator, can be such a tracer. Analogously, palaeontological research should put more effort into diagnosing Cenozoic fossils with the aim of including them into modern systematic frameworks.
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Affiliation(s)
| | - Paschalia Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Wien, Austria
| | - Guido W. Grimm
- Department of Palaeontology, University of Vienna, Wien, Austria
- Orléans, France
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18
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Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 2017; 33:1630-1638. [PMID: 28108445 PMCID: PMC5447239 DOI: 10.1093/bioinformatics/btx025] [Citation(s) in RCA: 226] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/27/2016] [Accepted: 01/17/2017] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences. RESULTS We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size. AVAILABILITY AND IMPLEMENTATION mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org . CONTACT : paschalia.kapli@h-its.org or alexandros.stamatakis@h-its.org or tomas.flouri@h-its.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- P Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - S Lutteropp
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - J Zhang
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - K Kobert
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - P Pavlidis
- Foundation for Research and Technology, Hellas Institute of Computer Science GR, Heraklion, Crete, Greece
| | - A Stamatakis
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - T Flouri
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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19
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Renner SS, Grimm GW, Kapli P, Denk T. Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth-death clock model. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150135. [PMID: 27325832 PMCID: PMC4920336 DOI: 10.1098/rstb.2015.0135] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2016] [Indexed: 11/12/2022] Open
Abstract
The fossilized birth-death (FBD) model can make use of information contained in multiple fossils representing the same clade, and we here apply this model to infer divergence times in beeches (genus Fagus), using 53 fossils and nuclear sequences for all nine species. We also apply FBD dating to the fern clade Osmundaceae, with about 12 living species and 36 fossils. Fagus nuclear sequences cannot be aligned with those of other Fagaceae, and we therefore use Bayes factors to choose among alternative root positions. The crown group of Fagus is dated to 53 (62-43) Ma; divergence of the sole American species to 44 (51-39) Ma and divergence between Central European F. sylvatica and Eastern Mediterranean F. orientalis to 8.7 (20-1.8) Ma, unexpectedly old. The FBD model can accommodate fossils as sampled ancestors or as extinct or unobserved lineages; however, this makes its raw output, which shows all fossils on short or long branches, problematic to interpret. We use hand-drawn depictions and a bipartition network to illustrate the uncertain placements of fossils. Inferred speciation and extinction rates imply approximately 5× higher evolutionary turnover in Fagus than in Osmundaceae, fitting a hypothesized low turnover in plants adapted to low-nutrient conditions.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- S S Renner
- Systematic Botany and Mycology, University of Munich, Menzinger Street 67, 80638 Munich, Germany
| | - Guido W Grimm
- Department of Palaeontology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Paschalia Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 68159 Heidelberg, Germany
| | - Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History, Svante Arrhenius Väg 9, 10405 Stockholm, Sweden
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Skourtanioti E, Kapli P, Ilgaz Ç, Kumlutaş Y, Avcı A, Ahmadzadeh F, Crnobrnja-Isailović J, Gherghel I, Lymberakis P, Poulakakis N. A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes. Mol Phylogenet Evol 2016; 103:199-214. [PMID: 27404043 DOI: 10.1016/j.ympev.2016.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 02/25/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Morphological and DNA data support that the East Mediterranean snake-eyed skink Ablepharus kitaibelii represents a species complex that includes four species A. kitaibelii, A. budaki, A. chernovi, and A. rueppellii, highlighting the need of its taxonomic reevaluation. Here, we used Bayesian and Maximum Likelihood methods to estimate the phylogenetic relationships of all members of the complex based on two mitochondrial (cyt b, 16S rRNA) and two nuclear markers (MC1R, and NKTR) and using Chalcides, Eumeces, and Eutropis as outgroups. The biogeographic history of the complex was also investigated through the application of several phylogeographic (BEAST) and biogeographic (BBM) analyses. Paleogeographic and paleoclimatic data were used to support the inferred phylogeographic patterns. The A. kitaibelli species complex exhibits high genetic diversity, revealing cases of hidden diversity and cases of non-monophyletic species such as A. kitaibelii and A. budaki. Our results indicate that A. pannonicus branches off first and a group that comprises specimens of A. kitaibelli and A. budaki from Kastelorizo Island group (southeast Greece) and southwest Turkey, respectively is differentiated from the rest A. kitaibelli and A. budaki populations and may represent a new species. The estimated divergence times place the origin of the complex in the Middle Miocene (∼16Mya) and the divergence of most currently recognized species in the Late Miocene. The inferred ancestral distribution suggests that the complex originated in Anatolia, supposing that several vicariance and dispersal events that are related with the formation of the Mid-Aegean Trench, the Anatolian Diagonal and the orogenesis of the mountain chains in southern and eastern Anatolia have led to current distribution pattern of A. kitaibelii species complex in the Balkans and Middle East.
