cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/1f677c39993cbdd2739cef7ad8dd758e
title: Combined data on plant species abundance and composition from LTER and other grasslands in the United States, 1943 - 2010

description: Understanding how biotic mechanisms confer stability in variable environments is a fundamental quest in ecology, and one that is becoming increasingly urgent with global change. Several mechanisms, notably a portfolio effect associated with species richness, compensatory dynamics generated by negative species covariance and selection for stable dominant species populations can increase the stability of the overall community. While the importance of these mechanisms is debated, few studies have contrasted their importance in an environmental context. We compiled nine long-term datasets of grassland species composition to evaluate the strength of biotic mechanisms of community stability and assess how these mechanisms change across precipitation gradients. Data were collected in replicate plots over time at nine different sites throughout the US (replicates within a site range from 5-100, plot sizes from 0.1 m² to 17 m²; minimum 9 years, maximum 30 years). Species abundance was measured as either percent cover, biomass, or allometrically-derived biomass. At all sites the measurement techniques and management regimes remained constant over the collection period, and the data collection methods were not relativized. For example, sites in which species composition were measured as percent cover do not require their estimates to sum to 100. For sites with long-term experimental treatments, only the control plots were included. These data have been presented in: Lauren M. Hallett, Joanna S. Hsu, Elsa E. Cleland, Scott L. Collins, Timothy L. Dickson, Emily C. Farrer, Laureano A. Gherardi, Katherine L. Gross, Richard J. Hobbs, Laura Turnbull, Katharine N. Suding. 2014. Biotic mechanisms of community stability shift along a precipitation gradient. Ecology 95:1693–1700. http://dx.doi.org/10.1890/13-0895.1
DOI: 10.6073/pasta/4a7b654d265cca39fabaac3f4aeb55b2
title: Shell geochemistry and environmental instability along the Georgia Coast during the Late Archaic Period (5000 - 3800 BP)

description: This dataset includes stable oxygen isotope (δ18O) data collected from eastern oysters (n=19) (Crassostrea virginica) and hard clams (n=59) (Mercenaria spp.) from the Late Archaic (ca. 50000-3500 cal. BP) Sapelo Shell Rings on Sapelo Island, Georgia. A total of 1064 isotope samples were collected and analyzed from these shells. The data are part of a larger project reconstructing paleo-climate and Native American adaption and resilience in the context of climate instability along the South Atlantic coast of North America during the Late Archaic Period. Shell isotope samples were collected by multiple researchers over the last decade. Carey Garland added to and cleaned the data between June 2020 and December 2021. The dataset was structured to include site name, location, and provenience (e.g., unit, level, etc.) associated with each shell analyzed, as well as all raw isotope data. The original database contains sensitive information, such as the specific location of archaeological sites. If a professional archaeologist needs site location information, they can contact the Georgia Archaeological Site File.
DOI: 10.6084/m9.figshare.18282497
title: Geography and climate drive the distribution and diversification of the cosmopolitan cyanobacterium <i>Microcoleus</i> (Oscillatoriales, Cyanobacteria)

description: Despite the extensive diversity of bacteria and their importance to the fundamental functioning of terrestrial ecosystems, their distribution patterns are still not fully known. To fill the gap and further understand the biogeographic patterns in bacteria, we investigated the phylogeographic structure and the underlying drivers of diversification among populations of the cyanobacterium <i>Microcoleus</i> spp. The phylogenetic history was reconstructed using 16S rRNA genes and the 16S–23S internal transcribed spacer (ITS) of 495 <i>Microcoleus</i> spp. isolates. Ancestral area and state reconstruction was employed to investigate the distributional and ecological patterns within <i>Microcoleus</i>. Both isolation by distance and isolation by environment were tested with distance matrices analysis. The phylogenetic signal tests were conducted in order to assess the influence of the climatic preferences on the diversification of <i>Microcoleus</i> isolates. The distribution and phylogenetic diversification of <i>Microcoleus</i> are driven by both isolation by distance and environment, leading to at least 13 distinct lineages that could represent novel cyanobacterial species. <i>Microcoleus</i> spp. exhibited a distinct phylogeographic structure within the respective lineages. The ancestral area and state reconstruction revealed that <i>Microcoleus</i> most likely arose in Europe in terrestrial habitats. The phylogenetic signal showed that the phylogeny significantly affects the climatic preferences of <i>Microcoleus</i> strains. Geographic distance and contemporary climatic conditions play significant roles in shaping the distribution and diversification of <i>Microcoleus</i>. The observed patterns of distribution may shift in the future due to the impact of climate change. Highlights <i>Microcoleus</i> exhibited distinct phylogeographic structure within the respective lineages.Geographic and environmental heterogeneity affect <i>Microcoleus</i> distribution and diversification.Genetically distinct lineages coexist at the same site. <i>Microcoleus</i> exhibited distinct phylogeographic structure within the respective lineages. Geographic and environmental heterogeneity affect <i>Microcoleus</i> distribution and diversification. Genetically distinct lineages coexist at the same site.
DOI: 10.6084/m9.figshare.19137380
title: Biogeography of six species in the planktonic diatom genus <i>Bacteriastrum</i> (Bacillariophyta)

