Showing papers by "Paul R. Berg published in 2012"

Candidate genes for colour and vision exhibit signals of selection across the pied flycatcher (Ficedula hypoleuca) breeding range

Abstract: The role of natural selection in shaping adaptive trait differentiation in natural populations has long been recognized. Determining its molecular basis, however, remains a challenge. Here, we search for signals of selection in candidate genes for colour and its perception in a passerine bird. Pied flycatcher plumage varies geographically in both its structural and pigment-based properties. Both characteristics appear to be shaped by selection. A single-locus outlier test revealed 2 of 14 loci to show significantly elevated signals of divergence. The first of these, the follistatin gene, is expressed in the developing feather bud and is found in pathways with genes that determine the structure of feathers and may thus be important in generating variation in structural colouration. The second is a gene potentially underlying the ability to detect this variation: SWS1 opsin. These two loci were most differentiated in two Spanish pied flycatcher populations, which are also among the populations that have the highest UV reflectance. The follistatin and SWS1 opsin genes thus provide strong candidates for future investigations on the molecular basis of adaptively significant traits and their co-evolution.

Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon

Abstract: Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar) strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Most of the identified candidate regions were rather small ranging from zero to a few centimorgans (cM) in the female Atlantic salmon linkage map. We also evaluated how adaptation from standing variation affects adjacent SNP and microsatellite variation along the chromosomes and, by using forward simulations with strong selection, we were able to generate genetic differentiation patterns comparable to the observed data. This study highlights the significance of standing genetic variation during the early stages of adaptation and represents a useful step towards identifying functional variants involved in domestication of Atlantic salmon.

Spatial structure and climatic adaptation in African maize revealed by surveying SNP diversity in relation to global breeding and landrace panels.

Abstract: Background Climate change threatens maize productivity in sub-Saharan Africa. To ensure food security, access to locally adapted genetic resources and varieties is an important adaptation measure. Most of the maize grown in Africa is a genetic mix of varieties introduced at different historic times following the birth of the trans-Atlantic economy, and knowledge about geographic structure and local adaptations is limited. Methodology A panel of 48 accessions of maize representing various introduction routes and sources of historic and recent germplasm introductions in Africa was genotyped with the MaizeSNP50 array. Spatial genetic structure and genetic relationships in the African panel were analysed separately and in the context of a panel of 265 inbred lines representing global breeding material (based on 26,900 SNPs) and a panel of 1127 landraces from the Americas (270 SNPs). Environmental association analysis was used to detect SNPs associated with three climatic variables based on the full 43,963 SNP dataset. Conclusions The genetic structure is consistent between subsets of the data and the markers are well suited for resolving relationships and admixture among the accessions. The African accessions are structured in three clusters reflecting historical and current patterns of gene flow from the New World and within Africa. The Sahelian cluster reflects original introductions of Meso-American landraces via Europe and a modern introduction of temperate breeding material. The Western cluster reflects introduction of Coastal Brazilian landraces, as well as a Northeast-West spread of maize through Arabic trade routes across the continent. The Eastern cluster most strongly reflects gene flow from modern introduced tropical varieties. Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season. The associations located in genes of known importance for abiotic stress tolerance are interesting candidates for local adaptations.

Complex mixtures: a critical examination of a paper by Homer et al.

Abstract: DNA evidence in criminal cases may be challenging to interpret if several individuals have contributed to a DNA-mixture. The genetic markers conventionally used for forensic applications may be insufficient to resolve cases where there is a small fraction of DNA (say less than 10%) from some contributors or where there are several (say more than 4) contributors. Recently methods have been proposed that claim to substantially improve on existing approaches [1]. The basic idea is to use high-density single nucleotide polymorphism (SNP) genotyping arrays including as many as 500,000 markers or more and explicitly exploit raw allele intensity measures. It is claimed that trace fractions of less than 0.1% can be reliably detected in mixtures with a large number of contributors. Specific forensic issues pertaining to the amount and quality of DNA are not discussed in the paper and will not be addressed here. Rather our paper critically examines the statistical methods and the validity of the conclusions drawn in Homer et al. (2008) [1]. We provide a mathematical argument showing that the suggested statistical approach will give misleading results for important cases. For instance, for a two person mixture an individual contributing less than 33% is expected to be declared a non-contributor. The quoted threshold 33% applies when all relative allele frequencies are 0.5. Simulations confirmed the mathematical findings and also provide results for more complex cases. We specified several scenarios for the number of contributors, the mixing proportions and allele frequencies and simulated as many as 500,000 SNPs. A controlled, blinded experiment was performed using the Illumina GoldenGate ® 360 SNP test panel. Twenty-five mixtures were created from 2 to 5 contributors with proportions ranging from 0.01 to 0.99. The findings were consistent with the mathematical result and the simulations. We conclude that it is not possible to reliably infer the presence of minor contributors to mixtures following the approach suggested in Homer et al. (2008) [1]. The basic problem is that the method fails to account for mixing proportions.