The complex history of genome duplication and hybridization in North American gray treefrogs

Polyploid speciation has played an important role in evolutionary history
across the tree of life, yet there remain large gaps in our understanding
of how polyploid species form and persist. While systematic studies have
been conducted in numerous polyploid complexes, recent advances in
sequencing technology have demonstrated that conclusions from data-limited
studies may be spurious and misleading. The North American gray treefrog
complex, consisting of the diploid Hyla chrysoscelis and the
tetraploid Hyla versicolor, has long been used as a model system
in a variety of biological fields, yet all taxonomic studies to date were
conducted with only a few loci from nuclear and mitochondrial genomes.
Here, we utilized anchored hybrid enrichment and high-throughput
sequencing to capture hundreds of loci along with whole mitochondrial
genomes to investigate the evolutionary history of this complex. We used
several phylogenetic and population genetic methods, including coalescent
simulations and testing of polyploid speciation models with Approximate
Bayesian Computation (ABC), to determine that H. versicolor was most
likely formed via autopolyploidization from a now extinct lineage of H.
chrysoscelis. We also uncovered evidence of significant hybridization
between diploids and tetraploids where they co-occur, and show that
historical hybridization between these groups led to the re-formation of
distinct polyploid lineages following the initial whole genome duplication
event. Our study indicates that a wide variety of methods and explicit
model testing of polyploid histories can greatly facilitate efforts to
uncover the evolutionary history of polyploid complexes.