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opencc-by-4.0May 2020View details →

Seed morphology in the Vitaceae based on geometric models

Images of the seeds in the Vitaceae used in the experiments corresponding to the article entitled: Seed morphology in the Vitaceae based on geometric models, by José Javier Martín-Gómez et al. (Agronomy, 2020 submitted)

opencc-by-4.0Nov 2020View details →

Replication R code and data for "Geometric morphometric investigation of craniofacial morphological change in domesticated silver foxes"

This repository holds various files and R code used in the publication of the manuscript entitled "Geometric morphometric investigation of craniofacial morphological change in domesticated silver foxes". Data files include: The 3D landmark coordinates of each individual specimen (Fox_data_Morphologika.txt), the linear measurement data associated with those foxes (fox_linear_volume_data.csv), and replication data measurements.  The following files include the R code used to perform the analyses contained within the paper: 1_Procrustes_analysis - details the Geometric morphometrics analyses performed 2_linear_models - details the model specification for the GLS models employed in the paper 3_graph_code - contains R script for the creation of the graphs displayed in the paper 4_repeatability_script - contains R code that details the statistical calculations made with the repeatability measurements indicated above.

Fig. 7 in Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry

Fig. 7. Evolution of the relative contribution of ammonoid superfamilies to diversity and disparity (mean squared Euclidean distance to the centroid) through the Early and Middle Devonian; based on the analysis of the whorl profiles. A. Relative contribution of ammonoid superfamilies to diversity (sampled-in-bin). B. Fluctuations of the mean squared Euclidean distance to the centroid (black line with grey area showing the confidence intervals computed after 1000 bootstraps) and sampled-in-bin diversity (blue bars). C. Relative contribution of ammonoid superfamilies to disparity (mean squared Euclidean distance to the centroid). See Fig. 2 for interval labels.

Fig. 9 in Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry

Fig. 9. Evolution of the relative contribution of ammonoid superfamilies to diversity and disparity (mean squared Euclidean distance to the centroid) through the Early and Middle Devonian ammonoid zones (biozones numbered from 1 to 30, see Fig. 2); based on the analysis of the whorl profiles. A. Relative contribution of ammonoid superfamilies to diversity (sampled-in-bin). B. Fluctuations of the mean squared Euclidean distance to the centroid (black line with grey area showing the confidence intervals computed after 1000 bootstraps) and sampled-in-bin diversity (blue bars). C. Relative contribution of ammonoid superfamilies to disparity (mean squared Euclidean distance to the centroid).

Fig. 6 in Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry

Fig. 6. Evolution of the morphospace occupation through the seven intervals constituting the Early and Middle Devonian, showing the distribution of ammonoid superfamilies; based on the analysis of the whorl profiles (on each diagram, the horizontal axis corresponds to PC1 and the vertical axis to PC2). See Fig. 2 for interval labels.

Fig. 11 in Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry

Fig. 11. Variations of the convex hull area computed for PC1 and PC2, based on the analysis of the whorl profiles through the Early and Middle Devonian. Comparison of the measured values with the expected values given diversity, computed by applying the null model of Whalen et al. (2020). A. Fluctuations computed at the interval resolution. B. Fluctuations computed at the biozone resolution. See Fig. 2 for interval labels and biozones.

Fig. 5 in Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry

Fig. 5. Diagrams showing the morphospace occupation observed for the three stages constituting the Early and Middle Devonian (A–C), with level contours and density curves; based on the analysis of the whorl profiles. The grey dots correspond to the data recorded for the entire studied time interval (Early and Middle Devonian); the black dots refer to the data recorded for each of the studied stage (respectively, Emsian, Eifelian, and Givetian). The colours refer to the density of the data in the morphospace; the red-yellowwhite gradient indicates the decreasing density of occupied areas. Compare also with density curves (in grey) above and to the right of the diagrams.

Fig. 4 in Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry

Fig. 4. Morphospace occupation observed for the Early and Middle Devonian, based on the analysis of the whorl profiles, with representative examples of shapes. The first two axes explain 95.7% of the variance.

Fig. 3. Ammonoid morphology and dataset. A in Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry

Fig. 3. Ammonoid morphology and dataset. A. Morphology of an ammonoid; as an example, the outline of the whorl profile taken at the maximum conch diameter is highlighted by a thick black line (modified from De Baets et al. 2010). B. Dataset analysed here; compilation of drawings of whorl profile outlines corresponding to Early and Middle Devonian ammonoids from Morocco.

