cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3938536_d4.v1
title: Additional file 4: Table S4. of Genome-wide segregation of single nucleotide and structural variants into single cancer cells

description: List of Amplicon Primers used in Resequencing. This file provides a list of the primers used for interrogating the bulk and single cell samples for single-nucleotide and structural variants. (XLSX 57Â kb)
DOI: 10.3535/4zk-4mg-evw
title: Rhabdias ranae Walton, 1929

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cq8-hsw-raf
title: Valencinia longirostris Quatrefages, 1846

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5517/ccdc.csd.cc2jrpll
title: CCDC 2346470: Experimental Crystal Structure Determination

description: Related Article: Jieli Lin, Shihua Liu, Shunlin Zheng, Hansjörg Grützmacher, Cheng-Yong Su, Zhongshu Li|2024|Chemical Science|15|20030|doi:10.1039/D4SC06462C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.c.3938536_d4
title: Additional file 4: Table S4. of Genome-wide segregation of single nucleotide and structural variants into single cancer cells

description: List of Amplicon Primers used in Resequencing. This file provides a list of the primers used for interrogating the bulk and single cell samples for single-nucleotide and structural variants. (XLSX 57Â kb)
DOI: 10.3535/5az-2tl-5w9
title: Anoplocephalidae Cholodkovsky, 1902

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q4t-hj5-dbl
title: Serratosagitta serratodentata (Krohn, 1853)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ah6-1k6-f5p
title: Acanthocephalus Koelreuter, 1771

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/k74-qeq-w02
title: Dugesia japonica Ichikawa & Kawakatsu, 1964

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cg6-60d-2el
title: Phyllodoce maculata (Linnaeus, 1767)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rm1-hn5-ler
title: Dugesia japonica Ichikawa & Kawakatsu, 1964

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xvq-vec-2a5
title: Labiosthenolepis sibogae (Horst, 1917)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5517/ccdc.csd.cc2k4n7m
title: CCDC 2357960: Experimental Crystal Structure Determination

description: Related Article: haotian  Gao|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.25152483
title: A hint on the unknown diversity of eastern Andes: high endemicity and new species of mammals revealed through DNA barcoding

description: The eastern Andean slopes harbours a diverse fauna with multiple endemic and endangered species. The region is identified as a biodiversity hotspot with high conservation priority. However, it remains one of the least studied in South America regarding the diversity of mammals. Here we present new data on the diversity of non-volant small mammals (marsupials and rodents) from Parque Nacional del Río Abiseo (PNRA), a poorly known, remote site located in the eastern Andean slopes in central-northern Peru. We sequenced the mitochondrial gene cytochrome b to provide identification of the collected specimens, and to discuss zoogeographic patterns of the species from PNRA and closely related taxa. In 15 days of sampling at PRNA we registered 16 species (12 rodents, 4 marsupials) on montane forests between 2500 and 2800 m above sea level (asl). Combined with results from previous surveys, the diversity of non-volant small mammals at PNRA (23 species) is the highest ever recorded for high Andes. Remarkably, only four of the 16 species recorded in our expedition could be assigned to described species based on molecular identification. The remaining 12 species need urgent taxonomic attention, several of which are potentially new to science. Moreover, 11 of the 16 species (69%) registered are currently unknown from other sites, suggesting a large beta diversity. A combination of exceptional levels of endemism in Andean montane forests and an obvious sampling bias resultant of the lack of comprehensive surveys explain the high number of ‘unique’ species at PNRA. Our phylogenetic analyses suggest that the non-volant small mammals from PNRA seem to have diverse phylogeographic affinities, with a closer proximity with central Andes. The scarcity of sequenced samples for comparative analyses from multiple Andean sites is, however, a major barrier to the development of accurate historical reconstructions for these endemic faunas.
DOI: 10.6084/m9.figshare.25152483.v1
title: A hint on the unknown diversity of eastern Andes: high endemicity and new species of mammals revealed through DNA barcoding

