The occurrence of the hover fly genus <i>Eristalis </i>Latreille, 1804 (Diptera: Syrphidae) in the Afrotropical region

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The Afrotropical hover flies placed in the genus Eristalis Latreille, 1804 (Diptera: Syrphidae) are revised and the taxonomic history of the placement, and identity, of the different species is presented. Five species are recognised, of which only three can be clearly defined: E. pallidibasis (Bigot, 1891), E. plumipes Bezzi ,1912, and E. tenax (Linnaeus, 1758). Eristalis apis Curran, 1939 syn. nov. is proposed as a junior synonym of E. pallidibasis (Bigot, 1891). Eristalis convexifacies Macquart, 1850 is known only from a badly damaged holotype. The identity of Simoides trichopus Bigot, 1891, (now considered to be an Eristalis) is uncertain as its type material could not be traced and the original description lacks sufficient detail. For the time being, S. trichopus is considered a nomen dubium. An identification key and detailed redescriptions are provided. Eristalis pallidibasis, E. plumipes and E. tenax are easily identified using DNA barcoding. The relationship of Afrotropical Eristalis with Afrotropical representatives of other eristaline genera is briefly discussed based on morphological data.

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  • 10.1111/j.1440-6055.2008.00645.x
DNA barcoding demystified
  • Aug 1, 2008
  • Australian Journal of Entomology
  • Andrew Mitchell

Only 10% of the earth’s biota has been described despite250 yearsoftaxonomicresearch(Wilson2000).Thisisinlargepart a reflection of the extent and complexity of biologicaldiversity,butitisalsotruethattraditionaltaxonomictechniquesare labourious and highly specialised, and taxonomic expertiseis very thinly spread across the myriad groups of life (Scotland

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  • Cite Count Icon 110
  • 10.11646/zootaxa.3083.1.1
A taxonomic revision of the Neotropical poison frog genus Ranitomeya (Amphibia: Dendrobatidae)
  • Oct 28, 2011
  • Zootaxa
  • Jason L Brown + 13 more

The Neotropical poison frog genus Ranitomeya is revised, resulting in one new genus, one new species, five synonymies and one species classified as nomen dubium. We present an expanded molecular phylogeny that contains 235 terminals, 104 of which are new to this study. Notable additions to this phylogeny include seven of the 12 species in the minuta group, 15 Ranitomeya amazonica, 20 R. lamasi, two R. sirensis, 30 R. ventrimaculata and seven R. uakarii. Previous researchers have long recognized two distinct, reciprocally monophyletic species groups contained within Ranitomeya, sensu Grant et al. 2006: the ventrimaculata group, which is distributed throughout much of the Amazon, and the minuta group of the northern Andes and Central America. We restrict Ranitomeya to the former group and erect a new genus, Andinobates Twomey, Brown, Amézquita & Mejía-Vargas gen. nov., for members of the minuta group. Other major taxonomic results of the current revision include the following: (i) A new species, Ranitomeya toraro Brown, Caldwell, Twomey, Melo-Sampaio & Souza sp. nov., is described from western Brazil. This species has long been referred to as R. ventrimaculata but new morphological and phylogenetic data place it sister to R. defleri. (ii) Examination of the holotype of R. ventrimaculata revealed that this specimen is in fact a member of what is currently referred to as R. duellmani, therefore, Dendrobates duellmani Schulte 1999 is considered herein a junior synonym of D. ventrimaculatus Shreve 1935 (= R. ventrimaculata). (iii) For the frogs that were being called R. ventrimaculata prior to this revision, the oldest available and therefore applicable name is R. variabilis. Whereas previous definitions of R. variabilis were restricted to spotted highland frogs near Tarapoto, Peru, our data suggest that this color morph is conspecific with lowland striped counterparts. Therefore, the definition of R. variabilis is greatly expanded to include most frogs which were (prior to this revision) referred to as R. ventrimaculata. (iv) Phylogenetic and bioacoustic evidence support the retention of R. amazonica as a valid species related to R. variabilis as defined in this paper. Based on phylogenetic data, R. amazonica appears to be distributed throughout much of the lower Amazon, as far east as French Guiana and the Amazon Delta and as far west as Iquitos, Peru. (v) Behavioral and morphological data, as well as phylogenetic data which includes topotypic material of R. sirensis and numerous samples of R. lamasi, suggest that the names sirensis, lamasi and biolat are applicable to a single, widespread species that displays considerable morphological variation throughout its range. The oldest available name for this group is sirensis Aichinger; therefore, we expand the definition of R. sirensis. (vi) Ranitomeya ignea and R. intermedia, elevated to the species status in a previous revision, are placed as junior synonyms of R. reticulata and R. imitator, respectively. (vii) Ranitomeya rubrocephala is designated as nomen dubium. In addition to taxonomic changes, this revision includes the following: (i) Explicit definitions of species groups that are consistent with our proposed taxonomy. (ii) A comprehensive dichotomous key for identification of ‘small’ aposematic poison frogs of South and Central America. (iii) Detailed distribution maps of all Ranitomeya species, including unpublished localities for most species. In some cases, these records result in substantial range extensions (e.g., R. uakarii, R. fantastica). (iv) Tadpole descriptions for R. amazonica, R. flavovittata, R. imitator, R. toraro sp. nov., R. uakarii and R. variabilis; plus a summary of tadpole morphological data for Andinobates and Ranitomeya species. (v) A summary of call data on most members of Andinobates and Ranitomeya, including call data of several species that have not been published before. (vi) A discussion on the continued impacts of the pet trade on poison frogs (vii) A discussion on several cases of potential Müllerian mimicry within the genus Ranitomeya. We also give opinions regarding the current debate on recent taxonomic changes and the use of the name Ranitomeya.

