|Id||Title||Authors||Abstract||Picture||Thematic fields||Recommender||Reviewers||Submission date|
29 Sep 2017
Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of the South American continentMichael D. Pirie, Paul J. M. Maas, Rutger A. Wilschut, Heleen Melchers-Sharrott & Lars W. Chatrou 10.1101/141127
Unravelling the history of Neotropical plant diversificationRecommended by Hervé Sauquet based on reviews by Thomas Couvreur and Hervé Sauquet
South American rainforests, particularly the Tropical Andes, have been recognized as the hottest spot of plant biodiversity on Earth, while facing unprecedented threats from human impact [1,2]. Considerable research efforts have recently focused on unravelling the complex geological, bioclimatic, and biogeographic history of the region [3,4]. While many studies have addressed the question of Neotropical plant diversification using parametric methods to reconstruct ancestral areas and patterns of dispersal, Pirie et al.  take a distinct, complementary approach. Based on a new, near-complete molecular phylogeny of two Neotropical genera of the flowering plant family Annonaceae, the authors modelled the ecological niche of each species and reconstructed the history of niche differentiation across the region. The main conclusion is that, despite similar current distributions and close phylogenetic distance, the two genera experienced rather distinct processes of diversification, responding differently to the major geological events marking the history of the region in the last 20 million years (Andean uplift, drainage of Lake Pebas, and closure of the Panama Isthmus).
As a researcher who has not personally worked on Neotropical biogeography, I found this paper captivating and especially enjoyed very much reading the Introduction, which sets out the questions very clearly. The strength of this paper is the near-complete diversity of species the authors were able to sample in each clade and the high-quality data compiled for the niche models. I would recommend this paper as a nice example of a phylogenetic study aimed at unravelling the detailed history of Neotropical plant diversification. While large, synthetic meta-analyses of many clades should continue to seek general patterns [4,6], careful studies restricted on smaller, but well controlled and sampled datasets such as this one are essential to really understand tropical plant diversification in all its complexity.
 Antonelli A, and Sanmartín I. 2011. Why are there so many plant species in the Neotropics? Taxon 60, 403–414.
 Mittermeier RA, Robles-Gil P, Hoffmann M, Pilgrim JD, Brooks TB, Mittermeier CG, Lamoreux JL and Fonseca GAB. 2004. Hotspots revisited: Earths biologically richest and most endangered ecoregions. CEMEX, Mexico City, Mexico 390pp
 Antonelli A, Nylander JAA, Persson C and Sanmartín I. 2009. Tracing the impact of the Andean uplift on Neotropical plant evolution. Proceedings of the National Academy of Science of the USA 106, 9749–9754. doi: 10.1073/pnas.0811421106
 Hoorn C, Wesselingh FP, ter Steege H, Bermudez MA, Mora A, Sevink J, Sanmartín I, Sanchez-Meseguer A, Anderson CL, Figueiredo JP, Jaramillo C, Riff D, Negri FR, Hooghiemstra H, Lundberg J, Stadler T, Särkinen T and Antonelli A. 2010. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330, 927–931. doi: 10.1126/science.1194585
 Pirie MD, Maas PJM, Wilschut R, Melchers-Sharrott H and Chatrou L. 2017. Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of the South American continent. bioRxiv, 141127, ver. 3 of 28th Sept 2017. doi: 10.1101/141127
 Bacon CD, Silvestro D, Jaramillo C, Tilston Smith B, Chakrabartye P and Antonelli A. 2015. Biological evidence supports an early and complex emergence of the Isthmus of Panama. Proceedings of the National Academy of Science of the USA 112, 6110–6115. doi: 10.1073/pnas.1423853112
|Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of the South American continent||Michael D. Pirie, Paul J. M. Maas, Rutger A. Wilschut, Heleen Melchers-Sharrott & Lars W. Chatrou||Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of lake Peba...||Phylogenetics / Phylogenomics, Phylogeography & Biogeography||Hervé Sauquet||Hervé Sauquet, Thomas Couvreur||2017-06-03 21:25:48||View|
26 Sep 2017
Lacking conservation genomics in the giant Galápagos tortoiseEtienne Loire, Nicolas Galtier https://doi.org/10.1101/101980
A genomic perspective is needed for the re-evaluation of species boundaries, evolutionary trajectories and conservation strategies for the Galápagos giant tortoisesRecommended by Michael C. Fontaine based on reviews by 4 anonymous reviewers
Genome-wide data obtained from even a small number of individuals can provide unprecedented levels of detail about the evolutionary history of populations and species , determinants of genetic diversity , species boundaries and the process of speciation itself . Loire and Galtier  present a clear example, using the emblematic Galápagos giant tortoise (Chelonoidis nigra), of how multi-species comparative population genomic approaches can provide valuable insights about population structure and species delimitation even when sample sizes are limited but the number of loci is large and distributed across the genome.
