Nature, Science, PNAS, Cell, PLoS Biology, eLife, Current Biology, Evolution, Genetics Evolution of the new head by gradual acquisition of neural crest regulatory circuits Megan L. Martik, Shashank Gandhi, Benjamin R. Uy, J. Andrew Gillis, Stephen A. Green, Marcos Simoes-Costa & Marianne E. Bronner Nature volume 574, pages675–678(2019)Cite this article https://www.nature.com/articles/s41586-019-1691-4 The neural crest, an embryonic stem-cell population, is a vertebrate innovation that has been proposed to be a key component of the ‘new head’, which imbued vertebrates with predatory behaviour1,2. Here, to investigate how the evolution of neural crest cells affected the vertebrate body plan, we examined the molecular circuits that control neural crest development along the anteroposterior axis of a jawless vertebrate, the sea lamprey. Gene expression analysis showed that the cranial subpopulation of the neural crest of the lamprey lacks most components of a transcriptional circuit that is specific to the cranial neural crest in amniotes and confers the ability to form craniofacial cartilage onto non-cranial neural crest subpopulations3. Consistent with this, hierarchical clustering analysis revealed that the transcriptional profile of the lamprey cranial neural crest is more similar to the trunk neural crest of amniotes. Notably, analysis of the cranial neural crest in little skate and zebrafish embryos demonstrated that the transcriptional circuit that is specific to the cranial neural crest emerged via the gradual addition of network components to the neural crest of gnathostomes, which subsequently became restricted to the cephalic region. Our results indicate that the ancestral neural crest at the base of the vertebrate lineage possessed a trunk-like identity. We propose that the emergence of the cranial neural crest, by progressive assembly of an axial-specific regulatory circuit, allowed the elaboration of the new head during vertebrate evolution. Genome editing retraces the evolution of toxin resistance in the monarch butterfly Marianthi Karageorgi, Simon C. Groen, Fidan Sumbul, Julianne N. Pelaez, Kirsten I. Verster, Jessica M. Aguilar, Amy P. Hastings, Susan L. Bernstein, Teruyuki Matsunaga, Michael Astourian, Geno Guerra, Felix Rico, Susanne Dobler, Anurag A. Agrawal & Noah K. Whiteman Nature volume 574, pages409–412(2019)Cite this article https://www.nature.com/articles/s41586-019-1610-8 Identifying the genetic mechanisms of adaptation requires the elucidation of links between the evolution of DNA sequence, phenotype, and fitness1. Convergent evolution can be used as a guide to identify candidate mutations that underlie adaptive traits2,3,4, and new genome editing technology is facilitating functional validation of these mutations in whole organisms1,5. We combined these approaches to study a classic case of convergence in insects from six orders, including the monarch butterfly (Danaus plexippus), that have independently evolved to colonize plants that produce cardiac glycoside toxins6,7,8,9,10,11. Many of these insects evolved parallel amino acid substitutions in the α-subunit (ATPα) of the sodium pump (Na+/K+-ATPase)7,8,9,10,11, the physiological target of cardiac glycosides12. Here we describe mutational paths involving three repeatedly changing amino acid sites (111, 119 and 122) in ATPα that are associated with cardiac glycoside specialization13,14. We then performed CRISPR–Cas9 base editing on the native Atpα gene in Drosophila melanogaster flies and retraced the mutational path taken across the monarch lineage11,15. We show in vivo, in vitro and in silico that the path conferred resistance and target-site insensitivity to cardiac glycosides16, culminating in triple mutant ‘monarch flies’ that were as insensitive to cardiac glycosides as monarch butterflies. ‘Monarch flies’ retained small amounts of cardiac glycosides through metamorphosis, a trait that has been optimized in monarch butterflies to deter predators17,18,19. The order in which the substitutions evolved was explained by amelioration of antagonistic pleiotropy through epistasis13,14,20,21,22. Our study illuminates how the monarch butterfly evolved resistance to a class of plant toxins, eventually becoming unpalatable, and changing the nature of species interactions within ecological communities2,6,7,8,9,10,11,15,17,18,19. Coordination between stochastic and deterministic specification in the Drosophila visual system Maximilien Courgeon, Claude Desplan* Science 18 Oct 2019: Vol. 366, Issue 6463, eaay6727 DOI: 10.1126/science.aay6727 Structured Abstract INTRODUCTION Neuronal fate decisions must be coordinated across brain regions so that the proper stoichiometry of distinct afferents and their target neurons is established. Many sensory systems rely on stochastic fate specification to increase their repertoire of neuronal types and/or to establish the mosaic of distinct sensory receptors. Once these stochastic fate decisions have been made at the periphery, they must be conveyed to processing centers in the brain to ensure that the correct information is retained. This in turn requires that the proper number of target neurons of the proper type are generated and are connected to their cognate sensory receptors. How these stochastically determined sensory systems transmit their decision to their targets in the brain—as when red (L) and green (M) cone photoreceptors connect to their appropriate bipolar cells in the human retina, or when randomly specified olfactory receptors project to their correct glomeruli in the mouse olfactory bulb—has remained unknown. RATIONALE In the Drosophila retina, different types of color-sensitive R7 photoreceptors with different ultraviolet spectral sensitivities are stochastically specified and distributed. By contrast, neurogenesis of the optic lobes that receive input from photoreceptors is highly deterministic: A fixed number of neuroblasts produces sequentially the same types of neurons following a rigid temporal program as well as a spatial program of determination. We asked how the stochastic choices made in the retina are propagated to the optic lobes—that is, how stochastically specified photoreceptors project and connect to their neuronal targets that