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DNA barcoding and integrative taxonomy of Macrobiotus hufelandi C.A.S. Schultze 1834, the first tardigrade species to be described, and some related species
  • Aug 17, 2011
  • Zootaxa
  • Roberto Bertolani + 3 more

Within the framework of a DNA barcoding project on tardigrade species, a study was carried out on Macrobiotus hufelandi C.A.S. Schultze 1834, the first formally described tardigrade species. We used samples collected from the type locality and additional material from other European sites containing species of the “M. hufelandi group”. The study was performed by integrating morphological, karyological and molecular (mt-DNA cox1) information and comparing these data with morphological data from the type material. Several species from this group were found in the type locality of M. hufelandi (near Freiburg, Black Forest, Germany) and these were all barcoded. One was M. hufelandi, the other two were: Macrobiotus sandrae Bertolani & Rebecchi 1993 (originally described from the same locality), and Macrobiotus vladimiri Bertolani, Biserov, Rebecchi & Cesari in press (type locality Andalo, Italy), all with interspecific genetic distances of more than 19%. A fourth cryptic species, which had the same morphology as M. hufelandi but a genetic distance of 6.7%, was not described as a new taxon but named M. cf. hufelandi sp.1 for this study. Macrobiotus sandrae and M. vladimiri were also present (and barcoded) in Italy (Alps). Additional individuals (animals and eggs) were also found, and barcoded, in Italy (Apennines) and Switzerland that belonged to the haplogroup Macrobiotus cf. hufelandi sp. 1. These data together with other recent studies on tardigrade DNA barcoding represent a starting point for further studies on tardigrade biogeography, phylogeography and diversity.

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  • Cite Count Icon 11
  • 10.1111/j.1463-6409.2006.00241.x
Taxonomic revision and phylogenetic analysis of the genusTambjaBurn, 1962 (Mollusca, Nudibranchia, Polyceridae)
  • Aug 24, 2006
  • Zoologica Scripta
  • Marta Pola + 2 more

This paper discusses the systematics and phylogeny of the genusTambjaBurn, 1962 throughout tropical and temperate areas in the Atlantic, eastern Pacific and Indo‐Pacific. The phylogenetic relationships withinTambjaare unknown and a comprehensive taxonomic revision is necessary in order to construct a phylogeny of the genus. To date,Tambjacomprises 28 nominal species, 22 of which have been examined morphologically based on newly collected and type material. The reproductive systems of four species (T. limaciformis(Eliot, 1908),T. sagamiana(Baba, 1955),T. amakusana, Baba, 1987 andT. olivaria, Yonow, 1993) were studied for the first time and two species previously considered as valid,Tambja morosa(Bergh, 1877) andTambja kushimotoensisBaba, 1987, are here synonymized. Of the remaining six nominal species, no additional material has been found since their original description. The holotypes of three (T. diaphana(Bergh, 1877),T. gratiosa(Bergh, 1890) andT. marbellensisSchick & Cervera, 1998) have been re‐examined and the original descriptions improved.Tambja diaphanais regarded asnomen dubium.Tambja amitina(Eliot, 1905),T. divae(Marcus, 1958) andT. anayanaOrtea, 1989 remain as valid species until further comparison with new specimens can be made. New structures are also described for several taxa. Morphological and anatomical data from 22 nominalTambjaspecies have been used to construct a phylogeny. The phylogenetic analysis rejects the monophyly ofTambjaand shows its preliminary relationships within the subfamily Nembrothinae.

