cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29040427
title: Integrative systematics of the Brazilian tree “sucupira”: morphological, cytogenetic and genomic boundaries of <i>Pterodon emarginatus</i> Vogel and <i>P. pubescens</i> (Benth.) Benth. (Leguminosae, Papilionoideae)

description: In the genus <i>Pterodon</i> (Leguminosae, Papilionoideae) <i>P. emarginatus</i> and <i>P. pubescens</i> (both known as “sucupira”) exhibit unclear boundaries due to their incomplete isolation barriers and phylogenetic proximity. Both species have a conserved karyotype with 2<i>n</i> = 16, featuring small and morphologically similar chromosomes, and they form hybrids in sympatric areas of distribution in the Neotropical Savanna. Here, we aimed to revisit the systematics of <i>P. emarginatus</i> and <i>P. pubescens</i> based on morphometry of vegetative and reproductive characters, cytogenetics and genome skimming (low coverage Illumina sequencing). The morphometric analysis based on continuous data resulted in unclear distinctiveness between <i>P. emarginatus</i> and <i>P. pubescens</i>. However, the discrete characters of pubescence on leaves and flowers allow us to distinguish these species and individuals with intermediate morphology. The species presented similar genome sizes (1 C = ca. 0.64 pg) and stable karyotypes with two pairs of CMA<sup>+</sup>/DAPI<sup>−</sup> bands/35S rDNA and one pair of 5S rDNA sites. Similarities were also observed in the repetitive genomic fraction (∼25%) with few differences in the retrotransposons (RTs) abundances. The most representative RTs in both species were Ty1/copia-SIRE, Ty3/gypsy-Athila and Ty3/gypsy-Tekay. Remarkably, we found a difference in the 5S rDNA cluster, with the nontranscribed spacer (NTS) regions varying in length and similarity between <i>P. emarginatus</i> and <i>P. pubescens</i>. Six satellite DNAs were found, two of which were exclusive to <i>P. emarginatus</i> and four were shared by both species. <i>In situ</i> hybridization revealed that the most abundant repeats were enriched in proximal CMA<sup>+</sup> heterochromatin in both species, except for the Ty1/copia-Ale retroelement, which was widely dispersed across all <i>P. pubescens</i> chromosomes. Our morphological, cytogenetic and genomic data revealed that <i>Pterodon</i> species boundaries are complex corroborating the evolutionary proximity between these species. We suggest that the cytogenetic and genomic stability found in <i>Pterodon</i> may facilitate the natural interspecific gene flow reported in sympatric populations, complicating the interpretation of morphological traits and the understanding of their systematics and evolution.
DOI: 10.6084/m9.figshare.30784842
title: Diversity and molecular phylogeny of the Indo-West Pacific rock dwelling <i>Smaragdinella</i> snails (Cephalaspidea, Haminoeidae)

description: <i>Smaragdinella</i> A. Adams, 1848 is a genus of marine gastropods belonging to the family Haminoeidae (order Cephalaspidea), confined to tidal zones of the tropical and sub-tropical Indo-West Pacific region. These snails are of special evolutionary interest because they are the only lineage of Cephalaspidea adapted to living directly on hard substrates. However, with only three valid species and 17 nominal names currently recognized, the taxonomy of Haminoeidae is problematic. This study presents the first global phylogenetic analyses of <i>Smaragdinella</i> based on 84 specimens from across the geographic range of the genus using complete mitochondrial genomes and partial nuclear ribosomal complex data (18S rRNA + 28S rRNA). Maximum likelihood, Bayesian inference and species delimitation analyses using the Assemble Species by Automatic Partitioning (ASAP) method, were employed to estimate the number of candidate species and infer their relationships. In addition, morphological analysis of shells and anatomical structures was performed in targeted specimens using dissections and scanning electron microscopy. The results suggest the presence of 13 or 14 candidate species clustering in two main clades largely separated by geography: one comprising Pacific Ocean and Red Sea species, and another consisting of Indian Ocean species. These clades are defined by synapomorphic traits with specimens from the Indian and Pacific clades having unique features of the shell, digestive and reproductive systems.
DOI: 10.6084/m9.figshare.30784842.v2
title: Diversity and molecular phylogeny of the Indo-West Pacific rock dwelling <i>Smaragdinella</i> snails (Cephalaspidea, Haminoeidae)

