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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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2
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Heinicke MP, Lemmon AR, Lemmon EM, McGrath K, Hedges SB. Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae). Mol Phylogenet Evol 2018; 118:145-155. [DOI: 10.1016/j.ympev.2017.09.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/15/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
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3
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Sansom RS, Wills MA. Differences between hard and soft phylogenetic data. Proc Biol Sci 2017; 284:20172150. [PMID: 29237859 PMCID: PMC5745416 DOI: 10.1098/rspb.2017.2150] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/15/2017] [Indexed: 11/20/2022] Open
Abstract
When building the tree of life, variability of phylogenetic signal is often accounted for by partitioning gene sequences and testing for differences. The same considerations, however, are rarely applied to morphological data, potentially undermining its use in evolutionary contexts. Here, we apply partition heterogeneity tests to 59 animal datasets to demonstrate that significant differences exist between the phylogenetic signal conveyed by 'hard' and 'soft' characters (bones, teeth and shells versus myology, integument etc). Furthermore, the morphological partitions differ significantly in their consistency relative to independent molecular trees. The observed morphological differences correspond with missing data biases, and as such their existence presents a problem not only for phylogeny reconstruction, but also for interpretations of fossil data. Evolutionary inferences drawn from clades in which hard, readily fossilizable characters are relatively less consistent and different from other morphology (mammals, bivalves) may be less secure. More secure inferences might be drawn from the fossil record of clades that exhibit fewer differences, or exhibit more consistent hard characters (fishes, birds). In all cases, it will be necessary to consider the impact of missing data on empirical data, and the differences that exist between morphological modules.
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Affiliation(s)
- Robert S Sansom
- School of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Matthew A Wills
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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4
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Paddock CD, Allerdice MEJ, Karpathy SE, Nicholson WL, Levin ML, Smith TC, Becker T, Delph RJ, Knight RN, Ritter JM, Sanders JH, Goddard J. Unique Strain of Rickettsia parkeri Associated with the Hard Tick Dermacentor parumapertus Neumann in the Western United States. Appl Environ Microbiol 2017; 83:e03463-16. [PMID: 28213544 PMCID: PMC5394329 DOI: 10.1128/aem.03463-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/13/2017] [Indexed: 11/20/2022] Open
Abstract
In 1953, investigators at the Rocky Mountain Laboratories in Hamilton, MT, described the isolation of a spotted fever group Rickettsia (SFGR) species from Dermacentor parumapertus ticks collected from black-tailed jackrabbits (Lepus californicus) in northern Nevada. Several decades later, investigators characterized this SFGR (designated the parumapertus agent) by using mouse serotyping methods and determined that it represented a distinct rickettsial serotype closely related to Rickettsia parkeri; nonetheless, the parumapertus agent was not further characterized or studied. To our knowledge, no isolates of the parumapertus agent remain in any rickettsial culture collection, which precludes contemporary phylogenetic placement of this enigmatic SFGR. To rediscover the parumapertus agent, adult-stage D. parumapertus ticks were collected from black-tailed jackrabbits shot or encountered as roadkills in Arizona, Utah, or Texas from 2011 to 2016. A total of 339 ticks were collected and evaluated for infection with Rickettsia species. Of 112 D. parumapertus ticks collected in south Texas, 16 (14.3%) contained partial ompA sequences with the closest identity (99.6%) to Rickettsia sp. strain Atlantic rainforest Aa46, an SFGR that is closely related or identical to an SFGR species that causes a mild rickettsiosis in several states of Brazil. A pure isolate, designated strain Black Gap, was cultivated in Vero E6 cells, and sequence analysis of the rrs, gltA, sca0, sca5, and sca4 genes also revealed the closest genetic identity to Rickettsia sp. Atlantic rainforest Aa46. Phylogenetic analysis of the five concatenated rickettsial genes place Rickettsia sp. strain Black Gap and Rickettsia sp. Atlantic rainforest Aa46 with R. parkeri in a distinct and well-supported clade.IMPORTANCE We suggest that Rickettsia sp. Black Gap and Rickettsia sp. Atlantic rainforest Aa46 represent nearly identical strains of R. parkeri and that Rickettsia sp. Black Gap or a very similar strain of R. parkeri represents the parumapertus agent. The close genetic relatedness among these taxa, as well as the response of guinea pigs infected with the Black Gap strain, suggests that R. parkeri Black Gap could cause disease in humans. The identification of this organism could also account, at least in part, for the remarkable differences in severity ascribed to Rocky Mountain spotted fever (RMSF) among various regions of the American West during the early 20th century. We suggest that the wide variation in case fatality rates attributed to RMSF could have occurred by the inadvertent inclusion of cases of milder disease caused by R. parkeri Black Gap.
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Affiliation(s)
- Christopher D Paddock
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michelle E J Allerdice
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sandor E Karpathy
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - William L Nicholson
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael L Levin
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Travis C Smith
- Texas Parks and Wildlife Department, Black Gap Wildlife Management Area, Alpine, Texas, USA
| | - Tom Becker
- Utah Division of Wildlife Resources, Springville, Utah, USA
| | - Robert J Delph
- Center for Environmental Management of Military Lands, United States Army Dugway Proving Ground, Utah, USA
| | - Robert N Knight
- Environmental Department, United States Army Dugway Proving Ground, Utah, USA
| | - Jana M Ritter
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jeanine H Sanders
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jerome Goddard
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, Mississippi, USA
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5
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Kjer KM, Simon C, Yavorskaya M, Beutel RG. Progress, pitfalls and parallel universes: a history of insect phylogenetics. J R Soc Interface 2016; 13:20160363. [PMID: 27558853 PMCID: PMC5014063 DOI: 10.1098/rsif.2016.0363] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/19/2016] [Indexed: 11/12/2022] Open
Abstract
The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.
