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836 results for “species limits”
Data from: The thermal limits of native plant species in California Coastal Sage Scrub
<p>Field and laboratory data for Goldsmith et al. (<em>In Review</em>) entitled, "The thermal limits of native plant species in California Coastal Sage Scrub." Four data files are included: </p> <p><strong><em>Goldsmithetal_PlantFunctionalTraitMetaData-18July24.xlsx </em></strong>-Provides metadata (header, description, units, measurement type, and expample) for each column of the file entitled "<em>Goldsmithetal_PlantFunctionalTraitData-18July24.csv." </em></p> <p><em><strong>Goldsmithetal_PlantFunctionalTraitData-18July24.csv </strong>- </em>Provides raw data for field and lab observations of plant functional traits as described in the methods section of this data record. </p> <p><em><strong>Goldsmithetal_PlantFvFmLabData-29March24.csv </strong>- </em>Provides raw data for experimental lab observations of leaf fv/fm following experimental heat treatments as described in the methods section of this data record. <em><br></em></p> <p><em><strong>Goldsmithetal_PlantFvFmLabMetaData-2Aug23.xlsx</strong> - </em>Provides metadata (header, description, units, measurement type, and expample) for each column of the file entitled "Goldsmithetal_PlantFvFmLabData-29March24.csv." </p> <p> </p> <p>Contact Greg Goldsmith (goldsmith at chapman dot edu) for additional information. </p>
Data from: Genomic analysis reveals limited hybridization among three giraffe species in Kenya
<p>The data deposited here was generated by and reported in Coimbra <em>et al.</em> (2023).</p> <p><em>SNP calling and linkage pruning</em></p> <ul> <li><strong>snp_calling_per_species.tar.gz:</strong> includes a genotype likelihoods (GL) file estimated with ANGSD for each giraffe species.</li> <li><strong>sampled_ld.tar.gz:</strong> contains a random sample of estimated pairwise <em>r<sup>2</sup></em> values for each species used to fit linkage disequilibrium (LD) decay curves.</li> <li><strong>ld_pruned_snps.tar.gz:</strong> contains an LD-pruned ANGSD GL file per species.</li> <li><strong>snp_calling_combined.tar.gz:</strong> includes a single LD-pruned ANGSD GL file comprising all sampled individuals of the three giraffe species analyzed in this study.</li> </ul> <p><em>Relatedness</em></p> <ul> <li><strong>relatedness.tar.gz:</strong> contains the input and output files used with NGSremix to estimate relatedness among giraffe in the dataset.</li> <li><strong>snp_calling_combined_unrelated.tar.gz:</strong> includes a single LD-pruned ANGSD GL file comprising all unrelated individuals of the three giraffe species analyzed in this study.</li> </ul> <p><em>Population structure and admixture</em></p> <ul> <li><strong>pcangsd.tar.gz:</strong> contains the covariance matrix generated by PCAngsd.</li> <li><strong>ngsadmix.tar.gz:</strong> includes run likelihood lists for each K value ranging from 1 to 11, as well as the admixture proportions (stored in '.qopt' files) inferred from the run with the highest log-likelihood for each K in NGSadmix.</li> <li><strong>evaladmix.tar.gz:</strong> contains the pairwise correlation of residuals between individuals estimated with evalAdmix for the NGSadmix runs with the highest log-likelihood run for each K.</li> </ul> <p><em>SNP-based phylogenomic inference</em></p> <ul> <li><strong>snp_phylogeny.tar.gz:</strong> contains the input PHYLIP file and the IQ-TREE output tree and log files.</li> </ul> <p><em>Phylogeny of mitochondrial genomes</em></p> <ul> <li><strong>mtdna_phylogeny.tar.gz:</strong> includes the 13 mitochondrial protein-coding gene alignments, the partitions file, and the IQ-TREE output tree and log files.</li> </ul> <p><em>Inference of migration events</em></p> <ul> <li><strong>admixture_graphs.tar.gz:</strong> contains the TreeMix / OrientAGraph input file ('treemix.frq.strat.gz'), the output files for all TreeMix and OrientAGraph runs, and the OptM summary table of TreeMix runs ('optm.tsv').</li> </ul> <p><em>Test for introgression</em></p> <ul> <li><strong>dsuite_introgression.tar.gz:</strong> includes the input VCF, the admixture graph topology reconstructed by OrientAGraph, and the Dsuite output files for the estimation of Patterson's D, f4-ratio, and f-branch statistics.</li> </ul> <p><em>Contemporary migration rates</em></p> <ul> <li><strong>ba3-snps.tar.gz:</strong> contains the input and output files for the BA3-SNPs-autotune and BA3-SNPs runs.</li> </ul> <p><em>Demographic reconstruction</em></p> <ul> <li><strong>demographic_inference.tar.gz:</strong> includes the SFS files generated with ANGSD and realSFS and the StairwayPlot2 blueprint and output files.</li> </ul> <p>Other:</p> <ul> <li><strong>metadata.csv:</strong> a companion file containing sample information used in conjunction with R scripts to plot the figures in the paper.</li> </ul>
