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BIGG universal model in COBRAPY format
<p>This provides the BIGG universal model in COBRAPY JSON format. The notebook for conversion is provided along with the converted model as well.</p>
Figure 5 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status
Figure 5. Global phylogenetic trees of killer whales based on (a) haplotypes from 452 mitogenomes and (b) 49 nuclear genome sequences. Reprinted with permission from Morin et al. [15] (figure 2; by permission from John Wiley & Sons, licence 5458310335802) and [9] (electronic supplementary material, figure S3b, by permission from Andrew D. Foote). Black branches in (a) lead to haplotypes that are from animals that have not been identified to ecotype (see electronic supplementary material, table S1 from [15]).
Figure 3 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status
Figure 3. PCA plot of first two principal components based on (a) 88 SNPs: offshore (n = 3), resident (n = 11), Bigg's (n = 30) from data in Morin et al. [15]; (b) 26 microsatellites: offshore (n = 5), resident (n = 250), Bigg's (n = 116) (samples genotyped at ≥20 loci) [56]; unpublished); (c) 3678 RADseq SNPs: offshore (n = 7), resident (n = 52) and Bigg's (n = 37) populations [57,62]; (d) 1 00 000 (subset from 6 371 282) SNPs from 147 high-coverage genomes of offshore (n = 7), Bigg's (n = 14) and resident (n = 126) samples from multiple geographically and behaviourally defined subpopulations (Alaska, northern and southern resident populations) (based on subset of SNP genotype data from [113]. See Supplementary Materials for methods and data set information.
Figure 7 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status
Figure 7. Photographs of neotype skulls for (a) Orcinus rectipinnus (USNM 594671) and (b) Orcinus ater (USNM 594672).
Figure 1 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status
Figure 1. Expected range maps for (a) resident and (b) Bigg's killer whales, including locations of samples used for mitogenome analysis (figure 5a, resident n = 106, Bigg's n = 93) [15]. Distribution ranges have been inferred based on published identifications of individuals that are identified by ecotype [48–53]. Sample distributions cover the known ranges of both ecotypes, with the exception of residents of Oregon and northern California, and both ecotypes off northern Japan (Hokkaido) in the western Pacific [48,54]. Sample maps for microsatellite data are in electronic supplementary material, figure S2.
Figure 8 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status
Figure 8. Vertical images of (a) an adult male Bigg's killer whale (BKW) from the West Coast Transient population of Bigg's killer whales and (b) an adult male resident killer whale (RKW) from the sympatric Southern Resident population of resident killer whales. Images are scaled to the estimated asymptotic lengths of 7.3 m [20] and 6.9 m [145], respectively. Vertical images were collected using an octocopter drone using methods described by Durban et al. [146], provided by John Durban and Holly Fearnbach.
Figure 6 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status
Figure 6. Illustrations of (a) O. ater and (b) O. rectipinnus from Scammon [138,140]. These illustrations were likely made by Scammon, or made under his guidance from his field notes and sketches. Whether they represent renderings of specific specimens, or composite sketches, is unknown.
Figure 2. Canonical variate 1 and 2 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status
Figure 2. Canonical variate 1 and 2 plots for cranial shape features that distinguish among ecotypes for (a) skull morphology (resident (n = 17), Bigg's (n = 13) and offshore (n = 6)) and (b) dentary bone morphology (resident (n = 21), Bigg's (n = 12) and offshore (n = 8) specimens) (reprinted from [103]).
Figure 4. Structure assignment probability plots for K in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status
Figure 4. Structure assignment probability plots for K = 3 groups from (a) 26 microsatellites: offshore (n = 5), resident (n = 250), Bigg's (n = 116) samples genotyped at ≥ 20 loci) (56; unpublished); (b) 3340 RADseq SNPs (polymorphic in sample set): offshore (n = 7), resident (n = 52) and Bigg's (n = 37) populations [57,62]. Vertical bars represent the individual assignment probability for each group inferred by Structure (groups identified by shading), with samples sorted by a priori ecotype assignment. See electronic supplementary material for methods and data set information.
