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Samaradiwakara NP, de Farias ARG, Tennakoon DS, Aluthmuhandiram JVS, Bhunjun CS, Chethana KWT, Kumla J, Lumyong S. Appendage-Bearing Sordariomycetes from Dipterocarpus alatus Leaf Litter in Thailand. J Fungi (Basel) 2023; 9:625. [PMID: 37367561 DOI: 10.3390/jof9060625] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Leaf litter is an essential functional aspect of forest ecosystems, acting as a source of organic matter, a protective layer in forest soils, and a nurturing habitat for micro- and macro-organisms. Through their successional occurrence, litter-inhabiting microfungi play a key role in litter decomposition and nutrient recycling. Despite their importance in terrestrial ecosystems and their abundance and diversity, information on the taxonomy, diversity, and host preference of these decomposer taxa is scarce. This study aims to clarify the taxonomy and phylogeny of four saprobic fungal taxa inhabiting Dipterocarpus alatus leaf litter. Leaf litter samples were collected from Doi Inthanon National Park in Chiang Mai, northern Thailand. Fungal isolates were characterized based on morphology and molecular phylogeny of the nuclear ribosomal DNA (ITS, LSU) and protein-coding genes (tub2, tef1-α, rpb2). One novel saprobic species, Ciliochorella dipterocarpi, and two new host records, Pestalotiopsis dracontomelon and Robillarda australiana, are introduced. The newly described taxa are compared with similar species, and comprehensive descriptions, micrographs, and phylogenetic trees are provided.
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Affiliation(s)
- Nethmini P Samaradiwakara
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | | | - Danushka S Tennakoon
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Janith V S Aluthmuhandiram
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chitrabhanu S Bhunjun
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - K W Thilini Chethana
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Jaturong Kumla
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
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2
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Beck RMD, de Vries D, Janiak MC, Goodhead IB, Boubli JP. Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. J Hum Evol 2023; 174:103293. [PMID: 36493598 DOI: 10.1016/j.jhevol.2022.103293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022]
Abstract
There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.
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Affiliation(s)
- Robin M D Beck
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK.
| | - Dorien de Vries
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Mareike C Janiak
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Ian B Goodhead
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Jean P Boubli
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
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3
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Pugh KD. Phylogenetic analysis of Middle-Late Miocene apes. J Hum Evol 2022; 165:103140. [DOI: 10.1016/j.jhevol.2021.103140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 01/18/2023]
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4
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Blotto BL, Lyra ML, Cardoso MCS, Trefaut Rodrigues M, R Dias I, Marciano-Jr E, Dal Vechio F, Orrico VGD, Brandão RA, Lopes de Assis C, Lantyer-Silva ASF, Rutherford MG, Gagliardi-Urrutia G, Solé M, Baldo D, Nunes I, Cajade R, Torres A, Grant T, Jungfer KH, da Silva HR, Haddad CFB, Faivovich J. The phylogeny of the Casque-headed Treefrogs (Hylidae: Hylinae: Lophyohylini). Cladistics 2021; 37:36-72. [PMID: 34478174 DOI: 10.1111/cla.12409] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2019] [Indexed: 12/24/2022] Open
Abstract
The South American and West Indian Casque-headed Treefrogs (Hylidae: Hylinae: Lophyohylini) include 85 species. These are notably diverse in morphology (e.g. disparate levels of cranial hyperossification) and life history (e.g. different reproductive modes, chemical defences), have a wide distribution, and occupy habitats from the tropical rainforests to semiarid scrubland. In this paper, we present a phylogenetic analysis of this hylid tribe based on sequence fragments of up to five mitochondrial (12S, 16S, ND1, COI, Cytb) and six nuclear genes (POMC, RAG-1, RHOD, SIAH, TNS3, TYR). We included most of its species (> 96%), in addition to a number of new species. Our results indicate: (i) the paraphyly of Trachycephalus with respect to Aparasphenodon venezolanus; (ii) the nonmonophyly of Aparasphenodon, with Argenteohyla siemersi, Corythomantis galeata and Nyctimantis rugiceps nested within it, and Ap. venezolanus nested within Trachycephalus; (iii) the polyphyly of Corythomantis; (iv) the nonmonophyly of the recognized species groups of Phyllodytes; and (v) a pervasive low support for the deep relationships among the major clades of Lophyohylini, including C. greeningi and the monotypic genera Itapotihyla and Phytotriades. To remedy the nonmonophyly of Aparasphenodon, Corythomantis, and Trachycephalus, we redefined Nyctimantis to include Aparasphenodon (with the exception of Ap. venezolanus, which we transferred to Trachycephalus), Argenteohyla, and C. galeata. Additionally, our results indicate the need for taxonomic work in the following clades: (i) Trachycephalus dibernardoi and Tr. imitatrix; (ii) Tr. atlas, Tr. mambaiensis and Tr. nigromaculatus; and (iii) Phyllodytes. On the basis of our phylogenetic results, we analyzed the evolution of skull hyperossification and reproductive biology, with emphasis on the multiple independent origins of phytotelm breeding, in the context of Anura. We also analyzed the inter-related aspects of chemical defences, venom delivery, phragmotic behaviour, co-ossification, and prevention of evaporative water loss.