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  • Cite Count Icon 9
  • 10.3897/bdj.8.e59177
A revision of European species of the genus Tetrastichus Haliday (Hymenoptera: Eulophidae) using integrative taxonomy.
  • Dec 16, 2020
  • Biodiversity data journal
  • Christer Hansson + 1 more

BackgroundThe European species of the genus Tetrastichus (Insecta, Hymenoptera, Eulophidae, Tetrastichinae) are revised with 93 species, including 50 species described as new. The revision was conducted using an integrative taxonomic approach, based on DNA barcoding in combination with morphological characters. The Tetrastichinae are a biologically diverse and species-rich group of parasitoid wasps with numerous complexes of morphologically often very similar species that attack a wide range of hosts in over 100 insect families in 10 different orders. The genus Tetrastichus is, with almost 500 described species, the third largest genus of Tetrastichinae. Although biological information is lacking for most species, current data indicate that Tetrastichus species are gregarious koinobiont endoparasitoids developing on juvenile stages of mainly holometabolous insects. Due to their host specificity, several species of Tetrastichus are used as biological control agents.New informationThe European species of Tetrastichus Haliday (Hymenoptera: Eulophidae) are revised using a combination of externo-morphological and DNA barcoding data. This is the first integrative approach for any of the large genera of the Tetrastichinae. A total of 93 species are included, of which 50 are described as new: T. agonus sp. n., T. antonjanssoni sp. n., T. argei sp. n., T. argutus sp. n., T. asilis sp. n., T. ballotus sp. n., T. bledius sp. n., T. broncus sp. n., T. calcarius sp. n., T. calmius sp. n., T. clisius sp. n., T. cosidis sp. n., T. cumulus sp. n., T. cyprus sp. n., T. delvarei sp. n., T. doczkali sp. n., T. elanus sp. n., T. elodius sp. n., T. ennis sp. n., T. enodis sp. n., T. erinus sp. n., T. evexus sp. n., T. fadus sp. n., T. fenrisi sp. n., T. flaccius sp. n., T. gredius sp. n., T. iasi sp. n., T. illydris sp. n., T. incanus sp. n., T. inscitus sp. n., T. intruitus sp. n., T. johnnoyesi sp. n., T. lacustrinus sp. n., T. ladrus sp. n., T. lanius sp. n., T. lazius sp. n., T. lixalius sp. n., T. lycus sp. n., T. marcusgrahami sp. n., T. minius sp. n., T. mixtus sp. n., T. nataliedaleskeyae sp. n., T. nymphae sp. n., T. pixius sp. n., T. scardiae sp. n., T. splendens sp. n., T. sti sp. n., T. suecus sp. n., T. tacitus sp. n. and T. tartus sp. n. Two keys for the identification of species are presented, one for females and one for males. Based on DNA barcode sequences for 70 of the species, a Maximum Likelihood tree to assess phylogenetic relationships within the genus is presented. These 70 species are also characterised by a combination of CO1 and morphological data. The remaining 23 species, without a DNA barcode, are characterised by morphological data. Using a combination of data from the morphology and CO1 or morphological data only, the species are separated into three species groups (clito-, hylotomarum-, murcia-groups) with 41 unplaced species outside these groups. Hosts are known for 27 of the species and they are gregarious, koinobiont endoparasitoids on a wide range of immature stages of holometabolous insects and appear to be very host specific. The first host record for Lepidoptera (Tineidae) in Europe is included.

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  • Cite Count Icon 61
  • 10.1093/sysbio/syab076
Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks.
  • Sep 15, 2021
  • Systematic Biology
  • Bing Yang + 6 more

Integrative taxonomy is central to modern taxonomy and systematic biology, including behavior, niche preference, distribution, morphological analysis, and DNA barcoding. However, decades of use demonstrate that these methods can face challenges when used in isolation, for instance, potential misidentifications due to phenotypic plasticity for morphological methods, and incorrect identifications because of introgression, incomplete lineage sorting, and horizontal gene transfer for DNA barcoding. Although researchers have advocated the use of integrative taxonomy, few detailed algorithms have been proposed. Here, we develop a convolutional neural network method (morphology-molecule network [MMNet]) that integrates morphological and molecular data for species identification. The newly proposed method (MMNet) worked better than four currently available alternative methods when tested with 10 independent data sets representing varying genetic diversity from different taxa. High accuracies were achieved for all groups, including beetles (98.1% of 123 species), butterflies (98.8% of 24 species), fishes (96.3% of 214 species), and moths (96.4% of 150 total species). Further, MMNet demonstrated a high degree of accuracy ($>$98%) in four data sets including closely related species from the same genus. The average accuracy of two modest subgenomic (single nucleotide polymorphism) data sets, comprising eight putative subspecies respectively, is 90%. Additional tests show that the success rate of species identification under this method most strongly depends on the amount of training data, and is robust to sequence length and image size. Analyses on the contribution of different data types (image vs. gene) indicate that both morphological and genetic data are important to the model, and that genetic data contribute slightly more. The approaches developed here serve as a foundation for the future integration of multimodal information for integrative taxonomy, such as image, audio, video, 3D scanning, and biosensor data, to characterize organisms more comprehensively as a basis for improved investigation, monitoring, and conservation of biodiversity. [Convolutional neural network; deep learning; integrative taxonomy; single nucleotide polymorphism; species identification.].

