Contrasting phylogeographic patterns of sandy vs. rocky sympatric sister species of supralittoral Tylos isopods in Chile

Sister taxa that have diverged and persisted in sympatry have likely been
exposed to the same general environmental changes throughout their
evolutionary history and may thus exhibit similar phylogeographies. Here
we compare the phylogeographic patterns of two sister species of isopods
(genus Tylos) that have broadly overlapping distributions but distinct
habitat preferences in the supralittoral zone of Chile. The dynamic
geoclimatic history of this region during the Quaternary has been
implicated in shaping the evolutionary histories of other coastal taxa.
Tylos spinulosus is found in sandy beaches at latitudes ~27–30°S, whereas
Tylos chilensis has been found in rocky shores at ~27–33°S and at
~39–42°S. We sampled both species across their ranges (collectively from
20 localities) and obtained sequences from at least one mitochondrial gene
for 95 T. chilensis and 41 T. spinulosus. We used phylogenetics and
population genetics methods to analyze four single-gene and one
concatenated datasets: 12S rDNA (n=130); 16S rDNA (n=31); Cytochrome
oxidase subunit I (n=28); Cytochrome b (n=24); concatenation of the four
genes (n=24). Both species show high levels of isolation of local
populations, consistent with expectations from their limited autonomous
dispersal potential. However, they exhibit strikingly different
mitochondrial phylogeographic patterns. Tylos chilensis shows evidence of
multiple relatively deep divergence events leading to geographically
restricted lineages that appear to have persisted over multiple
glaciations. Surprisingly, one lineage of T. chilensis was found in
geographically distant localities, suggesting the possibility of
human-mediated dispersal. Tylos spinulosus appears to have undergone a
relatively recent bottleneck followed by a population/range expansion.
Differences in life histories and habitat preferences or stochasticity may
have contributed to these striking phylogeographic differences. Finally,
the high levels of differentiation and isolation among populations
indicate that they are highly vulnerable to extirpation. We discuss
threats to their persistence, and recommendations for their conservation.
This dataset includes: details about each of the specimens used in this
study (Supporting Table S1); input and output files used to generate the
haplotype networks depicted in the manuscripts; input and output files of
the analyses used to generate the rooted phylogenies depicted in this
manuscript (5 datasets: four single-gene and one concatenated); command
line and input files used to infer isolation by distance in Tylos
spinulosus (Mante test); and input and output files and detailed
methodology for testing the molecular clock hypothesis and inferring
genetic distances for two genes.