Thomas Pape | University of Copenhagen (original) (raw)

Teaching Documents by Thomas Pape

Papers by Thomas Pape

Insecta Mundi, Dec 1, 2000

BMC Biology, Oct 27, 2021

European Journal of Entomology, Jan 3, 2007

Journal of Arachnology, Dec 1, 2000

Zoological Studies, Aug 1, 2014

Scientific Reports, Jan 29, 2021

Scientific Reports, Oct 5, 2016

European Journal of Entomology, Oct 23, 2017

Systematic Entomology, Mar 21, 2019

Stomach bot flies (Calyptratae: Oestridae, Gasterophilinae) are obligate endoparasitoids of Probo... more Stomach bot flies (Calyptratae: Oestridae, Gasterophilinae) are obligate endoparasitoids of Proboscidea (i.e. elephants), Rhinocerotidae (i.e. rhinos) and Equidae (i.e. horses and zebras, etc.), with their larvae developing in the digestive tract of hosts with very strong host specificity. They represent an extremely unusual diversity among dipteran, or even insect parasites in general, and therefore provide significant insights into the evolution of parasitism. The phylogeny of stomach bot flies was reconstructed based on extensive mitochondrial genomic data for Cobboldia, Gyrostigma and six of the eight known species of Gasterophilus. The phylogenetic tree, i.e. {Cobboldia, [Gyrostigma, (Gasterophilus pecorum, (Gasterophilus intestinalis, (Gasterophilus haemorrhoidalis, Gasterophilus inermis)), (Gasterophilus nasalis, Gasterophilus nigricornis))]}, provides a strong evolutionary reference to infer several biological patterns for the first time for this group: (i) host shifts of stomach bot flies from elephants to rhinoceroses and then from rhinoceroses to equids; (ii) dispersal with their hosts from the Afrotropical region into the Palaearctic and Oriental regions; (iii) oviposition site, originally on the host head, and egg production positively correlated with distance from the mouth; (iv) attachment of third-instar larva originally in the stomach, with duodenal and large intestinal positions secondarily derived; and (v) guanine and cytosine enrichment of the mitogenome as an adaptation to larval life in the warm environment of the host digestive tract, combined with the need for a high evolutionary rate to cope with the fast evolution of their mammalian hosts.

Zenodo (CERN European Organization for Nuclear Research), Nov 17, 2019

The first instar larva is described for Miltogramma pardalina (ROHDENDORF, 1934). Using a combina... more The first instar larva is described for Miltogramma pardalina (ROHDENDORF, 1934). Using a combination of light microscopy and scanning electron microscopy, the habitus is documented along with all important exoskeletal and cephaloskeletal structures. The first instar larva of M. pardalina fits well within the morphological diversity of the genus Miltogramma MEIGEN and is the most similar to larvae of M. margiana (ROHDENDORF, 1925) and M. punctata MEIGEN, 1824. Larvae of these species share at least six larval character states but all of them may be treated as typical for ancestral larva of Miltogramminae and cannot be interpreted as synapomorphies. Information about larval morphology of M. pardalina will assist future evolutionary studies of the genus Miltogramma based on the application of methods of the next generation sequencing.

The twenty-nine species-group names of Sarcophagidae proposed by Chien-ming Chao and Xue-zhong Zh... more The twenty-nine species-group names of Sarcophagidae proposed by Chien-ming Chao and Xue-zhong Zhang are reviewed. Of these names, twenty-four are available, while five are unavailable nomina nuda. Of the twenty-four available names, nine are considered valid, fifteen as invalid: thirteen junior synonyms, one unnecessary replacement name and one junior primary homonym. Holotypes of all species, and allotypes when available, are photographed and the species redescribed based on the type material. Eight new synonyms are proposed:

Zoological Journal of the Linnean Society, Dec 19, 2017

The first comprehensive genus-level phylogeny of the subfamily Sarcophaginae is presented. A morp... more The first comprehensive genus-level phylogeny of the subfamily Sarcophaginae is presented. A morphology-based phylogenetic analysis using parsimony is performed with 141 terminal taxa representing all 50 nominal genera of Sarcophaginae. In total, 222 morphological characters are coded, 150 of which are from the male terminalia. The homology of relevant male terminalia structures is assessed for the first time across the entire subfamily. Of 38 polyspecific genera represented by more than one species, the monophyly of 33 genera was recovered. This cladistic study found the genera Lepidodexia, Retrocitomyia, Sarcodexiopsis and Titanogrypa to be non-monophyletic as currently defined. Of nine monospecific genera, Mecynocorpus changes its status from monospecific to polyspecific with the discovery of a new species, Promayoa also becomes polyspecific with the transfer of one Titanogrypa species, and the remaining seven monospecific genera remain as such. Support was obtained for treating Sarcodexia as a subgenus of Peckia, and for treating Helicobia and Lipoptilocnema as valid genera rather than subgenera of Sarcophaga, and Halliosca as a valid genus rather than a subgenus of Lepidodexia. Morphological synapomorphies are discussed for all genera, including reviewed character interpretations of previous authors. We are here presenting a much more unifying interpretation of the Sarcophaginae acrophallus. New insights into the functional aspects of the sarcophagine phallus are presented. Our phylogeny shows the early lineages in Sarcophaginae as being mostly dung breeding, while lineages emerging later have more diverse life habits, including necrophagy and parasitism. Based on our phylogeny, 46 genera are recognized. The following nominal genus-group taxa are synonymized, with the junior synonym receiving a new status as subgenus under its respective senior synonym: under genus Dexosarcophaga

