cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13603472
title: Justification for a taxonomic conservation update of the rodent genus <i>Tamiasciurus</i>: addressing marginalization and mis-prioritization of research efforts and conservation <i>laissez-faire</i> for a sustainability outlook

description: Taxonomy presents itself as the critical basis of any modern scientific decision-making approach in the living world, and therefore accurate classifications have to be sought. Due to ongoing species naming debates, here we would like to facilitate a discussion on the methods and validity used for taxonomic claims and their influence on conservation, ecology, and management for squirrels in the western world as a wider example. Following the established epigenetic approach, we examine the rodent genus <i>Tamiasciurus</i>. We include in our assessment all relevant species-interfering characteristics and present one new perspective, ecological niches. The ecological niche is essential for explaining the species’ behavior patterns and their discrepancies among the congeners, adding insights into phylogenesis. We add the usage of mapping software such as geographic information systems (ArcGIS, Open QGIS) for this genus, as well as best-available open access data and the statistical aid from R. Misclassifications in the taxonomy are known to lead to conservation failures on a continental and societal scale, in part caused by a lack of knowledge by the public and the miscommunication between scientists and the public. As one possible solution, here we suggest a reclassification for Mearns’s squirrel (<i>Tamiasciurus mearnsi</i>) and a description update for the entire <i>Tamiasciurus</i> genus to improve conservation success. Additional solutions are presented to simplify classification with reduced errors and confusion in the animal kingdom. A larger future effort of this style is sought to greatly decrease marginalization, to improve the current lack of research priority and “<i>laissez-faire”</i> attitudes on environmental issues for a better relationship between humans and the biotic world. In conclusion we present important topics and yet unaddressed problems, such as how the rodent’s marginalization influences the pandemic disease transmission to humans (e.g. Covid-19, rabies, and bubonic plague), appropriately assigned budgets for their conservation, and the data transparency in a continuously accelerating climate-changing world.
DOI: 10.6084/m9.figshare.13721686.v1
title: Puzzling over spurdogs: molecular taxonomy assessment of the <i>Squalus</i> species in the Strait of Sicily

description: The actual occurrence of <i>Squalus megalops</i> in the Mediterranean Sea has recently been questioned. Several research works which sought to assess available morphological and meristic features that differentiate <i>S. megalops</i> from other <i>Squalus</i> species in the Mediterranean Sea, revealed poor discriminatory power and high variability of the assessed characters, especially when comparing <i>S. megalops</i> and <i>S. blainville</i>. The application of molecular tools does not support the presence of <i>S. megalops</i>. In the present study, we screened spurdog species from the Strait of Sicily using a molecular taxonomy approach based on two mitochondrial DNA markers and we report the occurrence of two <i>Squalus</i> lineages characterizing specimens collected from the stretch of sea between Tunisia, southern Sicily, Malta and Libya. The results support the hypothesis that a common species, <i>S. blainville</i>, currently inhabits the Mediterranean Sea, while a second and rare species is probably an occasional visitor with high morphological similarity to the <i>S. megalops</i> and <i>S. blainville</i> but is genetically distinct from both. Within this perspective, the occurrence of <i>S. megalops</i> in the Mediterranean Sea is not confirmed and our study highlights the taxonomic uncertainties in relation to the occurrence and distribution of <i>Squalus</i> species in this region. We encourage the establishment of a coordinated international effort to implement a comprehensive and integrated taxonomic assessment on this genus which represents an irreplaceable component of the biodiversity of the area.
DOI: 10.6084/m9.figshare.13721686
title: Puzzling over spurdogs: molecular taxonomy assessment of the <i>Squalus</i> species in the Strait of Sicily