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  • Cite Count Icon 97
  • 10.1071/mf9580372
A Monograph of the Freshwater Mussels (Mollusca: Pelecypoda) of the Australian Region
  • Jan 1, 1958
  • Australian Journal of Marine and Freshwater Research
  • Df Mcmichael + 1 more

This monograph incorporates a systematic revision of the freshwater mussels of the Australian Region (Australia, New Zealand, New Guinea and the Solomon Islands). Previous systematic works are revised and discussed. Details of the taxonomic procedures used in the present work are presented. One aberrant New Guinea genus, Haasodonta, with two species is referred provisionally to the family Unionidae Fleming, subfamily Rectidentinae Modell. The remainder of the Australasian species are assigned to the family Mutelidae Gray. Four subfamilies, Velesunioninae Iredale, Lortiellinae Iredale, Hyridellinae Iredale, and Cucumerunioninae Iredale, are recognized. These include eight genera, Velesunio Iredale, Alathyria Iredale, Weatralunio Iredale, Microdontia Tapparone Canefri, Lortiella Iredale, Hyridella Swainson, Cucumerunio Iredale, and Virgus Simpson. The genus Hyridella includes four subgenera, Hyridella s.s., Protohyridella Cotton & Gabriel, Nesonaia Haas, and a new subgenus for H. menziesi Gray. These eight genera include 27 species, three of which are polytypic. Three additional species are considered of doubtful validity and two nominal species are listed as nomina dubia. Each taxon is redescribed and all available data of shell morphology, soft anatomy, larval stages, distribution, and type material are presented. The distribution of the Australian and New Guinea species in relation to the fluvifaunal provinces of Iredale and Whitley is considered and a new name is proposed for the fluvifaunula of southern New Guinea. The evolutionary relationships of the Australasian freshwater mussels are discussed and it is suggested that, with one exception, they arose from a single ancestral stock and have subsequently differentiated into four subfamilies within this region. This view is supported by the close anatomical similarity between them.

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  • Research Article
  • Cite Count Icon 11
  • 10.30963/aramit5904
How to deal with destroyed type material? The case of Embrik Strand (Arachnida: Araneae)
  • Mar 6, 2020
  • Arachnologische Mitteilungen: Arachnology Letters
  • Wolfgang Nentwig + 4 more

When the museums of Lübeck, Stuttgart, Tübingen and partly of Wiesbaden were destroyed during World War II between 1942 and 1945, also all or parts of their type material were destroyed, among them types from spider species described by Embrik Strand between 1906 and 1917. He did not illustrate type material from 181 species and one subspecies and described them only in an insufficient manner. These species were never recollected during more than 110 years and no additional taxonomically relevant information was published in the arachnological literature. It is impossible to recognize them, so we declare these 181 species here as nomina dubia. Four of these species belong to monotypic genera, two of them to a ditypic genus described by Strand in the context of the mentioned species descriptions. Consequently, without including valid species, the five genera Carteroniella Strand, 1907, Eurypelmella Strand, 1907, Theumella Strand, 1906, Thianella Strand, 1907 and Tmeticides Strand, 1907 are here also declared as nomina dubia. Palystes modificus minor Strand, 1906 is a junior synonym of P. superciliosus L. Koch, 1875 syn. nov.

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  • Cite Count Icon 16
  • 10.4081/jlimnol.2013.s1.e23
A DNA barcoding approach in the study of tardigrades
  • Jul 24, 2013
  • Journal of Limnology
  • Michele Cesari + 4 more

DNA barcoding is a technique proposed by Hebert and co-workers in 2003 for discriminating species through analysis of a single gene barcode locus. It aims to obtain a better taxonomic resolution than that achieved through morphological studies, and to avoid the decline in taxonomic knowledge. Today DNA barcoding is a global enterprise, and the implementation of the idea has seen a rapid rise (more than 1900 papers published to date on different organisms). Nonetheless, controversy still arises regarding barcoding and taxonomy. It is important to note that DNA barcoding does not focus on building a tree-of-life or on doing DNA taxonomy, even though sometimes it has been used for these purposes. DNA barcoding rather focuses on producing a universal molecular identification key based on strong taxonomic knowledge that should be included in the barcode reference library. In the phylum Tardigrada, DNA barcoding represents a recent approach to species identification and to help in solving taxonomic problems, especially considering the diminutive size of these animals and the paucity of morphological characters useful for taxonomy. In the framework of the MoDNA Project (Morphology and DNA), carried out by our research group in collaboration with several colleagues, we are combining the study of a fragment of the mitochondrial cytochrome c oxidase subunit I gene ( cox1 ) with morphological data, in a wide sense (cuticular structures, chromosomes, data on sex ratio and reproduction), to form an integrative taxonomy approach for tardigrade species identification. We believe that without verified reference sequences from voucher specimens that have been authenticated by qualified taxonomists, there is no reliable library for newly generated sequences with which to be compared. Methods and protocols for standardized results are focused on obtaining tight correspondence between tardigrade morphology (and egg shell morphology, when useful), possibly both light and scanning electron microscopy images, and molecular sequence. This approach is particularly useful in describing new species, and important when applied on material collected in species type localities. Results using this approach are presented, primarily focusing on a number of species from the so-called Macrobiotus hufelandi group.