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Affiliation(s)
- Boris L Blotto
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A 1515, 13506-900, Rio Claro, São Paulo, Brazil.,Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, São Paulo, Brazil
| | - Mariana L Lyra
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A 1515, 13506-900, Rio Claro, São Paulo, Brazil
| | - Monica C S Cardoso
- Setor de Herpetologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, CEP 20940-040, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, São Paulo, Brazil
| | - Iuri R Dias
- Tropical Herpetology Laboratory, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP 45662-900, Ilhéus, Bahia, Brazil
| | - Euvaldo Marciano-Jr
- Tropical Herpetology Laboratory, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP 45662-900, Ilhéus, Bahia, Brazil
| | - Francisco Dal Vechio
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, São Paulo, Brazil
| | - Victor G D Orrico
- Tropical Herpetology Laboratory, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP 45662-900, Ilhéus, Bahia, Brazil
| | - Reuber A Brandão
- Laboratório de Fauna e Unidades de Conservação, Departamento de Engenharia Florestal, Universidade de Brasília, 70910-900, Brasília, Distrito Federal, Brazil
| | - Clodoaldo Lopes de Assis
- Museu de Zoologia João Moojen, Departamento de Biologia Animal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Amanda S F Lantyer-Silva
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A 1515, 13506-900, Rio Claro, São Paulo, Brazil
| | - Mike G Rutherford
- Department of Life Sciences, The University of The West Indies Zoology Museum, The University of The West Indies, St. Augustine, Trinidad & Tobago
| | - Giussepe Gagliardi-Urrutia
- Laboratorio de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Prédio 40, sala 110, 90619-900, Porto Alegre, Rio Grande do Sul, Brazil
| | - Mirco Solé
- Tropical Herpetology Laboratory, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP 45662-900, Ilhéus, Bahia, Brazil
| | - Diego Baldo
- Laboratorio de Genetica Evolutiva "Claudio Juan Bidau", Instituto de Biologıa Subtropical (CONICET-UNaM), Félix de Azara, 1552, CPA N3300LQF Posadas, Misiones, Argentina
| | - Ivan Nunes
- Laboratório de Herpetologia, Instituto de Biociências, Universidade Estadual Paulista, Campus do Litoral Paulista, CEP 11330-900, São Vicente, São Paulo, Brazil
| | - Rodrigo Cajade
- Laboratorio de Herpetología, Departamento de Biología, Facultad de Ciencias Exactas y Naturales y Agrimensura, CONICET, Universidad Nacional del Nordeste, Av. Libertad 5470, 3400, Corrientes, Argentina
| | - Ambrosio Torres
- Unidad Ejecutora Lillo, CONICET - Fundación Miguel Lillo, Miguel Lillo 251, 4000, San Miguel de Tucumán, Argentina
| | - Taran Grant
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, São Paulo, Brazil
| | - Karl-Heinz Jungfer
- Department of Biology, Institute of Integrated Sciences, University of Koblenz-Landau, Universitätsstr. 1, 56070, Koblenz, Germany
| | - Helio R da Silva
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Federal Rural do Rio de Janeiro, Caixa Postal 74524, 23851-970, Seropédica, Rio de Janeiro, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A 1515, 13506-900, Rio Claro, São Paulo, Brazil
| | - Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Angel Gallardo 470, C1405DJR, Buenos Aires, Argentina.,Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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5
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Echevarría LY, De la Riva I, Venegas PJ, Rojas-Runjaic FJM, R Dias I, Castroviejo-Fisher S. Total evidence and sensitivity phylogenetic analyses of egg-brooding frogs (Anura: Hemiphractidae). Cladistics 2021; 37:375-401. [PMID: 34478194 DOI: 10.1111/cla.12447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2020] [Indexed: 01/06/2023] Open
Abstract
We study the phylogenetic relationships of egg-brooding frogs, a group of 118 neotropical species, unique among anurans by having embryos with large bell-shaped gills and females carrying their eggs on the dorsum, exposed or inside a pouch. We assembled a total evidence dataset of published and newly generated data containing 51 phenotypic characters and DNA sequences of 20 loci for 143 hemiphractids and 127 outgroup terminals. We performed six analytical strategies combining different optimality criteria (parsimony and maximum likelihood), alignment methods (tree- and similarity-alignment), and three different indel coding schemes (fifth character state, unknown nucleotide, and presence/absence characters matrix). Furthermore, we analyzed a subset of the total evidence dataset to evaluate the impact of phenotypic characters on hemiphractid phylogenetic relationships. Our main results include: (i) monophyly of Hemiphractidae and its six genera for all our analyses, novel relationships among hemiphractid genera, and non-monophyly of Hemiphractinae according to our preferred phylogenetic hypothesis; (ii) non-monophyly of current supraspecific taxonomies of Gastrotheca, an updated taxonomy is provided; (iii) previous differences among studies were mainly caused by differences in analytical factors, not by differences in character/taxon sampling; (iv) optimality criteria, alignment method, and indel coding caused differences among optimal topologies, in that order of degree; (v) in most cases, parsimony analyses are more sensitive to the addition of phenotypic data than maximum likelihood analyses; (vi) adding phenotypic data resulted in an increase of shared clades for most analyses.
