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159 results for “diversity determinants”
Data from: Pyramids of species richness: the determinants and distribution of species diversity across trophic levels
How species richness is distributed across trophic levels determines several dimensions of ecosystem functioning, including herbivory, predation, and decomposition rates. We perform a meta-analysis of 72 large published food webs to investigate their trophic diversity structure and possible endogenous, exogenous, and methodological causal variables. Consistent with classic theory, we found that published food webs can generally be described as 'pyramids of species richness'. The food webs were more predator-poor, prey-rich and hierarchical than is expected by chance or by the niche or cascade models. The trophic species richness distribution also depended on centrality, latitude, ecosystem-type and methodological bias. Although trophic diversity structure is generally pyramidal, under many conditions the structure is consistently uniform or inverse-pyramidal. Our meta-analysis adds nuance to classic assumptions about food web structure: diversity decreases with trophic level, but not under all conditions, and the decrease may be scale-dependent.
Data from: Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen-forming family Parmeliaceae
Microbial symbionts are instrumental to the ecological and long-term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species-rich lichen-forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer (ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units (OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study.
Data from: Population size and time since island isolation determine genetic diversity loss in insular frog populations
Understanding the factors that contribute to loss of genetic diversity in fragmented populations is crucial for conservation measurements. Land-bridge archipelagoes offer ideal model systems for identifying the long-term effects of these factors on genetic variations in wild populations. In this study, we used 9 microsatellite markers to quantify genetic diversity and differentiation of 810 pond frogs (Pelophylax nigromaculataus) from 24 islands of the Zhoushan Archipelago and 3 sites on nearby mainland China and estimated the effects of the island area, population size, time since island isolation, distance to the mainland and distance to the nearest larger island on reduced genetic diversity of insular populations. The mainland populations displayed higher genetic diversity than insular populations. Genetic differentiations and no obvious gene flow were detected among the frog populations on the islands. Hierarchical partitioning analysis showed that only time since island isolation (square root transformed) and population size (log transformed) significantly contributed to insular genetic diversity. These results suggest that decreased genetic diversity and genetic differentiations among insular populations may have been caused by random genetic drift following isolation by rising sea levels during the Holocene. The results provide strong evidence for a relationship between retained genetic diversity and population size and time since island isolation for pond frogs on the islands, consistent with the prediction of the neutral theory for finite populations. Our study highlights the importance of the size and estimated isolation time of populations in understanding the mechanisms of genetic diversity loss and differentiation in fragmented wild populations.
Supplementary Material: Decoding sequence determinants of gene expression in diverse cellular and disease states
<p>Supplementary material for the following publication:</p> <p><strong>Decoding sequence determinants of gene expression in diverse cellular and disease states</strong></p> <p>Avantika Lal*,1, Alexander Karollus*,1,2,3, Laura Gunsalus1, David Garfield4, Surag Nair1, Alex M Tseng1, M Grace Gordon5, John Blischak6, Bryce van de Geijn6, Tushar Bhangale6, Jenna L Collier1, Nathaniel Diamant1, Tommaso Biancalani1, Hector Corrada Bravo1, Gabriele Scalia1, Gokcen Eraslan1</p> <p>*Equal contributions</p> <p>1Biology Research | AI Development, gRED Computational Sciences, Genentech, South San Francisco, CA 94080, USA</p> <p>2School of Computation, Information and Technology, Technical University of Munich, Germany</p> <p>3Munich Center for Machine Learning </p> <p>4OMNI Bioinformatics and Department of Regenerative Medicine, Genentech, South San Francisco, CA 94080, USA</p> <p>5 Department of Cellular and Tissue Genomics, Genentech Research and Early Development, Genentech, South San Francisco, CA 94080, USA</p> <p>6 Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA</p> <p><strong><br></strong>Correspondence: Avantika Lal (<a href="mailto:lal.avantika@gene.com">lal.avantika@gene.com</a>), Gokcen Eraslan (<a href="mailto:eraslan.gokcen@gene.com">eraslan.gokcen@gene.com</a>)</p>
Figure 3 from: Santos-Silva C, Louro R, Natário B, Nobre T (2021) Lack of knowledge on ecological determinants and cryptic lifestyles hinder our understanding of Terfezia diversity. MycoKeys 84: 1-14. https://doi.org/10.3897/mycokeys.84.71372
Figure 3 Terfezia species collected in the present work AT. arenariaBT. fanfaniCT. cistophilaDT. griseaET. dunensisFT. extremadurensisGT. lusitanicaHT. piniIT. solaris-libera.
