Tuesday, December 22, 2015

Merry Christmas and Happy New EXEB-year!

Posted by Erik Svensson

The year 2015 is approaching the end, and I wish all EXEB-members a Merry Christmas and a Happy New Year. I think we have had a great year and many exciting and intellectually stimulating lab-meetings where (at least I) have learned a lot and got many new insights. EXEB has grown rapidly in short time - particularly since Tobias Uller have recruited several new co-workers - and we do now also have several hardworking interns, field assistants, laboratory assistants, PhD-students, Master's students and postdocs. All our permanent and temporary co-workers - nobody mentioned, nobody forgotten - do a tremendous job, both in terms of actual work performed, but also in contributing to a friendly and intellectually stimulating research environment.

Some statistics: If we count only the "core" EXEB members (who are in Lund and have formal positions), we are 11 in total (3 PI:s, 3 PhD-students, 4 postdocs and one research engineer). Counting a bit more generously, we are 13, since we have two affiliated PhD-students from Sussex University (Katrine Lund-Hansen)  and Manchester University (Miguel Gomez), who Jessica Abbott and I are co-advisors of, respectively.

Looking back upon 2015 in terms of research achievements, it has been a very succesful year, I think we can say without any hesitation. I have not made an official tally of joint publications, but I note that Tobias team had an interesting article about asymmetric species interactions in hybrid zones of lizards in Ecology Letters, and Jessica published a model paper about how self-fertilization and inbreeding might limit sexual antagonism in Journal of Evolutionary Biology. As for myself, I was happy to get our long-term time-series analysis of the signature of negative frequency-dependent selection in damselfly morphs published in American Naturalist. John Waller got his first thesis-chapter about imperfect detection and mark-recapture analysis of selection published in Methods in Ecology & Evolution. Lastly, and importantly, Jessica Abbott was awarded an ERC Starting Grant in October, the first of two at the Biology Department in Lund. All in all, a very succesful year for EXEB and its members, I think.

The future looks bright, I think, if the trend in 2015 will continue, but now for something lighter: the evolutionary origin of Santa Claus. It was Beatriz Willink pointed me to this very interesting blog post, which aims to do a phylogenetic analysis of the evolutionary origin and allopatric divergence of different Santa Claus phenotypes. It is from the blog "EEB and Flow", and R-code is provided, should you be interested in exploring this fascinating topic in depth. Enjoy!

Friday, December 4, 2015

Lab meeting on 8th of December: Genomic targets of natural selection on bill morphology

Posted by Hanna Laakkonen

Martin Stervander's cool PhD is out and since there is a lot of interesting reading in the book I suggest we pick a paper from there for next Tuesday. This topic is a manuscript, but Martin was kind to provide us the pdf for reading. I'll print out a few copies and put them into my pigeon hole, pick one from there if your missing the actual thesis!

Title: Identifying the genomic targets of natural selection on bill morphology in the Inaccessible Island finch Nesospiza acunhae

Abstract: Adaptation to food sources is a key element in divergence processes, and may promote ecological speciation in the face of gene flow. In birds, the size and shape of the bill is the target for natural selection on feeding efficiency, and it can also affect male song, a sexually selected trait. Here, we investigate the Inaccessible Island finch Nesospiza acunhae, part of a small radiation endemic to the South Atlantic islands of Tristan da Cunha. Inaccessible Island hosts two subspecies: a smallbilled generalist feeding mainly on grass seeds, and a large-billed specialist foraging on the seeds of Phylica trees. Notably, despite the extremely small geographic scale – Inaccessible Island is only 16 km2 – there is simultaneous occurrence of strong bill size-associated assortative mating, and parallel hybridization between the two subspecies in confined parts of the highland plateau. Here we report on the genomic landscape of bill morphology and detect two genomic regions with significantly elevated differentiation between small- and large-billed birds. The first region, on chromosome 1, contains 4–6 genes, of which one (KPNA3) is part of a large pathway where several bill morphology candidate genes are included. The second region, residing on the sex chromosome Z, contains 8 genes, all of which are associated with previously known bill morphology candidate genes. One of them is ISL1, a homeobox transcription factor included in the neural crest differentiation pathway, which affects bill morphology in Darwin’s finches through the expression of bone morphogenetic proteins. The effect of the combined chromosome 1/Z genotypes on bill phenotype indicates an epistatic interaction between the regions. Our results show that minute proportions of the genome contribute to extreme bill variation in the Inaccessible Island finch, which in turn is associated with strong differential food preference, habitat selection and assortative mating.