description: Marine planktonic diatom species can exhibit contrasting distribution patterns, from endemic to cosmopolitan. Endemicity is counter-intuitive for planktonic species given their potentially large population sizes and ample migration opportunities by means of ocean currents. Here, we analyse the biogeography of six species of the diatom genus <i>Bacteriastrum</i> with apparently contrasting distribution patterns. Occurrence data obtained from metabarcode reads in samples from Ocean Sampling Day (OSD) sites and from <i>Tara</i> Oceans stations as well as from their observational records included in biodiversity data repositories of GBIF and OBIS were plotted in occurrence maps. According to metabarcoding data, the six species examined here occur all over the temperate and tropical parts of the oceans. Observational records corroborate this finding for <i>B. elegans</i>, <i>B. furcatum</i>, <i>B. hyalinum</i> and <i>B. mediterraneum</i>. Instead, atypical colony former <i>B. jadranum</i> is encountered at just a few distant sites, and solitary <i>B. parallelum</i> only in the Gulf of Naples. The metabarcoding data reveal that the latter two species are far more widely distributed than their actual sightings according to GBIF and OBIS, and that <i>B. hyalinum</i> also occurs in the Arctic. The most likely reasons for the discrepancies among the different data sources are the relatively recent description of <i>B. jadranum</i> and <i>B. parallelum</i>, their diminutive and inconspicuous habitus, and their possible misidentification in routine plankton counting. HIGHLIGHTS • Metabarcoding data of <i>Tara</i> Oceans and OSD discern <i>Bacteriastrum</i> species.• Pan-oceanic distribution of <i>Bacteriastrum</i> species according to global metabarcoding data.• Distribution patterns of phytoplankton species can be inferred from global metabarcode datasets.
DOI: 10.6084/m9.figshare.19137380.v1
title: Biogeography of six species in the planktonic diatom genus <i>Bacteriastrum</i> (Bacillariophyta)

description: Marine planktonic diatom species can exhibit contrasting distribution patterns, from endemic to cosmopolitan. Endemicity is counter-intuitive for planktonic species given their potentially large population sizes and ample migration opportunities by means of ocean currents. Here, we analyse the biogeography of six species of the diatom genus <i>Bacteriastrum</i> with apparently contrasting distribution patterns. Occurrence data obtained from metabarcode reads in samples from Ocean Sampling Day (OSD) sites and from <i>Tara</i> Oceans stations as well as from their observational records included in biodiversity data repositories of GBIF and OBIS were plotted in occurrence maps. According to metabarcoding data, the six species examined here occur all over the temperate and tropical parts of the oceans. Observational records corroborate this finding for <i>B. elegans</i>, <i>B. furcatum</i>, <i>B. hyalinum</i> and <i>B. mediterraneum</i>. Instead, atypical colony former <i>B. jadranum</i> is encountered at just a few distant sites, and solitary <i>B. parallelum</i> only in the Gulf of Naples. The metabarcoding data reveal that the latter two species are far more widely distributed than their actual sightings according to GBIF and OBIS, and that <i>B. hyalinum</i> also occurs in the Arctic. The most likely reasons for the discrepancies among the different data sources are the relatively recent description of <i>B. jadranum</i> and <i>B. parallelum</i>, their diminutive and inconspicuous habitus, and their possible misidentification in routine plankton counting. HIGHLIGHTS • Metabarcoding data of <i>Tara</i> Oceans and OSD discern <i>Bacteriastrum</i> species.• Pan-oceanic distribution of <i>Bacteriastrum</i> species according to global metabarcoding data.• Distribution patterns of phytoplankton species can be inferred from global metabarcode datasets.
DOI: 10.6084/m9.figshare.19207766
title: Ten new species of <i>Ulva</i> (Ulvophyceae, Chlorophyta) discovered in New Caledonia: genetic and morphological diversity, and bloom potential