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  • Cite Count Icon 39
  • 10.1111/syen.12444
The omission of critical data in the pursuit of ‘revolutionary’ methods to accelerate the description of species
  • Aug 3, 2020
  • Systematic Entomology
  • Alireza Zamani + 3 more

Recently, Meierotto et al. (2019) proposed a 'revolutionary' protocol for the description of understudied hyperdiverse taxa. The premise of their study was to champion exclusively DNA-barcode-based species descriptions (=diagnoses), which would dramatically increase the rate of description and provide a 'human-readable record in the literature' (unlike a Barcode Index Number, BIN; Ratnasingham & Hebert, 2013) that can later be supplemented with additional information. Species are always delimited against already known species (Linnaeus, 1753, 1758; Mayr, 1992; ICZN, 1999; Naciri & Linder, 2015; Renner, 2016). This was also recognized by Meierotto et al. (2019, p. 120): 'Requirements for the publication of new species include (…) that they be accompanied by either a description or diagnosis which can separate them from any known species with which they are likely to be confused'. However, the latter authors failed to diagnose their 15 new Zelomorpha Ashmead, 1900 species from 51 out of 52 previously known species (only the type species was used in the analysis) and their three new Hemichoma Enderlein, 1920 species from any of the five previously known species. This is not the first case of its kind in zoology; Hebert et al. (2004) proposed to recognize ten species of skipper butterflies (genus Astraptes) based on DNA characters and ecology and some morphological characters, but the species were not formally named until Brower (2010) described them based exclusively on unique mutations in the DNA barcode region. Brower (2010) hailed this method as a flagship example of DNA barcoding's success in overcoming the 'taxonomic impediment' (Brower, 2010). However, it has received extensive criticism (DeSalle et al., 2005; Pons et al., 2006; Rubinoff et al., 2006; Elias et al., 2007; Dupérré, 2020). Meierotto et al. (2019) have taken this approach one step further by immediately assigning names to the lineages. This is, in our opinion, a step too far. Each description includes a lateral habitus image of a single specimen, a short diagnosis based solely on COI barcode nucleotide differences, brief notes on biology, and largely unannotated type specimen information except for brief mention of the locality and host caterpillar of the holotype. There are no morphological descriptions, and as mentioned, the 'molecular diagnosis' of their new Zelomorpha spp. are compared only with that of the type species, and not to the other 51 already known species of that genus, and in the case of Hemichoma, with none of the five species that were already described. We consider this poor taxonomic practice, and their approach to be fundamentally flawed. We urge innovators to pursue revolutionary new approaches that do not undermine the value of taxonomic expertise or produce sloppy results, but rather seek to draw on the latest methodological advancements to increase the rate of taxonomy without compromising on quality. Over the last 20 years, there have been many calls for an increase in the rate of taxonomic description (Mora et al., 2011). Few have delivered on that promise. Undoubtedly, the single steepest increase in this rate was made possible by DNA barcoding (Hebert et al., 2003). Yet, in the wake of the genetic revolution, there were already concerns that too much emphasis might be placed on DNA barcoding data alone, leading taxonomists to neglect the importance of other data—integrative approaches, taking the congruence of genetic signals with other datasets, would be required to keep describing biologically meaningful units (Dayrat, 2005; Ebach & Holdrege, 2005; Will et al., 2005). DNA barcoding is a rapid means to sort specimens into clusters, identify species and discover new ones (when a library of the relevant named species is already available), but does not overcome the bottleneck of the description process itself. Proposals for methods to speed up that process were dubbed 'turbo' or 'fast-track' taxonomy—an approach that does not differ fundamentally from previous species descriptions, but relies more heavily on formulaic descriptions of large numbers of new species (Butcher et al., 2012; Riedel et al., 2013). In essence, the approach of Meierotto et al. (2019) is simply another one of these turbo-taxonomic approaches except in three key aspects: Fundamentally, a diagnosis should identify features or combinations of features of a new species that are unique, that is, that allow it to be distinguished from all previously named taxa. It thereby gives a means not only to identify the new species but also to demonstrate that the new taxon is not a synonym of an existing one. The diagnoses of Meierotto et al. (2019) are based solely on DNA barcodes, but no barcodes are presented for 51 of the 52 existing species of Zelomorpha. Indeed, the existing taxa are summarily ignored, except for a statement that the notes of the second author (M.J. Sharkey) were used to verify that the new species are distinct from the existing taxa, without providing any evidence. As a result, it is impossible, based on the study of Meierotto et al. (2019), to assess whether or not their 15 new Zelomorpha names are distinct from 51 of the 52 species that were already described. In our opinion, Meierotto et al. (2019) have impeded, not enhanced, the taxonomy of these wasps. Ignoring almost all previously described species in a genus is indeed a way to speed up taxonomy—the process of comparison becomes very easy when you neglect practically all existing names—but it also creates chaos. Even the fastest approach to taxonomy will always require consideration of existing names before new ones can be established. Morphologically homogeneous ('cryptic') species are difficult to diagnose from one another, even when substantial differences exist in their DNA barcodes. This can delay taxonomy, because more effort must be invested per species to identify characters that do indeed differ. To overcome this problem, Renner (2016) recently called for more widespread inclusion of DNA sequence data in diagnoses. However, we do not believe that Renner (2016) envisioned the complete replacement of the diagnosis by single nucleotide changes, but rather expansion of concise but comprehensive diagnoses with such information. In some cases, restriction exclusively to genetic markers may be appropriate (e.g. where morphology is highly plastic, or where extremely distinctive genetic lineages are demonstrably cryptic in all other available lines of evidence), but such cases are likely to be the exception rather than the rule. Having complementary lines of evidence, such as morphology, is particularly important when, as is the case