cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27223616.v1
title: Integrative taxonomy of <i>Tethya</i>: description of four new species based on morphology, phylogeny and microbiome diversity

description: The genus <i>Tethya</i>, one of the most iconic groups in the phylum Porifera. includes nearly 100 valid species. <i>Tethya</i> shows a nearly cosmopolitan distribution, and thus this clade could help elucidate global mechanisms of speciation in sponges. Contrasting with many other marine organisms, <i>Tethya</i> peaks in diversity in the temperate region, with only ∼30% of diversity occurring in the tropics. This pattern may however be related to a lack of studies in the tropics, masked by dubious taxonomic identifications. To address this question, we studied new collections from the Western Atlantic (Caribbean and Brazil) and the Northeastern Atlantic, as well as museum material from the Indian Ocean. Combining morphological investigation with molecular phylogenetics and the study of the sponge’s microbial communities, we conclude that four constitute new species that we describe here: <i>Tethya martini</i> Riesgo, Giribet, & Santodomingo, sp. nov.; <i>Tethya simoni</i> Santodomingo, Zea, & Riesgo, sp. nov.; <i>Tethya erici</i> Díez-Vives, Santodomingo, Moles, & Riesgo, sp. nov.; <i>Tethya orioni</i> Kenny, Santodomingo & Riesgo, sp. nov. Some species thought to be widespread (e.g., <i>T. aurantium</i> and <i>T. seychellensis</i>), each represent multiple species with unique geographic distributions. A phylogenetic analysis of <i>Tethya</i> (based on COI and 28S rRNA sequence data) recovered five main clades, which were also characterized by distinct prokaryotic communities. This suggests that microbiomes could be used as a guide for taxonomic identification in <i>Tethya</i>. We finally explored the existence of a phylosymbiotic pattern in sponges at different levels of prokaryotic taxonomic resolution (i.e., at phylum, class, and genus-level analysis of prokaryotes). Remarkably, our analysis revealed high levels of coevolution of <i>Tethya</i> and their associated microbial communities, even when microbiomes were analysed at the genus level. Our findings support the use of an integrative approach to better understand the evolutionary history of sponges. http://zoobank.org/urn:lsid:zoobank.org:pub:54F80E5E-99A4-43CE-BA3A-BCD01E715595
DOI: 10.6084/m9.figshare.27917312
title: A new large predator (Amphipoda, Eusiridae) hidden at hadal depths of the Atacama Trench

description: The deep ocean is a vast reservoir of new species to science, and each discovery improves our ecological understanding of these remote ecosystems. One island-like ecosystem is the Atacama Trench (Southeast Pacific Ocean), where the hadal depths (&gt;6000 m) host a distinctive endemic community. Unlike the communities of other hadal subduction trenches, predatory (non-scavenging) amphipods have not been documented or collected from the Atacama Trench. In this study, we applied an integrative taxonomic approach to describe a new predatory amphipod in the Eusiridae Stebbing, 1888 family collected from 7902 m during the 2023 IDOOS Expedition and provide an updated global Eusiridae key with the 14th genus. Morphology and DNA barcoding robustly supported raising a new genus separate from the systematically similar genera <i>Dorotea. Dulcibella camanchaca</i> gen. nov. sp. nov. is a large amphipod (holotype: 38.9 mm length) with diagnostic features that include: a smooth dorsal body, 12 spines on the outer maxilla 1 plate, subsimilar and strongly subchelate gnathopods with broad carpus lobes, the pereopods 3 and 4 dactyli are 0.45× of the respective propodus and pereopods 5 to 7 dactyli are 0.6×, a distal spiniform process on the peduncle of uropod 1, and an elongated but weakly cleft telson. Together, <i>Dulcibella camanchaca</i> gen. nov. sp. nov. is a novel predator and reinforces the eco-evolutionary distinctiveness of the Atacama Trench. http://zoobank.org/urn:lsid:zoobank.org:pub:95A6C497-AC8E-4C24-B451-C4B7F76CE687
DOI: 10.15468/dl.pnagu8
title: Occurrence Download

description: A dataset containing 2430 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Batrachoseps gavilanensis Jockusch, Yanev & Wake, 2001)"
 ]
}