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Affiliation(s)
- Karl M Kjer
- Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Margarita Yavorskaya
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
| | - Rolf G Beutel
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
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6
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Dallai R, Mercati D, Mashimo Y, Machida R, Beutel RG. The fine structure of the rectal pads of Zorotypus caudelli Karny (Zoraptera, Insecta). ARTHROPOD STRUCTURE & DEVELOPMENT 2016; 45:380-388. [PMID: 27368527 DOI: 10.1016/j.asd.2016.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/16/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
The rectal pads of a species of the controversial polyneopteran order Zoraptera were examined using histological sections and TEM micrographs. Six pads are present along the thin rectal epithelium. Each pad consists of a few large principal cells surrounded by flattened junctional cells, which extend also beneath the principal cells. The cells are lined by a thin apical cuticle. No basal cells and no cavity have been observed beneath the pad. Principal cells have a regular layer of apical microvilli and are joined by intercellular septate junctions, which are interrupted by short dilatations of the intercellular space. At these levels the two adjacent plasma membranes are joined by short zonulae adhaerentes. In the cytoplasm, a rich system of strict associations between lateral plasma membranes and mitochondria forms scalariform junctions. Rectal pads share ultrastructural features with similar excretory organs of several neopteran groups, in particular with Blattodea (roaches and termites) and Thysanoptera, and are involved in fluid reabsorption and ion regulation.
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Affiliation(s)
- R Dallai
- Department of Life Sciences, Via A. Moro 2, University of Siena, I-53100 Siena, Italy.
| | - D Mercati
- Department of Life Sciences, Via A. Moro 2, University of Siena, I-53100 Siena, Italy
| | - Y Mashimo
- Sugadaira Montane Research Center, University of Tsukuba, Nagano 386-2204, Japan
| | - R Machida
- Sugadaira Montane Research Center, University of Tsukuba, Nagano 386-2204, Japan
| | - R G Beutel
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, Erbertstraße 1, 07743 Jena, Germany
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7
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Ford E, Wheeler WC. Comparison of heuristic approaches to the generalized tree alignment problem. Cladistics 2015; 32:452-460. [DOI: 10.1111/cla.12142] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2015] [Indexed: 11/27/2022] Open
Affiliation(s)
- Eric Ford
- Department of Mathematics & Computer Science; Lehman College; CUNY; Bronx NY 10468 USA
- Division of Invertebrate Zoology; American Museum of Natural History; New York NY 10024 USA
| | - Ward C. Wheeler
- Division of Invertebrate Zoology; American Museum of Natural History; New York NY 10024 USA
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8
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Baeza JA, Bauer RT, Okuno J, Thiel M. Molecular phylogeny of hinge-beak shrimps (Decapoda: Caridea:RhynchocinetesandCinetorhynchus) and allies: a formal test of familiar and generic monophyly using a multilocus phylogeny. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12173] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- J. Antonio Baeza
- Department of Biological Sciences; Clemson University; 132 Long Hall Clemson South Carolina 29634 USA
- Smithsonian Marine Station at Fort Pierce; 701 Seaway Drive Fort Pierce Florida 34949 USA
- Departamento de Biología Marina; Facultad de Ciencias del Mar; Universidad Católica del Norte; Larrondo 1281 Coquimbo Chile
| | - Raymond T. Bauer
- Department of Biology; University of Louisiana at Lafayette; P.O. Box 42451 Lafayette Louisiana USA
| | - Junji Okuno
- Coastal Branch of Natural History Museum and Institute; Chiba, 123 Yoshio, Katsuura Chiba 299-5242 Japan
| | - Martin Thiel
- Departamento de Biología Marina; Facultad de Ciencias del Mar; Universidad Católica del Norte; Larrondo 1281 Coquimbo Chile
- Centro de Estudios Avanzados en Zonas Aridas CEAZA; Coquimbo Chile
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9
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Dallai R, Gottardo M, Mercati D, Machida R, Mashimo Y, Matsumura Y, Rafael JA, Beutel RG. Comparative morphology of spermatozoa and reproductive systems of zorapteran species from different world regions (Insecta, Zoraptera). ARTHROPOD STRUCTURE & DEVELOPMENT 2014; 43:371-383. [PMID: 24657729 DOI: 10.1016/j.asd.2014.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 06/03/2023]
Abstract
The male and female reproductive apparatus of Zorotypus magnicaudelli (Malaysia), Zorotypus huxleyi (Ecuador) and Zorotypus weidneri (Brazil) were examined and documented in detail. The genital apparatus and sperm of the three species show only minor differences. The testes are larger in Z. magnicaudelli. Z. huxleyi lacks the helical appendage in the accessory glands. A long cuticular flagellum is present in Z. magnicaudelli and in the previously studied Zorotypus caudelli like in several other species, whereas it is absent in Z. weidneri, Z. huxleyi, Zorotypus hubbardi, Zorotypus impolitus and Zorotypus guineensis. Characteristic features of the very similar sperm are the presence of: a) two dense arches above the axoneme; b) a 9 + 9+2 axoneme with detached subtubules A and B of doublets 1 and 6; c) the axonemal end degenerating with enlarging accessory tubules; d) accessory tubules with 17 protofilaments; e) three accessory bodies beneath the axoneme; and f) two mitochondrial derivatives of equal shape. The first characteristic (a) is unknown outside of Zoraptera and possibly autapomorphic. The sperm structure differs distinctly in Z. impolitus and Z. hubbardi, which produce giant sperm and possess a huge spermatheca. The presence of the same sperm type in species either provided with a sclerotized coiled flagellum in males or lacking this structure indicates that a different organization of the genital apparatus does not necessarily affect the sperm structure. The flagellum and its pouch has probably evolved within Zoraptera, but it cannot be excluded that it is a groundplan feature and was reduced several times. The fossil evidence and our findings suggest that distinct modifications in the genital apparatus occurred before the fragmentation of the Gondwanan landmass in the middle Cretaceous.
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Affiliation(s)
- Romano Dallai
- Department of Life Sciences, Via A. Moro 2, University of Siena, I-53100 Siena, Italy.
| | - Marco Gottardo
- Department of Life Sciences, Via A. Moro 2, University of Siena, I-53100 Siena, Italy.
| | - David Mercati
- Department of Life Sciences, Via A. Moro 2, University of Siena, I-53100 Siena, Italy.
| | - Ryuichiro Machida
- Sugadaira Montane Research Center, University of Tsukuba, Nagano 386-2204, Japan.
| | - Yuta Mashimo
- Sugadaira Montane Research Center, University of Tsukuba, Nagano 386-2204, Japan.
| | - Yoko Matsumura
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, Erbertstr. 1, D-07743 Jena, Germany.
| | - José Albertino Rafael
- Instituto Nacional de Pesquisas da Amazonia, Caixa Postal 478, 69011-970 Manaus, AM, Brazil.
| | - Rolf Georg Beutel
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, Erbertstr. 1, D-07743 Jena, Germany.
