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Long-term dynamics of trace elements concentrations in the organism of the shrews (Sorex) during the periods of high and reduction emissions from the copper smelter
<p>Data and code for mixed-model analysis for the article: </p> <p>Mukhacheva S.V. (2022) Long-term dynamics of trace elements concentrations in the organism of the shrews (Sorex) during the periods of high and reduction emissions from the copper smelter" // Russian Journal of Ecology. Vol. 5. </p> <p>Data provided by S.V. Mukhacheva</p> <p>Code provided by A.N. Sozontov</p>
Fig. 1 in Patterns Of Craniometric Variability Of Six Common Species Of Shrews (Soricidae: Crocidura, Neomys, Sorex)
Fig. 1. Geographical origin of the materials examined. Dashed lines denote putative borders between eastern and western clades in the species of genus Crocidura, established on
Fig. 3 in Patterns Of Craniometric Variability Of Six Common Species Of Shrews (Soricidae: Crocidura, Neomys, Sorex)
Fig. 3. Crocidura: results of PCA and model-based clustering. a: Specimen scores for the first two Principal Components. Ellipses
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).
FIGURE A3-1 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE A3-1. Landmarks position on the medial surface of the dentary in relation to the teeth in recent materials and the alveoli edges in fossils. The image admits a similar position of the landmarks with and without teeth. For an unambiguous definition of the landmarks position is required a marking the alveoli edge before a photo acquisition.
FIGURE 1 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE 1. Geographic location of paleontological sites (red dots) and recent samples of S. araneus (dark blue dots) and S. tundrensis (green dots), with diagrammatic drawings of modern boundaries of the species geographic ranges. A, Modern geographic ranges of S. araneus (red line) and S. tundrensis (dark blue line) in Palearctic by source: https:/ /www.iucnredlist.org/ (Hutterer and Kryštufek, 2016; Tsytsulina et al., 2016). B1, Location of samples and fossil sites in Pre-Ural, Ural and West Siberia regions. B2, Location of recent samples in Arkhangelskaya Oblast' and Komi Republic (magnified inset from B1). C, Eastern samples of S. tundrensis. Key: A1–A2, S. araneus samples; Cher1, Cheremukhovo-1 Cave; Da, Dan' sample; DKS, Dyrovatyi Kamen' Grot; F, data by Fadeeva (2016); PtU, sample of the Pechora chromocomal race of S. araneus, 'Ulashevo'; Ra, Ramen'e sample; SeF, sample of the Serov race, 'Foothill'; SeH, sample of the Serov race, 'Hill'; SeV, sample of the Serov race, 'Valley'; Sim3, Sim III Cave; T1–T7, S. tundrensis samples. Detailed information see in Appendices 1–2. Map source: ESRI (http://www.esri.com/) via SASPlanet Application (ver. 160707.9476).
FIGURE A4-1 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE A4-1. Result of principal component analyses based on the m1 shape. The tooth data represented as three repetition of four samples within space of PC1 and PC2: SeV, SeF, SeH and PtU.
FIGURE 7 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE 7. Result of regression analyses and the normality test of two linear characters, aLML and MRH. A, Fitting data (aLML vs MRH; n = 138) to a von Bertalanffy growth model. B, aLML values distribution histogram with a gap marking between two subsamples. C, Visual combination of the result of four separate regression analyses: line d1, von Bertalanffy (n = 138); d2 line, bivariate linear regression (BLR; S. tundrensis, n = 20); d3 line, BLR (PtU, n = 56); d4 line, BLR (Serov, n = 45). D, The regression line parameters, d1–d4. Key: a, line of Gaussian distribution; b, gap, detected by the W-test; c, an overlapping zone, calculated by the predicted values (μ ± 2σ); PtU (1063), re-defined specimen (from S. araneus to S. tundrensis).
FIGURE 10 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE 10. Combined plot of three-dimensional landmarks data set of m1 (A), visualization of two first axes of PCA (phylomorphospace) performed on three-dimensional data set of the m1 shape with phylogenetic projection (B), molecular phylogeny (concatenated tree based on seven mitochondrial and nuclear genes; source: Bannikova et al., 2018; see Appendix 6), displaying the estimated phylogenetic relationships among Sorex species (C), and visualization of the shape changes between S. tundrensis (upper teeth, red points) (D) and S. araneus (lower teeth, blue points) (E). A, m1 in subocclusal (upper) and subapical (bottom) views with landmarks position (Appendix 3: Table A3-3). B, Phylomorphospace of 7 soricine species (six Sorex, ingroup; Neomys outgroup). C, Phylogenetic tree. D1(E1), Shape transformation in the apical view. D2 (E2), Shape transformation in the lingual view. D3(E3), Shape transformation in the posterior view. Key: i, elongation of the tooth crown base in S. tundrensis; ii, narrowing the crown base in S. tundrensis; iii, posterior shifting of the paraconid of S. tundrensis; iv, swallowing the protocristid notch of S. tundrensis; v, shortening of the hypolophid of S. tundrensis. D, E unscaled.
FIGURE A3-3 in Morphospace dynamics and intraspecies variety of Sorex araneus and S. tundrensis according to recent and fossil data
FIGURE A3-3. Key points of the m1 alignment into 'Functional View.' A, Reference image that prepared before a mass processing of the images (is opening during the image processing within a separate window for collation). B, Four key points that help m1 alignment: overall view of the paraconid and the anterior edge of m1; the functional view of the protoconid, i.e. the pre- and postprotocristid external edges hide a buccal surface of the trigonid; a view of the oblique cristid contact in manner of two planes as shown in C; and a shape (narrow triangle) of the posterobuccal surface of the talonid. D, m1 conids. Abbreviations: a, b — planes of oblique cristid and the trigonid posterior border.
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