A practical guide to environmental association analysis in landscape genomics. Molecular Ecology

Seleccionado por: Alicia 

Rellstab, C., F. Gugerli, A. J. Eckert, A. M. Hancock, and R. Holderegger. 2015. A practical guide to environmental association analysis in landscape genomics. Molecular Ecology 24:4348–4370.

Abstract
Landscape genomics is an emerging research field that aims to identify the environmental factors that shape adaptive genetic variation and the gene variants that drive local adaptation. Its development has been facilitated by next-generation sequencing, which allows for screening thousands to millions of single nucleotide polymorphisms in many individuals and populations at reasonable costs. In parallel, data sets describing environmental factors have greatly improved and increasingly become publicly accessible. Accordingly, numerous analytical methods for environmental association studies have been developed. Environmental association analysis identifies genetic variants associated with particular environmental factors and has the potential to uncover adaptive patterns that are not discovered by traditional tests for the detection of outlier loci based on population genetic differentiation. We review methods for conducting environmental association analysis including categorical tests, logistic regressions, matrix correlations, general linear models and mixed effects models. We discuss the advantages and disadvantages of different approaches, provide a list of dedicated software packages and their specific properties, and stress the importance of incorporating neutral genetic structure in the analysis. We also touch on additional important aspects such as sampling design, environmental data preparation, pooled and reduced-representation sequencing, candidate-gene approaches, linearity of allele–environment associations and the combination of environmental association analyses with traditional outlier detection tests. We conclude by summarizing expected future directions in the field, such as the extension of statistical approaches, environmental association analysis for ecological gene annotation, and the need for replication and post hoc validation studies. 

Se trata de una revisión de los métodos para realizar análisis de asociación ambiental, que incluye métodos estadísticos, métodos moleculares, diseño experimental, manejo de datos ambientales y otros. Lo escogí porque sé que muchos de ustedes están realizando o podrían realizar este tipo de análisis. Sugiero entonces que la dinámica del próximo viernes sea un poco diferente a lo normal:

Propongo que cada quién piense como podría aplicar estos métodos en su proyecto y el viernes nos lo comente de forma breve. Quienes no estarán utilizando este tipo de análisis podrían comentar si les parece o no lo que sugirieron los otros.

The Accumulation of Deleterious Mutations as a Consequence of Domestication and Improvement in Sunflowers and Other Compositae Crops

Seleccionado por: José Luis

Renaut S, Rieseberg LH (2015) The Accumulation of Deleterious Mutations as a Consequence of Domestication and Improvement in Sunflowers and Other Compositae Crops. Molecular Biology and Evolution, 32, 2273–2283.

 

Abstract

       For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism (SNP) data. While we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased towards non-synonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Lastly, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. While the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.

 

        Envío adjunto el artículo que propongo para nuestro próximo seminario junto con una entrada de The Molecular Ecologist que habla del artículo y que amablemente Alicia me mostró en un reciente viaje

La razón por la cuál elegí este artículo es que muchos de los miembros del seminario tenemos un interés especial en la domesticación y los cambios que ésta ocasiona en el genoma de las especies domesticadas. Tal vez nuestra perspectiva de la domesticación vista desde el humano hace que tengamos un prejuicio que tiende a buscar mutaciones "benéficas" asociadas a la domesticación. Sin embargo en este artículo se demuestra que acompañando a la domesticación, se acumulan una alta proporción de mutaciones deletéreas. Este efecto puede ser explicado por cuellos de botella acompañado de expansiones poblacionales rápidas y un cambio en el entorno selectivo que ocasiona una relajación de la selección sobre algunas regiones genómicas durante la domesticación. Además del enfoque en la "parte deletérea" que trae la consigo la domesticación, algo que me parece interesante para discutir es si se pueden aplicar los mismos parámetros para definir mutaciones deletéreas en especies domesticadas y silvestres. Dado que las especies domesticadas se encuentran en un entorno selectivo principalmente guiado por el hombre, ¿las mutaciones deletéreas no se deberían definir desde la perspectiva de la interacción de la planta con el hombre?

link a la nota en The Molecular Ecologist