are generated through a highly deterministic program. RESULTS We identified distinct subtypes of the main postsynaptic target of the ultraviolet-sensitive R7 photoreceptors, the Dm8 neurons. Each Dm8 subtype is specific to one of the three different subtypes of R7, and their organization in the optic lobe mirrors the topographic organization of R7s in the retina. The three subtypes of Dm8 are prespecified early in neurogenesis by distinct neural progenitors, independently from (and before) any photoreceptor input. These neurons are produced in excess, but only when the correct photoreceptor-Dm8 pairs form do Dm8s survive. This allows them to accommodate random variations in the production of the subtypes of R7s. Those Dm8s that do not find their correct R7 partner are culled by programmed cell death. We then showed that matching of one of the R7-Dm8 subtypes is mediated by two complementary cell adhesion molecules: Dpr11 in one of the subtypes of R7, and its cognate receptor DIPγ in the corresponding subclass of Dm8. Loss of either molecule leads to the death of that Dm8 subtype or its mispairing with the wrong R7 subtype; these phenotypes are similar to the loss of the corresponding subtype of R7 photoreceptors. These mechanisms allow the qualitative and quantitative matching of R7 subtypes with their target in the brain, and thus permit the stochastic choice made in R7 to be propagated to the deterministically specified downstream circuit to support color vision. CONCLUSION Our data reveal two fundamental principles in circuit formation: (i) The neurotrophic theory suggests that neuronal survival depends on trophic factors provided by the targets. We show that apoptosis is also involved in the quantitative and qualitative matching of target neurons with their afferent sensory receptors, providing a direct link between correct synaptic partner choice and cell survival. (ii) As Sperry’s chemoaffinity theory proposed, we show that synaptic partner choice is controlled by two interacting cell adhesion molecules, which are part of two large families of interacting proteins. Rapid, large-volume, thermally controlled 3D printing using a mobile liquid interface David A. Walker1,2,*, James L. Hedrick2,3,*, Chad A. Mirkin1,2,3,† Science 18 Oct 2019: Vol. 366, Issue 6463, pp. 360-364 DOI: 10.1126/science.aax1562 We report a stereolithographic three-dimensional printing approach for polymeric components that uses a mobile liquid interface (a fluorinated oil) to reduce the adhesive forces between the interface and the printed object, thereby allowing for a continuous and rapid print process, regardless of polymeric precursor. The bed area is not size-restricted by thermal limitations because the flowing oil enables direct cooling across the entire print area. Continuous vertical print rates exceeding 430 millimeters per hour with a volumetric throughput of 100 liters per hour have been demonstrated, and proof-of-concept structures made from hard plastics, ceramic precursors, and elastomers have been printed. Global distribution of earthworm diversity Helen R. P. Phillips1,2,*, Carlos A. Guerra1,3, Marie L. C. Bartz4, Maria J. I. Briones5, George Brown6, Thomas W. Crowther7, Olga Ferlian1,2, Konstantin B. Gongalsky8,9, Johan van den Hoogen7, Julia Krebs1,2, Alberto Orgiazzi10, Devin Routh7, Benjamin Schwarz11, Elizabeth M. Bach12,13, Joanne Bennett1,3, Ulrich Brose1,14, Thibaud Decaëns15, Birgitta König-Ries1,16, Michel Loreau17, Jérôme Mathieu18, Christian Mulder19, Wim H. van der Putten20,21, Kelly S. Ramirez20, Matthias C. Rillig22,23, David Russell24, Michiel Rutgers25, Madhav P. Thakur20, Franciska T. de Vries26, Diana H. Wall12,13, David A. Wardle27, Miwa Arai28, Fredrick O. Ayuke29, Geoff H. Baker30, Robin Beauséjour31, José C. Bedano32, Klaus Birkhofer33, Eric Blanchart34, Bernd Blossey35, Thomas Bolger36,37, Robert L. Bradley31, Mac A. Callaham38, Yvan Capowiez39, Mark E. Caulfield40, Amy Choi41, Felicity V. Crotty42,43, Andrea Dávalos35,44, Darío J. Diaz Cosin45, Anahí Dominguez32, Andrés Esteban Duhour46, Nick van Eekeren47, Christoph Emmerling48, Liliana B. Falco49, Rosa Fernández50, Steven J. Fonte51, Carlos Fragoso52, André L. C. Franco12, Martine Fugère31, Abegail T. Fusilero53,54, Shaieste Gholami55, Michael J. Gundale56, Mónica Gutiérrez López45, Davorka K. Hackenberger57, Luis M. Hernández58, Takuo Hishi59, Andrew R. Holdsworth60, Martin Holmstrup61, Kristine N. Hopfensperger62, Esperanza Huerta Lwanga63,64, Veikko Huhta65, Tunsisa T. Hurisso51,66, Basil V. Iannone III67, Madalina Iordache68, Monika Joschko69, Nobuhiro Kaneko70, Radoslava Kanianska71, Aidan M. Keith72, Courtland A. Kelly51, Maria L. Kernecker73, Jonatan Klaminder74, Armand W. Koné75, Yahya Kooch76, Sanna T. Kukkonen77, H. Lalthanzara78, Daniel R. Lammel23,79, Iurii M. Lebedev8,9, Yiqing Li80, Juan B. Jesus Lidon45, Noa K. Lincoln81, Scott R. Loss82, Raphael Marichal83, Radim Matula84, Jan Hendrik Moos85,86, Gerardo Moreno87, Alejandro Morón-Ríos88, Bart Muys89, Johan Neirynck90, Lindsey Norgrove91, Marta Novo45, Visa Nuutinen92, Victoria Nuzzo93, Mujeeb Rahman P94, Johan Pansu95,96, Shishir Paudel82, Guénola Pérès97, Lorenzo Pérez-Camacho98, Raúl Piñeiro99, Jean-François Ponge100, Muhammad Imtiaz Rashid101,102, Salvador Rebollo98, Javier Rodeiro-Iglesias103, Miguel Á. Rodríguez104, Alexander M. Roth105,106, Guillaume X. Rousseau58,107, Anna Rozen108, Ehsan Sayad55, Loes van Schaik109, Bryant C. Scharenbroch110, Michael Schirrmann111, Olaf Schmidt37,112, Boris Schröder22,113, Julia Seeber114,115, Maxim P. Shashkov116,117, Jaswinder Singh118, Sandy M. Smith119, Michael Steinwandter115, José A. Talavera120, Dolores Trigo45, Jiro Tsukamoto121, Anne W. de Valença122, Steven J. Vanek51, Iñigo Virto123, Adrian A. Wackett124, Matthew W. Warren125, Nathaniel H. Wehr126, Joann K. Whalen127, Michael B. Wironen128, Volkmar Wolters129, Irina V. Zenkova130, Weixin Zhang131, Erin K. Cameron132,133,†, Nico Eisenhauer1,2,† Science 25 Oct 2019: Vol. 366, Issue 6464, pp. 480-485 DOI: 10.1126/science.aax4851 Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide. Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster View ORCID ProfileSeth M. Rudman, Sharon Greenblum, Rachel C. Hughes, Subhash Rajpurohit, Ozan Kiratli, Dallin B. Lowder, Skyler G. Lemmon, Dmitri A. Petrov, View ORCID ProfileJohn M. Chaston, and Paul Schmidt PNAS October 1, 2019 116 (40) 20025-20032; first published September 16, 2019 https://doi.org/10.1073/pnas.1907787116 Edited by Harmit S. Malik, Fred Hutchinson Cancer Research Center, Seattle, WA, and approved August 21, 2019 (received for review May 5, 2019) Population genomic data has revealed patterns of genetic variation associated with adaptation in many taxa. Yet understanding the adaptive process that drives such patterns is challenging; it requires disentangling the ecological agents of selection, determining the relevant timescales over which evolution occurs, and elucidating the genetic architecture of adaptation. Doing so for the adaptation of hosts to their microbiome is of particular interest with growing recognition of the importance and complexity of host–microbe interactions. Here, we track the pace and genomic architecture of adaptation to an experimental microbiome manipulation in replicate populations of Drosophila melanogaster in field mesocosms. Shifts in microbiome composition altered population dynamics and led to divergence between treatments in allele frequencies, with regions showing strong divergence found on all chromosomes. Moreover, at divergent loci previously associated with adaptation across natural populations, we found that the more common allele in fly populations experimentally enriched for a certain microbial group was also more common in natural populations with high relative abundance of that microbial group. These results suggest that microbiomes may be an agent of selection that shapes the pattern and process of adaptation and, more broadly, that variation in a single ecological factor within a complex environment can drive rapid, polygenic adaptation over short timescales. Molecular control limiting sensitivity of sweet taste neurons in Drosophila Hsueh-Ling Chen, Ulrich Stern, and Chung-Hui Yang PNAS October 1, 2019 116 (40) 20158-20168; first published September 16, 2019 https://doi.org/10.1073/pnas.1911583116 Edited by L. B. Vosshall, The Rockefeller University, New York, NY, and approved August 22, 2019 (received for review July 9, 2019) To assess the biological value of environmental stimuli, animals’ sensory systems must accurately decode both the identities and the intensities of these stimuli. While much is known about the mechanism by which sensory neurons detect the identities of stimuli, less is known about the mechanism that controls how sensory neurons respond appropriately to different intensities of stimuli. The ionotropic receptor IR76b has been shown to be expressed in different Drosophila chemosensory neurons for sensing a variety of chemicals. Here, we show that IR76b plays an unexpected role in lowering the sensitivity of Drosophila sweet taste neurons. First, IR76b mutants exhibited clear behavioral responses to sucrose and acetic acid (AA) at concentrations that were too low to trigger observable behavioral responses from WT animals. Second, IR76b is expressed in many sweet neurons on the labellum, and these neurons responded to both sucrose and AA. Removing IR76b from the sweet neurons increased their neuronal responses as well as animals’ behavioral responses to sucrose and AA. Conversely, overexpressing IR76b in the sweet neurons decreased their neuronal as well as animals’ behavioral responses to sucrose and AA. Last, IR76b’s response-lowering ability has specificity: IR76b mutants and WT showed comparable responses to capsaicin when the mammalian capsaicin receptor VR1 was ectopically expressed in their sweet neurons. Our findings suggest that sensitivity of Drosophila sweet neurons to their endogenous ligands is actively limited by IR76b and uncover a potential molecular target by which contexts can modulate sensitivity of sweet neurons. QnAs QnAs with Günter P. Wagner Sandeep Ravindran PNAS October 8, 2019 116 (41) 20250-20251; first published September 30, 2019 https://doi.org/10.1073/pnas.1914920116 Günter P. Wagner works at the interface of population genetics and evolutionary developmental biology, and has made several key contributions to both fields. A professor of ecology and evolutionary biology at Yale University, Wagner was elected to the National Academy of Sciences in 2018. Wagner focuses on the evolution of complex organisms and traits, providing a mechanistic understanding of the concept of evolutionary homology. Wagner and his colleagues recently suggested an evolutionary link between the human female orgasm and copulation-induced ovulation in other mammals. In his Inaugural Article, Wagner describes an experimental test of this ovulatory homolog model of female orgasm (1). Crystal growth kinetics as an architectural constraint on the evolution of molluscan shells Vanessa Schoeppler, Robert Lemanis, Elke Reich, Tamás Pusztai, László Gránásy, and View ORCID ProfileIgor Zlotnikov PNAS October 8, 2019 116 (41) 20388-20397; first published September 24, 2019 https://doi.org/10.1073/pnas.1907229116 Molluscan shells are a classic model system to study formation–structure–function relationships in biological materials and the process of biomineralized tissue morphogenesis. Typically, each shell consists of a number of highly mineralized ultrastructures, each characterized by a specific 3D mineral–organic architecture. Surprisingly, in some cases, despite the lack of a mutual biochemical toolkit for biomineralization or evidence of homology, shells from different independently evolved species contain similar ultrastructural motifs. In the present study, using a recently developed physical framework, which is based on an analogy to the process of directional solidification and simulated by phase-field modeling, we compare the process of ultrastructural morphogenesis of shells from 3 major molluscan classes: A bivalve Unio pictorum, a cephalopod Nautilus pompilius, and a gastropod Haliotis asinina. We demonstrate that the fabrication of these tissues is guided by the organisms by regulating the chemical and physical boundary conditions that control the growth kinetics of the mineral phase. This biomineralization concept is postulated to act as an architectural constraint on the