description: The eastern Andean slopes harbours a diverse fauna with multiple endemic and endangered species. The region is identified as a biodiversity hotspot with high conservation priority. However, it remains one of the least studied in South America regarding the diversity of mammals. Here we present new data on the diversity of non-volant small mammals (marsupials and rodents) from Parque Nacional del Río Abiseo (PNRA), a poorly known, remote site located in the eastern Andean slopes in central-northern Peru. We sequenced the mitochondrial gene cytochrome b to provide identification of the collected specimens, and to discuss zoogeographic patterns of the species from PNRA and closely related taxa. In 15 days of sampling at PRNA we registered 16 species (12 rodents, 4 marsupials) on montane forests between 2500 and 2800 m above sea level (asl). Combined with results from previous surveys, the diversity of non-volant small mammals at PNRA (23 species) is the highest ever recorded for high Andes. Remarkably, only four of the 16 species recorded in our expedition could be assigned to described species based on molecular identification. The remaining 12 species need urgent taxonomic attention, several of which are potentially new to science. Moreover, 11 of the 16 species (69%) registered are currently unknown from other sites, suggesting a large beta diversity. A combination of exceptional levels of endemism in Andean montane forests and an obvious sampling bias resultant of the lack of comprehensive surveys explain the high number of ‘unique’ species at PNRA. Our phylogenetic analyses suggest that the non-volant small mammals from PNRA seem to have diverse phylogeographic affinities, with a closer proximity with central Andes. The scarcity of sequenced samples for comparative analyses from multiple Andean sites is, however, a major barrier to the development of accurate historical reconstructions for these endemic faunas.
DOI: 10.3535/129-zhb-jl7
title: Spiculopteragia spiculoptera (Guschanskaja, 1931) Orloff, 1933

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5517/ccdc.csd.cc2k6fx4
title: CCDC 2359686: Experimental Crystal Structure Determination

description: Related Article: Guanlun Zhang, Xu Wu, Shiyu Mao, Mengqi Li, Honglong Hu, Bing-Feng Shi, Wei-Hong Zhu|2024|Chemical Science|15|20013|doi:10.1039/D4SC05375C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/gsk-a5s-yxw
title: Heteromastus filiformis (Claparède, 1864)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.25040248
title: When looks can be deceiving: a new cryptic land planarian species of <i>Choeradoplana</i> Graff, 1896 (Platyhelminthes: Geoplanidae) from Argentina

description: A new species of the genus <i>Choeradoplana</i> found in the east-central region of Argentina is herein described, <i>Choeradoplana malaria</i> sp. nov. This new entity shows a striking similarity regarding the pigment pattern with other land planarian species of this genus, viz. <i>Choeradoplana langi</i>, <i>Choeradoplana gladismariae</i>, and <i>Choeradoplana minima</i>. Besides, the internal anatomy of <i>Ch. malaria</i> sp. nov. is remarkably similar to that of <i>Ch. gladismariae</i>, a species recorded in southeastern Brazil, some 2300 km distant from the new species. Although there are minimal differences in the colour pattern of the dorsum, both species can be differentiated by some anatomical and histological details, such as the thickness of the cutaneous musculature, the width of the creeping sole, and some features related to the reproductive system. This low morphological disparity between both species fits within the term ‘cryptic species’. These subtle differences were also corroborated in a phylogenetic analysis using Cox-1 gene sequences. Likewise, species delimiters reinforced the identity of the new taxon herein proposed and allowed us to differentiate <i>Ch. malaria</i> sp. nov. from <i>Ch. gladismariae</i> at the genetic level. http://zoobank.org/urn:lsid:zoobank.org:pub:DF432618-A85B-4C99-8E64-EC9C581B0714
DOI: 10.6084/m9.figshare.25040248.v1
title: When looks can be deceiving: a new cryptic land planarian species of <i>Choeradoplana</i> Graff, 1896 (Platyhelminthes: Geoplanidae) from Argentina