in Meierotto et al. (2019), only a tiny portion of the available names have DNA sequence data available. The lack of overlap between morphological and genetic data will further delay the process of clarifying whether or not the new names are synonyms of existing species. It is also important to note that DNA barcoding relies wholly on mitochondrial markers (usually cytochrome oxidase-I). Mitochondrial trees often disagree with nuclear species trees, especially in taxa where Wolbachia may be altering mtDNA introgression (Klopfstein et al., 2016). In these cases, and especially when genetic data are the sole basis of species-level recognition, congruence between nuclear and mitochondrial signal should be tested to better reinforce the species units identified. Moreover, as explained by Dupérré (2020), purely DNA-based descriptions will not only make the identification of millions of historical specimens impossible, it will impair this science in developing countries which house most of the undiscovered portion of biodiversity, due to high costs and lack of staff and technology. Considering the status of taxonomy as a fundamental science, this would drastically affect other related fields of study and, importantly, conservation. Renner (2016) also called for more emphasis on diagnosis and not description. With highly descriptive taxonomy, a great deal of time is invested in description of features that are not informative for the distinction of species from one another, which is time that could be spent instead diagnosing substantially more species. Instead, she and others have emphasized the importance of high-resolution photographs as supplements to diagnoses. We agree that detailed high-resolution photographs of specimens can indeed be highly valuable, but we contend that (i) there must be several photographs available, not a single lateral photograph of a single specimen, as provided by Meierotto et al. (2019), and (ii) some text highlighting important diagnostic features is valuable to experts, and of paramount importance to nonexperts, who must instead play a game of 'spot-the-difference' when such information is lacking. Experts might know the difference between variable and nonvariable characters, whereas such features cannot be distinguished by nonexperts, and it is the purpose of the diagnosis, if not the description, to point such features out. Moreover, we note that the photographs of Meierotto et al. (2019) are sometimes blurry and almost all of them cut off the tips of the antennae! Finally, it has been shown that (e.g. in case of tropical parasitoid wasps) the most time-consuming part of species discovery is field sampling (Sääksjärvi et al., 2004; Hopkins et al., 2019), and the actual description of the species may be written within minutes when material and expertise are already available. To make up the gaps in the existing barcode database, which contains maybe 2% of currently named species worldwide (see http://www.boldsystems.org/), far more survey work needs to be undertaken. A comprehensive barcoding database for a given taxon is a prerequisite to contemplating a DNA-only approach akin to that of Meierotto et al. (2019), and one that will require substantial further work to assemble. In the face of the Holocene (=sixth) extinction, taxonomists are racing to describe the 8 million unnamed eukaryotes that lie between the 2.07 million species currently named (Frid & Caswell, 2016), and the estimated ten million extant species (Mora et al., 2011; but see also Larsen et al., 2017 for well-reasoned estimates orders of magnitude higher). Currently, the rate of description is around 18 000 species per year (IISE, 2011), but with species going extinct at a rate 1000 times higher than the natural background rate of extinction, the annual species loss is clearly within or even higher than the rate of new descriptions (Dirzo & Raven, 2003; Mora et al., 2011), and thousands of species will undoubtedly go extinct before they can be described to science (IPBES, 2019). As the current average shelf life of new species between discovery and description is about 21 years (Fontaine et al., 2012), we do indeed need revolutionary new approaches to the discovery and description of new species. BINs and candidate species numbers (Vieites et al., 2009) already serve a valuable purpose as alphanumeric placeholders to recognize potentially evolutionarily significant diversity before it is taxonomically described. Simply assigning all BINs taxonomic names as Meierotto et al. (2019) propose would indeed complete the inventory of life on Earth extremely quickly (at precisely the same pace as the rate of barcoding)—that we do not dispute. But it would also remove the quantitative and qualitative difference between these preliminary identifiers (based on a single DNA marker) and full taxonomic recognition (based on a more comprehensive diagnosis, ideally supported by multiple lines of evidence including genetic data) that lend taxonomy its value. It would supplant taxonomists with technicians, who need to know nothing of the biology of the units with which they are dealing. The purpose of inclusion of molecular data in species descriptions should be to produce more precise taxonomic framework. A species description can be thought of as a hypothesis that can be supported or rejected when more data are obtained. Other researchers must have an opportunity to scientifically evaluate the status of the species in question. In our eyes, methodological changes to the way species are delineated and described are an important component of increasing the rate of species description, but dismissing the existing literature, and producing 'descriptions' that contain almost no information on the morphology of species, its variation, their unique features, their biology, or other aspects, do not constitute a revolution, and cannot be adopted. We note that real revolutions are undoubtedly coming, especially from the fields of machine learning and integrative species delimitation (Solís-Lemus et al., 2015; Favret & Sieracki, 2016), and also that it is possible to produce massive, rapidly assembled taxonomic monographs without compromising on quality (Rakotoarison et al., 2017). But we also want to emphasize that there is no shortcut to nirvana, and a true paradigm shift in taxonomy will come only when there is a revolution in the level of financial investment in taxonomy and the natural history museums that house the described and undescribed reference material of life on Earth (Wheeler, 2020), and when legislature stops acting to prohibit the collecting work of dedicated taxonomists while turning a blind eye to the innumerable organisms destroyed with every hectare of habitat that is lost (Britz et al., 2020). The authors declare no conflicts of interest. The data that support the findings of this study are available from the corresponding author upon reasonable request.