evolution of molluscan shells by defining a morphospace of possible shell ultrastructures that is bounded by the thermodynamics and kinetics of crystal growth. Dronc-independent basal executioner caspase activity sustains Drosophila imaginal tissue growth Natsuki Shinoda, Nozomi Hanawa, View ORCID ProfileTakahiro Chihara, Akiko Koto, and Masayuki Miura PNAS October 8, 2019 116 (41) 20539-20544; first published September 23, 2019 https://doi.org/10.1073/pnas.1904647116 Edited by Junying Yuan, Harvard Medical School, Boston, MA, and approved September 4, 2019 (received for review March 18, 2019) Caspase is best known as an enzyme involved in programmed cell death, which is conserved among multicellular organisms. In addition to its role in cell death, caspase is emerging as an indispensable enzyme in a wide range of cellular functions, which have recently been termed caspase-dependent nonlethal cellular processes (CDPs). In this study, we examined the involvement of cell death signaling in tissue-size determination using Drosophila wing as a model. We found that the Drosophila executioner caspases Dcp-1 and Decay, but not Drice, promoted wing growth independently of apoptosis. Most of the reports on CDPs argue the importance of the spatiotemporal regulation of the initiator caspase, Dronc; however, this sublethal caspase function was independent of Dronc, suggesting a more diverse array of CDP regulatory mechanisms. Tagging of TurboID, an improved promiscuous biotin ligase that biotinylates neighboring proteins, to the C terminus of caspases revealed the differences among the neighbors of executioner caspases. Furthermore, we found that the cleavage of Acinus, a substrate of the executioner caspase, was important in promoting wing growth. These results demonstrate the importance of executioner caspase-mediated basal proteolytic cleavage of substrates in sustaining tissue growth. Given the existence of caspase-like DEVDase activity in a unicellular alga, our results likely highlight the original function of caspase—not cell death, but basal proteolytic cleavages for cell vigor. A marine plasmid hitchhiking vast phylogenetic and geographic distances Jörn Petersen, John Vollmers, Victoria Ringel, Henner Brinkmann, Claire Ellebrandt-Sperling, Cathrin Spröer, Alexandra M. Howat, J. Colin Murrell, and View ORCID ProfileAnne-Kristin Kaster PNAS October 8, 2019 116 (41) 20568-20573; first published September 23, 2019 https://doi.org/10.1073/pnas.1905878116 Edited by Nils Chr. Stenseth, University of Oslo, Oslo, Norway, and approved September 3, 2019 (received for review April 9, 2019) Horizontal gene transfer (HGT) plays an important role in bacterial evolution and serves as a driving force for bacterial diversity and versatility. HGT events often involve mobile genetic elements like plasmids, which can promote their own dissemination by associating with adaptive traits in the gene pool of the so-called mobilome. Novel traits that evolve through HGT can therefore lead to the exploitation of new ecological niches, prompting an adaptive radiation of bacterial species. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized RepL-type plasmid found in diverse members of the marine Roseobacter group across the globe. Noteworthy, 100% identical plasmids were detected in phylogenetically and geographically distant bacteria, revealing a so-far overlooked, but environmentally highly relevant vector for HGT. The genomic and functional characterization of this plasmid showed a completely conserved backbone dedicated to replication, stability, and mobilization as well as an interchangeable gene cassette with highly diverse, but recurring motifs. The majority of the latter appear to be involved in mechanisms coping with toxins and/or pollutants in the marine environment. Furthermore, we provide experimental evidence that the plasmid has the potential to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment. An experimental test of the ovulatory homolog model of female orgasm Mihaela Pavlicev, Andreja Moset Zupan, Amanda Barry, Savannah Walters, Kristin M. Milano, View ORCID ProfileHarvey J. Kliman, and View ORCID ProfileGünter P. Wagner PNAS October 8, 2019 116 (41) 20267-20273; first published September 30, 2019 https://doi.org/10.1073/pnas.1910295116 Contributed by Günter P. Wagner, August 22, 2019 (sent for review June 17, 2019; reviewed by Martin J. Cohn and Scott F. Gilbert) The ovulatory homolog model of female orgasm posits that the neuro-endocrine mechanisms underlying female orgasm evolved from and are homologous to the mechanisms mediating copulation-induced ovulation in some mammals. This model predicts that pharmacological agents that affect human orgasm, such as fluoxetine, should also affect ovulation in animals with copulation-induced ovulation, such as rabbits. We tested this prediction by treating rabbits with daily doses of fluoxetine for 2 wk and found that fluoxetine treatment reduces the number of ovulations postcopulation by 30%. In a second experiment we tested whether this result was mediated by an effect on the brain or via peripheral serotonin functions. We treated animals with fluoxetine and induced ovulation with a single injection of human chorionic gonadotropin. In this experiment ovulation rate was nominally reduced by only 8%, which is statistically not significant. We conclude that the effect of fluoxetine on copulation-induced ovulation rate supports the ovulatory homolog model of female orgasm, suggesting that female orgasm has very deep evolutionary roots among the early eutherian mammals. Reviving rare chicken breeds using genetically engineered sterility in surrogate host birds Mark E. Woodcock, Almas A. Gheyas, Andrew S. Mason, Sunil Nandi, Lorna Taylor, Adrian Sherman, Jacqueline Smith, Dave W. Burt, Rachel Hawken, and View ORCID ProfileMichael J. McGrew PNAS October 15, 2019 116 (42) 20930-20937; first published October 1, 2019 https://doi.org/10.1073/pnas.1906316116 Edited by Martin M. Matzuk, Baylor College of Medicine, Houston, TX, and approved September 6, 2019 (received for review April 15, 2019) In macrolecithal species, cryopreservation of the oocyte and zygote is not possible due to the large size and quantity of lipid deposited within the