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Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family
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Asian mock vipers of the genus Psammodynastes and African forest snakes of the genus Buhoma are two genera belonging to the snake superfamily Elapoidea. The phylogenetic placements of Psammodynastes and Buhoma within Elapoidea has been extremely unstable which has resulted in their uncertain and debated taxonomy. We used ultraconserved elements and traditional nuclear and mitochondrial markers to infer the phylogenetic relationships of these two genera with other elapoids. Psammodynastes, for which a reference genome has been sequenced, were found, with strong branch support, to be a relatively early diverging split within Elapoidea that is sister to a clade consisting of Elapidae, Micrelapidae and Lamprophiidae. Hence, we allocate Psammodynastes to its own family, Psammodynastidae new family. However, the phylogenetic position of Buhoma could not be resolved with a high degree of confidence. Attempts to identify the possible sources of conflict in the rapid radiation of elapoid snakes suggest that both hybridisation/introgression during the rapid diversification, including possible ghost introgression, as well as incomplete lineage sorting likely have had a confounding role. The usual practice of combining mitochondrial loci with nuclear genomic data appears to mislead phylogeny reconstructions in rapid radiation scenarios, especially in the absence of genome scale data.
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RBINS Staff Publications 2024
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Taxonomie and nomenclatorial revision within the Neotropical genera of the subtribe Odontocheilina W. Horn in a new sense- 18 Six Mexican and Central American species reltated to odontocheila mexicana Laporte de Casternau and O. ignita Chaudoir, with a de
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A Paleocene occurrence of cornelian cherries Cornus subg. Cornus in the land-mammal site of Berru (Paris Basin, France)
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Cornus subgenus Cornus, also called cornelian cherries, is a relatively ancient clade of dogwoods with a complex biogeographic history. Their fossil record attests to a distribution in North America during the Late Cretaceous and Paleocene, whereas the earliest fossil record in Europe is dated as early as the Eocene. Here, we describe a new occurrence of cornelian cherries based on permineralized endocarps from the late Paleocene (ca. 58 Ma) land-mammal locality of Berru, in Northwest France. The 48 studied specimens possess characteristic cornelian cherry endocarp morphology with locules associated with a dorsal germination valve, no central vascularization, and the presence of numerous secretory cavities in the endocarp wall. In addition, the presence of (three)-four locules and a large apical depression strongly suggest affinities with the early Eocene species Cornus multilocularis from the London Clay Formation. This new occurrence expands the stratigraphic range of the species by approximately four to six million years and is the first unequivocal evidence of cornelian cherries in Europe during the Paleocene. The biogeographical history of cornelian cherries remains complex to explore because of its ancient distribution in the Cretaceous and a geographically and stratigraphically patchy Cenozoic record.
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RBINS Staff Publications 2025
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A Neogene succession in the city centre of Antwerp (Belgium): stratigraphy, palaeontology and geotechnics of the Rubenshuis temporary outcrop
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A temporary outcrop near the “Rubenshuis” in the centre of Antwerp (northern Belgium) facilitated the study of the Neogene glauconitic sand of the Berchem and Kattendijk formations, west and south of their respective stratotype sections. In contrast to the latter sections, the exposed Kiel Member of the Berchem Formation contains a relatively silty interval in its upper part, which is also reflected in Cone Penetration Tests. This silty interval is rich in molluscs, including the subspecies Glossus lunulatus cf. lunulatus and Ennucula haesendoncki haesendoncki, previously unknown from this member. Dinoflagellate cysts indicate that the main body of the Kiel Member was deposited during the middle Burdigalian, while only the upper part was deposited during the late Burdigalian. The Kiel Member is covered by the shell-rich, silty sand of the Langhian Antwerpen Member (Berchem Formation). Both members display soft-sediment deformation structures, probably caused by differences in silt content between and within these units. The Antwerpen Member is incised by the Lower Pliocene Kattendijk Formation, which reduced the thickness of the former to only 1.1 m, compared to 7 m in northeastern Antwerp. As a result, the basal gravel of the Kattendijk Formation contains many fossils reworked from the Antwerpen Member, in addition to autochthonous molluscs and Ditrupa. The Zanclean fauna resembles associations known from the highest part of the Kattendijk Formation in the former Oosterweel outcrop north of Antwerp, while it differs from the fauna of the lowermost Kattendijk Formation near Doel and Kallo. Hence, the palaeontological observations corroborate the regional depositional model of this unit, suggesting that only the youngest gully sequence of the Kattendijk Formation was deposited across the city of Antwerp.