Fig. 8 in Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry

Fig. 8. Disparity and diversity fluctuations through the Early and Middle Devonian; based on the analysis of the whorl profiles. A. Sum of ranges (black line with grey area showing the confidence intervals) and sampled-in-bin diversity (blue bars). B. Sum of variances (black line with grey area showing the confidence intervals) and sampled-in-bin diversity (blue bars). C. Average displacement (black line with grey area showing the confidence intervals) and sampled-in-bin diversity (blue bars). Confidence intervals (error bars) are computed after 1000 bootstraps. See Fig. 2 for interval labels.

Fig. 1 in Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry

Fig. 1. Simplified geological map of Morocco (modified from Klug 2002b). The square shows the area where Early and Middle Devonian ammonoids are reported (Tafilalt and Ma'der basins).

Fig. 2 in Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry

Fig. 2. Stratigraphic scheme for the Early and Middle Devonian of the Anti-Atlas of Morocco, showing the distribution of superfamilies through time. Ammonoid biozonation from (Klug 2002a; Aboussalam and Becker 2011; Bockwinkel et al. 2015; Becker et al. 2019). Absolute ages from the Geological Time Scale v. 5.0 (Walker et al. 2018). "Sobolewia sp. nov." and "Afromaenioceras sp. nov" have been introduced by Becker et al. (2004), and Lunupharciceras sp. nov." by Aboussalam and Becker (2011); these new taxa have not yet been formally described but they are mentioned in several studies where they are used to establish the biozonation (e.g., Becker et al. 2004; Aboussalam and Becker 2011).

Fig. 10 in Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry

Fig. 10. Disparity and diversity fluctuations through the Early and Middle Devonian ammonoid zones (biozones numbered from 1 to 30, see Fig. 2); based on the analysis of the whorl profiles. A. Sum of ranges (black line with grey area showing the confidence intervals) and sampled-in-bin diversity (blue bars). B. Sum of variances (black line with grey area showing the confidence intervals) and sampled-in-bin diversity (blue bars). C. Average displacement black line with grey area showing the confidence intervals) and sampled-in-bin diversity (blue bars). Confidence intervals (error bars) are computed after 1000 bootstraps.

Figure 14 in Integrative approach of morphology and geometric morphometrics to species delimiation in Torrenticolidae (Acari: Hydrachnidiae)

Figure 14. Monatractides macrocorpis Gu & Guo, 2019, female. A. Dorsal view. B. Ventral view. C. Palp, lateral view. D. Infracapitulum and chelicera. Scale bars = 100 μm.

Figure 11 in Integrative approach of morphology and geometric morphometrics to species delimiation in Torrenticolidae (Acari: Hydrachnidiae)

Figure 11. Torrenticola brevisuturae Gu & Guo, sp. nov., female. A. Dorsal view. B. Ventral view. C. Palp, lateral view. D. Infracapitulum and chelicera. Scale bars = 100 μm.

Figure 10 in Integrative approach of morphology and geometric morphometrics to species delimiation in Torrenticolidae (Acari: Hydrachnidiae)

Figure 10. Torrenticola brevisuturae Gu & Guo, sp. nov., male. A. Leg-I. B. Leg-II. C. Leg-III. D. Ejaculatory complex. E. Leg-IV- 1–4. F. Leg-IV-5–6. Scale bars = 100 μm.

Figure 1. Landmark definition. A. Dorsoglandularia 1–4. B in Integrative approach of morphology and geometric morphometrics to species delimiation in Torrenticolidae (Acari: Hydrachnidiae)

Figure 1. Landmark definition. A. Dorsoglandularia 1–4. B. Infracapitulum (Torrenticola). C. Infracapitulum (Monatractides).

Figure 13 in Integrative approach of morphology and geometric morphometrics to species delimiation in Torrenticolidae (Acari: Hydrachnidiae)

Figure 13. Monatractides macrocorpis Gu & Guo, 2019, male. A. Dorsal view. B. Ventral view. C. Palp, lateral view. D. Ejaculatory complex. E. Infracapitulum and chelicera. Scale bars = 100 μm.

Figure 9 in Integrative approach of morphology and geometric morphometrics to species delimiation in Torrenticolidae (Acari: Hydrachnidiae)

Figure 9. Torrenticola brevisuturae Gu & Guo, sp. nov., male. A. Dorsal view. B. Ventral view. C. Palp, lateral view. D. Infracapitulum and chelicera. Scale bars = 100 μm.

Figure 12 in Integrative approach of morphology and geometric morphometrics to species delimiation in Torrenticolidae (Acari: Hydrachnidiae)

Figure 12. Torrenticola brevisuturae Gu & Guo, sp. nov., female. A. Leg-I. B. Leg-II. C. Leg-III-1–4. D. Leg-III-5–6. E. Leg-IV-1–4. F. Leg-IV-5–6. Scale bars = 100 μm.