description: The actual occurrence of <i>Squalus megalops</i> in the Mediterranean Sea has recently been questioned. Several research works which sought to assess available morphological and meristic features that differentiate <i>S. megalops</i> from other <i>Squalus</i> species in the Mediterranean Sea, revealed poor discriminatory power and high variability of the assessed characters, especially when comparing <i>S. megalops</i> and <i>S. blainville</i>. The application of molecular tools does not support the presence of <i>S. megalops</i>. In the present study, we screened spurdog species from the Strait of Sicily using a molecular taxonomy approach based on two mitochondrial DNA markers and we report the occurrence of two <i>Squalus</i> lineages characterizing specimens collected from the stretch of sea between Tunisia, southern Sicily, Malta and Libya. The results support the hypothesis that a common species, <i>S. blainville</i>, currently inhabits the Mediterranean Sea, while a second and rare species is probably an occasional visitor with high morphological similarity to the <i>S. megalops</i> and <i>S. blainville</i> but is genetically distinct from both. Within this perspective, the occurrence of <i>S. megalops</i> in the Mediterranean Sea is not confirmed and our study highlights the taxonomic uncertainties in relation to the occurrence and distribution of <i>Squalus</i> species in this region. We encourage the establishment of a coordinated international effort to implement a comprehensive and integrated taxonomic assessment on this genus which represents an irreplaceable component of the biodiversity of the area.
DOI: 10.6084/m9.figshare.13628050
title: The activity of hydrolytic enzymes in the digestive system of Acanthobdellida, Branchiobdellida and Hirudinida (Annelida, Clitellata) – considerations on similarity and phylogeny

description: Activities of nineteen hydrolases were measured in the digestive systems of predatory and blood-feeding true leeches (Hirudinida) and their closest relatives, Branchiobdellida and Acanthobdellida. Hydrolase activities were analyzed in different parts of the digestive systems: the species-specific anterior part, i.e. jaws, pharynx or proboscis, crop and intestine. The results obtained suggest that food digestion and possible absorption predominate in the intestine of most of the studied Hirudinida and <i>A. peledina</i>, whereas in <i>B. astaci</i> these processes take place in the anterior part of the digestive system and crop. In Erpobdellidae and <i>Piscicola respirans</i>, the activity of acid and alkaline phosphatases, N-acetyl-β-glucosaminidase, leucine and valine arylamidases, and α-fucosidase was also detected in the anterior part of the digestive system. We also detected differences in enzyme occurrence between the studied species, which are probably connected with their different food preferences. Moreover, the presence of the whole spectrum of enzymes in predatory leeches and the absence of trypsin and α-chymotrypsin activity in the crop of all the leeches support the hypothesis that the leech ancestor was a blood-feeder. Our study showed that “Rhynchobdellida” constitute a paraphyletic group which confirms the previous results based on molecular phylogenetics, while Arhynchobdellida appears to be a non-monophyletic group which is not consistent with previous molecular results.
DOI: 10.6084/m9.figshare.13628050.v1
title: The activity of hydrolytic enzymes in the digestive system of Acanthobdellida, Branchiobdellida and Hirudinida (Annelida, Clitellata) – considerations on similarity and phylogeny

description: Activities of nineteen hydrolases were measured in the digestive systems of predatory and blood-feeding true leeches (Hirudinida) and their closest relatives, Branchiobdellida and Acanthobdellida. Hydrolase activities were analyzed in different parts of the digestive systems: the species-specific anterior part, i.e. jaws, pharynx or proboscis, crop and intestine. The results obtained suggest that food digestion and possible absorption predominate in the intestine of most of the studied Hirudinida and <i>A. peledina</i>, whereas in <i>B. astaci</i> these processes take place in the anterior part of the digestive system and crop. In Erpobdellidae and <i>Piscicola respirans</i>, the activity of acid and alkaline phosphatases, N-acetyl-β-glucosaminidase, leucine and valine arylamidases, and α-fucosidase was also detected in the anterior part of the digestive system. We also detected differences in enzyme occurrence between the studied species, which are probably connected with their different food preferences. Moreover, the presence of the whole spectrum of enzymes in predatory leeches and the absence of trypsin and α-chymotrypsin activity in the crop of all the leeches support the hypothesis that the leech ancestor was a blood-feeder. Our study showed that “Rhynchobdellida” constitute a paraphyletic group which confirms the previous results based on molecular phylogenetics, while Arhynchobdellida appears to be a non-monophyletic group which is not consistent with previous molecular results.
DOI: 10.6084/m9.figshare.14238013.v1
title: Differential genetic variability at two mtDNA COI regions does not imply mismatches in Odonata molecular identification performances

