cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24639630
title: Ancestral state reconstruction reveals extensive homoplasy in nutlet characters of Cynoglossinae (Boraginaceae, subfam. Cynoglossoideae, tribe Cynoglosseae)

description: Recent phylogenetic studies have challenged the traditional classification of the subtribe Cynoglossinae, which was based on nutlet characteristics. To investigate the evolution of fruit traits related to dispersal modes in this complex group, we conducted a study using scanning electron microscopy to examine 28 taxa representing all previously recognized lineages of the subtribe. Cynoglossinae displays four main types of nutlets: marginate, emarginate, flat wing, and incurved wing. Our findings reveal the arrangement of glochids and their structure, including the number of apical hooks, and their surface ornamentation is highly variable both across and within these four main types. We reconstructed the phylogenetic tree with four main clades (i.e., Clades I–IV) using Maximum likelihood analysis. In addition, we mapped four nutlet traits (i.e., nutlet margin, nutlet glochid, glochid sculpture, and glochid hooks) associated with different dispersal modes using ancestral state reconstruction analysis. The ancestor of subtribe Cynoglossinae was inferred to have marginate and glochidiate nutlets, with glochids externally provided with complex spiny tubercles and bearing at least four hooks at the tip as well as epizoochory dispersal mode. These ancestral states have been retained in Clade II (East Asian-Australian-African <i>Cynoglossum</i>-<i>Lindelofia</i> clade) and Clade III (Mediterranean-Asian <i>Cynoglossum</i>-<i>Solenanthus</i>-<i>Trachelanthus</i> clade), with several independent shifts to emarginate fruits. Transitions from marginate to wide-winged nutlets have occurred at least four independent times, facilitating wind-assisted dispersal in Clade I (<i>Microparacaryum</i> clade), Clade IV (<i>Paracaryum</i>-<i>Mattiastrum</i>-<i>Rindera</i> clade), <i>Rindera tetraspis</i>, and <i>Mattiastrum crista-galli</i> (both belonging to Clade III), where a transition from tuberculate to papillate surface has also occurred.
DOI: 10.6084/m9.figshare.24639630.v1
title: Ancestral state reconstruction reveals extensive homoplasy in nutlet characters of Cynoglossinae (Boraginaceae, subfam. Cynoglossoideae, tribe Cynoglosseae)

description: Recent phylogenetic studies have challenged the traditional classification of the subtribe Cynoglossinae, which was based on nutlet characteristics. To investigate the evolution of fruit traits related to dispersal modes in this complex group, we conducted a study using scanning electron microscopy to examine 28 taxa representing all previously recognized lineages of the subtribe. Cynoglossinae displays four main types of nutlets: marginate, emarginate, flat wing, and incurved wing. Our findings reveal the arrangement of glochids and their structure, including the number of apical hooks, and their surface ornamentation is highly variable both across and within these four main types. We reconstructed the phylogenetic tree with four main clades (i.e., Clades I–IV) using Maximum likelihood analysis. In addition, we mapped four nutlet traits (i.e., nutlet margin, nutlet glochid, glochid sculpture, and glochid hooks) associated with different dispersal modes using ancestral state reconstruction analysis. The ancestor of subtribe Cynoglossinae was inferred to have marginate and glochidiate nutlets, with glochids externally provided with complex spiny tubercles and bearing at least four hooks at the tip as well as epizoochory dispersal mode. These ancestral states have been retained in Clade II (East Asian-Australian-African <i>Cynoglossum</i>-<i>Lindelofia</i> clade) and Clade III (Mediterranean-Asian <i>Cynoglossum</i>-<i>Solenanthus</i>-<i>Trachelanthus</i> clade), with several independent shifts to emarginate fruits. Transitions from marginate to wide-winged nutlets have occurred at least four independent times, facilitating wind-assisted dispersal in Clade I (<i>Microparacaryum</i> clade), Clade IV (<i>Paracaryum</i>-<i>Mattiastrum</i>-<i>Rindera</i> clade), <i>Rindera tetraspis</i>, and <i>Mattiastrum crista-galli</i> (both belonging to Clade III), where a transition from tuberculate to papillate surface has also occurred.
DOI: 10.13145/bacdive14089.20230509.8
title: Solirubrobacter ginsenosidimutans An et al. 2011