  • Research Article
  • Cite Count Icon 9
  • 10.1002/zoos.200900018
An annotated catalogue of the tongue worms (Pentastomida) held in the Museum für Naturkunde Berlin
  • Mar 24, 2010
  • Zoosystematics and Evolution
  • Doreen Röhlig + 3 more

An annotated catalogue of the type and non-type material belonging to the enigmatic arthropod group Pentastomida (tongue worms) in the Museum fur Naturkunde Berlin is presented. Aspects of human infection, current ideas on their affinities and some recent developments in the study of these animals are briefly reviewed. Types of eight species have been recorded: Raillietiella affinis Bovien, 1927, Raillietiella bicaudata Heymons & Vitzthum, 1935, “Pentastomum ” javanicum Bovien, 1927, Raillietella kochi Heymons, 1926, Elenia lialisi Heymons, 1939a, Raillietiella mabuiae Heymons, 1922, Raillietella shipleyi Heymons, 1926 and Cephalobaena tetrapoda Heymons, 1922. Five of these types are currently considered valid species. According to the literature, type material from Elenia travassosi (Heymons, 1932) should be in Berlin, but could not be traced during the present review and may have to be considered lost. A further twenty-six non-type species were recorded, plus specimens assigned to two names currently regarded as nomina dubia. This yields a total of 31 currently valid species in Berlin, representing nearly 25 % of the known world fauna. Much of the Berlin material derives from the important Richard Heymons collection, but significant historical specimens collected in Brazil in the early nineteenth century by Johann Natterer was also discovered during the course of this project. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

  • Research Article
  • 10.3897/aca.4.e64709
Unheeded biodiversity: perspectives of DNA barcoding of Trichoptera in Bosnia and Herzegovina
  • Mar 4, 2021
  • ARPHA Conference Abstracts
  • Dalila Destanović + 4 more

