Selection on Visual Opsin Genes in Diurnal Neotropical Frogs and Loss of the SWS2 Opsin in Poison Frogs.

"data availability raw illumina sequencing data are deposited in the sequence read archive (bioproject prjna856227). all scripts and other data are available in the supporting material on datadryad (doi: 10 5061/dryad zw3r2289j). estimated gene trees were largely concordant with recent family-level phylogenies ( ; ) and hypothesized interspecific relationships ( ; ; ; see supplementary data s3 supplementary material online).; we first compared the dn value estimated for transition branches between nocturnal and diurnal lineages (the stem branches of dendrobatidae of atelopus and of brachycephalus ) to a dn value estimated for all other branches; no sites were identified as under different patterns of selection (see supplementary data s1 supplementary material online).; input files and results are available in supplementary data s1 supplementary material online a the numbering system used in our alignments can be determined by adding 17 to the bovine rh1 number for lws adding 9 for sws2 and subtracting 5 for sws1 b amino acid sites reported by as under positive selection.; based on published data 3 of the 44 sites are known spectral tuning sites including site 217 in lws and sites124 and 164 in rh1 ; 12 other sites are within three amino acids from a known spectral tuning site ( table 2 ; supplementary data s1 supplementary material online; supplementary table s3 supplementary material online).; fel results are indicated using + to indicate positive selection and - to indicate negative selection (negative selection results are only shown for sites found to be under positive selection by other analyses; see supplementary data s1 supplementary material online for full fel results).; for dendrobatids we explored the reassembled o pumilio scaffolds and found that scaffold70671 contained lws and was syntenic with other amphibians (two short and highly conserved regions between sws2 and lws could be aligned between nanorana and o pumilio [ supplementary data s2 supplementary material online]) but we could not identify any coding region of sws2 .; in contrast using the same methods we were able to detect sws2 upstream of lws in other hyloid frogs including bufo eleutherodactylus engystomops and rhinella ( fig 2 b supplementary data s4 supplementary material online).; the data matrix iqtree2 scripts constraint tree and analysis log files are included in supplementary data s3 supplementary material online in the folder iqtree.; we also compared substitution rates between transition branches (the stem branches of dendrobatidae of atelopus and of brachycephalus ) and all other branches but no sites were identified to be under different selection regimes in this foreground (see supplementary data s1 supplementary material online).; following convention the amino acid sites are numbered based on the bovine rhodopsin sequence (np_001014890 1); sequences from each opsin gene were aligned with bovine rhodopsin using mafft v7 419 and the numbering of the amino acid site was determined by referring to the numbering of bovine rhodopsin starting with the start codon as1 (see supplementary data s1 supplementary material online).; this analysis is implemented in the dryad folder named "synteny" (see supplementary data s4 supplementary material online).; this analysis is implemented in the dryad folders named "sws2_search" and "lws_search" (see supplementary data s4 supplementary material online) msad206_supplementary_data click here for additional data file. data availability raw illumina sequencing data are deposited in the sequence read archive (bioproject prjna856227"

"Conflict of interest: This publication is based in part on work by D.C.C. while serving at the National Science Foundation. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation or United States government."

"This research was funded by NSF DEB-1556967 to D.C.C.; NSF GROW, NSF DDIG (DEB-1404409), National Geographic Society 2014 Young Explorer Grant, and UC Berkeley start-up to RDT; NIH 5P50GM068763, NSF IOS-1822025, and William F. Milton Fund from Harvard Medical School to L.A.O.; L.A.O. is a New York Stem Cell Foundation—Robertson Investigator. J.C.S. was supported by SJU start-up funds and NSF DEB-2016372. M.J.N. was supported by the American Association of University Women. We thank Roberto Ibañez and Brian Gratwicke (Amphibian Rescue and Conservation Project), Vicky Poole, and Kevin Barrett (The Maryland Zoo), Luis A. Coloma (Fundación Otonga and Centro Jambatu de Investigación y Conservación de Anfibios; Quito, Ecuador), César Aguilar (Universidad Nacional Mayor de San Marcos; Lima, Peru), and Travis LaDuc (Biodiversity Center, UT Austin) for facilitating access to tissues and specimens. We thank two anonymous reviewers for critiques that improved the quality of this article. We also acknowledge and express gratitude for the lives of the animals involved in this study. The publication of this article was made possible in part by support from the Berkeley Research Impact Initiative (BRII) sponsored by the UC Berkeley Library. De novo sequence assembly was then completed using Trinity () on the Odyssey cluster supported by the FAS Science Division Research Computing Group at Harvard University. We remapped reads to the raw assembly using BWA () and then used eXpress (http://bio.math.berkeley.edu/eXpress/) to generate FPKM (fragments per kilobase per million mapped) scores for each contig. Low-confidence contigs that had an FPKM value of less than one were removed from the draft assembly. After removing contigs with low confidence, we used CD-HIT-EST () to remove contig redundancy. Given that redundant contigs can represent alternative splice variants, polymorphisms among the pooled individuals, or sequencing errors, we used a conservative threshold of 98% sequence similarity. The final assembly was annotated using Trinotate (); it was found to contain only three opsin genes: RH1, LWS, and SWS1. The SWS2 gene was absent. Thus, we hypothesized that SWS2 might have been lost in the ancestor of dendrobatids."