The Genomic Analyses Club

This week we will discuss graph-based variant discovery in bovines. Note the change of day to Thursday.

We will discuss the new review about structural variation in Nature: https://www.nature.com/articles/s41576-019-0180-9

TGAC has been revived and we will again meet up to discuss interesting science. First up is this very interesting paper by Therkildsen et al. 2019 in Science

Abstract

For the human population to maintain a constant size from generation to generation, an increase in fertility must compensate for the reduction in the mean fitness of the population caused, among others, by deleterious mutations. The required increase in fertility due to this mutational load depends on the number of sites in the genome that are functional, the mutation rate, and the fraction of deleterious mutations among all mutations in functional regions. These dependencies and the fact that there exists a maximum tolerable replacement level fertility can be used to put an upper limit on the fraction of the human genome that can be functional. Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 25%, and is probably considerably lower.

paper

Continuing the discussion of papers related to graph based representation of reference genomes, we will read a paper on the cortex assembler, which actually builds a graph based on sequencing data from multiple samples.

Continuing the discussion of papers related to graph based representation of reference genomes, we will read a more practical paper this week on applying graph-based references to a complex variable region in the human genome.

Continuing the discussion of papers related to graph based representation of reference genomes, we will read a technical paper this week on a new way to look at the structure of reference genomes. Note the time!

One of the upcoming CELS projects is around Graph based representation of reference genomes. In the next episodes of the TGAC journal club, we will therefore discuss several papers around this subject. Some are very technical, some more applied.

It is time for this year's last TGAC meeting, where we'll discuss the current "Flock of genomes" special issue of Science about 48 newly released bird genomes. With eight research articles and one review, this special issue could keep the TGAC busy for weeks, but for now I propose to focus on the article of Jarvis et al. entitled "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Bank et al. (2014) looks like the perfect paper for a TGAC discussion: Highly relevant (arguing that selective sweep detection needs to take demography and background selection into account), brand new (currently in press corrected proof), and short (7 pages). So let's have a TGAC meeting on Tuesday, at 1 pm as usual.

In a second edition of TGAC-with-original-authors, we'll discuss Marcussen et al. (2014), a recent Science paper on ancient hybridization of polyploid wheat genomes. The first author Thomas Marcussen will join our discussion, and since Kjetill Jakobsen was involved in the study, we may even have two authors present to answer all our questions. We're switching back to the old meeting time, starting at 1 pm.

In a sort of a special edition of the TGAC journal club, we hope to finally find out whether Thor Heyerdahl was right after all with his claims regarding early contact between the cultures of South America and Easter Island, whether his Kon-Tiki expedition in 1947 was just a fun cruise across the Pacific without any scientific substantiation, or whether genomic data actually supports his ideas. We will find the answers in the very recent paper by Moreno-Mayar et al. (2014), which just came out in Current Biology and comes with a commentary in Science. Four of the authors are working at the University Hospital here in Oslo, and at least two of them will join our discussion!

As there will be a CELS meeting this Tuesday at 1 pm, the TGAC discussion will be earlier than usual, at 11 am.

We feel that it's time to find out about the Pairwise Sequential Markovian Coalescent and it derivations. How does it magically infer demography from single genomes? Why does the original author recommend other tools? Why do all these demography plots look the same? And can I use it for my data? Once more, we'll need more than one paper to find out. We'll focus on the first publication to present the PSMC, Li & Durbin (2011) in Nature, but we invite participants with a bit of extra time to check out and report on updates on the method, which were published by Schiffels & Durbin (2014) in Nature Genetics, and by Harris et al. (2014) on arXiv.

This tuesday, we'll discuss genome resequencing and hybrid origin of pig populations, as recently reported by Bosse et al. (2014) in Molecular Ecology, Bosse et al. (2014) in Nature Communications, and Ramírez et al. (2014) in Heredity. We'll focus on the Molecular Ecology paper, but try to provide a brief summary of the other two studies as well.

As we are starting to worry about bias in branch lengths when phylogenetic approaches are used with genomic data, we'll have a look at McGill et al. (2013), which discusses the influence of minor allele frequency thresholds on estimates of demography.

As a follow-up to our discussion on genomic islands of speciation two weeks ago, we'll continue along the same lines with a recent paper by Ruegg et al. (2014) that came out recently in Molecular Evolution.

In this weeks edition of the TGAC journal club, we'll focus on African cichlid fishes, and the "genomic substrate" of their adaptive radiation: The paper by Brawand et al. (2014), was published last week in Nature.

We restart the TGAC+CELS journal club series with a discussion of a recent review (Cruickshank & Hahn 2014) on genome divergence between closely related species. A substantial paper, but a highly relevant one, also for our friends from the speciation journal club!