Figure 1 from: Santos-Silva C, Louro R, Natário B, Nobre T (2021) Lack of knowledge on ecological determinants and cryptic lifestyles hinder our understanding of Terfezia diversity. MycoKeys 84: 1-14. https://doi.org/10.3897/mycokeys.84.71372
Figure 1 a Phylogenetic relationship between Terfezia species. The reconstructed phylogeny corresponds to the majority rule consensus tree higher than 0.50 of trees sampled in a Bayesian analysis, and the posterior probability values are shown for main nodes b clades with new sequenced specimens collected within the present study.
Figure 2 from: Santos-Silva C, Louro R, Natário B, Nobre T (2021) Lack of knowledge on ecological determinants and cryptic lifestyles hinder our understanding of Terfezia diversity. MycoKeys 84: 1-14. https://doi.org/10.3897/mycokeys.84.71372
Figure 2 Phylogenetic reconstruction of intra-species diversity (Fig. 1) linking to soil properties and putative host plant aT. arenariabT. fanfanicT. grisea [specimens in the circle represent deviations from the ecological grouping, see text for details] dT. lusitanica. The other species are identified and their relation to soil and host plant are presented in the main text.
Supplementary material 1 from: Santos-Silva C, Louro R, Natário B, Nobre T (2021) Lack of knowledge on ecological determinants and cryptic lifestyles hinder our understanding of Terfezia diversity. MycoKeys 84: 1-14. https://doi.org/10.3897/mycokeys.84.71372
Table S1
Linked collectors and determiners for: Complex diversity in a mainly tropical group of ant parasitoids: Revision of the Orasema stramineipes species group (Hymenoptera: Chalcidoidea: Eucharitidae).
Natural history specimen data linked to collectors and determiners held within, "Complex diversity in a mainly tropical group of ant parasitoids: Revision of the Orasema stramineipes species group (Hymenoptera: Chalcidoidea: Eucharitidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/d89af63d-c093-4908-bd61-2b26133bb7d6">https://bionomia.net/dataset/d89af63d-c093-4908-bd61-2b26133bb7d6</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/d89af63d-c093-4908-bd61-2b26133bb7d6">https://gbif.org/dataset/d89af63d-c093-4908-bd61-2b26133bb7d6</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches.
Natural history specimen data linked to collectors and determiners held within, "First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/0bb8a532-1b00-45e6-99ea-774b47eae650">https://bionomia.net/dataset/0bb8a532-1b00-45e6-99ea-774b47eae650</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/0bb8a532-1b00-45e6-99ea-774b47eae650">https://gbif.org/dataset/0bb8a532-1b00-45e6-99ea-774b47eae650</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: A review of Augochlora (Oxystoglossella) bees from South America: unexpected Amazonian diversity and assessment of vulnerable species.
Natural history specimen data linked to collectors and determiners held within, "A review of Augochlora (Oxystoglossella) bees from South America: unexpected Amazonian diversity and assessment of vulnerable species". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/0f7f9d5d-4eaf-4464-83d9-d30749f03fc5">https://bionomia.net/dataset/0f7f9d5d-4eaf-4464-83d9-d30749f03fc5</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/0f7f9d5d-4eaf-4464-83d9-d30749f03fc5">https://gbif.org/dataset/0f7f9d5d-4eaf-4464-83d9-d30749f03fc5</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: The morphological diversity of Mymaridae (Hymenoptera): an atlas of scanning electron micrographs. Part 1. General overview and structure of the head.