Galápagos giant tortoises are endemic to the Galápagos Islands and are currently recognized as an endangered, multi-species complex including both extant and extinct taxa. Taxonomic definitions are based on morphology, geographic isolation and population genetic evidence based on short DNA sequences of the mitochondrial genome (mtDNA) and/or a dozen or so nuclear microsatellite loci [5-8]. The species complex enjoys maximal protection. Population recoveries have been quite successful and spectacular conservation programs based on mitochondrial genes and microsatellites are ongoing. This includes for example individual translocations, breeding program, “hybrid” sterilization or removal, and resurrection of extinct lineages).
In 2013, Loire et al.  provided the first population genomic analyses based on genome scale data (~1000 coding loci derived from blood-transcriptomes) from five individuals, encompassing three putative “species”: Chelonnoidis becki, C. porteri and C. vandenburghi. Their results raised doubts about the validity/accuracy of the currently accepted designations of “genetic distinctiveness”. However, the implications for conservation and management have remained unnoticed.
In 2017, Loire and Galtier  have re-appraised this issue using an original multi-species comparative population genomic analysis of their previous data set . Based on a comparison of 53 animal species, they show that both the level of genome-wide neutral diversity (πS) and level of population structure estimated using the inbreeding coefficient (F) are much lower than would be expected from a sample covering multiple species. The observed values are more comparable to those typically reported at the “among population” level within a single species such as human (Homo sapiens). The authors go to great length to assess the sensitivity of their method to detect population structure (or lack thereof) and show that their results are robust to potential issues, such as contamination and sequencing errors that can occur with Next Generation Sequencing techniques; and biases related to the small sample size and sub-sampling of individuals. They conclude that published mtDNA and microsatellite-based assessment of population structure and species designations may be biased towards over-splitting.
This manuscript is a very good read as it shows the potential of the now relatively affordable genome-wide data for helping to both resolve and clarify population and species boundaries, illuminate demographic trends, evolutionary trajectories of isolated groups, patterns of connectivity among them, and test for evidence of local adaptation and even reproductive isolation. The comprehensive information provided by genome-wide data can critically inform and assist the development of the best strategies to preserve endangered populations and species. Loire and Galtier  make a strong case for applying genomic data to the Galápagos giant tortoises, which is likely to redirect conservation efforts more effectively and at lower cost. The case of the Galápagos giant tortoises is certainly a very emblematic example, which will find an echo in many other endangered species conservation programs.
 Li H and Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature, 475: 493–496. doi: 10.1038/nature10231
 Romiguier J, Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, Chiari Y, Dernat R, Duret L, Faivre N, Loire E, Lourenco JM, Nabholz B, Roux C, Tsagkogeorga G, Weber AA-T, Weinert LA, Belkhir K, Bierne N, Glémin S and Galtier N. 2014. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature, 515: 261–263. doi: 10.1038/nature13685
 Roux C, Fraïsse C, Romiguier J, Anciaux Y, Galtier N and Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology, 14: e2000234. doi: 10.1371/journal.pbio.2000234
 Loire E and Galtier N. 2017. Lacking conservation genomics in the giant Galápagos tortoise. bioRxiv 101980, ver. 4 of September 26, 2017. doi: 10.1101/101980