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10
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Mashimo Y, Beutel RG, Dallai R, Lee CY, Machida R. Embryonic development of Zoraptera with special reference to external morphology, and its phylogenetic implications (Insecta). J Morphol 2013; 275:295-312. [DOI: 10.1002/jmor.20215] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/02/2013] [Accepted: 09/06/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Yuta Mashimo
- Sugadaira Montane Research Center; University of Tsukuba; Sugadaira Kogen, Ueda Nagano 386-2204 Japan
| | - Rolf G. Beutel
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; Friedrich-Schiller-Universität Jena; Erbertstrasse 1 Jena 07743 Germany
| | - Romano Dallai
- Department of Life Sciences; University of Siena; Via A. Moro 2 Siena I-53100 Italy
| | - Chow-Yang Lee
- School of Biological Sciences; Universiti Sains Malaysia; Penang 11800 Malaysia
| | - Ryuichiro Machida
- Sugadaira Montane Research Center; University of Tsukuba; Sugadaira Kogen, Ueda Nagano 386-2204 Japan
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11
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Friedemann K, Spangenberg R, Yoshizawa K, Beutel RG. Evolution of attachment structures in the highly diverse Acercaria (Hexapoda). Cladistics 2013; 30:170-201. [DOI: 10.1111/cla.12030] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2013] [Indexed: 11/26/2022] Open
Affiliation(s)
- Katrin Friedemann
- Entomology Group; Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; FSU Jena 07743 Germany
- Max Planck Institute for Chemical Ecology; 07745 Jena Germany
| | - Rico Spangenberg
- Entomology Group; Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; FSU Jena 07743 Germany
- Max Planck Institute for Chemical Ecology; 07745 Jena Germany
| | - Kazunori Yoshizawa
- Laboratory of Systematic Entomology; Graduate School of Agriculture; Hokkaido University; Sapporo 060-8589 Japan
| | - Rolf G. Beutel
- Entomology Group; Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; FSU Jena 07743 Germany
- Max Planck Institute for Chemical Ecology; 07745 Jena Germany
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12
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Khademvatan S, Rahim F, Tavalla M, Abdizadeh R, Hashemitabar M. PCR-based molecular characterization of Toxocara spp. using feces of stray cats: a study from Southwest Iran. PLoS One 2013; 8:e65293. [PMID: 23755213 PMCID: PMC3670902 DOI: 10.1371/journal.pone.0065293] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 04/22/2013] [Indexed: 11/18/2022] Open
Abstract
Feces of stray cat are potential sources of gastrointestinal parasites and play a crucial role in spreading and transmitting parasite eggs, larvae, and oocysts through contamination of soil, food, or water. In this study, we investigated the prevalence of Toxocara spp. infection in stray cats in Ahvaz city, southwest Iran. Eggs of Toxocara spp. in feces of stray cats were detected by the sucrose flotation method, and identification was conducted by polymerase chain reaction (PCR) and DNA sequencing. Of the 140 fecal samples that were randomly collected from public environments during the months of January to May 2012, 45% were found to harbour Toxocara spp. eggs. The highest prevalence of Toxocara spp. eggs was found in the central area of Ahvaz city (28.6%). T. canis eggs were found in 4 (6.34%) of the 63 positive samples. Stray cats are found in parks, playgrounds, and other public places and may be a potential contamination risk. Identification of Toxocara spp. using molecular methods is sufficiently sensitive to detect low levels of parasites and identify the different Toxocara spp. in feces. The relatively high prevalence of Toxocara spp. infection may continue to increase due to lack of effective environmental hygiene control in Iran. Consequently, there is a need to plan adequate programs to detect, identify, and control this infection as well as stray cats in the region.
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Affiliation(s)
- Shahram Khademvatan
- Cellular and Molecular Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Medical Parasitology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- * E-mail: (SK); (FR)
| | - Fakher Rahim
- Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- * E-mail: (SK); (FR)
| | - Mahdi Tavalla
- Department of Medical Parasitology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Rahman Abdizadeh
- Department of Medical Parasitology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahmoud Hashemitabar
- Cellular and Molecular Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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13
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Varón A, Wheeler WC. Local search for the generalized tree alignment problem. BMC Bioinformatics 2013; 14:66. [PMID: 23441880 PMCID: PMC3637488 DOI: 10.1186/1471-2105-14-66] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 01/31/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relationships between organisms? At the core of every biological problem lies a phylogenetic component. The patterns that can be observed in nature are the product of complex interactions, constrained by the template that our ancestors provide. The problem of simultaneous tree and alignment estimation under Maximum Parsimony is known in combinatorial optimization as the Generalized Tree Alignment Problem (GTAP). The GTAP is the Steiner Tree Problem for the sequence edit distance. Like many biologically interesting problems, the GTAP is NP-Hard. Typically the Steiner Tree is presented under the Manhattan or the Hamming distances. RESULTS Experimentally, the accuracy of the GTAP has been subjected to evaluation. Results show that phylogenies selected using the GTAP from unaligned sequences are competitive with the best methods and algorithms available. Here, we implement and explore experimentally existing and new local search heuristics for the GTAP using simulated and real data. CONCLUSIONS The methods presented here improve by more than three orders of magnitude in execution time the best local search heuristics existing to date when applied to real data.