description: <i>Smaragdinella</i> A. Adams, 1848 is a genus of marine gastropods belonging to the family Haminoeidae (order Cephalaspidea), confined to tidal zones of the tropical and sub-tropical Indo-West Pacific region. These snails are of special evolutionary interest because they are the only lineage of Cephalaspidea adapted to living directly on hard substrates. However, with only three valid species and 17 nominal names currently recognized, the taxonomy of Haminoeidae is problematic. This study presents the first global phylogenetic analyses of <i>Smaragdinella</i> based on 84 specimens from across the geographic range of the genus using complete mitochondrial genomes and partial nuclear ribosomal complex data (18S rRNA + 28S rRNA). Maximum likelihood, Bayesian inference and species delimitation analyses using the Assemble Species by Automatic Partitioning (ASAP) method, were employed to estimate the number of candidate species and infer their relationships. In addition, morphological analysis of shells and anatomical structures was performed in targeted specimens using dissections and scanning electron microscopy. The results suggest the presence of 13 or 14 candidate species clustering in two main clades largely separated by geography: one comprising Pacific Ocean and Red Sea species, and another consisting of Indian Ocean species. These clades are defined by synapomorphic traits with specimens from the Indian and Pacific clades having unique features of the shell, digestive and reproductive systems.
DOI: 10.6084/m9.figshare.30888523.v1
title: Revisiting Chilean gorgonians (Cnidaria: Octocorallia: Gorgoniidae): taxonomic clarification and molecular phylogeny of <i>Leptogorgia chilensis</i> and <i>Phycogorgia fucata</i>

description: Most biodiversity studies of eastern Pacific octocorals have focused on the tropical shallow waters from Mexico to Peru, and more recently, on those off Chile. The first description of a Chilean octocoral dates back to the H.M.S. Challenger expedition (1873–1876), and since then, only a few descriptions of new coral species have been published from this region. In addition, the taxonomic status of most gorgonians reported from the temperate Pacific coast of South America remains uncertain due to the loss of the original type material. In this study, we use morphological characters and nuclear and mitochondrial markers to re-evaluate the taxonomy of the Chilean gorgonians <i>Phycogorgia fucata</i> and <i>Leptogorgia chilensis</i>. Our findings support the monophyly of Chilean <i>Leptogorgia</i>, confirm that <i>Leptogorgia chilensis</i> from Chile is distinct from specimens identified as the same species in California, and reveal that <i>P. fucata</i>, despite its unique morphology, should be included in the genus <i>Leptogorgia</i>.
DOI: 10.6084/m9.figshare.28431173
title: Collecting and cataloguing the world: the botanical collections of Hans Sloane (1660–1753)

description: Botanical collections assembled before the widespread adoption of the ‘Linnaean’ system of binomial naming often have nomenclatural significance, are increasingly utilized to investigate genetic and environmental change, and are important sources for the history of science and medicine. However, such early collections may be difficult to access and interpret, and few have machine-readable metadata or images. The natural history collections of Hans Sloane (1660–1753), assembled between the 1680s and his death in 1753, constitute the <i>de facto</i> foundation collections of the Natural History Museum, London. This study analyses Sloane’s Herbarium and ‘Vegetable Substances’ which make up the largest surviving components of Sloane’s natural history materials and the largest pre-Linnaean botanical collection in existence. The collections contain specimens contributed by hundreds of people from over 70 countries and territories worldwide. New data sets are presented that enable novel research and a comparison of their parts. The data provide details of the people and places mentioned in these sources, along with a complete transcription of the Vegetable Substances catalogue, and new folio-level metadata for the entire Herbarium. The results provide precise estimates of the scale of the collections (8812 surviving specimens of the Vegetable Substances, and 121 506 specimens in the herbarium) and demonstrate their heterogeneity, reflecting their complex histories. Aspects of the collections’ histories can be read from the data and reveal some of the organization and management practices that shaped the collections as we have them today. However, we show that there is frequent ambiguity and uncertainty in the provenance of specimens, while the human histories connected with their assembly are often opaque, embedded in the trading networks of colonialism and enslavement. These data permit analyses of the collections at scale for the first time, yet also suggest that multi-disciplinary approaches are required to fully unlock such historical collections.
DOI: 10.6084/m9.figshare.28431173.v1
title: Collecting and cataloguing the world: the botanical collections of Hans Sloane (1660–1753)