 Beheregaray LB, Ciofi C, Caccone A, Gibbs JP and Powell JR. 2003. Genetic divergence, phylogeography and conservation units of giant tortoises from Santa Cruz and Pinzón, Galápagos Islands. Conservation Genetics, 4: 31–46. doi: 10.1023/A:1021864214375
 Ciofi C, Milinkovitch MC, Gibbs JP, Caccone A and Powell JR. 2002. Microsatellite analysis of genetic divergence among populations of giant Galápagos tortoises. Molecular Ecology, 11: 2265–2283. doi: 10.1046/j.1365-294X.2002.01617.x
 Garrick RC, Kajdacsi B, Russello MA, Benavides E, Hyseni C, Gibbs JP, Tapia W and Caccone A. 2015. Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises. Ecology and Evolution, 5: 676–694. doi: 10.1002/ece3.1388
 Poulakakis N, Edwards DL, Chiari Y, Garrick RC, Russello MA, Benavides E, Watkins-Colwell GJ, Glaberman S, Tapia W, Gibbs JP, Cayot LJ and Caccone A. 2015. Description of a new Galápagos giant tortoise species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz island. PLoS ONE, 10: e0138779. doi: 10.1371/journal.pone.0138779
 Loire E, Chiari Y, Bernard A, Cahais V, Romiguier J, Nabholz B, Lourenço JM and Galtier N. 2013. Population genomics of the endangered giant Galápagos tortoise. Genome Biology, 14: R136. doi: 10.1186/gb-2013-14-12-r136
|Lacking conservation genomics in the giant Galápagos tortoise||Etienne Loire, Nicolas Galtier||<p>Conservation policy in the giant Galápagos tortoise, an iconic endangered animal, has been assisted by genetic markers for ~15 years: a dozen loci have been used to delineate thirteen (sub)species, between which hybridization is prevented. Here...||Evolutionary Applications, Population Genetics / Genomics, Speciation, Systematics / Taxonomy||Michael C. Fontaine||2017-01-21 15:34:00||View|
20 Sep 2017
An interaction between cancer progression and social environment in DrosophilaErika H. Dawson, Tiphaine P.M. Bailly, Julie Dos Santos , Céline Moreno, Maëlle Devilliers, Brigitte Maroni, Cédric Sueur, Andreu Casali, Beata Ujvari, Frederic Thomas, Jacques Montagne, Frederic Mery 10.1101/143560
Cancer and loneliness in DrosophilaRecommended by Ana Rivero based on reviews by Ana Rivero and Silvie Huijben
Drosophila flies may not be perceived as a quintessentially social animal, particularly when compared to their eusocial hymenopteran cousins. Although they have no parental care, division of labour or subfertile caste, fruit flies nevertheless exhibit an array of social phenotypes that are potentially comparable to those of their highly social relatives. In the wild, Drosophila adults cluster around food resources where courtship, mating activity and oviposition occur. Recent work has shown not only that social interactions in these clusters condition many aspects of the behaviour and physiology of the flies  but also, and perhaps more unexpectedly, that social isolation has a negative impact on their fitness .
Many studies in humans point to the role of social isolation as a source of stress that can induce and accelerate disease progression. The ultimate proof of the connection between social interaction and disease is however mired in confounding variables and alternative explanations so the subject, though crucial, remains controversial. With a series of elegant experiments using Drosophila flies that develop an inducible form of intestinal cancer, Dawson et al  show that cancer progresses more rapidly in flies maintained in isolation than in flies maintained with other cancerous flies. Further, cancerous flies kept with non-cancerous flies, fare just as badly as when kept alone. Their experiments suggest that this is due to the combined effect of healthy flies avoiding contact with cancerous flies (even though this is a non-contagious disease), and of cancerous flies having higher quality interactions with other cancerous flies than with healthy ones. Perceived isolation is therefore as pernicious as real isolation when it comes to cancer progression in these flies. Like all good research, this study opens up as many questions as it answers, in particular the why and wherefores of the flies’ extraordinary social behaviour in the face of disease.
