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131 results for “species-richness”
Data from: Species abundance fluctuations over 31 years are associated with plant-soil feedback in a species-rich mountain meadow
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Data from: Phylogeny does not predict the outcome of heterospecific pollen-pistil interactions in a species-rich alpine plant community
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Species-rich old grasslands have beneficial effects on the health and gut microbiome of bumblebees
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Data from: Coevolution and the diversification of nestling ornamentation in a species-rich avian radiation
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Anther modes influence diversification rates in the animal-pollinated species-rich Didymocarpoideae
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Data from: Small-scale variation in fuel loads differentially affects two co-dominant bunchgrasses in a species-rich pine savanna
Ecological disturbances frequently control the occurrence and patterning of dominant plants in high-diversity communities like C4 grasslands and savannas. In such ecosystems disturbance-related processes can have important implications for species, and for whole communities when those species are dominant, yet mechanistic understanding of such processes remains fragmentary. Multiple bunchgrass species commonly co-dominate disturbance-dependent and species-rich pine savannas, where small-scale fuel heterogeneity may influence bunchgrass survival and growth following fires. We quantified how fire in locally varying fuel loads influenced dynamics of dominant C4 bunchgrasses in a species-rich pine savanna in southeastern Louisiana, USA. We focused on two congeneric, co-dominant species (Schizachyrium scoparium and S. tenerum) with similar growth forms, functional traits and reproductive strategies to highlight effects of fuel heterogeneity during fires. In experimental plots with either reduced or increased fuels versus controls with unmanipulated fuels, we compared: 1) bunchgrass damage and 2) mortality from fires; 3) subsequent growth and 4) flowering. Compared to controls, fire with increased fuels caused greater damage, mortality and subsequent flowering, but did not affect post-fire growth. Fire with reduced fuels had no effect on any of the four measures. The two species responded differently to fire with increased fuels – S. scoparium incurred measurably more damage and mortality than S. tenerum. Logistic regression indicated that the larger average size of S. tenerum tussocks made them resistant to more severe burning where fuels were increased. We speculate that locally increased fuel loading may be important in pine savannas for creating colonization sites because where fuels are light or moderate, dominant bunchgrasses persist through fires. Small-scale heterogeneity in fires, and differences in how species tolerate fire may together promote shared local dominance by different bunchgrasses.
Data from: Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards
Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus. To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic diversity. Using a phylogenetically informed approach, we tested whether variation in genetic diversity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic diversity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic diversity, suggesting that genetic diversity might be difficult to predict at shallower phylogenetic scales.
Data from: Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities
Freshwater habitats are of high conservation value and provide a wide range of ecosystem services. Effective management requires regular monitoring. However, conventional methods based on direct observation or specimen collection are so invasive, expensive and labour-intensive that frequent monitoring is uncommon. Here, we test whether the evaluation of environmental DNA (eDNA) from water based on a simple protocol can be used for assessing biodiversity. We use universal metazoan primers for characterizing water eDNA across horizontal and vertical spatial dimensions in two reservoirs with known species diversity for two key taxa. eDNA obtained directly from 42 samples × 15 ml water (total = 630 ml) per reservoir yielded DNA signatures for more than 500 metazoan species, of which 105 could be identified to species/genus based on DNA barcodes. We show that eDNA can be used to assign each water sample to its reservoir of origin, and that eDNA outperforms conventional survey methods in single-sample richness comparisons, while revealing evidence for hundreds of unknown species that are undetected by conventional bioassessment methods. eDNA also confirms the presence of a recently discovered invasive snail species and provides evidence for the continued survival of a rare native species of goby not sighted in that habitat since 2007. eDNA thus promises to be a useful addition to the bioassessment toolbox for freshwater systems.
Data from: A pre-Miocene Irano-Turanian cradle: origin and diversification of the species-rich monocot genus Gagea (Liliaceae)
The Irano‐Turanian (IT) floristic region is considered an important centre of origin for many taxa. However, there is a lack of studies dealing with typical IT genera that also occur in neighbouring areas. The species-rich monocot genus Gagea Salisb. shows a centre of diversity in IT region and a distribution in adjacent regions, therefore representing a good study object to investigate spatial and temporal relationships among IT region and its neighbouring areas (East-Asia, Euro-Siberia, Himalaya, and Mediterranean). We aimed at (i) testing the origin of the genus and of its major lineages in the IT region, (ii) reconstructing divergence times and (iii) reconstructing colonisation events. To address these problems, sequences of the ribosomal DNA internal transcribed spacer (ITS) region of 418 individuals and chloroplast intergenic spacers sequences (psbA-trnH, trnL-trnF) of 497 individuals, representing 116 species from all sections of the genus and nearly its entire distribution area were analysed. Divergence times were estimated under a random molecular clock based on nrITS phylogeny, which was the most complete data set regarding the representation of species and distribution areas. Ancestral distribution ranges were estimated for the nrITS data set as well as for a combined data set, revealing that Gagea most likely originated in southwestern Asia. This genus first diversified there starting in the Early Miocene. In the Middle Miocene, Gagea migrated to the Mediterranean and to East Asia, while migration into Euro-Siberia took place in the Late Miocene. During the Pleistocene, the Arctic was colonised and Gagea serotina, the most widespread species, reached North America. The Mediterranean basin was colonised multiple times from southwestern Asia or Euro-Siberia. Most of the currently existing species originated during the last 3 Ma.
