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Inferred genetic architecture underlying evolution in a fossil stickleback lineage

Citation

Stuart, Yoel; Travis, Matthew; Bell, Michael (2020), Inferred genetic architecture underlying evolution in a fossil stickleback lineage, Dryad, Dataset, https://doi.org/10.5061/dryad.02v6wwq18

Abstract

Inferring the genetic architecture of evolution in the fossil record is difficult because genetic crosses are impossible, the acquisition of DNA is usually impossible, and phenotype-genotype maps are rarely obvious. However, such inference is valuable because it reveals the genetic basis of microevolutionary change across many more generations than is possible in studies of extant taxa, thereby integrating microevolutionary process and macroevolutionary pattern. Here, we infer the genetic basis of pelvic skeleton reduction in Gasterosteus doryssus, a Miocene stickleback fish from a finely resolved stratigraphic sequence that spans nearly 17,000 years. Reduction in pelvic score, a categorical measure of pelvic structure, resulted primarily from reciprocal frequency changes of two discrete phenotypic classes. Pelvic vestiges also showed left-side-larger asymmetry. These patterns implicate Pitx1, a large-effect gene whose deletion generates left-larger asymmetry of pelvic vestiges in extant, closely-related Gasterosteus aculeatus. In contrast, reductions in lengths of the pelvic girdle and pelvic spines resulted from directional shifts of unimodal, continuous trait distributions, suggesting an additional suite of genes with minor, additive pelvic effects, again like G. aculeatus. Similar genetic architectures explain shared but phyletically independent patterns across 10 million years of stickleback evolution.

Methods

Please see the manuscript for details.

Usage Notes

Phenotypic.data.for.analysis.no.sc.csv

Univariate traits measured for fossil specimens from 18 sections of temporal sequence K. Missing data are due to taphonomic reasons or because traits have been lost, and are indicated by NAs. Trait abbreviations are described in KSeries_abbreviations.doc.

Sample_L_Pelvic_Frequencies_fromTravis_May2019.csv

This table is equivalent to Supplementary Table S2. It is a frequency table of pelvic score by section.

univariate.data.L.fromTableS4_forAnalysis.csv

This is the temporal sequence L data set used for pelvic asymmetry analysis. In the R code, we've noted that times reported in YEAR (col D) and INT (col E) are miscalibrated. This is okay, however, as chronology is not necessary for the asymmetry analyses, except to make sure that only lineage II fish are analyzed. The arrival of lineage II can be correlated with Supplementary Table S2 by finding where mean PS goes from ~1 to exactly 3.0 for several thousand years. This happens at INT = 5250 years, which means that fish from earlier in the sequence are lineage I and were excluded for the analyses.

Dryad_StuartTravisBell.R

This R script should recreate the results and figures in the paper. You will have to set your working directory define the path to the data files. Otherwise, it should run cleanly. If there are errors, or if results insconsistent with the manuscript appear, please write to Yoel Stuart (ystuart@luc.edu).

 

Funding

National Science Foundation, Award: DEB-1456462

National Science Foundation, Award: DEB-2003457

National Science Foundation, Award: BSR-8111013

National Institutes of Health, Award: GM124330-01

National Geographic Society, Award: 2869-84

National Institutes of Health, Award: EAR-9870337

National Science Foundation, Award: EAR-9870337

National Science Foundation, Award: DEB-0322818

Center for Field Research (Earthwatch)

Center for Field Research (Earthwatch)