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Evolutionary Biology
The coevolutionary biology of brood parasitism: a call for integration.
Apr 12, 2019   Philosophical Transactions Of The Royal Society Of London. Series B, Biological Sciences
Thorogood R, Spottiswoode CN, Portugal SJ, Gloag R
The coevolutionary biology of brood parasitism: a call for integration.
Apr 12, 2019
Philosophical Transactions Of The Royal Society Of London. Series B, Biological Sciences
Obligate brood-parasitic cheats have fascinated natural historians since ancient times. Passing on the costs of parental care to others occurs widely in birds, insects and fish, and often exerts selection pressure on hosts that in turn evolve defences. Brood parasites have therefore provided an illuminating system for researching coevolution. Nevertheless, much remains unknown about how ecology and evolutionary history constrain or facilitate brood parasitism, or the mechanisms that shape or respond to selection. In this special issue, we bring together examples from across the animal kingdom to illustrate the diverse ways in which recent research is addressing these gaps. This special issue also considers how research on brood parasitism may benefit from, and in turn inform, related fields such as social evolution and immunity. Here, we argue that progress in our understanding of coevolution would benefit from the increased integration of ideas across taxonomic boundaries and across Tinbergen's Four Questions: mechanism, ontogeny, function and phylogeny of brood parasitism. We also encourage renewed vigour in uncovering the natural history of the majority of the world's brood parasites that remain little-known. Indeed, it seems very likely that some of nature's brood parasites remain entirely unknown, because otherwise we are left with a puzzle: if parental care is so costly, why is brood parasitism not more common? This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.
Global effects of non-native tree species on multiple ecosystem services.
Apr 11, 2019   Biological Reviews Of The Cambridge Philosophical Society
Castro-Díez P, Vaz AS, Silva JS, van Loo M, Alonso Á,   . . . . . .   , Vicente JR, Vilà M, Ylioja T, Zenni RD, Godoy O
Global effects of non-native tree species on multiple ecosystem services.
Apr 11, 2019
Biological Reviews Of The Cambridge Philosophical Society
Non-native tree (NNT) species have been transported worldwide to create or enhance services that are fundamental for human well-being, such as timber provision, erosion control or ornamental value; yet NNTs can also produce undesired effects, such as fire proneness or pollen allergenicity. Despite the variety of effects that NNTs have on multiple ecosystem services, a global quantitative assessment of their costs and benefits is still lacking. Such information is critical for decision-making, management and sustainable exploitation of NNTs. We present here a global assessment of NNT effects on the three main categories of ecosystem services, including regulating (RES), provisioning (PES) and cultural services (CES), and on an ecosystem disservice (EDS), i.e. pollen allergenicity. By searching the scientific literature, country forestry reports, and social media, we compiled a global data set of 1683 case studies from over 125 NNT species, covering 44 countries, all continents but Antarctica, and seven biomes. Using different meta-analysis techniques, we found that, while NNTs increase most RES (e.g. climate regulation, soil erosion control, fertility and formation), they decrease PES (e.g. NNTs contribute less than native trees to global timber provision). Also, they have different effects on CES (e.g. increase aesthetic values but decrease scientific interest), and no effect on the EDS considered. NNT effects on each ecosystem (dis)service showed a strong context dependency, varying across NNT types, biomes and socio-economic conditions. For instance, some RES are increased more by NNTs able to fix atmospheric nitrogen, and when the ecosystem is located in low-latitude biomes; some CES are increased more by NNTs in less-wealthy countries or in countries with higher gross domestic products. The effects of NNTs on several ecosystem (dis)services exhibited some synergies (e.g. among soil fertility, soil formation and climate regulation or between aesthetic values and pollen allergenicity), but also trade-offs (e.g. between fire regulation and soil erosion control). Our analyses provide a quantitative understanding of the complex synergies, trade-offs and context dependencies involved for the effects of NNTs that is essential for attaining a sustained provision of ecosystem services.
Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches.
Apr 13, 2019   Zoology (Jena, Germany)
Jaspers C, Fraune S, Arnold AE, Miller DJ, Bosch TCG, Voolstra CR, Consortium of Australian Academy of Science Boden Research Conference Participants
Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches.
