cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28062901
title: Phyto-metabolomic investigation of biologically active fraction of <i>Phanera vahlii (Wight & Arn.) Benth.</i> leaf

description: <i>Phanera vahlii</i> (Wight & Arn.) Benth., leaves are used traditionally in variety of diseases. Chemical examination of the leaves yielded Davinvolunol B (1) and Quercetin-3-O-rhamnoside (2). Compared with the other extracts, the aqueous methanol extract significantly inhibited <i>Streptococcus aureus</i> with an IC<sub>50</sub> of 8 µg/mL. In the anticancer activity assay, the ethyl acetate extract was effective against HeLa cells (IC<sub>50</sub> 19 µg/mL), the methanol extract was effective against A549 cells (IC<sub>50</sub> of 19 µg/mL), the aqueous methanol extract was effective against PANC-1 cells (IC<sub>50</sub> of 17 µg/mL) and the chloroform extract was effective against HT1080 cells (IC<sub>50</sub> of 19 µg/mL). The polar extracts which showed good antioxidant activity exhibited strong bioactivity. This finding was supported by untargeted phytometabolite profiling of extracts using UPLC-ESI-Q-TOF-MSE. The PCA score plot and the Ven diagram revealed that the extracts had a distinctive and adequate number of polar molecules that likely contributed to their observed inhibitory activity.
DOI: 10.6084/m9.figshare.28062901.v1
title: Phyto-metabolomic investigation of biologically active fraction of <i>Phanera vahlii (Wight & Arn.) Benth.</i> leaf

description: <i>Phanera vahlii</i> (Wight & Arn.) Benth., leaves are used traditionally in variety of diseases. Chemical examination of the leaves yielded Davinvolunol B (1) and Quercetin-3-O-rhamnoside (2). Compared with the other extracts, the aqueous methanol extract significantly inhibited <i>Streptococcus aureus</i> with an IC<sub>50</sub> of 8 µg/mL. In the anticancer activity assay, the ethyl acetate extract was effective against HeLa cells (IC<sub>50</sub> 19 µg/mL), the methanol extract was effective against A549 cells (IC<sub>50</sub> of 19 µg/mL), the aqueous methanol extract was effective against PANC-1 cells (IC<sub>50</sub> of 17 µg/mL) and the chloroform extract was effective against HT1080 cells (IC<sub>50</sub> of 19 µg/mL). The polar extracts which showed good antioxidant activity exhibited strong bioactivity. This finding was supported by untargeted phytometabolite profiling of extracts using UPLC-ESI-Q-TOF-MSE. The PCA score plot and the Ven diagram revealed that the extracts had a distinctive and adequate number of polar molecules that likely contributed to their observed inhibitory activity.
DOI: 10.6084/m9.figshare.27604661
title: Hyracoidea from the Oligocene of Topernawi, Turkana Basin, Kenya

description: The Topernawi area of west Turkana, northern Kenya, preserves a number of recently discovered vertebrate fossil localities of mid-Oligocene age. The Topernawi fauna provides important new data on mammalian evolution in equatorial eastern Africa during the mid-Cenozoic. Here, we describe five new species of hyracoids from Topernawi: <i>Nengohyrax josephi</i>, <i>Abdahyrax philipi</i>, <i>Geniohyus ewoii</i>, <i>Thyrohyrax lokutani</i>, and <i>Thyrohyrax ekaii</i>. These species range in reconstructed body mass from ∼8 to ∼150 kg, comparable to the body size range that has been observed at other hyracoid-rich Paleogene sites. We use Bayesian tip-dating phylogenetic analyses to estimate hyracoid relationships. We find that non-<i>Thyrohyrax</i> species from Topernawi are members of Geniohyidae, a clade of bunodont, Paleogene hyracoids. Despite being approximately the same age as some of the youngest and best-sampled horizons in the Jebel Qatrani Formation (Fayum, northern Egypt), the Topernawi hyracoid fauna is distinct, and shows no overlap at the species level; it also shows no species overlap with the ∼1.5–2.5 Ma younger Chilga localities in northern Ethiopia. The hyracoid assemblage from Topernawi adds to a growing body of evidence which suggests that certain distinctive clades known from earlier Oligocene horizons in northern Africa (<i>Saghatherium</i>, <i>Selenohyrax</i>, <i>Titanohyrax</i>) did not persist into the late Oligocene.
DOI: 10.6084/m9.figshare.27604661.v1
title: Hyracoidea from the Oligocene of Topernawi, Turkana Basin, Kenya