Biodiversity Information Science and Standards

From its birth as the ‘Biosystematic Database of World Diptera’ in 1984, the ‘Systema Dipterorum’... more From its birth as the ‘Biosystematic Database of World Diptera’ in 1984, the ‘Systema Dipterorum’ (Evenhuis and Pape 2023) has grown into one of the largest databases currently maintained for the taxonomy and nomenclature of a single order of insects. Systema Dipterorum covers all two-winged insects (Diptera), and with almost a quarter of a million names representing more than 170,000 valid species distributed in some 13,000 valid genera, we cover about 10% of the described and named Animalia. About 1,000 new nominal species are described annually within Diptera. Data are entered in FileMaker Pro (database) and served through an online portal*1 with an updated version currently provided every two months. Names are harvested and reviewed through a four-tier quality assurance hierarchy with entries eventually reaching taxonomic and nomenclatural standards equivalent to being published online. The nomenclatural status of each name is shown using 50 different codes, and at this moment a...

PLOS Biology

Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms ... more Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms at ever finer precision but have come with challenges as the major Codes of bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, species diagnoses), which is particularly problematic for DNA-based taxonomy. We, the commissioners of the International Commission on Zoological Nomenclature, advocate a tightening of the definition of “species diagnosis” in future editions of Codes of bionomenclature, for example, through the introduction of requirements for specific information on the character states of differentiating traits in comparison with similar species. Such new provisions would enhance taxonomic standards and ensure that all diagnoses, including DNA-based ones, contain adequate taxonomic context. Our recommendations are intended to spur discussion among biologists, as broad community consensus is critical ahead of the implementation ...

The Bulletin of Zoological Nomenclature

BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access t... more BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences published by nonprofit societies, associations, museums, institutions, and presses.

PLOS ONE, Sep 18, 2023

Phylogenetic relationships within the oestroid subclades Rhinophorinae (Calliphoridae) and Pollen... more Phylogenetic relationships within the oestroid subclades Rhinophorinae (Calliphoridae) and Polleniidae were reconstructed for the first time, applying a Sanger sequencing approach using the two protein-coding nuclear markers CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase; 1794 bp) and MCS (molybdenum cofactor sulfurase; 2078 bp). Three genera of Polleniidae and nineteen genera of Rhinophorinae were analyzed together with a selection of taxa representing the major lineages of Oestroidea (non-rhinophorine Calliphoridae, Oestridae, Sarcophagidae, Tachinidae). The selected markers provide good resolution and moderate to strong support of the distal branches, but weak support for several deeper nodes. Polleniidae (cluster flies) emerge as monophyletic and their sister-group relationship to Tachinidae is confirmed. Morinia Robineau-Desvoidy as currently circumscribed emerges as paraphyletic with regard to Melanodexia Williston, and Pollenia Robineau-Desvoidy is the sister taxon of the Morinia-Melanodexia clade. We propose a classification with two subfamilies, Moriniinae Townsend (including Morinia, Melanodexia, and Alvamaja Rognes), and Polleniinae Brauer & Bergenstamm (including Pollenia, Dexopollenia Townsend, and Xanthotryxus Aldrich). Anthracomyza Malloch and Nesodexia Villeneuve are considered as Oestroidea incertae sedis pending further study. Rhinophorinae (woodlouse flies) emerge as monophyletic and sister to a clade composed of (Ameniinae + (Ameniinae + Phumosiinae)), and a tribal classification is proposed with the subfamily divided into Rhinophorini Robineau-Desvoidy, 1863 and Phytonini Robineau-Desvoidy, 1863 (the Stevenia-group and the Phyto-group of authors, respectively). Oxytachina Brauer & Bergenstamm, 1891, stat. rev. is resurrected to contain nine Afrotropical rhinophorine species currently assigned to genus Rhinomorinia Brauer & Bergenstamm, 1891:

