Zoological Taxonomy Research Articles

The natural cytotoxicity receptor genes in the family Felidae.

Natural killer (NK) cells belong to the innate immune system. The germline-encoded natural killer cell receptors represent activating and inhibitory receptors regulating multiple NK cell activities. The natural cytotoxicity receptors (NCRs) are activating natural cytotoxicity triggering receptors 1, 2, and 3 (NKp46, NKp44, and NKp30), encoded by the genes NCR1, NCR2, and NCR3, respectively. NCRs may be expressed in different cell types engaged in mechanisms of innate and adaptive immunity. The family Felidae, comprising the domestic cat and a wide variety of free-ranging species represents a well-suited model for biomedical and evolutionary studies. We characterized the NCR1, NCR2, and NCR3 genes in a panel of felid species. We confirmed the presence of potentially functional genes NCR1, NCR2, and NCR3 in all species. All three genes are conserved within the family and are similar to other phylogenetically related mammalian families. The NCR1 and NCR2 phylogenetic trees based on both nucleotide and protein sequences corresponded to the current zoological taxonomy, with some exceptions suggesting effects of different selection pressures in some species. Highly conserved NCR3 sequences did not allow a robust phylogenetic analysis. Most interspecific differences both at the nucleotide and protein level were found in NCR2. Within species, the most polymorphic CDS was detected in NCR1. Selection analyses indicated the effects of purifying selection on individual amino acid sites in all three genes. In stray cats, a rather high intraspecific diversity was observed.

The deadly face of felid killer cells: The cytotoxic proteins and their genes.

Natural killer cells and cytotoxic T lymphocytes are the main cell populations of the immune system able to directly kill target cells via cytotoxic granules. Different mammalian species may differ in specific features of their pore-forming protein (perforin) and granule-bound serine proteases (granzymes). One perforin gene (PRF1) and four genes encoding granzymes A, B, H, and K (GZMA, GZMB, GZMH, GZMK) were identified in the reference genomes of felids. The objective of this work was to characterize the genes PRF1, GZMA and GZMB in a panel of 17 felid species by next-generation re-sequencing. A search of available felid genomes (17 species) retrieved the coding sequences of these genes for comparison to our data. Both sets of sequences or their combinations (23 species) were used for phylogenetic and selection analyses. Nucleotide PRF1, GZMA and GZMB sequences showed high similarities between felid species (over 95% identity). All trees derived from coding sequences expressed phylogenetic relationships corresponding to the zoological taxonomy of the Felidae, except GZMA. No effects of positive selection were detected in the genes studied, however, effects of purifying selection were observed for PRF1 and GZMA. The conservation of PRF1 is in agreement with its critical biological function. The differentiation observed between granzyme sub-families may reflect an adaptation to pathogen variation. The need to maintain important gene functions and at the same time cope with various pathogens may lead to an equilibrium between positive and negative selective pressures acting on GZMB. The within-species variability in wild felid populations merits further investigation.

Phylogenetic signal in characters from Aristotle’s History of Animals

The influential Greek philosopher Aristotle (384-322 BCE) is almost unanimously acclaimed as the founder of zoology. There is a consensus that he was interested in attributes of animals, but whether or not he tried to develop a zoological taxonomy remains controversial. Fürst von Lieven and Humar compiled a data matrix from Aristotle’s Historia animalium and showed, through a parsimony analysis published in 2008, that these data produced a hierarchy that matched several taxa recognized by Aristotle. However, their analysis leaves some questions unanswered because random data can sometimes yield fairly resolved trees. In this study, we update the scores of many cells and add four new characters to the data matrix (147 taxa scored for 161 characters) and quote passages from Aristotle’s Historia animalium to justify these changes. We confirm the presence of a phylogenetic signal in these data through a test using skewness in length distribution of a million random trees, which shows that many of the characters discussed by Aristotle were systematically relevant. Our parsimony analyses on the updated matrix recover far more trees than reported by Fürst von Lieven and Humar, but their consensus includes many taxa that Aristotle recognized and apparently named for the first time, such as selachē (selachians) and dithyra (Bivalvia Linnaeus, 1758). This study suggests that even though taxonomy was obviously not Aristotle’s chief interest in Historia animalium, it was probably among his secondary interests. These results may pave the way for further taxonomic studies in Aristotle’s zoological writings in general. Despite being almost peripheral to Aristotle’s writings, his taxonomic contributions are clearly major achievements.