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Affiliation(s)
- Andrés Varón
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY - 10024, USA
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY - 10024, USA
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14
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Warnow T. Large-Scale Multiple Sequence Alignment and Phylogeny Estimation. MODELS AND ALGORITHMS FOR GENOME EVOLUTION 2013. [DOI: 10.1007/978-1-4471-5298-9_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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15
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Nagy LG, Kocsubé S, Csanádi Z, Kovács GM, Petkovits T, Vágvölgyi C, Papp T. Re-mind the gap! Insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi. PLoS One 2012; 7:e49794. [PMID: 23185439 PMCID: PMC3501463 DOI: 10.1371/journal.pone.0049794] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/12/2012] [Indexed: 01/09/2023] Open
Abstract
Rapidly evolving, indel-rich phylogenetic markers play a pivotal role in our understanding of the relationships at multiple levels of the tree of life. There is extensive evidence that indels provide conserved phylogenetic signal, however, the range of phylogenetic depths for which gaps retain tree signal has not been investigated in detail. Here we address this question using the fungal internal transcribed spacer (ITS), which is central in many phylogenetic studies, molecular ecology, detection and identification of pathogenic and non-pathogenic species. ITS is repeatedly criticized for indel-induced alignment problems and the lack of phylogenetic resolution above species level, although these have not been critically investigated. In this study, we examined whether the inclusion of gap characters in the analyses shifts the phylogenetic utility of ITS alignments towards earlier divergences. By re-analyzing 115 published fungal ITS alignments, we found that indels are slightly more conserved than nucleotide substitutions, and when included in phylogenetic analyses, improved the resolution and branch support of phylogenies across an array of taxonomic ranges and extended the resolving power of ITS towards earlier nodes of phylogenetic trees. Our results reconcile previous contradicting evidence for the effects of data exclusion: in the case of more sophisticated indel placement, the exclusion of indel-rich regions from the analyses results in a loss of tree resolution, whereas in the case of simpler alignment methods, the exclusion of gapped sites improves it. Although the empirical datasets do not provide to measure alignment accuracy objectively, our results for the ITS region are consistent with previous simulations studies alignment algorithms. We suggest that sophisticated alignment algorithms and the inclusion of indels make the ITS region and potentially other rapidly evolving indel-rich loci valuable sources of phylogenetic information, which can be exploited at multiple taxonomic levels.
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Affiliation(s)
- László G Nagy
- University of Szeged, Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary.
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16
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Abstract
BACKGROUND The inference of homologies among DNA sequences, that is, positions in multiple genomes that share a common evolutionary origin, is a crucial, yet difficult task facing biologists. Its computational counterpart is known as the multiple sequence alignment problem. There are various criteria and methods available to perform multiple sequence alignments, and among these, the minimization of the overall cost of the alignment on a phylogenetic tree is known in combinatorial optimization as the Tree Alignment Problem. This problem typically occurs as a subproblem of the Generalized Tree Alignment Problem, which looks for the tree with the lowest alignment cost among all possible trees. This is equivalent to the Maximum Parsimony problem when the input sequences are not aligned, that is, when phylogeny and alignments are simultaneously inferred. RESULTS For large data sets, a popular heuristic is Direct Optimization (DO). DO provides a good tradeoff between speed, scalability, and competitive scores, and is implemented in the computer program POY. All other (competitive) algorithms have greater time complexities compared to DO. Here, we introduce and present experiments a new algorithm Affine-DO to accommodate the indel (alignment gap) models commonly used in phylogenetic analysis of molecular sequence data. Affine-DO has the same time complexity as DO, but is correctly suited for the affine gap edit distance. We demonstrate its performance with more than 330,000 experimental tests. These experiments show that the solutions of Affine-DO are close to the lower bound inferred from a linear programming solution. Moreover, iterating over a solution produced using Affine-DO shows little improvement. CONCLUSIONS Our results show that Affine-DO is likely producing near-optimal solutions, with approximations within 10% for sequences with small divergence, and within 30% for random sequences, for which Affine-DO produced the worst solutions. The Affine-DO algorithm has the necessary scalability and optimality to be a significant improvement in the real-world phylogenetic analysis of sequence data.
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Affiliation(s)
- Andrés Varón
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY - 10024, USA
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY - 10024, USA
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Hünefeld F, Missbach C, Beutel RG. The morphology and evolution of the female postabdomen of Holometabola (Insecta). ARTHROPOD STRUCTURE & DEVELOPMENT 2012; 41:361-371. [PMID: 22583791 DOI: 10.1016/j.asd.2012.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 05/02/2012] [Accepted: 05/02/2012] [Indexed: 05/31/2023]
Abstract
In the present article homology issues, character evolution and phylogenetic implications related to the female postabdomen of the holometabolan insects are discussed, based on an earlier analysis of a comprehensive morphological data set. Hymenoptera, the sistergroup of the remaining Holometabola, are the only group where the females have retained a fully developed primary ovipositor of the lepismatid type. There are no characters of the female abdomen supporting a clade Coleopterida + Neuropterida. The invagination of the terminal segments is an autapomorphy of Coleoptera. The ovipositor is substantially modified in Raphidioptera and distinctly reduced in Megaloptera and Neuroptera. The entire female abdomen is extremely simplified in Strepsiptera. The postabdomen is tapering posteriorly in Mecopterida and retractile in a telescopic manner (oviscapt). The paired ventral sclerites of segments VIII and IX are preserved, but valvifers and valvulae are not distinguishable. In Amphiesmenoptera sclerotizations derived from the ventral appendages VIII are fused ventromedially, forming a solid plate, and the appendages IX are reduced. The terminal segments are fused and form a terminal unit which bears the genital opening subapically. The presence of two pairs of apophyses and the related protraction of the terminal unit by muscle force are additional autapomorphies, as is the fusion of the rectum with the posterior part of the genital chamber (cloaca). Antliophora are supported by the presence of a transverse muscle between the ventral sclerites of segment VIII. Secondary egg laying tubes have evolved independently within Boreidae (absent in Caurinus) and in Tipulomorpha. The loss of two muscle associated with the genital chamber are likely autapomorphies of Diptera. The secondary loss of the telescopic retractability of the postabdomen is one of many autapomorphies of Siphonaptera.
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Affiliation(s)
- Frank Hünefeld
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, Erbertstr. 1, D-07743 Jena, Germany.