description: The Topernawi area of west Turkana, northern Kenya, preserves a number of recently discovered vertebrate fossil localities of mid-Oligocene age. The Topernawi fauna provides important new data on mammalian evolution in equatorial eastern Africa during the mid-Cenozoic. Here, we describe five new species of hyracoids from Topernawi: <i>Nengohyrax josephi</i>, <i>Abdahyrax philipi</i>, <i>Geniohyus ewoii</i>, <i>Thyrohyrax lokutani</i>, and <i>Thyrohyrax ekaii</i>. These species range in reconstructed body mass from ∼8 to ∼150 kg, comparable to the body size range that has been observed at other hyracoid-rich Paleogene sites. We use Bayesian tip-dating phylogenetic analyses to estimate hyracoid relationships. We find that non-<i>Thyrohyrax</i> species from Topernawi are members of Geniohyidae, a clade of bunodont, Paleogene hyracoids. Despite being approximately the same age as some of the youngest and best-sampled horizons in the Jebel Qatrani Formation (Fayum, northern Egypt), the Topernawi hyracoid fauna is distinct, and shows no overlap at the species level; it also shows no species overlap with the ∼1.5–2.5 Ma younger Chilga localities in northern Ethiopia. The hyracoid assemblage from Topernawi adds to a growing body of evidence which suggests that certain distinctive clades known from earlier Oligocene horizons in northern Africa (<i>Saghatherium</i>, <i>Selenohyrax</i>, <i>Titanohyrax</i>) did not persist into the late Oligocene.
DOI: 10.6084/m9.figshare.27239955
title: Postcranial anatomy of <i>Dsungaripterus weii</i> (Pterosauria: Ornithocheiroidea) from the Lower Cretaceous of Wuerho, China

description: Ornithocheiroidea was a globally diverse group of pterosaurs during the Cretaceous. However, well-documented ornithocheiroids are highly derived, hampering our understanding on the morphological evolution of this clade. <i>Dsungaripterus weii</i> Young, 1964 from the Lower Cretaceous Tugulu Group (Valanginian) of the Junggar Basin is an iconic early member of Ornithocheiroidea. <i>Dsungaripterus</i> is known from numerous three-dimensionally preserved specimens, ranging from isolated bones to partially articulated individuals. Here we provide a comprehensive description of the postcranium of <i>Dsungaripterus</i>. We find that <i>Dsungaripterus</i> has many autapomorphies in the postcranial skeleton parallelling its unique skull, including the asynchronous fusion between the sacrum and pelvis and a posterodorsal fossa of the humerus with a paper-thin bone wall. <i>Dsungaripterus</i> also displays some plesiomorphic features of Ornithoecheiroidea, for example, limb bones with relatively thick bone walls, variably reduced pneumatic features in cervical vertebrae and appendicular skeletons, absence of spinoprezygapophyseal and spinopostzygapophyseal ridges in middle-series cervical vertebrae, at least one metacarpal articulating with the distal syncarpal, and a distally displaced adductor ridge on the femur. Additionally, <i>Dsungaripterus</i> possesses some unexpected features possibly convergent with other members of Ornithocheiroidea. Although the postcranial skeletons of <i>Dsungaripterus</i> are represented by osteologically mature specimens, notable morphological variation is present. Functional reconstructions of several aspects of the postcranial skeleton of <i>Dsungaripterus</i> are elucidated, including the arrangement of the metacarpophalangeal region during terrestrial locomotion. Niche partitioning between the two dsungaripterids from the Tugulu Group of Wuerho, <i>Dsungaripterus</i> and <i>Noripterus</i>, is supported by their distinct dentitions, neck morphology, and limb proportions.
DOI: 10.6084/m9.figshare.27239955.v2
title: Postcranial anatomy of <i>Dsungaripterus weii</i> (Pterosauria: Ornithocheiroidea) from the Lower Cretaceous of Wuerho, China

