cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.13145/bacdive14073.20230509.8
title: Shewanella gaetbuli Yoon et al. 2004

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14074.20230509.8
title: Shewanella sediminis Zhao et al. 2005

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14075.20230509.8
title: Shewanella kaireitica Miyazaki et al. 2006

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14076.20230509.8
title: Shewanella abyssi Miyazaki et al. 2006

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14077.20230509.8
title: Shewanella surugensis Miyazaki et al. 2006

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14078.20230509.8
title: Shewanella halifaxensis Zhao et al. 2006

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14079.20230509.8
title: Shewanella loihica Gao et al. 2006

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14080.20230509.8
title: Shewanella canadensis Zhao et al. 2007

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14081.20230509.8
title: Shewanella atlantica Zhao et al. 2007

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14082.20230509.8
title: Shewanella colwelliana (Weiner et al. 1988) Coyne et al. 1990

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14083.20230509.8
title: Shewanella fidelis Ivanova et al. 2003

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.24211509
title: Revision of the Indo-West Pacific crab genus <i>Soliella</i> (Brachyura: Xanthidae: Etisinae): ‘pseudocryptic species’ and basinal speciation

description: Etisine crabs are some of the most abundant cryptobionts in Indo-West Pacific coral reef systems. Despite their ecological importance and abundance in museum collections, several recent systematic studies have indicated family- to subspecies-level taxonomic problems. One such case involves the former chlorodielline genus <i>Soliella</i> Lasley, Klaus & Ng, 2015 (treated here as part of Etisinae), which currently comprises two valid species and three available names that have been in flux in recent literature. The validity of these taxa has only been cursorily discussed. To resolve species limits and distributions, a thorough morphological examination of hundreds of specimens was conducted, including scanning electron microscopy of male gonopods, along with analysis of sequence data of the mitochondrial marker cytochrome c oxidase subunit I (COI) from 84 exemplars across the distribution of the genus. The status of two species that have Indian Ocean versus Pacific Ocean distributions with overlap in the Indo-Australian Archipelago and adjacent regions is confirmed. While external morphology is not reliable for identification, a few discrete, although slight, differences in gonopod morphology were found, and these results are consistent with a ‘pseudocryptic species’ designation. Speciation conforms to a previously published etisine model of allopatric differentiation followed by subsequent divergence of gonopod morphology upon secondary sympatry. This pattern, the biogeography of the two species and the concept of ‘pseudocryptic species’ are discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:ABEC01C7-EA5B-4BB6-87E0-405FE3895D95
DOI: 10.6084/m9.figshare.24211509.v1
title: Revision of the Indo-West Pacific crab genus <i>Soliella</i> (Brachyura: Xanthidae: Etisinae): ‘pseudocryptic species’ and basinal speciation

description: Etisine crabs are some of the most abundant cryptobionts in Indo-West Pacific coral reef systems. Despite their ecological importance and abundance in museum collections, several recent systematic studies have indicated family- to subspecies-level taxonomic problems. One such case involves the former chlorodielline genus <i>Soliella</i> Lasley, Klaus & Ng, 2015 (treated here as part of Etisinae), which currently comprises two valid species and three available names that have been in flux in recent literature. The validity of these taxa has only been cursorily discussed. To resolve species limits and distributions, a thorough morphological examination of hundreds of specimens was conducted, including scanning electron microscopy of male gonopods, along with analysis of sequence data of the mitochondrial marker cytochrome c oxidase subunit I (COI) from 84 exemplars across the distribution of the genus. The status of two species that have Indian Ocean versus Pacific Ocean distributions with overlap in the Indo-Australian Archipelago and adjacent regions is confirmed. While external morphology is not reliable for identification, a few discrete, although slight, differences in gonopod morphology were found, and these results are consistent with a ‘pseudocryptic species’ designation. Speciation conforms to a previously published etisine model of allopatric differentiation followed by subsequent divergence of gonopod morphology upon secondary sympatry. This pattern, the biogeography of the two species and the concept of ‘pseudocryptic species’ are discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:ABEC01C7-EA5B-4BB6-87E0-405FE3895D95
DOI: 10.6084/m9.figshare.24298552
title: Unveiling hidden diversity of <i>Oecomys</i> (Rodentia: Cricetidae) from Brazilian Central Amazonia: description of a new species and new lineages

