2
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Blackburn DC, Nielsen SV, Barej MF, Doumbia J, Hirschfeld M, Kouamé NG, Lawson D, Loader S, Ofori‐Boateng C, Stanley EL, Rödel M. Evolution of the African slippery frogs (Anura:
Conraua
), including the world’s largest living frog. ZOOL SCR 2020. [DOI: 10.1111/zsc.12447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- David C. Blackburn
- Department of Natural History Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Stuart V. Nielsen
- Department of Natural History Florida Museum of Natural History University of Florida Gainesville FL USA
- Department of Biological Sciences Marquette University Milwaukee WI USA
| | - Michael F. Barej
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | | | - Mareike Hirschfeld
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | | | - Dwight Lawson
- Oklahoma City Zoo and Botanical Garden Oklahoma City OK USA
| | | | | | - Edward L. Stanley
- Department of Natural History Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Mark‐Oliver Rödel
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
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3
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Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 2019; 7:e6399. [PMID: 30783571 PMCID: PMC6378093 DOI: 10.7717/peerj.6399] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022] Open
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alexandre Antonelli
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
| | - Christine D. Bacon
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stella Huynh
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Hélène Morlon
- Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France
| | - Luay K. Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alexander Schliep
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | | | - Fernanda P. Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil
| | - John Wiedenhoeft
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
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5
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Whelan NV, Halanych KM. Who Let the CAT Out of the Bag? Accurately Dealing with Substitutional Heterogeneity in Phylogenomic Analyses. Syst Biol 2018; 66:232-255. [PMID: 27633354 DOI: 10.1093/sysbio/syw084] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 09/04/2016] [Indexed: 11/14/2022] Open
Abstract
As phylogenetic datasets have increased in size, site-heterogeneous substitution models such as CAT-F81 and CAT-GTR have been advocated in favor of other models because they purportedly suppress long-branch attraction (LBA). These models are two of the most commonly used models in phylogenomics, and they have been applied to a variety of taxa, ranging from Drosophila to land plants. However, many arguments in favor of CAT models have been based on tenuous assumptions about the true phylogeny, rather than rigorous testing with known trees via simulation. Moreover, CAT models have not been compared to other approaches for handling substitutional heterogeneity such as data partitioning with site-homogeneous substitution models. We simulated amino acid sequence datasets with substitutional heterogeneity on a variety of tree shapes including those susceptible to LBA. Data were analyzed with both CAT models and partitioning to explore model performance; in total over 670,000 CPU hours were used, of which over 97% was spent running analyses with CAT models. In many cases, all models recovered branching patterns that were identical to the known tree. However, CAT-F81 consistently performed worse than other models in inferring the correct branching patterns, and both CAT models often overestimated substitutional heterogeneity. Additionally, reanalysis of two empirical metazoan datasets supports the notion that CAT-F81 tends to recover less accurate trees than data partitioning and CAT-GTR. Given these results, we conclude that partitioning and CAT-GTR perform similarly in recovering accurate branching patterns. However, computation time can be orders of magnitude less for data partitioning, with commonly used implementations of CAT-GTR often failing to reach completion in a reasonable time frame (i.e., for Bayesian analyses to converge). Practices such as removing constant sites and parsimony uninformative characters, or using CAT-F81 when CAT-GTR is deemed too computationally expensive, cannot be logically justified. Given clear problems with CAT-F81, phylogenies previously inferred with this model should be reassessed. [Data partitioning; phylogenomics, simulation, site-heterogeneity, substitution models.].
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Affiliation(s)
- Nathan V Whelan
- Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA
| | - Kenneth M Halanych
- Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA
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6
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Bittencourt-Silva GB, Conradie W, Siu-Ting K, Tolley KA, Channing A, Cunningham M, Farooq HM, Menegon M, Loader SP. The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura). Mol Phylogenet Evol 2016; 99:89-102. [PMID: 27001603 DOI: 10.1016/j.ympev.2016.03.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 03/14/2016] [Accepted: 03/16/2016] [Indexed: 11/18/2022]
Abstract
The phylogenetic relationships of the African mongrel frog genus Nothophryne are poorly understood. We provide the first molecular assessment of the phylogenetic position of, and diversity within, this monotypic genus from across its range-the Afromontane regions of Malawi and Mozambique. Our analysis using a two-tiered phylogenetic approach allowed us to place the genus in Pyxicephalidae. Within the family, Nothophryne grouped with Tomopterna, a hypothesis judged significantly better than alternative hypotheses proposed based on morphology. Our analyses of populations across the range of Nothophryne suggest the presence of several cryptic species, at least one species per mountain. Formal recognition of these species is pending but there is a major conservation concern for these narrowly distributed populations in an area impacted by major habitat change. The phylogenetic tree of pyxicephalids is used to examine evolution of life history, ancestral habitat, and biogeography of this group.