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Affiliation(s)
- Lourdes Y Echevarría
- Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, Porto Alegre, RS, 90619-900, Brazil.,División de Herpetología-Centro de Ornitología y Biodiversidad (CORBIDI), Urb. Huertos de San Antonio, Santa Rita No. 105 Of. 202, Surco, Lima, Perú
| | - Ignacio De la Riva
- Museo Nacional de Ciencias Naturales-CSIC, C/José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Pablo J Venegas
- División de Herpetología-Centro de Ornitología y Biodiversidad (CORBIDI), Urb. Huertos de San Antonio, Santa Rita No. 105 Of. 202, Surco, Lima, Perú
| | | | - Iuri R Dias
- Graduate Program in Zoology, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, Ilhéus, Bahia, 45662-900, Brazil
| | - Santiago Castroviejo-Fisher
- Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, Porto Alegre, RS, 90619-900, Brazil.,Department of Herpetology, American Museum of Natural History, New York, NY, 10024, USA
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6
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Torres A, Goloboff PA, Catalano SA. Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology). Cladistics 2021; 38:103-125. [DOI: 10.1111/cla.12477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
- Ambrosio Torres
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
| | - Pablo A. Goloboff
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
- American Museum of Natural History 200 Central Park West New York NY 10024 USA
| | - Santiago A. Catalano
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo Universidad Nacional de Tucumán Miguel Lillo 205 S. M. de Tucumán Tucumán 4000 Argentina
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7
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Smith BT, Mauck WM, Benz BW, Andersen MJ. Uneven Missing Data Skew Phylogenomic Relationships within the Lories and Lorikeets. Genome Biol Evol 2021; 12:1131-1147. [PMID: 32470111 PMCID: PMC7486955 DOI: 10.1093/gbe/evaa113] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2020] [Indexed: 01/21/2023] Open
Abstract
The resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense taxon sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally degraded, which presents various challenges. In this study, we evaluated how the coverage at variant sites and missing data among historical and modern samples impacts phylogenomic inference. We explored these patterns in the brush-tongued parrots (lories and lorikeets) of Australasia by sampling ultraconserved elements in 105 taxa. Trees estimated with low coverage characters had several clades where relationships appeared to be influenced by whether the sample came from historical or modern specimens, which were not observed when more stringent filtering was applied. To assess if the topologies were affected by missing data, we performed an outlier analysis of sites and loci, and a data reduction approach where we excluded sites based on data completeness. Depending on the outlier test, 0.15% of total sites or 38% of loci were driving the topological differences among trees, and at these sites, historical samples had 10.9× more missing data than modern ones. In contrast, 70% data completeness was necessary to avoid spurious relationships. Predictive modeling found that outlier analysis scores were correlated with parsimony informative sites in the clades whose topologies changed the most by filtering. After accounting for biased loci and understanding the stability of relationships, we inferred a more robust phylogenetic hypothesis for lories and lorikeets.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, New York
| | - William M Mauck
- Department of Ornithology, American Museum of Natural History, New York, New York.,New York Genome Center, New York, New York
| | - Brett W Benz
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico
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8
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Perera N, Galhena G, Ranawaka G. X-chromosomal STR based genetic polymorphisms and demographic history of Sri Lankan ethnicities and their relationship with global populations. Sci Rep 2021; 11:12748. [PMID: 34140598 PMCID: PMC8211843 DOI: 10.1038/s41598-021-92314-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 06/03/2021] [Indexed: 11/23/2022] Open
Abstract
A new 16 X-short tandem repeat (STR) multiplex PCR system has recently been developed for Sr Lankans, though its applicability in evolutionary genetics and forensic investigations has not been thoroughly assessed. In this study, 838 unrelated individuals covering all four major ethnic groups (Sinhalese, Sri Lankan Tamils, Indian Tamils and Moors) in Sri Lanka were successfully genotyped using this new multiplex system. The results indicated a high forensic efficiency for the tested loci in all four ethnicities confirming its suitability for forensic applications of Sri Lankans. Allele frequency distribution of Indian Tamils showed subtle but statistically significant differences from those of Sinhalese and Moors, in contrast to frequency distributions previously reported for autosomal STR alleles. This suggest a sex biased demographic history among Sri Lankans requiring a separate X-STR allele frequency database for Indian Tamils. Substantial differences observed in the patterns of LD among the four groups demand the use of a separate haplotype frequency databases for each individual ethnicity. When analysed together with other 14 world populations, all Sri Lankan ethnicities except Indian Tamils clustered closely with populations from Indian Bhil tribe, Bangladesh and Europe reflecting their shared Indo-Aryan ancestry.
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Affiliation(s)
- Nandika Perera
- Genetech Molecular Diagnostics, Colombo 08, Sri Lanka
- Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
| | - Gayani Galhena
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03, Sri Lanka.
| | - Gaya Ranawaka
- Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
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9
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Assessing topological congruence among concatenation-based phylogenomic approaches in empirical datasets. Mol Phylogenet Evol 2021; 161:107086. [PMID: 33609710 DOI: 10.1016/j.ympev.2021.107086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/25/2020] [Accepted: 01/22/2021] [Indexed: 10/22/2022]
Abstract
Assessing the effect of methodological decisions on the resulting hypotheses is critical in phylogenetics. Recent studies have focused on evaluating how model selection, orthology definition and confounding factors affect phylogenomic results. Here, we compare the results of three concatenated phylogenetic methods (Maximum Likelihood, ML; Bayesian Inference, BI; Maximum Parsimony, MP) in 157 empirical phylogenomic datasets. The resulting trees were very similar, with 96.7% of all nodes shared between BI and ML (90.6% for ML-MP and 89.1% for BI-MP). Differing nodes were predominantly those of lower support. The main conclusions of most of the studies agreed for the three phylogenetic methods and the discordance involved nodes considered as recalcitrant problems in systematics. The differences between methods were proportionally larger in datasets that analyze the relationships at higher taxonomic levels (particularly phyla and kingdoms), and independent of the number of characters included in the datasets. Note: a spanish version of this article is available in the Supplementary material (Supplementary material online).