egg. For birds, this signifies that cryopreserving and regenerating a species from frozen cellular material are currently technically unfeasible. Diploid primordial germ cells (PGCs) are a potential means to freeze down the entire genome and reconstitute an avian species from frozen material. Here, we examine the use of genetically engineered (GE) sterile female layer chicken as surrogate hosts for the transplantation of cryopreserved avian PGCs from rare heritage breeds of chicken. We first amplified PGC numbers in culture before cryopreservation and subsequent transplantation into host GE embryos. We found that all hatched offspring from the chimera GE hens were derived from the donor rare heritage breed broiler PGCs, and using cryopreserved semen, we were able to produce pure offspring. Measurement of the mutation rate of PGCs in culture revealed that 2.7 × 10−10 de novo single-nucleotide variants (SNVs) were generated per cell division, which is comparable with other stem cell lineages. We also found that endogenous avian leukosis virus (ALV) retroviral insertions were not mobilized during in vitro propagation. Taken together, these results show that mutation rates are no higher than normal stem cells, essential if we are to conserve avian breeds. Thus, GE sterile avian surrogate hosts provide a viable platform to conserve and regenerate avian species using cryopreserved PGCs. Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae Andrea Hodgins-Davis, Fabien Duveau, Elizabeth A. Walker, and View ORCID ProfilePatricia J. Wittkopp PNAS October 15, 2019 116 (42) 21085-21093; first published September 30, 2019 https://doi.org/10.1073/pnas.1902823116 Edited by Michael Lynch, Arizona State University, Tempe, AZ, and approved September 4, 2019 (received for review February 16, 2019) Understanding how phenotypes evolve requires disentangling the effects of mutation generating new variation from the effects of selection filtering it. Tests for selection frequently assume that mutation introduces phenotypic variation symmetrically around the population mean, yet few studies have tested this assumption by deeply sampling the distributions of mutational effects for particular traits. Here, we examine distributions of mutational effects for gene expression in the budding yeast Saccharomyces cerevisiae by measuring the effects of thousands of point mutations introduced randomly throughout the genome. We find that the distributions of mutational effects differ for the 10 genes surveyed and are inconsistent with normality. For example, all 10 distributions of mutational effects included more mutations with large effects than expected for normally distributed phenotypes. In addition, some genes also showed asymmetries in their distribution of mutational effects, with new mutations more likely to increase than decrease the gene’s expression or vice versa. Neutral models of regulatory evolution that take these empirically determined distributions into account suggest that neutral processes may explain more expression variation within natural populations than currently appreciated. Genetic dissection of active forgetting in labile and consolidated memories in Drosophila Yang Gao, Yichun Shuai, Xuchen Zhang, Yuwei Peng, Lianzhang Wang, Jing He, Yi Zhong, and Qian Li PNAS October 15, 2019 116 (42) 21191-21197; first published September 5, 2019 https://doi.org/10.1073/pnas.1903763116 Edited by Ralph J. Greenspan, University of California San Diego, La Jolla, CA, and accepted by Editorial Board Member Yuh Nung Jan August 9, 2019 (received for review March 4, 2019) Different memory components are forgotten through distinct molecular mechanisms. In Drosophila, the activation of 2 Rho GTPases (Rac1 and Cdc42), respectively, underlies the forgetting of an early labile memory (anesthesia-sensitive memory, ASM) and a form of consolidated memory (anesthesia-resistant memory, ARM). Here, we dissected the molecular mechanisms that tie Rac1 and Cdc42 to the different types of memory forgetting. We found that 2 WASP family proteins, SCAR/WAVE and WASp, act downstream of Rac1 and Cdc42 separately to regulate ASM and ARM forgetting in mushroom body neurons. Arp2/3 complex, which organizes branched actin polymerization, is a canonical downstream effector of WASP family proteins. However, we found that Arp2/3 complex is required in Cdc42/WASp-mediated ARM forgetting but not in Rac1/SCAR-mediated ASM forgetting. Instead, we identified that Rac1/SCAR may function with formin Diaphanous (Dia), a nucleator that facilitates linear actin polymerization, in ASM forgetting. The present study, complementing the previously identified Rac1/cofilin pathway that regulates actin depolymerization, suggests that Rho GTPases regulate forgetting by recruiting both actin polymerization and depolymerization pathways. Moreover, Rac1 and Cdc42 may regulate different types of memory forgetting by tapping into different actin polymerization mechanisms. Fitness effects but no temperature-mediated balancing selection at the polymorphic Adh gene of Drosophila melanogaster Mohammad A. Siddiq and Joseph W. Thornton PNAS October 22, 2019 116 (43) 21634-21640; first published October 8, 2019 https://doi.org/10.1073/pnas.1909216116 Edited by Detlef Weigel, Max Planck Institute for Developmental Biology, Tübingen, Germany, and approved September 17, 2019 (received for review May 29, 2019) Polymorphism in the alcohol dehydrogenase (ADH) protein of Drosophila melanogaster, like genetic variation in many other enzymes, has long been hypothesized to be maintained by a selective trade-off between thermostability and enzyme activity. Two major Adh variants, named Fast and Slow, are distributed along latitudinal clines on several continents. The balancing selection trade-off hypothesis posits that Fast is favored at high latitudes because it metabolizes alcohol faster, whereas Slow is favored at low latitudes because it is more stable at high temperatures. Here we use biochemical and physiological assays of precisely engineered genetic variants to directly test this hypothesis. As predicted, the Fast protein has higher catalytic activity than Slow, and both the Fast protein and regulatory variants linked to it confer greater ethanol tolerance