description: Molecular-based approaches for species identification and delimitation strongly rely, in terms of universality and efficiency, on the selected markers. Conventionally, when adopting a DNA barcoding approach to discriminate (or identify) metazoans species, the marker choice falls on the 658 base pair region at the 5ʹ end of the mitochondrial COI gene. However, a growing number of studies suggest to use alternative and more variable genetic regions, even from the same gene, such as the 3ʹ end of the COI. In this work, we compared the identification performance of the 5ʹ and 3ʹ end COI regions on a large sequence dataset of odonate species, an order of arthropods among the most studied in terms of conservation importance for aquatic ecosystems. The genetic datasets comprised a total of 236 specimens, 113 species, 51 genera and 12 families spanning the two odonate suborders Zygoptera and Anisoptera, and were analysed under an integrative multiple approach including descriptive statistics and variability of the sequences, phylogenetic reconstructions, DNA-based species delimitations, genetic distances, identification of diagnostic characters and saturation plots. All analyses were congruent in recovering the COI-3ʹ region to be slightly more variable than the COI-5ʹ one, and both regions showed a saturation of transversion at the third codon position. However, phylogenetic reconstructions, genetic distances, and diagnostic characters identification resulted in a similar discrimination power for the two COI regions. Therefore, the COI-3ʹ region does not add much information to the standard COI-5ʹ barcode region, which has in turn largely been demonstrated to successfully delineate invertebrate communities through DNA and eDNA metabarcoding, and to have a much more extensive taxonomic coverage in public databases. Overall, the DNA barcoding inventory assembled in this study will provide valuable insights into the systematics and conservation of many odonate species with implications for future DNA and eDNA monitoring-based studies.
DOI: 10.6084/m9.figshare.14238013
title: Differential genetic variability at two mtDNA COI regions does not imply mismatches in Odonata molecular identification performances

description: Molecular-based approaches for species identification and delimitation strongly rely, in terms of universality and efficiency, on the selected markers. Conventionally, when adopting a DNA barcoding approach to discriminate (or identify) metazoans species, the marker choice falls on the 658 base pair region at the 5ʹ end of the mitochondrial COI gene. However, a growing number of studies suggest to use alternative and more variable genetic regions, even from the same gene, such as the 3ʹ end of the COI. In this work, we compared the identification performance of the 5ʹ and 3ʹ end COI regions on a large sequence dataset of odonate species, an order of arthropods among the most studied in terms of conservation importance for aquatic ecosystems. The genetic datasets comprised a total of 236 specimens, 113 species, 51 genera and 12 families spanning the two odonate suborders Zygoptera and Anisoptera, and were analysed under an integrative multiple approach including descriptive statistics and variability of the sequences, phylogenetic reconstructions, DNA-based species delimitations, genetic distances, identification of diagnostic characters and saturation plots. All analyses were congruent in recovering the COI-3ʹ region to be slightly more variable than the COI-5ʹ one, and both regions showed a saturation of transversion at the third codon position. However, phylogenetic reconstructions, genetic distances, and diagnostic characters identification resulted in a similar discrimination power for the two COI regions. Therefore, the COI-3ʹ region does not add much information to the standard COI-5ʹ barcode region, which has in turn largely been demonstrated to successfully delineate invertebrate communities through DNA and eDNA metabarcoding, and to have a much more extensive taxonomic coverage in public databases. Overall, the DNA barcoding inventory assembled in this study will provide valuable insights into the systematics and conservation of many odonate species with implications for future DNA and eDNA monitoring-based studies.
DOI: 10.5281/zenodo.4784352
title: Análisis del comportamiento de los contaminantes atmosféricos en las estaciones Puente Aranda y Jazmín y su relación con las variables meteorológicas (Datos y código)