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Affiliation(s)
- Eirini Skourtanioti
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece; Biology Department, School of Sciences and Engineering, University of Crete, Vassilika Vouton, GR-70013 Herakleio, Crete, Greece
| | - Paschalia Kapli
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece; Biology Department, School of Sciences and Engineering, University of Crete, Vassilika Vouton, GR-70013 Herakleio, Crete, Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, TR-35160, Buca-İzmir, Turkey
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, TR-35160, Buca-İzmir, Turkey
| | - Aziz Avcı
- Adnan Menderes University, Faculty of Science and Arts, Department of Biology, 09010 Aydın, Turkey
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Jelka Crnobrnja-Isailović
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, Niš 18000, Serbia; Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", Despota Stefana 142, Beograd 11000, Serbia
| | - Iulian Gherghel
- Department of Biology, Case Western Reserve University, 2080 Adelbert Road, Cleveland 44106, Ohio, USA
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece; Biology Department, School of Sciences and Engineering, University of Crete, Vassilika Vouton, GR-70013 Herakleio, Crete, Greece.
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Kornilios P, Thanou E, Kapli P, Parmakelis A, Chatzaki M. Peeking through the trapdoor: Historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae. Mol Phylogenet Evol 2016; 98:300-13. [DOI: 10.1016/j.ympev.2016.01.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 11/23/2015] [Accepted: 01/31/2016] [Indexed: 10/22/2022]
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Kjer KM, Ware JL, Rust J, Wappler T, Lanfear R, Jermiin LS, Zhou X, Aspöck H, Aspöck U, Beutel RG, Blanke A, Donath A, Flouri T, Frandsen PB, Kapli P, Kawahara AY, Letsch H, Mayer C, McKenna DD, Meusemann K, Niehuis O, Peters RS, Wiegmann BM, Yeates DK, von Reumont BM, Stamatakis A, Misof B. Response to Comment on “Phylogenomics resolves the timing and pattern of insect evolution”. Science 2015; 349:487. [DOI: 10.1126/science.aaa7136] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- K. M. Kjer
- University of California, Davis, CA, USA
| | - J. L. Ware
- Rutgers University, New Brunswick, NJ, USA
| | | | | | | | - L. S. Jermiin
- Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - X. Zhou
- China National GeneBank, BGI–Shenzhen, China
- BGI-Shenzhen, China
| | | | - U. Aspöck
- Universität Wien, Vienna, Austria
- Naturhistorisches Museum Wien, Vienna, Austria
| | - R. G. Beutel
- Phyletischem Museum Jena, Friedrich-Schiller-Universität Jena, Germany
| | | | - A. Donath
- Universität Bonn, Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | - T. Flouri
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - P. B. Frandsen
- Rutgers University, New Brunswick, NJ, USA
- Smithsonian Institution, Washington, DC, USA
| | - P. Kapli
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | | | - C. Mayer
- Universität Bonn, Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | | | - K. Meusemann
- Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | - O. Niehuis
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
- Arizona State University, Tempe, AZ, USA
| | - R. S. Peters
- Universität Bonn, Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | | | - D. K. Yeates
- Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - B. M. von Reumont
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
- Natural History Museum London, London, UK
| | - A. Stamatakis
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - B. Misof
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
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Grimm GW, Kapli P, Bomfleur B, McLoughlin S, Renner SS. Using More Than the Oldest Fossils: Dating Osmundaceae with Three Bayesian Clock Approaches. Syst Biol 2014; 64:396-405. [DOI: 10.1093/sysbio/syu108] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/01/2014] [Indexed: 11/13/2022] Open
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Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O, Petersen M, Izquierdo-Carrasco F, Wappler T, Rust J, Aberer AJ, Aspock U, Aspock H, Bartel D, Blanke A, Berger S, Bohm A, Buckley TR, Calcott B, Chen J, Friedrich F, Fukui M, Fujita M, Greve C, Grobe P, Gu S, Huang Y, Jermiin LS, Kawahara AY, Krogmann L, Kubiak M, Lanfear R, Letsch H, Li Y, Li Z, Li J, Lu H, Machida R, Mashimo Y, Kapli P, McKenna DD, Meng G, Nakagaki Y, Navarrete-Heredia JL, Ott M, Ou Y, Pass G, Podsiadlowski L, Pohl H, von Reumont BM, Schutte K, Sekiya K, Shimizu S, Slipinski A, Stamatakis A, Song W, Su X, Szucsich NU, Tan M, Tan X, Tang M, Tang J, Timelthaler G, Tomizuka S, Trautwein M, Tong X, Uchifune T, Walzl MG, Wiegmann BM, Wilbrandt J, Wipfler B, Wong TKF, Wu Q, Wu G, Xie Y, Yang S, Yang Q, Yeates DK, Yoshizawa K, Zhang Q, Zhang R, Zhang W, Zhang Y, Zhao J, Zhou C, Zhou L, Ziesmann T, Zou S, Li Y, Xu X, Zhang Y, Yang H, Wang J, Wang J, Kjer KM, Zhou X. Phylogenomics resolves the timing and pattern of insect evolution. Science 2014; 346:763-7. [DOI: 10.1126/science.1257570] [Citation(s) in RCA: 1672] [Impact Index Per Article: 167.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Poulakakis N, Kapli P, Lymberakis P, Trichas A, Vardinoyiannis K, Sfenthourakis S, Mylonas M. A review of phylogeographic analyses of animal taxa from the Aegean and surrounding regions. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12071] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nikos Poulakakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Paschalia Kapli