on transgenic animals. But we found no evidence of a temperature-mediated trade-off: The Fast protein is not less stable or active at high temperatures, and Fast alleles increase ethanol tolerance and survivorship at all temperatures tested. Further, analysis of a population genomic dataset reveals no signature of balancing selection in the Adh gene. These results provide strong evidence against balancing selection driven by a stability/activity trade-off in Adh, and they justify caution about this hypothesis for other enzymes except those for which it has been directly tested. Our findings tentatively suggest that environment-specific selection for the Fast allele, coupled with demographic history, may have produced the observed pattern of Adh variation. Cellular defects resulting from disease-related myosin II mutations in Drosophila View ORCID ProfileKaren E. Kasza, Sara Supriyatno, and Jennifer A. Zallen PNAS October 29, 2019 116 (44) 22205-22211; first published October 15, 2019 https://doi.org/10.1073/pnas.1909227116 Edited by Elaine Fuchs, Rockefeller University, New York, NY, and approved September 22, 2019 (received for review May 31, 2019) The nonmuscle myosin II motor protein produces forces that are essential to driving the cell movements and cell shape changes that generate tissue structure. Mutations in myosin II that are associated with human diseases are predicted to disrupt critical aspects of myosin function, but the mechanisms that translate altered myosin activity into specific changes in tissue organization and physiology are not well understood. Here we use the Drosophila embryo to model human disease mutations that affect myosin motor activity. Using in vivo imaging and biophysical analysis, we show that engineering human MYH9-related disease mutations into Drosophila myosin II produces motors with altered organization and dynamics that fail to drive rapid cell movements, resulting in defects in epithelial morphogenesis. In embryos that express the Drosophila myosin motor variants R707C or N98K and have reduced levels of wild-type myosin, myosin motors are correctly planar polarized and generate anisotropic contractile tension in the tissue. However, expression of these motor variants is associated with a cellular-scale reduction in the speed of cell intercalation, resulting in a failure to promote full elongation of the body axis. In addition, these myosin motor variants display slowed turnover and aberrant aggregation at the cell cortex, indicating that mutations in the motor domain influence mesoscale properties of myosin organization and dynamics. These results demonstrate that disease-associated mutations in the myosin II motor domain disrupt specific aspects of myosin localization and activity during cell intercalation, linking molecular changes in myosin activity to defects in tissue morphogenesis. Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa Deepti Gurdasani 32 Tommy Carstensen 32 Segun Fatumo 32 Pontiano Kaleebu 33 Ines Barroso 33 Manj S. Sandhu 33, 34 Show all authors Show footnotes DOI:https://doi.org/10.1016/j.cell.2019.10.004 Genomic studies in African populations provide unique opportunities to understand disease etiology, human diversity, and population history. In the largest study of its kind, comprising genome-wide data from 6,400 individuals and whole-genome sequences from 1,978 individuals from rural Uganda, we find evidence of geographically correlated fine-scale population substructure. Historically, the ancestry of modern Ugandans was best represented by a mixture of ancient East African pastoralists. We demonstrate the value of the largest sequence panel from Africa to date as an imputation resource. Examining 34 cardiometabolic traits, we show systematic differences in trait heritability between European and African populations, probably reflecting the differential impact of genes and environment. In a multi-trait pan-African GWAS of up to 14,126 individuals, we identify novel loci associated with anthropometric, hematological, lipid, and glycemic traits. We find that several functionally important signals are driven by Africa-specific variants, highlighting the value of studying diverse populations across the region. Symmetry breaking in the embryonic skin triggers directional and sequential plumage patterning PLoS Biology https://doi.org/10.1371/journal.pbio.3000448 Richard Bailleul, Camille Curantz, Carole Desmarquet-Trin Dinh, Magdalena Hidalgo, Jonathan Touboul , Marie Manceau The development of an organism involves the formation of patterns from initially homogeneous surfaces in a reproducible manner. Simulations of various theoretical models recapitulate final states of natural patterns, yet drawing testable hypotheses from those often remains difficult. Consequently, little is known about pattern-forming events. Here, we surveyed plumage patterns and their emergence in Galliformes, ratites, passerines, and penguins, together representing the three major taxa of the avian phylogeny, and built a unified model that not only reproduces final patterns but also intrinsically generates shared and varying directionality, sequence, and duration of patterning. We used in vivo and ex vivo experiments to test its parameter-based predictions. We showed that directional and sequential pattern progression depends on a species-specific prepattern: an initial break in surface symmetry launches a travelling front of sharply defined, oriented domains with self-organising capacity. This front propagates through the timely transfer of increased cell density mediated by cell proliferation, which controls overall patterning duration. These results show that universal mechanisms combining prepatterning and self-organisation govern the timely emergence of the plumage pattern in birds. Mating induces switch from hormone-dependent to hormone-independent steroid receptor–mediated growth in Drosophila secondary cells PLoS Biology Aaron Leiblich , Josephine E. E. U. Hellberg , Aashika Sekar , Carina Gandy, Claudia C. Mendes, Siamak Redhai, John Mason, Mark Wainwright, Pauline Marie, Deborah C. I. Goberdhan, Freddie C. Hamdy, Clive Wilson Male reproductive glands like the mammalian prostate and the paired Drosophila melanogaster accessory