Apr 13, 2019
Zoology (Jena, Germany)
Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e., microbial eukaryotes, archaea, bacteria, and viruses), the so-called metaorganism, as the biological entity. While recent research supports and encourages the adoption of such an integrative view, it must be understood that microorganisms are not involved in all host processes and not all associated microorganisms are functionally important. As such, our intention here is to provide a critical review and evaluation of perspectives and limitations relevant to studying organisms in a metaorganism framework and the functional toolbox available to do so. We note that marker gene-guided approaches that primarily characterize microbial diversity are a first step in delineating associated microbes but are not sufficient to establish proof of their functional relevance. More sophisticated tools and experiments are necessary to reveal the specific functions of associated microbes. This can be accomplished through the study of metaorganisms in less complex environments, the targeted manipulation of microbial associates, or work at the mechanistic level with the toolbox available in model systems. We conclude that the metaorganism framework is a powerful new concept to help provide answers to longstanding biological questions such as the evolution and ecology of organismal complexity and the importance of organismal symbioses to ecosystem functioning. The intricacy of the metaorganism requires a holistic framework combining reductionist and integrative approaches to resolve the structure and function of its member species and to disclose the various roles that microorganisms play in the biology of their hosts.
Accounting for ambiguity in ancestral sequence reconstruction.
Apr 12, 2019   Bioinformatics (Oxford, England)
Oliva A, Pulicani S, Lefort V, Bréhélin L, Gascuel O, Guindon S
Accounting for ambiguity in ancestral sequence reconstruction.
Apr 12, 2019
Bioinformatics (Oxford, England)
MOTIVATION: The reconstruction of ancestral genetic sequences from the analysis of contemporaneous data is a powerful tool to improve our understanding of molecular evolution. Various statistical criteria defined in a phylogenetic framework can be used to infer nucleotide, amino-acid or codon states at internal nodes of the tree, for every position along the sequence. These criteria generally select the state that maximizes (or minimizes) a given criterion. Although it is perfectly sensible from a statistical perspective, that strategy fails to convey useful information about the level of uncertainty associated to the inference. RESULTS: The present study introduces a new criterion for ancestral sequence reconstruction, the minimum posterior expected error (MPEE), that selects a single state whenever the signal conveyed by the data is strong, and a combination of multiple states otherwise. We also assess the performance of a criterion based on the Brier scoring scheme which, like MPEE, does not rely on any tuning parameters. The precision and accuracy of several other criteria that involve arbitrarily set tuning parameters are also evaluated. Large scale simulations demonstrate the benefits of using the MPEE and Brier-based criteria with a substantial increase in the accuracy of the inference of past sequences compared to the standard approach and realistic compromises on the precision of the solutions returned. AVAILABILITY: The software package PhyML (https://github.com/stephaneguindon/phyml) provides an implementation of the Maximum A Posteriori (MAP) and MPEE criteria for reconstructing ancestral nucleotide and amino-acid sequences.
Environmental heterogeneity can tip the population genetics of range expansions.
Apr 12, 2019   ELife
Gralka M, Hallatschek O
Environmental heterogeneity can tip the population genetics of range expansions.
Apr 12, 2019
ELife
The population genetics of most range expansions is thought to be shaped by the competition between Darwinian selection and random genetic drift at the range margins. Here, we show that the evolutionary dynamics during range expansions is highly sensitive to additional fluctuations induced by environmental heterogeneities. Tracking mutant clones with a tunable fitness effect in bacterial colonies grown on randomly patterned surfaces we found that environmental heterogeneity can dramatically reduce the efficacy of selection. Time-lapse microscopy and computer simulations suggest that this effect arises generically from a local 'pinning' of the expansion front, whereby stretches of the front are slowed down on a length scale that depends on the structure of the environmental heterogeneity. This pinning focuses the range expansion into a small number of 'lucky' individuals with access to expansion paths, altering the neutral evolutionary dynamics and increasing the importance of chance relative to selection.
Counties not countries: Variation in host specificity among populations of an aphid parasitoid.
Apr 14, 2019   Evolutionary Applications
Hopper KR, Oppenheim SJ, Kuhn KL, Lanier K, Hoelmer KA, Heimpel GE, Meikle WG, O'Neil RJ, Voegtlin DG, Wu K, Woolley JB, Heraty JM
Counties not countries: Variation in host specificity among populations of an aphid parasitoid.