Mammalian herbivores restrict the altitudinal range limits of three alpine grass species (transplant and herbivore exclusion experiment and demographic data from natural populations), West Elk Mountains, Colorado, USA 2015-2018
Though rarely experimentally tested, biotic interactions have long been hypothesized to limit low-elevation range boundaries of species. We tested the effects of herbivory on three alpine-restricted plant species by transplanting plants below (novel), at the edge (limit), or in the center (core) of their current elevational range and factorially fencing-out above- and belowground mammals in the West Elk Mountains, Colorado, USA from 2015-2018. Herbivore damage was greater in range limit and novel habitats than in range cores. Exclosures increased plant biomass and reproduction more in novel habitats than in range cores, suggesting demographic costs of novel interactions with herbivores. We then used demographic models to project population growth rates, which increased 5-20% more under herbivore exclosure at range limit and novel sites than in core habitats. Our results identify mammalian herbivores as key drivers of the low-elevation range limits of alpine plants and indicate that upward encroachment of herbivores could trigger local extinctions by depressing plant population growth.
Variations in tree growth provide limited evidence of species mixture effects in Interior West U.S.A. mixed-conifer forests
<p>1. In mixed stands, species complementarity (e.g., facilitation and competition reduction) may enhance forest tree productivity. Although positive mixture effects have been identified in forests worldwide, the majority of studies have focused on two-species interactions in managed systems with high functional diversity. We extended this line of research to examine mixture effects on tree productivity across landscape-scale compositional and environmental gradients in the low functional diversity, fire-suppressed, mixed-conifer forests of the U.S. Interior West.</p> <p>2. We investigated mixture effects on the productivity of <i>Pinus ponderosa</i>, <i>Pseudotsuga menziesii</i>, and <i>Abies concolor</i>. Using region-wide forest inventory data, we created individual-tree generalized linear mixed models and examined the growth of these species across community gradients. We compared the relative influences of stand structure, age, competition, and environmental stress on mixture effects using multi-model inference. We analyzed growth of neighboring tree species to infer whether a mixture effect in a single species translated to the stand-level.</p> <p>3. We found support for a positive mixture effect in <i>P. menziesii</i>, although our results were equivocal in light of a weaker but still plausible alternative model. Growth of <i>P. menziesii</i> neighboring species in mixed stands declined or held constant depending on aridity, suggesting that a positive mixture effect in <i>P. menziesii</i> does not necessarily extend to the stand level. We found no evidence for mixture effects in <i>P. ponderosa</i>, <i>A. concolor</i> or their neighboring species.</p> <p>4. Complementarity appears to have a limited influence on tree growth in the mixed-conifer systems of the U.S. Interior West, reflecting limited functional diversity. Historical changes in stand structure following fire exclusion, particularly high stand densities, may limit the potential for positive species mixture effects. The limited species pool of Interior West forests increases the risk that, without careful management, what functional diversity exists could be lost to compositional changes resulting from stand dynamics or disturbance.</p>
Fig. 5. PrincipalComponentAnalysisbasedon 15 craniodentalcharactersof M in The Subspecies Of Myotis Montivagus - Taxonomic Revision And Species Limits (Mammalia: Chiroptera: Vespertilionidae)
Fig. 5. PrincipalComponentAnalysisbasedon 15 craniodentalcharactersof M. borneoensis (blackcircles), M. federatus (blacksquares), M. montivagus (emptysquares) and M. peytoni
Fig. 4 in The Subspecies Of Myotis Montivagus - Taxonomic Revision And Species Limits (Mammalia: Chiroptera: Vespertilionidae)
Fig. 4. Occlusal view of left upper premolar rows: a = M. annectans BM(NH) 78.2355 from Thailand, b = M. annectans BM(NH) 16.3.25.30 (holotype of M. primula), c = M. borneoensis BM(NH) 83.349 (holotype), d = M. federatus BM(NH) 16.4.20.5 (holotype), e = M. montivagus BM(NH) 76.3.10.5 (holotype), f = M. peytoni BM(NH) 12.8.25.1 (holotype). Scale = 3 mm.
