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Harbach RE. An Anopheles by Any Other Name …? JOURNAL OF MEDICAL ENTOMOLOGY 2018; 55:1069-1070. [PMID: 30020514 DOI: 10.1093/jme/tjy108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Indexed: 06/08/2023]
Abstract
The physical characteristics of a nematoceran fly that evokes the image of a mosquito of the genus Anopheles Meigen (Diptera: Culicidae) has existed since the genus was defined in the early part of the twentieth century. Is that image likely to change with the recent proposal to elevate four Neotropical subgenera to generic status based on relationships generated by phylogenetic analyses of mitochondrial protein-coding genes? Reasons for retaining the traditional concept of Anopheles, with its traditionally recognized subgenera, are presented. However, as the ranking of taxa as genera or subgenera is subjective, the choice of rank of a genus-group name may be considered a subjective decision and a matter of user preference.
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Affiliation(s)
- Ralph E Harbach
- Department of Life Sciences, Natural History Museum, London, UK
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Kalousová B, Hasegawa H, Petrželková KJ, Sakamaki T, Kooriyma T, Modrý D. Adult hookworms (Necator spp.) collected from researchers working with wild western lowland gorillas. Parasit Vectors 2016; 9:75. [PMID: 26858023 PMCID: PMC4746918 DOI: 10.1186/s13071-016-1357-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 02/02/2016] [Indexed: 01/27/2023] Open
Abstract
Background In general, studies on the diversity of strongylid nematodes in endangered host species are complicated as material obtained by non-invasive sampling methods has limited value for generic and species identification. While egg morphology barely allows assignment to family, the morphology of cultivated infective third stage larvae provides a better resolution at the generic level but cannot be used for exact species identification. Morphology-based taxonomic approaches greatly depend on the examination of adult worms that are usually not available. Methods Hookworm parasites in two European researchers, who participated in gorilla research in the Central African Republic, were expelled after anthelmintic treatment to the faeces, collected and morphologically examined. A male worm discharged naturally from a wild bonobo (Pan paniscus) in Congo was also examined for comparison. Results Two species of Necator were identified in researchers’ faecal material: Necator americanus (Stiles, 1902) and N. gorillae Noda & Yamada, 1964; the latter species differed in having a smaller body, smaller buccal cavity and shorter spicules with spade-shaped membranes situated distally. Males of N. gorillae also possessed unusual cuticular thickenings on the dorsal side of the prebursal region of the body. These characters, shared with the male worm from the bonobo, correspond well to the description of N. gorillae described from gorillas in Congo. Conclusions Based on the morphology of the hookworms recovered in this study and previous molecular analyses of larvae developed from both humans and western lowland gorillas (Gorilla gorilla gorilla) from this locality, we conclude that the researchers became infected with gorilla hookworms during their stay in the field. This is the first report of infection with a Necator species other than N. americanus in humans.
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Affiliation(s)
- Barbora Kalousová
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Palackeho tr. 1946/1, 612 42, Brno, Czech Republic.
| | - Hideo Hasegawa
- Department of Biology, Faculty of Medicine, Oita University, Hasama, Yufu, Oita, 879-5593, Japan.
| | - Klára J Petrželková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Kvetna 8, 603 65, Brno, Czech Republic. .,Biology Centre, Institute of Parasitology, Academy of Sciences of the Czech Republic, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic. .,Liberec Zoo, Lidove sady 425/1, 460 01, Liberec, Czech Republic.
| | - Tetsuya Sakamaki
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan.
| | - Takanori Kooriyma
- Department of Veterinary Science, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midori, Ebetsu, Hokkaido, 069-8501, Japan.
| | - David Modrý
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Palackeho tr. 1946/1, 612 42, Brno, Czech Republic. .,Biology Centre, Institute of Parasitology, Academy of Sciences of the Czech Republic, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic. .,Central European Institute for Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences, Palackeho 1946/1, 612 42, Brno, Czech Republic.
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Molecular systematics: A synthesis of the common methods and the state of knowledge. Cell Mol Biol Lett 2010; 15:311-41. [PMID: 20213503 PMCID: PMC6275913 DOI: 10.2478/s11658-010-0010-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2009] [Accepted: 03/01/2010] [Indexed: 11/21/2022] Open
Abstract
The comparative and evolutionary analysis of molecular data has allowed researchers to tackle biological questions that have long remained unresolved. The evolution of DNA and amino acid sequences can now be modeled accurately enough that the information conveyed can be used to reconstruct the past. The methods to infer phylogeny (the pattern of historical relationships among lineages of organisms and/or sequences) range from the simplest, based on parsimony, to more sophisticated and highly parametric ones based on likelihood and Bayesian approaches. In general, molecular systematics provides a powerful statistical framework for hypothesis testing and the estimation of evolutionary processes, including the estimation of divergence times among taxa. The field of molecular systematics has experienced a revolution in recent years, and, although there are still methodological problems and pitfalls, it has become an essential tool for the study of evolutionary patterns and processes at different levels of biological organization. This review aims to present a brief synthesis of the approaches and methodologies that are most widely used in the field of molecular systematics today, as well as indications of future trends and state-of-the-art approaches.
