Pervasive hybridization with local wild relatives in Western European grapevine varieties

Grapevine (Vitis vinifera L.) diversity richness results from a complex domestication history over multiple historical periods. Here, we used whole-genome resequencing to elucidate different aspects of its recent evolutionary history. Our results support a model in which a central domestication event in grapevine was followed by postdomestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties showing large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by gene flow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.info:eu-repo/semantics/publishedVersio

Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates.

Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present in the avian iris are lacking from the integument of birds or mammals, but are remarkably similar to those found in the skin of ectothermic vertebrates. To investigate molecular mechanisms associated with eye coloration in birds, we took advantage of a Mendelian mutation found in domestic pigeons that alters the deposition of yellow pterin pigments in the iris. Using a combination of genome-wide association analysis and linkage information in pedigrees, we mapped variation in eye coloration in pigeons to a small genomic region of ~8.5kb. This interval contained a single gene, SLC2A11B, which has been previously implicated in skin pigmentation and chromatophore differentiation in fish. Loss of yellow pigmentation is likely caused by a point mutation that introduces a premature STOP codon and leads to lower expression of SLC2A11B through nonsense-mediated mRNA decay. There were no substantial changes in overall gene expression profiles between both iris types as well as in genes directly associated with pterin metabolism and/or chromatophore differentiation. Our findings demonstrate that SLC2A11B is required for the expression of pterin-based pigmentation in the avian iris. They further highlight common molecular mechanisms underlying the production of coloration in the iris of birds and skin of ectothermic vertebrates

Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates

Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present in the avian iris are lacking from the integument of birds or mammals, but are remarkably similar to those found in the skin of ectothermic vertebrates. To investigate molecular mechanisms associated with eye coloration in birds, we took advantage of a Mendelian mutation found in domestic pigeons that alters the deposition of yellow pterin pigments in the iris. Using a combination of genome-wide association analysis and linkage information in pedigrees, we mapped variation in eye coloration in pigeons to a small genomic region of ~8.5kb. This interval contained a single gene, SLC2A11B, which has been previously implicated in skin pigmentation and chromatophore differentiation in fish. Loss of yellow pigmentation is likely caused by a point mutation that introduces a premature STOP codon and leads to lower expression of SLC2A11B through nonsense-mediated mRNA decay. There were no substantial changes in overall gene expression profiles between both iris types as well as in genes directly associated with pterin metabolism and/or chromatophore differentiation. Our findings demonstrate that SLC2A11B is required for the expression of pterin-based pigmentation in the avian iris. They further highlight common molecular mechanisms underlying the production of coloration in the iris of birds and skin of ectothermic vertebrates

Is the future of peer review automated?

The rising rate of preprints and publications, combined with persistent inadequate reporting practices and problems with study design and execution, have strained the traditional peer review system. Automated screening tools could potentially enhance peer review by helping authors, journal editors, and reviewers to identify beneficial practices and common problems in preprints or submitted manuscripts. Tools can screen many papers quickly, and may be particularly helpful in assessing compliance with journal policies and with straightforward items in reporting guidelines. However, existing tools cannot understand or interpret the paper in the context of the scientific literature. Tools cannot yet determine whether the methods used are suitable to answer the research question, or whether the data support the authors’ conclusions. Editors and peer reviewers are essential for assessing journal fit and the overall quality of a paper, including the experimental design, the soundness of the study’s conclusions, potential impact and innovation. Automated screening tools cannot replace peer review, but may aid authors, reviewers, and editors in improving scientific papers. Strategies for responsible use of automated tools in peer review may include setting performance criteria for tools, transparently reporting tool performance and use, and training users to interpret reports.</p

Mating system and extra-pair paternity in the Fan-tailed Gerygone <i>Gerygone flavolateralis</i> in relation to parasitism by the Shining Bronze-cuckoo <i>Chalcites lucidus</i> - Fig 2

<p><b>Genetic constitution of 127 Fan-tailed Gerygones of 36 breeding attempts in New Caledonia with single (a) and mixed (b) paternity.</b> First two columns consist of broods with bright skin coloration, third column–dark skin coloration, and fourth column–polymorphic broods. The number in upper left corner of each plot corresponds to breeding attempt ID in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194059#pone.0194059.g001" target="_blank">Fig 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194059#pone.0194059.t001" target="_blank">Table 1</a>. Squares indicate females, triangles males, and circles offspring. Position of the individuals within the graph is determined by two first Principal Coordinates calculated based on Euclidean distances. The colours correspond to the three first Principal Coordinates transformed into RGB.</p

Is the future of peer review automated?

The rising rate of preprints and publications, combined with persistent inadequate reporting practices and problems with study design and execution, have strained the traditional peer review system. Automated screening tools could potentially enhance peer review by helping authors, journal editors, and reviewers to identify beneficial practices and common problems in preprints or submitted manuscripts. Tools can screen many papers quickly, and may be particularly helpful in assessing compliance with journal policies and with straightforward items in reporting guidelines. However, existing tools cannot understand or interpret the paper in the context of the scientific literature. Tools cannot yet determine whether the methods used are suitable to answer the research question, or whether the data support the authors’ conclusions. Editors and peer reviewers are essential for assessing journal fit and the overall quality of a paper, including the experimental design, the soundness of the study’s conclusions, potential impact and innovation. Automated screening tools cannot replace peer review, but may aid authors, reviewers, and editors in improving scientific papers. Strategies for responsible use of automated tools in peer review may include setting performance criteria for tools, transparently reporting tool performance and use, and training users to interpret reports

Internal relatedness and standardized heterozygosity in Fan-tailed Gerygone nestlings in New Caledonia grouped by skin coloration (49 bright and 15 dark), based on analysis of all 17 microsatellite loci and seven loci associated with skin colour.

<p>Internal relatedness and standardized heterozygosity in Fan-tailed Gerygone nestlings in New Caledonia grouped by skin coloration (49 bright and 15 dark), based on analysis of all 17 microsatellite loci and seven loci associated with skin colour.</p

Locations of sampled Fan-tailed Gerygone nests in the Parc des Grandes Fougères and surroundings.

<p>The colours of dots indicate the mean genetic constitution of breeding attempts, based on Principal Coordinates calculated on Euclidean distances and transformed into RGB values. White background indicates open areas, grey forest.</p

Genetic diversity measures of 17 microsatellite markers in 69 Fan-tailed Gerygone nestlings and the results of association analysis performed in CLUMP 2.4 with skin coloration of the offspring.

<p>HE: unbiased expected heterozygosity; HO: observed heterozygosity; p: level of significance of the chi-squared value from the table obtained by comparing χ² of the allele frequencies in dark and bright chicks with χ² calculated based on simulated (100x) tables with the same row and column totals, after collapsing low allele frequencies (<5%, [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194059#pone.0194059.ref045" target="_blank">45</a>]). Significant results (loci associated with skin coloration) after Bonferroni correction (adjusted P < 0.003) are marked with asterisk.</p