 Camiletti AL and Thompson GJ. 2016. Drosophila as a genetically tractable model for social insect behavior. Frontiers in Ecology and Evolution, 4: 40. doi: 10.3389/fevo.2016.00040
 Ruan H and Wu C-F. 2008. Social interaction-mediated lifespan extension of Drosophila Cu/Zn superoxide dismutase mutants. Proceedings of the National Academy of Sciences, USA, 105: 7506-7510. doi: 10.1073/pnas.0711127105
 Dawson E, Bailly T, Dos Santos J, Moreno C, Devilliers M, Maroni B, Sueur C, Casali A, Ujvari B, Thomas F, Montagne J, Mery F. 2017. An interaction between cancer progression and social environment in Drosophila. BiorXiv, 143560, ver. 3 of 19th September 2017. doi: 10.1101/143560
|An interaction between cancer progression and social environment in Drosophila||Erika H. Dawson, Tiphaine P.M. Bailly, Julie Dos Santos , Céline Moreno, Maëlle Devilliers, Brigitte Maroni, Cédric Sueur, Andreu Casali, Beata Ujvari, Frederic Thomas, Jacques Montagne, Frederic Mery||The ecological benefits of sociality in gregarious species are widely acknowledged. However, only limited data is available on how the social environment influences non-communicable disease outcomes. For instance, despite extensive research over t...||Behavior & Social Evolution, Evolutionary Ecology, Phenotypic Plasticity||Ana Rivero||2017-05-30 08:55:16||View|
11 Sep 2017
Less effective selection leads to larger genomesTristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N. Pierre Charrier, David Eme, Florian Mermillod-Blondin, Laurent Duret, Cristina Vieira, Ludovic Orlando and Christophe Douady 10.1101/gr.212589.116
Colonisation of subterranean ecosystems leads to larger genome in waterlouse (Aselloidea)Recommended by Benoit Nabholz and Jochen B. W. Wolf
The total amount of DNA utilized to store hereditary information varies immensely among eukaryotic organisms. Single copy genome sizes – disregarding differences due to ploidy - differ by more than three orders of magnitude ranging from a few million nucleotides (Mb) to hundreds of billions (Gb). With the ever-increasing availability of fully sequenced genomes we now know that most of the difference is due either to whole genome duplication or to variation in the abundance of repetitive elements. Regarding repetitive elements, the evolutionary forces underlying the large variation 'allowing' more or less elements in a genome remain largely elusive. A tentative correlation between an organism's complexity (however this may be adequately measured) and genome size, the so called C-value paradox , has long been dismissed. Studies testing for selection on secondary phenotypic effects associated with genome size (cell size, metabolic rates, nutrient availability) have yielded mixed results. Nonadaptive theories capitalizing on a role of deleterious insertion-deletion mutations and genetic drift as the main drivers have likewise received mixed support [2-3]. Overall, most evidence was derived from analyses across broad taxonomical scales [4-6].
Lefébure and colleagues  take a different approach. They confine their considerations to a homogeneous, restricted taxonomical group, isopod crustaceans of the superfamily Aselloidea. This taxonomic focus allows the authors to circumvent many of the confounding factors such as phylogenetic inertia, life history divergence and mutation rate variation that tend to trouble analyses across broad taxonomic timescales. Another important feature of the chosen system is the evolutionary independent transition of habitat use that has occurred at least 11 times. One group of species inhabits subterranean ecosystems (groundwater), another group thrives on surface water. Populations of the former live in low-energy habitats and are expected to be outnumbered by their surface dwelling relatives. Interestingly – and a precondition for the study - the groundwater species have significantly larger genomes (up to 137%). With this unique set-up, the authors are able to investigate the link between genome size and evolutionary forces related to a proxy of long-term population size by removing many of the confounding factors a priori.
Upfront, we learn that the dN/dS ratio is higher in the groundwater species. This may either suggest prevalent positive selection or lower efficacy of purifying selection (relaxed constraint) in the group of species in which population sizes are expected to be low. Using a series of population genetic analyses the authors provide compelling evidence for the latter. Analyses are carefully conducted and include models for estimating the intensity and frequency of purifying and positive selection, the DoS (direction of selection) and α statistic. Next the authors also exclude the possibility that increased dN/dS of the subterranean groundwater species may be due to nonfunctionalization, which may result from the subterranean lifestyle.
Overall, these analyses suggest relaxed constraint in smaller populations as the most plausible alternative to explain increased dN/dS ratios. In addition to the efficacy of selection, the authors estimate the timing of the ecological transition under the rationale that the amount of time a species may have been exposed to the subterranean habitat may reflect long term population sizes. To calibrate the 'colonization clock' they apply a neat trick based on the degree of degeneration of the opsin gene (as vision tends to get lost in these habitats). When finally testing which parameters may explain differences in genome size all factors – ecological status, selection efficiency as measured by dN/dS and colonization time - turned out to be significant predictors. Direct estimates of the short term effective population size Ne from polymorphism data, however, did not correlate with genome size. Ruling out the effect of other co-variates such as body size and growth rate the authors conclude that genome size was overall best predicted by long-term population size change upon habitat shift. In that the authors provide convincing evidence that the increase in genome size is linked to a decrease in long-term reduction of selection efficiency of subterranean species. Assuming a bias for insertion mutations over deletion mutations (which is usually the case in eukaryotes) this result is in agreement with the theory of mutational hazard [4-6]. This theory proposed by Michael Lynch postulates that the accumulation of non-functional DNA has a weak deleterious effect that can only be efficiently opposed by natural selection in species with high Ne.
