DOI: 10.5061/dryad.bj7n9
title: 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)

description: Background: High morphological diversity can occur in closely related
 animals when selection favors morphologies that are subject to intrinsic
 biological constraints. A good example is subterranean rodents of the
 genus Thomomys, one of the most taxonomically and morphologically diverse
 mammalian genera. Highly procumbent, tooth-digging rodent skull shapes are
 often geometric consequences of increased body size. Indeed, larger-bodied
 Thomomys species tend to inhabit harder soils. We used geometric
 morphometric analyses to investigate the interplay between soil hardness
 (the main extrinsic selection pressure on fossorial mammals) and allometry
 (i.e. shape change due to size change; generally considered the main
 intrinsic factor) on crania and humeri in this fast-evolving mammalian
 clade. Results: Larger Thomomys species/subspecies tend to have more
 procumbent cranial shapes with some exceptions, including a small-bodied
 species inhabiting hard soils. Counter to earlier suggestions, cranial
 shape within Thomomys does not follow a genus-wide allometric pattern as
 even regional subpopulations differ in allometric slopes. In contrast,
 humeral shape varies less with body size and with soil hardness. Soft-soil
 taxa have larger humeral muscle attachment sites but retain an orthodont
 (non-procumbent) cranial morphology. In intermediate soils, two pairs of
 sister taxa diverge through differential modifications on either the
 humerus or the cranium. In the hardest soils, both humeral and cranial
 morphology are derived through large muscle attachment sites and a high
 degree of procumbency. Conclusions: Our results show that conflict between
 morphological function and intrinsic allometric patterning can quickly and
 differentially alter the rodent skeleton, especially the skull. In
 addition, we found a new case of convergent evolution of incisor
 procumbency among large-, medium-, and small-sized species inhabiting hard
 soils. This occurs through different combinations of allometric and
 non-allometric changes, contributing to shape diversity within the genus.
 The strong influence of allometry on cranial shape appears to confirm
 suggestions that developmental change underlies mammalian cranial shape
 divergences, but this requires confirmation from ontogenetic studies. Our
 findings illustrate how a variety of intrinsic processes, resulting in
 species-level convergence, could sustain a genus-level range across a
 variety of extrinsic environments. This might represent a mechanism for
 observations of genus-level niche conservation despite species extinctions
 in mammals.
description: Photographs of Northern
 California Thomomys pocket gopher lateral humeri for 2D Geometric
 MorphometricsZipped 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.Humerus_Lateral.zipPhotographs of Northern California Thomomys pocket gopher anterior humeri for 2D Geometric MorphometricsZipped 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.Humerus_Anterior.zipLandmark coordinates and slider identifications for each specimen view for geometric morphometricsLandmark 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.Landmark Coordinates.zipPhotographs of Northern California genus Thomomys subgenus Megascapheus pocket gopher lateral crania for 2D Geometric MorphometricsZipped 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.Crania_Lateral_Megascapheus.zipPhotographs of Northern California Thomomys subgenus Thomomys pocket gopher lateral crania for 2D Geometric MorphometricsZipped 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.Crania_Lateral_Thomomys.zipPhotographs of Northern California genus Thomomys subgenus Megascapheus pocket gopher ventral crania for 2D Geometric MorphometricsZipped 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.Crania_Ventral_Megascapheus.zipPhotographs of Northern California Thomomys subgenus Thomomys pocket gopher ventral crania for 2D Geometric MorphometricsZipped 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.Crania_Ventral_Thomomys.zipGeo-referrenced NRCS Soil Data for Northern California genus Thomomys pocket gophersThis 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.0064935GeoreferrencedNRCSSoilData.csv