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Bayzid MDS, Warnow T. Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence. J Comput Biol 2012; 19:591-605. [DOI: 10.1089/cmb.2012.0037] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
| | - Tandy Warnow
- Department of Computer Science, University of Texas at Austin, Austin
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19
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Abstract
The standard approach to phylogeny estimation uses two phases, in which the first phase produces an alignment on a set of homologous sequences, and the second phase estimates a tree on the multiple sequence alignment. POY, a method which seeks a tree/alignment pair minimizing the total treelength, is the most widely used alternative to this two-phase approach. The topological accuracy of trees computed under treelength optimization is, however, controversial. In particular, one study showed that treelength optimization using simple gap penalties produced poor trees and alignments, and suggested the possibility that if POY were used with an affine gap penalty, it might be able to be competitive with the best two-phase methods. In this paper we report on a study addressing this possibility. We present a new heuristic for treelength, called BeeTLe (Better Treelength), that is guaranteed to produce trees at least as short as POY. We then use this heuristic to analyze a large number of simulated and biological datasets, and compare the resultant trees and alignments to those produced using POY and also maximum likelihood (ML) and maximum parsimony (MP) trees computed on a number of alignments. In general, we find that trees produced by BeeTLe are shorter and more topologically accurate than POY trees, but that neither POY nor BeeTLe produces trees as topologically accurate as ML trees produced on standard alignments. These findings, taken as a whole, suggest that treelength optimization is not as good an approach to phylogenetic tree estimation as maximum likelihood based upon good alignment methods.
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Affiliation(s)
| | - Tandy Warnow
- Department of Computer Science, University of Texas at Austin, Austin, Texas, United States of America
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Warnow T. Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent. PLOS CURRENTS 2012; 4:RRN1308. [PMID: 22453901 PMCID: PMC3299439 DOI: 10.1371/currents.rrn1308] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/12/2012] [Indexed: 12/04/2022]
Abstract
BackgroundMost statistical methods for phylogenetic estimation in use today treat a gap (generally representing an insertion or deletion, i.e., indel) within the input sequence alignment as missing data. However, the statistical properties of this treatment of indels have not been fully investigated.ResultsWe prove that maximum likelihood phylogeny estimation, treating indels as missing data, can be statistically inconsistent for a general (and rather simple) model of sequence evolution, even when given the true alignment. Therefore, accurate phylogeny estimation cannot be guaranteed for maximum likelihood analyses, even given arbitrarily long sequences, when indels are present and treated as missing data.ConclusionsOur result shows that the standard statistical techniques used to estimate phylogenies from sequence alignments may have unfavorable statistical properties, even when the sequence alignment is accurate and the assumed substitution model matches the generation model. This suggests that the recent research focus on developing statistical methods that treat indel events properly is an important direction for phylogeny estimation.
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Affiliation(s)
- Tandy Warnow
- Professor of Computer Science, Department of Computer Science, University of Texas at Austin
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Dallai R, Mercati D, Gottardo M, Machida R, Mashimo Y, Beutel RG. The fine structure of the female reproductive system of Zorotypus caudelli Karny (Zoraptera). ARTHROPOD STRUCTURE & DEVELOPMENT 2012; 41:51-63. [PMID: 21996134 DOI: 10.1016/j.asd.2011.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 08/02/2011] [Accepted: 08/13/2011] [Indexed: 05/31/2023]
Abstract
The general structure of the female genital system of Zorotypus caudelli is described. The ovarioles are of the panoistic type. Due to the reduction of the envelope (tunica externa) the ovarioles are in direct contact with the hemolymph like in some other insect groups, Plecoptera included. The calices are much larger in Z. caudelli then in Zorotypus hubbardi and their epithelial cells produce large amounts of secretions, probably protecting the surface of the eggs deposited on the substrate. Eggs taken from the calyx bear a series of long fringes, which are missing in the eggs found in the ovariole, and in other zorapteran species. The long sperm of Z. caudelli and the long spermathecal duct are likely related to a sexual isolating mechanism (cryptic female choice), impeding female re-mating. The apical receptacle and the spermathecal duct - both of ectodermal origin - consist of three cell types. In addition to the cells beneath the cuticle lining the lumen, two other cell types are visible: secretory and canal cells. The cytoplasm of the former is rich in rough endoplasmic reticulum cisterns and Golgi complexes, which produce numerous discrete dense secretory bodies. These products are released into the receiving canal crossing the extracellular cavity of secretory cells, extending over a series of long microvilli. The secretion is transported towards the lumen of the apical receptacle of the spermatheca or to that of the spermathecal duct by a connecting canal formed by the canal cells. It is enriched by material produced by the slender canal cells. Before mating, the sperm cells are enveloped by a thick glycocalyx produced at the level of the male accessory glands, but it is absent when they have reached the apical receptacle, and also in the spermathecal duct lumen. It is likely removed by secretions of the spermatheca. The eggs are fertilized at the level of the common oviduct where the spermathecal duct opens. Two micropyles at the dorsal side of the equator level possibly facilitate fertilization. The presence of these two micropyles is a presumably derived feature shared with Phasmatodea. The fine structure of the female reproductive system of Z. caudelli does not allow to assess the phylogenetic position at the present stage of knowledge. The enlarged calyx and the temporary presence of long fringes on the eggs are potential autapomorphies of Z. caudelli or may indicate relationships with other Zorotypus species.
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Affiliation(s)
- R Dallai
- Department of Evolutionary Biology, Via A. Moro 2, I-53100 Siena, Italy.
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Abstract
Basic taste qualities like sour, salty, sweet, bitter and umami serve specific functions in identifying food components found in the diet of humans and animals, and are recognized by proteins in the oral cavity. Recognition of bitter taste and aversion to it are thought to protect the organism against the ingestion of poisonous food compounds, which are often bitter. Interestingly, bitter taste receptors are expressed not only in the mouth but also in extraoral tissues, such as the gastrointestinal tract, indicating that they may play a role in digestive and metabolic processes. BitterDB database, available at http://bitterdb.agri.huji.ac.il/bitterdb/, includes over 550 compounds that were reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. These studies may contribute to predicting bitterness of unknown compounds, predicting ligands for bitter receptors from different species and rational design of bitterness modulators.
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Affiliation(s)
- Ayana Wiener
- The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
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Wang LS, Leebens-Mack J, Kerr Wall P, Beckmann K, dePamphilis CW, Warnow T. The impact of multiple protein sequence alignment on phylogenetic estimation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011; 8:1108-1119. [PMID: 21566256 DOI: 10.1109/tcbb.2009.68] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. Over the last decade or so, new multiple sequence alignment methods have been developed to improve comparative analyses of protein structure, but these new methods have not been typically used in phylogenetic analyses. In this paper, we report on a simulation study that we performed to evaluate the consequences of using these new multiple sequence alignment methods in terms of the resultant phylogenetic reconstruction. We find that while alignment accuracy is positively correlated with phylogenetic accuracy, the amount of improvement in phylogenetic estimation that results from an improved alignment can range from quite small to substantial. We observe that phylogenetic accuracy is most highly correlated with alignment accuracy when sequences are most difficult to align, and that variation in alignment accuracy can have little impact on phylogenetic accuracy when alignment error rates are generally low. We discuss these observations and implications for future work.