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10
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Evidence of absence treated as absence of evidence: The effects of variation in the number and distribution of gaps treated as missing data on the results of standard maximum likelihood analysis. Mol Phylogenet Evol 2020; 154:106966. [PMID: 32971285 DOI: 10.1016/j.ympev.2020.106966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/15/2020] [Accepted: 09/15/2020] [Indexed: 11/23/2022]
Abstract
Although numerous studies have demonstrated the theoretical and empirical importance of treating gaps as insertion/deletion (indel) events in phylogenetic analyses, the standard approach to maximum likelihood (ML) analysis employed in the vast majority of empirical studies codes gaps as nucleotides of unknown identity ("missing data"). Therefore, it is imperative to understand the empirical consequences of different numbers and distributions of gaps treated as missing data. We evaluated the effects of variation in the number and distribution of gaps (i.e., no base, coded as IUPAC "." or "-") treated as missing data (i.e., any base, coded as "?" or IUPAC "N") in standard ML analysis. We obtained alignments with variable numbers and arrangements of gaps by aligning seven diverse empirical datasets under different gap opening costs using MAFFT. We selected the optimal substitution model for each alignment using the corrected Akaike Information Criterion in jModelTest2 and searched for optimal trees using GARLI. We also employed a Monte Carlo approach to randomly replace nucleotides with gaps (treated as missing data) in an empirical dataset to understand more precisely the effects of varying their number and distribution. To compare alignments, we developed four new indices and used several existing measures to quantify the number and distribution of gaps in all alignments. Our most important finding is that ML scores correlate negatively with gap opening costs and the amount of missing data. However, this negative relationship is not due to the increase in missing data per se-which increases ML scores-but instead to the effect of gaps on nucleotide homology. These variables also cause significant but largely unpredictable effects on tree topology.
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11
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King B. Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit. Syst Biol 2020; 70:283-294. [PMID: 32692834 DOI: 10.1093/sysbio/syaa057] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 11/14/2022] Open
Abstract
The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip dating affects the recovery of evolutionary relationships has yet to be fully explored. Here I show, through analysis of several data sets with multiple phylogenetic methods, that topologies produced by tip dating are outliers as compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip dating have better fit to stratigraphy than trees recovered by other methods under both the Gap Excess Ratio (GER) and the Stratigraphic Completeness Index (SCI). This is because trees with better stratigraphic fit are assigned a higher likelihood by the fossilized birth-death tree model. However, the degree to which the tree model favors tree topologies with high stratigraphic fit metrics is modulated by the diversification dynamics of the group under investigation. In particular, when net diversification rate is low, the tree model favors trees with a higher GER compared to when net diversification rate is high. Differences in stratigraphic fit and tree topology between tip dating and other methods are concentrated in parts of the tree with weaker character signal, as shown by successive deletion of the most incomplete taxa from two data sets. These results show that tip dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit an expectation that can be overturned by strong evidence from character data. [fossilized birth-death; fossils; missing data; morphological clock; morphology; parsimony; phylogenetics.].
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Affiliation(s)
- Benedict King
- Naturalis Biodiversity Center, Postbus 9517, 2300 RA, Leiden, The Netherlands.,College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
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12
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Smirnov V, Warnow T. Phylogeny Estimation Given Sequence Length Heterogeneity. Syst Biol 2020; 70:268-282. [PMID: 32692823 PMCID: PMC7875441 DOI: 10.1093/sysbio/syaa058] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/21/2022] Open
Abstract
Phylogeny estimation is a major step in many biological studies, and has many well known challenges. With the dropping cost of sequencing technologies, biologists now have increasingly large datasets available for use in phylogeny estimation. Here we address the challenge of estimating a tree given large datasets with a combination of full-length sequences and fragmentary sequences, which can arise due to a variety of reasons, including sample collection, sequencing technologies, and analytical pipelines. We compare two basic approaches: (1) computing an alignment on the full dataset and then computing a maximum likelihood tree on the alignment, or (2) constructing an alignment and tree on the full length sequences and then using phylogenetic placement to add the remaining sequences (which will generally be fragmentary) into the tree. We explore these two approaches on a range of simulated datasets, each with 1000 sequences and varying in rates of evolution, and two biological datasets. Our study shows some striking performance differences between methods, especially when there is substantial sequence length heterogeneity and high rates of evolution. We find in particular that using UPP to align sequences and RAxML to compute a tree on the alignment provides the best accuracy, substantially outperforming trees computed using phylogenetic placement methods. We also find that FastTree has poor accuracy on alignments containing fragmentary sequences. Overall, our study provides insights into the literature comparing different methods and pipelines for phylogenetic estimation, and suggests directions for future method development. [Phylogeny estimation, sequence length heterogeneity, phylogenetic placement.]