Apr 14, 2019
Evolutionary Applications
Parasitic wasps are among the most species-rich groups on Earth. A major cause of this diversity may be local adaptation to host species. However, little is known about variation in host specificity among populations within parasitoid species. Not only is such knowledge important for understanding host-driven speciation, but because parasitoids often control pest insects and narrow host ranges are critical for the safety of biological control introductions, understanding variation in specificity and how it arises are crucial applications in evolutionary biology. Here, we report experiments on variation in host specificity among 16 populations of an aphid parasitoid, Aphelinus certus. We addressed several questions about local adaptation: Do parasitoid populations differ in host ranges or in levels of parasitism of aphid species within their host range? Are differences in parasitism among parasitoid populations related to geographical distance, suggesting clinal variation in abundances of aphid species? Or do nearby parasitoid populations differ in host use, as would be expected if differences in aphid abundances, and thus selection, were mosaic? Are differences in parasitism among parasitoid populations related to genetic distances among them? To answer these questions, we measured parasitism of a taxonomically diverse group of aphid species in laboratory experiments. Host range was the same for all the parasitoid populations, but levels of parasitism varied among aphid species, suggesting adaptation to locally abundant aphids. Differences in host specificity did not correlate with geographical distances among parasitoid populations, suggesting that local adaption is mosaic rather than clinal, with a spatial scale of less than 50 kilometers. We sequenced and assembled the genome of A. certus, made reduced-representation libraries for each population, analyzed for single nucleotide polymorphisms, and used these polymorphisms to estimate genetic differentiation among populations. Differences in host specificity correlated with genetic distances among the parasitoid populations.
Y-chromosomal analysis of clan structure of Kalmyks, the only European Mongol people, and their relationship to Oirat-Mongols of Inner Asia.
Apr 12, 2019   European Journal Of Human Genetics : EJHG
Balinova N, Post H, Kushniarevich A, Flores R, Karmin M,   . . . . . .   , Khomyakova I, Spitsina N, Zinchenko R, Villems R, Rootsi S
Y-chromosomal analysis of clan structure of Kalmyks, the only European Mongol people, and their relationship to Oirat-Mongols of Inner Asia.
Apr 12, 2019
European Journal Of Human Genetics : EJHG
Kalmyks, the only Mongolic-speaking population in Europe, live in the southeast of the European Plain, in Russia. They adhere to Buddhism and speak a dialect of the Mongolian language. Historical and linguistic evidence, as well a shared clan names, suggests a common origin with Oirats of western Mongolia; yet, only a limited number of genetic studies have focused on this topic. Here we compare the paternal genetic relationship of Kalmyk clans with ethnographically related groups from Mongolia, Kyrgyzstan and China, within the context of their neighbouring populations. A phylogeny of 37 high-coverage Y-chromosome sequences, together with further genotyping of larger sample sets, reveals that all the Oirat-speaking populations studied here, including Kalmyks, share, as a dominant paternal lineage, Y-chromosomal haplogroup C3c1-M77, which is also present in several geographically distant native Siberian populations. We identify a subset of this clade, C3c1b-F6379, specifically enriched in Kalmyks as well as in Oirat-speaking clans in Inner Asia. This sub-clade coalesces at around 1500 years before present, before the Genghis Khan era, and significantly earlier than the split between Kalmyks and other Oirat speakers about 400 years ago. We also show that split between the dominant hg C variant among Buryats-C3-M407-and that of C3-F6379, took place in the Early Upper Palaeolithic, suggesting an extremely long duration for the dissipation of hg C3-M217 carriers across northern Eurasia, which cuts through today's major linguistic phyla.
Biodiversity loss in a Mediterranean ecosystem due to an extreme warming event unveils the role of an engineering gorgonian species.
Apr 17, 2019   Scientific Reports
Verdura J, Linares C, Ballesteros E, Coma R, Uriz MJ, Bensoussan N, Cebrian E
Biodiversity loss in a Mediterranean ecosystem due to an extreme warming event unveils the role of an engineering gorgonian species.
Apr 17, 2019
Scientific Reports
Stochastic perturbations can trigger major ecosystem shifts. Marine systems have been severely affected in recent years by mass mortality events related to positive thermal anomalies. Although the immediate effects in the species demography affected by mortality events are well known, information on the mid- to long-term effects at the community level is much less documented. Here, we show how an extreme warming event replaces a structurally complex habitat, dominated by long-lived species, by a simplified habitat (lower species diversity and richness) dominated by turf-forming species. On the basis of a study involving the experimental manipulation of the presence of the gorgonian Paramuricea clavata, we observed that its presence mitigated the effects of warming by maintaining the original assemblage dominated by macroinvertebrates and delaying the proliferation and spread of the invasive alga Caulerpa cylindracea. However, due to the increase of sediment and turf-forming species after the mortality event we hypothesize a further degradation of the whole assemblage as both factors decrease the recruitment of P.clavata, decrease the survival of encrusting coralligenous-dwelling macroinvertebrates and facilitate the spreading of C. cylindracea.
Urbanity and the dynamics of language shift in Galicia.