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.23459204
title: Integrative taxonomy provides evidence for a cryptic lineage in the velvet worm <i>Peripatopsis birgeri</i> species complex (Onychophora: Peripatopsidae) in KwaZulu-Natal, South Africa

description: During the present study, species boundaries in the velvet worm <i>Peripatopsis birgeri</i> species complex in KwaZulu-Natal, South Africa, were examined with the use of DNA sequence data, gross morphology, scanning electron microscopy (SEM) and ecological niche modelling. Mitochondrial <i>CO1</i> and nuclear <i>18S</i> rRNA sequence data were used to generate a phylogeny using both a Bayesian inference and maximum likelihood approaches. Both the <i>CO1</i> sequence data and the combined DNA sequence topology (<i>CO1</i> +<i> 18S</i> rRNA) revealed the presence of two geographically distinct clades within the <i>P. birgeri</i> species complex. Results from three species delimitation methods (GMYC, PTP and ASAP), were incongruent in determining the number of species within the species complex and generally overestimated the number of operational taxonomic units. The latter result can be attributed to the marked genetic structure within the species complex, a result corroborated by the <i>CO1</i> haplotype network and statistically significant <i>F</i><sub>ST</sub> values. Divergence time estimation suggests that the two clades diverged during the Plio/Pleistocene. Niche modelling revealed that the two clades were differentially impacted by bioclimatic variables and occupied different habitats. Gross morphological characteristics, such as leg pair numbers and colour revealed no fixed differences between the two clades, however, a creamy white headband/collar occurred exclusively in specimens of clade 1 (<i>P. birgeri</i>). In contrast, SEM revealed fixed dorsal and ventral scale rank differences between the two clades. The results corroborate the presence of a novel species within the <i>P. birgeri s.s.</i> species complex. <i>Peripatopsis birgeri s.s.</i> is revised and restricted to the southern Drakensberg and a new species, <i>P. polychroma</i> sp. nov. (clade 2), from the northern Drakensberg and adjacent Afrotemperate forests in the interior of KwaZulu-Natal is described. https://zoobank.org/urn:lsid:zoobank:org:pub:569557AB-8BC8-49B6-B8AA-96507371297B
DOI: 10.6084/m9.figshare.23459204.v1
title: Integrative taxonomy provides evidence for a cryptic lineage in the velvet worm <i>Peripatopsis birgeri</i> species complex (Onychophora: Peripatopsidae) in KwaZulu-Natal, South Africa

description: During the present study, species boundaries in the velvet worm <i>Peripatopsis birgeri</i> species complex in KwaZulu-Natal, South Africa, were examined with the use of DNA sequence data, gross morphology, scanning electron microscopy (SEM) and ecological niche modelling. Mitochondrial <i>CO1</i> and nuclear <i>18S</i> rRNA sequence data were used to generate a phylogeny using both a Bayesian inference and maximum likelihood approaches. Both the <i>CO1</i> sequence data and the combined DNA sequence topology (<i>CO1</i> +<i> 18S</i> rRNA) revealed the presence of two geographically distinct clades within the <i>P. birgeri</i> species complex. Results from three species delimitation methods (GMYC, PTP and ASAP), were incongruent in determining the number of species within the species complex and generally overestimated the number of operational taxonomic units. The latter result can be attributed to the marked genetic structure within the species complex, a result corroborated by the <i>CO1</i> haplotype network and statistically significant <i>F</i><sub>ST</sub> values. Divergence time estimation suggests that the two clades diverged during the Plio/Pleistocene. Niche modelling revealed that the two clades were differentially impacted by bioclimatic variables and occupied different habitats. Gross morphological characteristics, such as leg pair numbers and colour revealed no fixed differences between the two clades, however, a creamy white headband/collar occurred exclusively in specimens of clade 1 (<i>P. birgeri</i>). In contrast, SEM revealed fixed dorsal and ventral scale rank differences between the two clades. The results corroborate the presence of a novel species within the <i>P. birgeri s.s.</i> species complex. <i>Peripatopsis birgeri s.s.</i> is revised and restricted to the southern Drakensberg and a new species, <i>P. polychroma</i> sp. nov. (clade 2), from the northern Drakensberg and adjacent Afrotemperate forests in the interior of KwaZulu-Natal is described. https://zoobank.org/urn:lsid:zoobank:org:pub:569557AB-8BC8-49B6-B8AA-96507371297B
DOI: 10.6084/m9.figshare.24018972.v1
title: Unity in diversity: morphological and genetic variability, integrative systematics, and phylogeography of the widespread nudibranch mollusc <i>Onchidoris muricata</i>