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Affiliation(s)
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), Humewood 6013, South Africa; South African Institute for Aquatic Biodiversity, Grahamstown 6140, South Africa
| | - Karen Siu-Ting
- Ecological and Evolutionary Genomics Lab, IBERS, Aberystwyth University, Aberystwyth SY23 3FG, United Kingdom; School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland; Departamento de Herpetología, Museo de Historia Natural UNMSM, Av. Arenales 1256, Jesus María, Lima, Peru
| | - Krystal A Tolley
- South African National Biodiversity Institute, Rhodes Drive, Private Bag X7, Newlands, Claremont 7735, Cape Town, South Africa
| | - Alan Channing
- Biodiversity and Conservation Biology Department, University of the Western Cape, Bellville 7525, South Africa
| | - Michael Cunningham
- South African Institute for Aquatic Biodiversity, Grahamstown 6140, South Africa; Department of Genetics, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Harith M Farooq
- Faculty of Natural Sciences, Lúrio University, Pemba 958, Mozambique
| | - Michele Menegon
- Tropical Biodiversity Section, Museo delle Scienze, Viale del Lavoro e della Scienza, 3, 38122 Trento, Italy
| | - Simon P Loader
- Department of Environmental Sciences, University of Basel, Basel 4056, Switzerland; University of Roehampton, London SW15 4JD, United Kingdom
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7
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Barej MF, Schmitz A, Günther R, Loader SP, Mahlow K, Rödel MO. The first endemic West African vertebrate family - a new anuran family highlighting the uniqueness of the Upper Guinean biodiversity hotspot. Front Zool 2014; 11:8. [PMID: 24485269 PMCID: PMC3925359 DOI: 10.1186/1742-9994-11-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 12/21/2013] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Higher-level systematics in amphibians is relatively stable. However, recent phylogenetic studies of African torrent-frogs have uncovered high divergence in these phenotypically and ecologically similar frogs, in particular between West African torrent-frogs versus Central (Petropedetes) and East African (Arthroleptides and Ericabatrachus) lineages. Because of the considerable molecular divergence, and external morphology of the single West African torrent-frog species a new genus was erected (Odontobatrachus). In this study we aim to clarify the systematic position of West African torrent-frogs (Odontobatrachus). We determine the relationships of torrent-frogs using a multi-locus, nuclear and mitochondrial, dataset and include genera of all African and Asian ranoid families. Using micro-tomographic scanning we examine osteology and external morphological features of West African torrent-frogs to compare them with other ranoids. RESULTS Our analyses reveal Petropedetidae (Arthroleptides, Ericabatrachus, Petropedetes) as the sister taxon of the Pyxicephalidae. The phylogenetic position of Odontobatrachus is clearly outside Petropedetidae, and not closely related to any other ranoid family. According to our time-tree estimation Odontobatrachus has been separated from other frog lineages since the Cretaceous (90.1 Ma; confidence interval: 84.2-97.1 Ma). Along with this molecular evidence, osteological and external diagnostic characters recognize West African torrent-frogs as distinct from other ranoids and provide strong support for the necessity of the recognition of a new family of frogs. This is the only endemic vertebrate family occurring in the Upper Guinea biodiversity hotspot. CONCLUSION Based on molecular and morphological distinctiveness, the West African torrent-frog Odontobatrachus natator is allocated to a newly described anuran family. The discovery of an endemic vertebrate family in West Africa highlights the Upper Guinean forests as an outstanding, but highly endangered biodiversity hotspot.
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Affiliation(s)
- Michael F Barej
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstrasse 43, D-10115 Berlin, Germany
| | - Andreas Schmitz
- Department of Herpetology and Ichthyology, Natural History Museum of Geneva, CP 6434, 1211 Geneva 6, Switzerland
| | - Rainer Günther
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstrasse 43, D-10115 Berlin, Germany
| | - Simon P Loader
- Department of Environmental Sciences (Biogeography), University of Basel, Klingelbergstr. 27, Basel 4056, Switzerland
| | - Kristin Mahlow
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstrasse 43, D-10115 Berlin, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstrasse 43, D-10115 Berlin, Germany
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