Apr 16, 2019   Nature Communications
Mussa Juane M, Seoane LF, Muñuzuri AP, Mira J
Urbanity and the dynamics of language shift in Galicia.
Apr 16, 2019
Nature Communications
Sociolinguistic phenomena often involve interactions across different scales and result in social and linguistic changes that can be tracked over time. Here, we focus on the dynamics of language shift in Galicia, a bilingual community in northwest Spain. Using historical data on Galician and Spanish speakers, we show that the rate at which shift dynamics unfold correlates inversely with the internal complexity of a region (approximated by the proportion of urban area). Less complex areas converge faster to steady states, while more complex ones sustain transitory dynamics longer. We further explore the contextual relevance of each region within the network of regions that constitute Galicia. The network is observed to sustain or reverse the dynamic rates. This model can introduce a competition between the internal complexity of a region and its contextual relevance in the network. Harnessing these sociodynamic features may prove useful in policy making to limit conflicts.
Pollinators, herbivores, and the evolution of floral traits.
Apr 16, 2019   Science (New York, N.Y.)
Ågren J
Stroke genetics: discovery, biology, and clinical applications.
Apr 12, 2019   The Lancet. Neurology
Dichgans M, Pulit SL, Rosand J
Stroke genetics: discovery, biology, and clinical applications.
Apr 12, 2019
The Lancet. Neurology
Stroke, a leading cause of long-term disability and death worldwide, has a heritable component. Recent gene discovery efforts have expanded the number of known single-gene disorders associated with stroke and have linked common variants at approximately 35 genetic loci to stroke risk. These discoveries have highlighted novel mechanisms and pathways implicated in stroke related to large artery atherosclerosis, cardioembolism, and small vessel disease, and defined shared genetic influences with related vascular traits. Genetics has also successfully established causal relationships with risk factors and holds promise for prioritising targets for exploration in clinical trials. Genome-wide polygenic scores enable the identification of high-risk individuals before the emergence of vascular risk factors. Challenges ahead include a better understanding of rare variants and ancestral differences for integration of genetics into precision medicine, integration with other omics data, uncovering the genetic factors that govern stroke recurrence and stroke outcome, and the conversion of genetic discoveries to novel therapies.
Molecular phylogeny of Oreochromis (Cichlidae: Oreochromini) reveals mito-nuclear discordance and multiple colonisation of adverse aquatic environments.
Apr 11, 2019   Molecular Phylogenetics And Evolution
Ford AGP, Bullen TR, Pang L, Genner MJ, Bills R, Flouri T, Ngatunga BP, Rüber L, Schliewen UK, Seehausen O, Shechonge A, Stiassny MLJ, Turner GF, Day JJ
Molecular phylogeny of Oreochromis (Cichlidae: Oreochromini) reveals mito-nuclear discordance and multiple colonisation of adverse aquatic environments.
Apr 11, 2019
Molecular Phylogenetics And Evolution
Although the majority of cichlid diversity occurs in the African Great Lakes, these fish have also diversified across the African continent. Such continental radiations, occurring in both rivers and lakes have received far less attention than lacustrine radiations despite some members, such as the oreochromine cichlids (commonly referred to as 'tilapia'), having significant scientific and socio-economic importance both within and beyond their native range. Unique among cichlids, several species of the genus Oreochromis exhibit adaptation to soda conditions (including tolerance of elevated temperatures and salinity), which are of interest from evolutionary biology research and aquaculture perspectives. Questions remain regarding the factors facilitating the diversification of this group, which to date have not been addressed within a phylogenetic framework. Here we present the first comprehensive (32/37 described species) multi-marker molecular phylogeny of Oreochromis and closely related Alcolapia, based on mitochondrial (1583 bp) and nuclear (3092 bp) sequence data. We show widespread discordance between nuclear DNA and mitochondrial DNA trees. This could be the result of incomplete lineage sorting and/or introgression in mitochondrial loci, although we didn't find a strong signal for the latter. Based on our nuclear phylogeny we demonstrate that adaptation to adverse conditions (elevated salinity, temperature, or alkalinity) has occurred multiple times within Oreochromis, but that adaptation to extreme (soda) conditions (high salinity, temperature, and alkalinity) has likely arisen once in the lineage leading to O. amphimelas and Alcolapia. We also show Alcolapia is nested within Oreochromis, which is in agreement with previous studies, and here revise the taxonomy to synonymise the genus in Oreochromis, retaining the designation as subgenus Oreochromis (Alcolapia).
Network motifs and their origins.
Apr 11, 2019   PLoS Computational Biology
Stone L, Simberloff D, Artzy-Randrup Y
Network motifs and their origins.