description: The arboreal rice rat of the genus <i>Oecomys</i> Thomas, 1906 is one of the most speciose genera of the subfamily Sigmodontinae, with 19 species currently recognized and occurring from eastern Panama to northern Argentina, Paraguay, and in northern, central and eastern Brazil. Herein we describe a new species using an integrative approach based on molecular, morphological, and morphometric data. We used in our assessment recently collected specimens from the states of Pará and Rondônia, one of the most deforested regions in Brazil. We examined 51 specimens of <i>Oecomys</i> from museum collections including name-bearing types from most of the distributional range of the genus. We also sequenced 32 specimens of <i>Oecomys</i>, and for the molecular analyses, we used the mitochondrial marker Cytochrome <i>b</i> and the nuclear marker intron 7 of β-fibrinogen. Our mitochondrial marker results recovered a strongly supported clade composed of two divergent clades (3.78%), one including lineages of <i>O. bicolor</i> and <i>O. cleberi</i>, and the other clade representing the new species. The topology of concatenated mitochondrial and nuclear data also recovered <i>Oecomys</i> sp. nov. as a sister lineage of the <i>O. bicolor</i> and <i>O. cleberi</i> clade. Also, both markers recovered new lineages from the <i>O. bicolor</i> and <i>O. cleberi</i> species group. The new species can be discriminated from other <i>Oecomys</i> species by pelage colour and craniodental characters, such as absent or small mastoid fenestra, and the presence of alisphenoid strut, small subsquamosal fenestra, presence of sphenopalatine vacuities, and presence of accessory loph of M1 and M2 paracones. The new species occurs exclusively in the Rondônia centre of endemism, delimited by the rivers Amazon to the north, Tapajós to the east, and Madeira to the west. The description of this new <i>Oecomys</i> increases the diversity, and also contributes to elevate Amazonian Sigmodontinae species richness and endemism in this still poorly known biome. http://zoobank.org/urn:lsid:zoobank.org:7477D37A-4D02-443F-B0FB-149379BEDE92
DOI: 10.6084/m9.figshare.23182704
title: Clarifying the identity of the <i>Cleistes rosea</i> complex (Orchidaceae) based on integrative taxonomy

description: <i>Cleistes rosea</i> and 10 other taxa comprise a complex widely distributed in various open vegetation types from eastern South America to Panama. The taxonomic identity of most of these taxa is unclear and their relationships with <i>C. rosea</i> have never been satisfactorily discussed or tested. Here, we employ molecular phylogenetics, morphometrics and morphological, ecological and geographic distribution data to investigate the relationships and taxonomy of <i>Cleistes rosea</i> and related species. Our results confirm that <i>Cleistes rosea</i> and <i>Cleistes castaneoides</i> are sister species and although highly similar in general floral morphology, they differ in vegetative characters, distribution, habitat, floral scent, and lip characters. Both species show local variations regarding floral characters, particularly the flower colour, and such differences were used here to delimit infraspecific taxa within the <i>C. rosea</i>/<i>C. castaneoides</i> clade. While <i>C. rosea</i> var. <i>guianensis</i> var. nov. is restricted to French Guiana, and <i>C. rosea</i> var. <i>buenaventurae</i> stat. & comb. nov. is restricted to low altitudes on the western side of the Cordillera Occidental in the Chocó region of Colombia, <i>C. castaneoides</i> var. <i>castaneoides</i> and <i>C. castaneoides</i> var. <i>augusta</i> comb. nov. are sympatric throughout their distribution. <i>Cleistes abdita</i>, formerly known as <i>C. rosea</i> f. <i>pallida</i>, is similar to <i>C. castaneoides</i> but distinguished by the smaller flowers and restricted distribution to Amazonian savannas. <i>Cleistes rosea</i> is distributed throughout the north of the Andes and northern South America. In turn, <i>C. castaneoides</i> occurs mainly in South-eastern and Central-western Brazil. Still, the distribution of these three species overlaps in the Guiana Shield, where the differentiation between them is less evident. Our results provide evidence of the plasticity of the floral morphology of <i>Cleistes</i>, especially the lip, and highlight that hitherto neglected characters, such as vegetative morphology, habitat, and floral scent, are particularly informative for the characterization of species and taxonomy of the genus.
DOI: 10.6084/m9.figshare.23182704.v1
title: Clarifying the identity of the <i>Cleistes rosea</i> complex (Orchidaceae) based on integrative taxonomy