Insecta Mundi, Dec 1, 2000

BMC Biology, Oct 27, 2021

European Journal of Entomology, Jan 3, 2007

Journal of Arachnology, Dec 1, 2000

Zoological Studies, Aug 1, 2014

Scientific Reports, Jan 29, 2021

Scientific Reports, Oct 5, 2016

European Journal of Entomology, Oct 23, 2017

Systematic Entomology, Mar 21, 2019

Stomach bot flies (Calyptratae: Oestridae, Gasterophilinae) are obligate endoparasitoids of Probo... more Stomach bot flies (Calyptratae: Oestridae, Gasterophilinae) are obligate endoparasitoids of Proboscidea (i.e. elephants), Rhinocerotidae (i.e. rhinos) and Equidae (i.e. horses and zebras, etc.), with their larvae developing in the digestive tract of hosts with very strong host specificity. They represent an extremely unusual diversity among dipteran, or even insect parasites in general, and therefore provide significant insights into the evolution of parasitism. The phylogeny of stomach bot flies was reconstructed based on extensive mitochondrial genomic data for Cobboldia, Gyrostigma and six of the eight known species of Gasterophilus. The phylogenetic tree, i.e. {Cobboldia, [Gyrostigma, (Gasterophilus pecorum, (Gasterophilus intestinalis, (Gasterophilus haemorrhoidalis, Gasterophilus inermis)), (Gasterophilus nasalis, Gasterophilus nigricornis))]}, provides a strong evolutionary reference to infer several biological patterns for the first time for this group: (i) host shifts of stomach bot flies from elephants to rhinoceroses and then from rhinoceroses to equids; (ii) dispersal with their hosts from the Afrotropical region into the Palaearctic and Oriental regions; (iii) oviposition site, originally on the host head, and egg production positively correlated with distance from the mouth; (iv) attachment of third-instar larva originally in the stomach, with duodenal and large intestinal positions secondarily derived; and (v) guanine and cytosine enrichment of the mitogenome as an adaptation to larval life in the warm environment of the host digestive tract, combined with the need for a high evolutionary rate to cope with the fast evolution of their mammalian hosts.

Zenodo (CERN European Organization for Nuclear Research), Nov 17, 2019

The first instar larva is described for Miltogramma pardalina (ROHDENDORF, 1934). Using a combina... more The first instar larva is described for Miltogramma pardalina (ROHDENDORF, 1934). Using a combination of light microscopy and scanning electron microscopy, the habitus is documented along with all important exoskeletal and cephaloskeletal structures. The first instar larva of M. pardalina fits well within the morphological diversity of the genus Miltogramma MEIGEN and is the most similar to larvae of M. margiana (ROHDENDORF, 1925) and M. punctata MEIGEN, 1824. Larvae of these species share at least six larval character states but all of them may be treated as typical for ancestral larva of Miltogramminae and cannot be interpreted as synapomorphies. Information about larval morphology of M. pardalina will assist future evolutionary studies of the genus Miltogramma based on the application of methods of the next generation sequencing.

The twenty-nine species-group names of Sarcophagidae proposed by Chien-ming Chao and Xue-zhong Zh... more The twenty-nine species-group names of Sarcophagidae proposed by Chien-ming Chao and Xue-zhong Zhang are reviewed. Of these names, twenty-four are available, while five are unavailable nomina nuda. Of the twenty-four available names, nine are considered valid, fifteen as invalid: thirteen junior synonyms, one unnecessary replacement name and one junior primary homonym. Holotypes of all species, and allotypes when available, are photographed and the species redescribed based on the type material. Eight new synonyms are proposed:

Zoological Journal of the Linnean Society, Dec 19, 2017

The first comprehensive genus-level phylogeny of the subfamily Sarcophaginae is presented. A morp... more The first comprehensive genus-level phylogeny of the subfamily Sarcophaginae is presented. A morphology-based phylogenetic analysis using parsimony is performed with 141 terminal taxa representing all 50 nominal genera of Sarcophaginae. In total, 222 morphological characters are coded, 150 of which are from the male terminalia. The homology of relevant male terminalia structures is assessed for the first time across the entire subfamily. Of 38 polyspecific genera represented by more than one species, the monophyly of 33 genera was recovered. This cladistic study found the genera Lepidodexia, Retrocitomyia, Sarcodexiopsis and Titanogrypa to be non-monophyletic as currently defined. Of nine monospecific genera, Mecynocorpus changes its status from monospecific to polyspecific with the discovery of a new species, Promayoa also becomes polyspecific with the transfer of one Titanogrypa species, and the remaining seven monospecific genera remain as such. Support was obtained for treating Sarcodexia as a subgenus of Peckia, and for treating Helicobia and Lipoptilocnema as valid genera rather than subgenera of Sarcophaga, and Halliosca as a valid genus rather than a subgenus of Lepidodexia. Morphological synapomorphies are discussed for all genera, including reviewed character interpretations of previous authors. We are here presenting a much more unifying interpretation of the Sarcophaginae acrophallus. New insights into the functional aspects of the sarcophagine phallus are presented. Our phylogeny shows the early lineages in Sarcophaginae as being mostly dung breeding, while lineages emerging later have more diverse life habits, including necrophagy and parasitism. Based on our phylogeny, 46 genera are recognized. The following nominal genus-group taxa are synonymized, with the junior synonym receiving a new status as subgenus under its respective senior synonym: under genus Dexosarcophaga