description: A new species of the genus <i>Choeradoplana</i> found in the east-central region of Argentina is herein described, <i>Choeradoplana malaria</i> sp. nov. This new entity shows a striking similarity regarding the pigment pattern with other land planarian species of this genus, viz. <i>Choeradoplana langi</i>, <i>Choeradoplana gladismariae</i>, and <i>Choeradoplana minima</i>. Besides, the internal anatomy of <i>Ch. malaria</i> sp. nov. is remarkably similar to that of <i>Ch. gladismariae</i>, a species recorded in southeastern Brazil, some 2300 km distant from the new species. Although there are minimal differences in the colour pattern of the dorsum, both species can be differentiated by some anatomical and histological details, such as the thickness of the cutaneous musculature, the width of the creeping sole, and some features related to the reproductive system. This low morphological disparity between both species fits within the term ‘cryptic species’. These subtle differences were also corroborated in a phylogenetic analysis using Cox-1 gene sequences. Likewise, species delimiters reinforced the identity of the new taxon herein proposed and allowed us to differentiate <i>Ch. malaria</i> sp. nov. from <i>Ch. gladismariae</i> at the genetic level. http://zoobank.org/urn:lsid:zoobank.org:pub:DF432618-A85B-4C99-8E64-EC9C581B0714
DOI: 10.6084/m9.figshare.25133769
title: Integrative species delimitation and biogeography of the <i>Rhinella margaritifera</i> species group (Amphibia, Anura, Bufonidae) suggest an intense diversification throughout Amazonia during the last 10 million years

description: The accumulation of studies delimiting species in Amazonia has not only shed light on the patterns of its outstanding species richness but also allowed a better understanding of the processes of diversification within this immense region. Nevertheless, vast knowledge gaps remain even for prominent anuran species complexes, such as the <i>Rhinella margaritifera</i> species group. This clade of toads comprises 23 valid species-level taxa, mainly distributed in Amazonia but also in South America’s Dry Diagonal and Atlantic and trans-Andean rainforests. Species boundaries and taxonomy in this group are notoriously complex, with studies suggesting the existence of several unnamed species. Available phylogenetic information suggests an Andean-western Amazonian origin of the group with subsequent diversification within Amazonian lowlands during the last 10 Myr and secondary dispersals into other Neotropical regions. To further test this biogeographic scenario and improve knowledge on species diversity, we used an unprecedentedly large mtDNA sampling (&gt;800 16S sequences) across the clade’s distribution and comprising all but one described species. We delimited 54 Molecular Operational Taxonomic Units, which we tested further based on patterns of variation of a nuclear locus and acoustic and morphological data. This approach confirmed the existence of at least 25 candidate species, 19 of which correspond to currently recognized taxa whereas 30 remained ‘unconfirmed’. Our results clarify the taxonomic status of some species but also suggest multiple introgression events that blur some mtDNA-based species boundaries. Lastly, to provide a temporal framework for the clade’s diversification, we generated a time-calibrated phylogenetic tree based on a mitogenomic matrix, which confirmed a Miocene (∼9 Ma) western Amazonian origin and six major clades in the group, each having initially diversified in different regions within Amazonia. Most of these clades have later dispersed throughout Amazonia during the establishment of the modern Amazonian hydrographic system, i.e., in the last 6 Myr.
DOI: 10.3535/4q8-dxl-59j
title: Echiurus echiurus (Pallas, 1766)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vl3-6c0-x18
title: Lamellibrachia luymesi van der Land & Nørrevang, 1975