glands secrete seminal fluid components that enhance fecundity. In humans, the prostate, stimulated by environmentally regulated endocrine and local androgens, grows throughout adult life. We previously showed that in fly accessory glands, secondary cells (SCs) and their nuclei also grow in adults, a process enhanced by mating and controlled by bone morphogenetic protein (BMP) signalling. Here, we demonstrate that BMP-mediated SC growth is dependent on the receptor for the developmental steroid ecdysone, whose concentration is reported to reflect sociosexual experience in adults. BMP signalling appears to regulate ecdysone receptor (EcR) levels via one or more mechanisms involving the EcR’s N terminus or the RNA sequence that encodes it. Nuclear growth in virgin males is dependent on ecdysone, some of which is synthesised in SCs. However, mating induces additional BMP-mediated nuclear growth via a cell type–specific form of hormone-independent EcR signalling, which drives genome endoreplication in a subset of adult SCs. Switching to hormone-independent endoreplication after mating allows growth and secretion to be hyperactivated independently of ecdysone levels in SCs, permitting more rapid replenishment of the accessory gland luminal contents. Our data suggest mechanistic parallels between this physiological, behaviour-induced signalling switch and altered pathological signalling associated with prostate cancer progression. Dynamic turnover of centromeres drives karyotype evolution in Drosophila Ryan Bracewell, Kamalakar Chatla, Matthew J Nalley, Doris Bachtrog Is a corresponding author University of California, Berkeley, United States eLife Centromeres are the basic unit for chromosome inheritance, but their evolutionary dynamics is poorly understood. We generate high-quality reference genomes for multiple Drosophila obscura group species to reconstruct karyotype evolution. All chromosomes in this lineage were ancestrally telocentric and the creation of metacentric chromosomes in some species was driven by de novo seeding of new centromeres at ancestrally gene-rich regions, independently of chromosomal rearrangements. The emergence of centromeres resulted in a drastic size increase due to repeat accumulation, and dozens of genes previously located in euchromatin are now embedded in pericentromeric heterochromatin. Metacentric chromosomes secondarily became telocentric in the pseudoobscura subgroup through centromere repositioning and a pericentric inversion. The former (peri)centric sequences left behind shrunk dramatically in size after their inactivation, yet contain remnants of their evolutionary past, including increased repeat-content and heterochromatic environment. Centromere movements are accompanied by rapid turnover of the major satellite DNA detected in (peri)centromeric regions. https://doi.org/10.7554/eLife.49002.001 The yellow gene influences Drosophila male mating success through sex comb melanization Cite as: eLife 2019;8:e49388 doi: 10.7554/eLife.49388 Jonathan H Massey, Daayun Chung, Igor Siwanowicz, David L Stern Is a corresponding author , Patricia J Wittkopp Is a corresponding author University of Michigan, United States; Janelia Research Campus, Howard Hughes Medical Institute, United States eLife Drosophila melanogaster males perform a series of courtship behaviors that, when successful, result in copulation with a female. For over a century, mutations in the yellow gene, named for its effects on pigmentation, have been known to reduce male mating success. Prior work has suggested that yellow influences mating behavior through effects on wing extension, song, and/or courtship vigor. Here, we rule out these explanations, as well as effects on the nervous system more generally, and find instead that the effects of yellow on male mating success are mediated by its effects on pigmentation of male-specific leg structures called sex combs. Loss of yellow expression in these modified bristles reduces their melanization, which changes their structure and causes difficulty grasping females prior to copulation. These data illustrate why the mechanical properties of anatomy, not just neural circuitry, must be considered to fully understand the development and evolution of behavior. Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment Lydia J Baker Is a corresponding author , Lindsay L Freed, Cole G Easson, Jose V Lopez, Danté Fenolio, Tracey T Sutton, Spencer V Nyholm, Tory A Hendry Is a corresponding author Cornell University, United States; Nova Southeastern University, United States; Middle Tennessee State University, United States; Center for Conservation and Research, San Antonio Zoo, United States; University of Connecticut, United States eLife 2019;8:e47606 doi: 10.7554/eLife.47606 Deep-sea anglerfishes are relatively abundant and diverse, but their luminescent bacterial symbionts remain enigmatic. The genomes of two symbiont species have qualities common to vertically transmitted, host-dependent bacteria. However, a number of traits suggest that these symbionts may be environmentally acquired. To determine how anglerfish symbionts are transmitted, we analyzed bacteria-host codivergence across six diverse anglerfish genera. Most of the anglerfish species surveyed shared a common species of symbiont. Only one other symbiont species was found, which had a specific relationship with one anglerfish species, Cryptopsaras couesii. Host and symbiont phylogenies lacked congruence, and there was no statistical support for codivergence broadly. We also recovered symbiont-specific gene sequences from water collected near hosts, suggesting environmental persistence of symbionts. Based on these results we conclude that diverse anglerfishes share symbionts that are acquired from the environment, and that these bacteria have undergone extreme genome reduction although they are not vertically transmitted. Natural Variation and Genetic Determinants of Caenorhabditis elegans Sperm Size View ORCID ProfileClotilde Gimond, Anne Vielle, View ORCID ProfileNuno Silva-Soares, Stefan Zdraljevic, Patrick T. McGrath, View ORCID ProfileErik C. Andersen and View ORCID ProfileChristian Braendle Genetics October 1, 2019 vol. 213 no. 2 615-632; https://doi.org/10.1534/genetics.119.302462 