description: <i>Onchidoris muricata</i> (Gastropoda: Nudibranchia: Onchidorididae) is a well-known nudibranch species, which has a wide amphiboreal range confirmed by molecular data. However, <i>O. muricata</i> shows a high degree of variation in external morphology among distant populations, which may indicate the presence of cryptic diversity within this species. There are also two closely related species with an unconfirmed taxonomic status, which were recently described from the northwestern Pacific based on morphological data. In this paper we study the taxonomic status and population structure of <i>O. muricata</i> based on an integrative approach combining morphological and molecular data and using <i>O. muricata</i> as a model we explore issues of boreal marine fauna connectivity and glaciation-driven isolation. The external morphology, spicule composition, and features of the buccal armature and the reproductive system were studied using light microscopy, scanning electron microscopy and mCT scan technology. The molecular study included various population genetic analyses as well as divergence time estimation and ancestral area reconstruction analyses. <i>Onchidoris muricata</i> represents a true amphiboreal species, which shows a high degree of heterogeneity in morphological characters, especially in the radular morphology and in features of the reproductive system. Our new data question the validity of the North-West Pacific species <i>O. macropompa</i> and <i>O. pavli</i> as the morphology of both these species fall within the phenotypic diversity of <i>O. muricata.</i> Although our sampling does not include the type localities of these two species, the observed morphological variability in <i>O. muricata</i> and the lack of molecular data for the North Pacific species <i>O. macropompa</i> and <i>O. pavli</i> suggest the latter two species are in fact part of <i>O. muricata</i> morphological diversity. Phylogeographic analyses indicate a genetic separation of the North Pacific and North Atlantic-Arctic populations of <i>O. muricata</i>, suggesting restricted gene flow between these areas. We show that this divergence may be a result of glacial cycles during the late Pleistocene, which were a key factor in the reduction of gene flow across the Arctic Ocean. Our molecular results also suggest that the White Sea population experienced a bottleneck event during the last Glacial Maximum.
DOI: 10.6084/m9.figshare.24972767
title: Reappraisal of the systematics of two sympatric coral snakes (Reptilia: Elapidae) from Northeast India

description: Systematics of the Asian coral snake genus <i>Sinomicrurus</i> Slowinski et al., 2001, was recently reviewed; however, the lack of molecular data for <i>S. macclellandi</i> (Reinhardt, 1844), especially topotypical specimens, renders most taxonomic revisions mutable. This largely hinders the reappraisal of the putative synonyms of <i>S. macclellandi</i> which may be distinct and deserve recognition to highlight their evolutionary importance and eventual conservation. We reassessed the systematic status of Northeast Indian populations of <i>S. macclellandi</i> that also included topotypic material, based on the combination of morphology and genetic data (mitochondrial and nuclear genes). We uncovered morphological and genetic evidence for resurrecting <i>S. gorei</i> comb. nov., from the synonymy of <i>S. macclellandi</i> and elevating it to a full species rank, previously recognised as a colour variant of <i>S. macclellandi</i>. We redescribed the species based on a total of 36 adult specimens examined from Mizoram, along with the type material from Assam, as well as specimens from Bangladesh. Apart from the genetic distinction of <i>S. gorei</i> from the other congeners, it is also morphologically diagnosable from its closest sympatric species <i>S. macclellandi</i> var. typica, in bearing a suit of somatic and osteological features.
DOI: 10.6084/m9.figshare.24972767.v1
title: Reappraisal of the systematics of two sympatric coral snakes (Reptilia: Elapidae) from Northeast India