Apr 11, 2019
PLoS Computational Biology
Modern network science is a new and exciting research field that has transformed the study of complex systems over the last 2 decades. Of particular interest is the identification of small "network motifs" that might be embedded in a larger network and that indicate the presence of evolutionary design principles or have an overly influential role on system-wide dynamics. Motifs are patterns of interconnections, or subgraphs, that appear in an observed network significantly more often than in compatible randomized networks. The concept of network motifs was introduced into Systems Biology by Milo, Alon and colleagues in 2002, quickly revolutionized the field, and it has had a huge impact in wider scientific domains ever since. Here, we argue that the same concept and tools for the detection of motifs were well known in the ecological literature decades into the last century, a fact that is generally not recognized. We review the early history of network motifs, their evolution in the mathematics literature, and their recent rediscoveries.
Defences against brood parasites from a social immunity perspective.
Apr 12, 2019   Philosophical Transactions Of The Royal Society Of London. Series B, Biological Sciences
Cotter SC, Pincheira-Donoso D, Thorogood R
Defences against brood parasites from a social immunity perspective.
Apr 12, 2019
Philosophical Transactions Of The Royal Society Of London. Series B, Biological Sciences
Parasitic interactions are so ubiquitous that all multicellular organisms have evolved a system of defences to reduce their costs, whether the parasites they encounter are the classic parasites which feed on the individual, or brood parasites which usurp parental care. Many parallels have been drawn between defences deployed against both types of parasite, but typically, while defences against classic parasites have been selected to protect survival, those against brood parasites have been selected to protect the parent's inclusive fitness, suggesting that the selection pressures they impose are fundamentally different. However, there is another class of defences against classic parasites that have specifically been selected to protect an individual's inclusive fitness, known as social immunity. Social immune responses include the anti-parasite defences typically provided for others in kin-structured groups, such as the antifungal secretions produced by termite workers to protect the brood. Defences against brood parasites, therefore, are more closely aligned with social immune responses. Much like social immunity, host defences against brood parasitism are employed by a donor (a parent) for the benefit of one or more recipients (typically kin), and as with social defences against classic parasites, defences have therefore evolved to protect the donor's inclusive fitness, not the survival or ultimately the fitness of individual recipients This can lead to severe conflicts between the different parties, whose interests are not always aligned. Here, we consider defences against brood parasitism in the light of social immunity, at different stages of parasite encounter, addressing where conflicts occur and how they might be resolved. We finish with considering how this approach could help us to address longstanding questions in our understanding of brood parasitism. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.
Non-fertilizing sperm in Lepidoptera show little evidence for recurrent positive selection.
Apr 13, 2019   Molecular Ecology
Mongue AJ, Hansen ME, Gu L, Sorenson CE, Walters JR
Non-fertilizing sperm in Lepidoptera show little evidence for recurrent positive selection.
Apr 13, 2019
Molecular Ecology
Sperm are among the most variable cells in nature. Some of this variation results from non-adaptive errors in spermatogenesis, but many species consistently produce multiple sperm morphs, the adaptive significance of which remains unknown. Here, we investigate the evolution of dimorphic sperm in Lepidoptera, the butterflies and moths. Males of this order produce both fertilizing sperm and a secondary, non-fertilizing type that lacks DNA. Previous organismal studies suggested a role for non-fertilizing sperm in sperm competition, but this hypothesis has never been evaluated from a molecular framework. We combined published datasets with new sequencing in two species, the monandrous Carolina sphinx moth and the highly polyandrous monarch butterfly. Based on population genetic analyses, we see evidence for increased adaptive evolution in fertilizing sperm, but only in the polyandrous species. This signal comes primarily from a decrease in non-synonymous polymorphism in sperm proteins compared to the rest of the genome, suggesting stronger purifying selection, consistent with selection via sperm competition. Non-fertilizing sperm proteins, in contrast, do not show an effect of mating system and do not appear to evolve differently from the background genome in either species, arguing against the involvement of non-fertilizing sperm in direct sperm competition. Based on our results and previous work, we suggest that non-fertilizing sperm may be used to delay female remating in these insects and decrease the risk of sperm competition rather than directly affect its outcome.
Gene expression shifts in yellow-bellied marmots prior to natal dispersal.
Apr 14, 2019   Behavioral Ecology : Official Journal Of The International Society For Behavioral Ecology
Armenta TC, Cole SW, Geschwind DH, Blumstein DT, Wayne RK
Gene expression shifts in yellow-bellied marmots prior to natal dispersal.
