Thursday, September 22, 2016

Thinking about homology

Homology has had its ups and downs in the history of evolutionary thought, but the last few years Gunter Wagner and others have forcefully argued that it should take on a central role in evolutionary biology. Let us see why!

Link to paper:

10.00, Argumentet, and fika as usual.

Thursday, September 15, 2016

Meeting 20 Sept: Genomic variation and admixture in grey wolf

For next week's EXEB meeting (Sept 20, 2016), I think it might be a good opportunity to discuss a paper on genomic variation and admixture in grey wolf (ancestor of domestic dog) by using population genomics approach.

Time & place & "FIKA" as usual!

Title: Worldwide patterns of genomic variation and admixture in gray wolves

Abstract: The gray wolf (Canis lupus) is a widely distributed top predator and ancestor of the domestic dog. To address questions about wolf relationships to each other and dogs, we assembled and analyzed a data set of 34 canine genomes. The divergence between New and Old World wolves is the earliest branching event and is followed by the divergence of Old World wolves and dogs, confirming that the dog was domesticated in the Old World. However, no single wolf population is more closely related to dogs, supporting the hypothesis that dogs were derived from an extinct wolf population. All extant wolves have a surprisingly recent common ancestry and experienced a dramatic population decline beginning at least ∼30 thousand years ago (kya). We suggest this crisis was related to the colonization of Eurasia by modern human hunter–gatherers, who competed with wolves for limited prey but also domesticated them, leading to a compensatory population expansion of dogs. We found extensive admixture between dogs and wolves, with up to 25% of Eurasian wolf genomes showing signs of dog ancestry. Dogs have influenced the recent history of wolves through admixture and vice versa, potentially enhancing adaptation. Simple scenarios of dog domestication are confounded by admixture, and studies that do not take admixture into account with specific demographic models are problematic.


Thursday, September 8, 2016

Meeting 13 Sept: Transparency in Ecology and Evolution

For next meeting I would like to discuss concerns about transparency in empirical sciences in general and ecology and evolution specifically. The next paper highlights those issues and discusses some solutions.

Title: Transparency in Ecology and Evolution: Real Problems, Real Solutions

TREE Vol. 31, Issue 9, September 2016, Pages 711–719

Abstract: To make progress scientists need to know what other researchers have found and how they found it. However, transparency is often insufficient across much of ecology and evolution. Researchers often fail to report results and methods in detail sufficient to permit interpretation and meta-analysis, and many results go entirely unreported. Further, these unreported results are often a biased subset. Thus the conclusions we can draw from the published literature are themselves often biased and sometimes might be entirely incorrect. Fortunately there is a movement across empirical disciplines, and now within ecology and evolution, to shape editorial policies to better promote transparency. This can be done by either requiring more disclosure by scientists or by developing incentives to encourage disclosure.

Tuesday 13 September at 10.00, Argumentet

Thursday, September 1, 2016

Meeting Sept 6th: Updating population genetics

D. melanogaster, by Qinyang Li
Posted by Jessica Abbott

Like many other researchers who use experimental evolution today, I plan to investigate the genetic changes that have occurred in our experimental populations using sequencing. That's why I found this paper particularly interesting - it deals with how the assumptions of standard population genetics models don't fit well with current empirical data on rapid evolution, and how genomics studies might help to solve this problem.

Title: Can population genetics adapt to rapid evolution?

Abstract: Population genetics largely rests on a ‘standard model’ in which random genetic drift is the dominant force, selective sweeps occur infrequently, and deleterious mutations are purged from the population by purifying selection. Studies of phenotypic evolution in nature reveal a very different picture, with strong selection and rapid heritable trait changes being common. The time-rate scaling of phenotypic evolution suggests that selection on phenotypes is often fluctuating in direction, allowing phenotypes to respond rapidly to environmental fluctuations while remaining within relatively constant bounds over longer periods. Whether such rapid phenotypic evolution undermines the standard model will depend on how many genomic loci typically contribute to strongly selected traits and how phenotypic evolution impacts the dynamics of genetic variation in a population. Population-level sequencing will allow us to dissect the genetic basis of phenotypic evolution and study the evolutionary dynamics of genetic variation through direct measurement of polymorphism trajectories over time.

Tuesday September 5th at 10.00 in Argumentet, as usual.