description: Análisis comparativo del comportamiento de los contaminantes atmosféricos, variables meteorológicas y la relación entre ellos, usando el lenguaje de programación Python, en el entorno Spyder.
DOI: 10.5281/zenodo.4784351
title: Análisis del comportamiento de los contaminantes atmosféricos en las estaciones Puente Aranda y Jazmín y su relación con las variables meteorológicas (Datos y código)

description: Análisis comparativo del comportamiento de los contaminantes atmosféricos, variables meteorológicas y la relación entre ellos, usando el lenguaje de programación Python, en el entorno Spyder.
DOI: 10.6084/m9.figshare.12854210
title: The species identification problem in mirids (Hemiptera: Heteroptera) highlighted by DNA barcoding and species delimitation studies

description: Due to the difficulties associated with detecting and correctly identifying mirids, developing an accurate species identification approach is crucial, especially for potential harmful species. Accurate identification is often hampered by inadequate morphological key characters, invalid and/or outdated systematics, and biases in the molecular data available in public databases. This study aimed to verify whether molecular characterization (i.e. DNA barcoding) is able to identify mirid species of economic relevance and if species delimitation approaches are reliable tools for species discrimination. Cytochrome c oxydase 1 (<i>cox1</i>) data from public genetic databases were compared with new data obtained from mirids sampled in different Italian localities, including an old specimen from private collection, showing contrasting results. Based on the DNA barcoding approach, for the genus <i>Orthops</i>, all sequences were unambiguously assigned to the same species, while in <i>Adelphocoris, Lygus</i> and <i>Trigonotylus</i> there were over-descriptions and/or misidentifications of species. On the other hand, in <i>Polymerus</i> and <i>Deraeocoris</i> there was an underestimation of the taxonomic diversity. The present study highlighted an important methodological problem: DNA barcoding can be a good tool for pest identification and discrimination, but the taxonomic unreliability of public DNA databases can make this method useless or even misleading.
DOI: 10.6084/m9.figshare.11981616
title: Ethanolic extract of propolis and vitamin E attenuates metal-induced testicular necrosis: time-related study on male reproductive system in albino mice

description: This study was designed to investigate the protective effects of propolis and vitamin E against time-related metal (aluminum chloride)-induced toxicity on the male reproductive system in albino mice (n = 63). Animals were randomly divided into seven groups (n = 9 each). Group I (control) received 0.9% saline solution; group II was given 50 mg/kg of aluminum chloride (AlCl<sub>3</sub>); groups III and IV were administered vitamin E (150 mg/kg) and propolis (50 mg/kg), respectively; and groups V, VI and VII were administered AlCl<sub>3</sub> + vitamin E, AlCl<sub>3</sub> + propolis, and AlCl<sub>3</sub> + vitamin E + propolis, respectively, for 45 days. Animals were sacrificed; blood and tissue samples were collected (thrice; fortnightly) for the estimation of hormones i.e., Follicle stimulating hormone (FSH), Luteinizing hormone (LH) and testosterone using Enzyme linked immunosorbent assay (ELISA). Testicular histology, testicular weight, sperm count and motility were estimated. Group II revealed a highly significant decrease in LH, FSH, testosterone, testis weight, sperm count and motility. Groups III–VII showed a significant increase in LH, FSH, testosterone, organ weight, sperm count and motility in the 3<sup>rd</sup> sampling, as compared to group II. Hence, it is concluded that vitamin E and propolis, acting individually as well as synergistically, mitigate metal-induced time-related toxicity on the reproductive system and testicular histology of male mice.
DOI: 10.6084/m9.figshare.11981616.v1
title: Ethanolic extract of propolis and vitamin E attenuates metal-induced testicular necrosis: time-related study on male reproductive system in albino mice