description: <i>Ulva</i> is a green macroalgal genus with rich species diversity and worldwide distribution. While current knowledge on <i>Ulva</i> diversity focuses on temperate regions, genetic and morphological data in tropical and subtropical areas are scarce and the species richness is not clearly defined. The genus is known for its bloom-forming ability that can induce green tides leading to severe environmental and economic damage. In the last two decades, several important blooms of <i>Ulva</i> spp. have occurred in New Caledonia, requiring further investigations to identify the species involved. As knowledge of New Caledonian <i>Ulva</i> diversity is limited, an update to the <i>Ulva</i> spp. inventory in the area is essential. Based on <i>Ulva</i> specimens collected throughout New Caledonia (Grande Terre, Isle of Pines and Loyalty Islands), we (1) reassessed species diversity using species delimitation methods, (2) analysed morpho-anatomical characters to identify species and/or enrich their diagnosis, and (3) reconstructed a multilocus phylogeny (ITS, <i>rbc</i>L, <i>tuf</i>A) of the genus. We found 21 secondary species hypotheses (SSHs) among our dataset, from which five were successfully assigned to <i>U. lactuca, U. ohnoi, U. tepida, U. meridionalis</i> and <i>U. taeniata</i>. Ten SSHs were defined as new species for which we provided taxonomic description, and six other SSHs were singletons that will need to be data-enriched for better interpretation. Our concatenated multilocus matrix included 61 <i>Ulva</i> species. Of these, 15 species were found in New Caledonia and were moderately to strongly supported. Among the <i>Ulva</i> species found in New Caledonia, seven are known to be bloom-forming which highlights the need for strict regulation and regular monitoring of water quality, particularly in areas exposed to strong nutrient input where these species can form green tides. <i>Ulva</i> diversity in New Caledonia was reassessed with 15 species highlighted.Ten new species have been discovered in New Caledonia.Indigenous species caused recent green tides in New Caledonia. <i>Ulva</i> diversity in New Caledonia was reassessed with 15 species highlighted. Ten new species have been discovered in New Caledonia. Indigenous species caused recent green tides in New Caledonia.
DOI: 10.6084/m9.figshare.19207766.v2
title: Ten new species of <i>Ulva</i> (Ulvophyceae, Chlorophyta) discovered in New Caledonia: genetic and morphological diversity, and bloom potential

description: <i>Ulva</i> is a green macroalgal genus with rich species diversity and worldwide distribution. While current knowledge on <i>Ulva</i> diversity focuses on temperate regions, genetic and morphological data in tropical and subtropical areas are scarce and the species richness is not clearly defined. The genus is known for its bloom-forming ability that can induce green tides leading to severe environmental and economic damage. In the last two decades, several important blooms of <i>Ulva</i> spp. have occurred in New Caledonia, requiring further investigations to identify the species involved. As knowledge of New Caledonian <i>Ulva</i> diversity is limited, an update to the <i>Ulva</i> spp. inventory in the area is essential. Based on <i>Ulva</i> specimens collected throughout New Caledonia (Grande Terre, Isle of Pines and Loyalty Islands), we (1) reassessed species diversity using species delimitation methods, (2) analysed morpho-anatomical characters to identify species and/or enrich their diagnosis, and (3) reconstructed a multilocus phylogeny (ITS, <i>rbc</i>L, <i>tuf</i>A) of the genus. We found 21 secondary species hypotheses (SSHs) among our dataset, from which five were successfully assigned to <i>U. lactuca, U. ohnoi, U. tepida, U. meridionalis</i> and <i>U. taeniata</i>. Ten SSHs were defined as new species for which we provided taxonomic description, and six other SSHs were singletons that will need to be data-enriched for better interpretation. Our concatenated multilocus matrix included 61 <i>Ulva</i> species. Of these, 15 species were found in New Caledonia and were moderately to strongly supported. Among the <i>Ulva</i> species found in New Caledonia, seven are known to be bloom-forming which highlights the need for strict regulation and regular monitoring of water quality, particularly in areas exposed to strong nutrient input where these species can form green tides. <i>Ulva</i> diversity in New Caledonia was reassessed with 15 species highlighted.Ten new species have been discovered in New Caledonia.Indigenous species caused recent green tides in New Caledonia. <i>Ulva</i> diversity in New Caledonia was reassessed with 15 species highlighted. Ten new species have been discovered in New Caledonia. Indigenous species caused recent green tides in New Caledonia.
DOI: 10.6084/m9.figshare.19307137
title: Insight into the morphology and genetic diversity of the <i>Chaetoceros tenuissimus</i> (Bacillariophyta) species complex