Sunday, November 29, 2015

Meeting 1 dec: Can invertebrates have personalities?

Posted by Jessica Abbot on behalf of Alexander Hegg

This is an interesting essay on the topic of animal personalities, published last year in Animal Behaviour. Most personality studies have focused on vertebrates, but here the authors point out the possible advantages of studying personality variation in invertebrates. What are your thoughts on this? I think it would be an interesting topic to discuss at the next lab meeting.

Link: doi:10.1016/j.anbehav.2014.02.016

Title: Studying personality variation in invertebrates: why bother?

Abstract: Research on animal personality variation has been burgeoning in the last 20 years but surprisingly few studies have investigated personalities in invertebrate species although they make up 98% of all animal species. Such lack of invertebrate studies might be due to a traditional belief that invertebrates are just ‘minirobots’. Lately, studies highlighting personality differences in a range of invertebrate species have challenged this idea. However, the number of invertebrate species investigated still contrasts markedly with the effort that has been made studying vertebrates, which represent only a single subphylum. We describe how investigating proximate, evolutionary and ecological correlates of personality variation in invertebrates may broaden our understanding of personality variation in general. In our opinion, personality studies on invertebrates are much needed, because invertebrates exhibit a range of aspects in their life histories, social and sexual behaviours that are extremely rare or absent in most studied vertebrates, but that offer new avenues for personality research. Examples are complete metamorphosis, male emasculation during copulation, asexual reproduction, eusociality and parasitism. Further invertebrate personality studies could enable a comparative approach to unravel how past selective forces have driven the evolution of personality differences. Finally, we point out the advantages of studying personality variation in many invertebrate species, such as easier access to relevant data on proximate and ultimate factors, arising from easy maintenance, fast life cycles and short generation times.

Friday, November 20, 2015

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.

Thursday, November 5, 2015

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!

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.

Friday, October 30, 2015

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


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 :)

Thursday, October 22, 2015

Lab meeting on Oct. 27th at 10:00 on turtle development and evolution.

Hello all,

Next week I will give a talk on my PhD research:

Developmental and genetic underpinnings of parallel evolution in turtles

Abstract:The repeated evolution of form and function suggests commonality in processes that influence organismal diversity. Recent studies revealed convergent (dissimilar) or parallel (similar) change in genes linked to similar adult traits in unrelated species. Still, how genes interact during embryogenesis to ultimately give rise to strikingly similar adult morphologies is unclear. We tested the prediction that parallel morphological evolution reflects similar changes in gene activity. By examining expression of nearly 16,000 genes, we uncovered similarity in vast gene networks governing development of a specialized shoulder blade in turtles that independently evolved complex shell-closing systems. Remarkably, in embryos of those species, similar gene networks associated with skeletal differentiation and muscle contraction were temporally and spatially congruent with the de novo formation of a synovial joint, normally found in knees and elbows of vertebrates. This further corroborated that repeated morphological evolution often arises via evolutionarily conserved developmental processes. To our knowledge, our study is the first to sample natural populations to indentify similar developmental origins, cell and molecular, of parallel skeletal evolution in unrelated vertebrate species. Integration of genetics, development, and evolution is crucial to illuminating processes that underlie macroevolutionary patterns of similarity across the tree of life.

See you at the same time and place next week! (coffee and snacks included)