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RBINS Staff Publications 2024 OA
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Describing novel mitochondrial genomes of Antarctic amphipods
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To date, only one mitogenome from an Antarctic amphipod has been published. Here, novel complete mitochondrial genomes (mitogenomes) of two morphospecies are assembled, namely, Charcotia amundseni and Eusirus giganteus. For the latter species, we have assembled two mitogenomes from different genetic clades of this species. The lengths of Eusirus and Charcotia mitogenomes range from 15,534 to 15,619 base pairs and their mitogenomes are composed of 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 1 putative control region CR. Some tRNAs display aberrant structures suggesting that minimalization is also ongoing in amphipod mitogenomes. The novel mitogenomes of the two Antarctic species have features distinguishing them from other amphipod mitogenomes such as a lower AT-richness in the whole mitogenomes and a negative GC- skew in both strands of protein coding genes. The genetically most variable mitochondrial regions of amphipods are nad6 and atp8, while cox1 shows low nucleotide diversity among closely and more distantly related species. In comparison to the pancrustacean mitochondrial ground pattern, E. giganteus shows a translocation of the nad1 gene, while cytb and nad6 genes are translocated in C. amundseni. Phylogenetic analysis based on mitogenomes illustrates that Eusirus and Charcotia cluster together with other species belonging to the same amphipod superfamilies. In the absence of reference nuclear genomes, mitogenomes can be useful to develop markers for studying population genetics or evolutionary relationships at higher taxonomic levels.
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RBINS Staff Publications 2022
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On an endemic species flock of cypridopsine ostracods (Crustacea, Ostracoda) from the ancient Lake Malawi (Africa), with the description of a new genus and three new species
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We describe Malawidopsis gen. nov., a new genus of Cypridopsinae Kaufmann, 1900 from the African ancient Lake Malawi. The genus comprises at least 17 new species, which makes it a significant ostracod radiation in this lake, parallel to a similar (but independent) cypridopsine radiation in Lake Tanganyika. Three of these new species are here described: Malawidopsis stellae gen. et. sp. nov., the type species of the new genus; M. ruwaydae gen. et. sp. nov. and M. antoniae gen. et. sp. nov.. The other new species are briefly illustrated and described, but are left in open nomenclature (sp. A, B, C, etc.). Cypridopsis cunningtoni Sars, 1910 and Potamocypris fuelleborni Daday, 1910 are transferred to Malawidopsis gen. nov. and are identical to Malawidopsis spec. F and Malawidopsis spec. N, respectively. The new tribe Plesiocyprisopsini trib. nov. is erected, and comprises the cypridopsine genera previously in the Cypridopsini s.l. with the right valve overlapping the left valve, at least anteriorly. Potential drivers of speciation within this endemic clade in Lake Malawi are briefly discussed. Bathymetry might have been important, with most species being restricted to shallower depths and only four species also occurring at depths of 75 m or more, but very few specimens were retrieved from greater depths. Most species occurred on coarse sand, but this sediment category coincides with shallower stations. Overall, most species appear to have a wide geographical distribution in the lake, so no geographical parapatric speciation is apparent. The occurrence of all species in sexual populations and the significant differences in the male sexual organs and the valves suggest that sexual selection might have been the most important driver in the speciation process of this species flock, but this should be further explored. Following deep coring results in Lake Malawi, the present clade could be (at least) c one million years old.
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On a new species of Pseudocypretta Klie, 1932 (Crustacea, Ostracoda) from the Neotropical region, with a discussion on the position of the genus.