description: Among the marine planktonic diatoms, <i>Chaetoceros</i> is among the most species-rich genera, and many <i>Chaetoceros</i> species are considered important primary producers. However, little is known about the ecology and distribution of the few small solitary species within this genus, including <i>Chaetoceros tenuissimus</i>. This article describes a minute <i>Chaetoceros</i> strain, identified as <i>C. tenuissimus</i> (named CT16ED) that was isolated at a coastal lagoon in Corsica Island, Western Mediterranean. The strain was characterized by light microscopy and scanning and transmission electron microscopy, with a specific focus on the fine structure and construction of setae and its behaviour in culture. The CT16ED strain was compared with other strains we isolated from the species type locality (Ostend Harbour, North Sea) by sequencing a fragment of the nuclear ribosomal DNA (rDNA) spanning from the 18S rDNA to the D3 region of the 28S rDNA, and the plastid <i>rbc</i>L gene that codes the large RuBisCO subunit. Based on the literature and the available sequence data, the analysed strains were similar to <i>C. tenuissimus</i> but the phylogenetic analysis indicated a <i>C. tenuissimus</i> species complex that contained several clades, therefore the current taxonomic status of <i>C. tenuissimus</i> is discussed. The comparison with the available rDNA and <i>rbc</i>L sequencing data of strains assigned to species considered as synonyms of <i>C. tenuissimus</i>, including <i>Chaetoceros simplex</i> var. <i>calcitrans, Chaetoceros calcitrans</i> and <i>Chaetoceros calcitrans</i> f. <i>pumilus</i>, suggested that these taxa are paraphyletic within the genus <i>Chaetoceros</i>.
DOI: 10.6084/m9.figshare.19307137.v1
title: Insight into the morphology and genetic diversity of the <i>Chaetoceros tenuissimus</i> (Bacillariophyta) species complex

description: Among the marine planktonic diatoms, <i>Chaetoceros</i> is among the most species-rich genera, and many <i>Chaetoceros</i> species are considered important primary producers. However, little is known about the ecology and distribution of the few small solitary species within this genus, including <i>Chaetoceros tenuissimus</i>. This article describes a minute <i>Chaetoceros</i> strain, identified as <i>C. tenuissimus</i> (named CT16ED) that was isolated at a coastal lagoon in Corsica Island, Western Mediterranean. The strain was characterized by light microscopy and scanning and transmission electron microscopy, with a specific focus on the fine structure and construction of setae and its behaviour in culture. The CT16ED strain was compared with other strains we isolated from the species type locality (Ostend Harbour, North Sea) by sequencing a fragment of the nuclear ribosomal DNA (rDNA) spanning from the 18S rDNA to the D3 region of the 28S rDNA, and the plastid <i>rbc</i>L gene that codes the large RuBisCO subunit. Based on the literature and the available sequence data, the analysed strains were similar to <i>C. tenuissimus</i> but the phylogenetic analysis indicated a <i>C. tenuissimus</i> species complex that contained several clades, therefore the current taxonomic status of <i>C. tenuissimus</i> is discussed. The comparison with the available rDNA and <i>rbc</i>L sequencing data of strains assigned to species considered as synonyms of <i>C. tenuissimus</i>, including <i>Chaetoceros simplex</i> var. <i>calcitrans, Chaetoceros calcitrans</i> and <i>Chaetoceros calcitrans</i> f. <i>pumilus</i>, suggested that these taxa are paraphyletic within the genus <i>Chaetoceros</i>.
DOI: 10.6084/m9.figshare.19207766.v1
title: Ten new species of <i>Ulva</i> (Ulvophyceae, Chlorophyta) discovered in New Caledonia: genetic and morphological diversity, and bloom potential