description: Ornithocheiroidea was a globally diverse group of pterosaurs during the Cretaceous. However, well-documented ornithocheiroids are highly derived, hampering our understanding on the morphological evolution of this clade. <i>Dsungaripterus weii</i> Young, 1964 from the Lower Cretaceous Tugulu Group (Valanginian) of the Junggar Basin is an iconic early member of Ornithocheiroidea. <i>Dsungaripterus</i> is known from numerous three-dimensionally preserved specimens, ranging from isolated bones to partially articulated individuals. Here we provide a comprehensive description of the postcranium of <i>Dsungaripterus</i>. We find that <i>Dsungaripterus</i> has many autapomorphies in the postcranial skeleton parallelling its unique skull, including the asynchronous fusion between the sacrum and pelvis and a posterodorsal fossa of the humerus with a paper-thin bone wall. <i>Dsungaripterus</i> also displays some plesiomorphic features of Ornithoecheiroidea, for example, limb bones with relatively thick bone walls, variably reduced pneumatic features in cervical vertebrae and appendicular skeletons, absence of spinoprezygapophyseal and spinopostzygapophyseal ridges in middle-series cervical vertebrae, at least one metacarpal articulating with the distal syncarpal, and a distally displaced adductor ridge on the femur. Additionally, <i>Dsungaripterus</i> possesses some unexpected features possibly convergent with other members of Ornithocheiroidea. Although the postcranial skeletons of <i>Dsungaripterus</i> are represented by osteologically mature specimens, notable morphological variation is present. Functional reconstructions of several aspects of the postcranial skeleton of <i>Dsungaripterus</i> are elucidated, including the arrangement of the metacarpophalangeal region during terrestrial locomotion. Niche partitioning between the two dsungaripterids from the Tugulu Group of Wuerho, <i>Dsungaripterus</i> and <i>Noripterus</i>, is supported by their distinct dentitions, neck morphology, and limb proportions.
DOI: 10.6084/m9.figshare.27239955.v1
title: Postcranial anatomy of <i>Dsungaripterus weii</i> (Pterosauria: Ornithocheiroidea) from the Lower Cretaceous of Wuerho, China

description: Ornithocheiroidea was a globally diverse group of pterosaurs during the Cretaceous. However, well-documented ornithocheiroids are highly derived, hampering our understanding on the morphological evolution of this clade. <i>Dsungaripterus weii</i> Young, 1964 from the Lower Cretaceous Tugulu Group (Valanginian) of the Junggar Basin is an iconic early member of Ornithocheiroidea. <i>Dsungaripterus</i> is known from numerous three-dimensionally preserved specimens, ranging from isolated bones to partially articulated individuals. Here we provide a comprehensive description of the postcranium of <i>Dsungaripterus</i>. We find that <i>Dsungaripterus</i> has many autapomorphies in the postcranial skeleton parallelling its unique skull, including the asynchronous fusion between the sacrum and pelvis and a posterodorsal fossa of the humerus with a paper-thin bone wall. <i>Dsungaripterus</i> also displays some plesiomorphic features of Ornithoecheiroidea, for example, limb bones with relatively thick bone walls, variably reduced pneumatic features in cervical vertebrae and appendicular skeletons, absence of spinoprezygapophyseal and spinopostzygapophyseal ridges in middle-series cervical vertebrae, at least one metacarpal articulating with the distal syncarpal, and a distally displaced adductor ridge on the femur. Additionally, <i>Dsungaripterus</i> possesses some unexpected features possibly convergent with other members of Ornithocheiroidea. Although the postcranial skeletons of <i>Dsungaripterus</i> are represented by osteologically mature specimens, notable morphological variation is present. Functional reconstructions of several aspects of the postcranial skeleton of <i>Dsungaripterus</i> are elucidated, including the arrangement of the metacarpophalangeal region during terrestrial locomotion. Niche partitioning between the two dsungaripterids from the Tugulu Group of Wuerho, <i>Dsungaripterus</i> and <i>Noripterus</i>, is supported by their distinct dentitions, neck morphology, and limb proportions.
DOI: 10.6084/m9.figshare.27330919
title: A platypterygiid ichthyosaur from the Cenomanian of central New Zealand

description: Understanding of Cretaceous ichthyosaur diversity has substantially increased in recent years; however, Eastern Gondwana’s ichthyosaur fauna is still poorly understood, particularly in New Zealand where only scarce fragmentary material is known. A Cenomanian-aged partial ichthyosaur skeleton has been recovered from the northeastern South Island of New Zealand and is described here. Whilst the specimen is too fragmentary to formally name, this taxon shows an extreme reduction of the basioccipital extracondylar area, a scapula with a prominent acromion process and a strap-like scapula shaft, as well as a complete left pelvic girdle with an elongated depression on the anteroproximal face of the ischiopubis. We suggest that it is a late branching member of the platypterygiid ichthyosaurs, closely related to the Eastern Gondwanan ichthyosaur <i>Platypterygius australis</i> and to many European Cretaceous taxa. However, it appears to be unrelated to the Cretaceous ichthyosaurs of Western Gondwana, suggesting potential regionalism amongst the Gondwanan Cretaceous ichthyosaur populations.
DOI: 10.6084/m9.figshare.27330919.v2
title: A platypterygiid ichthyosaur from the Cenomanian of central New Zealand

