Lab-meeting on Drosophila evolution: epistatic networks and thermal adaptation

Posted by Erik Svensson

There is now a lot of activity in the Drosophila-lab, with one undergraduate student, one postdoc (Natsu) and yesterday also a PRAO-student (my daughter My). Given this, Jessica and I felt it was time to have a lab-meeting focussed on some interesting new research in evolutionary biology, focussed on the Drosophila-system.

We have therefore picked two recent PNAS-papers for discussion, one more genetic and molecular (dealing with epistasis and gene regulatory networks of starvation resistance and chill coma recovery) and one more macroevolutionary, dealing with the evolution of upper thermal limits in a phylogenetic context. Both have in common a focus on thermal adaptation. You will find Abstracts here and here, and Abstracts and titles below.

In addition, we hope Natsu could bring anbd show some printout pictures of the beatiful Wing Interference Patterns (WIP:s) of Drosophila melanogaster inbred lines. This will just be a taster, however, as Natsu will give a more formal seminar later in November telling the lab-group about the ongoing work and some preliminary results.

Time: Tuesday October 23 at 10.30
Place: "Argumentet", 2nd floor

Epistasis dominates the genetic architecture of Drosophila quantitative traits              

Abstract

Epistasis—nonlinear genetic interactions between polymorphic loci—is the genetic basis of canalization and speciation, and epistatic interactions can be used to infer genetic networks affecting quantitative traits. However, the role that epistasis plays in the genetic architecture of quantitative traits is controversial. Here, we compared the genetic architecture of three Drosophila life history traits in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and a large outbred, advanced intercross population derived from 40 DGRP lines (Flyland). We assessed allele frequency changes between pools of individuals at the extremes of the distribution for each trait in the Flyland population by deep DNA sequencing. The genetic architecture of all traits was highly polygenic in both analyses. Surprisingly, none of the SNPs associated with the traits in Flyland replicated in the DGRP and vice versa. However, the majority of these SNPs participated in at least one epistatic interaction in the DGRP. Despite apparent additive effects at largely distinct loci in the two populations, the epistatic interactions perturbed common, biologically plausible, and highly connected genetic networks. Our analysis underscores the importance of epistasis as a principal factor that determines variation for quantitative traits and provides a means to uncover genetic networks affecting these traits. Knowledge of epistatic networks will contribute to our understanding of the genetic basis of evolutionarily and clinically important traits and enhance predictive ability at an individualized level in medicine and agriculture.

Upper thermal limits of Drosophila are linked to species distributions and strongly constrained phylogenetically

Abstract

Upper thermal limits vary less than lower limits among related species of terrestrial ectotherms. This pattern may reflect weak or uniform selection on upper limits, or alternatively tight evolutionary constraints. We investigated this issue in 94 Drosophila species from diverse climates and reared in a common environment to control for plastic effects that may confound species comparisons. We found substantial variation in upper thermal limits among species, negatively correlated with annual precipitation at the central point of their distribution and also with the interaction between precipitation and maximum temperature, showing that heat resistance is an important determinant of Drosophila species distributions. Species from hot and relatively dry regions had higher resistance, whereas resistance was uncorrelated with temperature in wetter regions. Using a suite of analyses we showed that phylogenetic signal in heat resistance reflects phylogenetic inertia rather than common selection pressures. Current species distributions are therefore more likely to reflect environmental sorting of lineages rather than local adaptation. Similar to previous studies, thermal safety margins were small at low latitudes, with safety margins smallest for species occupying both humid and dry tropical environments. Thus, species from a range of environments are likely to be at risk owing to climate change. Together these findings suggest that this group of insects is unlikely to buffer global change effects through marked evolutionary changes, highlighting the importance of facilitating range shifts for maintaining biodiversity.

 

 

On ancestral temperature tolerances, butterfly colonization, Lolita and Vladimir Nabokov

Picture sources from Wikipedia.

This week's lab-meeting will take place at 13.30 on Wednesday February 9 in "Darwin", in accordance with our new schedule. We will discuss a very interesting article from Naomi Pierce's laboratory, which deals with biogeography and multiple "waves" of colonization of Polyommatus blues (butterflies belonging to the family Lycaenidae), as they crossed the Bering's Strait in North America. This beatiful paper integrates ancestral state reconstructions of an ecological important trait (thermal tolerance), biogeography, phylogeny and is of also of litterary interest, as the authors confirm a hypothesis by amateur lepidopterist and famous russian author Nabokov. 

Vladimir Nabokov worked at the museum in Harvard (where Naomi Pierce is active today), during the middle part of the last century. Nabokov is mainly known as an important figure in litterature for his famous but controversial erotic novel "Lolita", about the sexual attraction a middle-age man felt towards a young 12-year old girl. Then and now quite a forbidden topic. But Nabokov was also an excellent amateur entomologist and systematist, whose expertise in butterflies exceeded many professional systematists.

Nabokovs biogeographical hypothesis about multiple waves of colonization of bluets to the New World was based on considerations of genital morphology, but has now proven to be largely correct and validated by molecular data. An excellent example how natural history, systematics and museum expertise can be predictive sciences and complement molecular systematics, rather than being replaced by it. I think our former postdoc and beloved co-worker Shawn Kuchta will love this paper. There is an interesting popular essay in New York Times as well, which might be of interest and worth reading prior to the lab-meeting. You can find that excellent essay by Carl Zimmer here. A blog post on the interesting phylogenetic blog "Dechronization" also comments on Zimmer's paper.  