The diversity in sperm shape and size represents a powerful paradigm to understand how selection drives the evolutionary diversification of cell morphology. Experimental work on the sperm biology of the male-hermaphrodite nematode Caenorhabditis elegans has elucidated diverse factors important for sperm fertilization success, including the competitive superiority of larger sperm. Yet despite extensive research, the molecular mechanisms regulating C. elegans sperm size and the genetic basis underlying natural variation in sperm size remain unknown. To address these questions, we quantified male sperm size variation of a worldwide panel of 97 genetically distinct C. elegans strains, allowing us to uncover significant genetic variation in male sperm size. Aiming to characterize the molecular genetic basis of C. elegans male sperm size variation using a genome-wide association study, we did not detect any significant quantitative trait loci. We therefore focused on the genetic analysis of pronounced sperm size differences observed between recently diverged laboratory strains (N2 vs. LSJ1/2). Using mutants and quantitative complementation tests, we demonstrate that variation in the gene nurf-1 underlies the evolution of small sperm in the LSJ lineage. Given the previous discovery that this same nurf-1 variation was central for hermaphrodite laboratory adaptation, the evolution of reduced male sperm size in LSJ strains likely reflects a pleiotropic consequence. Together, our results provide a comprehensive quantification of natural variation in C. elegans sperm size and first insights into the genetic determinants of Caenorhabditis sperm size, pointing at an involvement of the NURF chromatin remodeling complex. Planar cell polarity signaling in the development of left–right asymmetry Jeffrey D.Axelrod https://doi.org/10.1016/j.ceb.2019.09.002 Current Opinion in Cell Biology Volume 62, February 2020, Pages 61-69 The planar cell polarity (PCP) signaling pathway, principally understood from work in Drosophila, is now known to contribute to development in a broad swath of the animal kingdom, and its impairment leads to developmental malformations and diseases affecting humans. The ‘core’ mechanism underlying PCP signaling polarizes sheets of cells, aligning them in a head-to-tail fashion within the sheet. Cells use the resulting directional information to guide a wide variety of processes. One such process is lateralization, the determination of left–right asymmetry that guides the asymmetric morphology and placement of internal organs. Recent evidence extends the idea that PCP signaling underlies the earliest steps in lateralization and that PCP is invoked again during asymmetric morphogenesis of organs including the heart and gut. The Coding Loci of Evolution and Domestication: Current Knowledge and Implications for Bio-Inspired Genome Editing Virginie Courtier-Orgogozo 1 Arnaud Martin HAL One promising application of CRISPR/Cas9 is to create targeted mutations to introduce traits of interest into domesticated organisms. However, a major current limitation for crop and livestock improvement is to identify the precise genes and genetic changes that must be engineered to obtain traits of interest. Here we discuss the advantages of bio-inspired genome editing, i.e. the engineered introduction of natural mutations that have already been associated with traits of interest in other lineages (breeds, populations, or species). To get a landscape view of potential targets for genome editing, we used Gephebase (www.gephebase.org), a manually-curated database compiling published data about the genes responsible for evolutionary and domesticated changes across Eukaryotes, and examined the >1,200 mutations that have been identified in the coding regions of more than 700 genes in animals, plants and yeasts. We observe that our genetic knowledge is relatively important for certain traits, such as xenobiotic resistance, and poor for others. We also note that protein-null alleles, often due to nonsense and frameshift mutations, represent a large fraction of the known loci of domestication (42% of identified coding mutations), compared to intraspecific (27%) and interspecific evolution (11%). While this trend may be subject to detection, publication, and curation biases, it is consistent with the idea that breeders have selected large-effect mutations underlying adaptive traits in specific settings, but that these mutations and associated phenotypes would not survive the vagaries of changing external and internal environments. Our compilation of the loci of evolution and domestication uncovers interesting options for bio-inspired and transgene-free genome editing. A primary sexual trait involved in courtship in insects: Male genital lobe morphology affects the chance to copulate in Drosophila pachea Bénédicte M. Lefèvre, Diane Catté, Virginie Courtier-Orgogozo, Michael Lang doi: https://doi.org/10.1101/816538 Male genitalia are thought to ensure transfer of sperm through direct physical contact with female during copulation. Such primary sexual traits were also observed to affect pre-copulatory female mate-choice in some Vertebrates species, but whether this also occurs in insects is unknown. Males of the fruitfly Drosophila pachea have a pair of asymmetric external genital lobes, which are primary sexual structures and stabilize the copulatory complex of female and male genitalia. We tested for a pre-copulatory courtship role of these lobes with a D. pachea stock where males have variable lobe lengths. In 111 mate competition experiments with a single female and two males, females preferentially engaged into a first copulation with males that had a longer left lobe. Courtship durations increased with female age and when two males courted the female simultaneously, compared to experiments with only one courting male. In 54 additional experiments with both males having partially amputated left lobes, we observed a similar but weaker effect of left lobe length on copulation success. We conclude that left lobe length affects male mating success before genital contact. Our results suggest that primary male sexual traits in insects can serve as a signal for pre-copulatory mate-choice.