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  • Biodiversity Informatics, 2, 2005, pp. 70-78 RESOLVING TAXONOMIC DISCREPANCIES: ROLE OF ELECTRONIC CATALOGUES OF KNOWN ORGANISMS VISHWAS CHAVAN, NILESH RANE, APARNA WATVE Information Division, National Chemical Laboratory, Pune 411008, India. AND MICHAEL RUGGIERO Integrated Taxonomic Information System, U.S. Geological Survey, Smithsonian Institution, Washington D.C., USA Abstract. —There is a disparity in availability of nomenclature change literature to the taxonomists of the developing world and availability of taxonomic papers published by developing world scientists to their counterparts in developed part of the globe. This has resulted in several discrepancies in the naming of organisms. Development of electronic catalogues of names of known organisms would help in pointing out these issues. We have attempted to highlight a few such discrepancies found while developing IndFauna, an electronic catalogue of known Indian fauna, and comparing it with existing global and regional databases. Key words.—Biodiversity informatics, electronic catalogue, taxonomic discrepancies, Indian fauna Identification of organisms is fundamental to needed from the international authority. Similarly, biodiversity studies. Owing to this, the discipline discrepancies in the nomenclature are brought to of taxonomy, especially scientific nomenclature, the notice of the ICZN and ICBN by scientists, has gained immense importance. Taxonomy which are later reviewed. This process requires a provides a vocabulary to discuss the world (Knapp long time and the availability of a large amount of et al., 2002). Each name is unique and its literature to the scientists discussing nomenclature. representative organism is precisely described. It is In several cases, especially for taxonomists in estimated that about 1.8 million species of developing countries, recent taxonomic literature organisms have been formally named from the including the codes themselves are unavailable. world (May, 1999) and each is recognized by a Very few libraries around the world have the unique binomial. More than 2000 new generic financial capacity to carry the full range of names and 15000 new specific names alone are literature in which systematic results are published added to the zoological literature every year, and (Agosti and Johnson, 2002). Hence, nomenclature with such a multiplicity of names, problems are changes are in many cases unavailable or become bound to occur. International mechanisms such as available much later to the developing country the International Code of Zoological Nomenclature scientists than to their counterparts in developed (ICZN, 1999) and the International Code of world. This leads to use of old or outdated Botanical Nomenclature (ICBN) are rulebooks that nomenclature. govern how organisms are named and they provide On the other hand taxonomic papers by clear instructions on how to go about the process developing country scientists published in journals (Knapp et al., 2002). with regional scope, which are not scientifically International codes of nomenclature require abstracted, remain isolated and unnoticed by the taxonomic actions to be published and the data wider scientific audience and taxonomic changes thus made available (Agosti and Johnson, 2002). proposed or used in such papers are often However, nomenclatural additions or changes have neglected. This obviously leads to many to be conveyed to the ICZN or ICBN by the discrepancies in the information available, authors and is usually done when ratification is especially about the current or correct taxonomic 70
  • CHAVAN ET AL. – RESOLVING TAXONOMIC DISCREPANCIES hierarchy of organisms. It is thus necessary to TAXONOMIC DISCREPANCIES create a system, which will lead to rapid During this project we have noticed several identification of taxonomic discrepancies and their taxonomic discrepancies, which need to be resolution. In addition, a permanent mechanism for resolved by application of nomenclatural rules. registering and validating scientific names of These discrepancies can be grouped in 3 organisms needs to be created at national as well as categories: hierarchical differences, spelling global levels. Web-based electronic catalogues can differences and homonymies. be effective in creating such a central repository of taxonomic information. In this paper, we Difference in taxonomic hierarchies demonstrate the use of web-based electronic Several examples were found where the catalogues (ELECATs) in identifying taxonomic taxonomic hierarchy of organisms followed in discrepancies in an Indian context. India did not match that used by ITIS. This is The NCL Center for Biodiversity Informatics especially true in case of some fishes, nematodes (NCBI) is developing an Electronic Catalogue of and insects. This is the result of differences in Known Indian Fauna (IndFauna) (NCL, 2005). So taxonomic opinions or the provisional nature of far