The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.

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Antigen processing and presentation by major histocompatibility complex (MHC) molecules is a cornerstone in vertebrate immunity. Like mammals, teleosts possess both classical MHC class I and multiple families of divergent MHC class I genes. However, while certain mammalian MHC class I-like molecules have proven to be integral in immune regulation against a broad array of pathogens, the biological relevance of the different MHC class I lineages in fish remains elusive. This work focuses on MHC class I L lineage genes and reveals unique regulatory patterns of six genes (Sasa-lia, Sasa-lda, Sasa-lca, Sasa-lga, Sasa-lha, and Sasa-lfa) in antimicrobial immunity of Atlantic salmon (Salmo salar L.). Using two separate in vivo challenge models with different kinetics and immune pathologies combined with in vitro stimulation using viral and bacterial TLR ligands, we show that de novo synthesis of different L lineage genes is distinctly regulated in response to various microbial stimuli. Prior to the onset of classical MHC class I gene expression, lia was rapidly and systemically induced in vivo by the single-stranded (ss) RNA virus salmonid alpha virus 3 (SAV3) but not in response to the intracellular bacterium Piscirickettsia salmonis. In contrast, lga expression was upregulated in response to both viral and bacterial stimuli. A role for distinct MHC class I L-lineage genes in anti-microbial immunity in salmon was further substantiated by a marked upregulation of lia and lga gene expression in response to type I IFNa stimulation in vitro. Comparably, lha showed no transcriptional induction in response to IFNa stimulation but was strongly induced in response to a variety of viral and bacterial TLR ligands. In sharp contrast, lda showed no response to viral or bacterial challenge. Similarly, induction of lca, which is predominantly expressed in primary and secondary lymphoid tissues, was marginal with the exception of a strong and transient upregulation in pancreas following SAV3 challenge Together, these findings suggest that certain Atlantic salmon MHC class I L lineage genes play important and divergent roles in early anti-microbial response and that their regulation, in response to different activation signals, represents a system for selectively promoting the expression of distinct non-classical MHC class I genes in response to different types of immune challenges.

40The field of ancient DNA is taxonomically dominated by studies focusing on mammals. This 41 taxonomic bias limits our understanding of endogenous DNA preservation for vertebrate taxa 42 with different bone physiology, such as teleost fish. In contrast to most mammalian bone, teleost 43 bone is typically brittle, porous, lightweight and is characterized by a lack of bone remodeling 44 during growth. Using high-throughput shotgun sequencing, we here investigate the preservation 45 of DNA in a range of different bone elements from over 200 archaeological Atlantic cod (Gadus 46 morhua) specimens from 38 sites in northern Europe, dating up to 8000 years before present. We 47 observe that the majority of archaeological sites (79%) yield endogenous DNA, with 40% of sites 48 providing samples that contain high levels (> 20%). Library preparation success and levels of 49 endogenous DNA depend mainly on excavation site and pre-extraction laboratory treatment. The 50 use of pre-extraction treatments lowers the rate of library success, although -if successful -the 51 fraction of endogenous DNA can be improved by several orders of magnitude. This trade-off 52 between library preparation success and levels of endogenous DNA allows for alternative 53 extraction strategies depending on the requirements of down-stream analyses and research 54 questions. Finally, we find that -in contrast to mammalian bones -different fish bone elements 55 yield similar levels of endogenous DNA. Our results highlight the overall suitability of 56 archaeological fish bone as a source for ancient DNA and provide novel evidence for a possible 57 role of bone remodeling in the preservation of endogenous DNA across different classes of 58 vertebrates. 59 60 Dabney et al., 2013), with the inclusion of a pre-digestion step (DD, Damgaard et al., 2015), or with 129