description: Botanical collections assembled before the widespread adoption of the ‘Linnaean’ system of binomial naming often have nomenclatural significance, are increasingly utilized to investigate genetic and environmental change, and are important sources for the history of science and medicine. However, such early collections may be difficult to access and interpret, and few have machine-readable metadata or images. The natural history collections of Hans Sloane (1660–1753), assembled between the 1680s and his death in 1753, constitute the <i>de facto</i> foundation collections of the Natural History Museum, London. This study analyses Sloane’s Herbarium and ‘Vegetable Substances’ which make up the largest surviving components of Sloane’s natural history materials and the largest pre-Linnaean botanical collection in existence. The collections contain specimens contributed by hundreds of people from over 70 countries and territories worldwide. New data sets are presented that enable novel research and a comparison of their parts. The data provide details of the people and places mentioned in these sources, along with a complete transcription of the Vegetable Substances catalogue, and new folio-level metadata for the entire Herbarium. The results provide precise estimates of the scale of the collections (8812 surviving specimens of the Vegetable Substances, and 121 506 specimens in the herbarium) and demonstrate their heterogeneity, reflecting their complex histories. Aspects of the collections’ histories can be read from the data and reveal some of the organization and management practices that shaped the collections as we have them today. However, we show that there is frequent ambiguity and uncertainty in the provenance of specimens, while the human histories connected with their assembly are often opaque, embedded in the trading networks of colonialism and enslavement. These data permit analyses of the collections at scale for the first time, yet also suggest that multi-disciplinary approaches are required to fully unlock such historical collections.
DOI: 10.6084/m9.figshare.30784842.v1
title: Diversity and molecular phylogeny of the Indo-West Pacific rock dwelling <i>Smaragdinella</i> snails (Cephalaspidea, Haminoeidae)

description: <i>Smaragdinella</i> A. Adams, 1848 is a genus of marine gastropods belonging to the family Haminoeidae (order Cephalaspidea), confined to tidal zones of the tropical and sub-tropical Indo-West Pacific region. These snails are of special evolutionary interest because they are the only lineage of Cephalaspidea adapted to living directly on hard substrates. However, with only three valid species and 17 nominal names currently recognized, the taxonomy of Haminoeidae is problematic. This study presents the first global phylogenetic analyses of <i>Smaragdinella</i> based on 84 specimens from across the geographic range of the genus using complete mitochondrial genomes and partial nuclear ribosomal complex data (18S rRNA + 28S rRNA). Maximum likelihood, Bayesian inference and species delimitation analyses using the Assemble Species by Automatic Partitioning (ASAP) method, were employed to estimate the number of candidate species and infer their relationships. In addition, morphological analysis of shells and anatomical structures was performed in targeted specimens using dissections and scanning electron microscopy. The results suggest the presence of 13 or 14 candidate species clustering in two main clades largely separated by geography: one comprising Pacific Ocean and Red Sea species, and another consisting of Indian Ocean species. These clades are defined by synapomorphic traits with specimens from the Indian and Pacific clades having unique features of the shell, digestive and reproductive systems.
DOI: 10.6084/m9.figshare.30530947
title: Molecular phylogeny of the genus <i>Tamsita</i> Kiriakoff, 1954 (Lepidoptera: Erebidae) unveils its systematic position and cryptic diversity in East Africa

description: The Afrotropical genus <i>Tamsita</i> Kiriakoff, 1954 (Erebidae) currently comprises only two recognized species, occurring in East Africa. Here, we shed light on the diversity of these moths using an integrative approach based on the combination of morphological characters and molecular data. For the reconstruction of the molecular phylogeny, we used mitochondrial cytochrome C oxidase subunit I (COI) and nuclear wingless (Wg) markers. The results of the phylogenetic analyses place the genus <i>Tamsita</i> in the subfamily Arctiinae, in contrast to its previous assignment to Lymantriinae, and reveal the existence of seven species, five of which are herein described, <i>Tamsita kivuana</i> sp. nov., <i>T. barnsi</i> sp. nov., <i>T. vulcanicola</i> sp. nov., <i>T. udzungwana</i> sp. nov. and <i>T. smithi</i> sp. nov. Furthermore, we found a deep split between the clusters of <i>T. ochthoeba</i> and <i>T. habrotima</i>, to which all five newly discovered species belonged. Our results also indicate clear genetic separation among all recovered species and a high level of endemicity. http://zoobank.org/urn:lsid:zoobank.org:pub:07E34AFD-A443-4D2F-8057-A088C50B5912
DOI: 10.6084/m9.figshare.30530947.v1
title: Molecular phylogeny of the genus <i>Tamsita</i> Kiriakoff, 1954 (Lepidoptera: Erebidae) unveils its systematic position and cryptic diversity in East Africa