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Affiliation(s)
- Vladimir Smirnov
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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13
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Simmons MP, Kessenich J. Divergence and support among slightly suboptimal likelihood gene trees. Cladistics 2019; 36:322-340. [DOI: 10.1111/cla.12404] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Mark P. Simmons
- Department of Biology Colorado State University Fort Collins CO 80523‐1878 USA
| | - John Kessenich
- 305 W. Magnolia Street PMB 134 Fort Collins CO 80521 USA
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14
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Zhou Y, Zhang YQ, Xing XC, Zhang JQ, Ren Y. Straight From the Plastome: Molecular Phylogeny and Morphological Evolution of Fargesia (Bambusoideae: Poaceae). FRONTIERS IN PLANT SCIENCE 2019; 10:981. [PMID: 31447865 PMCID: PMC6691181 DOI: 10.3389/fpls.2019.00981] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/11/2019] [Indexed: 06/04/2023]
Abstract
Fargesia is ecologically and economically important in mountainous forests. Many Fargesia species are also important sources of food for some endangered animals such as the giant panda. Recent molecular phylogenetic analyses have revealed Fargesia as a polyphyletic group despite some unclear lineage affinities. In the present study, we reconstructed the phylogeny of Fargesia and its allies, including Thamnocalamus, Arundinaria (incl. Bashania), Yushania, Indocalamus, Ampelocalamus and Phyllostachys, from a plastome sequence matrix that contained 20 Fargesia and five Yushania species as ingroups, 16 species from nine other bamboo genera plus Oryza sativa and Zea mays as outgroups. Fargesia and its allies were broken into eight clades. Several Fargesia species were clustered into the Thamnocalamus clade and the Drepanostachyum + Himalayacalamus clade that rendered the polyphyly of Fargesia. The remaining six clades, including the Fargesia spathe clade, the Phyllostachys clade, Arundinaria fargesii, the Ampelocalamus clade, the Fargesia grossa clade, and the Fargesia macclureana clade, were identified. Molecular phylogenetic analyses supported that Yushania should be included in Fargesia (s.l.) which had synapomorphy of expanded leaf sheaths in varying degree at the basis of inflorescences, and further divided into the Fargesia spathe clade, the Fargesia grossa clade, and the Fargesia macclureana clade. All sampled species of Yushania were nested within the Fargesia grossa clade. The probable model of the origin of the species in the Fargesia spathe clade with spathe-like leaf sheath syndrome was proposed. Moreover, the formation of the spathe-like leaf sheath syndrome may be correlated with cold climatic conditions in Quaternary. Our results provide new sight into the phylogenetic relationship within Fargesia.
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Affiliation(s)
| | | | | | - Jian-Qiang Zhang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Yi Ren
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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15
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King B. Which morphological characters are influential in a Bayesian phylogenetic analysis? Examples from the earliest osteichthyans. Biol Lett 2019; 15:20190288. [PMID: 31311486 PMCID: PMC6684994 DOI: 10.1098/rsbl.2019.0288] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/19/2019] [Indexed: 12/12/2022] Open
Abstract
There has been much recent debate about which method is best for reconstructing the tree of life from morphological datasets. However, little attention has been paid to which characters, if any, are responsible for topological differences between trees recovered from competing methods on empirical datasets. Indeed, a simple procedure for finding characters supporting conflicting tree topologies is available in a parsimony framework, but an equivalent procedure in a model-based framework is lacking. Here, I introduce such a procedure and apply it to the problem of the 'psarolepid' osteichthyans. The 'psarolepids', which include the earliest known osteichthyans, are weakly supported as stem osteichthyans under parsimony but strongly supported as sarcopterygians in Bayesian analysis. The Bayesian result is driven by just two characters, both of which relate to the intracranial joint of sarcopterygians. Important characters that support a stem osteichthyan affinity for 'psarolepids', such as the absence of tooth enamel, have virtually no effect in a Bayesian framework. This is because of a bias towards characters with relatively complete sampling, a bias that has previously been reported for molecular data. This has important implications for Bayesian analysis of morphological datasets in general, as characters from different body parts commonly have different levels of coding completeness. Methods to critically appraise character support for conflicting phylogenetic hypotheses, such as that used here, should form an important part of phylogenetic analyses.
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Affiliation(s)
- Benedict King
- Naturalis Biodiversity Center, Postbus 9517, 2300 RA Leiden, The Netherlands
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16
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Goloboff PA, Arias JS. Likelihood approximations of implied weights parsimony can be selected over the Mk model by the Akaike information criterion. Cladistics 2019; 35:695-716. [DOI: 10.1111/cla.12380] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 01/09/2023] Open
Affiliation(s)
- Pablo A. Goloboff
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas Fundación Miguel Lillo Miguel Lillo 251 4000 S.M. de Tucumán Argentina
| | - J. Salvador Arias
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas Fundación Miguel Lillo Miguel Lillo 251 4000 S.M. de Tucumán Argentina
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17
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Simmons MP, Sloan DB, Springer MS, Gatesy J. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Mol Phylogenet Evol 2019; 131:80-92. [DOI: 10.1016/j.ympev.2018.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023]
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18
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Alda F, Tagliacollo VA, Bernt MJ, Waltz BT, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P. Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting. Syst Biol 2018; 68:573-593. [DOI: 10.1093/sysbio/syy085] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Fernando Alda
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA
| | - Victor A Tagliacollo
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Ipirianga, 04263-000, São Paulo, São Paulo, Brazil
| | - Maxwell J Bernt
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - Brandon T Waltz
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - William B Ludt
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Brant C Faircloth
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - James S Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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19
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Crouch NMA, Ramanauskas K, Igić B. Tip-dating and the origin of Telluraves. Mol Phylogenet Evol 2018; 131:55-63. [PMID: 30385308 DOI: 10.1016/j.ympev.2018.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 09/05/2018] [Accepted: 10/09/2018] [Indexed: 10/28/2022]
Abstract
Despite a relatively vast accumulation of molecular data, the timing of diversification of modern bird lineages remains elusive. Accurate dating of the origination of Telluraves-a clade of birds defined by their arboreality-is of particular interest, as it contains the most species-rich avian group, the passerines. Historically, neontological studies have estimated a Cretaceous origin for the group, but more recent studies have recovered Cenozoic dates, closer to the oldest known fossils for the group. We employ total-evidence dating to estimate divergence times that are expected to be both less sensitive to prior assumptions and more accurate. Specifically, we use a large collection of morphological character data from arboreal bird fossils, along with combined molecular sequence and morphological character data from extant taxa. Our analyses recover a Late Cretaceous origin for crown Telluraves, with a few lineages crossing the K-Pg boundary. Following the K-Pg boundary, our results show the group underwent rapid diversification, likely benefiting from increased ecological opportunities in the aftermath of the extinction event. We find very little confidence for the precise topological placement of many extinct taxa, possibly due to rapid diversification, paucity of character data, and rapid morphological differentiation during the early history of the group.
