Meeting Nov 24th: sex-bias, X-linkage, and rates of evolution

Posted by Jessica Abbott

D. melanogaster. Photo by Qinyang Li.

Although a number of members of the group are currently away, I thought it would be nice to have a meeting next week anyway. I don't think anyone else has planned anything, so I figured I might as well take the initiative. I suggest that we read the following short paper on the "faster-X effect" - how sex-biased gene expression and X-linkage affect rates of evolution.


Title: The effects of sex-biased gene expression and X-linkage on rates of adaptive protein sequence evolution in Drosophila

Abstract: A faster rate of adaptive evolution of X-linked genes compared with autosomal genes may be caused by the fixation of new recessive or partially recessive advantageous mutations (the Faster-X effect). This effect is expected to be largest for mutations that affect only male fitness and absent for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using genes with different levels of sex-biased expression and by estimating the extent of adaptive evolution of non-synonymous mutations from polymorphism and divergence data. We detected both a Faster-X effect and an effect of male-biased gene expression. There was no evidence for a strong association between the two effects—modest levels of male-biased gene expression increased the rate of adaptive evolution on both the autosomes and the X chromosome, but a Faster-X effect occurred for both unbiased genes and female-biased genes. The rate of genetic recombination did not influence the magnitude of the Faster-X effect, ruling out the possibility that it reflects less Hill–Robertson interference for X-linked genes.

Lab meeting on November 10th at 10.00 on Phylogeography of marine animals

Next Tuesday I'll tell you a little about my past PhD-project in Helsinki University. Fika included, see you there!

-Hanna

My thesis in nutshell:

Phylogeography of amphi-boreal marine fauna

The Northern Atlantic and Pacific Oceans share a faunal element consisting of pairs of closely related vicariant taxa, known as the amphi-boreal fauna. The inter-oceanic systematic affinities reflect a history of shared ancestry since dispersal through the Bering Strait and across the Arctic basin, which was initiated by the opening of the Bering Strait at the end of the Miocene. In my PhD I examined the dynamics and consequences of the faunal interchange between the Atlantic and Pacific Oceans since that time up to the present. This was done by comparing differences in the mitochondrial gene sequence variation in different taxonomic groups and across the circum-boreal geographical scale, comprising both newly produced sequences and data from literature, from altogether 70 species or species groups (molluscs, crustaceans, echinoderms, polychaetes, fishes and mammals). Two exemplary genera, pelagic fish genus Clupea and boreal-arctic bivalve Hiatella were examined more closely and with additional markers.

The phylogeographical histories of the Pacific–Atlantic amphi-boreal taxa were found to be remarkably variable. A simple vicariant history since an early, Pliocene or Early Pleistocene (6–3 My ago) dispersal was inferred only in about half of the examined taxa, whereas signatures of more than one trans-Arctic dispersal were found in a third of the cases. A close inter-oceanic relationship that would reflect recent trans-Arctic dispersal or ongoing gene flow was found to be common for amphi-boreal genera (40% of cases). Overall the estimates of inter-oceanic mitochondrial divergence within each of the broader taxonomic groups varied greatly, up to 10–20 fold, and suggest that trans-Arctic faunal dispersal has been a repeated process through the time frame considered. Based on the molecular divergence, several instances of putative new allopatric species were detected in the invertebrates.

Repeated trans-Arctic invasions have practically always resulted in secondary contacts of diverged lineages (for this data, in all cases but one). The Pacific herring C. pallasii, of East Asian origin, invaded the Northeast European seas post-glacially and then differentiated into separate regional populations. In Europe, hybridization with the native sister species C. harengus, the Atlantic herring, has also taken place. The amount of introgression from the Atlantic to the Pacific herring was variable between the various contact regions of the taxa. Most heavily introgressed fjord population in northern Norway has parallels in the boreal bivalves Macoma and Mytilus, for which similar repeated invasion history has been inferred.