In conclusion, Lefébure and colleagues provide novel and welcome evidence supporting a 'neutralist' hypothesis of genome size evolution without the need to invoke an adaptive component. Methodologically, the study cautions against the common use of polymorphism-based estimates of Ne which are often obfuscated by transitory demographic change. Instead, alternative measures of selection efficacy linked to long-term population size may serve as better predictors of genome size. We hope that this study will stimulate additional work testing the link between Ne and genome size variation in other taxonomical groups [8-9]. Using genome sequences instead of the transcriptome approach applied here may concomitantly further our understanding of the molecular mechanisms underlying genome size change.
 Thomas, CA Jr. 1971. The genetic organization of chromosomes. Annual Review of Genetics 5: 237–256. doi: 10.1146/annurev.ge.05.120171.001321
 Ågren JA, Greiner S, Johnson MTJ, Wright SI. 2015. No evidence that sex and transposable elements drive genome size variation in evening primroses. Evolution 69: 1053–1062. doi: 10.1111/evo.12627
 Bast J, Schaefer I, Schwander T, Maraun M, Scheu S, Kraaijeveld K. 2016. No accumulation of transposable elements in asexual arthropods. Molecular Biology and Evolution 33: 697–706. doi: 10.1093/molbev/msv261
 Lynch M. 2007. The Origins of Genome Architecture. Sinauer Associates.
 Lynch M, Bobay LM, Catania F, Gout JF, Rho M. 2011. The repatterning of eukaryotic genomes by random genetic drift. Annual Review of Genomics and Human Genetics 12: 347–366. doi: 10.1146/annurev-genom-082410-101412
 Lynch M, Conery JS. 2003. The origins of genome complexity. Science 302: 1401–1404. doi: 10.1126/science.1089370
 Lefébure T, Morvan C, Malard F, François C, Konecny-Dupré L, Guéguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Der Sarkissian C, Charrier NP, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, and Douady CJ. 2017. Less effective selection leads to larger genomes. Genome Research 27: 1016-1028. doi: 10.1101/gr.212589.116
 Lower SS, Johnston JS, Stanger-Hall KF, Hjelmen CE, Hanrahan SJ, Korunes K, Hall D. 2017. Genome size in North American fireflies: Substantial variation likely driven by neutral processes. Genome Biolology and Evolution 9: 1499–1512. doi: 10.1093/gbe/evx097
 Sessegolo C, Burlet N, Haudry A. 2016. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies. Biology Letters 12: 20160407. doi: 10.1098/rsbl.2016.0407
|Less effective selection leads to larger genomes||Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N. Pierre Charrier, David Eme, Florian Mermillod-Blondin, Lau...||The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However...||Evolutionary Theory, Genome Evolution, Molecular Evolution, Population Genetics / Genomics||Benoit Nabholz||2017-09-08 09:39:23||View|
03 Aug 2017
Fisher's geometrical model and the mutational patterns of antibiotic resistance across dose gradientsNoémie Harmand, Romain Gallet, Roula Jabbour-Zahab, Guillaume Martin, Thomas Lenormand 10.1111/evo.13111
What doesn’t kill us makes us stronger: can Fisher’s Geometric model predict antibiotic resistance evolution?Recommended by Inês Fragata and Claudia Bank
The increasing number of reported cases of antibiotic resistance is one of today’s major public health concerns. Dealing with this threat involves understanding what drives the evolution of antibiotic resistance and investigating whether we can predict (and subsequently avoid or circumvent) it .
