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: http://onlinelibrary.wiley.com/doi/10.1002/jez.b.22656/abstract

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.


Link: http://genome.cshlp.org/content/26/2/163


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.

Wednesday, August 31, 2016

Thankyou, goodbye and good luck Mireia, Skye, Tammy and Anna!











 













(Photos shamelessly stolen from Facebook)

Posted by Erik Svensson 

As some of you already know, we have had some amazing and hard-working undergraduate internship students working in our labs and helping our PhD-students and postdocs who have now left EXEB to continue their education and work elsewhere. You probably already know who I am talking about: Mireia Ballesta (from Spain), Skye Butterson (from South Africa), Tammy Ho (from Singapore, studying at Manchester University, UK) and Anna Kell (from Wales, studying at Manchester University, UK). 

Mireia, Skye, Tammy and Anna have all been extremely helpful in both the field and the laboratory, helping and assisting mainly Anna Nordén, John Waller and Beatriz Willink in their day-to-day research. As an advisor of John and Beatriz I am of course very happy to see them getting this  help, and also getting training in teaching and advising, and I think I speak also for Jessica Abbott, who is main advisor for Anna in that respect. 

We have valued your contributions a lot, as well as your enthusiasm, good working spirit and humour. We wish all four of you good luck in your future careers, and we hope you will keep your time in Lund as one of happy memories. Thankyou!!!!






Friday, August 26, 2016

Eco-Evo-Devo

Next Tuesday I thought we could read a paper that has been on my to-read list for a while. It's a review by Scott Gilbert et al. entitled 'Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents'.

I'm not sure if the paper says anything radically new, but I think it might be a nice entry point to a discussion about how ecology, evolution and development fit together and what the future of this interdisciplinary field might hold for us.

You can find the paper here and below the abstract:


The integration of research from developmental biology and ecology into evolutionary theory has given rise to a relatively new field, ecological evolutionary developmental biology (Eco-Evo-Devo). This field integrates and organizes concepts such as developmental symbiosis, developmental plasticity, genetic accommodation, extragenic inheritance and niche construction. This Review highlights the roles that developmental symbiosis and developmental plasticity have in evolution. Developmental symbiosis can generate particular organs, can produce selectable genetic variation for the entire animal, can provide mechanisms for reproductive isolation, and may have facilitated evolutionary transitions. Developmental plasticity is crucial for generating novel phenotypes, facilitating evolutionary transitions and altered ecosystem dynamics, and promoting adaptive variation through genetic accommodation and niche construction. In emphasizing such non-genomic mechanisms of selectable and heritable variation, Eco-Evo-Devo presents a new layer of evolutionary synthesis.

When: Tuesday August 30 at 10.00
Where: "Argumentet", 2nd floor, Ecology Building

There might be some fika ;-)

Tuesday, August 23, 2016

EXEB seminar schedule autumn 2016!

Posted by Erik Svensson

The EXEB-schedule for autumn 2016 has now been finalized, based on the "Doodle"-poll. As usual, feel free to have a mix between journal club and articles to discuss, give a short research presentation or raise some topic for discussion or invite temporary visitors for short and informal seminars.

The person(-s) responsible for a Tuesday meeting should announce the topic on the blog, preferably in good time and ideally on Thursday or Friday the preceeding week so that people have time to read the article.

As usual,  meetings take place on Tuesdays at 10.00 and "fika" is compulsory :). If you have to change your date, you'll have to talk to some other on the list who can replace you.


Day                                           Person(-s)

Tuesday August 30                 Nathalie Feiner
Tuesday September 6             Jessica Abbott
Tuesday September 13           Reinder Radersma
Tuesday September 20           Weizhao Yang
Tuesday September 27           Tobias Uller
Tuesday October 4                 Antonio Cordero
Tuesday October 11                Seminar by Ayana Martins (visiting Erik's group)
Tuesday  October 18              Alexander Hegg & Qinyang Li
Tuesday  October 25               Beatriz Willink
Tuesday November 1              Anna Nordén
Tuesday November 8               John Waller
Tuesday November 15             Seminar by Stephen De Lisle (new postdoc in Erik's group)
Tuesday November 22             Nathalie Feiner
Tuesday November 29             Jessica Abbott
Tuesday December 6                Reinder Radersma
Tuesday December 13              Weizhao Yang