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Affiliation(s)
- Nicholas M A Crouch
- Dept. of Biological Sciences, University of Illinois at Chicago, 840 West Taylor St. MC067, Chicago, IL 60607, USA; Department of Zoology, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
| | - Karolis Ramanauskas
- Dept. of Biological Sciences, University of Illinois at Chicago, 840 West Taylor St. MC067, Chicago, IL 60607, USA; Department of Zoology, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
| | - Boris Igić
- Dept. of Biological Sciences, University of Illinois at Chicago, 840 West Taylor St. MC067, Chicago, IL 60607, USA; Department of Zoology, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
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20
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Sayyari E, Whitfield JB, Mirarab S. Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction. Mol Biol Evol 2018; 34:3279-3291. [PMID: 29029241 DOI: 10.1093/molbev/msx261] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Species tree reconstruction from genome-wide data is increasingly being attempted, in most cases using a two-step approach of first estimating individual gene trees and then summarizing them to obtain a species tree. The accuracy of this approach, which promises to account for gene tree discordance, depends on the quality of the inferred gene trees. At the same time, phylogenomic and phylotranscriptomic analyses typically use involved bioinformatics pipelines for data preparation. Errors and shortcomings resulting from these preprocessing steps may impact the species tree analyses at the other end of the pipeline. In this article, we first show that the presence of fragmentary data for some species in a gene alignment, as often seen on real data, can result in substantial deterioration of gene trees, and as a result, the species tree. We then investigate a simple filtering strategy where individual fragmentary sequences are removed from individual genes but the rest of the gene is retained. Both in simulations and by reanalyzing a large insect phylotranscriptomic data set, we show the effectiveness of this simple filtering strategy.
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Affiliation(s)
- Erfan Sayyari
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA
| | | | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA
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21
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Donath A, Stadler PF. Split-inducing indels in phylogenomic analysis. Algorithms Mol Biol 2018; 13:12. [PMID: 30026791 PMCID: PMC6047143 DOI: 10.1186/s13015-018-0130-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 06/16/2018] [Indexed: 11/13/2022] Open
Abstract
Background Most phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps. Results Here we show that gap patterns in large-scale, genome-wide alignments are themselves phylogenetically informative and can be used to infer reliable phylogenies provided the gap data are properly filtered to reduce noise introduced by the alignment method. We introduce here the notion of split-inducing indels (splids) that define an approximate bipartition of the taxon set. We show both in simulated data and in case studies on real-life data that splids can be efficiently extracted from phylogenomic data sets. Conclusions Suitably processed gap patterns extracted from genome-wide alignment provide a surprisingly clear phylogenetic signal and an allow the inference of accurate phylogenetic trees. Electronic supplementary material The online version of this article (10.1186/s13015-018-0130-7) contains supplementary material, which is available to authorized users.
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22
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Affiliation(s)
- David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
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23
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Breinholt JW, Earl C, Lemmon AR, Lemmon EM, Xiao L, Kawahara AY. Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics. Syst Biol 2018; 67:78-93. [PMID: 28472519 DOI: 10.1093/sysbio/syx048] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 04/28/2017] [Indexed: 11/12/2022] Open
Abstract
The advent of next-generation sequencing technology has allowed for thecollection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels. We combine AHE and transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea $+$ Gelechioidea $+$ Thyridoidea) $+$ (Papilionoidea $+$ Pyraloidea $+$ Macroheterocera). To examine the efficacy of AHE at a shallow taxonomic level, phylogenetic analyses were also conducted on a sister group representing a more recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; resulting trees supported new phylogenetics relationships, especially within the Saturniidae and Sphingidae (e.g., Hemarina derived in the latter). We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community.
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Affiliation(s)
- Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.,RAPiD Genomics, Gainesville, FL 32601, USA
| | - Chandra Earl
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Lei Xiao
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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24
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Tripp EA, Tsai YE, Zhuang Y, Dexter KG. RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia. Ecol Evol 2017; 7:7920-7936. [PMID: 29043045 PMCID: PMC5632676 DOI: 10.1002/ece3.3274] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/16/2017] [Accepted: 06/20/2017] [Indexed: 01/04/2023] Open
Abstract
Deserts, even those at tropical latitudes, often have strikingly low levels of plant diversity, particularly within genera. One remarkable exception to this pattern is the genus Petalidium (Acanthaceae), in which 37 of 40 named species occupy one of the driest environments on Earth, the Namib Desert of Namibia and neighboring Angola. To contribute to understanding this enigmatic diversity, we generated RADseq data for 47 accessions of Petalidium representing 22 species. We explored the impacts of 18 different combinations of assembly parameters in de novo assembly of the data across nine levels of missing data plus a best practice assembly using a reference Acanthaceae genome for a total of 171 sequence datasets assembled. RADseq data assembled at several thresholds of missing data, including 90% missing data, yielded phylogenetic hypotheses of Petalidium that were confidently and nearly fully resolved, which is notable given that divergence time analyses suggest a crown age for African species of 3.6-1.4 Ma. De novo assembly of our data yielded the most strongly supported and well-resolved topologies; in contrast, reference-based assembly performed poorly, perhaps due in part to moderate phylogenetic divergence between the reference genome, Ruellia speciosa, and the ingroup. Overall, we found that Petalidium, despite the harshness of the environment in which species occur, shows a net diversification rate (0.8-2.1 species per my) on par with those of diverse genera in tropical, Mediterranean, and alpine environments.