Fig. 3 in The Subspecies Of Myotis Montivagus - Taxonomic Revision And Species Limits (Mammalia: Chiroptera: Vespertilionidae)
Fig. 3. Detail of the rostral part of skulls: a = M. annectans BM(NH) 78.2355 from Thailand, b = M. borneoensis BM(NH) 83.349 (holotype), c = M. federatus BM(NH) 16.4.20.5 (holotype), d = M. montivagus BM(NH) 76.3.10.5 (holotype), e = M. peytoni BM(NH) 12.8.25.1 (holo-
Fig. 2 in The Subspecies Of Myotis Montivagus - Taxonomic Revision And Species Limits (Mammalia: Chiroptera: Vespertilionidae)
Fig. 2. Lateral view of skulls: a = M. annectans BM(NH) 78.2355 from Thailand, b = M. borneoensis BM(NH) 83.349 (holotype), c = M. federatus BM(NH) 16.4.20.5 (holotype), d = M. montivagus BM(NH) 76.3.10.5 (holotype), e = M. peytoni BM(NH) 12.8.25.1 (holotype). Scale = 5 mm.
Fig. 1 in Interspecific Interactions as a Factor of Limitation of Geographical Distribution: Evidence Obtained by Modeling Home Ranges of Vole Twin Species Microtus Arvalis – M. Levis (Rodentia, Microtidae)
Fig. 1. Potential distribution of the Common vole Microtus arvalis. White circles are georeferenced occurrences of genetically identified individuals; black indicates areas of maximum habitat suitability, white are areas of lowest suitability.
Figure 7 in Taxonomic status of the Western Hemispingus Sphenopsis ochracea (Thraupidae) and a review of species limits in the genus Sphenopsis P. L. Sclater, 1861
Figure 7. Lateral view of Western Hemispingus Sphenopsis ochracea (von Berlepsch & Taczanowski, 1884). From left to right, (1) DMNH 85570, adult female prepared by Fred C. Sibley on 12 June 1976 at 'Chiriboga, km. 45, Quito-Santo Domingo (Old Rd.) 2000 m, Pichincha, Ecuador'. YPM field series = C 184. (2) DMNH 59270 (YPM N-604), adult male, prepared by Keith B. Aubry on 15 August 1976 at 'Chiraborga [= Chiriboga], 2000 m, Old Quito-Santo Domingo Rd., Pichincha, Ecuador'. At the time it was prepared, the bird weighed 21.5 g and had enlarged testes ('5 mm'). (3) DMNH 85569, adult male, prepared by Fred C. Sibley on 12 June 1976 at 'Chiriboza [= Chiriboga], km. 45, Quito-Santo Domingo (Old Road) 2000 m, Pichincha, Ecuador'. YPM field series = C 202. When prepared, the bird weighed 16 g and testes were not enlarged ('1 mm'). (4) ANSP 149722, adult male, prepared by Kjell von Sneidern on 3 April 1941 at 'Mayasquer, Nariño, Colombia, Pac[ific] side / 7800 ft.' [=2,377 m] (Matthew R. Halley)
Figure 5 in Taxonomic status of the Western Hemispingus Sphenopsis ochracea (Thraupidae) and a review of species limits in the genus Sphenopsis P. L. Sclater, 1861
Figure 5 (left). Lateral view of Oleaginous Hemispingus Sphenopsis frontalis (Chapman, 1923). From left to right, (1) ANSP 141983, adult female S. f. frontalis prepared by Kjell von Sneidern on 20 March 1939 at 'La Costa, Huila, Colombia'. (2) ANSP 185826, adult male S. f. frontalis, prepared by Tristan J. Davis on 22 July 1992 at 'Panguri; ca. 12 km NE San Francisco del Vergel', Zamora Chinchipe, Ecuador. (3) ANSP 83780, adult male S. f. frontalis, collected on 15 September 1922 at 'Baeza, Ecuador'. (4) ANSP 