Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.

/pdf/the-oyster-genome-reveals-stress-adaptation-and-complexity-21k1krsbun.pdf

The oyster genome reveals stress adaptation and complexity of shell formation

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.

/pdf/the-genomic-basis-of-adaptive-evolution-in-threespine-27yq6s7i0b.pdf

The genomic basis of adaptive evolution in threespine sticklebacks

What is ecological speciation

Increased rates of inbreeding have been observed in several Holstein populations across the world since genomic selection (GS) was implemented into the breeding programs. The objective of this study was to test whether this is also the case in the Nordic Holstein population using pedigree data. Rates of inbreeding were estimated before, during and after the GS implementation. We could not detect any increase in inbreeding or coancestry rates in Nordic Holstein. Effective population size increased over the studied time periods from 68 to 104, despite fewer sires being used. This might be because more of sires of sons have been used to produce AI bulls compared to the time before implementation of GS. 

/pdf/230-inbreeding-and-coancestry-trends-in-nordic-holstein-3kepswsv.pdf

230. Inbreeding and coancestry trends in Nordic Holstein

Increased rates of inbreeding have been observed in several Holstein populations across the world since genomic selection (GS) was implemented into the breeding programs. The objective of this study was to test whether this is also the case in the Nordic Holstein population using pedigree data. Rates of inbreeding were estimated before, during and after the GS implementation. We could not detect any increase in inbreeding or coancestry rates in Nordic Holstein. Effective population size increased over the studied time periods from 68 to 104, despite fewer sires being used. This might be because more of sires of sons have been used to produce AI bulls compared to the time before implementation of GS.

Inbreeding and coancestry trends in Nordic Holstein

Irish Wolfhound (IW) is a large dog breed developed several centuries ago with an average longevity of 7 years The genetics behind the short lifespan is poorly understood. Based on data from the Irish Wolfhound database (IWDB) on 118,095 pedigreed IW and data from the IW Longevity Study including 10,122 dogs with known longevity and 6,057 of these having a known cause of death (COD), longevity and the two most common COD were analysed. Heritability, maternal effects, and correlations were estimated accounting for sex, birthyear, country of origin and inbreeding coefficient. Both longevity (0.27) and COD (0.17-0.20) were moderately heritable. Longevity and COD showed low correlations, both genetic and residual correlations. We argue that this is likely due to short longevity being caused by early aging and COD being specific expressions of early aging. In addition, inbreeding was found to significantly reduce longevity. Implications for increasing longevity in IW are discussed. 

/pdf/755-longevity-and-major-causes-of-death-are-heritable-in-1dykg78h.pdf

Paul R. Berg

Papers

230. Inbreeding and coancestry trends in Nordic Holstein

Inbreeding and coancestry trends in Nordic Holstein

755. Longevity and major causes of death are heritable in Irish Wolfhound