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Figure 4 in Notes on a recently described subspecies, and the poorly known nominate subspecies of Rüppell's Parrot, Poicephalus rueppellii mariettae and P. r. rueppellii
Figure 4. Female of the recently described Poicephalus rueppellii mariettae, Namibia, 4 March 2018; this taxon, with dark ultramarine-blue plumage in females, is better known and more widespread than the nominate subspecies (© Charles James Sharp)
Figure 1 in Notes on a recently described subspecies, and the poorly known nominate subspecies of Rüppell's Parrot, Poicephalus rueppellii mariettae and P. r. rueppellii
Figure 1. Distribution map of Rüppell's Parrot Poicephalus rueppellii based on e-Bird (https://ebird. org/species/ruepar1?siteLanguage=de). P. r. rueppellii (red dots) occurs only in north-west and west-central Angola around Luanda and Benguela, whereas P. r. mariettae (green dots) is widespread in Namibia and south-west Angola (© Thomas Arndt)
Data and source code for: Recent adaptation in a threatened salmonid revealed by museum genomics
<p>Steelhead/rainbow trout (Oncorhynchus mykiss) is an imperiled salmonid with two main life history strategies: migrate to the ocean or remain in freshwater. Domesticated hatchery forms of this species have been stocked into almost all California waterbodies, possibly resulting in introgression into natural populations and altered population structure. </p> <p>We compared whole-genome sequence data from contemporary populations against a set of museum population samples of steelhead from the same locations that were collected prior to most hatchery stocking. </p> <p>We observed minimal introgression and few steelhead-hatchery trout hybrids despite a century of extensive stocking. Our historical data show signals of introgression with a sister species and indications of an early hatchery facility. Finally, we found that migration-associated haplotypes have become less frequent over time, a likely adaptation to decreased opportunities for migration. Since contemporary migration-associated haplotype frequencies have been used to guide species management, we consider this to be a rare example of shifting baseline syndrome that has been validated with historical data. </p> <p>We suggest cautious optimism that a century of hatchery stocking has had minimal impact on California steelhead population genetic structure, but we note that continued shifts in life history may lead to further declines in the ocean-going form of the species. </p>
Figure 1 in Phylogenetic placement of a recently discovered population of the threatened alpine she-oak skink Cyclodomorphus praealtus (Squamata: Scincidae) in Victoria
Figure 1: Elevation map of the mainland Australian alpine region indicating the five major populations of Cyclodomorphus praealtus, including the new location of Wellington Plains. Elevation is indicated by light, mid and dark grey areas at 500 m intervals, with highest elevations at or above 1500 m above sea level. Adapted from fig. 1; Koumoundouros et al. (2009).
Figure 3 in Phylogenetic placement of a recently discovered population of the threatened alpine she-oak skink Cyclodomorphus praealtus (Squamata: Scincidae) in Victoria
Figure 3: Population structure of Victorian Cyclodomorphus praealtus according to ND4 mitochondrial haplotype network. Black indicates individuals from Lankey Plain, dark grey indicates those from Mt Hotham, white indicates those from Bogong High Plains and diagonal stripes indicate those from Wellington Plains. The network structure indicates 3 haplogroups (i, ii and iii) within Victoria. Each circle represents a unique haplotype, with the circle size indicative of frequency and sample sizes within each circle. Empty circles represent missing haplotypes and differ by one base pair from the closest haplotype.
Figure 2 in Phylogenetic placement of a recently discovered population of the threatened alpine she-oak skink Cyclodomorphus praealtus (Squamata: Scincidae) in Victoria
Figure 2: A Bayesian consensus tree of the mtDNA ND4 sequences, depicting the relationship between unique haplotypes at each locality (Bogong High Plains, Lankey Plain, Mt Hotham, Wellington Plains and Kosciuszko National Park) for Cyclodomorphus praealtus. Bayesian posterior probabilities are shown at major nodes.
