DOI: 10.5061/dryad.c342rg7
title: Data from: Phylogenomics of an extra-Antarctic notothenioid radiation reveals a previously unrecognized lineage and diffuse species boundaries

description: Background: The impressive adaptive radiation of notothenioid fishes in
 Antarctic waters is generally thought to have been facilitated by an
 evolutionary key innovation, antifreeze glycoproteins, permitting the
 rapid evolution of more than 120 species subsequent to the Antarctic
 glaciation. By way of contrast, the second-most species-rich notothenioid
 genus, Patagonotothen, which is nested within the Antarctic clade of
 Notothenioidei, is almost exclusively found in the non-Antarctic waters of
 Patagonia. While the drivers of the diversification of Patagonotothen are
 currently unknown, they are unlikely to be related to antifreeze
 glycoproteins, given that water temperatures in Patagonia are well above
 freezing point. Here we performed a phylogenetic analysis based on
 genome-wide single nucleotide polymorphisms (SNPs) derived from
 restriction site-associated DNA sequencing (RADseq) in a total of twelve
 Patagonotothen species. Results: We present a well-supported,
 time-calibrated phylogenetic hypothesis including closely and distantly
 related outgroups, confirming the monophyly of the genus Patagonotothen
 with an origin approximately 3 million year ago and the paraphyly of both
 the sister genus Lepidonotothen and the family Notothenidae. Our
 phylogenomic and population genetic analyses highlight a previously
 unrecognized linage and provide evidence for shared genetic variation
 between some closely related species. We also provide a mitochondrial
 phylogeny showing mitonuclear discordance. Conclusions: Based on a
 combination of phylogenomic and population genomic approaches, we provide
 evidence for the existence of a new, potentially cryptic, Patagonotothen
 species, and demonstrate that genetic boundaries between some closely
 related species are diffuse, likely due to recent introgression and/or
 incomplete linage sorting. The detected mitonuclear discordance highlights
 the limitations of relying on a single locus for species barcoding. In
 addition, our time calibrated phylogenetic hypothesis shows that the early
 burst of diversification roughly coincides with the onset of the
 intensification of Quaternary glacial cycles and that the rate of species
 accumulation may have been stepwise rather than constant. Our phylogenetic
 framework not only advances our understanding of the origin of a
 high-latitude marine radiation, but also provides the basis for the study
 of the ecology and life history of the genus Patagonotothen, as well as
 for their conservation and commercial management.
description: SNPs_Figure1_MLSNPs used to generate the ML tree shown in Figure 1.SNPs_Figure2_MLSNPs used to generate the ML tree shown in Figure 2.P. guntheri - P. brevicauda_Figure3a.structureSNPs used in STRUCTURE to generate Figure 3 aguntheri-brevicauda_Figure3a.structure.tsvP. ramsayi - P. wiltoni_Figure3b.structureSNPs used in STRUCTURE to generate Figure 3 bramsayi-wiltoni_Figure3b.structure.tsvL. squamifrons - L. kempi_Figure3c.structureSNPs used in STRUCTURE to generate Figure 3 csquamifrons-kempi_Figure3c.structure.tsvSNPs_Figure4_SNAPPSNPs used in SNAPP to generate tree shown in Figure 4Additional_file4_PoMoInput file used in the software IQtree to generate the tree shown in the additional file4.