Apr 14, 2019
Behavioral Ecology : Official Journal Of The International Society For Behavioral Ecology
The causes and consequences of vertebrate natal dispersal have been studied extensively, yet little is known about the molecular mechanisms involved. We used RNA-seq to quantify transcriptomic gene expression in blood of wild yellow-bellied marmots (Marmota flaviventer) prior to dispersing from or remaining philopatric to their natal colony. We tested 3 predictions. First, we hypothesized dispersers and residents will differentially express genes and gene networks since dispersal is physiologically demanding. Second, we expected differentially expressed genes to be involved in metabolism, circadian processes, and immune function. Finally, in dispersing individuals, we predicted differentially expressed genes would change as a function of sampling date relative to dispersal date. We detected 150 differentially expressed genes, including genes that have critical roles in lipid metabolism and antigen defense. Gene network analysis revealed a module of 126 coexpressed genes associated with dispersal that was enriched for extracellular immune function. Of the dispersal-associated genes, 22 altered expression as a function of days until dispersal, suggesting that dispersal-associated genes do not initiate transcription on the same time scale. Our results provide novel insights into the fundamental molecular changes required for dispersal and suggest evolutionary conservation of functional pathways during this behavioral process.
Transposon molecular domestication and the evolution of the RAG recombinase.
Apr 11, 2019   Nature Add nature.com free-link Cancel
Zhang Y, Cheng TC, Huang G, Lu Q, Surleac MD, Mandell JD, Pontarotti P, Petrescu AJ, Xu A, Xiong Y, Schatz DG
Transposon molecular domestication and the evolution of the RAG recombinase.
Apr 11, 2019
Nature
Domestication of a transposon (a DNA sequence that can change its position in a genome) to give rise to the RAG1-RAG2 recombinase (RAG) and V(D)J recombination, which produces the diverse repertoire of antibodies and T cell receptors, was a pivotal event in the evolution of the adaptive immune system of jawed vertebrates. The evolutionary adaptations that transformed the ancestral RAG transposase into a RAG recombinase with appropriately regulated DNA cleavage and transposition activities are not understood. Here, beginning with cryo-electron microscopy structures of the amphioxus ProtoRAG transposase (an evolutionary relative of RAG), we identify amino acid residues and domains the acquisition or loss of which underpins the propensity of RAG for coupled cleavage, its preference for asymmetric DNA substrates and its inability to perform transposition in cells. In particular, we identify two adaptations specific to jawed-vertebrates-arginine 848 in RAG1 and an acidic region in RAG2-that together suppress RAG-mediated transposition more than 1,000-fold. Our findings reveal a two-tiered mechanism for the suppression of RAG-mediated transposition, illuminate the evolution of V(D)J recombination and provide insight into the principles that govern the molecular domestication of transposons.
Maelstrom regulates spermatogenesis of the silkworm, Bombyx mori.
Apr 16, 2019   Insect Biochemistry And Molecular Biology
Chen K, Chen S, Xu J, Yu Y, Liu Z, Tan A, Huang Y
Maelstrom regulates spermatogenesis of the silkworm, Bombyx mori.
Apr 16, 2019
Insect Biochemistry And Molecular Biology
The spermatogenesis of animal is essential for the reproduction and a very large number of genes participate in this procession. The Maelstrom (Mael) is identified essential for spermatogenesis in both Drosophila and mouse, though the mechanisms appear to differ. It was initially found that Mael gene is necessary for axis specification of oocytes in Drosophila, and recent studies suggested that Mael participates in the piRNA pathway. In this study, we obtained Bombyx mori Mael mutants by using a binary transgenic CRISPR/Cas9 system and analyzed the function of Mael in B. mori, a model lepidopteran insect. The results showed that BmMael is not necessary for piRNA pathway in the ovary of silkworm, whereas it might be essential for transposon elements (TEs) repression in testis. The BmMael mutation resulted in male sterility, and further analysis established that BmMael was essential for spermatogenesis. The spermatogenesis defects occurred in the elongation stage and resulted in nuclei concentration arrest. RNA-seq and qRT-PCR analyses demonstrated that spermatogenesis defects were associated with tight junctions and apoptosis. We also found that BmMael was not involved in the silkworm sex determination pathway. Our data provide insights into the biological function of BmMael in male spermatogenesis and might be useful for developing novel methods to control lepidopteron pests.
Ancestral sequences from an elite neutralizer proximal to the development of neutralization resistance as a potential source of HIV vaccine immunogens.