description: <i>Ulva</i> is a green macroalgal genus with rich species diversity and worldwide distribution. While current knowledge on <i>Ulva</i> diversity focuses on temperate regions, genetic and morphological data in tropical and subtropical areas are scarce and the species richness is not clearly defined. The genus is known for its bloom-forming ability that can induce green tides leading to severe environmental and economic damage. In the last two decades, several important blooms of <i>Ulva</i> spp. have occurred in New Caledonia, requiring further investigations to identify the species involved. As knowledge of New Caledonian <i>Ulva</i> diversity is limited, an update to the <i>Ulva</i> spp. inventory in the area is essential. Based on <i>Ulva</i> specimens collected throughout New Caledonia (Grande Terre, Isle of Pines and Loyalty Islands), we (1) reassessed species diversity using species delimitation methods, (2) analysed morpho-anatomical characters to identify species and/or enrich their diagnosis, and (3) reconstructed a multilocus phylogeny (ITS, <i>rbc</i>L, <i>tuf</i>A) of the genus. We found 21 secondary species hypotheses (SSHs) among our dataset, from which five were successfully assigned to <i>U. lactuca, U. ohnoi, U. tepida, U. meridionalis</i> and <i>U. taeniata</i>. Ten SSHs were defined as new species for which we provided taxonomic description, and six other SSHs were singletons that will need to be data-enriched for better interpretation. Our concatenated multilocus matrix included 61 <i>Ulva</i> species. Of these, 15 species were found in New Caledonia and were moderately to strongly supported. Among the <i>Ulva</i> species found in New Caledonia, seven are known to be bloom-forming which highlights the need for strict regulation and regular monitoring of water quality, particularly in areas exposed to strong nutrient input where these species can form green tides. <i>Ulva</i> diversity in New Caledonia was reassessed with 15 species highlighted.Ten new species have been discovered in New Caledonia.Indigenous species caused recent green tides in New Caledonia. <i>Ulva</i> diversity in New Caledonia was reassessed with 15 species highlighted. Ten new species have been discovered in New Caledonia. Indigenous species caused recent green tides in New Caledonia.
DOI: 10.6084/m9.figshare.19355074
title: Molecular diversity of the genus <i>Cryptomonas</i> (Cryptophyceae) in Russia

description: Molecular data were used to revise the diversity of the genus <i>Cryptomonas</i> in Russia, using samples collected across nine geographic regions within Russia from 2015–2019. Several molecular markers were used: nuclear SSU, LSU and ITS2 rDNA, and plastid <i>psb</i>A. In total, 24 species of the genus <i>Cryptomonas</i> were identified in the country’s fresh waters based on 122 different strains. Six new species were identified and are described here (<i>Cryptomonas matvienkoae</i> sp. nov., <i>C. furtiva</i> sp. nov., <i>C. paludosa</i> sp. nov., <i>C. ursina</i> sp. nov., <i>C. kisselevii</i> sp. nov. and <i>C. meshchorana</i> sp. nov.), and three taxa are emended (<i>Cryptomonas skujae, C. platyuris</i> and <i>C. obovata</i>). These new and emended species group in clades with the previously described species or represent new lineages on the phylogenetic tree. Seven morphospecies, previously reported in Russia, are confirmed by molecular methods, and two unidentified taxa are also reported. <b>HIGHLIGHTS</b> Molecular investigations of the genus <i>Cryptomonas</i> in Russia revealed 24 species.Descriptions of three species were emended.Six species new to science were described. Molecular investigations of the genus <i>Cryptomonas</i> in Russia revealed 24 species. Descriptions of three species were emended. Six species new to science were described.
DOI: 10.6084/m9.figshare.19355074.v1
title: Molecular diversity of the genus <i>Cryptomonas</i> (Cryptophyceae) in Russia

description: Molecular data were used to revise the diversity of the genus <i>Cryptomonas</i> in Russia, using samples collected across nine geographic regions within Russia from 2015–2019. Several molecular markers were used: nuclear SSU, LSU and ITS2 rDNA, and plastid <i>psb</i>A. In total, 24 species of the genus <i>Cryptomonas</i> were identified in the country’s fresh waters based on 122 different strains. Six new species were identified and are described here (<i>Cryptomonas matvienkoae</i> sp. nov., <i>C. furtiva</i> sp. nov., <i>C. paludosa</i> sp. nov., <i>C. ursina</i> sp. nov., <i>C. kisselevii</i> sp. nov. and <i>C. meshchorana</i> sp. nov.), and three taxa are emended (<i>Cryptomonas skujae, C. platyuris</i> and <i>C. obovata</i>). These new and emended species group in clades with the previously described species or represent new lineages on the phylogenetic tree. Seven morphospecies, previously reported in Russia, are confirmed by molecular methods, and two unidentified taxa are also reported. <b>HIGHLIGHTS</b> Molecular investigations of the genus <i>Cryptomonas</i> in Russia revealed 24 species.Descriptions of three species were emended.Six species new to science were described. Molecular investigations of the genus <i>Cryptomonas</i> in Russia revealed 24 species. Descriptions of three species were emended. Six species new to science were described.