 Palmer AC, and Kishony R. 2013. Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance. Nature Review Genetics 14: 243—248. doi: 10.1038/nrg3351
 Tenaillon O. 2014. The utility of Fisher’s geometric model in evolutionary genetics. Annual Review of Ecology, Evolution and Systematics 45: 179—201. doi: 10.1146/annurev-ecolsys-120213-091846
 Blanquart F and Bataillon T. 2016. Epistasis and the structure of fitness landscapes: are experimental fitness landscapes compatible with Fisher’s geometric model? Genetics 203: 847—862. doi: 10.1534/genetics.115.182691
 Harmand N, Gallet R, Jabbour-Zahab R, Martin G and Lenormand T. 2017. Fisher’s geometrical model and the mutational patterns of antibiotic resistance across dose gradients. Evolution 71: 23—37. doi: 10.1111/evo.13111
 de Visser, JAGM, and Krug J. 2014. Empirical fitness landscapes and the predictability of evolution. Nature 15: 480—490. doi: 10.1038/nrg3744
 Palmer AC, Toprak E, Baym M, Kim S, Veres A, Bershtein S and Kishony R. 2015. Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes. Nature Communications 6: 1—8. doi: 10.1038/ncomms8385
|Fisher's geometrical model and the mutational patterns of antibiotic resistance across dose gradients||Noémie Harmand, Romain Gallet, Roula Jabbour-Zahab, Guillaume Martin, Thomas Lenormand||Fisher's geometrical model (FGM) has been widely used to depict the fitness effects of mutations. It is a general model with few underlying assumptions that gives a large and comprehensive view of adaptive processes. It is thus attractive in sever...||Adaptation||Inês Fragata||2017-08-01 16:06:02||View|
31 Jul 2017
Selection on morphological traits and fluctuating asymmetry by a fungal parasite in the yellow dung flyWolf U. Blanckenhorn 10.1101/136325
Parasite-mediated selection promotes small body size in yellow dung fliesRecommended by Rodrigo Medel based on reviews by Rodrigo Medel and 1 anonymous reviewer
Body size has long been considered as one of the most important organismic traits influencing demographical processes, population size, and evolution of life history strategies [1, 2]. While many studies have reported a selective advantage of large body size, the forces that determine small-sized organisms are less known, and reports of negative selection coefficients on body size are almost absent at present. This lack of knowledge is unfortunate as climate change and energy demands in stressful environments, among other factors, may produce new selection scenarios and unexpected selection surfaces . In this manuscript, Blanckenhorn  reports on a potential explanation for the surprising 10% body size decrease observed in a Swiss population of yellow dung flies during 1993 - 2009. The author took advantage of a fungus outbreak in 2002 to assess the putative role of the fungus Entomopthora scatophagae, a specific parasite of adult yellow dung flies, as selective force acting upon host body size. His findings indicate that, as expected by sexual selection theory, large males experience a mating advantage. However, this positive sexual selection is opposed by a strong negative selection on male and female body size through the viability fitness component. This study provides the first evidence of parasite-mediated disadvantage of large adult body size in the field. While further experimental work is needed to elucidate the exact causes of body size reduction in the population, the author proposes a variation of the trade-off hypothesis raised by Rantala & Roff  that large-sized individuals face an immunity cost due to their high absolute energy demands in stressful environments.
 Peters RH. 1983. The ecological implications of body size. Cambridge University Press, Cambridge.
 Schmidt-Nielsen K. 1984. Scaling: why is animal size so important? Cambridge University Press, Cambridge.
 Ohlberger J. 2013. Climate warming and ectotherm body size: from individual physiology to community ecology. Functional Ecology 27: 991-1001. doi: 10.1111/1365-2435.12098
 Blanckenhorn WU. 2017. Selection on morphological traits and fluctuating asymmetry by a fungal parasite in the yellow dung fly. bioRxiv 136325, ver. 2 of 29th June 2017. doi: 10.1101/136325
 Rantala MJ & Roff DA. 2005. An analysis of trade-offs in immune function, body size and development time in the Mediterranean field cricket, Gryllus bimaculatus. Functional Ecology 19: 323-330. doi: 10.1111/j.1365-2435.2005.00979.x
|Selection on morphological traits and fluctuating asymmetry by a fungal parasite in the yellow dung fly||Wolf U. Blanckenhorn||Evidence for selective disadvantages of large body size remains scarce in general. Previous phenomenological studies of the yellow dung fly *Scathophaga stercoraria* have demonstrated strong positive sexual and fecundity selection on male and fema...||Behavior & Social Evolution, Evolutionary Ecology, Life History, Sexual Selection||Rodrigo Medel||Rodrigo Medel||2017-05-10 11:16:26||View|
12 Jul 2017
Assortment of flowering time and defense alleles in natural Arabidopsis thaliana populations suggests co-evolution between defense and vegetative lifespan strategiesGlander S, He F, Schmitz G, Witten A, Telschow A, de Meaux J 10.1101/131136
Towards an integrated scenario to understand evolutionary patterns in A. thalianaRecommended by Xavier Picó based on reviews by Rafa Rubio de Casas and Xavier Picó
Nobody can ignore that a full understanding of evolution requires an integrated approach from both conceptual and methodological viewpoints. Although some life-history traits, e.g. flowering time, have long been receiving more attention than others, in many cases because the former are more workable than the latter, we must acknowledge that our comprehension about how evolution works is strongly biased and limited. In the Arabidopsis community, such an integration is making good progress as an increasing number of research groups worldwide are changing the way in which evolution is put to the test.