The nomenclatural status of the amphibian and reptile nomina introduced by  La Cepède in his Histoire Naturelle des Quadrupèdes Ovipares et des Serpens, with comments on various questions of zoological nomenclature

The ‘suppression’ (invalidation) for nomenclatural purposes by the International Commission on Zoological Nomenclature of the work Histoire Naturelle des Quadrupèdes Ovipares et des Serpens first published by La Cepède from 1788 to 1790 brought no benefit of any kind to zoological taxonomy and nomenclature but generated several nomenclatural problems. Here we review the history of the many discussions and proposals, as well as the successive and contradictory decisions of the Commission, regarding this work and the new nomina it contains, and we make new proposals to solve some of the problems created by these decisions. We suggest the Commission should take the initiative to restore nomenclatural availability to 18 nomina of La Cepède invalidated or of unclear status following its previous actions. More generally, we think that the use of the Plenary Power by the Commission should be more strictly regulated and made less easy and straightforward, and that the whole invalidation of complete works that have been considered as nomenclaturally available for a very long time in many works (e.g., 100 works in the 100 immediately preceding years) should be forbidden, and that the Commission should rather concentrate its attention and action on nomina rather than on works. Besides, we show that the snake nomen Coluber trigonocephalus Donndorff, 1798, currently considered valid, is invalid, and should be replaced by the nomen Coluber capitetriangulatus Bonnaterre, 1790.

<p class="ZootaxaTitle">New concepts and methods for phylogenetic taxonomy and nomenclature in zoology, exemplified by a new ranked cladonomy of recent amphibians (Lissamphibia)

Although currently most taxonomists claim to adhere to the concept of ‘phylogenetic taxonomy’, in fact most of the zoological classifications currently published are only in part ‘phylogenetic’ but include also phenetic or gradist approaches, in their arbitrary choices of the nodes formally recognised as taxa and in their attribution of ranks to these taxa. We here propose a new approach to ‘phylogenetic taxonomy and nomenclature’, exemplified by a phylogenetic classification or cladonomy of the extant amphibians (subclass Lissamphibia of the class Amphibia) derived from a supermatrix-based phylogenetic analysis using 4060 amphibian species, i.e. about half of the 8235 species recognised on 31 October 2020. These taxa were represented by a mean of 3029 bp (range: 197–13849 bp) of DNA sequence data from a mean of 4 genes (range: 1‒15). The cladistic tree thus generated was transferred into a classification according to a new taxonomic and nomenclatural methodology presented here, which allows a bijective or isomorphic relationship between the phylogenetic hypothesis and the classification through a rigorous use of suprageneric ranks, in which their hierarchy mirrors the structure of the tree. Our methodology differs from all previous ones in several particulars: [1] whereas the current International Code of Zoological Nomenclature uses only three ‘groups of names’ (species, genus and family), we recognise four nominal-series (species, genus, family and class); [2] we strictly follow the Code for the establishment of the valid nomen (scientific name) of taxa in the three lower nominal-series (however, in a few situations, we suggest improvements to the current Rules of the Code); [3] we provide precise and unambiguous Criteria for the assignment of suprageneric nomina to either the family- or the class-series, excluding nomina proposed expressly under unranked or pseudoranked nomenclatural systems; [4] in the class-series, for which the Code provides only incomplete Rules concerning availability, we provide precise, complete and unambiguous Criteria for the nomenclatural availability, taxonomic allocation and nomenclatural validity and correctness of nomina; [5] we stress the fact that nomenclatural ranks do not have biological definitions or meanings and that they should never be used in an ‘absolute’ way (e.g., to express degrees of genetic or phenetic divergence between taxa or hypothesised ages of cladogeneses) but in a ‘relative’ way: two taxa which are considered phylogenetically as sister-taxa should always be attributed to the same nomenclatural rank, but taxa bearing the same rank in different ‘clades’ are by no means ‘equivalent’, as the number of ranks depends largely on the number of terminal taxa (species) and on the degree of phylogenetic resolution of the tree; [6] because of this lack of ‘equivalence’, some arbitrary criteria are necessary to fix a starting point for assigning a given suprageneric rank to some taxa, from which the ranks of all other taxa will automatically derive through a simple implementation of the hierarchy of ranks: for this purpose we chose the rank family and we propose a ‘Ten Criteria Procedure’ allowing to fix the position of this rank in any zoological classification. As a result of the implementation of this set of Criteria, we obtained a new ranked classification of extant lissamphibians using 25 suprageneric ranks below the rank class (11 class-series and 14 family-series ranks), and including 34 class-series and 573 family-series taxa, and where the 575 genera we recognise are referred to 69 families and 87 subfamilies. We provide new nomina and diagnoses for 10 class-series taxa, 171 family-series taxa, 14 genus-series taxa and 1 species. As many new species of amphibians are permanently described, this classification and its nomenclature will certainly have to change many times in the future but, using the clear, explicit, complete, automatic and unambiguous methodology presented here, these changes will be easy to implement, and will not depend on subjective and arbitrary choices as it has too often been the case in the last decades. We suggest that applying this methodology in other zoological groups would improve considerably the homogeneity, clarity and usefulness of zoological taxonomy and nomenclature.