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.25551194
title: Genetics, geography, and subspecies status of American mink in Florida, with an emphasis on <i>Neogale vison evergladensis</i>

description: Historical records of American mink (<i>Neogale vison</i>) in Florida suggest they occur in four populations, each currently recognized as a separate subspecies. The Everglades mink (<i>N. v. evergladensis</i>) is a state-listed threatened subspecies, and the Atlantic salt marsh mink (<i>N. v. lutensis</i>) and Gulf salt marsh mink (<i>N. v. halilimnetes</i>) are both Species of Greatest Conservation Need, but support for their taxonomic status is limited. We acquired 62 samples of mink for genetic analysis using mtDNA and microsatellite data with the objective of assessing the subspecies status of mink in Florida with an emphasis on <i>evergladensis</i>. We also compared historical and current range estimates of mink subspecies in Florida using museum specimens, public sightings, and detection records from scientific studies. All estimates of FST were significant when <i>evergladensis</i> was paired with other subspecies and both assignment tests and the Principal Coordinate Analysis separated <i>evergladensis</i> from other subspecies. The single mtDNA haplotype from <i>evergladensis</i> was not found elsewhere in Florida but was present in a subspecies outside of Florida (<i>vulgivaga</i>). Genetic diversity was lowest in <i>evergladensis</i> and highest for <i>vulgivaga</i> from Louisiana. We found support for <i>lutensis</i> as a separate taxonomic unit and assignment tests found some support for the genetic distinctiveness of <i>halilimnetes</i>. Sample sizes limited analyses in <i>halilimnetes</i> and prevented any conclusions about the subspecies status of mink in the Panhandle. Based on current range estimates, mink from <i>evergladensis</i>, <i>lutensis</i>, and <i>halilimnetes</i> are geographically isolated from one another and supports the genetic analysis. Using a more modern definition of subspecies that includes genetics, distribution, and ecology, we conclude that the data supports multiple subspecies of mink in Florida.
DOI: 10.6084/m9.figshare.25551194.v1
title: Genetics, geography, and subspecies status of American mink in Florida, with an emphasis on <i>Neogale vison evergladensis</i>

description: Historical records of American mink (<i>Neogale vison</i>) in Florida suggest they occur in four populations, each currently recognized as a separate subspecies. The Everglades mink (<i>N. v. evergladensis</i>) is a state-listed threatened subspecies, and the Atlantic salt marsh mink (<i>N. v. lutensis</i>) and Gulf salt marsh mink (<i>N. v. halilimnetes</i>) are both Species of Greatest Conservation Need, but support for their taxonomic status is limited. We acquired 62 samples of mink for genetic analysis using mtDNA and microsatellite data with the objective of assessing the subspecies status of mink in Florida with an emphasis on <i>evergladensis</i>. We also compared historical and current range estimates of mink subspecies in Florida using museum specimens, public sightings, and detection records from scientific studies. All estimates of FST were significant when <i>evergladensis</i> was paired with other subspecies and both assignment tests and the Principal Coordinate Analysis separated <i>evergladensis</i> from other subspecies. The single mtDNA haplotype from <i>evergladensis</i> was not found elsewhere in Florida but was present in a subspecies outside of Florida (<i>vulgivaga</i>). Genetic diversity was lowest in <i>evergladensis</i> and highest for <i>vulgivaga</i> from Louisiana. We found support for <i>lutensis</i> as a separate taxonomic unit and assignment tests found some support for the genetic distinctiveness of <i>halilimnetes</i>. Sample sizes limited analyses in <i>halilimnetes</i> and prevented any conclusions about the subspecies status of mink in the Panhandle. Based on current range estimates, mink from <i>evergladensis</i>, <i>lutensis</i>, and <i>halilimnetes</i> are geographically isolated from one another and supports the genetic analysis. Using a more modern definition of subspecies that includes genetics, distribution, and ecology, we conclude that the data supports multiple subspecies of mink in Florida.
DOI: 10.3535/76p-2vs-6vw
title: Lamellibrachia luymesi van der Land & Nørrevang, 1975

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qzz-nyc-nfc
title: Filogranula exilis Imajima, 1979

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g5f-evm-6qh
title: Sangiria hystrix Horst, 1911