Fig. 1 in Recent Range Expansion Of Pomatias Rivulare (Eichwald, 1829) (Mollusca: Pomatiidae) In Central-Eastern Europe
Fig. 1. Distribution area of Pomatias rivulare according to SCHÜTT (2001), LIKHAREV and RAM- MELMEIER (1952), DAMJANOV and LIKHAREV (1975), GROSSU (1986) and ŠTAMOL and JOVANO- VIĆ (1990). Filled squares indicate sampling sites of examined material, empty squares indicate subfossil occurrences in the Pannonian region according to BERTALAN et al. (1995), arrows indicate
Fig. 2 in Recent Range Expansion Of Pomatias Rivulare (Eichwald, 1829) (Mollusca: Pomatiidae) In Central-Eastern Europe
Fig. 2. Bayesian tree of COI genes of the examined Pomatias samples. Littorina plena (AJ622948) was used as an outgroup. Numbers at the branches indicate Bayesian posterior probabilities. Scalebar
Materials Attagenus (Attagenus) ziegleri Herrmann & Háva, 2009 (Figs. 1-3) Faro: Carrapateira-Amado, 9-03-2007, 1 male (M. MAntič leg.; J. Háva det. et coll.) Distribution: Species recently described from Spain (Herrmann & Háva 2009). New species for Portugal. Fig. 1.- Habitus of Attagenus (Attagenus) ziegleri Herrmann & Háva, 2009 in Attagenus (Attagenus) ziegleri Herrmann & Háva, 2009 (Coleoptera: Dermestidae), new species for Portugal.
Materials Attagenus (Attagenus) ziegleri Herrmann & Háva, 2009 (Figs. 1-3) Faro: Carrapateira-Amado, 9-03-2007, 1 male (M. MAntič leg.; J. Háva det. et coll.) Distribution: Species recently described from Spain (Herrmann & Háva 2009). New species for Portugal. Fig. 1.- Habitus of Attagenus (Attagenus) ziegleri Herrmann & Háva, 2009
FIGURE A5-2 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE A5-2. Results of the principal component analysis based on the hemimandible shape dataset, combined of S. araneus and S. tundrensis samples. Samples dispersion displayed as convex hulls. Key: ars, specimens of S. araneus from 'non-chromosomal' samples; Dan'(D), sample of S. tundrensis from Dan' village; tdr, S. tundrensis. See the main text and Figure 5B.
FIGURE A5-1 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE A5-1. Results of the principal component analysis based on the skull shape, combined of S. araneus and S. tundrensis samples. A. Morphospace within PC1–2 with clear separation both species; B1. Skull shape (in ventral view) in a transformation frame on the negative end of PC1 that corresponding to S. tundrensis; B2. Skull shape (in a transformation frame on the positive end of PC1 that corresponding to S. araneus. Abbreviations: A1–A5 — upper antemolar row; Dan' — Dan' sample; for. ovale — foramen ovale (lm19); I1 — first upper incisor; lm — landmark; M — upper molar; P4 — fourth upper premolar; pal — palatinum; PtU — Ulashevo sample (Pechora race); SeV — reference sample of S. araneus; tdr — reference sample of S. tundrensis; zpmx — zygomatic proce ss of the maxilla.
FIGURE A3-4 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE A3-4. 'Specimen conglomerator' (SC). A, Autodesk 3Ds Max screen with three variants of conlomerator. B, The conglomerator dimensions supposed to be used 15 mL Falcon Centrifuge Tubes as a transportable container (Falcon used without cap). C, A view of four hemimandibles, scanned with SC in the CTVox software ver. 3.3.0 r1403 (64-bit) (Brucker microCT). D, Transversal digital section of SC, with the four mounted hemimandibles. E, An overall view of the Falcon tubes (source: https://www.amazon.in/Falcon-Centrifuge-Tubes-Polypropylene-352096/). Abbreviations: a — SC with a cross- shaped bearing part (for 4, 8 or 12 small [width <6 mm] items); b, c — SC with a flatted bearing pa rt (for 2 or 4 flat and width items, e.g., skull of tiny shrews); d — a mounting area; e — an inner diameter of SC that is inserted into the Falcon tube. An outer diameter (4 mm) serves as a cap; f — a transversal section of the dentary; g — a layer of the Dental Orthodontic Wax used for the bones mounting; h — part of the cro ss-shaped SC. SC models in STL-format are available by the request (Leonid.Voyta@zin.ru).
FIGURE A3-2. m1 images preparation protocol. A in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE A3-2. m1 images preparation protocol. A, Two-dimensional images of m1 give from three-dimensional model of a hemimandible. B, Interface MorphoDig software (Lebrun, 2020) for work with the models. C, Model alignment to the 'Functional View' in sense to Polly (2003), see details in Figure A3-3. D, Obtaining separate images via 'Snipping Tool' for three repeats, A, B, and C. E, Landmarking ready images via tpsDig software (Rohlf, 2007). F, Obtaining three separate data sets required for assessing the 'metering error' influence or obtaining a final work data set as a mean between repeats. Abbreviations: a, b — rotation along of the space planes for a model alignment.