it has documented baseline information on certain data in ITIS and a consensus is often more than 91,000 scientific names of the known difficult. In this case, the information managers Indian faunal species. The data incorporated in the can display the placement of the taxon according to database is collected from multiple sources. The alternative schemes. In spite of this option, it is main focus is on published literature including necessary to conform to the international research papers, faunas, and monographs as taxonomic opinion, to make the datasets sources of authentic and reviewed information. For interoperable with those developed in other parts those taxa especially invertebrates, on which of the world. This is an issue that needs to be published literature is not readily available, discussed and resolved by taxonomists working in preserved collections from natural history India. Although making changes in taxonomic museums, web-based databases and checklists are hierarchy is technically possible in case of the also being referenced. Thus, when collecting electronic datasets, each change needs to be information, highest importance is given to validated by the taxonomic community as some “faunas” and “monographs” followed by taxa may or may not be conforming to that change. “published research papers”, then “online and Some of the examples where taxonomic hierarchy offline databases” followed by “region- and taxon- is different are given in Table 1. specific web sites” followed by “personal As per ITIS and other taxonomic resources communications with experts”, and finally to “non- Sub Class Elasmobranchii is placed under Class taxonomic publications”. Chondricthyes, while Systema Naturae 2000 The information is carefully scrutinized for (Brands, S. J., 1989-2005) still recognizes it as validity and accepted only if it is from reputed Class Elasmobranchii. taxonomic institutions or experts. For each species, the taxonomic hierarchy used by Indian faunas is Differences in spelling crosschecked diligently with that used in global The most common problem faced while taxonomic inventories such as Integrated digitizing the data was different spellings of Taxonomic Information System (ITIS, 2005), organisms’ names. Some examples are given in Species2000 (Species2000, 2005), Catalogue of Table 2. Life: 2005 Annual Checklist (Bisby et al., 2005), Order Cheilostomata as per ITIS is named Index to Organism Names (ION, 2005), European differently as Order Cheilostomida by ERMS Register for Marine Species (ERMS, 2005), (2005). Even the hierarchy under this order is not Systema Naturae 2000 (Brands, S. J., 1989-2005) same for many species given in these two etc. In case of any problems regarding taxonomic databases. placement of the species concerned taxonomy experts are contacted and as per their suggestions the species are being entered in the database. 71
  • CHAVAN ET AL. – RESOLVING TAXONOMIC DISCREPANCIES Table 1. Difference in hierarchies used in various sources. Sr. Taxon or Scientific name Indian sources Integrated Taxonomic No. Information System 1 Appendicularia histnae Kingdom: Animalia Kingdom: Animalia Phylum: Chordata Phylum: Chordata Subphylum:Urochordata Subphylum:Tunicata Class: Larvacea Class: Appendicularia Order: Oikopleurida Order: Copelata Family: Appendicularidae ITIS does not include genus Genus: Appendicularia Appendicularia Species: histnae (Das, 2003; Dhandapani, 1977) 2 Pillaia indica Pillaia khajuriai Kingdom: Animalia Kingdom: Animalia Genus Pillaia is placed Phylum: Chordata Phylum: Chordata under different order of Class: Actinopterygii Class: Actinopterygii Class Actinopterygii Order: Perciformes Order: Synbranchiformes Family: Chaudhuriidae Family: Chaudhuriidae Genus Pillaia Genus Pillaia (Rao, 2000) 3 Zenarchopterus ectuntio and Kingdom: Animalia Kingdom: Animalia Zenarchopterus striga Phylum: Chordata Phylum: Chordata Genus Zenarchopterus is Class: Actinopterygii Class: Actinopterygii placed under different Order: Atheriniformes Order: Beloniformes order Sub Order: Exocoetoidei Sub Order: Belonoidei Family: Hemiramphidae Family: Hemiramphidae Genus Zenarchopterus Genus Zenarchopterus (Rao, 2000) In some cases these were misspellings, Homonyms especially typographical errors. However, to A few homonyms were identified in the follow the taxonomic norms, each misspelling cataloguing process. For instance, genus needs to be reported along with the valid scientific Chaunoproctus and genus Microcosmus were name for avoiding future problems. Usually such observed to be used in different regions for wrongly spelled scientific names are reported as different taxa. This is a direct contradiction to synonyms with a prefix “sic” as per the nomenclature rules. Closer scrutiny of literature International Code of Zoological Nomenclature and taxonomic opinion revealed interesting facts of (ICZN, 1999). In some case the difference in uses of these two genera. According to ITIS (ITIS, spelling was due to different taxonomic opinions, 2005) and the Taxonomicon of Systema Naturae and choosing which to use requires discussion with 2000 (Brands, S. J., 1989-2005), genus taxonomists. For example the Blue Whale Shark Chaunoproctus Bonaparte, 1850 (Aves: Rhincodon which is spelled Rhiniodon (Talwar and Passeriformes: Fringillidae) is a bird, Kacker, 1984; Talwar, P. K., 1991) in Indian Chaunoproctus ferreorostris Vigors, 1829, which literature. ITIS shows Rhiniodon as a synonym of is now extinct as per the IUCN Redlist of Rhincodon that was suppressed by a ruling (ITIS, Threatened Species (IUCN, 2005). 2005). 72