description: Systematics of the Asian coral snake genus <i>Sinomicrurus</i> Slowinski et al., 2001, was recently reviewed; however, the lack of molecular data for <i>S. macclellandi</i> (Reinhardt, 1844), especially topotypical specimens, renders most taxonomic revisions mutable. This largely hinders the reappraisal of the putative synonyms of <i>S. macclellandi</i> which may be distinct and deserve recognition to highlight their evolutionary importance and eventual conservation. We reassessed the systematic status of Northeast Indian populations of <i>S. macclellandi</i> that also included topotypic material, based on the combination of morphology and genetic data (mitochondrial and nuclear genes). We uncovered morphological and genetic evidence for resurrecting <i>S. gorei</i> comb. nov., from the synonymy of <i>S. macclellandi</i> and elevating it to a full species rank, previously recognised as a colour variant of <i>S. macclellandi</i>. We redescribed the species based on a total of 36 adult specimens examined from Mizoram, along with the type material from Assam, as well as specimens from Bangladesh. Apart from the genetic distinction of <i>S. gorei</i> from the other congeners, it is also morphologically diagnosable from its closest sympatric species <i>S. macclellandi</i> var. typica, in bearing a suit of somatic and osteological features.
DOI: 10.6084/m9.figshare.21829605
title: Phylogenetic and morphological evidence reveals the association between diet and the evolution of the venom delivery system in Neotropical goo-eating snakes

description: Advanced endoglyptodont snakes share a complex but homologous venom delivery system associated with the upper jaw and its dentition. Recently, a remarkable novel lower jaw venom delivery system was described for the Neotropical dipsadine radiation of goo-eating snakes. While most dipsadines are opistoglyphous and exhibit large, mainly serous venom glands associated with the upper jaw and supralabial glands, goo-eating dipsadine snakes are aglyphous and lack serous upper labial venom glands. Here, we provide new morphological and histological information on the oral glands and maxillary dentition of representatives of the major lineages of dipsadines that help trace the evolutionary steps that shaped the venom delivery system of dipsadines. We performed a maximum likelihood analysis on a molecular dataset that includes 443 terminals and seven loci. Our results show that goo-eating dipsadines form a monophyletic assemblage that includes the genus <i>Adelphicos</i> for the first time, along with <i>Geophis</i>, <i>Atractus</i>, <i>Ninia</i>, <i>Chersodromus</i>, <i>Tropidodipsas</i>, <i>Sibon</i>, and <i>Dipsas</i>. We also provide the first evidence of a complete shift from an upper jaw to a lower jaw venom delivery system associated with their specialized feeding behaviour. Unlike other dipsadines who exhibit typical endoglyptodont anteroposteriorly ridged posterior maxillary teeth, goo-eating dipsadines have uniform lateromedially ridged teeth throughout their maxilla. Our results indicate that the loss of the endoglyptodont venom delivery system occurred in the most recent common ancestor of goo-eating dipsadines, probably resulting from the loss of the embryonic posterior maxillary lamina responsible for the development of the venom delivery system.
DOI: 10.6084/m9.figshare.21829605.v1
title: Phylogenetic and morphological evidence reveals the association between diet and the evolution of the venom delivery system in Neotropical goo-eating snakes

description: Advanced endoglyptodont snakes share a complex but homologous venom delivery system associated with the upper jaw and its dentition. Recently, a remarkable novel lower jaw venom delivery system was described for the Neotropical dipsadine radiation of goo-eating snakes. While most dipsadines are opistoglyphous and exhibit large, mainly serous venom glands associated with the upper jaw and supralabial glands, goo-eating dipsadine snakes are aglyphous and lack serous upper labial venom glands. Here, we provide new morphological and histological information on the oral glands and maxillary dentition of representatives of the major lineages of dipsadines that help trace the evolutionary steps that shaped the venom delivery system of dipsadines. We performed a maximum likelihood analysis on a molecular dataset that includes 443 terminals and seven loci. Our results show that goo-eating dipsadines form a monophyletic assemblage that includes the genus <i>Adelphicos</i> for the first time, along with <i>Geophis</i>, <i>Atractus</i>, <i>Ninia</i>, <i>Chersodromus</i>, <i>Tropidodipsas</i>, <i>Sibon</i>, and <i>Dipsas</i>. We also provide the first evidence of a complete shift from an upper jaw to a lower jaw venom delivery system associated with their specialized feeding behaviour. Unlike other dipsadines who exhibit typical endoglyptodont anteroposteriorly ridged posterior maxillary teeth, goo-eating dipsadines have uniform lateromedially ridged teeth throughout their maxilla. Our results indicate that the loss of the endoglyptodont venom delivery system occurred in the most recent common ancestor of goo-eating dipsadines, probably resulting from the loss of the embryonic posterior maxillary lamina responsible for the development of the venom delivery system.
DOI: 10.6084/m9.figshare.23910325
title: Systematics, biogeography and phylogenomics of northern bog lemmings (Cricetidae), cold-temperate rodents of conservation concern under global change

