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1. Transcriptomic responses to extreme low salinity among locally adapted populations of Olympia oyster ( Ostrea lurida )

   https://doi.org/10.1111/mec.14863  

   Maynard, Ashley ; Bible, Jillian M. ; Pespeni, Melissa H. ; Sanford, Eric ; Evans, Tyler G. ( October 2018 , Molecular Ecology)

   The Olympia oyster (Ostrea lurida) is a foundation species inhabiting estuaries along the North American west coast. In California estuaries,O. luridais adapted to local salinity regimes and populations differ in low salinity tolerance. In this study, oysters from three California populations were reared for two generations in a laboratory common garden and subsequently exposed to low salinity seawater. Comparative transcriptomics was then used to understand species‐level responses to hyposmotic stress and population‐level mechanisms underlying divergent salinity tolerances. Gene expression patterns indicate Olympia oysters are sensitive to hyposmotic stress: All populations respond to low salinity by up‐regulating transcripts indicative of protein unfolding,DNAdamage and cell cycle arrest after sub‐lethal exposure. AmongO. luridapopulations, transcriptomic profiles differed constitutively and in response to low salinity. Despite two generations in common‐garden conditions, transcripts encoding apoptosis modulators were constitutively expressed at significantly different levels in the most tolerant population. Expression of cell death regulators may facilitate cell fate decisions when salinity declines. Following low salinity exposure, oysters from the more tolerant population expressed a small number of mRNAs at significantly higher levels than less tolerant populations. Proteins encoded by these transcripts regulate ciliary activity within the mantle cavity and may function to prolong valve closure and reduce mortality in low salinity seawater. Collectively, gene expression patterns suggest sub‐lethal impacts of hyposmotic stress in Olympia oysters are considerable and that even oysters with greater low salinity tolerance may be vulnerable to future freshwater flooding events.

    

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2. The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex

   https://doi.org/10.1111/mec.13763  

   Ferris, Kathleen G. ; Barnett, Laryssa L. ; Blackman, Benjamin K. ; Willis, John H. ( August 2016 , Molecular Ecology)

   The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters of smaller effect loci. In this study, we investigate the genetic architecture of divergence in flowering time, mating system‐related traits, and leaf shape betweenMimulus laciniatusand a sympatric population of its close relativeM. guttatus. These three traits are probably involved inM. laciniatus’adaptation to a dry, exposed granite outcrop environment. Flowering time and mating system differences are also reproductive isolating barriers making them ‘magic traits’. Phenotypic hybrids in this population provide evidence of recent gene flow. Using next‐generation sequencing, we generate denseSNPmarkers across the genome and map quantitative trait loci (QTLs) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to fewQTLof large effect including a highly pleiotropicQTLon chromosome 8. ThisQTLregion contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in otherMimulusspecies. Our results are consistent with theory, indicating that local adaptation and reproductive isolation with gene flow should be due to few loci with large and pleiotropic effects.

    

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3. Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

   https://doi.org/10.1111/mec.13517  

   Hand, Brian K. ; Muhlfeld, Clint C. ; Wade, Alisa A. ; Kovach, Ryan P. ; Whited, Diane C. ; Narum, Shawn R. ; Matala, Andrew P. ; Ackerman, Michael W. ; Garner, Brittany A. ; Kimball, John S. ; et al ( February 2016 , Molecular Ecology)

   Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population‐specific and pairwiseF_ST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin,USA. Using 151 putatively neutral and 29 candidate adaptiveSNPloci, we found that climate‐related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables andF_STacross all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin‐wide to the metapopulation scale). Sensitivity analysis (leave‐one‐population‐out) revealed consistent relationships between climate variables andF_STwithinthree metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

    

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4. Effects of assortative mate choice on the genomic and morphological structure of a hybrid zone between two bird subspecies

   https://doi.org/10.1111/mec.14376  

   Semenov, Georgy A. ; Scordato, Elizabeth S. C. ; Khaydarov, David R. ; Smith, Chris C. R. ; Kane, Nolan C. ; Safran, Rebecca J. ( November 2017 , Molecular Ecology)

   Phenotypic differentiation plays an important role in the formation and maintenance of reproductive barriers. In some cases, variation in a few key aspects of phenotype can promote and maintain divergence; hence, the identification of these traits and their associations with patterns of genomic divergence is crucial for understanding the patterns and processes of population differentiation. We studied hybridization between thealbaandpersonatasubspecies of the white wagtail (Motacilla alba), and quantified divergence and introgression of multiple morphological traits and 19,437SNPloci on a 3,000 km transect. Our goal was to identify traits that may contribute to reproductive barriers and to assess how variation in these traits corresponds to patterns of genome‐wide divergence. Variation in only one trait—head plumage patterning—was consistent with reproductive isolation. Transitions in head plumage were steep and occurred over otherwise morphologically and genetically homogeneous populations, whereas cline centres for other traits and genomic ancestry were displaced over 100 km from the head cline. Field observational data show that social pairs mated assortatively by head plumage, suggesting that these phenotypes are maintained by divergent mating preferences. In contrast, variation in all other traits and genetic markers could be explained by neutral diffusion, although weak ecological selection cannot be ruled out. Our results emphasize that assortative mating may maintain phenotypic differences independent of other processes shaping genome‐wide variation, consistent with other recent findings that raise questions about the relative importance of mate choice, ecological selection and selectively neutral processes for divergent evolution.

    

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5. Population connectivity across east Australia's bioregions and larval duration of the range‐extending sea star Meridiastra calcar

   https://doi.org/10.1002/aqc.3973  

   Klanten, O. Selma ; Gall, Mailie ; Barbosa, Sergio S. ; Hart, Michael W. ; Keever, Carson C. ; Puritz, Jonathan B. ; Harantio, Januar ; Toonen, Robert J. ; Selvakumaraswamy, Paulina ; Grosberg, Richard K. ; et al ( July 2023 , Aquatic Conservation: Marine and Freshwater Ecosystems)

   The diversity and distribution of marine species in eastern Australia is influenced by one of the world's strongest western boundary currents, the East Australia Current, which propels water and propagules poleward, a flow intensifying due to climate change.

   Population genetic structure of the asterinid sea starMeridiastra calcarwas investigated across its range in eastern Australia (12° of latitude, 2,500 km) from northern New South Wales to its poleward‐extending range in Tasmania at the southern edge influence of the East Australia Current.

   Population structure and connectivity ofM. calcarwere examined across six bioregions using six microsatellite loci (nuclear DNA) and the control region (mitochondrial DNA). The potential influence of the extent ofM. calcar's intertidal rock platform habitat was also assessed.

   Genetic structure analysis indicated that the Hawkesbury Shelf contained distinct genetic clusters, whereas the two sites in the Batemans Shelf differed from each other, with Jervis Bay Marine Park having just one genetic cluster. The Manning Shelf, Twofold Shelf, and Bruny bioregions all had similar genetic composition.

   Strong self‐seeding (68–98%) was indicated by microsatellite loci for all bioregions, with lower (0.3–6.5%) migration between bioregions. Poleward (New South Wales to Tasmania) migration was low except from the Manning Shelf (30%).

   Contemporary population connectivity and genetic structure ofM. calcarappear to be influenced by ocean currents, habitat distribution, and its short planktonic larval duration, which was a minimum of 12–14 days, depending on availability of a settlement cue.

   The dominance of unique genetic groups in the Hawkesbury bioregion shows the importance of this region forM. calcarand possibly a diversity of co‐distributed rock platform species. This highlights how important it is to have a large marine park in the Hawkesbury bioregion, which is presently lacking.

    

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