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Affiliation(s)
- Erin A. Tripp
- Department of Ecology & Evolutionary BiologyUCB 334University of ColoradoBoulderCOUSA
- Museum of Natural HistoryUCB 350University of ColoradoBoulderCOUSA
| | - Yi‐Hsin Erica Tsai
- Department of Ecology & Evolutionary BiologyUCB 334University of ColoradoBoulderCOUSA
- Museum of Natural HistoryUCB 350University of ColoradoBoulderCOUSA
| | - Yongbin Zhuang
- Department of Ecology & Evolutionary BiologyUCB 334University of ColoradoBoulderCOUSA
- Museum of Natural HistoryUCB 350University of ColoradoBoulderCOUSA
| | - Kyle G. Dexter
- School of GeoSciencesUniversity of EdinburghEdinburghUK
- Royal Botanic Garden EdinburghEdinburghUK
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25
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Revised classification and phylogeny of an Afrotropical species group based on molecular and morphological data, with the description of a new genus (Coleoptera: Scarabaeidae: Onthophagini). ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-016-0297-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Zhao L, Li X, Zhang N, Zhang SD, Yi TS, Ma H, Guo ZH, Li DZ. Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids. Mol Phylogenet Evol 2016; 105:166-176. [DOI: 10.1016/j.ympev.2016.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 06/06/2016] [Accepted: 06/27/2016] [Indexed: 12/28/2022]
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27
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Hosner PA, Faircloth BC, Glenn TC, Braun EL, Kimball RT. Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes). Mol Biol Evol 2015; 33:1110-25. [PMID: 26715628 DOI: 10.1093/molbev/msv347] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Production of massive DNA sequence data sets is transforming phylogenetic inference, but best practices for analyzing such data sets are not well established. One uncertainty is robustness to missing data, particularly in coalescent frameworks. To understand the effects of increasing matrix size and loci at the cost of increasing missing data, we produced a 90 taxon, 2.2 megabase, 4,800 locus sequence matrix of landfowl using target capture of ultraconserved elements. We then compared phylogenies estimated with concatenated maximum likelihood, quartet-based methods executed on concatenated matrices and gene tree reconciliation methods, across five thresholds of missing data. Results of maximum likelihood and quartet analyses were similar, well resolved, and demonstrated increasing support with increasing matrix size and sparseness. Conversely, gene tree reconciliation produced unexpected relationships when we included all informative loci, with certain taxa placed toward the root compared with other approaches. Inspection of these taxa identified a prevalence of short average contigs, which potentially biased gene tree inference and caused erroneous results in gene tree reconciliation. This suggests that the more problematic missing data in gene tree-based analyses are partial sequences rather than entire missing sequences from locus alignments. Limiting gene tree reconciliation to the most informative loci solved this problem, producing well-supported topologies congruent with concatenation and quartet methods. Collectively, our analyses provide a well-resolved phylogeny of landfowl, including strong support for previously problematic relationships such as those among junglefowl (Gallus), and clarify the position of two enigmatic galliform genera (Lerwa, Melanoperdix) not sampled in previous molecular phylogenetic studies.
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Affiliation(s)
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia
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28
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Zhang S, Bian Y, Li L, Sun K, Wang Z, Zhao Q, Zha L, Cai J, Gao Y, Ji C, Li C. Population genetic study of 34 X-Chromosome markers in 5 main ethnic groups of China. Sci Rep 2015; 5:17711. [PMID: 26634331 PMCID: PMC4669481 DOI: 10.1038/srep17711] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/04/2015] [Indexed: 01/09/2023] Open
Abstract
As a multi-ethnic country, China has some indigenous population groups which vary in culture and social customs, perhaps as a result of geographic isolation and different traditions. However, upon close interactions and intermarriage, admixture of different gene pools among these ethnic groups may occur. In order to gain more insight on the genetic background of X-Chromosome from these ethnic groups, a set of X-markers (18 X-STRs and 16 X-Indels) was genotyped in 5 main ethnic groups of China (HAN, HUI, Uygur, Mongolian, Tibetan). Twenty-three private alleles were detected in HAN, Uygur, Tibetan and Mongolian. Significant differences (p < 0.0001) were all observed for the 3 parameters of heterozygosity (Ho, He and UHe) among the 5 ethnic groups. Highest values of Nei genetic distance were always observed at HUI-Uygur pairwise when analyzed with X-STRs or X-Indels separately and combined. Phylogenetic tree and PCA analyses revealed a clear pattern of population differentiation of HUI and Uygur. However, the HAN, Tibetan and Mongolian ethnic groups were closely clustered. Eighteen X-Indels exhibited in general congruent phylogenetic signal and similar cluster among the 5 ethnic groups compared with 16 X-STRs. Aforementioned results proved the genetic polymorphism and potential of the 34 X-markers in the 5 ethnic groups.