FIGURE 9 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE 9. Results of PCA based on the combined 'Fossil/Recent' datasets of hemimandible shape. A, Mandibular morphospace of PC1-2. B, 'Timespan inset' with information on the supposed shape changes between fossil Uralian samples of S. tundrensis from DKS3, Sim3 and the recent Dan' localities (see details in Figure 2, Table 3). Time scale has been reversed due to corresponding the samples position in the morphospace. C, Inset with information on the supposed shape changes between fossil Uralian samples of S. araneus from DKS3, Sim3 and the recent Dan' localities. Key: a, re-defined specimens of S. araneus (to S. tundrensis: Sim3, S18 and S19); b, magnified relationships between specimens from DKS3 sample; c, common area of DK08 and DK09 (DKS3), repeating by the m1 and mandibular shape (cf. Figure 8); d, cooling in the Late Holocene stage (see Figure 2: arrow 'a'); e, warming from the Early to Middle Holocene stages (see Figure 2: arrow 'b'); f, shape changes trajectory, associated with size increasing between the Early Holocene DKS3 and the Late Holocene Sim3 samples of S. tundrensis; g, shape changes trajectory, associated with size decreasing between the Late Holocene Sim3 sample and the recent Dan' sample of S. tundrensis; h, shape similarity between the Early Holocene DKS3 and the Late Holocene Sim3 samples of S. araneus; hatched area displays the overall convex hull of Dan' S. tundrensis subsample; y, the shape changes trajectory, associated with size decreasing between the Late Holocene Sim3 sample and the recent Dan' sample of S. araneus (changes weaker than 'g'); see also Figures 5, 8.
FIGURE 6 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE 6. Hemimandible shape transformation along of PC1 (morphospace see on Figure 5B). A1, Shape transformation toward of the negative end of PC1 (corresponding to S. tundrensis). A2, Hemimandible of S. tundrensis (ZIN 107833/1149, PtU) in medial view, with an impose mandibular ramus contour of S. araneus (B2). B1, Shape transformation toward of the positive end of PC1 (corresponding to S. araneus). B2, Hemimandible of S. araneus (ZIN 96960; Ser'ga Riv., Mid. Ural). C, Inset from Figure 5B: result of PCA. Key: a, shape change in the posterior shift of the whole cheek-teeth row, with shortening the 'angle' between the m3 posterior alveolus and the mandibular ramus base; b, shape change in the anterior overall inclination of the mandibular ramus; c, shape change in the anterior shift of the condylar process.
FIGURE 3 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE 3. Two-dimensional-landmarks and semilandmarks position on the occlusal view of the first lower molar (m1) and medial view of the hemimandible of shrews, and three linear measurements. A1, Diagrammatic image of m1 in occlusal view, with the conids marking. A2, Landmarked m1 in the 'functional view' sense Polly (2003). B1, Right hemimandible, with teeth and parts marking. B2, Landmarked right hemimandible (6 lms, 42 sms). Key: aLm1-m3, alveolar length of the lower molars row(aLML); cn, carnassial notch (notches nomenclature by Lopatin, 2006); lm, landmark (pl. lms); Lm1, lingual length of m1; MRH, mandibular ramus height; pn, protocristid notch; pr., process; sm, semilandmark (pl. sms). Description of the landmarks position see in Appendix 3; some problems that may arise with landmarking the fossil and recent specimens graphically resolving in Appendix 3 (Figure A3-1). Mandible of S. araneus (ZIN 107833/1001, PtU; 2D-image of 3D-model). Unscaled.
