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Low resolution scans provide a sufficiently accurate, cost- and time-effective alternative to high resolution scans for interspecific 3D shape analyses

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222 days ago
Low resolution scans provide a sufficiently accurate, cost- and time-effective alternative to high resolution scans for interspecific 3D shape analyses https://t.co/s9fFVdVfU6
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Supplemental Information

Catalogue numbers and sex information for all specimens

Catalogue numbers are searchable in the Queensland Museum database, which also provided the sex information for the 19 delicate mouse (Pseudomys delicatulus) specimens we used in our study.

DOI: 10.7287/peerj.preprints.26696v1/supp-1

Supplementary methods for optimal use of an HD109 3D surface scanner for small biological specimens

This standard operating procedures outlines the best practices for 3D scanning, which we chose after extensive trial and error.

DOI: 10.7287/peerj.preprints.26696v1/supp-2

Landmark, semi-landmark curve, and patch point names and definitions

There are a total of 289 points used to capture crania shape. 58 are fixed landmarks (LM): the first 12 are centrally located and the remaining 46 come in right and left pairs (right is odd, left is even in the table numbering system). 145 points were placed along 39 curves as semi-landmarks: the first 7 curves are centrally located and the remaining 32 curves come in right and left pairs (right is even, left is odd). 86 points were placed on 12 surface patches, all of which come in right and left pairs (right is even, left is odd).

DOI: 10.7287/peerj.preprints.26696v1/supp-3

R script for analyses presented in this study

This file should be copied into R or Rstudio. All datasets required to run the analyses are contained in the supplementary information. Some analyses must be run in MorphoJ, an outside software freely available at: http://www.flywings.org.uk/morphoj_page.htm.

DOI: 10.7287/peerj.preprints.26696v1/supp-4

Raw landmark coordinates produced by digitizing 3D files in Viewbox

This is the raw format of our shape data produced by exporting the landmark coordinates once landmarking in Viewbox was finished.

DOI: 10.7287/peerj.preprints.26696v1/supp-5

Definitions of semilandmarks as required for sliding in geomorph during Procrustes superimposition

This table simply encodes the two neighboring points that a semi-landmark can slide between. Point numbers can be related to their position on the cranium using Fig. 3 or Table S2. This table is necessary to treat sliding semi-landmarks correcting during Procrustes alignment using geomorph's gpagen() function.

DOI: 10.7287/peerj.preprints.26696v1/supp-6

Table of digitized points with bilateral symmetry for symmetric shape analysis

This table only includes the points which have bilateral symmetry (i.e. a symmetric pair on the other left/right side of the skull). Point numbers can be related to their position on the cranium using Fig. 3 or Table S2. This table is necessary to isolate the symmetric component of shape in geomorph using the bilat.symmetry() function.

DOI: 10.7287/peerj.preprints.26696v1/supp-7

Sex identification for specimens in intra-specific analyses

This table is nearly identical to Table S1 except that the "Catalogue Number" column heading is shortened to "CatNum" to ease the merging datasets. This dataset is necessary to perform the intra-specific analyses presented here.

DOI: 10.7287/peerj.preprints.26696v1/supp-8

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Ariel E Marcy conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Carmelo Fruciano conceived and designed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Matthew J Phillips analyzed the data, approved the final draft.

Karine Mardon performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Vera Weisbecker conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

1) MorphoSource (www.morphosource.org)

2) P458 "3D surface scanning versus microCT scanning in very small vertebrate crania"

3) https://www.morphosource.org/MyProjects/Dashboard/dashboard/select_project_id/458

Login with username marcy.reviewer@gmail.com and password 12345; the project will appear on the right hand side of the dashboard

Funding

This work was supported by an Australian Research Council Discovery Grant (DP170103227) to VW and MJP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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