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Affiliation(s)
- Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai 200063, P.R. China.,State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai 200063, P.R. China
| | - Li Li
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai 200063, P.R. China
| | - Kuan Sun
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, P.R.China
| | - Zheng Wang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai 200063, P.R. China
| | - Qi Zhao
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai 200063, P.R. China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, P.R. China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, P.R. China
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou 215123, P.R. China
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai 200063, P.R. China
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29
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Xi Z, Liu L, Davis CC. The Impact of Missing Data on Species Tree Estimation. Mol Biol Evol 2015; 33:838-60. [DOI: 10.1093/molbev/msv266] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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30
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Jones LR, Sede M, Manrique JM, Quarleri J. Virus evolution during chronic hepatitis B virus infection as revealed by ultradeep sequencing data. J Gen Virol 2015; 97:435-444. [PMID: 26581478 DOI: 10.1099/jgv.0.000344] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Despite chronic hepatitis B virus (HBV) infection (CHB) being a leading cause of liver cirrhosis and cancer, HBV evolution during CHB is not fully understood. Recent studies have indicated that virus diversity progressively increases along the course of CHB and that some virus mutations correlate with severe liver conditions such as chronic hepatitis, cirrhosis and hepatocellular carcinoma. Using ultradeep sequencing (UDS) data from an intrafamilial case, we detected such mutations at low frequencies among three immunotolerant patients and at high frequencies in an inactive carrier. Furthermore, our analyses indicated that the HBV population from the seroconverter patient underwent many genetic changes in response to virus clearance. Together, these data indicate a potential use of UDS for developing non-invasive biomarkers for monitoring disease changes over time or in response to specific therapies. In addition, our analyses revealed that virus clearance seemed not to require the virus effective population size to decline. A detailed genetic analysis of the viral lineages arising during and after the clearance suggested that mutations at or close to critical elements of the core promoter (enhancer II, epsilon encapsidation signal, TA2, TA3 and direct repeat 1-hormone response element) might be responsible for a sustained replication. This hypothesis requires the decline in virus load to be explained by constant clearance of virus-producing hepatocytes, consistent with the sustained progress towards serious liver conditions experienced by many CHB patients.
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Affiliation(s)
- Leandro R Jones
- Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales sede Trelew, Universidad Nacional de la Patagonia San Juan Bosco, 9 de Julio y Begrano S/N (9100) Trelew, Chubut, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917 (C1083ACA) Buenos Aires, Argentina
| | - Mariano Sede
- Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917 (C1083ACA) Buenos Aires, Argentina.,Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155-Piso 11 (C1121ABG) Buenos Aires, Argentina
| | - Julieta M Manrique
- Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917 (C1083ACA) Buenos Aires, Argentina.,Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales sede Trelew, Universidad Nacional de la Patagonia San Juan Bosco, 9 de Julio y Begrano S/N (9100) Trelew, Chubut, Argentina
| | - Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155-Piso 11 (C1121ABG) Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917 (C1083ACA) Buenos Aires, Argentina
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31
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Dillman CB, Sidlauskas BL, Vari RP. A morphological supermatrix‐based phylogeny for the Neotropical fish superfamily Anostomoidea (Ostariophysi: Characiformes): phylogeny, missing data and homoplasy. Cladistics 2015; 32:276-296. [DOI: 10.1111/cla.12127] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 11/30/2022] Open
Affiliation(s)
- Casey B. Dillman
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution PO Box 37012 MRC‐159 Washington DC 20013‐7012 USA
| | - Brian L. Sidlauskas
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution PO Box 37012 MRC‐159 Washington DC 20013‐7012 USA
- Department of Fisheries and Wildlife Oregon State University 104 Nash Hall Corvallis OR 97331‐3803 USA
- National Evolutionary Synthesis Center 2024 W. Main St. A200 Durham NC 27705 USA
| | - Richard P. Vari
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution PO Box 37012 MRC‐159 Washington DC 20013‐7012 USA
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32
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Zheng Y, Wiens JJ. Do missing data influence the accuracy of divergence-time estimation with BEAST? Mol Phylogenet Evol 2015; 85:41-9. [PMID: 25681677 DOI: 10.1016/j.ympev.2015.02.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/26/2015] [Accepted: 02/01/2015] [Indexed: 10/24/2022]
Abstract
Time-calibrated phylogenies have become essential to evolutionary biology. A recurrent and unresolved question for dating analyses is whether genes with missing data cells should be included or excluded. This issue is particularly unclear for the most widely used dating method, the uncorrelated lognormal approach implemented in BEAST. Here, we test the robustness of this method to missing data. We compare divergence-time estimates from a nearly complete dataset (20 nuclear genes for 32 species of squamate reptiles) to those from subsampled matrices, including those with 5 or 2 complete loci only and those with 5 or 8 incomplete loci added. In general, missing data had little impact on estimated dates (mean error of ∼5Myr per node or less, given an overall age of ∼220Myr in squamates), even when 80% of sampled genes had 75% missing data. Mean errors were somewhat higher when all genes were 75% incomplete (∼17Myr). However, errors increased dramatically when only 2 of 9 fossil calibration points were included (∼40Myr), regardless of missing data. Overall, missing data (and even numbers of genes sampled) may have only minor impacts on the accuracy of divergence dating with BEAST, relative to the dramatic effects of fossil calibrations.
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Affiliation(s)
- Yuchi Zheng
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-088, USA.
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-088, USA.
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