67191, adult male S. f. hanieli, collected on 3 March 1914 at 'Galeparo; Curro Del Avito, Venezuela' (Matthew R. Halley) Figure 6 (right). Lateral view of Piura Hemispingus Sphenopsis piurae (Chapman, 1923). From left to right, (1) ANSP 116357, adult female prepared by M. A. Carriker, Jr., on 21 June 1933 at 'Palambla, D. Piura', Peru. (2) ANSP 116352, adult male, prepared by M. A. Carriker, Jr., on 22 June 1933 at 'Palambla, D. Piura', Peru. (3) ANSP 116358, adult male, prepared by M. A. Carriker, Jr., on 24 August 1933 at 'Chira, D. Cajamarca', Peru (Matthew R. Halley)
Figure 2 in Taxonomic status of the Western Hemispingus Sphenopsis ochracea (Thraupidae) and a review of species limits in the genus Sphenopsis P. L. Sclater, 1861
Figure 2. Four published illustrations of Western Hemispingus Sphenopsis ochracea: (A) lithograph by 'J. Smit', imprint by 'Hanhart', in von Berlepsch & Taczanowski (1884); (B) Ridgley & Greenfield (2001a); (C) Isler & Isler (1987); and (D) Hilty (2011).
Figure 3 in Taxonomic status of the Western Hemispingus Sphenopsis ochracea (Thraupidae) and a review of species limits in the genus Sphenopsis P. L. Sclater, 1861
Figure 3 (left). Lateral view of (Northern) Black-eared Hemispingus Sphenopsis melanotis melanotis (P. L. Sclater, 1855). From left to right, (1) ANSP 154444, adult female prepared by Kjell von Sneidern on 25 April 1942 at 'Toche, Tolima, Colombia'. (2) ANSP 154443, adult male, prepared by Kjell von Sneidern on 28 April 1942 at 'Toche, Tolima, Colombia'. (3) ANSP 165629, adult male, collected on 30 November 1950 on the 'Rio Rumiyaco, [Nariño] Colombia' (Matthew R. Halley) Figure 4 (right). Lateral view of (Southern) Black-eared Hemispingus Sphenopsis melanotis castaneicollis (P. L. Sclater, 1858). From left to right, (1) ANSP 102295, adult female collected on 30 May 1931 at 'Oconeque, [Puno] Peru'. (2) ANSP 102285, adult male collected on 30 May 1931 at 'Oconeque, [Puno] Peru'. (3) ANSP 119323, adult male collected on 15 September 1922 at 'Sandillani, Yungas', La Paz, Bolivia. (4) ANSP 119336, adult incubating female collected on 9 December 1934 at 'Sandillani, Yungas', La Paz, Bolivia (Matthew R. Halley)
FIGURES 1–4 in A Re-evaluation of the Generic Limits of Pison Jurine, and a New Species of the Genus Aulacophilinus Lomholdt (Hymenoptera: Crabronidae: Trypoxylini)
FIGURES 1–4, Aulacophilinus rennellensis, male features. 1, lateral profile of abdomen. 2, front view of head. 3 and 4, mandible, clypeus, and labrum
Figure 4 in New insights on the impact of earthworm extract on the growth of beneficial soil fungi: species-specific alteration of the nematophagous fungal growth and limitation of an entomopathogenic fungus
Figure 4. Growth of Purpureocillium lilacinum after 20 days postexposer to two different earthworm based media: fresh earthworms (FE) (four concentration C1, C2, C3, and C4), and earthworms devoid of gut contents (EDG) (four concentration C1, C2, C3, and C4), C1 = 40 g/L, C2 = 20 g/L, C3 = 10 g/L, C4 = 5 g/L, and two rich media: potato dextrose agar (PDA), and brain heart infusion (BHI).