Regional assemblages shaped by historical and contemporary factors: evidence from a species-rich insect group
<p><span><span><span><span><span><span><span><span><span><span><span>Understanding the complex diversity patterns is one of the main aims of community ecology. It is important to take both historical and contemporary factors into account in investigating the potential roles in assembling diversity patterns. Here, We compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State-Speciation and Extinction model to track the origins of these patterns. We subsequently estimate diversification rates of the two moth assemblages. Finally, we explored the effects of contemporary ecological factors on diversity patterns.<b> </b>From 7788 specimens we identified to 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Overall, moths in YS mountains showed higher species diversity and phylogenetic diversity than in TH mountains. Ancestral range analysis indicated YS as the origin. Significant historical dispersals from YS to TH mountains were detected. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow, were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we showed that a combined analysis of diversity patterns at multiples scales, including community, population and species levels, incorporating both historical and contemporary factors, are very informative for understanding factors of shaping diversity patterns.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Information dropout patterns in restriction site associated DNA phylogenomics and a comparison with multilocus Sanger data in a species-rich moth genus
A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, RAD (Restriction site Associated DNA) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for non-model species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely un-investigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6,172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3,256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.
FIGURE 3 in Iguanian species-richness in the Andes of boreal Patagonia: Evidence for an additional new Liolaemus lizard from Argentina lacking precloacal glands (Iguania, Liolaeminae)
FIGURE 3. Variation in morphological traits in the holotype male (a, c, e) and allotype female (b, d, f) of Liolaemus tregenzai. Dorsal body scales in the holotype (a) and in the allotype, ventral body scales in the holotype (c) and in the allotype, and cloacal region in the holotype (e) and in the allotype (f).
FIGURE 1 in Iguanian species-richness in the Andes of boreal Patagonia: Evidence for an additional new Liolaemus lizard from Argentina lacking precloacal glands (Iguania, Liolaeminae)
FIGURE 1. Holotype (a; MLP.R. 5274) and female paratype (b; MLP.R. 5276) of Liolaemus tregenzai in dorsal view.
FIGURE 4 in Iguanian species-richness in the Andes of boreal Patagonia: Evidence for an additional new Liolaemus lizard from Argentina lacking precloacal glands (Iguania, Liolaeminae)
FIGURE 4. Map of the North-Western Patagonia of Argentina and Chile, showing the distribution of Liolaemus tregenzai and L. neuquensis (black circle; Copahue Volcano) and L. coeruleus (both black triangles; Pino Hachado, Primeros Pinos)
FIGURES 130–140 in Species-richness in the Oriental fungus-feeding thrips of the genus Azaleothrips (Thysanoptera, Phlaeothripidae)
FIGURES 130–140. Azaleothrips species. simulans sp.n. female 130–135: (130) head, macroptera; (131) pronotum, macroptera; (132) mesonotum, metanotum & pelta, macroptera; (133) tergite II, macroptera; (134) mesonotum, metanotum & pelta, microptera; (135) tergite II, microptera. sulawesicus sp.n. 136–140: (136) head, female; (137) pronotum, female; (138) meso & metanotum, female; (139) tergite II, female; (140) sternite VIII, male.
FIGURES 153–161 in Species-richness in the Oriental fungus-feeding thrips of the genus Azaleothrips (Thysanoptera, Phlaeothripidae)
FIGURES 153–161. Azaleothrips species. toshifumii sp.n. female 153–156: (153) head; (154) pronotum; (155) meso & metanotum; (156) tergite II. vietnamensis sp.n. female 157–161: (157) head; (158) pronotum; (159) meso & metanotum; (160) tergite II; (161) tergite V.
FIGURES 111–122 in Species-richness in the Oriental fungus-feeding thrips of the genus Azaleothrips (Thysanoptera, Phlaeothripidae)
FIGURES 111–122. Azaleothrips species. reticulatus sp.n. female 111–116: (111) head; (112) antennal segments VII & VIII; (113) pronotum; (114) meso & metanotum; (115) tergite II; (116) tergite V. richardi sp.n., female 117–122: (117) head; (118) antennal segments VII & VIII; (119) pronotum; (120) right fore leg; (121) meso & metanotum; (122) tergite II.
FIGURES 123–129 in Species-richness in the Oriental fungus-feeding thrips of the genus Azaleothrips (Thysanoptera, Phlaeothripidae)
FIGURES 123–129. Azaleothrips siamensis, female. (123) head; (124) pronotum; (125–128) mouth cone; (129) meso & metanotum.
FIGURES 141–152 in Species-richness in the Oriental fungus-feeding thrips of the genus Azaleothrips (Thysanoptera, Phlaeothripidae)
FIGURES 141–152. Azaleothrips species. taiwanus sp.n. female 141–146: (141) head; (142) antennal segments VII & VIII; (143) pronotum; (144) meso & metanotum; (145) right fore leg; (146) tergite II. templeri sp.n. female 147–152: (147) head; (148) antennal segments VII & VIII; (149) pronotum; (150) meso & metanotum; (151) right fore leg; (152) tergite II.
FIGURES 87–96 in Species-richness in the Oriental fungus-feeding thrips of the genus Azaleothrips (Thysanoptera, Phlaeothripidae)
FIGURES 87–96. Azaleothrips species. mindanaoensis sp.n. female 87–91: (87) head; (88) antennal segments III & IV; (89) antennal segments VII & VIII; (90) pronotum; (91) meso & metanotum. philippinensis sp.n. 92–96: (92) head, female; (93) pronotum, female; (94) meso & metanotum, female; (95) tergite II, female; (96) sternite VIII, male.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.