description: The Afrotropical genus <i>Tamsita</i> Kiriakoff, 1954 (Erebidae) currently comprises only two recognized species, occurring in East Africa. Here, we shed light on the diversity of these moths using an integrative approach based on the combination of morphological characters and molecular data. For the reconstruction of the molecular phylogeny, we used mitochondrial cytochrome C oxidase subunit I (COI) and nuclear wingless (Wg) markers. The results of the phylogenetic analyses place the genus <i>Tamsita</i> in the subfamily Arctiinae, in contrast to its previous assignment to Lymantriinae, and reveal the existence of seven species, five of which are herein described, <i>Tamsita kivuana</i> sp. nov., <i>T. barnsi</i> sp. nov., <i>T. vulcanicola</i> sp. nov., <i>T. udzungwana</i> sp. nov. and <i>T. smithi</i> sp. nov. Furthermore, we found a deep split between the clusters of <i>T. ochthoeba</i> and <i>T. habrotima</i>, to which all five newly discovered species belonged. Our results also indicate clear genetic separation among all recovered species and a high level of endemicity. http://zoobank.org/urn:lsid:zoobank.org:pub:07E34AFD-A443-4D2F-8057-A088C50B5912
DOI: 10.6084/m9.figshare.29390275
title: Integrative taxonomy reveals lack of phylogenetic signal of the clavulate acanthostyles in <i>Ectyoplasia ferox</i> and non-monophyly of the genus <i>Ectyoplasia</i> (Demospongiae: Raspailiidae)

description: Morphological plasticity stands out as a primary source of difficulty in sponge taxonomy. <i>Ectyoplasia ferox</i> is an abundant sponge in tropical marine ecosystems, known for producing a diverse array of bioactive compounds with allelopathic, antipredation, and pharmacological properties. However, the taxonomy of <i>E. ferox</i> is complex, as specimens with and without clavulate acanthostyles have been observed in both the Caribbean and Brazil. To assess the phylogeny of <i>Ectyoplasia</i> and the phylogenetic signal of the clavulate acanthostyles in <i>E. ferox</i>, we describe and compare the external morphology, skeletal organization, spicule composition, and sequences of the nuclear gene 28S rRNA (regions D3–D5) and the mitochondrial gene <i>cox-1</i> in Caribbean and Brazilian specimens of <i>E. ferox</i>, both with and without clavulate acanthostyles. Phylogenetic analyses of both genes supported that all specimens examined belong to the same species, and therefore the presence/absence of clavulate acanthostyles lacks phylogenetic signal in this species. Moreover, the 28S tree strongly supported the non-monophyly of the genus <i>Ectyoplasia</i>, because <i>E. ferox</i> and the type species of the genus, <i>Ectyoplasia tabula</i>, fell into widely separate clades. Morphological evidences also support this non-monophyly, as <i>E. ferox</i> exhibits undifferentiated axial and extra-axial skeletons without ectosomal specialization, which are inconsistent with the current diagnosis of the genus. The placement of <i>E. ferox</i> in the Raspailiidae was supported by the phylogenetic analysis, despite the absence of a typical “raspailiid” ectosomal skeleton and the lack of acanthostyles in some specimens. Our study, like many others, highlights the need to integrate both morphological and molecular data from various specimens across different localities for sponge species delimitation and phylogeny.
DOI: 10.6084/m9.figshare.29390275.v1
title: Integrative taxonomy reveals lack of phylogenetic signal of the clavulate acanthostyles in <i>Ectyoplasia ferox</i> and non-monophyly of the genus <i>Ectyoplasia</i> (Demospongiae: Raspailiidae)