  • CHAVAN ET AL. – RESOLVING TAXONOMIC DISCREPANCIES Table 2. Misspellings and difference in hierarchies in various sources. Sr. No. Scientific names as per: Integrated Taxonomic Information Indian sources System 1 Kingdom: Animalia Corynosoma streemosum Phylum: Acanthocephala (Bhattacharya, 1998) Class: Palaeacanthocephala Order: Polymorphida Family: Polymorphidae Genus: Corynosoma Species: strumosum 2 Kingdom: Animalia Class Mammalia Phylum: Chordata Order: Cetacea Class: Mammalia Genus: Psudorca Order: Cetacea Species: crassidens Family: Delphinidae (Agarwal V.C., 1998) Genus: Pseudorca Species: crassidens 3 Genus: Amblypharyngodon Phylum: Chordata Genus previously present in ITIS but not Class: Actinopterygii found as on date. Family: Cyprinidae Genus: Ambylopharyngodon (Aditya and Raut, 2001) 4 Kingdom: Animalia Kingdom: Animalia Phylum: Chordata Phylum: Chordata Class: Actinopterygii Class: Actinopterygii Order: Beloniformes Order: Cyprinodontiformes Family: Adrianichthyidae Family: Cyprinodontidae Genus: Oryzias Genus: Oryzias Species: melastigma Species: melanostigma [Family: Cyprinodontidae is present under (Nandi, 1993) Order Cyprinodontiformes] 73
  • CHAVAN ET AL. – RESOLVING TAXONOMIC DISCREPANCIES Chaunoproctus Pearce, 1906 (Arachnida: today the carabid species is cited as Acari) is a group of orabitid mites as per the Microcosmodes flavopilosus. Thus, Indian Indian Faunas (Sanyal and Bhaduri, 1986; records (Saha, et al., 1992) which show presence Sanyal et al., 2003). The type species designated of Microcosmus instead of Microschemus needs for this genus is Chaunoproctus cancellatus to be updated. Pearce, 1906 collected from Sikkim, India. Polypodium hydriforme, which is under Interestingly, genus Zetorchella Berlese, 1916 phylum Cnidaria, is still considered as a valid reported from Somaliland, and genus Callopia scientific name under Phylum Pisces along with Balogh, 1958 reported from Angola, Africa were Phylum Cnidaria by ION (2005). Genus Doto regarded as synonyms of the genus described by Oken, 1815 is considered valid for Chaunoproctus by Balogh (1965) (Sanyal et.al., phylum Mollusca while; U.S. National Museum 2003). Later in 1972 he again considered them of Natural History database (2005) displays it as distinct genera. Recently, J. Balogh and P. under phylum Arthropoda as well as phylum Balogh (1992) again concluded that genus Mollusca. In these cases it is really difficult to Zetorchella and genus Caloppia as synonyms of place the organism in a specific hierarchy. genus Chaunoproctus. In 2003, Sanyal and team Another example is of the Genus Cyaniris, described three new species Chaunoproctus which is present under family Lycaenidae, order orientalis, C. sisiri, and C. amarpurensis Lepidoptera, class Insecta (Bingham, 1907). The belonging to genus Chaunoproctus from same genus name Cyaniris is also given to Tripura, India (Sanyal et.al., 2003). Genus insects belonging to family Chrysomelidae, Chaunoproctus is also reported from other parts order Coleoptera, class Insecta as per the of the globe as valid genus of Order Acari database of the holotype collections from India (Mahunka, S., 1987). As per the International present in the Belgium Museum (Drugmand, Code of Zoological Nomenclature (ICZN, 2002). The genus is not included in the ITIS 1999), generic name Chaunoproctus Pearce, database while the other web sites and literature 1906 (Arachnida: Acari) can be a junior sources shows presence of genus Cyaniris in homonym of Chaunoproctus Bonaparte, 1850 order Lepidoptera. (Aves: Passeriformes: Fringillidae). While checking hierarchy for a species, Similarly the generic name namely Idia pristis, which is placed under class Microcosmus Heller, 1878 (ITIS, 2005) [1877 Hydrozoa (Ritchie, 1910), surprisingly we came (ION, 2005)] (Chordata, Ascidiacea) is a across genus Idia which is also present under homonym of Microcosmus Chaudoir 1879 class Insecta, order Lepidoptera, family (Insecta, Coleoptera, Carabidae) (Saha, et.al., Noctuidae as per the checklist of Noctuoidea of 1992). Both names are in use and refer, Ontario present on the website hosted by respectively, to Ascidiacea as per the ITIS Canadian Biodiversity Information Facility (2005) and ION (2005), and for a beetle as per (Troubridge and Lafontaine, 2003). There is also Indian literature (Saha, et al., 1992). Opinion no ready reference available