description: <i>Cleistes rosea</i> and 10 other taxa comprise a complex widely distributed in various open vegetation types from eastern South America to Panama. The taxonomic identity of most of these taxa is unclear and their relationships with <i>C. rosea</i> have never been satisfactorily discussed or tested. Here, we employ molecular phylogenetics, morphometrics and morphological, ecological and geographic distribution data to investigate the relationships and taxonomy of <i>Cleistes rosea</i> and related species. Our results confirm that <i>Cleistes rosea</i> and <i>Cleistes castaneoides</i> are sister species and although highly similar in general floral morphology, they differ in vegetative characters, distribution, habitat, floral scent, and lip characters. Both species show local variations regarding floral characters, particularly the flower colour, and such differences were used here to delimit infraspecific taxa within the <i>C. rosea</i>/<i>C. castaneoides</i> clade. While <i>C. rosea</i> var. <i>guianensis</i> var. nov. is restricted to French Guiana, and <i>C. rosea</i> var. <i>buenaventurae</i> stat. & comb. nov. is restricted to low altitudes on the western side of the Cordillera Occidental in the Chocó region of Colombia, <i>C. castaneoides</i> var. <i>castaneoides</i> and <i>C. castaneoides</i> var. <i>augusta</i> comb. nov. are sympatric throughout their distribution. <i>Cleistes abdita</i>, formerly known as <i>C. rosea</i> f. <i>pallida</i>, is similar to <i>C. castaneoides</i> but distinguished by the smaller flowers and restricted distribution to Amazonian savannas. <i>Cleistes rosea</i> is distributed throughout the north of the Andes and northern South America. In turn, <i>C. castaneoides</i> occurs mainly in South-eastern and Central-western Brazil. Still, the distribution of these three species overlaps in the Guiana Shield, where the differentiation between them is less evident. Our results provide evidence of the plasticity of the floral morphology of <i>Cleistes</i>, especially the lip, and highlight that hitherto neglected characters, such as vegetative morphology, habitat, and floral scent, are particularly informative for the characterization of species and taxonomy of the genus.
DOI: 10.6084/m9.figshare.24298552.v1
title: Unveiling hidden diversity of <i>Oecomys</i> (Rodentia: Cricetidae) from Brazilian Central Amazonia: description of a new species and new lineages

description: The arboreal rice rat of the genus <i>Oecomys</i> Thomas, 1906 is one of the most speciose genera of the subfamily Sigmodontinae, with 19 species currently recognized and occurring from eastern Panama to northern Argentina, Paraguay, and in northern, central and eastern Brazil. Herein we describe a new species using an integrative approach based on molecular, morphological, and morphometric data. We used in our assessment recently collected specimens from the states of Pará and Rondônia, one of the most deforested regions in Brazil. We examined 51 specimens of <i>Oecomys</i> from museum collections including name-bearing types from most of the distributional range of the genus. We also sequenced 32 specimens of <i>Oecomys</i>, and for the molecular analyses, we used the mitochondrial marker Cytochrome <i>b</i> and the nuclear marker intron 7 of β-fibrinogen. Our mitochondrial marker results recovered a strongly supported clade composed of two divergent clades (3.78%), one including lineages of <i>O. bicolor</i> and <i>O. cleberi</i>, and the other clade representing the new species. The topology of concatenated mitochondrial and nuclear data also recovered <i>Oecomys</i> sp. nov. as a sister lineage of the <i>O. bicolor</i> and <i>O. cleberi</i> clade. Also, both markers recovered new lineages from the <i>O. bicolor</i> and <i>O. cleberi</i> species group. The new species can be discriminated from other <i>Oecomys</i> species by pelage colour and craniodental characters, such as absent or small mastoid fenestra, and the presence of alisphenoid strut, small subsquamosal fenestra, presence of sphenopalatine vacuities, and presence of accessory loph of M1 and M2 paracones. The new species occurs exclusively in the Rondônia centre of endemism, delimited by the rivers Amazon to the north, Tapajós to the east, and Madeira to the west. The description of this new <i>Oecomys</i> increases the diversity, and also contributes to elevate Amazonian Sigmodontinae species richness and endemism in this still poorly known biome. http://zoobank.org/urn:lsid:zoobank.org:7477D37A-4D02-443F-B0FB-149379BEDE92
DOI: 10.13145/bacdive14084.20230509.8
title: Shewanella xiamenensis Huang et al. 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.23624241
title: A population genetic-level approach to endemic species of <i>Oxalis</i> section <i>Palmatifoliae</i> (Oxalidaceae) in Patagonia

description: <i>Oxalis</i> section <i>Palmatifoliae</i> (wood sorrel) includes five species that are well differentiated morphologically. A previous population study in one of the species (<i>O. laciniata</i>) suggested a complex phylogeographic history and highlighted the need to explore the genetic variability of all the species in the section. Thus, we performed a population level study of the five species to (1) determine the population structure within and among species, (2) model their current and paleoclimatic distributions, and (3) assess the historical processes that influenced their current genetic and morphological variation. We generated inter-simple sequence repeat (ISSR) polymorphism data and DNA sequences for the plastid region <i>trn</i>H<i>-psb</i>A and used those data to obtain a haplotype network, and used georeferenced coordinates and Maxent to obtain present and past species distribution models. Our major results included: 1) ISSR data showed a significant level of genetic differentiation among the five species and a degree of admixture within species; 2) plastid region <i>trn</i>H-<i>psb</i>A shows that one haplotype is the most frequent and widespread among all the species; 3) modelling of species present distributions showed different climatic variables for each species, whereas modelling of past distribution scenarios suggests broader distributions of all species.
DOI: 10.6084/m9.figshare.23624241.v1
title: A population genetic-level approach to endemic species of <i>Oxalis</i> section <i>Palmatifoliae</i> (Oxalidaceae) in Patagonia