Are publications on zoological taxonomy under attack?

Taxonomy is essential to biological sciences and the priority field in face of the biodiversity crisis. The industry of scientific publications has made extensive promotion and display of bibliometric indexes, resulting in side effects such as the Journal Impact Factor™ (JIF) mania. Inadequacies of the widely used indexes to assess taxonomic publications are among the impediments for the progress of this field. Based on an unusually high proportion of self-citations, the mega-journal Zootaxa, focused on zoological taxonomy, was suppressed from the Journal Citation Reports (JCR, Clarivate™). A prompt reaction from the scientific community against this decision took place exposing myths and misuses of bibliometrics. Our goal is to shed light on the impact of misuse of bibliometrics to the production in taxonomy. We explored JCR's metrics for 2010–2018 of 123 zoological journals publishing taxonomic studies. Zootaxa, with around 15 000 citations, received 311% more citations than the second most cited journal, and shows higher levels of self-citations than similar journals. We consider Zootaxa's scope and the fact that it is a mega-journal are insufficient to explain its high level of self-citation. Instead, this result is related to the ‘Zootaxa phenomenon', a sociological bias that includes visibility and potentially harmful misconceptions that portray the journal as the only one that publishes taxonomic studies. Menaces to taxonomy come from many sources and the low bibliometric indexes, including JIF, are only one factor among a range of threats. Instead of being focused on statistically illiterate journal metrics endorsing the villainy of policies imposed by profit-motivated companies, taxonomists should be engaged with renewed strength in actions directly connected to the promotion and practice of this science without regard for citation analysis.

Species names based on photographs: debate closed.

Discussions of current issues of broad interest in zoological taxonomy are encouraged in Zootaxa (Zhang 2007). One recent topic examines species names based on photographs without preserved specimens. This is not a new topic: as Ceríaco et al. (2016) correctly noted, this topic was previously discussed about a decade ago in Zootaxa (Dubois & Nemésio 2007; Donegan 2008), and was soon followed by a series of opinions and rebuttals when the critically endangered species Galápagos pink land iguana-Conolophus marthae Gentile & Snell, 2009-was named without a preserved holotype (Donegan 2009; Nemésio 2009a,b; Dubois 2009; Gentile & Snell 2009; Minelli 2009).

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences.

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a-b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016.

Chengru Feng: The founder of biological illustration in China.

Chengru Feng: The founder of biological illustration in China.