Bosnia and Herzegovina has valuable natural resources with a high percentage of endemic and autochthonous species (Kučinić et al. 2008, Đug and Drešković 2012). The freshwater fauna of Trichoptera in this area is under-investigated, with a lack of morphological description of different life stages and DNA barcode data. Public data show 58,993 barcode entries for Trichoptera in the Barcode of Life Data Systems (BOLD) submitted from 92 countries, and none from Bosnia and Herzegovina (B&H) (BOLD 2021). Previous research in Bosnia and Herzegovina has provided the first DNA barcode for the endemic speciesRhyacophila bosnica, stored in GeneBank, under accession number MK211322 by a domestic institution (Kalamujić Stroil et al. 2018). A few DNA barcodes of adult individuals of Trichoptera from Bosnia and Herzegovina were found in BOLD. However, these specimens were collected on B&H territory, but analyzed, processed, and stored by foreign institutions. To change the current state of DNA barcoding of Trichoptera in Bosnia and Herzegovina, we aimed to employ this approach in investigating caddisflies in selected habitats in the Sarajevo Canton.Our fieldwork was done in all five protected areas (spring of the Bosna River, Bijambare, Trebević, Skakavac, and Bentbaša) in which larvae samples were collected according to the AQEM sampling methodology. The standard animal DNA barcode was successfully obtained using degenerated primers LCO1490- JJ and HCO2198-JJ (Astrin and Stüben 2008).Out of 684 collected individuals (313 Trebević, 130 spring of the Bosna River, 117 Bijambare, 71 Bentbaša, 53 Skakavac), a subset of specimens were sequenced. We uncovered 14 different taxa, 11 genera and six families (Limnephilidae, Glossosomatidae, Rhyacophilidae, Goeridae, Hydropsychidae, Polycentropodidae). The preliminary data of Trichoptera composition in the Sarajevo Canton indicated species richness. Based on our sequential data, a new subspecies was discovered in two investigated areas (Valladolid et al. 2020), proving that Trichoptera species diversity in our country is far from entirely uncovered. The benefit and power of the DNA barcoding approach are that it can pinpoint the areas of vast and unknown species diversity more economically, both financially and temporarily, than the morphological approach. Therefore, we believe that it is critical to support the development of DNA barcoding for the bioassessment of freshwater ecosystems in Bosnia and Herzegovina.Several problems prevented us from exploiting sequential data to the fullest. Despite a general notion among scientists that European Trichoptera species are well covered in the BOLD database, most of the sequences we obtained were absent from the database. Secondly, we recognized that morphological data about the larval developmental stage of B&H Trichoptera species are largely missing. The unified, updated, and complete data on this order of insects is urgently needed. However, insufficient financial support by governmental institutions and lack of systematic approach to barcoding the wildlife of Bosnia and Herzegovina hampers this process.Further attempts to collaborate with the stakeholders can be crucial with profound and substantial implications for biomonitoring of aquatic macroinvertebrates in general. New approaches, such as novel DNA barcoding-based methodology can fill an important gap in our knowledge of Balkan caddisflies haplotypes, lineages, and their diversification and distribution patterns.

  • Research Article
  • 10.3389/conf.fmars.2016.05.00079
Deeply divergent DNA barcode lineages within Dynamene edwardsi (Isopoda) from the Northeast Atlantic suggest between four to eight cryptic species
  • Jan 1, 2016
  • Frontiers in Marine Science
  • Vieira Pedro + 4 more

This work is part of the DiverseShores (PTDC/BIA-BIC/114526/2009) research project, funded by (FCT) under the COMPETE programme supported by the European Regional Development Fund. FCT also supported a Ph. D. grant to P.V. (SFRH/BD/86536/2012). Part of this work was funded by FEDER through COMPETE and by national funds through FCT/MEC in the scope of the projects FCOMP-01-0124-FEDER-015429 (ref. FCT: PTDC/MAR/113435/2009) and PEst-OE/BIA/UI4050/2014.

  • Research Article
  • Cite Count Icon 1
  • 10.1111/jse.70021
Deep learning for Fabaceae identification by integrating molecular and morphological data and a solution for barcode selection
  • Oct 29, 2025
  • Journal of Systematics and Evolution
  • Kawtar Lhayani + 2 more

Identification of Fabaceae family plants traditionally relies on either morphological traits or DNA barcoding, each with limitations in accuracy and efficiency. Deep learning has emerged as a promising tool for integrating multiple data sources, but its full potential remains underexplored. This study aimed to utilize a deep learning model that integrates morphological and molecular data for species identification within the Fabaceae family, bridging the gap between the two methods of identification. The research involved four main phases: (i) data collection; (ii) data preprocessing; (iii) training and testing the model; and (iv) analysis of results. The data comprised DNA barcode sequences retrieved from the BOLD database, and images were collected from different websites. The model was trained for identification on the genera and species levels, with two different barcodes: ITS2 and matK+rbcL . Only species with four available copies of ITS2, matK , and rbcL sequences were selected to ensure consistent input across samples. The final data set included seven genera and 21 species. While the model achieved high accuracy during training, test accuracy remained low (14%–19%), indicating overfitting, likely due to the limited data set size. However, the model demonstrated the ability to evaluate barcode discrimination across genera. Specifically, it highlighted ITS2 and matK+rbcL as having varying levels of effectiveness depending on the genus. These findings introduce a new application for deep learning in plant systematics not only for species identification but also for evaluating barcodes. This approach could help reduce the reliance on trial‐and‐error in barcode selection and enhance the efficiency of molecular taxonomy.

  • Research Article
  • Cite Count Icon 10
  • 10.1016/j.bse.2009.09.010
AFLPs are incompatible with RAPD and morphological data in Pennisetum purpureum (Napier grass)
  • Oct 21, 2009
  • Biochemical Systematics and Ecology
  • M Struwig + 4 more

AFLPs are incompatible with RAPD and morphological data in Pennisetum purpureum (Napier grass)

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