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Affiliation(s)
- Li-San Wang
- Department of Pathology and Laboratory Medicine and Penn Center for Bioinformatics, 1424 Blockley Hall, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Enghoff H, Petersen G, Seberg O. Phylogenetic relationships in the millipede family Julidae. Cladistics 2011; 27:606-616. [DOI: 10.1111/j.1096-0031.2011.00360.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Lücking R, Hodkinson BP, Stamatakis A, Cartwright RA. PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination. BMC Bioinformatics 2011; 12:10. [PMID: 21214904 PMCID: PMC3024941 DOI: 10.1186/1471-2105-12-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 01/07/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by 'Pairwise Identity and Cost Scores Ordination' (PICS-Ord). The method works via ordination of sequence identity or cost scores matrices by means of Principal Coordinates Analysis (PCoA). After identification of ambiguous regions, the method computes pairwise distances as sequence identities or cost scores, ordinates the resulting distance matrix by means of PCoA, and encodes the principal coordinates as ordered integers. Three biological and 100 simulated datasets were used to assess the performance of the new method. RESULTS Including ambiguous regions coded by means of PICS-Ord increased topological accuracy, resolution, and bootstrap support in real biological and simulated datasets compared to the alternative of excluding such regions from the analysis a priori. In terms of accuracy, PICS-Ord performs equal to or better than previously available methods of ambiguous region coding (e.g., INAASE), with the advantage of a practically unlimited alignment size and increased analytical speed and the possibility of PICS-Ord scores to be analyzed together with DNA data in a partitioned maximum likelihood model. CONCLUSIONS Advantages of PICS-Ord over step matrix-based ambiguous region coding with INAASE include a practically unlimited number of OTUs and seamless integration of PICS-Ord codes into phylogenetic datasets, as well as the increased speed of phylogenetic analysis. Contrary to word- and frequency-based methods, PICS-Ord maintains the advantage of pairwise sequence alignment to derive distances, and the method is flexible with respect to the calculation of distance scores. In addition to distance and maximum parsimony, PICS-Ord codes can be analyzed in a Bayesian or maximum likelihood framework. RAxML (version 7.2.6 or higher that was developed for this study) allows up to 32-state ordered or unordered characters. A GTR, MK, or ORDERED model can be applied to analyse the PICS-Ord codes partition, with GTR performing slightly better than MK and ORDERED. AVAILABILITY An implementation of the PICS-Ord algorithm is available from http://scit.us/projects/ngila/wiki/PICS-Ord. It requires both the statistical software, R http://www.r-project.org and the alignment software Ngila http://scit.us/projects/ngila.
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Affiliation(s)
- Robert Lücking
- Department of Botany, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA.
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26
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Lehtonen S. Phylogeny estimation and alignment via POY versus Clustal + PAUP*: a response to Ogden and Rosenberg (2007). Syst Biol 2010; 57:653-7. [PMID: 18709601 DOI: 10.1080/10635150802302476] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Samuli Lehtonen
- Department of Biology, Section of Biodiversity and Environmental Science, University of Turku, Turku, Finland.
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27
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Blair C, Murphy RW. Recent trends in molecular phylogenetic analysis: where to next? J Hered 2010; 102:130-8. [PMID: 20696667 DOI: 10.1093/jhered/esq092] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The acquisition of large multilocus sequence data is providing researchers with an unprecedented amount of information to resolve difficult phylogenetic problems. With these large quantities of data comes the increasing challenge regarding the best methods of analysis. We review the current trends in molecular phylogenetic analysis, focusing specifically on the topics of multiple sequence alignment and methods of tree reconstruction. We suggest that traditional methods are inadequate for these highly heterogeneous data sets and that researchers employ newer more sophisticated search algorithms in their analyses. If we are to best extract the information present in these data sets, a sound understanding of basic phylogenetic principles combined with modern methodological techniques are necessary.
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Affiliation(s)
- Christopher Blair
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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Pepato AR, da Rocha CEF, Dunlop JA. Phylogenetic position of the acariform mites: sensitivity to homology assessment under total evidence. BMC Evol Biol 2010; 10:235. [PMID: 20678229 PMCID: PMC2933639 DOI: 10.1186/1471-2148-10-235] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 08/02/2010] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Mites (Acari) have traditionally been treated as monophyletic, albeit composed of two major lineages: Acariformes and Parasitiformes. Yet recent studies based on morphology, molecular data, or combinations thereof, have increasingly drawn their monophyly into question. Furthermore, the usually basal (molecular) position of one or both mite lineages among the chelicerates is in conflict to their morphology, and to the widely accepted view that mites are close relatives of Ricinulei. RESULTS The phylogenetic position of the acariform mites is examined through employing SSU, partial LSU sequences, and morphology from 91 chelicerate extant terminals (forty Acariformes). In a static homology framework, molecular sequences were aligned using their secondary structure as guide, whereby regions of ambiguous alignment were discarded, and pre-aligned sequences analyzed under parsimony and different mixed models in a Bayesian inference. Parsimony and Bayesian analyses led to trees largely congruent concerning infra-ordinal, well-supported branches, but with low support for inter-ordinal relationships. An exception is Solifugae + Acariformes (P. P = 100%, J. = 0.91). In a dynamic homology framework, two analyses were run: a standard POY analysis and an analysis constrained by secondary structure. Both analyses led to largely congruent trees; supporting a (Palpigradi (Solifugae Acariformes)) clade and Ricinulei as sister group of Tetrapulmonata with the topology (Ricinulei (Amblypygi (Uropygi Araneae))). Combined analysis with two different morphological data matrices were run in order to evaluate the impact of constraining the analysis on the recovered topology when employing secondary structure as a guide for homology establishment. The constrained combined analysis yielded two topologies similar to the exclusively molecular analysis for both morphological matrices, except for the recovery of Pedipalpi instead of the (Uropygi Araneae) clade. The standard (direct optimization) POY analysis, however, led to the recovery of trees differing in the absence of the otherwise well-supported group Solifugae + Acariformes. CONCLUSIONS Previous studies combining ribosomal sequences and morphology often recovered topologies similar to purely morphological analyses of Chelicerata. The apparent stability of certain clades not recovered here, like Haplocnemata and Acari, is regarded as a byproduct of the way the molecular homology was previously established using the instrumentalist approach implemented in POY. Constraining the analysis by a priori homology assessment is defended here as a way of maintaining the severity of the test when adding new data to the analysis. Although the strength of the method advocated here is keeping phylogenetic information from regions usually discarded in an exclusively static homology framework; it still has the inconvenience of being uninformative on the effect of alignment ambiguity on resampling methods of clade support estimation. Finally, putative morphological apomorphies of Solifugae + Acariformes are the reduction of the proximal cheliceral podomere, medial abutting of the leg coxae, loss of sperm nuclear membrane, and presence of differentiated germinative and secretory regions in the testis delivering their products into a common lumen.