description: Understanding of Cretaceous ichthyosaur diversity has substantially increased in recent years; however, Eastern Gondwana’s ichthyosaur fauna is still poorly understood, particularly in New Zealand where only scarce fragmentary material is known. A Cenomanian-aged partial ichthyosaur skeleton has been recovered from the northeastern South Island of New Zealand and is described here. Whilst the specimen is too fragmentary to formally name, this taxon shows an extreme reduction of the basioccipital extracondylar area, a scapula with a prominent acromion process and a strap-like scapula shaft, as well as a complete left pelvic girdle with an elongated depression on the anteroproximal face of the ischiopubis. We suggest that it is a late branching member of the platypterygiid ichthyosaurs, closely related to the Eastern Gondwanan ichthyosaur <i>Platypterygius australis</i> and to many European Cretaceous taxa. However, it appears to be unrelated to the Cretaceous ichthyosaurs of Western Gondwana, suggesting potential regionalism amongst the Gondwanan Cretaceous ichthyosaur populations.
DOI: 10.6084/m9.figshare.27330919.v1
title: A platypterygiid ichthyosaur from the Cenomanian of central New Zealand

description: Understanding of Cretaceous ichthyosaur diversity has substantially increased in recent years; however, Eastern Gondwana’s ichthyosaur fauna is still poorly understood, particularly in New Zealand where only scarce fragmentary material is known. A Cenomanian-aged partial ichthyosaur skeleton has been recovered from the northeastern South Island of New Zealand and is described here. Whilst the specimen is too fragmentary to formally name, this taxon shows an extreme reduction of the basioccipital extracondylar area, a scapula with a prominent acromion process and a strap-like scapula shaft, as well as a complete left pelvic girdle with an elongated depression on the anteroproximal face of the ischiopubis. We suggest that it is a late branching member of the platypterygiid ichthyosaurs, closely related to the Eastern Gondwanan ichthyosaur <i>Platypterygius australis</i> and to many European Cretaceous taxa. However, it appears to be unrelated to the Cretaceous ichthyosaurs of Western Gondwana, suggesting potential regionalism amongst the Gondwanan Cretaceous ichthyosaur populations.
DOI: 10.6084/m9.figshare.27612136
title: <i>Romaleodelphis pollerspoecki</i>, gen. et sp. nov., an archaic dolphin from the Central Paratethys (Early Miocene, Austria)

description: A new long-snouted homodont odontocete fossil from the Lower Miocene of Austria (ca. 22.5–22.0 Ma) is formally described and interpreted based on external skull characteristics supplemented by CT and µCT data. The specimen was found in deposits from the Central Paratethys and includes an incomplete and fragmented cranium and mandible as well as ear bones. It differs markedly from previously identified long-snouted archaic dolphins with single-rooted, homodont dentition, and thus is suggestive of a new taxon, for which the name <i>Romaleodelphis pollerspoecki</i> proposed. The geological context of <i>R. pollerspoecki</i> hints at a neritic habitat in close vicinity to estuarine environments. <i>Romaleodelphis pollerspoecki</i> shares key features with certain members of the so-called ‘<i>Chilcacetus</i> clade’ such as the widening of the premaxillae at the rostrum base and the absence of a deep lateral groove along the rostrum; however, a phylogenetic analysis reconstructs <i>R. pollerspoecki</i> in a polytomy with members of this ‘clade’ and a larger clade including many other taxa. To better understand the phylogenetic relationships of these taxa, comprehensive reexamination of <i>Argryocetus</i> and <i>Macrodelphinus</i> will be necessary. Measurements obtained through µCT-based internal anatomical reconstruction of the bony labyrinth indicate that <i>R. pollerspoecki</i> had the ability to hear specialized high-frequency signals similar to modern narrow-band high-frequency (NBHF) specialists. This work further identifies several extinct platanistoids as hearing within the NBHF spectrum, increasing the understanding of the diversity of ecological adaptations in early-diverging odontocetes and providing more examples of convergent evolution of this hearing type.
DOI: 10.5281/zenodo.10973626
title: Script and data from: The best of two worlds: toward large-scale monitoring of biodiversity combining metabarcoding and optimised parataxonomic validation.