Below is the Abstract to the original article in Proc. R. Soc. Lond. B. that we will discuss on Wednesday. It is an "Open Acess"-article, so just follow the link to the abstract and then you should be able to download it.

Phylogeny and palaeoecology of Polyommatus blue butterflies show Beringia was a climate-regulated gateway to the New World

1. Roger Vila1,2,
2. Charles D. Bell3,
3. Richard Macniven1,4,
4. Benjamin Goldman-Huertas1,5,
5. Richard H. Ree6,
6. Charles R. Marshall1,7,
7. Zsolt Bálint8,
8. Kurt Johnson9,
9. Dubi Benyamini10 and
10. Naomi E. Pierce1,*

+ Author Affiliations

1. ¹Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
2. ²ICREA and Institute of Evolutionary Biology (CSIC-UPF), Passeig Marítim de la Barceloneta 37–49, Barcelona 08003, Spain
3. ³Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA
4. ⁴Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, USA
5. ⁵Department of Ecology and Evolution, The University of Arizona, 424 Biosciences West, Tucson, AZ 85721, USA
6. ⁶Department of Botany, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
7. ⁷University of California Museum of Paleontology, and Department of Integrative Biology, University of California, Berkeley, 1101 Valley Life Sciences Building, Berkeley, CA 02138, USA
8. ⁸Department of Zoology, Hungarian Natural History Museum H-1088, Budapest, Baross utca 13, Hungary
9. ⁹Florida State Collection of Arthropods/McGuire Center, University of Florida Cultural Plaza, Hull Road, Gainesville, FL 32611, USA
10. ¹⁰91 Levona Street, Bet Arye, 71947, Israel

1. * Author for correspondence (npierce@oeb.harvard.edu).

Abstract

Transcontinental dispersals by organisms usually represent improbable events that constitute a major challenge for biogeographers. By integrating molecular phylogeny, historical biogeography and palaeoecology, we test a bold hypothesis proposed by Vladimir Nabokov regarding the origin of Neotropical Polyommatus blue butterflies, and show that Beringia has served as a biological corridor for the dispersal of these insects from Asia into the New World. We present a novel method to estimate ancestral temperature tolerances using distribution range limits of extant organisms, and find that climatic conditions in Beringia acted as a decisive filter in determining which taxa crossed into the New World during five separate invasions over the past 11 Myr. Our results reveal a marked effect of the Miocene–Pleistocene global cooling, and demonstrate that palaeoclimatic conditions left a strong signal on the ecology of present-day taxa in the New World. The phylogenetic conservatism in thermal tolerances that we have identified may permit the reconstruction of the palaeoecology of ancestral organisms, especially mobile taxa that can easily escape from hostile environments rather than adapt to them.

Can phylogenetic methods from evolutionary biology inform us about how societies evolve?

This coming lab-meeting (Wednesday 27 October), I was thinking that we should discuss if and how methods from evolutionary biology can elucidate problems studied by political scientists: the rise and fall of societies. There is an interesting article published in Nature, where the authors used phylogenetic methods to investigate if societies evolved towards more complexity (or not). The study was performed on a set of societies in South-East Asia and in the Pacific.  

Evolutionary biologist and community ecologist Jared Diamond has an interesting perspective about the study. Read both the comment by Diamond and the original article so that we can have an interesting discussion on Wednesday. Time and place as usual: "Darwin" at 10.15. Below is the abstract and title of the original paper:

Rise and fall of political complexity in island South-East Asia and the Pacific  

Thomas E. Currie,Simon J. Greenhill, Russell D. Gray, Toshikazu Hasegawa & Ruth Mace 

There is disagreement about whether human political evolution has proceeded through a sequence of incremental increases in complexity, or whether larger, non-sequential increases have occurred. The extent to which societies have decreased in complexity is also unclear. These debates have continued largely in the absence of rigorous, quantitative tests. We evaluated six competing models of political evolution in Austronesian-speaking societies using phylogenetic methods. Here we show that in the best-fitting model political complexity rises and falls in a sequence of small steps. This is closely followed by another model in which increases are sequential but decreases can be either sequential or in bigger drops. The results indicate that large, non-sequential jumps in political complexity have not occurred during the evolutionary history of these societies. This suggests that, despite the numerous contingent pathways of human history, there are regularities in cultural evolution that can be detected using computational phylogenetic methods.

A new synthesis between community ecology and evolutionary biology?

On the lab-meeting this coming Wednesday (12 May, 2010), I would like to discuss a review article in TREE about the (possible) new and emerging synthesis between community ecology and evolutionary biology. You can download this article here. Hopefully, we can have a good and conceptually rich dicussion about the general message in this paper.

The lab-meeting the week after this one (i. e. May 17, 2010), I was planning to have a lab-meeting outdoors, meet the spring and (hopefully!) see the first emerged odonates of the year, followed by lunch at cosy outdooor museum and restaurant Kulturens Östarp. Stay tuned, more info soon.

Time and place for the coming lab-meeting the current week as usual:

Where: "Darwin"-room, 2nd floor, Ecology Building
When: May 10 2010, 10.15

Any fika-volunteer?