Cloning and characterization of DjPRPS gene in freshwater planarian Dugesia japonica

Objective: To clone the phosphoribosyl pyrophosphate synthetase gene from Dugesia japonica, and to do the bioinformatics and spatial expression analysis of the gene. Methods: The phosphoribosyl pyrophosphate synthetase gene (DjPRPS) was cloned from Dugesia japonica using the rapid amplification of cDNA ends method and its sequence was analyzed with biological softwares. Spatial expression pattern of the gene was detected by whole-mount in situ hybridization. Results: The full length cDNA of DjPRPS was 1,086 bp, containing a 80 bp of 5'-untranslated region, a 55 bp of 3'- untranslated region and a 951 bp of open reading frame encoding a protein of 316 amino acids with a calculated molecular mass of 35.18 kDa and isoelectric point of 8.14. The deduced amino acid sequence shared the conserved eukaryotic PRPS family motif. Phylogenetic analysis supported the traditional concept of zoological taxonomy in large scale. Intense positive signals were detected as bilateral lines of patches in the ventral side where the ovaries and yolk glands located in the intact sexual planarians. In the regenerating planarians, the expression pattern was similar to that of the intact samples, and no intense transcipt signals were detected in the blastema. Conclusion: DjPRPS sequence was highly homologous with that of other eukaryotic phosphoribosyl pyrophosphate synthetase gene. Intense transcript signals of DjPRPS were not detected in the blastema but in ovaries and yolk glands, suggesting that its function was probably reproduction-related and maybe not involved in regeneration.

Endangered: A Study of Morphological Drawing in Zoological Taxonomy

Drawing has long been the backbone of zoological taxonomy. Recently, however, morphological drawing has quietly fallen into a critical decline and is now an endangered practice. The author discusses the reasons for this decline and why morphological drawing is worth saving.

Symbolic Lizards: Forms of Special Purpose Classification of Animals among the Nage of Eastern Indonesia

ABSTRACTThe Nage people of Flores island, eastern Indonesia, recognize an unnamed (or “covert”) life-form category comprising several named kinds of lizards as a distinct component of their folk zoological taxonomy, a general purpose classification of animals based primarily on universally observable morphological and behavioral features. Exploring symbolic values of lizards evidenced in Nage thought and practice, this essay considers how far lizards might also compose a unitary symbolic class and whether symbolic similarity and contrast may inform Nage taxonomy. The answer is in both cases negative. Typically, symbolic classes cross-cut the major divisions of a folk taxonomy of animals, thereby associating, on symbolic grounds (such as common association with spiritual beings), animals belonging to diverse life-forms such as snakes, birds, and fish. With reference to this and other findings, exploration of Nage lizard classification serves to introduce a discussion of general differences between folk taxonomy and symbolic classification of animals as well as circumstances in which folk taxonomic and symbolic categories are likely to coincide. Attention is also given to utilitarian categories as another form of special purpose, non-taxonomic classification, and with reference to specific practical uses Nage make of lizards, it is shown how the various members of the Nage folk taxon “lizard” similarly do not compose a single class. Contradicting a time-honored view most closely associated with Mary Douglas, the essay thus provides a comprehensive, critical demonstration of how animal classification in a given society need not compose a conceptual unity.

Zygoidy, a new nomenclatural concept

In zoological taxonomy, unambiguous and universal designation of a given taxon at a given rank in a given classification requires to establish its valid nomen and the correct spelling of the latter. Consequently, a need to resolve the situations of conflict that may exist between available nomina and spellings arises. These situations of nomenclatural conflict are here designated as zygoidy. They are of three kinds: zygonymy (conflicts of omonymy or synonymy between nomina for validity), zygography (conflicts of parography between spellings for correctness) and zygophory (conflicts of airetophory between onomatophore designations for validity). The resolution of these conflicts relies on several basic Principles already formulated in the Code (the Principles of Homonymy, Priority and “First-Reviser”, here renamed “Airesy”), as well as additional ones not yet recognized in this text: the Principles of Zygoidy, Proedry, Nomography and Sozoidy. A detailed analysis of these ituations is provided. It allows to identify in which cases and under which conditions these Principles apply. This omplete inventory of possible situations and solutions will be of great usefulness for a forecoming utomatisation and computerization of the Rules of the Code in forthcoming databases and Web applications.

