DOI: 10.5061/dryad.612jm6452
title: Rapid reduction of Paraoxonase expression followed by inactivation across semiaquatic mammals suggests adaptive benefit of gene loss

description: Convergent adaptation to the same environment by multiple lineages
 frequently involves rapid evolutionary change at the same genes,
 implicating these genes as important for environmental adaptation. Such
 adaptive molecular changes may yield either change or loss of function;
 loss of protein function can eliminate newly deleterious proteins or
 reduce energy necessary for protein production. We previously found a
 striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1)
 gene among aquatic mammal lineages – Pon1 became a pseudogene at least six
 times independently in aquatic and semiaquatic mammals with clear genetic
 lesions, such as stop codons and frameshifts. Here, we assess the
 landscape and pace of pseudogenization by studying Pon1 sequences,
 expression levels, and blood plasma activity across four major aquatic and
 semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We
 also observed in beavers and pinnipeds an unexpected reduction in
 expression of Pon3, a paralog with similar expression patterns but
 different substrate preferences. Ultimately, in all lineages with
 aquatic/semiaquatic members, we find that preceding any coding level
 pseudogenization events in Pon1, there is a drastic decrease in
 expression, followed by relaxed selection, thus allowing for accumulation
 of disrupting mutations. The recurrent and rapid loss of Pon1 even
 suggests that it is adaptive in aquatic mammals. Accordingly, we examined
 diving and dietary traits across pinniped species as potential driving
 forces of Pon1 loss. We found that loss is best correlated with diving
 activity and is likely the result of selective pressures associated with
 hypoxia and hypoxia-induced inflammation.
description: Expression patterns using transcriptomic data were performed for
 RNA-seq libraries created from museum liver samples, as well as liver
 RNA-seq libraries available on the Short Read Archive (SRA). For museum
 samples, the extracted RNA for 4 samples was sent to Novogene for library
 preparation (polyA enrichment) and sequencing via NovaSeq PE150. An
 additional 13 individuals had RNA-seq libraries made using Swift
 Biosciences RNA library prep kit, before being sent to Novogene for
 sequencing – these libraries were trimmed for adapters and quality
 filtered via BBduk in the BBtools package. Data downloaded from the SRA
 included transcriptomic data derived exclusively from liver for other
 pinniped species, as well as other carnivores, cetaceans, ungulates,
 rodents and chiropterans. Each library was mapped using Salmon against the
 closest-related reference available – for pinnipeds, they were mapped to
 all 6 pinniped references available. When possible, multiple individuals
 were used for the same species to assess within-species expression
 variation. Regardless of origin, expression levels of PON1, PON2, PON3,
 and endogenous controls were assessed in all transcriptomes. There were a
 total of 43 different transcriptome references used, thus each transcript
 was renamed according to the closest BLAST hit from the human
 transcriptome (GCF_000001405.39_GRCh38.p13_rna), and then isoforms for
 each gene collapsed into one per gene. Included in this
 repository are... Raw TPM count files from
 SALMON for Carnivores, Rodents, Ungulates, Cetaceans, and
 Chiropterans. Scripts and files associated with the
 PGLS Trees associated with CODEML
 PON3 sequence alignments
description: BBtools Bushnell (2018) 
 https://jgi.doe.gov/data-and-tools/software-tools/bbtools/ SALMON Patro et al. (2017) https://salmon.readthedocs.io/en/latest/index.html NCBI SRA Toolkit Lam and Ane (2014) https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit PAML - CODEML Yang (2007) http://abacus.gene.ucl.ac.uk/software/paml.html