Temporal dynamics of mother-offspring relationships in Bigg's killer whales: opportunities for kin-directed help by post-reproductive females
<p>Age-related changes in the patterns of local relatedness (kinship dynamics) can be a significant selective force for shaping the evolution of life history and social behaviour. In humans and some species of toothed whales, average female relatedness increases with age which can select for a prolonged post-reproductive lifespan in older females due to both the costs of reproductive conflict and the benefits of late-life helping of kin. Killer whales (<em>Orcinus</em> <em>orca</em>) provide a valuable system for exploring social dynamics related to such costs and benefits in a mammal with an extended post-reproductive female lifespan. We use >40 years of demographic data to investigate the opportunities for helping and harming in the mammal-eating Bigg's killer whale by quantifying how mother-offspring social relationships change with offspring age. Our results suggest a high degree of male philopatry and female-biased budding dispersal in Bigg's killer whales, with some variability in the dispersal rate for both sexes. These patterns of dispersal provide opportunities for late-life helping of particularly adult sons, while partly mitigating the costs of mother-daughter reproductive conflict. This is an important step towards understanding the evolution of menopause in the few species it occurs.</p>
Temporal dynamics of mother-offspring relationships in Bigg’s killer whales: opportunities for kin-directed help by post-reproductive females
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Input and output data from numerical simulations associated to paper Biggs and Annen (2019)
<p>Input and output files produced by code Heat2D_Car and used to produce the results published in Biggs and Annen (2019)</p>
BiGG SBML Models for SynBioCAD
<p>Models of chassis on which SynBioCAD tools can run.</p> <p>Models come from BiGG database and are in SBML format.</p>
Table 1 in Revised taxonomy of eastern North Pacific killer whales (Orcinus orca): Bigg's and resident ecotypes deserve species status
<p><b>Table 1.</b> Measures of differentiation, divergence and diagnosability based on nuclear microsatellite and SNP data. All frequency-based metrics (FST, F’ST, G’ST) were significantly different from zero at p <0.05.</p><table><tbody><tr><th>divergence metric</th><th></th><th>reference</th></tr></tbody><tbody><tr><th>dA (CR)</th><td>0.007 46a</td><td>[114]</td></tr><tr><th>dA (mitogenome)</th><td>0.003 91b</td><td>[114]</td></tr><tr><th>FST (microsatellite)</th><td>0.21–0.23</td><td>[56,85]</td></tr><tr><th>F’ST (microsatellite)</th><td>0.47</td><td>[56]</td></tr><tr><th>G’ST (microsatellite)</th><td>0.28</td><td>[56]</td></tr><tr><th>FST (SNP)</th><td>0.28</td><td>[15]</td></tr><tr><th>F(RADseq, neutral)c ST</th><td>0.27</td><td>[58]</td></tr><tr><th>F(RADseq, selected)c ST</th><td>0.67</td><td>[58]</td></tr><tr><th>FST (genomes)</th><td>0.32</td><td>[9] (electronic supplementary material, table S2)</td></tr><tr><th>diagnosability (CR)</th><td>100%</td><td>[114]</td></tr><tr><th>diagnosability (mitogenome)</th><td>100%</td><td>[114]</td></tr><tr><th>fixed differences (mitogenome)</th><td>57</td><td>[7]</td></tr><tr><th>fixed differences (3281 nuclear SNPs)</th><td>2–7</td><td>[58]</td></tr><tr><th>fixed differences (6 435 100 nuclear SNPs)</th><td>6361d</td><td>[113]</td></tr></tbody></table><p>a 95% confidence interval:0.00727–0.00772. b 95% confidence interval: 0.00388–0.00393. c Alaska transients (Bigg’s) versus Alaska residents. d Based on analysis of raw SNP data from Kardos et al. [113].</p>
Modifiying Biggs (1999)'s diagram to include teacher's level of stimulation and creativity
<p>I upgraded Biggs (1999) diagram on teaching method, student orientation and level of engagement. I included teacher's level of stimulation and creativity. I proposed student's research proposal with breakout session as an optimal teaching method to reach the highest level of student's engagement.</p>
Bigge Adler-Apotheke
<p>Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a</p><p>German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf.</p><p>gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope):</p><p>https://kalliope-verbund.info/DE-611-BF-70963</p><p>[Funktion: Im Findbuch anzeigen]</p><p> </p><p>Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot</p><p>be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf</p><p>Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht</p><p>veröffentlicht werden dürfen).</p>
Distribution. NW Australia, patchily across the Kimberley region in Western Australia, from Kalumburu in the N to North Derby in the S, including Bigge and Boongaree Is. The species was recently confirmed to occur in the East Kimberley (Cockburn Ranges) for the first time since its initial scientific discovery in 1917. in Phalangeridae
Distribution. NW Australia, patchily across the Kimberley region in Western Australia, from Kalumburu in the N to North Derby in the S, including Bigge and Boongaree Is. The species was recently confirmed to occur in the East Kimberley (Cockburn Ranges) for the first time since its initial scientific discovery in 1917.
Distribution. Coastal NW Kimberley from Mitchell Plateau to Charnley River, Western Australia; also Bonaparte Archipelago (Bigge I, Katers I), and Boongaree I. in Macropodidae
Distribution. Coastal NW Kimberley from Mitchell Plateau to Charnley River, Western Australia; also Bonaparte Archipelago (Bigge I, Katers I), and Boongaree I.
Subspecies and Distribution. P d. delicatulus Gould, 1842 — monsoonal NW & NC Australia, from Pilbara to far NW Queensland, and including the islands of Tent, Augustus, Bigge, Sir Graham Moore, Bathurst, Melville, Marchinbar, Groote Eylandt, and Sir Edward Pellew Group (West, South West, North, and Vanderlin). P. d. pumilus Troughton, 1936 — NE & CE Australia from Cape York S to NE New South Wales, including Fraser I; also reported from Trans Fly plains in S New Guinea. in Muridae
Subspecies and Distribution. P d. delicatulus Gould, 1842 — monsoonal NW & NC Australia, from Pilbara to far NW Queensland, and including the islands of Tent, Augustus, Bigge, Sir Graham Moore, Bathurst, Melville, Marchinbar, Groote Eylandt, and Sir Edward Pellew Group (West, South West, North, and Vanderlin). P. d. pumilus Troughton, 1936 — NE & CE Australia from Cape York S to NE New South Wales, including Fraser I; also reported from Trans Fly plains in S New Guinea.
Revised taxonomy of eastern North Pacific killer whales (Orcinus orca): Bigg’s and resident ecotypes deserve species status
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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.