description: Publication abstract 




In a context of unprecedented biodiversity decline, there is a critical need for reliable monitoring tools to measure species diversity and their dynamic at large scales. DNA-based identification methods, e.g. metabarcoding, were proposed as an effective way to reach this aim. However, metabarcoding suffers from intrinsic limitations (e.g. false positive and false negative species identifications) that are difficult to quantify in the field, and do not allow the estimation of species abundance.  To overcome these obstacles, we propose the Human-Assisted Molecular Identification (HAMI) framework, based on a combination of metabarcoding and image-based parataxonomic validation of outputs and recording of abundance data. This approach was tested on beetles from a national biodiversity monitoring initiative. We assessed the advantages of using HAMI over the exclusive use of a metabarcoding approach by examining 491 samples. We show that an average of 23% of the specific composition is missed when relying exclusively on metabarcoding, this percent being consistently higher in the most species-rich samples. In addition, on average 20% of the species composition identified by molecular-only approaches correspond to false positives linked to cross-sample contaminations or mis-identified barcode sequences in databases. The combination of molecular methodologies and parataxonomic validation in HAMI significantly reduces metabarcoding’s intrinsic bias and recovers reliable abundance data. This approach also enabling users to engage in a virtuous circle of database improvement through the identification of specimens associated with missing barcodes or barcodes with erroneous assignations. As such, HAMI fills an important gap in large-scale biodiversity monitoring by providing appropriate data.



File description: 

MiSeq raw sequences of the COI barcode from 491 Coleoptera field samples :

The Raw_sequencage_data ZIP directory contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Coleoptera field samples in duplicate using the MiSeq platform GenSeq (ISEM - University of Montpellier)

 

The HAMI_data_script_results_R zip directory contains Rmarkdown script files (.Rmd and .html)  and associated data used to analyse the systemic errors of the metabarcoding approach (N= 491 Coleoptera field samples).

 

The HAMI_pipeline zip directory contains all the codes associated with the HAMI pipeline, as well as a ReadMe file and a test data set.
DOI: 10.5281/zenodo.12733191
title: Script and data from: The best of two worlds: toward large-scale monitoring of biodiversity combining metabarcoding and optimised parataxonomic validation.

description: Publication abstract 




In a context of unprecedented biodiversity decline, there is a critical need for reliable monitoring tools to measure species diversity and their dynamic at large scales. DNA-based identification methods, e.g. metabarcoding, were proposed as an effective way to reach this aim. However, metabarcoding suffers from intrinsic limitations (e.g. false positive and false negative species identifications) that are difficult to quantify in the field, and do not allow the estimation of species abundance.  To overcome these obstacles, we propose the Human-Assisted Molecular Identification (HAMI) framework, based on a combination of metabarcoding and image-based parataxonomic validation of outputs and recording of abundance data. This approach was tested on beetles from a national biodiversity monitoring initiative. We assessed the advantages of using HAMI over the exclusive use of a metabarcoding approach by examining 491 samples. We show that an average of 23% of the specific composition is missed when relying exclusively on metabarcoding, this percent being consistently higher in the most species-rich samples. In addition, on average 20% of the species composition identified by molecular-only approaches correspond to false positives linked to cross-sample contaminations or mis-identified barcode sequences in databases. The combination of molecular methodologies and parataxonomic validation in HAMI significantly reduces metabarcoding’s intrinsic bias and recovers reliable abundance data. This approach also enabling users to engage in a virtuous circle of database improvement through the identification of specimens associated with missing barcodes or barcodes with erroneous assignations. As such, HAMI fills an important gap in large-scale biodiversity monitoring by providing appropriate data.



File description: 

MiSeq raw sequences of the COI barcode from 491 Coleoptera field samples :

The Raw_sequencage_data ZIP directory contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Coleoptera field samples in duplicate using the MiSeq platform GenSeq (ISEM - University of Montpellier)

 

The HAMI_data_script_results_R zip directory contains Rmarkdown script files (.Rmd and .html)  and associated data used to analyse the systemic errors of the metabarcoding approach (N= 491 Coleoptera field samples).

 

The HAMI_pipeline zip directory contains all the codes associated with the HAMI pipeline, as well as a ReadMe file and a test data set.

 

The Residual_chimera.zip directory contains lists of residual chimeric sequences that were not filtered using FROGS pipeline but secondarily detected with the de novo approach implemented in HAMI pipeline with ‘isBimeraDenovo’ R function from DADA2 v1.28.0.  It contains two distinct files according to the two sequencing runs.