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.26348457
title: When a name changes everything: taxonomy and conservation of the Atlantic bushmaster (<i>Lachesis</i> Daudin, 1803) (Serpentes: Viperidae: Crotalinae)

description: The South American bushmaster <i>Lachesis muta</i> is currently considered a valid taxon with no recognized subspecies. However, its wide distribution with discontinuous populations, the restricted sampling of molecular data in previous studies, and the inherent difficulty in obtaining diagnostic data, preclude a detailed evaluation of the taxonomic status of this taxon. In this study, we use high-resolution genomics, as well as venomic, morphological, and ecological data to infer the speciation processes involved in the evolutionary history of <i>L. muta</i> populations. Our data recognize the Amazon populations as <i>L. muta</i> and the Atlantic Forest populations as <i>L. rhombeata. Lachesis rhombeata</i> has lower genetic diversity than <i>L. muta</i> and we recommend a critical evaluation to include this species in the national and international red lists of endangered species. Moreover, we propose classifying the <i>L. rhombeata</i> population from the Baturité massif (Ceará state) as an evolutionarily significant unit (ESU) for conservation and we also found genetic substructure within <i>L. muta</i> populations. We expect our results will contribute to the taxonomic stability of the Neotropical fauna and highlight the urgency of protecting Atlantic Forest populations of <i>Lachesis</i> species and, consequently, the landscape that this species and related biota inhabit.
DOI: 10.6084/m9.figshare.26348457.v1
title: When a name changes everything: taxonomy and conservation of the Atlantic bushmaster (<i>Lachesis</i> Daudin, 1803) (Serpentes: Viperidae: Crotalinae)

description: The South American bushmaster <i>Lachesis muta</i> is currently considered a valid taxon with no recognized subspecies. However, its wide distribution with discontinuous populations, the restricted sampling of molecular data in previous studies, and the inherent difficulty in obtaining diagnostic data, preclude a detailed evaluation of the taxonomic status of this taxon. In this study, we use high-resolution genomics, as well as venomic, morphological, and ecological data to infer the speciation processes involved in the evolutionary history of <i>L. muta</i> populations. Our data recognize the Amazon populations as <i>L. muta</i> and the Atlantic Forest populations as <i>L. rhombeata. Lachesis rhombeata</i> has lower genetic diversity than <i>L. muta</i> and we recommend a critical evaluation to include this species in the national and international red lists of endangered species. Moreover, we propose classifying the <i>L. rhombeata</i> population from the Baturité massif (Ceará state) as an evolutionarily significant unit (ESU) for conservation and we also found genetic substructure within <i>L. muta</i> populations. We expect our results will contribute to the taxonomic stability of the Neotropical fauna and highlight the urgency of protecting Atlantic Forest populations of <i>Lachesis</i> species and, consequently, the landscape that this species and related biota inhabit.
DOI: 10.6084/m9.figshare.28054860
title: Four freshwater cyrtophorids from the Lake Weishan Wetland, China (Protozoa, Ciliophora): taxonomy, phylogeny, and description of a new species

description: It has long been recognized that ciliates play a crucial role in microbial food webs in all kinds of biotopes. However, basic information about their species diversity, geographic distribution, and ecological function is scant, and molecular data are unavailable for most species. As a new contribution, a comprehensive survey of the diversity of ciliates in the Lake Weishan freshwater Wetland in northern China has recently been undertaken. In the present study, four species of the subclass Cyrtophoria were morphologically investigated including a new one, <i>Phascolodon paravorticella</i> sp. nov., which is characterized by having a body size 40–55 × 25–40 μm, 4 or 5 right and 4–7 left kineties, 20–22 nematodesmal rods, and two diagonally positioned contractile vacuoles. Three known forms, namely <i>Gastronauta aloisi</i>, <i>Trithigmostoma cucullulus</i>, and <i>Trithigmostoma steini</i>, are re-described based on the Lake Weishan Wetland populations. Additionally, phylogenetic analyses based on 18S rRNA gene sequences support the validity of the family Gastronautidae and imply that <i>Trithigmostoma cucullulus</i> contains cryptic species. The phylogenetic relationship between the families Chilodonellidae and Gastronautidae remains uncertain. http://zoobank.org/urn:lsid:zoobank.org:pub:6AF4F5E2-A7F1-4E32-A080-2B6B2435DC2A