@article{10568,
  abstract     = {Genetic adaptation and phenotypic plasticity facilitate the migration into new habitats and enable organisms to cope with a rapidly changing environment. In contrast to genetic adaptation that spans multiple generations as an evolutionary process, phenotypic plasticity allows acclimation within the life-time of an organism. Genetic adaptation and phenotypic plasticity are usually studied in isolation, however, only by including their interactive impact, we can understand acclimation and adaptation in nature. We aimed to explore the contribution of adaptation and plasticity in coping with an abiotic (salinity) and a biotic (Vibrio bacteria) stressor using six different populations of the broad-nosed pipefish Syngnathus typhle that originated from either high [14–17 Practical Salinity Unit (PSU)] or low (7–11 PSU) saline environments along the German coastline of the Baltic Sea. We exposed wild caught animals, to either high (15 PSU) or low (7 PSU) salinity, representing native and novel salinity conditions and allowed animals to mate. After male pregnancy, offspring was split and each half was exposed to one of the two salinities and infected with Vibrio alginolyticus bacteria that were evolved at either of the two salinities in a fully reciprocal design. We investigated life-history traits of fathers and expression of 47 target genes in mothers and offspring. Pregnant males originating from high salinity exposed to low salinity were highly susceptible to opportunistic fungi infections resulting in decreased offspring size and number. In contrast, no signs of fungal infection were identified in fathers originating from low saline conditions suggesting that genetic adaptation has the potential to overcome the challenges encountered at low salinity. Offspring from parents with low saline origin survived better at low salinity suggesting genetic adaptation to low salinity. In addition, gene expression analyses of juveniles indicated patterns of local adaptation, trans-generational plasticity and developmental plasticity. In conclusion, our study suggests that pipefish are locally adapted to the low salinity in their environment, however, they are retaining phenotypic plasticity, which allows them to also cope with ancestral salinity levels and prevailing pathogens.},
  author       = {Goehlich, Henry and Sartoris, Linda and Wagner, Kim-Sara and Wendling, Carolin C. and Roth, Olivia},
  issn         = {2296-701X},
  journal      = {Frontiers in Ecology and Evolution},
  keywords     = {ecology, evolution, behavior and systematics, trans-generational plasticity, genetic adaptation, local adaptation, phenotypic plasticity, Baltic Sea, climate change, salinity, syngnathids},
  publisher    = {Frontiers Media},
  title        = {{Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels}},
  doi          = {10.3389/fevo.2021.626442},
  volume       = {9},
  year         = {2021},
}

@misc{5757,
  abstract     = {File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.

File S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.

File S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.

File S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.

File S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-
synonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.

File S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.

File S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.

File S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%
frequency.

File S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.},
  author       = {Fraisse, Christelle},
  keywords     = {(mal)adaptation, pleiotropy, selective constraint, evo-devo, gene expression, Drosophila melanogaster},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Supplementary Files for "Pleiotropy modulates the efficacy of selection in Drosophila melanogaster"}},
  doi          = {10.15479/at:ista:/5757},
  year         = {2018},
}

@inbook{10899,
  author       = {Barton, Nicholas H},
  booktitle    = {Encyclopedia of Biodiversity},
  isbn         = {978-0-12-384720-1},
  keywords     = {Adaptive landscape, Cline, Coalescent process, Gene flow, Hybrid zone, Local adaptation, Natural selection, Neutral theory, Population structure, Speciation},
  pages        = {508--515},
  publisher    = {Elsevier},
  title        = {{Differentiation}},
  doi          = {10.1016/b978-0-12-384719-5.00031-9},
  year         = {2013},
}