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Pseudocypretta amor sp. nov. (named after the carapace spots resembling the word “Love”) is here described from all-female populations from the four major floodplains in Brazil. The new species is compared to the other two know species in the genus, P. maculata Klie (1932), the type species, and P. lineata Ma and Yu (2020). As the latter two species are thus far found exclusively in South East Asia and China, respectively, the present extension of the area of the genus to South America is considerable. Several morphological characters in this genus and species are discussed, especially the presence of marginal septa in the valves, the candonid type T3 with 3rd and 4th segment separated (candonid type) and the caudal ramus which is reduced to a flagellum (cypridopsine type) or is fully absent. Based on the combination of these and other characters, the genus Pseudocypretta is here transferred from the Cyprettinae to the tribe Cyprettadopsini in the Cypridopsinae, as it is closely related to the genus Cyprettadopsis Savatenalinton, 2020. The presence of the candonid type T3 in Cyprididae and Notodromadidae, where the T3 generally has a pincer-shaped tip by the fusion of the 3rd and the 4th segment, is further discussed.
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RBINS Staff Publications 2022
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A comparison of three main scientific literature databases using a search in aquatic ecology
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Online searches for relevant scientific references using keywords have become common practice. Several multidisciplinary scientific online databases are available, of which Web of Science, Scopus (both payable) and Google Scholar (free of charge) are the most commonly used. We test the hypothesis that results of highly similar searches in these three databases do not necessarily give comparable results. We set out to query the three databases with a real example on “diapause in microcrustaceans” (Cladocera, Copepoda and Ostracoda), using the same time period (2012–2021), the same keywords with the same syntaxis and the same sorting criterion (“relevance”), and compared the first 100 hits provided by each database. There were several references provided which were irrelevant to the search, especially in the Web of Science, and of the remaining relevant references, only 9.84% were provided by all three databases. Our survey showed significant differences amongst the results provided by the databases, especially for “hydroperiod” and “type of environment”. These differences can be the result of different coverage of the scientific literature by the databases, but also of the different ways by which the criterion “relevance” is calculated by the three algorithms. We, therefore, recommend that literature surveys must be based on several databases; otherwise, the results might become biased.
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Dried aquatic macrophytes are floating egg banks and potential dispersal vectors of ostracods (Crustacea) from pleuston communities.
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In aquatic ecosystems, such as Neotropical floodplains, it is common to find dried aquatic macrophytes along the margins of various environments (e.g. lakes and rivers) during the dry season. Here, we evaluate the potential of dried Eichhornia crassipes as a dispersal vector of ostracod resting eggs by assessing the abundance, richness and beta diversity of the dormant associated fauna. We test two hypotheses: (1) that the roots of E. crassipes shelter and disperse ostracod resting eggs and (2) that the abundance, richness and beta diversity of dormant assemblages will increase over the incubation time after re-hydration. Dried E. crassipes from floodplain lakes were hydrated with distilled water. The microcosms were kept in germinating chambers with controlled temperature and photoperiod during 147 days. A total of 397 ostracods representing seven species hatched from the resting eggs attached to dried macrophyte roots. An increase in richness and a decrease in abundance were observed over the weeks, although these trends were not significant. However, the beta diversity increased significantly over the incubation time. Our results show that the complex root systems of E. crassipes have the potential for storage and dispersal of ostracod resting eggs.
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A (very) brief vademecum on biological nomenclature
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This editorial is aimed at explaining why the editors of Hydrobiologia are so concerned with biological nomenclature and why we ask our authors the utmost precision when referring to species in their papers. In particular, the Instructions for Authors of the journal specify that “When a species name is used for the first time in an article, it should be stated in full, and the name of its describer should also be given” (https://www.springer.com/journal/10750/submission-guidelines?IFA#Instructions%20for%20Authors_Scientific%20style). In the next lines, we want to show that this is not just an old fashion formalism, but a necessity to correctly and univocally identify the biological subjects that are the basis of the research published in this journal. Moreover, Hydrobiologia is a generalist journal giving voice to research embedded in a wide ecological and evolutionary context, carried out in any kind of aquatic ecosystem, and considering all their biological entities from small viruses onwards to large whales! Thus, the work of a, for example, fish biologist, should be readable for a botanist and vice versa. This achievement can be reached by avoiding as much as possible the jargon typical of each discipline (as the so called “common names” can be considered) and allowing the unequivocal identification of the targeted biological entities.
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