Figure 5 in New insights on the impact of earthworm extract on the growth of beneficial soil fungi: species-specific alteration of the nematophagous fungal growth and limitation of an entomopathogenic fungus
Figure 5. Evaluation of conidial germination of the fungus Beauveria bassiana exposed to two different earthworm extracts: fresh earthworms (FE) and earthworms without gut contents, EDG, and two conventional media: potato dextrose agar (PDA), and brain heart infusion agar (BHI). A. Percentage germination on conventional and earthworm-based media. B. Percent germination as a function of concentration and earthworm-based medium. Concentrations are equivalent to C1 = 40 g/L, C2 = 20 g/L, C3 = 10 g/L, and C4 = 5 g/L. Results of one-way ANOVA (A) or two-way ANOVA (B), and differences are significant according to Tukey's test (HSD) and groups "a", "b" and "c".
Figure 3 in New insights on the impact of earthworm extract on the growth of beneficial soil fungi: species-specific alteration of the nematophagous fungal growth and limitation of an entomopathogenic fungus
Figure 3. Evaluation of vegetative growth, conidial production and germination in the fungus Purpureocillium lilacinum exposed to two earthworm extracts: fresh earthworm (FE), earthworms devoid of intestinal contents (EDG) and two conventional media: potato dextrose agar (PDA), and brain heart infusion agar (BHI). A. Cumulative growth from 3 to 18 days according to conventional and earthworm-based media. B. Cumulative growth as a function of concentration and earthworm-based medium. C. Conidia production (×10⁵ conidia/mL) according to conventional and earthworm-based media. D. Conidia production (×10⁵ conidia/mL) according to concentration and earthworm-based medium. E. Percent germination on conventional and earthworm-based media. F. Percent germination as a function of concentration and earthworm-based medium. Concentrations are equivalent to C1 = 40 g/L, C2 = 20 g/L, C3 = 10 g/L, and C4 = 5 g/L. Results of one-way ANOVA (A, C, E) or two-way ANOVA (B, D, F), and differences are significant at Tukey's test (HSD) and groups "a", "b" and "c".
Figure 1 in New insights on the impact of earthworm extract on the growth of beneficial soil fungi: species-specific alteration of the nematophagous fungal growth and limitation of an entomopathogenic fungus
Figure 1. Evaluation of vegetative growth, conidial production and germination in the fungus Arthrobotris musiformis exposed to two earthworms' extracts: fresh earthworm (FE), earthworms devoid of intestinal contents (EDG) and two conventional media: potato dextrose agar (PDA), and brain heart infusion agar (BHI). A. Cumulative growth from 3 to 18 days according to conventional and earthworm-based media. B. Cumulative growth as a function of concentration and earthworm-based medium. C. Conidia production (×10⁵ conidia/mL) according to conventional and earthworm-based media. D. Conidia production (×10⁵ conidia/mL) according to concentration and earthworm-based medium. E. Percent germination on conventional and earthworm-based media. F. Percent germination as a function of concentration and earthworm-based medium. Concentrations are equivalent to C1 = 40 g/L, C2 = 20 g/L, C3 = 10 g/L, and C4 = 5 g/L. Results of one-way ANOVA (A, C, E) or two-way ANOVA (B, D, F), and differences are significant at Tukey's test (HSD) and groups "a", "b" and "c".
Figure 6 in Species limits in the African Palm Swift Cypsiurus parvus
Figure 6. Type of Cypsiurus parvus laemostigma (ZMB 49.338; above) compared to an example of C. p. gracilis (ZMB 36.546); note the plain grey breast and belly of the former (Nigel J. Collar)
Figure 5 in Species limits in the African Palm Swift Cypsiurus parvus
Figure 5. Examples in NHMUK of six taxa treated as races of African Palm Swift Cypsiurus parvus, left to right: gracilis and griveaudi (Malagasy taxa), hyphaenes, myochrous, brachypterus and parvus African taxa). Note the stronger-marked throat and breast markings and paler, scaled bellies of the Malagasy taxa, but the longer wings of griveaudi than gracilis (Nigel J. Collar, © Natural History Museum, London)
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.