description: Northern bog lemmings, <i>Mictomys</i> (<i>Synaptomys</i>) <i>borealis</i>, are currently being assessed for protections under the U.S. Endangered Species Act. A major impediment to comprehensive evaluation is a deficiency of data towards understanding the biology of these rodents. Inherent rarity and scarce specimen sampling, despite a continent-wide distribution, has precluded our ability to implement modern methods for resolving taxonomy, evolutionary history, and investigating multiple other species traits. Here we use a maternally inherited locus (mitochondrial cytochrome b) and between 5939 and 11 513 nuclear loci from reduced representation sequencing (ddRADseq) to investigate the evolutionary history of northern bog lemmings. We (1) qualify evidence based on morphological and early molecular studies for the genus assignment of <i>Mictomys</i>, (2) test the validity of multiple sub-species designations, (3) provide spatial and temporal historical biogeographic perspectives, and (4) discuss how incomplete sampling might influence conservation efforts. Both mitochondrial and nuclear datasets exhibit deep divergence and paraphyly between two recognized species, the northern (<i>Mictomys borealis</i>) and southern (<i>Synaptomys cooperi</i>) bog lemmings. Based on mtDNA, the geographically isolated subspecies (<i>M. b. sphagnicola</i>) was found to be divergent from all other specimens. The remainder of the species exhibited shallow intra-specific differentiation in mtDNA, however, nuclear data supports genetic distinction consistent with four geographic subspecies. Recent coalescence of all northern bog lemmings (except for <i>M. b. sphagnicola</i>) reflects divergence in multiple refugia through the last glacial cycle, including a well-known coastal center of endemism and multiple regions south of continental ice sheets. Regional lineages across North America suggest strong latitudinal displacement with global climate change, coupled with isolation-reconnection dynamics. This taxon suffers from a lack of modern samples through most of its distribution, severely limiting the interpretation of ongoing evolutionary processes, particularly in southern portions of the species’ range. Limited voucher specimen sampling of vulnerable populations could aid in rigorous conservation decision-making.
DOI: 10.6084/m9.figshare.23910325.v1
title: Systematics, biogeography and phylogenomics of northern bog lemmings (Cricetidae), cold-temperate rodents of conservation concern under global change

description: Northern bog lemmings, <i>Mictomys</i> (<i>Synaptomys</i>) <i>borealis</i>, are currently being assessed for protections under the U.S. Endangered Species Act. A major impediment to comprehensive evaluation is a deficiency of data towards understanding the biology of these rodents. Inherent rarity and scarce specimen sampling, despite a continent-wide distribution, has precluded our ability to implement modern methods for resolving taxonomy, evolutionary history, and investigating multiple other species traits. Here we use a maternally inherited locus (mitochondrial cytochrome b) and between 5939 and 11 513 nuclear loci from reduced representation sequencing (ddRADseq) to investigate the evolutionary history of northern bog lemmings. We (1) qualify evidence based on morphological and early molecular studies for the genus assignment of <i>Mictomys</i>, (2) test the validity of multiple sub-species designations, (3) provide spatial and temporal historical biogeographic perspectives, and (4) discuss how incomplete sampling might influence conservation efforts. Both mitochondrial and nuclear datasets exhibit deep divergence and paraphyly between two recognized species, the northern (<i>Mictomys borealis</i>) and southern (<i>Synaptomys cooperi</i>) bog lemmings. Based on mtDNA, the geographically isolated subspecies (<i>M. b. sphagnicola</i>) was found to be divergent from all other specimens. The remainder of the species exhibited shallow intra-specific differentiation in mtDNA, however, nuclear data supports genetic distinction consistent with four geographic subspecies. Recent coalescence of all northern bog lemmings (except for <i>M. b. sphagnicola</i>) reflects divergence in multiple refugia through the last glacial cycle, including a well-known coastal center of endemism and multiple regions south of continental ice sheets. Regional lineages across North America suggest strong latitudinal displacement with global climate change, coupled with isolation-reconnection dynamics. This taxon suffers from a lack of modern samples through most of its distribution, severely limiting the interpretation of ongoing evolutionary processes, particularly in southern portions of the species’ range. Limited voucher specimen sampling of vulnerable populations could aid in rigorous conservation decision-making.