FIGURE A4-2 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE A4-2. Measurements of the m1 and m2 of Beremendiini specimens: A. Common graph for eight species (by Zazhigin and Voyta, 2019, with changes); B Magnified part of graph with variability area of European samples of B. fissidens (dark grey convex hull as for A, original material of B. fissidens (three- and four-digit numbers), Lunanosorex lii (Ll), B. pohaiensis (Pph), B. pliocaenica (Ppl); C. Measurements for each holotype. Abbreviations: Bf_B5 — B. fissidens from Beremend 5 locality (Hungary; late Pleistocene); L(m1) — m1 length; L(m2) — m2 length; Ll_QP — L. lii from Qipanshan Hill locality (China; late Pliocene); Ll_HX — L. lii from Houxushan Hill locality (China; late Pliocene); Pph_h1 — holotype dimensions from original description of B. pohaiensis; Pph_h2 — holotype of B. pohaiensis re-dimensions by Jin and Kawamura (1996); Pph_HAI — B. pohaiensis from Haimao locality (China; early Pleistocene); Pph_r — redemensions of replicated B. pohaiensis holotype by Zazhigin and Voyta (2019); Ppl_h4 — holotype dimen - sions from original description of B. pliocaenica; Ppl_h5 — re-dimensions of B. pliocaenica holotype by Jin, Kawamura (1996).
FIGURE 4 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE 4. Results of the principal component analysis based on the m1 shape. The tooth data set represented three repetitions of four samples within space of PC1 and PC2: SeV, SeF, SeH and PtU. A, PCA result (PC1 vs. PC2). B1, m1 shape in a transformation frame on the negative end of PC1. B2, ibid., on the positive end of PC1. B3, ibid., on the positive end of PC2. B4, ibid., on the negative end of PC2. C1, Simulation of the buccal inclination of the 3D-model during an image acquisition that partly corresponds to the shape variation along of PC1 (X-state). C2, Simulation of the lingual inclination of the 3D-model during an image acquisition (Y-state). C3, Consensus position (correct for image acquisition) of m1. D, Diagrammatic image of the maximal variance disparity definition among three repetitions. Key: a, MEr trajectory between repeats of the Serov race samples; b, MEr trajectory between repeats of the Pechora race sample; c, d, opposite swinging of the 3D-model during the image acquisition; R, repetition; i–vii, differences (see the main text).
FIGURE 5 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE 5. Results of the principal component analysis based on the m1 shape (A) and hemimandible shape (B) datasets, combined of S. araneus and S. tundrensis samples. Samples dispersion displayed as convex hulls. Key: ars, specimens of S. araneus from 'non-chromosomal' samples; Dan'(D), sample of S. tundrensis from Dan' village; tdr, S. tundrensis.
FIGURE 2 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE 2. Chronological ranges for the Late Pleistocene and Holocene fossil samples of soricids from North, Middle, South and Pre-Ural localities, with information on 14C dating (provided calibrated dates; used intCal20 Curve [Reimer et al., 2020]), geochronology of the Late Pleistocene and Holocene by GICC05 Project (Rasmussen et al., 2006; Andersen et al., 2006; Svensson et al., 2008) and climate-stratigraphic units (Bond and Lotti, 1995; Lisiecki and Raymo, 2005; Rasmussen et al., 2014; Railsback et al., 2015). Key: a, cooling in the Late Holocene stage; AT, Atlantic Climate-Stratigraphic Unit; b, warming from the Early to Middle Holocene stages; BAIC, BØlling-AllerØd Interstadial (= GI1); BO, Boreal Climate-Stratigraphic Unit; c, DO1 unit position; Inter., intermediate fauna between warm and cold (vice versa) intervals; GI1/GS1-GS4, Greenland Interstadials/Stadial Units (Rasmussen et al., 2014) that have been synchronized with the Marine Isotope Stages — MIS1-MIS2 (Lisiecki and Raymo, 2005; Railsback et al., 2015); GICC05, Isotope Curve of the Greenland Ice Core Chronology 2005 Project for 55 kyr BP interval (Rasmussen et al., 2006; Andersen et al., 2006; Svensson et al., 2008); LGM, Last Glacial Maximum (= GS4–GS2.1); LGT, Late Glacial Transition (= GS2.1); PB, Preboreal Climate-Stratigraphic Unit; SA, Subatlantic Climate-Stratigraphic Unit; SB, Subboreal Climate-Stratigraphic Unit; YD, Younger Dryas Stadial (= GS1). Acronyms of the samples see in Figure 1 and Appendix 2. The Late Pleistocene and Holocene Schema by Cohen and Gibbard (2019); *, data by Fadeeva (2016): B. Makh. — Bolshaya Makhnevskaya Cave (horizon 140–147 cm); Koz iy S. — Koziy Stone Rock (horizon 135–145 cm); Rasik/B21 — Rasik Grot (lay er 21); Rasik/B27 — Rasik Grot (layer 27).
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.