Lab meeting on Nov 3 (10.00h) on Transgenerational Epigenetic Inheritance

Hej,

For next week's lab meeting I would like to discuss the importance of transgenerational epigenetic inheritance in evolution. I selected a paper which gives a nice overview of potential mechanisms and some examples of transgenerational epigenetic inheritance. The paper is already a bit "old" (1.5 year already) and the discussion is focussing on human health, but it gives a nice overview.

Transgenerational Epigenetic Inheritance: Myths and Mechanisms
Cell: Volume 157, Issue 1, p95–109, 27 March 2014

Summary: Since the human genome was sequenced, the term “epigenetics” is increasingly being associated with the hope that we are more than just the sum of our genes. Might what we eat, the air we breathe, or even the emotions we feel influence not only our genes but those of descendants? The environment can certainly influence gene expression and can lead to disease, but transgenerational consequences are another matter. Although the inheritance of epigenetic characters can certainly occur—particularly in plants—how much is due to the environment and the extent to which it happens in humans remain unclear.

Fika will be provided :)

Lab-meeting by Weizhao Yang on Genetic signature of high-altitude adaptation for toads: October 20 (10.00)

Hej!

According to Erik's suggestion, next week on the EXEB-meeting on Tuesday October 20th (10.00 as usual), I will take the opportunity to introduce part of my PhD thesis, genetic signature of high-altitude adaptation for toads.

Asiatic toad  is one of the few amphibians living on the Tibetan Plateau. It has been a true Plateau dweller for approximate 2.5 millions of years and is well-adapted to the environments. In addition, it occupies a large elevational gradient from zero to 4,300m above sea level, which provides excellent opportunities to compare individuals or populations from various altitudes. I implemented a series of experiments to explore the evolutionary genetic signature of altitude adaptation in Asiatic toad, and hope the results could provide useful direction to understand how poikilotherms adapt to high-altitude.

"Fika" will be provided and time and place as usual: "Argumentet" at 10.00.

Congratulations to Jessica Abbott for receiving ERC Starting Grant!

Posted by Erik Svensson 

Last Friday (October 9, 2015), our colleague and one of EXEB:s three PI:s Jessica Abbott found out that she has been awarded an "Starting Grant" from the European Research Council (ERC). This is a very large grant of up to 1.5 million Euro, spread out over a five-year period, and it is highly competitive and prestiguous. 

This ERC-grant will give Jessica the opportunity to further consolidate her research group and hire more postdocs and PhD-students, and will also give her higher job security, as she has sofar only been on a temporary position as Junior Researcher, funded by the Swedish Research Council (VR). It means that we can hopefully soon look forward to see some new faces in the form of students and postdocs at future EXEB-meetings. This will of course further strengthen an already strong and intellectually stimulating scientific environment.

This was the third time Jessica applied for these ERC-grants, and likewise the third time she went to Brussels for an interview with the evaluation panel. Jessica has worked long and hard to get this grant, and she should therefore be proud of this strong achievement. It is the first ERC-grant awarded to any researcher at the Department of Biology in Lund, but hopefully Jessica's example will inspire others to follow in her footsteps.

On behalf of myself, EXEB and many other of our colleagues in the Biology Department and the Evolutionary Ecology Unit, we hereby congratulate Jessica to her achievement. Well done! I am sure you will use this grant money wisely to consolidate your group and develop your research programme further.

 

Lab-meeting 13 October 2015: on neutral theory, ecological drift and the utility of null models in ecology and evolution

Posted by Erik Svensson

For the lab-meeting this forthcoming week, I was thinking we should discuss a short - but hopefully provocative - opinion paper about the utility of the Unified Neutral Theory of Biodiversity (UNTB), which became famous but also controversial about 15 years ago when Stephen Hubbell published his Princeton-monographs. Proponents of the neutral theory, including Hubbel himself, sees UNTB as community ecology's counterpart to the neutral theory of molecular evolution in population genetics, and a rigorous point-of-departure and null model. Opponents - including some leading ecologists like Bob Ricklefs - dismiss UNTB on various empirical grounds. Who is right and who is wrong? Or can both sides be partly right? I hope we can have a good discussion about this.