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Affiliation(s)
- Almir R Pepato
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, travessa 14, 321, 05508-900, São Paulo, Brazil
| | - Carlos EF da Rocha
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, travessa 14, 321, 05508-900, São Paulo, Brazil
| | - Jason A Dunlop
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, Invalidenstrasse 43, 10115 Berlin, Germany
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An expanded phylogeny of treefrogs (Hylidae) based on nuclear and mitochondrial sequence data. Mol Phylogenet Evol 2010; 55:871-82. [DOI: 10.1016/j.ympev.2010.03.013] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 02/11/2010] [Accepted: 03/09/2010] [Indexed: 11/23/2022]
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Studying sources of incongruence in arthropod molecular phylogenies: Sea spiders (Pycnogonida) as a case study. C R Biol 2010; 333:438-53. [DOI: 10.1016/j.crvi.2010.01.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 01/14/2010] [Accepted: 01/15/2010] [Indexed: 11/18/2022]
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Aurahs R, Göker M, Grimm GW, Hemleben V, Hemleben C, Schiebel R, Kucera M. Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences. Bioinform Biol Insights 2009; 3:155-77. [PMID: 20140067 PMCID: PMC2808177 DOI: 10.4137/bbi.s3334] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequenced nucleotides prior to phylogenetic inference. Here, we investigate the potential of the multiple analysis approach to infer a molecular phylogeny of all modern planktonic foraminiferal taxa by using a matrix of 146 new and 153 previously published SSU rDNA sequences. Our multiple analysis approach is based on eleven different automated alignments, analysed separately under the maximum likelihood criterion. The high degree of congruence between the phylogenies derived from our novel approach, traditional manually homologized culled alignments and the fossil record indicates that poorly resolved nucleotide homology does not represent the most significant obstacle when exploring the phylogenetic structure of the SSU rDNA in planktonic foraminifera. We show that approaches designed to extract phylogenetically valuable signals from complete sequences show more promise to resolve the backbone of the planktonic foraminifer tree than attempts to establish strictly homologous base calls in a manual alignment.
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Affiliation(s)
- Ralf Aurahs
- Department of Micropaleontology, Institute of Geosciences, Eberhard Karls University of Tübingen, Sigwartstrabetae 10, 72076 Tübingen, Germany
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Prevosti FJ, Chemisquy MA. The impact of missing data on real morphological phylogenies: influence of the number and distribution of missing entries. Cladistics 2009; 26:326-339. [DOI: 10.1111/j.1096-0031.2009.00289.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Charles Darwin, beetles and phylogenetics. Naturwissenschaften 2009; 96:1293-312. [DOI: 10.1007/s00114-009-0601-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 06/11/2009] [Accepted: 08/07/2009] [Indexed: 10/20/2022]
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Wägele JW, Letsch H, Klussmann-Kolb A, Mayer C, Misof B, Wägele H. Phylogenetic support values are not necessarily informative: the case of the Serialia hypothesis (a mollusk phylogeny). Front Zool 2009; 6:12. [PMID: 19555513 PMCID: PMC2710323 DOI: 10.1186/1742-9994-6-12] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 06/26/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular phylogenies are being published increasingly and many biologists rely on the most recent topologies. However, different phylogenetic trees often contain conflicting results and contradict significant background data. Not knowing how reliable traditional knowledge is, a crucial question concerns the quality of newly produced molecular data. The information content of DNA alignments is rarely discussed, as quality statements are mostly restricted to the statistical support of clades. Here we present a case study of a recently published mollusk phylogeny that contains surprising groupings, based on five genes and 108 species, and we apply new or rarely used tools for the analysis of the information content of alignments and for the filtering of noise (masking of random-like alignment regions, split decomposition, phylogenetic networks, quartet mapping). RESULTS The data are very fragmentary and contain contaminations. We show that that signal-like patterns in the data set are conflicting and partly not distinct and that the reported strong support for a "rather surprising result" (monoplacophorans and chitons form a monophylum Serialia) does not exist at the level of primary homologies. Split-decomposition, quartet mapping and neighbornet analyses reveal conflicting nucleotide patterns and lack of distinct phylogenetic signal for the deeper phylogeny of mollusks. CONCLUSION Even though currently a majority of molecular phylogenies are being justified with reference to the 'statistical' support of clades in tree topologies, this confidence seems to be unfounded. Contradictions between phylogenies based on different analyses are already a strong indication of unnoticed pitfalls. The use of tree-independent tools for exploratory analyses of data quality is highly recommended. Concerning the new mollusk phylogeny more convincing evidence is needed.
