Data from: Getting a head in hard soils: convergent skull evolution and divergent allometric patterns explain shape variation in a highly diverse genus of pocket gophers (Thomomys)

Marcy AE, Hadly EA, Sherratt E, Garland K, Weisbecker V

Date Published: October 3, 2016

DOI: http://dx.doi.org/10.5061/dryad.bj7n9

 

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Title Photographs of Northern California Thomomys pocket gopher lateral humeri for 2D Geometric Morphometrics
Downloaded 4 times
Description Zipped folder containing photographs of lateral humerus specimens of genus Thomomys gophers from our Northern California study region housed in the UC Berkeley Museum of Vertebrate Zoology's (MVZ) mammal collections. Abbreviated taxonomic identification and the MVZ catalog numbers are given in the filenames of each specimen photo. Photos with a number at the end of the filename are photos taken of the same specimen at different times during the digitization process to assess operator error. Photos with "copy" at the end of the filename are photo files that were digitally duplicated to assess landmarking error specifically.
Download Humerus_Lateral.zip (302.0 Mb)
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Title Photographs of Northern California Thomomys pocket gopher anterior humeri for 2D Geometric Morphometrics
Downloaded 2 times
Description Zipped folder containing photographs of anterior humerus specimens of genus Thomomys gophers from our Northern California study region housed in the UC Berkeley Museum of Vertebrate Zoology's (MVZ) mammal collections. Abbreviated taxonomic identification and the MVZ catalog numbers are given in the filenames of each specimen photo. Photos with a number at the end of the filename are photos taken of the same specimen at different times during the digitization process to assess operator error. Photos with "copy" at the end of the filename are photo files that were digitally duplicated to assess landmarking error specifically.
Download Humerus_Anterior.zip (333.5 Mb)
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Title Landmark coordinates and slider identifications for each specimen view for geometric morphometrics
Downloaded 9 times
Description Landmark coordinates created by tpsdig2 software (Rohlf, Stony Brook) in TPS files the file format of landmark coordinates read in by geomorph, the R package for Geometric Morphometrics (GMM). Semilandmarks or "sliders" are indicated in the associated .CSV files for each view. Please read the ReadMe file for how to use R to combine the TPS and CSV files to recreate the collection of landmarks and semilandmarks we used for our GMM analyses.
Download Landmark Coordinates.zip (436.2 Kb)
Download README.rtf (9.044 Kb)
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Title Photographs of Northern California genus Thomomys subgenus Megascapheus pocket gopher lateral crania for 2D Geometric Morphometrics
Downloaded 3 times
Description Zipped folder containing photographs of lateral crania specimens of genus Thomomys subgenus Megascapheus gophers from our Northern California study region housed in the UC Berkeley Museum of Vertebrate Zoology's (MVZ) mammal collections. Abbreviated taxonomic identification and the MVZ catalog numbers are given in the filenames of each specimen photo. Photos with a number at the end of the filename are photos taken of the same specimen at different times during the digitization process to assess operator error. Photos with "copy" at the end of the filename are photo files that were digitally duplicated to assess landmarking error specifically. Combine with the subgenus Thomomys file of the same view before proceeding with analyses.
Download Crania_Lateral_Megascapheus.zip (829.2 Mb)
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Title Photographs of Northern California Thomomys subgenus Thomomys pocket gopher lateral crania for 2D Geometric Morphometrics
Downloaded 3 times
Description Zipped folder containing photographs of lateral crania specimens of genus Thomomys subgenus Thomomys gophers from our Northern California study region housed in the UC Berkeley Museum of Vertebrate Zoology's (MVZ) mammal collections. Abbreviated taxonomic identification and the MVZ catalog numbers are given in the filenames of each specimen photo. Photos with a number at the end of the filename are photos taken of the same specimen at different times during the digitization process to assess operator error. Photos with "copy" at the end of the filename are photo files that were digitally duplicated to assess landmarking error specifically. Combine with the subgenus Megascapheus file of the same view before proceeding with analyses.
Download Crania_Lateral_Thomomys.zip (825.5 Mb)
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Title Photographs of Northern California genus Thomomys subgenus Megascapheus pocket gopher ventral crania for 2D Geometric Morphometrics
Downloaded 4 times
Description Zipped folder containing photographs of ventral crania specimens of genus Thomomys subgenus Megascapheus gophers from our Northern California study region housed in the UC Berkeley Museum of Vertebrate Zoology's (MVZ) mammal collections. Abbreviated taxonomic identification and the MVZ catalog numbers are given in the filenames of each specimen photo. Photos with a number at the end of the filename are photos taken of the same specimen at different times during the digitization process to assess operator error. Photos with "copy" at the end of the filename are photo files that were digitally duplicated to assess landmarking error specifically. Combine with the subgenus Thomomys file of the same view before proceeding with analyses.
Download Crania_Ventral_Megascapheus.zip (849.6 Mb)
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Title Photographs of Northern California Thomomys subgenus Thomomys pocket gopher ventral crania for 2D Geometric Morphometrics
Downloaded 2 times
Description Zipped folder containing photographs of ventral crania specimens of genus Thomomys subgenus Thomomys gophers from our Northern California study region housed in the UC Berkeley Museum of Vertebrate Zoology's (MVZ) mammal collections. Abbreviated taxonomic identification and the MVZ catalog numbers are given in the filenames of each specimen photo. Photos with a number at the end of the filename are photos taken of the same specimen at different times during the digitization process to assess operator error. Photos with "copy" at the end of the filename are photo files that were digitally duplicated to assess landmarking error specifically. Combine with the subgenus Megascapheus file of the same view before proceeding with analyses.
Download Crania_Ventral_Thomomys.zip (849.2 Mb)
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Title Geo-referrenced NRCS Soil Data for Northern California genus Thomomys pocket gophers
Downloaded 2 times
Description This CSV file contains the soil information extracted from the US Department of Agriculture (USDA)'s Natural Resource Conservation Service (NRCS) STATSGO soil database. The soil characteristics of clay, silt, sand, bulk density, linear extensibility are given as a weighted average for both a depth of 20cm and of 1m; the total soil depth for the area is also reported. These characteristics are associated with all unique specimen localities in our study area. Unique ID refers to the specimen's unique ID number in the Arctos collaborative museum database. The CatNum ID is the Museum of Vertebrate Zoology (MVZ) catalog number we use to identify specimens throughout our analyses. For more information about this dataset, please see Marcy et al (2013) PLOS ONE doi: http://dx.doi.org/10.1371/journal.pone.0064935
Download GeoreferrencedNRCSSoilData.csv (114.1 Kb)
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When using this data, please cite the original publication:

Marcy AE, Hadly EA, Sherratt E, Garland K, Weisbecker V (2016) Getting a head in hard soils: convergent skull evolution and divergent allometric patterns explain shape variation in a highly diverse genus of pocket gophers (Thomomys). BMC Evolutionary Biology 16: 207. http://dx.doi.org/10.1186/s12862-016-0782-1

Additionally, please cite the Dryad data package:

Marcy AE, Hadly EA, Sherratt E, Garland K, Weisbecker V (2016) Data from: Getting a head in hard soils: convergent skull evolution and divergent allometric patterns explain shape variation in a highly diverse genus of pocket gophers (Thomomys). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.bj7n9
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