I also hope to show some  unpublished and preliminary data on these questions from our ongoing research on damselflies and the prospects for ecological drift in these insects. 

Time and place as usual: "Argumentet", October 13 at 10.00.

The case for ecological neutral theory

By:Rosindell, J (Rosindell, James)^{[ 1,2,3 ]} ; Hubbell, SP (Hubbell, Stephen P.)^{[ 4,5 ]} ; He, FL (He, Fangliang)^{[ 6,7 ]} ; Harmon, LJ (Harmon, Luke J.)^{[ 2,8 ]} ; Etienne, RS (Etienne, Rampal S.)^{[ 9 ]}

TRENDS IN ECOLOGY & EVOLUTION

27: 203-208

DOI: 10.1016/j.tree.2012.01.004

Published: APR 2012

Abstract

Ecological neutral theory has elicited strong opinions in recent years. Here, we review these opinions and strip away some unfortunate problems with semantics to reveal three major underlying questions. Only one of these relates to neutral theory and the importance of ecological drift, whereas the others involve the link between pattern and process, the tradeoff between simplicity and complexity in modeling, and the role of stochasticity and drift in ecology. We explain how neutral theory cannot be simultaneously used both as a null hypothesis and as an,approximation. However, we also show how neutral theory always has a valuable use in one of these two roles even though the real world is not neutral.

Visit by US colleague Eben Gering next week: invasion biology and colour evolution of damselflies and chickens

 


Posted by Erik Svensson

Next week (October 12-16), our colleague Dr. Eben Gering from Michigan State University in the US will visit EXEB and the Biology Department. Some of you have already met Eben before, and he visited three years ago during the ISBE Congress in Lund 2012. Eben obtained his PhD at University of Texas (Austin), under the supervision of Prof. Molly Cummings. His thesis-research focused on mechanisms of colour polymorphism maintenance in damselflies and island biogeography. He studied the damselfly Ischnura ramburi (a congener to Ischnura elegans, which we are working on in our lab), and he performed much of his field work on Hawaii.

Currently, Eben is a postdoc at MSU, but he collaborates with a Swedish research group working on chicken genomics at Linköping University, particularly Dominic Wright. On his way to Linköping, Eben thus stops by in Lund and he will participate in our lab-meeting on Tuesday next week (announced in a separate blog post). He will give next week's Thursday seminar on October 15 (13.15) in the "Blue Hall", which will contain data about colour evoution in both damselflies and chickens and a discussion about the evolutionary and genomic consequences of feralization (the opposite of domestication).  

If you are interested in meeting with Eben and discuss his or your research, please contact me (erik.svensson@biol.lu.se), so we can set up a meeting. We also plan to go out for beers at least one evening (tentatively on Wednesday October 14, to "Inferno"), and everybody who wants to attend are most welcome to join in. Below follows more information and an Abstract about Eben's talk.

A tale of two invasions: rapid evolution of color polymorphism in invasive damselflies and chickens

"Darwin and Wallace each struggled to explain the variation in evolution’s color palette. In Darwin’s view, colorful ornaments were a common outcome of sexual selection, whereas Wallace ascribed them to natural selection. A century later, we recognize that both forms of selection interact in complex ways to determine color phenotypes. Here I will describe two case studies of color evolution within invasive populations. Species invasions provide unique opportunities to characterize how traits respond to novel (and often extreme) forms of selection. Surprisingly, our syntheses of historical, genetic and experimental data from invasive chickens and damselflies suggest that density-dependent selection promoted color variability in both groups via very different mechanisms. In damselflies, color polymorphism allowed females to adapt to changes in social environment that ensued invasive spread.  In chickens, plumage variation that resulted from hybridization collapsed during colonization of marginal habitats. While our understanding of these complex systems is far from complete, patterns seen thus far reveal how demographic features of biotic invasions could facilitate rapid evolution by both Darwinian and Wallacian mechanisms."