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Petros Lymberakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | - Apostolos Trichas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | | | | | - Moisis Mylonas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
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Zhang J, Kapli P, Pavlidis P, Stamatakis A. A general species delimitation method with applications to phylogenetic placements. Bioinformatics 2013; 29:2869-76. [PMID: 23990417 PMCID: PMC3810850 DOI: 10.1093/bioinformatics/btt499] [Citation(s) in RCA: 1350] [Impact Index Per Article: 122.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION Sequence-based methods to delimit species are central to DNA taxonomy, microbial community surveys and DNA metabarcoding studies. Current approaches either rely on simple sequence similarity thresholds (OTU-picking) or on complex and compute-intensive evolutionary models. The OTU-picking methods scale well on large datasets, but the results are highly sensitive to the similarity threshold. Coalescent-based species delimitation approaches often rely on Bayesian statistics and Markov Chain Monte Carlo sampling, and can therefore only be applied to small datasets. RESULTS We introduce the Poisson tree processes (PTP) model to infer putative species boundaries on a given phylogenetic input tree. We also integrate PTP with our evolutionary placement algorithm (EPA-PTP) to count the number of species in phylogenetic placements. We compare our approaches with popular OTU-picking methods and the General Mixed Yule Coalescent (GMYC) model. For de novo species delimitation, the stand-alone PTP model generally outperforms GYMC as well as OTU-picking methods when evolutionary distances between species are small. PTP neither requires an ultrametric input tree nor a sequence similarity threshold as input. In the open reference species delimitation approach, EPA-PTP yields more accurate results than de novo species delimitation methods. Finally, EPA-PTP scales on large datasets because it relies on the parallel implementations of the EPA and RAxML, thereby allowing to delimit species in high-throughput sequencing data. AVAILABILITY AND IMPLEMENTATION The code is freely available at www.exelixis-lab.org/software.html. .
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Affiliation(s)
- Jiajie Zhang
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, D-68159 Heidelberg, Germany, Graduate School for Computing in Medicine and Life Sciences, University of Lübeck, Institut für Neuro- und Bioinformatik, University of Lübeck, 23538 Lübeck, Germany, Natural History Museum of Crete, University of Crete, GR-71409 Irakleio, Crete, Greece and Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas-FORTH, GR-70013 Heraklion, Crete, Greece
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Kapli P, Botoni D, Ilgaz Ç, Kumlutaş Y, Avcı A, Rastegar-Pouyani N, Fathinia B, Lymberakis P, Ahmadzadeh F, Poulakakis N. Corrigendum to “Molecular phylogeny and historical biogeography of the Anatolian lizard Apathya (Squamata, Lacertidae)” [Mol. Phylogenet. Evol. 66 (2013) 992–1001]. Mol Phylogenet Evol 2013. [DOI: 10.1016/j.ympev.2013.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Poulakakis N, Kapli P, Kardamaki A, Skourtanioti E, Göcmen B, Ilgaz Ç, Kumlutaş Y, Avci A, Lymberakis P. Comparative phylogeography of six herpetofauna species in Cyprus: late Miocene to Pleistocene colonization routes. Biol J Linn Soc Lond 2013. [DOI: 10.1111/j.1095-8312.2012.02039.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Nikos Poulakakis
- Molecular Systematics Lab; Natural History Museum of Crete; University of Crete; Iraklion Crete Greece
- Biology Department; University of Crete; Iraklion Crete Greece
| | - Paschalia Kapli
- Molecular Systematics Lab; Natural History Museum of Crete; University of Crete; Iraklion Crete Greece
- Biology Department; University of Crete; Iraklion Crete Greece
| | - Afroditi Kardamaki
- Molecular Systematics Lab; Natural History Museum of Crete; University of Crete; Iraklion Crete Greece
- Biology Department; University of Crete; Iraklion Crete Greece
| | - Eirini Skourtanioti
- Molecular Systematics Lab; Natural History Museum of Crete; University of Crete; Iraklion Crete Greece
- Biology Department; University of Crete; Iraklion Crete Greece
| | - Bayram Göcmen
- Faculty of Science; Department of Biology; Ege University; 35100 Bornova/İzmir Turkey
| | - Çetin Ilgaz
- Faculty of Science; Department of Biology; Dokuz Eylül University; 35160 Buca/İzmir Turkey
| | - Yusuf Kumlutaş
- Faculty of Science; Department of Biology; Dokuz Eylül University; 35160 Buca/İzmir Turkey
| | - Aziz Avci
- Faculty of Science and Arts; Department of Biology; Adnan Menderes University; 09010 Aydın Turkey
| | - Petros Lymberakis
- Molecular Systematics Lab; Natural History Museum of Crete; University of Crete; Iraklion Crete Greece
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