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Affiliation(s)
- J Wolfgang Wägele
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53313 Bonn, Germany
| | - Harald Letsch
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53313 Bonn, Germany
| | - Annette Klussmann-Kolb
- J. W. Goethe University, Institute for Ecology, Evolution and Diversity, Siesmayerstrasse 70, D – 60054 Frankfurt am Main, Germany
| | - Christoph Mayer
- Ruhr-University Bochum, Faculty of Biology, Universitätsstr., 44370 Bochum, Germany
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53313 Bonn, Germany
| | - Heike Wägele
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53313 Bonn, Germany
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Arnedo MA, Hormiga G, Scharff N. Higher-level phylogenetics of linyphiid spiders (Araneae, Linyphiidae) based on morphological and molecular evidence. Cladistics 2009; 25:231-262. [DOI: 10.1111/j.1096-0031.2009.00249.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Morrison DA. Why Would Phylogeneticists Ignore Computerized Sequence Alignment? Syst Biol 2009; 58:150-8. [DOI: 10.1093/sysbio/syp009] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Álvarez-Padilla F, Dimitrov D, Giribet G, Hormiga G. Phylogenetic relationships of the spider family Tetragnathidae (Araneae, Araneoidea) based on morphological and DNA sequence data. Cladistics 2009; 25:109-146. [DOI: 10.1111/j.1096-0031.2008.00242.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Yue F, Shi J, Tang J. Simultaneous phylogeny reconstruction and multiple sequence alignment. BMC Bioinformatics 2009; 10 Suppl 1:S11. [PMID: 19208110 PMCID: PMC2648791 DOI: 10.1186/1471-2105-10-s1-s11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to affect the quality of the inferred phylogeny. At the same time, all the current multiple sequence alignment programs use a guide tree to produce the alignment and experiments showed that good guide trees can significantly improve the multiple alignment quality. Results We devise a new algorithm to simultaneously align multiple sequences and search for the phylogenetic tree that leads to the best alignment. We also implemented the algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM250 or BLOSUM62. The performance of the new method are compared with those from other popular multiple sequence alignment tools, including the widely used programs such as ClustalW and T-Coffee. Experimental results suggest that this method has good performance in terms of both phylogeny accuracy and alignment quality. Conclusion We present an algorithm to align multiple sequences and reconstruct the phylogenies that minimize the alignment score, which is based on an efficient algorithm to solve the median problems for three sequences. Our extensive experiments suggest that this method is very promising and can produce high quality phylogenies and alignments.
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Affiliation(s)
- Feng Yue
- Ludwig Institute for Cancer Research, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Liu K, Nelesen S, Raghavan S, Linder CR, Warnow T. Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2009; 6:7-21. [PMID: 19179695 DOI: 10.1109/tcbb.2008.63] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Several methods have been developed for simultaneous estimation of alignment and tree, of which POY is the most popular. In a 2007 paper published in Systematic Biology, Ogden and Rosenberg reported on a simulation study in which they compared POY to estimating the alignment using ClustalW and then analyzing the resultant alignment using maximum parsimony. They found that ClustalW+MP outperformed POY with respect to alignment and phylogenetic tree accuracy, and they concluded that simultaneous estimation techniques are not competitive with two-phase techniques. Our paper presents a simulation study in which we focus on the NP-hard optimization problem that POY addresses: minimizing treelength. Our study considers the impact of the gap penalty and suggests that the poor performance observed for POY by Ogden and Rosenberg is due to the simple gap penalties they used to score alignment/tree pairs. Our study suggests that optimizing under an affine gap penalty might produce alignments that are better than ClustalW alignments, and competitive with those produced by the best current alignment methods. We also show that optimizing under this affine gap penalty produces trees whose topological accuracy is better than ClustalW+MP, and competitive with the current best two-phase methods.
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Affiliation(s)
- Kevin Liu
- The University of Texas at Austin, Austin, TX 78712, USA.
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Quicke DLJ, Sharkey MJ, Laurenne NM, Dowling A. A preliminary molecular phylogeny of the Sigalphinae (Hymenoptera: Braconidae), includingPselaphanusSzépligeti, based on 28S rDNA, with descriptions of new Afrotropical and MadagascanMinangaandMalasigalphusspecies. J NAT HIST 2008. [DOI: 10.1080/00222930802364042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Spagna JC, Álvarez-Padilla F. Finding an upper limit for gap costs in direct optimization parsimony. Cladistics 2008. [DOI: 10.1111/j.1096-0031.2008.00213.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Frost DR, Grant T, Faivovich J, Bain RH, Haas A, Haddad CFB, de Sa RO, Channing A, Wilkinson M, Donnellan SC, Raxworthy CJ, Campbell JA, Blotto BL, Moler P, Drewes RC, Nussbaum RA, Lynch JD, Green DM, Wheeler WC. Is The Amphibian Tree of Life really fatally flawed? Cladistics 2008. [DOI: 10.1111/j.1096-0031.2007.00181.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Spagna JC, Gillespie RG. More data, fewer shifts: Molecular insights into the evolution of the spinning apparatus in non-orb-weaving spiders. Mol Phylogenet Evol 2008; 46:347-68. [DOI: 10.1016/j.ympev.2007.08.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Revised: 07/31/2007] [Accepted: 08/08/2007] [Indexed: 10/22/2022]
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Krüger D, Gargas A. Secondary structure of ITS2 rRNA provides taxonomic characters for systematic studies--a case in Lycoperdaceae (Basidiomycota). ACTA ACUST UNITED AC 2007; 112:316-30. [PMID: 18342242 DOI: 10.1016/j.mycres.2007.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Revised: 09/24/2007] [Accepted: 10/30/2007] [Indexed: 11/26/2022]
Abstract
The secondary structure of the ITS2 rDNA transcript (pre-rRNA) could provide information for identifying homologous nucleotide characters useful for cladistic inference of relationships. Such structure data could become taxonomic characters. This work compares the effect of several modern nucleotide alignment strategies, including those making use of structure data, on phylogenetic inference. From both the phylogenetic analyses and comparative secondary structure, implications for taxonomy and evolution of puffball fungi are discussed. Lycoperdaceae remain insufficiently resolved with present taxon and data sampling. Neither alignment allows statistically robust phylogenetic hypotheses under any current optimality criterion. The secondary structure data at this time are best used as accessory taxonomic characters as their phylogenetic resolving power and confidence in validity is limited compared with underlying nucleotide characters. We introduce a preliminary nomenclature convention to describe secondary structure for defining consensus features. These consensus structures are illustrated for the clades /Calvatia, /Handkea-Echinatum, /Vascellum, /Morganella, and /Plumbea-Paludosa (Bovista).
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Affiliation(s)
- Dirk Krüger
- The Botany Department, University of Wisconsin, 430 Lincoln Drive, Madison, WI 53706, USA.
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