Apr 10, 2019   PloS One
Mesa KA, Yu B, Wrin T, Petropoulos CJ, Pogson GH, Alexander DL, Perez G, O'Rourke SM, Sinangil F, Robinson J, Conant MA, Berman PW
Ancestral sequences from an elite neutralizer proximal to the development of neutralization resistance as a potential source of HIV vaccine immunogens.
Apr 10, 2019
PloS One
A major challenge in HIV vaccine development is the identification of immunogens able to elicit broadly neutralizing antibodies (bNAbs). While remarkable progress has been made in the isolation and characterization of bNAbs, the epitopes they recognize appear to be poorly immunogenic. Thus, none of the candidate vaccines developed to date has induced satisfactory levels of neutralizing antibodies to the HIV envelope protein (Env). One approach to the problem of poor immunogenicity is to build vaccines based on envelope (env) genes retrieved from rare individuals termed elite neutralizers (ENs) who at one time possessed specific sequences that stimulated the formation of bNAbs. Env proteins selected from these individuals could possess uncommon, yet to be defined, structural features that enhance the immunogenicity of epitopes recognized by bNAbs. Here we describe the recovery of envs from an EN that developed unusually broad and potent bNAbs. As longitudinal specimens were not available, we combined plasma and provirus sequences acquired from a single time-point to infer a phylogenetic tree. Combining ancestral reconstruction data with virus neutralization data allowed us to sift through the myriad of virus quasi-species that evolved in this individual to identify envelope sequences from the nodes that appeared to define the transition from neutralization sensitive envs to the neutralization resistant envs that occur in EN plasma. Synthetic genes from these nodes were functional in infectivity assays and sensitive to neutralization by bNAbs, and may provide a novel source of immunogens for HIV vaccine development.
Importance of plant- and microbe-driven metabolic pathways for plant defence.
Apr 10, 2019   Molecular Ecology
O'Brien AM
Importance of plant- and microbe-driven metabolic pathways for plant defence.
Apr 10, 2019
Molecular Ecology
Expression of plant phenotypes can depend on both plant genomes and interactions between plants and the microbes living in, on and near their roots. We understand a growing number of the mechanistic links between plant genotypes and phenotypes, such as defence against herbivory (see brief review in Hubbard et al., ), yet the links between root microbiomes and the comprehensive swathe of plant phenotypes they affect (Friesen et al., ) remain less clear. In this issue of Molecular Ecology, Hubbard et al. () follow microbe- and plant-driven changes in plant defence against hervibory from molecular underpinnings to ecological consequences, contrasting both the metabolites affected and the magnitude of defensive impact. Naively, we might expect plant genomes to drive more variation in phenotype than the root microbiome, but Hubbard et al. () find the opposite, implying profound consequences for plant trait evolution and ecological interactions.
Author Correction: The genetic legacy of continental scale admixture in Indian Austroasiatic speakers.
Apr 16, 2019   Scientific Reports
Tätte K, Pagani L, Pathak AK, Kõks S, Ho Duy B,   . . . . . .   , Hadid Y, Villems R, Chaubey G, Kivisild T, Metspalu M
Author Correction: The genetic legacy of continental scale admixture in Indian Austroasiatic speakers.
Apr 16, 2019
Scientific Reports
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Mapping vaccination coverage to explore the effects of delivery mechanisms and inform vaccination strategies.
Apr 13, 2019   Nature Communications
Utazi CE, Thorley J, Alegana VA, Ferrari MJ, Takahashi S, Metcalf CJE, Lessler J, Cutts FT, Tatem AJ
Mapping vaccination coverage to explore the effects of delivery mechanisms and inform vaccination strategies.
Apr 13, 2019
Nature Communications
The success of vaccination programs depends largely on the mechanisms used in vaccine delivery. National immunization programs offer childhood vaccines through fixed and outreach services within the health system and often, additional supplementary immunization activities (SIAs) are undertaken to fill gaps and boost coverage. Here, we map predicted coverage at 1 × 1 km spatial resolution in five low- and middle-income countries to identify areas that are under-vaccinated via each delivery method using Demographic and Health Surveys data. We compare estimates of the coverage of the third dose of diphtheria-tetanus-pertussis-containing vaccine (DTP3), which is typically delivered through routine immunization (RI), with those of measles-containing vaccine (MCV) for which SIAs are also undertaken. We find that SIAs have boosted MCV coverage in some places, but not in others, particularly where RI had been deficient, as depicted by DTP coverage. The modelling approaches outlined here can help to guide geographical prioritization and strategy design.
Untangling posterior growth and segmentation by analyzing mechanisms of axis elongation in hemichordates.
