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Below you will find code/packages developed by the Pierce lab to explore various aspects of vertebrate anatomy, function and evolution.

APSE

Accelerated Pose Searching with Electrostatics (or APSE) is an iterative algorithm for rapidly and intelligently sampling high-dimensional joint pose space to quantify articular function and mobility. Developed by postdoctoral fellow Peter Bishop as a MATLAB GUI, APSE the algorithm simulateously searches rotations and translations, and integrates constraints to define the pose space.

  • Bishop, P.J., Brocklehurst, R.J. and Pierce, S.E., 2022. Intelligent sampling of high‐dimensional joint mobility space for analysis of articular function. Methods in Ecology and Evolution.

AUTOBEND

AutoBend is set of Maya-based python functions that estimates osteological range of motion at intervertebral joints based on a series of constraints on motion. The code was developed by postdoctoral fellow Katrina Jones to automate ROM estimation and reduce interobserver error.

  • Jones, K.E., Brocklehurst, R.J. and Pierce, S.E., 2021. AutoBend: an automated approach for estimating intervertebral joint function from bone-only digital models. Integrative Organismal Biology, 3(1), p.obab026.

EvoPhylo

R package to perform automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses. The package was developed by postdoctoral fellow Tiago Simoes to pre- and postprocess data using the software Mr. Bayes, but since version 0.3 it also handles data pre- and post-processing for the software package BEAST2.

  • Simões, T.R. and Pierce, S.E., 2021. Sustained high rates of morphological evolution during the rise of tetrapods. Nature Ecology & Evolution, 5(10), pp.1403-1414.
  • Simões, T.R., Greifer, N., Barido-Sottani, J. and Pierce, S.E., 2022. EvoPhylo: an R package for pre-and postprocessing of morphological data from relaxed clock Bayesian phylogenetics.

MORPHOSCAPE

R package that builds adaptive landscapes from performance surfaces to explore the functional trade-offs associated with morphologial variation. The package was developed by graduate student Blake Dickson and uses morphological and functional data measured across a morphospace to build adaptive landscapes that optimize performance.

  • Dickson, B.V. and Pierce, S.E., 2019. Functional performance of turtle humerus shape across an ecological adaptive landscape. Evolution, 73(6), pp.1265-1277.
  • Dickson, B.V., Clack, J.A., Smithson, T.R. and Pierce, S.E., 2021. Functional adaptive landscapes predict terrestrial capacity at the origin of limbs. Nature, 589(7841), pp.242-245.
  • Jones, K.E., Dickson, B.V., Angielczyk, K.D. and Pierce, S.E., 2021. Adaptive landscapes challenge the “lateral-to-sagittal” paradigm for mammalian vertebral evolution. Current Biology, 31(9), pp.1883-1892.
  • Dickson B, Pierce S, Greifer N (2022). Morphoscape: Computation and Visualization of Adaptive Landscapes. R package version 1.0.1, https://blakedickson.github.io/Morphoscape/.

REGIONS

R package that statistically finds "regions" in serially-homologous structures, such as the vertebral column. The package was developed by postdoctoral fellow Katrina Jones and uses segmented regressions on multivariate morphological or functional data to determine the number of "regions" or descrete segments.

  • Jones, K.E., Angielczyk, K.D., Polly, P.D., Head, J.J., Fernandez, V., Lungmus, J.K., Tulga, S. and Pierce, S.E., 2018. Fossils reveal the complex evolutionary history of the mammalian regionalized spine. Science, 361(6408), pp.1249-1252.
  • Jones, K.E., Gonzalez, S., Angielczyk, K.D. and Pierce, S.E., 2020. Regionalization of the axial skeleton predates functional adaptation in the forerunners of mammals. Nature Ecology & Evolution, 4(3), pp.470-478.