Natural history specimen data linked to collectors and determiners held within, "The morphological diversity of Mymaridae (Hymenoptera): an atlas of scanning electron micrographs. Part 1. General overview and structure of the head". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/1d5719a4-b5f9-46ff-8d27-4010f0eed663">https://bionomia.net/dataset/1d5719a4-b5f9-46ff-8d27-4010f0eed663</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/1d5719a4-b5f9-46ff-8d27-4010f0eed663">https://gbif.org/dataset/1d5719a4-b5f9-46ff-8d27-4010f0eed663</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: The Hercules pseudoscorpions from Madagascar: A systematic study of Feaellidae (Pseudoscorpiones: Feaelloidea) highlights regional endemism and diversity in one of the " hottest " biodiversity hotspots.
Natural history specimen data linked to collectors and determiners held within, "The Hercules pseudoscorpions from Madagascar: A systematic study of Feaellidae (Pseudoscorpiones: Feaelloidea) highlights regional endemism and diversity in one of the " hottest " biodiversity hotspots". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/bac17de6-baf9-4fee-9ded-268adbb26a61">https://bionomia.net/dataset/bac17de6-baf9-4fee-9ded-268adbb26a61</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/bac17de6-baf9-4fee-9ded-268adbb26a61">https://gbif.org/dataset/bac17de6-baf9-4fee-9ded-268adbb26a61</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: University of California, Davis, Center for Plant Diversity - Lichen Herbarium.
Natural history specimen data linked to collectors and determiners held within, "University of California, Davis, Center for Plant Diversity - Lichen Herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/cf6a5ca0-c9ca-4d99-85df-598bc118226d">https://bionomia.net/dataset/cf6a5ca0-c9ca-4d99-85df-598bc118226d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/cf6a5ca0-c9ca-4d99-85df-598bc118226d">https://gbif.org/dataset/cf6a5ca0-c9ca-4d99-85df-598bc118226d</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: University of California, Davis, Center for Plant Diversity - Bryophyte Herbarium.
Natural history specimen data linked to collectors and determiners held within, "University of California, Davis, Center for Plant Diversity - Bryophyte Herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/08ed4a7c-2948-48d1-98f1-8e395d8a5626">https://bionomia.net/dataset/08ed4a7c-2948-48d1-98f1-8e395d8a5626</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/08ed4a7c-2948-48d1-98f1-8e395d8a5626">https://gbif.org/dataset/08ed4a7c-2948-48d1-98f1-8e395d8a5626</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Targeting a portion of central European spider diversity for permanent preservation.
Natural history specimen data linked to collectors and determiners held within, "Targeting a portion of central European spider diversity for permanent preservation". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/caaa6bf4-c6a1-4960-8b40-c817be0caaf0">https://bionomia.net/dataset/caaa6bf4-c6a1-4960-8b40-c817be0caaf0</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/caaa6bf4-c6a1-4960-8b40-c817be0caaf0">https://gbif.org/dataset/caaa6bf4-c6a1-4960-8b40-c817be0caaf0</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Exceptional diversity of Tischeriidae (Lepidoptera) from a single tropical forest site in Belize, Central America.
Natural history specimen data linked to collectors and determiners held within, "Exceptional diversity of Tischeriidae (Lepidoptera) from a single tropical forest site in Belize, Central America". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/6b090571-aa68-41fc-b802-c650c6c2cb69">https://bionomia.net/dataset/6b090571-aa68-41fc-b802-c650c6c2cb69</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/6b090571-aa68-41fc-b802-c650c6c2cb69">https://gbif.org/dataset/6b090571-aa68-41fc-b802-c650c6c2cb69</a>. Formatted as a Frictionless Data package.
Figure 2 in Genetic diversity of Atherina hepsetus (Osteichthyes: Atherinidae) populations as determined by RFLP analysis of three mtDNA regions
Figure 2. Neighbor-joining (Saitou and Nei 1987) cladogram, based on the net nucleotide divergence.
Geographic patterns of Lucanus (Coleoptera: Lucanidae) species diversity and its environmental determinants in China
Open the record for dataset details and reuse information.
Data from: Pyramids of species richness: the determinants and distribution of species diversity across trophic levels
Open the record for dataset details and reuse information.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.
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