Taxonomy, Type Specimens, and the Making of Biological Property in Intellectual Property Rights Law

AbstractDespite remaining the most iconic and highly valorized metrical technology of the entire, now globally universalized, project of zoological and botanical taxonomy, very little attention has been given to highlighting the pivotal role that type specimens also play in constructing and disciplining contemporary relations to living property. Building on my earlier work on the relationship between biological classification and regulation,1 this article provides an overdue analysis of this technology's significance in introducing deposition, priority of publication, and authorship as the key conceptual and functional mechanisms not only of taxonomic classification, but also of the ascendant system for prosecuting rights to ownership of biological novelties in the contemporary era: the Euro-American system of intellectual property law.

Of Mice and Rats: The Place of Murids in Nage Animal Classification and Symbolism

Abstract The folk zoological taxonomy of the Nage people of central Flores (Indonesia) classifies wild mammals into thirteen named folk generic taxa (sensu Berlin). Of these, nearly half denote murids (rats and mice). In addition, Nage employ dheke, a name that can specifically refer to large commensal rats, to further designate a folk intermediate taxon that subsumes other murid folk generics, thus resulting in a notably more elaborate classification of mice and rats than of other mammals. Murids also receive comparably distinctive treatment in other, special purpose forms of animal classification, and they occupy an especially prominent place in Nage symbolism. The paper considers how these several conceptual orders may be connected, including whether the ethnotaxonomic elaboration of murids may either reflect or be reflected in their symbolic value.

When Is a Fish Not a Fish? Questions Raised by a Nage Life-Form Category

Speakers of a Central-Malayo-Polynesian language, the Nage inhabit the central region of the eastern Indonesian island of Flores. Their folk taxonomy of animals (ana wa) contains three named life-form taxa, one of which is ika, fish. A review of component folk-generic taxa, however, reveals that Nage do not classify five kinds of freshwater fish as ‘fish’ (ika), even though they further apply ika to various marine fish (including sharks and rays) as well as to marine mammals. The article considers this peculiarity of Nage folk zoological taxonomy, and how it might affect an understanding of ika as denoting a ‘fish’ life-form taxon. The main conclusion is that the five excluded categories—distinguished largely on morphological and behavioural grounds, and conveniently designated as the ‘tebhu cluster’, after one of their members—are contrasted primarily with freshwater species which Nage do classify as ‘fish’ (ika). Specified by name as ika lowo (‘river fish’), these are further contrasted with another named folk-intermediate taxon of ‘marine fish’ (ika mesi). From this, it is argued that, as a life-form category, ika should be understood as implicitly including the five members of the ‘tebhu cluster’ as a third, albeit covert, folk-intermediate taxon.

When Is a Fish Not a Fish? Questions Raised by a Nage Life-Form Category

Speakers of a Central-Malayo-Polynesian language, the Nage inhabit the central region of the eastern Indonesian island of Flores. Their folk taxonomy of animals (ana wa) contains three named life-form taxa, one of which is ika, fish. A review of component folk-generic taxa, however, reveals that Nage do not classify five kinds of freshwater fish as ‘fish’ (ika), even though they further apply ika to various marine fish (including sharks and rays) as well as to marine mammals. The article considers this peculiarity of Nage folk zoological taxonomy, and how it might affect an understanding of ika as denoting a ‘fish’ life-form taxon. The main conclusion is that the five excluded categories—distinguished largely on morphological and behavioural grounds, and conveniently designated as the ‘tebhu cluster’, after one of their members—are contrasted primarily with freshwater species which Nage do classify as ‘fish’ (ika). Specified by name as ika lowo (‘river fish’), these are further contrasted with another named folk-intermediate taxon of ‘marine fish’ (ika mesi). From this, it is argued that, as a life-form category, ika should be understood as implicitly including the five members of the ‘tebhu cluster’ as a third, albeit covert, folk-intermediate taxon.

