Inferring the evolution of reproductive isolation in a lineage of fossil threespine stickleback, Gasterosteus doryssus

Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr’s peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould’s original punctuated equilibrium model combined Darwin’s conjecture, Mayr’s model, and 124 years of unsuccessfully sampling the fossil record for transitions. Observing such divergence, however, could illustrate the tempo and mode of evolution during early speciation. Here, we investigate peripatric divergence in a Miocene stickleback fish, Gasterosteus doryssus. This lineage appeared and, over ~8,000 generations, evolved significant reduction of twelve of sixteen traits related to armor, swimming, and diet, relative to its ancestral population. This was greater morphological divergence than we observed between reprodu..., (a) Fossil specimen data
To quantify morphological divergence in the fossils, we compiled published data from the D (Bell et al. 1985), L (Bell et al. 2006), and K series (Stuart et al. 2020, Voje et al. 2022). See Figure 1A for stratigraphic correlations among series. Series D consisted of 26 samples spaced at ~5,000-year intervals over an estimated 108,275 years (Figure 1A). Six traits were measured from D: standard length, pelvic score, and the number of pre-dorsal pterygiophores, dorsal spines, anal-fin rays, and dorsal-fin rays (Bell et al. 1985). Series L comprised a section starting ~4,500 years before the replacement event until ~16,500 years after and was sampled continuously. Three armour traits were measured for series L: pelvic score, number of dorsal spines, and number of touching pre-dorsal pterygiophores. This series confirmed replacement of lineage I by lineage II within ~125 years (Bell et al. 2006) and that subsequent evolution of lineage II was probably caused by dire..., Microsoft Excel is helpful to open the data files.
R and R Studio are necessary to run the analysis scripts., # Inferring the evolution of reproductive isolation in a lineage of fossil threespine stickleback, Gasterosteus doryssus

Threespine stickleback data: Fossil and Species Pair Gasterosteus spp.

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The data are comprised of morphological traits (continuous, count, index) collected from samples of a fossil lineage of threespine stickleback (Gasterosteus doryssus) from a paleo lake in Nevada (Bell et al. 1985; Bell et al. 2006; Stuart et al. 2020) and extant threespine stickleback (Gasterosteus aculeates) from five lakes on Vancouver Island.

## Description of the data and file structure

RS.speciationPruned.for.sizecorrection.csv contains fossil data (Fos in the universal ID column) structured as temporal samples where T0 is time zero, k.19 is the next oldest sample, proceeding to K.03 as the youngest sample closest to the present. The mean age of each sample in years, relative to the first sample, is available in the the second column of KSampleMeanTimes.csv.

RS.speciationPruned.for.s...