description: Morphological plasticity stands out as a primary source of difficulty in sponge taxonomy. <i>Ectyoplasia ferox</i> is an abundant sponge in tropical marine ecosystems, known for producing a diverse array of bioactive compounds with allelopathic, antipredation, and pharmacological properties. However, the taxonomy of <i>E. ferox</i> is complex, as specimens with and without clavulate acanthostyles have been observed in both the Caribbean and Brazil. To assess the phylogeny of <i>Ectyoplasia</i> and the phylogenetic signal of the clavulate acanthostyles in <i>E. ferox</i>, we describe and compare the external morphology, skeletal organization, spicule composition, and sequences of the nuclear gene 28S rRNA (regions D3–D5) and the mitochondrial gene <i>cox-1</i> in Caribbean and Brazilian specimens of <i>E. ferox</i>, both with and without clavulate acanthostyles. Phylogenetic analyses of both genes supported that all specimens examined belong to the same species, and therefore the presence/absence of clavulate acanthostyles lacks phylogenetic signal in this species. Moreover, the 28S tree strongly supported the non-monophyly of the genus <i>Ectyoplasia</i>, because <i>E. ferox</i> and the type species of the genus, <i>Ectyoplasia tabula</i>, fell into widely separate clades. Morphological evidences also support this non-monophyly, as <i>E. ferox</i> exhibits undifferentiated axial and extra-axial skeletons without ectosomal specialization, which are inconsistent with the current diagnosis of the genus. The placement of <i>E. ferox</i> in the Raspailiidae was supported by the phylogenetic analysis, despite the absence of a typical “raspailiid” ectosomal skeleton and the lack of acanthostyles in some specimens. Our study, like many others, highlights the need to integrate both morphological and molecular data from various specimens across different localities for sponge species delimitation and phylogeny.
DOI: 10.6084/m9.figshare.28247875
title: Microendemism can be the rule in the Brazilian Caatinga: evidence from flat lizards of the <i>Tropidurus semitaeniatus</i> group (Squamata: Tropiduridae)

description: Microendemism remains a poorly studied phenomenon within Brazil’s Caatinga biome, yet recent research has revealed a number of species complexes with diverging lineages confined to narrow geographic ranges. These lineages often inhabit remote and undersampled regions lacking conservation efforts. Notable examples include the flat lizards from the <i>Tropidurus semitaeniatus</i> group, which comprises the broadly distributed <i>T. semitaeniatus</i> species complex plus <i>T. helenae</i>, <i>T. jaguaribanus</i>, and <i>T. pinima</i>, all endemic to the Caatinga biome. Incomplete knowledge of their taxonomic boundaries, phylogenetic relationships, and geographic distribution hinders both the formal description of new microendemic taxa and their conservation assessment. To address these gaps, we conducted a phylogenomic analysis of the <i>T. semitaeniatus</i> group employing ultra-conserved elements (UCEs) and investigated its microendemic diversity. Our analysis revealed that <i>T. semitaeniatus</i> is paraphyletic, with <i>T. helenae</i> emerging as sister to a clade formed by microendemic lineages of <i>T. semitaeniatus</i> (<i>sensu lato</i>), within which <i>T. jaguaribanus</i> is embedded. Additionally, the discovery of a new microendemic species, <i>Tropidurus galileii</i> sp. nov., from calcareous formations of Itaguaçu da Bahia, Brazil, exposed <i>T. pinima</i> as paraphyletic, revealing a novel species complex composed of multiple microendemic lineages. This finding led us to produce the first illustrated morphological guide for the <i>T. semitaeniatus</i> group, aimed at facilitating future comparative studies. Most species requiring taxonomic treatment in the <i>T. semitaeniatus</i> group exhibit morphological distinctiveness, and the number of microendemic taxa is significantly higher than previously estimated. Our findings suggest that range expansion followed by allopatric speciation is unlikely to be the sole driver of microendemism in this group. However, the specific biogeographic processes underlying the origin of microendemic lineages remain elusive. This study sheds light on the microendemic lizard diversity of the Caatinga, emphasizing the urgent need for enhanced systematic and conservation efforts. http://zoobank.org/urn:lsid:zoobank.org:pub:062DCEAA-67D9-41B9-B155-EC538BFE8182