for this generic was sought from carabidologists and finally designation anywhere. Wolfgang Schiller resolved this issue. Microcosmus has been described by Chaudoir DISCUSSION (Chaudoir, 1879) under tribe Panageini within A consensus on these issues is a matter of family Carabidae (Order Coleoptera: Class taxonomic discussion. They need to be resolved Insecta: Phylum Arthropoda) for the species M. by using nomenclatural rules, which requires flavopilosus. However, Heller already further detailed research. However these designated the same genus Microcosmus in 1877 examples effectively demonstrate the potential under family Pyuridae, (Class Ascidiacea, of electronic catalogues (ELECATs) in bringing Phylum Chordata). Hence, Emberik Strand issues or discrepancies to the attention of the proposed new name Microcosmodes (Strand, taxonomic community, starting a dialogue 1936). Later in 1940, Andrewes replaced it to between taxonomists across the globe and genus Microschemus (Yves, B., 2002). So until identifying issues of common concern. In order 74
  • CHAVAN ET AL. – RESOLVING TAXONOMIC DISCREPANCIES to notice such discrepancies and resolve them has already taken a step towards registering of quickly, it is essential that a wrapper be names (Anonymous, 2002) by requiring the developed which traverses through various authors of papers featuring new taxonomy to file electronic catalogues searching for taxonomic the information with a recognized institute such anomalies. This calls for increasing as Linnaean Society of London. Central registry collaboration among the various ELECATs. will be a repository of scientific name The information available so far on the information or an index for scientific names in Internet is largely limited to names and citations. use, along with their history. It will be a It is understood, however, that taxonomic dynamic register for proposed scientific names literature generated out of two centuries’ work (which will be provisionally accepted, noted), cannot be put on the Internet overnight. It is a which can later be added to the repository after formidable taxk, yet one that must be annotation. These will serve as references for accomplished as promptly as possible. With the scientists describing new taxa to check if the growing use of information and communication name has been used before, and in which technologies in biodiversity research, it should context. This will eliminate generation of be possible to make the taxonomic literature homonyms. It can also provide a point of itself available on the Internet, which can be “normalization” for data. used for checking inconsistency in taxonomy, ELECATs offer an effective method of used worldwide. Although taxonomists from creating unique electronic registers. Owing to around the world have been dealing with these the rules of acceptance of scientific names, discrepancies, it is time-consuming and tedious names cannot be registered as valid before the to identify, check, and correct them using the publication of taxon description in a journal. To traditional media such as published literature. solve this, a precedent can be set that in case of Modern information and communications tools each new description, together with the type can be of immense help in identifying taxonomic specimen deposition number, a provisional discrepancies quickly and resolving them in a registration number in the global, regional or collaborative manner leading to globally national web based ELECAT should be quoted. acceptable standardized inventories. With the There will be two-way information exchanges use of the Internet, there can be a truly two-way with other ELECATs. The registry will compare exchange of information between taxonomists between ELECATs information, find out any from developed and developing countries. points of mismatches or conflicting data, and Active collaboration and commitment of also pick up new information automatically from taxonomists and information managers are the ELECATs. Using this, a single number required to work towards the goal of developing reference system for each scientific name can be information systems to bring uniformity and developed. The central registry can provide a precision to taxonomic inventories across the minimum standard and starting point for use in world. Many of the discrepancies arise because other databases. taxonomists are unable or find it difficult to The Global Biodiversity Information check up on taxon names especially for taxa Facility (GBIF), together with the Taxonomic outside their field of expertise. Database Working Group (TDWG), is currently Hence, to build up easy communication seeking requirements for Globally Unique pathways and reduce the time input, it would be Identifiers (GUIDs) for biodiversity informatics extremely helpful to have a web-based central and to establish infrastructure to support their registry system for taxonomic names. Checking use. GUIDs once developed can overcome most of names being used in publication with the of the current problems, such as (a) central registry would definitely eliminate many identification of same data records served from of the commonly encountered discrepancies multiple locations, (b) referring to data from described above. Thorne (2003) also proposed outside network, irrespective of frequent change the need for registration of new taxa names in a of URLs, and (c) referring to taxon concepts in central registry of names. The journal Nature reliable and consistent way. Page (2005) 75