This manuscript  is a good example of that as the authors raise an important issue in evolutionary biology by combining gene expression and flowering time data from different sources. In particular, the authors explore how variation in flowering time, which determines lifespan, and host immunity defenses co-vary, which is interpreted in terms of co-evolution between the two traits. Interestingly, the authors go beyond that pattern by separating lifespan-dependent from lifespan–independent defense genes, and by showing that defense genes with variants known to impact fitness in the field are among the genes whose expression co-varies most strongly with flowering time. Finally, these results are supported by a simple mathematical model indicating that such a relationship can also be expected theoretically.
Overall, the readers will find many conceptual and methodological elements of interest in this manuscript. The idea that evolution is better understood under the scope of life history variation is really exciting and challenging, and in my opinion on the right track for disentangling the inherent complexities of evolutionary research. However, only when we face complexity, we also face its costs and burdens. In this particular case, the well-known co-variation between seed dormancy and flowering time is a missing piece, as well as the identification of (variation in) putative selective pressures accounting for the co-evolution between defense mechanisms and life history (seed dormancy vs. flowering time) along environmental gradients. More intellectual, technical and methodological challenges that with no doubt are totally worth it.
 Glander S, He F, Schmitz G, Witten A, Telschow A, de Meaux J. 2017. Assortment of flowering time and defense alleles in natural Arabidopsis thaliana populations suggests co-evolution between defense and vegetative lifespan strategies. bioRxiv ver.1 of June 19, 2017. doi: 10.1101/131136
|Assortment of flowering time and defense alleles in natural Arabidopsis thaliana populations suggests co-evolution between defense and vegetative lifespan strategies||Glander S, He F, Schmitz G, Witten A, Telschow A, de Meaux J||The selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits of immunity, which arbitrates the evolutio...||Adaptation, Evolutionary Ecology, Expression Studies, Life History, Phenotypic Plasticity, Quantitative Genetics, Species interactions||Xavier Picó||Sophie Karrenberg, Rafa Rubio de Casas, Xavier Picó||2017-06-21 10:57:14||View|
12 Jul 2017
Despite reproductive interference, the net outcome of reproductive interactions among spider mite species is not necessarily costlySalomé H. Clemente, Inês Santos, Rita Ponce, Leonor R. Rodrigues, Susana A. M. Varela and Sara Magalhães 10.1101/113274
The pros and cons of mating with strangersRecommended by Vincent Calcagno based on reviews by Joël Meunier and Michael D Greenfield
Interspecific matings are by definition rare events in nature, but when they occur they can be very important, and not only because they might condition gene flow between species. Even when such matings have no genetic consequence, for instance if they do not yield any fertile hybrid offspring, they can still have an impact on the population dynamics of the species involved . Such atypical pairings between heterospecific partners are usually regarded as detrimental or undesired; as they interfere with the occurrence or success of intraspecific matings, they are expected to cause a decline in absolute fitness.
 Gröning J. & Hochkirch A. 2008. Reproductive interference between animal species. The Quarterly Review of Biology 83: 257-282. doi: 10.1086/590510
 Clemente SH, Santos I, Ponce AR, Rodrigues LR, Varela SAM & Magalhaes S. 2017 Despite reproductive interference, the net outcome of reproductive interactions among spider mite species is not necessarily costly. bioRxiv 113274, ver. 4 of the 30th of June 2017. doi: 10.1101/113274
|Despite reproductive interference, the net outcome of reproductive interactions among spider mite species is not necessarily costly||Salomé H. Clemente, Inês Santos, Rita Ponce, Leonor R. Rodrigues, Susana A. M. Varela and Sara Magalhães||Reproductive interference is considered a strong ecological force, potentially leading to species exclusion. This supposes that the net effect of reproductive interactions is strongly negative for one of the species involved. Testing this requires...||Behavior & Social Evolution, Evolutionary Ecology, Species interactions||Vincent Calcagno||2017-03-06 11:48:08||View|
07 Jul 2017
Negative frequency-dependent selection is frequently confoundingDustin Brisson 10.1101/113324
Unmasking the delusive appearance of negative frequency-dependent selectionRecommended by Ignacio Bravo based on reviews by David Baltrus and 2 anonymous reviewers
Explaining the processes that maintain polymorphisms in a population has been a fundamental line of research in evolutionary biology. One of the main mechanisms identified that preserves genetic diversity is negative frequency-dependent selection (NFDS), which constitutes a powerful framework for interpreting the presence of persistent polymorphisms. Nevertheless, a number of patterns that are often explained by invoking NFDS may also be compatible with, and possibly more easily explained by, different processes.