description: <i>Oxalis</i> section <i>Palmatifoliae</i> (wood sorrel) includes five species that are well differentiated morphologically. A previous population study in one of the species (<i>O. laciniata</i>) suggested a complex phylogeographic history and highlighted the need to explore the genetic variability of all the species in the section. Thus, we performed a population level study of the five species to (1) determine the population structure within and among species, (2) model their current and paleoclimatic distributions, and (3) assess the historical processes that influenced their current genetic and morphological variation. We generated inter-simple sequence repeat (ISSR) polymorphism data and DNA sequences for the plastid region <i>trn</i>H<i>-psb</i>A and used those data to obtain a haplotype network, and used georeferenced coordinates and Maxent to obtain present and past species distribution models. Our major results included: 1) ISSR data showed a significant level of genetic differentiation among the five species and a degree of admixture within species; 2) plastid region <i>trn</i>H-<i>psb</i>A shows that one haplotype is the most frequent and widespread among all the species; 3) modelling of species present distributions showed different climatic variables for each species, whereas modelling of past distribution scenarios suggests broader distributions of all species.
DOI: 10.6084/m9.figshare.24989090
title: Phylogeny and ecological traits of the spider <i>Argiope trifasciata</i> (Araneidae) in Egypt clarifying the relationships with Afro-Eurasian and American populations

description: The orb-weaving spider <i>Argiope trifasciata</i> (Forsskål, 1775) was scientifically described in Egypt while it has been considered native to North America. The aim of this study was to analyse the phylogenetic relationships of the Egyptian population and shed light on its introduction and migration history. The <i>COX1</i> gene (mtDNA) of 49 samples from Egypt and Cyprus was analysed with 168 additional <i>COX1</i> sequences available in GenBank and BOLD originating from nineteen other countries. Selected ecological parameters were also studied in an Egyptian desert habitat for comparison with North American populations. We found that spiders oriented their webs in relation to the sun’s position (South and South-East) most likely to regulate their body temperature. The life cycle of <i>A. fasciata</i> in Egypt was found to be extended from what has been reported from other populations, partly possible because some individuals may survive throughout the winter. The phylogenetic analysis revealed that the sequences from Egypt and Cyprus clustered with Afro-Eurasian populations. Thirty haplotypes were found in Egypt and Cyprus of which 21 were unique. The analysis further revealed that the nearest American <i>COX1</i> sequence was separated by 18 mutations. The high <i>COXI</i> divergence (5.1%) as well as the low gene flow (<i>Fst</i> = 0.75) between Afro-Eurasian and American populations, indicated that <i>A. trifasciata</i> has not been recently dispersed from America to Africa and other continents, but the genetic isolation was estimated to have happened around 2.04 My ago. If these spiders represent unique species or subspecies will need further research.
DOI: 10.6084/m9.figshare.24989090.v1
title: Phylogeny and ecological traits of the spider <i>Argiope trifasciata</i> (Araneidae) in Egypt clarifying the relationships with Afro-Eurasian and American populations

description: The orb-weaving spider <i>Argiope trifasciata</i> (Forsskål, 1775) was scientifically described in Egypt while it has been considered native to North America. The aim of this study was to analyse the phylogenetic relationships of the Egyptian population and shed light on its introduction and migration history. The <i>COX1</i> gene (mtDNA) of 49 samples from Egypt and Cyprus was analysed with 168 additional <i>COX1</i> sequences available in GenBank and BOLD originating from nineteen other countries. Selected ecological parameters were also studied in an Egyptian desert habitat for comparison with North American populations. We found that spiders oriented their webs in relation to the sun’s position (South and South-East) most likely to regulate their body temperature. The life cycle of <i>A. fasciata</i> in Egypt was found to be extended from what has been reported from other populations, partly possible because some individuals may survive throughout the winter. The phylogenetic analysis revealed that the sequences from Egypt and Cyprus clustered with Afro-Eurasian populations. Thirty haplotypes were found in Egypt and Cyprus of which 21 were unique. The analysis further revealed that the nearest American <i>COX1</i> sequence was separated by 18 mutations. The high <i>COXI</i> divergence (5.1%) as well as the low gene flow (<i>Fst</i> = 0.75) between Afro-Eurasian and American populations, indicated that <i>A. trifasciata</i> has not been recently dispersed from America to Africa and other continents, but the genetic isolation was estimated to have happened around 2.04 My ago. If these spiders represent unique species or subspecies will need further research.
DOI: 10.13145/bacdive14085.20230509.8
title: Shewanella corallii Shnit-Orland et al. 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.