  • CHAVAN ET AL. – RESOLVING TAXONOMIC DISCREPANCIES suggests a system of Life Science Identifiers taxonomist’s time would be saved by having a (LSIDs) as unique numerical identifiers for tool that can readily compare data with that in scientific names and ITIS currently employs a the central file (such as ITIS’ Taxcompare tool). system of unique Taxonomic Serial Numbers The ability to check quickly for homonymies (TSNs). Databases could be mapped to TSNs or will also save time. In addition, development some parallel concept. and use of national ELECATs should be Many organizations are working towards encouraged to collate information at the national building up registers of published scientific levels and make it available to the global users. names of taxa such as for beetles (Vratislav, This is especially important, as these national 2005). Plant names can be checked using registers will be able to easily access locally International Plant Names Index (IPNI, 2005). available primary taxonomic information. Index to Organism Names (ION, 2005) database It is also necessary to track changes in can be used to check zoological names. The species concepts over time. ITIS has developed most holistic efforts are those of Species2000 a capability for change tracking, but has not yet and ITIS Catalogue of Life (Leslie, 2005) and implemented it. Availability of specimens, GBIF, which aim to create an index of at least images, protologues, and classifying characters 95% of the known species by 2011 (GBIF, in use in different countries, comparing between 2005). This is a major step towards developing a specimens of a species with wide distribution- central register of names, and increasing transcending political boundaries and building collaborations between similar efforts biogeographic distribution maps, language worldwide should shorten the time required. To barrier - translating Latin diagnoses, and picture complement these initiatives, International data are some of the capabilities required to Commission of Zoological Nomenclature ensure accurate results in biodiversity research announced its intention of setting up of web- projects. based, open access mandatory registration These advances suggest that, in the future, system called “ZooBank” to register descriptions the taxonomic discipline will make broad use of of all new taxa and nomenclatural acts in animal the web-based information and benefit greatly taxonomy. (Polaszek et al., 2005). While similar from it. Therefore, it is crucial at the moment to mandatory registration mechanism exists for build up or improve the collaborative activities descriptions of new bacteria, it needs to be among domain experts, information managers extended for other kingdoms viz., Plantae, and users of taxonomic information. This would Archaea, Chromista, Fungi, Protozoa, and ultimately help in strengthening the biodiversity Viruses. Similar to “ZooBank” these mandatory research necessary for conservation and registration mechanisms would facilitate management of global natural resources. retrospective registration of existing names, and of all nomenclatural acts in respective kingdom. CONCLUSIONS This can be achieved through active linkages The discrepancies found while developing and collaborations with existing projects, rather IndFauna, an electronic catalogue of known than replacing them. Indian fauna and comparing it with existing In addition, links to other databases like databases can help to solve several issues like image, DNA sequences, protein sequences, lipid taxonomic ambiguities, inadequate sequences, and collection locality maps, etc. will documentation and incorrect placements of be a major step forward. Further, linking valid species. Development of electronic catalogues of scientific names to collection accession numbers names of known organisms (ELECATs) will of type specimens will help scientists track all help in pointing out these issues. International collections quickly and know where they are organizations like GBIF are trying to make all deposited. Applications could be built such as biodiversity data accessible to the largest those on the ITIS Canada website or uBio1 that possible section of the human population. display multiple classifications. In addition, a Recently GBIF, Species 2000, ITIS and uBio (GBIF, 2005) have decided to cooperate on 1 http://www.ubio.org/. 76
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