 Brisson D. 2017. Negative frequency-dependent selection is frequently confounding. bioRxiv 113324, ver. 3 of 20th June 2017. doi: 10.1101/113324
 Heino M, Metz JAJ and Kaitala V. 1998. The enigma of frequency-dependent selection. Trends in Ecology & Evolution 13: 367-370. doi: 1016/S0169-5347(98)01380-9
|Negative frequency-dependent selection is frequently confounding||Dustin Brisson||The existence of persistent genetic variation within natural populations presents an evolutionary problem as natural selection and genetic drift tend to erode genetic diversity. Models of balancing selection were developed to account for the high ...||Evolutionary Applications, Evolutionary Theory, Population Genetics / Genomics||Ignacio Bravo||2017-03-03 18:46:42||View|
12 Jun 2017
Evolution and manipulation of vector host choiceSylvain Gandon 10.1101/110577
Modelling the evolution of how vector-borne parasites manipulate the vector's host choiceRecommended by Samuel Alizon based on reviews by Samuel Alizon and Nicole Mideo
Many parasites can manipulate their hosts, thus increasing their transmission to new hosts . This is particularly the case for vector-borne parasites, which can alter the feeding behaviour of their hosts. However, predicting the optimal strategy is not straightforward because three actors are involved and the interests of the parasite may conflict with that of the vector. There are few models that consider the evolution of host manipulation by parasites [but see 2-4], but there are virtually none that investigated how parasites can manipulate the host choice of vectors. Even on the empirical side, many aspects of this choice remain unknown. Gandon  develops a simple evolutionary epidemiology model that allows him to formulate clear and testable predictions. These depend on which actor controls the trait (the vector or the parasite) and, when there is manipulation, whether it is realised via infected hosts (to attract vectors) or infected vectors (to change host choice). In addition to clarifying the big picture, Gandon  identifies some nice properties of the model, for instance an independence of the density/frequency-dependent transmission assumption or a backward bifurcation at R0=1, which suggests that parasites could persist even if their R0 is driven below unity. Overall, this study calls for further investigation of the different scenarios with more detailed models and experimental validation of general predictions.
 Hughes D, Brodeur J, Thomas F. 2012. Host manipulation by parasites. Oxford University Press.
 Brown SP. 1999. Cooperation and conflict in host-manipulating parasites. Proceedings of the Royal Society of London B: Biological Sciences 266: 1899–1904. doi: 10.1098/rspb.1999.0864
 Lion S, van Baalen M, Wilson WG. 2006. The evolution of parasite manipulation of host dispersal. Proceedings of the Royal Society of London B: Biological Sciences. 273: 1063–1071. doi: 10.1098/rspb.2005.3412
 Vickery WL, Poulin R. 2010. The evolution of host manipulation by parasites: a game theory analysis. Evolutionary Ecology 24: 773–788. doi: 10.1007/s10682-009-9334-0
 Gandon S. 2017. Evolution and manipulation of vector host choice. bioRxiv 110577, ver. 3 of 7th June 2017. doi: 10.1101/110577
|Evolution and manipulation of vector host choice||Sylvain Gandon||The transmission of many animal and plant diseases relies on the behavior of arthropod vectors. In particular, the choice to feed on either infected or uninfected hosts can dramatically affect the epidemiology of vector-borne diseases. I develop a...||Evolutionary Ecology, Evolutionary Epidemiology, Evolutionary Theory||Samuel Alizon||2017-03-03 19:18:54||View|
Michael David Pirie
Alejandro Gonzalez Voyer