 The dataset includes 2430 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039622-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/9ss-364-gta
title: Baseodiscus delineatus (Delle Chiaje, 1822)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.27304687
title: Disentangling disjunctus: an integrated analysis of the patent leather beetle, <i>Odontotaenius disjunctus</i> complex (Passalidae: Coleoptera) with the description of two new species

description: The categorical rank of species is the fundamental taxonomic unit in characterizing biodiversity, and the accurate identification of species-level lineages is vital to all fields of biological research. This is particularly true for conservation biology, where state and federal agencies make conservation assessments based on recognized species’ distribution, ecology, and demography. Currently, there are two species of bess beetle in the conterminous United States, <i>Odontotaenius flordianus</i> (Schuster) and <i>O. disjunctus</i> (Illeger). Phylogeographic studies have proposed that <i>O. disjunctus</i> may represent a species complex harboring cryptic diversity. This study combines multi-locus species delimitation methods and multivariate analyses of morphological characters used to distinguish <i>O. floridanus</i>, to assess species diversity within the <i>O. disjunctus</i> complex. Delimitation methods inferred four well-supported species that diverged during the Pleistocene and whose formation was driven by historical isolation associated with shifting climatic conditions. We found a correlation between increased morphological differentiation and time since divergence. We described two new species, <i>Odontotaenius jackmanicus</i> sp. nov., based on morphological and molecular characters, and the cryptic species, <i>Odontotaenius cryptodisjunctus</i> sp. nov., diagnosed exclusively on molecular characters. We propose that the morphological similarities between <i>O. disjunctus</i> and <i>O. cryptodisjunctus</i> are due to a recent speciation combined with morphological conservatism and evolutionary stasis.
DOI: 10.6084/m9.figshare.27304687.v1
title: Disentangling disjunctus: an integrated analysis of the patent leather beetle, <i>Odontotaenius disjunctus</i> complex (Passalidae: Coleoptera) with the description of two new species

description: The categorical rank of species is the fundamental taxonomic unit in characterizing biodiversity, and the accurate identification of species-level lineages is vital to all fields of biological research. This is particularly true for conservation biology, where state and federal agencies make conservation assessments based on recognized species’ distribution, ecology, and demography. Currently, there are two species of bess beetle in the conterminous United States, <i>Odontotaenius flordianus</i> (Schuster) and <i>O. disjunctus</i> (Illeger). Phylogeographic studies have proposed that <i>O. disjunctus</i> may represent a species complex harboring cryptic diversity. This study combines multi-locus species delimitation methods and multivariate analyses of morphological characters used to distinguish <i>O. floridanus</i>, to assess species diversity within the <i>O. disjunctus</i> complex. Delimitation methods inferred four well-supported species that diverged during the Pleistocene and whose formation was driven by historical isolation associated with shifting climatic conditions. We found a correlation between increased morphological differentiation and time since divergence. We described two new species, <i>Odontotaenius jackmanicus</i> sp. nov., based on morphological and molecular characters, and the cryptic species, <i>Odontotaenius cryptodisjunctus</i> sp. nov., diagnosed exclusively on molecular characters. We propose that the morphological similarities between <i>O. disjunctus</i> and <i>O. cryptodisjunctus</i> are due to a recent speciation combined with morphological conservatism and evolutionary stasis.
DOI: 10.6084/m9.figshare.27917312.v2
title: A new large predator (Amphipoda, Eusiridae) hidden at hadal depths of the Atacama Trench