Biodiversity Information Science and Standards

From its birth as the ‘Biosystematic Database of World Diptera’ in 1984, the ‘Systema Dipterorum’... more From its birth as the ‘Biosystematic Database of World Diptera’ in 1984, the ‘Systema Dipterorum’ (Evenhuis and Pape 2023) has grown into one of the largest databases currently maintained for the taxonomy and nomenclature of a single order of insects. Systema Dipterorum covers all two-winged insects (Diptera), and with almost a quarter of a million names representing more than 170,000 valid species distributed in some 13,000 valid genera, we cover about 10% of the described and named Animalia. About 1,000 new nominal species are described annually within Diptera. Data are entered in FileMaker Pro (database) and served through an online portal*1 with an updated version currently provided every two months. Names are harvested and reviewed through a four-tier quality assurance hierarchy with entries eventually reaching taxonomic and nomenclatural standards equivalent to being published online. The nomenclatural status of each name is shown using 50 different codes, and at this moment a...

PLOS Biology

Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms ... more Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms at ever finer precision but have come with challenges as the major Codes of bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, species diagnoses), which is particularly problematic for DNA-based taxonomy. We, the commissioners of the International Commission on Zoological Nomenclature, advocate a tightening of the definition of “species diagnosis” in future editions of Codes of bionomenclature, for example, through the introduction of requirements for specific information on the character states of differentiating traits in comparison with similar species. Such new provisions would enhance taxonomic standards and ensure that all diagnoses, including DNA-based ones, contain adequate taxonomic context. Our recommendations are intended to spur discussion among biologists, as broad community consensus is critical ahead of the implementation ...

The Bulletin of Zoological Nomenclature

BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access t... more BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences published by nonprofit societies, associations, museums, institutions, and presses.

PLOS ONE, Sep 18, 2023

Phylogenetic relationships within the oestroid subclades Rhinophorinae (Calliphoridae) and Pollen... more Phylogenetic relationships within the oestroid subclades Rhinophorinae (Calliphoridae) and Polleniidae were reconstructed for the first time, applying a Sanger sequencing approach using the two protein-coding nuclear markers CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase; 1794 bp) and MCS (molybdenum cofactor sulfurase; 2078 bp). Three genera of Polleniidae and nineteen genera of Rhinophorinae were analyzed together with a selection of taxa representing the major lineages of Oestroidea (non-rhinophorine Calliphoridae, Oestridae, Sarcophagidae, Tachinidae). The selected markers provide good resolution and moderate to strong support of the distal branches, but weak support for several deeper nodes. Polleniidae (cluster flies) emerge as monophyletic and their sister-group relationship to Tachinidae is confirmed. Morinia Robineau-Desvoidy as currently circumscribed emerges as paraphyletic with regard to Melanodexia Williston, and Pollenia Robineau-Desvoidy is the sister taxon of the Morinia-Melanodexia clade. We propose a classification with two subfamilies, Moriniinae Townsend (including Morinia, Melanodexia, and Alvamaja Rognes), and Polleniinae Brauer & Bergenstamm (including Pollenia, Dexopollenia Townsend, and Xanthotryxus Aldrich). Anthracomyza Malloch and Nesodexia Villeneuve are considered as Oestroidea incertae sedis pending further study. Rhinophorinae (woodlouse flies) emerge as monophyletic and sister to a clade composed of (Ameniinae + (Ameniinae + Phumosiinae)), and a tribal classification is proposed with the subfamily divided into Rhinophorini Robineau-Desvoidy, 1863 and Phytonini Robineau-Desvoidy, 1863 (the Stevenia-group and the Phyto-group of authors, respectively). Oxytachina Brauer & Bergenstamm, 1891, stat. rev. is resurrected to contain nine Afrotropical rhinophorine species currently assigned to genus Rhinomorinia Brauer & Bergenstamm, 1891:

Fragmenta Faunistica, 2007

The dipteran family Rhinophoridae is recorded from North Korea for the first time. Acompomintho l... more The dipteran family Rhinophoridae is recorded from North Korea for the first time. Acompomintho lobata Villeneuve, 1927 is recorded from the mountains: Chonma-San, Myohyang, Pyongyang, Taesong and from areas surrounding them. Oplisa pollinosa Kugler, 1978 is recorded from the Ryongack Mountains. Some notes on the distribution o f A lobata are given. Illustrations o f A lobata and O. pollinosa females are presented for the first time.