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Blasco-Costa I, Balbuena JA, Kostadinova A, Olson PD. Interrelationships of the Haploporinae (Digenea: Haploporidae): A molecular test of the taxonomic framework based on morphology. Parasitol Int 2009; 58:263-9. [DOI: 10.1016/j.parint.2009.03.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/26/2009] [Accepted: 03/27/2009] [Indexed: 10/20/2022]
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Abstract
Classification of the Triatominae has become a complex balance between traditional approaches and a wide variety of evolutionary interpretations. On the one hand is the need for a stable classification of practical use for those involved in vector surveillance and control. On the other is the desire to adequately reflect evolutionary theory derived from a range of molecular, cytogenetic and morphometric comparisons, with additional complications raised by current interpretations of the subfamily as a recently derived polyphyletic assemblage. Here we review key aspects of triatomine systematics and evolution, to derive a pragmatic classification that seeks to build on traditional morphological concepts within the context of current evolutionary theories.
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Colbourn CJ, Kumar S. Lower bounds on multiple sequence alignment using exact 3-way alignment. BMC Bioinformatics 2007; 8:140. [PMID: 17470273 PMCID: PMC1890300 DOI: 10.1186/1471-2105-8-140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 04/30/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple sequence alignment is fundamental. Exponential growth in computation time appears to be inevitable when an optimal alignment is required for many sequences. Exact costs of optimum alignments are therefore rarely computed. Consequently much effort has been invested in algorithms for alignment that are heuristic, or explore a restricted class of solutions. These give an upper bound on the alignment cost, but it is equally important to determine the quality of the solution obtained. In the absence of an optimal alignment with which to compare, lower bounds may be calculated to assess the quality of the alignment. As more effort is invested in improving upper bounds (alignment algorithms), it is therefore important to improve lower bounds as well. Although numerous cost metrics can be used to determine the quality of an alignment, many are based on sum-of-pairs (SP) measures and their generalizations. RESULTS Two standard and two new methods are considered for using exact 2-way and 3-way alignments to compute lower bounds on total SP alignment cost; one new method fares well with respect to accuracy, while the other reduces the computation time. The first employs exhaustive computation of exact 3-way alignments, while the second employs an efficient heuristic to compute a much smaller number of exact 3-way alignments. Calculating all 3-way alignments exactly and computing their average improves lower bounds on sum of SP cost in v-way alignments. However judicious selection of a subset of all 3-way alignments can yield a further improvement with minimal additional effort. On the other hand, a simple heuristic to select a random subset of 3-way alignments (a random packing) yields accuracy comparable to averaging all 3-way alignments with substantially less computational effort. CONCLUSION Calculation of lower bounds on SP cost (and thus the quality of an alignment) can be improved by employing a mixture of 3-way and 2-way alignments.
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Affiliation(s)
- Charles J Colbourn
- Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, PO Box 875301, Tempe, AZ 85287-5301, USA
- School of Computing and Informatics, Arizona State University, PO Box 878809, Tempe, AZ 85287-8809, USA
| | - Sudhir Kumar
- Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, PO Box 875301, Tempe, AZ 85287-5301, USA
- School of Life Sciences, Arizona State University, PO Box 875301, Tempe, AZ 85287-5301, USA
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Abstract
Phylogenetic analysis has changed greatly in the last decade, and the most important themes in that change are reviewed here. Sequence data have become the most common source of phylogenetic information. This means that explicit models for evolutionary processes have been developed in a likelihood context, which allow more realistic data analyses. These models are becoming increasingly complex, both for nucleotides and for amino acid sequences, and so all such models need to be quantitatively assessed for each data set, to find the most appropriate one for use in any particular tree-building analysis. Bayesian analysis has been developed for tree-building and is greatly increasing in popularity. This is because a good heuristic strategy exists, which allows large data sets to be analyzed with complex evolutionary models in a practical time. Perhaps the most disappointing aspect of tree interpretation is the ongoing confusion between rooted and unrooted trees, while the effect of taxon and character sampling is often overlooked when constructing a phylogeny (especially in parasitology). The review finishes with a detailed consideration of the analysis of a multi-gene data set for several dozen taxa of Cryptosporidium (Apicomplexa), illustrating many of the theoretical and practical points highlighted in the review.