description: The deep ocean is a vast reservoir of new species to science, and each discovery improves our ecological understanding of these remote ecosystems. One island-like ecosystem is the Atacama Trench (Southeast Pacific Ocean), where the hadal depths (&gt;6000 m) host a distinctive endemic community. Unlike the communities of other hadal subduction trenches, predatory (non-scavenging) amphipods have not been documented or collected from the Atacama Trench. In this study, we applied an integrative taxonomic approach to describe a new predatory amphipod in the Eusiridae Stebbing, 1888 family collected from 7902 m during the 2023 IDOOS Expedition and provide an updated global Eusiridae key with the 14th genus. Morphology and DNA barcoding robustly supported raising a new genus separate from the systematically similar genera <i>Dorotea. Dulcibella camanchaca</i> gen. nov. sp. nov. is a large amphipod (holotype: 38.9 mm length) with diagnostic features that include: a smooth dorsal body, 12 spines on the outer maxilla 1 plate, subsimilar and strongly subchelate gnathopods with broad carpus lobes, the pereopods 3 and 4 dactyli are 0.45× of the respective propodus and pereopods 5 to 7 dactyli are 0.6×, a distal spiniform process on the peduncle of uropod 1, and an elongated but weakly cleft telson. Together, <i>Dulcibella camanchaca</i> gen. nov. sp. nov. is a novel predator and reinforces the eco-evolutionary distinctiveness of the Atacama Trench. http://zoobank.org/urn:lsid:zoobank.org:pub:95A6C497-AC8E-4C24-B451-C4B7F76CE687
DOI: 10.3535/1pr-h4m-lhw
title: Girardia tigrina (Girard, 1850)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/412-n5x-19b
title: Girardia tigrina (Girard, 1850)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.25605191
title: Molecular phylogeny and biogeography of the dwarf boas of the family Tropidophiidae (Serpentes: Alethinophidia)

description: Although present in the South American continent, dwarf boas (Tropidophiidae) show their greatest extant diversification in the Caribbean region, reaching their highest diversity in Cuba. Despite their remarkable species richness, phylogenetic affinities among species of <i>Tropidophis</i> and <i>Trachyboa</i> are still poorly known. Here, we provide a multi-locus phylogenetic hypothesis of the family that includes 25 of the 37 known continental and insular species, including most of its highly diverse Cuban endemic radiation (16 out of 17 species sampled). We also provide a time-calibrated tree derived from our molecular data. Our phylogenetic results indicate that the genus <i>Tropidophis</i> and its mainland and Cuban radiations are paraphyletic, while the Caribbean radiation forms a well-supported clade. We therefore synonymize <i>Trachyboa</i> with <i>Tropidophis</i> and provide new definitions for the species groups. Our time-calibrated tree suggests that tropidophiids originated along the northwestern Andean region of continental South America, diverging from its known sister-group genus <i>Anilius</i> during the late Cretaceous. The Atlantic Rainforest radiation diverged from the Andean radiation during the late Eocene. A mainland tropidophiid ancestor subsequently dispersed from northern South America to the Caribbean region in the latest Eocene. Dispersal likely took place through a near-continuous terrestrial land bridge that connected South America to the Greater Antilles during the late Eocene to early Oligocene (35–33 Ma). The existence of this land bridge, whether formed by the Aves Ridge (GAARlandia Hypothesis) or by a more southernly positioned landmass connecting the Greater Antilles and the northern Lesser Antilles Ridge (GRANoLA hypothesis), remains a topic of debate, which we address in this paper. After that main dispersal event, West Indian tropidophiids underwent over ten speciation events, rapidly colonizing the Caribbean islands. We also address the vertebral morphology of fossil and extant Tropidophiidae, with our observations challenging the current classification of several fossil taxa within crown-Tropidophiidae.
DOI: 10.6084/m9.figshare.25605191.v1
title: Molecular phylogeny and biogeography of the dwarf boas of the family Tropidophiidae (Serpentes: Alethinophidia)