description: This study was designed to investigate the protective effects of propolis and vitamin E against time-related metal (aluminum chloride)-induced toxicity on the male reproductive system in albino mice (n = 63). Animals were randomly divided into seven groups (n = 9 each). Group I (control) received 0.9% saline solution; group II was given 50 mg/kg of aluminum chloride (AlCl<sub>3</sub>); groups III and IV were administered vitamin E (150 mg/kg) and propolis (50 mg/kg), respectively; and groups V, VI and VII were administered AlCl<sub>3</sub> + vitamin E, AlCl<sub>3</sub> + propolis, and AlCl<sub>3</sub> + vitamin E + propolis, respectively, for 45 days. Animals were sacrificed; blood and tissue samples were collected (thrice; fortnightly) for the estimation of hormones i.e., Follicle stimulating hormone (FSH), Luteinizing hormone (LH) and testosterone using Enzyme linked immunosorbent assay (ELISA). Testicular histology, testicular weight, sperm count and motility were estimated. Group II revealed a highly significant decrease in LH, FSH, testosterone, testis weight, sperm count and motility. Groups III–VII showed a significant increase in LH, FSH, testosterone, organ weight, sperm count and motility in the 3<sup>rd</sup> sampling, as compared to group II. Hence, it is concluded that vitamin E and propolis, acting individually as well as synergistically, mitigate metal-induced time-related toxicity on the reproductive system and testicular histology of male mice.
DOI: 10.6084/m9.figshare.12854210.v1
title: The species identification problem in mirids (Hemiptera: Heteroptera) highlighted by DNA barcoding and species delimitation studies

description: Due to the difficulties associated with detecting and correctly identifying mirids, developing an accurate species identification approach is crucial, especially for potential harmful species. Accurate identification is often hampered by inadequate morphological key characters, invalid and/or outdated systematics, and biases in the molecular data available in public databases. This study aimed to verify whether molecular characterization (i.e. DNA barcoding) is able to identify mirid species of economic relevance and if species delimitation approaches are reliable tools for species discrimination. Cytochrome c oxydase 1 (<i>cox1</i>) data from public genetic databases were compared with new data obtained from mirids sampled in different Italian localities, including an old specimen from private collection, showing contrasting results. Based on the DNA barcoding approach, for the genus <i>Orthops</i>, all sequences were unambiguously assigned to the same species, while in <i>Adelphocoris, Lygus</i> and <i>Trigonotylus</i> there were over-descriptions and/or misidentifications of species. On the other hand, in <i>Polymerus</i> and <i>Deraeocoris</i> there was an underestimation of the taxonomic diversity. The present study highlighted an important methodological problem: DNA barcoding can be a good tool for pest identification and discrimination, but the taxonomic unreliability of public DNA databases can make this method useless or even misleading.
DOI: 10.6084/m9.figshare.13251563
title: Comparative morphology of labial cartilages in sharks (Chondrichthyes, Elasmobranchii)

description: During the last years, feeding mechanisms of sharks have been documented mainly based on their stomach contents supplemented by video footages of feeding behaviours in some species. Rare kinematic analyses of shark jaws contributed additionally to our knowledge. However, not all structures important to prey capture in sharks have been investigated yet. Here, we summarize the current knowledge about labial cartilages in sharks and compare them on a morphological base. Labial cartilages are considered a plesiomorph character found in extinct and extant species and their number and size varies a lot between species. We identified labial cartilages in representatives of 27 from 36 shark families and detected different numbers, sizes and forms of labial cartilages, as well as differing positioning along the jaws. The morphology of labial cartilages can help to identify suction-feeding in sharks and to estimate the quality of the suction generated by a species. We were able to summon different shark taxa according to their morphology and positioning of labial cartilages into eight groups, which we consider morphological modules. To determine if these modules bare a phylogenetic signal further testing with rigorous methodologies and more shark species as well as batomorphs needs to be done. This study therefore only can represent a first starting point providing future research pathways.