Insights from Zootaxa on potential trends in zoological taxonomic activity

BackgroundAn opinion currently shared by taxonomists and non taxonomists alike is that the work of inventorying biodiversity is unbalanced: firstly, in favour of countries in which taxonomy has been studied for a long time, and, secondly, in favour of vertebrates. In the current context of threats of species extinction, access for taxonomists to biological material and information becomes crucial if the scientific community really aims at a better knowledge of biological diversity before it is severely and irreversibly impoverished. We performed an analysis of 748 papers published in Zootaxa in 2006 and 2007, as well as 434 questionnaires sent to their authors to test these opinions. A generalization of these results to zoological taxonomy as a whole is discussed.DiscussionWe found that the disequilibrium is not exactly what it usually considered to be. The USA, China and Brazil are currently the three leading countries in zoological taxonomy. Each of them presents, however, a different pattern. Taxonomists from Asia and South America are younger and mainly work in universities, not museums. A bias in favour of vertebrates still exists if we refer to the effort invested in each group to produce taxonomic data, but not to the number of papers. Finally, we insist on the idea that "describing a species" is very different from "knowing a species".SummaryThe taxonomic involvement of a country, in terms of manpower and funding, appears to be a key factor in the development of fruitful taxonomic research. This message seems to have been understood by the countries that recently decided to increase considerably their taxonomic involvement. It still has to be received by those who did not.

Viva La Revolución! Designing the digital renaissance in zoological taxonomy

AbstractWeb‐based, digital taxonomy is developing rapidly, but the International Code of Zoological Nomenclature (ICZN) still requires that the primary data element of taxonomy, the description, be published in hard copy. If accepted, a recently proposed amendment to the ICZN allows for electronic publication of taxonomic names, with the names to be registered in a global, publicly accessible, web‐based archive called ZooBank. This proposal will allow for contemporary models of publication and begin the process of establishing a global register of zoological names. While on the surface this sounds like a reasonably minor step in the pathway to the new taxonomy, the logical implications of this proposal are many and far reaching. For example, this change may lead to further advances so that zoological taxonomy bypasses traditional journal publication entirely, with ZooBank or some other electronic web‐based outlet operating as the publishing vehicle and names register for the new taxonomy. While electronic publication is an important step in improving taxonomic practice, it is by no means a panacea for the critical shortage of taxonomic expertise in Australia or elsewhere.

Incorporation of nomina of higher-ranked taxa into the International Code of Zoological Nomenclature: the nomenclatural status of class-series zoological nomina published in a non-latinized form

Many new higher-ranked taxa are currently recognized by taxonomists as a result of the numerous phylogenetic hypotheses which are regularly published. The absence in the Code of Rules for the nomenclature of taxa above the rank superfamily (class-series nomenclature) is a factor of growing chaos in zoological taxonomy. This is why Dubois (2005) proposed a set of formal Rules for this nomenclature, which should be discussed and considered for incorporation into the Code. This paper focuses on a particular point regarding these proposed Rules, i.e., whether class-series nomina should be considered nomenclaturally available from their first publication in any modern language, provided they were latinized subsequently, or only from their first use in a latinized form. It is argued that the first solution should be retained, not only “to render unto Caesar the things which are Caesar’s”, but also for simple internal consistency within the Code. According to the Rules of the Code, generic nomina may be available, with their original authors and dates, even if directly transferred unchanged from modern languages, and family-series nomina, first published in a nonlatinized form, may be available, with their original authors and dates, provided they have been subsequently latinized. These general statements are illustrated with the higher nomenclature of several taxa including amphibians. According to the proposed Rules, the following nomina, authors and dates are the valid ones for the taxa they designate: VERTEBRATA Cuvier, 1800; AMPHIBIA De Blainville, 1816; GYMNOPHIONA Rafinesque-Schmaltz, 1814; BATRACHIA Brongniart, 1800; ANURA Duméril, 1806; URODELA Duméril, 1806; AMPHIPNEUSTA Merrem, 1820.