description: Although present in the South American continent, dwarf boas (Tropidophiidae) show their greatest extant diversification in the Caribbean region, reaching their highest diversity in Cuba. Despite their remarkable species richness, phylogenetic affinities among species of <i>Tropidophis</i> and <i>Trachyboa</i> are still poorly known. Here, we provide a multi-locus phylogenetic hypothesis of the family that includes 25 of the 37 known continental and insular species, including most of its highly diverse Cuban endemic radiation (16 out of 17 species sampled). We also provide a time-calibrated tree derived from our molecular data. Our phylogenetic results indicate that the genus <i>Tropidophis</i> and its mainland and Cuban radiations are paraphyletic, while the Caribbean radiation forms a well-supported clade. We therefore synonymize <i>Trachyboa</i> with <i>Tropidophis</i> and provide new definitions for the species groups. Our time-calibrated tree suggests that tropidophiids originated along the northwestern Andean region of continental South America, diverging from its known sister-group genus <i>Anilius</i> during the late Cretaceous. The Atlantic Rainforest radiation diverged from the Andean radiation during the late Eocene. A mainland tropidophiid ancestor subsequently dispersed from northern South America to the Caribbean region in the latest Eocene. Dispersal likely took place through a near-continuous terrestrial land bridge that connected South America to the Greater Antilles during the late Eocene to early Oligocene (35–33 Ma). The existence of this land bridge, whether formed by the Aves Ridge (GAARlandia Hypothesis) or by a more southernly positioned landmass connecting the Greater Antilles and the northern Lesser Antilles Ridge (GRANoLA hypothesis), remains a topic of debate, which we address in this paper. After that main dispersal event, West Indian tropidophiids underwent over ten speciation events, rapidly colonizing the Caribbean islands. We also address the vertebral morphology of fossil and extant Tropidophiidae, with our observations challenging the current classification of several fossil taxa within crown-Tropidophiidae.
DOI: 10.6084/m9.figshare.27917312.v1
title: A new large predator (Amphipoda, Eusiridae) hidden at hadal depths of the Atacama Trench

description: The deep ocean is a vast reservoir of new species to science, and each discovery improves our ecological understanding of these remote ecosystems. One island-like ecosystem is the Atacama Trench (Southeast Pacific Ocean), where the hadal depths (&gt;6000 m) host a distinctive endemic community. Unlike the communities of other hadal subduction trenches, predatory (non-scavenging) amphipods have not been documented or collected from the Atacama Trench. In this study, we applied an integrative taxonomic approach to describe a new predatory amphipod in the Eusiridae Stebbing, 1888 family collected from 7902 m during the 2023 IDOOS Expedition and provide an updated global Eusiridae key with the 14th genus. Morphology and DNA barcoding robustly supported raising a new genus separate from the systematically similar genera <i>Dorotea. Dulcinea camanchaca</i> gen. nov. sp. nov. is a large amphipod (holotype: 38.9 mm length) with diagnostic features that include: a smooth dorsal body, 12 spines on the outer maxilla 1 plate, subsimilar and strongly subchelate gnathopods with broad carpus lobes, the pereopods 3 and 4 dactyli are 0.45× of the respective propodus and pereopods 5 to 7 dactyli are 0.6×, a distal spiniform process on the peduncle of uropod 1, and an elongated but weakly cleft telson. Together, <i>Dulcinea camanchaca</i> gen. nov. sp. nov. is a novel predator and reinforces the eco-evolutionary distinctiveness of the Atacama Trench. http://zoobank.org/urn:lsid:zoobank.org:pub:95A6C497-AC8E-4C24-B451-C4B7F76CE687
DOI: 10.3535/aph-nnd-0fs
title: Hymenolepididae Ariola, 1899

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yt6-3s3-c3j
title: Tubulanus polymorphus Renier, 1804

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5517/ccdc.csd.cc2l9g0d
title: CCDC 2392363: Experimental Crystal Structure Determination

description: Related Article: Wei-Dong Liu, Han Xu, Chong-Yang Li, La-Sheng Long, Lan-Sun Zheng, Xiang-Jian Kong|2025|Inorg.Chem.Front.|12|253|doi:10.1039/D4QI02645D
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/d6r-lve-917
title: Pseudosagitta lyra (Krohn, 1853)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0yw-vb5-42d
title: Tubificoides heterochaetus (Michaelsen, 1926)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ey5-hxe-mz3
title: Scoloplos armiger (Müller, 1776)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/te7-8gt-7jb
title: Ostertagia (Ostertagia) mossi Dikmans, 1931