Apr 10, 2019   Proceedings Of The National Academy Of Sciences Of The United States Of America
Fritzenwanker JH, Uhlinger KR, Gerhart J, Silva E, Lowe CJ
Untangling posterior growth and segmentation by analyzing mechanisms of axis elongation in hemichordates.
Apr 10, 2019
Proceedings Of The National Academy Of Sciences Of The United States Of America
The trunk is a key feature of the bilaterian body plan. Despite spectacular morphological diversity in bilaterian trunk anatomies, most insights into trunk development are from segmented taxa, namely arthropods and chordates. Mechanisms of posterior axis elongation (PAE) and segmentation are tightly coupled in arthropods and vertebrates, making it challenging to differentiate between the underlying developmental mechanisms specific to each process. Investigating trunk elongation in unsegmented animals facilitates examination of mechanisms specific to PAE and provides a different perspective for testing hypotheses of bilaterian trunk evolution. Here we investigate the developmental roles of canonical Wnt and Notch signaling in the hemichordate Saccoglossus kowalevskii and reveal that both pathways play key roles in PAE immediately following the completion of gastrulation. Furthermore, our functional analysis of the role of Brachyury is supportive of a Wnt-Brachyury feedback loop during PAE in S. kowalevskii, establishing this key regulatory interaction as an ancestral feature of deuterostomes. Together, our results provide valuable data for testing hypotheses of bilaterian trunk evolution.
Monogamy without parental care? Social and genetic mating systems of avian brood parasites.
Apr 12, 2019   Philosophical Transactions Of The Royal Society Of London. Series B, Biological Sciences
Feeney WE, Riehl C
Monogamy without parental care? Social and genetic mating systems of avian brood parasites.
Apr 12, 2019
Philosophical Transactions Of The Royal Society Of London. Series B, Biological Sciences
Classic evolutionary theory predicts that monogamy should be intimately linked with parental care. It has long been assumed, therefore, that avian brood parasites-which lay their eggs in the nests of 'host' species and provide little, if any, parental care-should be overwhelmingly promiscuous. However, recent studies have revealed that the social mating systems of brood parasites are surprisingly diverse, encompassing lek polygyny, monogamy, polygamy and promiscuity. What ecological or phylogenetic factors explain this variation, and why are some brood parasites apparently monogamous? Here we review the social and genetic mating systems of all 75 brood parasitic species for which data are available and evaluate several hypotheses that may help explain these patterns. We find that social monogamy is widespread, often co-occurring with territoriality and cooperative behaviour by the mated pair. Comparative studies, though preliminary, suggest that in some species, monogamy is associated with low host density and polygamy with higher host density. Interestingly, molecular data show that genetic and social mating systems can be entirely decoupled: genetic monogamy can occur in parasitic species that lack behavioural pair-bonds, possibly as a by-product of territoriality; conversely, social monogamy has been reported in parasites that are genetically polygamous. This synthesis suggests that social and genetic monogamy may result from very different selective pressures, and that male-female cooperative behaviours, population density and territoriality may all interact to favour the evolution of monogamous mating in brood parasites. Given that detailed descriptive data of social, and especially genetic, mating systems are still lacking for the majority of brood parasitic species, definitive tests of these hypotheses await future work. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.
Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana).
Apr 13, 2019   Molecular Ecology
Aguirre-Liguori JA, Gaut BS, Jaramillo-Correa JP, Tenaillon MI, Montes-Hernández S, García-Oliva F, Hearne SJ, Eguiarte LE
Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana).
Apr 13, 2019
Molecular Ecology
Patterns of genomic divergence between hybridizing taxa can be heterogeneous along the genome. Both differential introgression and local adaptation may contribute to this pattern. Here we analysed two teosinte subspecies, Zea mays ssp. parviglumis and ssp. mexicana, to test whether their divergence has occurred in the face of gene flow and to infer which environmental variables have been important drivers of their ecological differentiation. We generated 9,780 DArTseqTM SNPs for 47 populations, and used an additional dataset containing 33,454 MaizeSNP50 SNPs for 49 populations. With these data, we inferred features of demographic history and performed genome wide scans to determine the number of outlier SNPs associated with climate and soil variables. The two datasets indicate that divergence has occurred or been maintained despite continuous gene flow and/or secondary contact. Most of the significant SNP associations were to temperature and to phosphorus concentration in the soil. A large proportion of these candidate SNPs were located in regions of high differentiation that had been identified previously as putative inversions. We therefore propose that genomic differentiation in teosintes has occurred by a process of adaptive divergence, with putative inversions contributing to reduced gene flow between locally adapted populations. This article is protected by copyright. All rights reserved.

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