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Affiliation(s)
- David A Morrison
- Department of Parasitology (SWEPAR), National Veterinary Institute and Swedish University of Agricultural Sciences, 751 89 Uppsala, Sweden
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Reconsideration of anopheline mosquito phylogeny (Diptera: Culicidae: Anophelinae) based on morphological data. SYST BIODIVERS 2005. [DOI: 10.1017/s147720000500174x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Abstract
Chagas disease control initiatives are yielding promising results. Molecular research has helped successful programs by identifying and characterizing introduced vector populations and by defining intervention targets accurately. However, researchers and health officials are facing new challenges throughout Latin America. Native vectors persistently reinfest insecticide-treated households, and sylvatic triatomines maintain disease transmission in humid forest regions (including Amazonia) without colonizing human dwellings. In these scenarios, fine-scale vector studies are essential to define epidemiological risk patterns and clarify the involvement of little-known triatomine taxa in disease transmission. These eco-epidemiological investigations, as well as the planning and monitoring of control interventions, rely by necessity on accurate taxonomic judgments. The problems of cryptic speciation and phenotypic plasticity illustrate this need - and how molecular systematics can provide the fitting answers. Molecular data analyses also illuminate basic aspects of vector evolution and adaptive trends. Here we review the applications of molecular markers (concentrating on allozymes and DNA sequencing) to the study of triatomines. We analyze the suitability, strengths and weaknesses of the various techniques for taxonomic, systematic and evolutionary investigations at different levels (populations, species, and higher taxonomic categories).
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Affiliation(s)
- Fernando Abad-Franch
- Coordenação de Biodiversidade em Saúde, Centro de Pesquisa Leônidas e Maria Deane Fiocruz-Amazônia, Manaus, AM 69057-070, Brasil
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Nolan MJ, Cribb TH. The Use and Implications of Ribosomal DNA Sequencing for the Discrimination of Digenean Species. ADVANCES IN PARASITOLOGY 2005; 60:101-63. [PMID: 16230103 DOI: 10.1016/s0065-308x(05)60002-4] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In just over a decade, the use of molecular approaches for the recognition of parasites has become commonplace. For trematodes, the internal transcribed spacer region of ribosomal DNA (ITS rDNA) has become the default region of choice. Here, we review the findings of 63 studies that report ITS rDNA sequence data for about 155 digenean species from 19 families, and then review the levels of variation that have been reported and how the variation has been interpreted. Overall, complete ITS sequences (or ITS1 or ITS2 regions alone) usually distinguish trematode species clearly, including combinations for which morphology gives ambiguous results. Closely related species may have few base differences and in at least one convincing case the ITS2 sequences of two "good" species are identical. In some cases, the ITS1 region gives greater resolution than the ITS2 because of the presence of variable repeat units that are generally lacking in the ITS2. Intraspecific variation is usually low and frequently apparently absent. Information on geographical variation of digeneans is limited but at least some of the reported variation probably reflects the presence of multiple species. Despite the accepted dogma that concerted evolution makes the individual representative of the entire species, a significant number of studies have reported at least some intraspecific variation. The significance of such variation is difficult to assess a posteriori, but it seems likely that identification and sequencing errors account for some of it and failure to recognise separate species may also be significant. Some reported variation clearly requires further analysis. The use of a "yardstick" to determine when separate species should be recognised is flawed. Instead, we argue that consistent genetic differences that are associated with consistent morphological or biological traits should be considered the marker for separate species. We propose a generalised approach to the use of rDNA to distinguish trematode species.
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Affiliation(s)
- Matthew J Nolan
- School of Molecular and Microbial Sciences and Centre for Marine Studies, Parasitology Section, The University of Queensland, Brisbane, Queensland 4072, Australia
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Abstract
Nematodes are considered among the most difficult animals to identify. DNA-based diagnostic methods have already gained acceptance in applications ranging from quarantine determinations to assessments of biodiversity. Researchers are currently in an information-gathering mode, with intensive efforts applied to accumulating nucleotide sequence of 18S and 28S ribosomal genes, internally transcribed spacer regions, and mitochondrial genes. Important linkages with collateral data such as digitized images, video clips and specimen voucher web pages are being established on GenBank and NemATOL, the nematode-specific Tree of Life database. The growing DNA taxonomy of nematodes has lead to their use in testing specific short sequences of DNA as a "barcode" for the identification of all nematode species.
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Affiliation(s)
- Tom Powers
- Department of Plant Pathology, University of Nebraska Lincoln, Lincoln, Nebraska 68583-0722, USA.
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