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xdm-qy6-k05
title: Spiculopteragia spiculoptera (Guschanskaja, 1931) Orloff, 1933

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zxg-770-tj7
title: Helobdella

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6vs-7z3-903
title: Filograna Berkeley, 1835

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tw7-5a5-0cs
title: Alitta succinea (Leuckart, 1847)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3938722_d2.v1
title: MOESM2 of Automated growth rate determination in high-throughput microbioreactor systems

description: Additional file 2. MATLAB live script executing all steps for automated growth rate calculation as annotated working example.
DOI: 10.3535/4b9-tjp-r00
title: Glossobalanus crozieri van der Horst, 1924

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3938722_d2
title: MOESM2 of Automated growth rate determination in high-throughput microbioreactor systems

description: Additional file 2. MATLAB live script executing all steps for automated growth rate calculation as annotated working example.
DOI: 10.3535/7sw-ybv-fpy
title: Tubulanus polymorphus Renier, 1804

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ale-5m4-mrg
title: Spiculopteragia spiculoptera (Guschanskaja, 1931) Orloff, 1933

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3938728_d1
title: Additional file 10: of A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa

description: List of MSU-RGAP genes that are not in the MAKER six HMMs annotation, functional descriptions and the lengths of the genes and their CDSes. (XLSX 221Â kb)
DOI: 10.6084/m9.figshare.c.3938728_d1.v1
title: Additional file 10: of A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa

description: List of MSU-RGAP genes that are not in the MAKER six HMMs annotation, functional descriptions and the lengths of the genes and their CDSes. (XLSX 221Â kb)
DOI: 10.3535/pwt-6lx-56k
title: Girardia Ball, 1974

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xp2-h33-dc7
title: Distomum Diesing, 1850

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jj8-4lm-f30
title: Diversibipalium Kawakatsu, Ogren, Froehlich & Sasaki, 2002

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tns-r54-nyn
title: Nephtys cirrosa Ehlers, 1868

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3938710_d3.v1
title: Additional file 3: of The gut mycobiome of the Human Microbiome Project healthy cohort

description: Fungi in metagenomic sequences. Description â   Table S2: Complete list of fungi found in metagenomic sequencing data. Table S3: Fungal reads found in metagenomic sequencing data. (XLSX 6137Â kb)
DOI: 10.3535/4xq-4zg-gkf
title: Phascolosoma (Phascolosoma) puntarenae Grübe & Oersted, 1858

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v4n-wcd-gev
title: Girardia Ball, 1974

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3938710_d3
title: Additional file 3: of The gut mycobiome of the Human Microbiome Project healthy cohort

description: Fungi in metagenomic sequences. Description â   Table S2: Complete list of fungi found in metagenomic sequencing data. Table S3: Fungal reads found in metagenomic sequencing data. (XLSX 6137Â kb)
DOI: 10.3535/len-9cx-584
title: Pseudosagitta lyra (Krohn, 1853)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0rf-ljj-gzq
title: Scoloplos armiger (Müller, 1776)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pet-bnm-4gk
title: Scoloplos armiger (Müller, 1776)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3938716_d3.v1
title: Additional file 3: Table S7. of Association of variation in the sugarcane transcriptome with sugar content

description: List of DEGs in the SUGIT, HST VS HSB. Table S8 List of DEGs in the SUGIT, LST VS LSB. Table S9 List of DEGs in the SUGIT, HST VS HSB. (XLSX 3817Â kb)
DOI: 10.3535/4ql-yjw-vwv
title: Octochaetidae Michaelsen, 1900

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d27-7rk-866
title: Ptychodera bahamensis Spengel, 1893

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3938716_d3
title: Additional file 3: Table S7. of Association of variation in the sugarcane transcriptome with sugar content

description: List of DEGs in the SUGIT, HST VS HSB. Table S8 List of DEGs in the SUGIT, LST VS LSB. Table S9 List of DEGs in the SUGIT, HST VS HSB. (XLSX 3817Â kb)