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Evolutionary Biology
Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman
Feb 22, 2017   Frontiers In Microbiology
Rempfert KR, Miller HM, Bompard N, Nothaft D, Matter JM, Kelemen P, Fierer N, Templeton AS
Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman
Feb 22, 2017
Frontiers In Microbiology
UNASSIGNED: Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite ("gabbro," "alkaline peridotite," "hyperalkaline peridotite," and "gabbro/peridotite contact") that vary strongly in pH and the concentrations of H
Genetic risk variants for social anxiety
Feb 22, 2017   American Journal Of Medical Genetics. Part B, Neuropsychiatric Genetics : The Official Publication Of The International Society Of Psychiatric Genetics
Stein MB, Chen CY, Jain S, Jensen KP, He F,   . . . . . .   , Thomas ML, Ursano RJ, Smoller JW, Gelernter J, Army STARRS Collaborators
Genetic risk variants for social anxiety
Feb 22, 2017
American Journal Of Medical Genetics. Part B, Neuropsychiatric Genetics : The Official Publication Of The International Society Of Psychiatric Genetics
UNASSIGNED: Social anxiety is a neurobehavioral trait characterized by fear and reticence in social situations. Twin studies have shown that social anxiety has a heritable basis, shared with neuroticism and extraversion, but genetic studies have yet to demonstrate robust risk variants. We conducted genomewide association analysis (GWAS) of subjects within the Army Study To Assess Risk and Resilience in Servicemembers (Army STARRS) to (i) determine SNP-based heritability of social anxiety; (ii) discern genetic risk loci for social anxiety; and (iii) determine shared genetic risk with neuroticism and extraversion. GWAS were conducted within ancestral groups (EUR, AFR, LAT) using linear regression models for each of the three component studies in Army STARRS, and then meta-analyzed across studies. SNP-based heritability for social anxiety was significant (h © 2017 Wiley Periodicals, Inc.
The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis
Feb 22, 2017   MBio
Olm MR, Butterfield CN, Copeland A, Boles TC, Thomas BC, Banfield JF
The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis
Feb 22, 2017
MBio
UNASSIGNED: In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Copyright © 2017 Olm et al.
Pathway-wide association study identifies five shared pathways associated with schizophrenia in three ancestral distinct populations
Feb 21, 2017   Translational Psychiatry
Liu C, Bousman CA, Pantelis C, Skafidas E, Zhang D, Yue W, Everall IP
Pathway-wide association study identifies five shared pathways associated with schizophrenia in three ancestral distinct populations
Feb 21, 2017
Translational Psychiatry
UNASSIGNED: Genome-wide association studies have confirmed the polygenic nature of schizophrenia and suggest that there are hundreds or thousands of alleles associated with increased liability for the disorder. However, the generalizability of any one allelic marker of liability is remarkably low and has bred the notion that schizophrenia may be better conceptualized as a pathway(s) disorder. Here, we empirically tested this notion by conducting a pathway-wide association study (PWAS) encompassing 255 experimentally validated Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways among 5033 individuals diagnosed with schizophrenia and 5332 unrelated healthy controls across three distinct ethnic populations; European-American (EA), African-American (AA) and Han Chinese (CH). We identified 103, 74 and 87 pathways associated with schizophrenia liability in the EA, CH and AA populations, respectively. About half of these pathways were uniquely associated with schizophrenia liability in each of the three populations. Five pathways (serotonergic synapse, ubiquitin mediated proteolysis, hedgehog signaling, adipocytokine signaling and renin secretion) were shared across all three populations and the single-nucleotide polymorphism sets representing these five pathways were enriched for single-nucleotide polymorphisms with regulatory function. Our findings provide empirical support for schizophrenia as a pathway disorder and suggest schizophrenia is not only a polygenic but likely also a poly-pathway disorder characterized by both genetic and pathway heterogeneity.
Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment
Feb 21, 2017   ELife
Gomez JE, Kaufmann-Malaga BB, Wivagg CN, Kim PB, Silvis MR, Renedo N, Ioerger TR, Ahmad R, Livny J, Fishbein S, Sacchettini JC, Carr SA, Hung DT
Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment
Feb 21, 2017
ELife
UNASSIGNED: Antibiotic resistance arising via chromosomal mutations is typically specific to a particular antibiotic or class of antibiotics. We have identified mutations in genes encoding ribosomal components in
Accelerated simulation of evolutionary trajectories in origin-fixation models
Feb 23, 2017   Journal Of The Royal Society, Interface
Teufel AI, Wilke CO
Accelerated simulation of evolutionary trajectories in origin-fixation models
Feb 23, 2017
Journal Of The Royal Society, Interface
We present an accelerated algorithm to forward-simulate origin-fixation models. Our algorithm requires, on average, only about two fitness evaluations per fixed mutation, whereas traditional algorithms require, per one fixed mutation, a number of fitness evaluations of the order of the effective population size, © 2017 The Author(s).
Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
Feb 23, 2017   Nature Communications
Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, Alm EJ
Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
Feb 23, 2017
Nature Communications
Whether mammal-microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary shifts have affected the distribution of different gut bacterial lineages and did so on vastly different bacterial phylogenetic resolutions. Diet mostly influences the acquisition of ancient and large microbial lineages. Conversely, correlation with host phylogeny is mostly seen among more recently diverged bacterial lineages, consistent with processes operating at similar timescales to host evolution. Considering microbiomes at appropriate phylogenetic scales allows us to model their evolution along the mammalian tree and to infer ancient diets from the predicted microbiomes of mammalian ancestors. Phylogenetic analyses support co-speciation as having a significant role in the evolution of mammalian gut microbiome compositions. Highly co-speciating bacterial genera are also associated with immune diseases in humans, laying a path for future studies that probe these co-speciating bacteria for signs of co-evolution.
Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein
Feb 24, 2017   Journal Of Molecular Evolution
Kacar B, Ge X, Sanyal S, Gaucher EA
Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein
Feb 24, 2017
Journal Of Molecular Evolution
The ability to design synthetic genes and engineer biological systems at the genome scale opens new means by which to characterize phenotypic states and the responses of biological systems to perturbations. One emerging method involves inserting artificial genes into bacterial genomes and examining how the genome and its new genes adapt to each other. Here we report the development and implementation of a modified approach to this method, in which phylogenetically inferred genes are inserted into a microbial genome, and laboratory evolution is then used to examine the adaptive potential of the resulting hybrid genome. Specifically, we engineered an approximately 700-million-year-old inferred ancestral variant of tufB, an essential gene encoding elongation factor Tu, and inserted it in a modern Escherichia coli genome in place of the native tufB gene. While the ancient homolog was not lethal to the cell, it did cause a twofold decrease in organismal fitness, mainly due to reduced protein dosage. We subsequently evolved replicate hybrid bacterial populations for 2000 generations in the laboratory and examined the adaptive response via fitness assays, whole genome sequencing, proteomics, and biochemical assays. Hybrid lineages exhibit a general adaptive strategy in which the fitness cost of the ancient gene was ameliorated in part by upregulation of protein production. Our results suggest that an ancient-modern recombinant method may pave the way for the synthesis of organisms that exhibit ancient phenotypes, and that laboratory evolution of these organisms may prove useful in elucidating insights into historical adaptive processes.
Evolutionary Origin of the Interferon-Immune Metabolic Axis: The Sterol-Vitamin D Link
Feb 24, 2017   Frontiers In Immunology
Newmark H, Dantoft W, Ghazal P
Evolutionary Origin of the Interferon-Immune Metabolic Axis: The Sterol-Vitamin D Link
Feb 24, 2017
Frontiers In Immunology
In vertebrate animals, the sterol metabolic network is emerging as a central player in immunity and inflammation. Upon infection, flux in the network is acutely moderated by the interferon (IFN) response through direct molecular and bi-directional communications. How sterol metabolism became linked to IFN control and for what purpose is not obvious. Here, we deliberate on the origins of these connections based on a systematic review of the literature. A narrative synthesis of publications that met eligibility criteria allowed us to trace an evolutionary path and functional connections between cholesterol metabolism and immunity. The synthesis supports an ancestral link between toxic levels of cholesterol-like products and the vitamin D receptor (VDR). VDR is an ancient nuclear hormone receptor that was originally involved in the recognition and detoxification of xenobiotic marine biotoxins exhibiting planar sterol ring scaffolds present in aquatic environments. Coadaptation of this receptor with the acquisition of sterol biosynthesis and IFNs in vertebrate animals set a stage for repurposing and linking a preexisting host-protection mechanism of harmful xenobiotics to become an important regulator in three key interlinked biological processes: bone development, immunity, and calcium homeostasis. We put forward the hypothesis that sterol metabolites, especially oxysterols, have acted as evolutionary drivers in immunity and may represent the first example of small-molecule metabolites linked to the adaptive coevolution and diversification of host metabolic and immune regulatory pathways.
The biogeography of tropical reef fishes: endemism and provinciality through time
Feb 23, 2017   Biological Reviews Of The Cambridge Philosophical Society
Cowman PF, Parravicini V, Kulbicki M, Floeter SR
The biogeography of tropical reef fishes: endemism and provinciality through time
Feb 23, 2017
Biological Reviews Of The Cambridge Philosophical Society
The largest marine biodiversity hotspot straddles the Indian and Pacific Oceans, driven by taxa associated with tropical coral reefs. Centred on the Indo-Australian Archipelago (IAA), this biodiversity hotspot forms the 'bullseye' of a steep gradient in species richness from this centre to the periphery of the vast Indo-Pacific region. Complex patterns of endemism, wide-ranging species and assemblage differences have obscured our understanding of the genesis of this biodiversity pattern and its maintenance across two-thirds of the world's oceans. But time-calibrated molecular phylogenies coupled with ancestral biogeographic estimates have provided a valuable framework in which to examine the origins of coral reef fish biodiversity across the tropics. Herein, we examine phylogenetic and biogeographic data for coral reef fishes to highlight temporal patterns of marine endemism and tropical provinciality. The ages and distribution of endemic lineages have often been used to identify areas of species creation and demise in the marine tropics and discriminate among multiple hypotheses regarding the origins of biodiversity in the IAA. Despite a general under-sampling of endemic fishes in phylogenetic studies, the majority of locations today contain a mixture of potential paleo- and neo-endemic fishes, pointing to multiple historical processes involved in the origin and maintenance of the IAA biodiversity hotspot. Increased precision and sampling of geographic ranges for reef fishes has permitted the division of discrete realms, regions and provinces across the tropics. Yet, such metrics are only beginning to integrate phylogenetic relatedness and ancestral biogeography. Here, we integrate phylogenetic diversity with ancestral biogeographic estimation of lineages to show how assemblage structure and tropical provinciality has changed through time.© 2017 Cambridge Philosophical Society.
Cooperation, decision time, and culture: Online experiments with American and Indian participants
Feb 23, 2017   PloS One
Nishi A, Christakis NA, Rand DG
Cooperation, decision time, and culture: Online experiments with American and Indian participants
Feb 23, 2017
PloS One
Two separate bodies of work have examined whether culture affects cooperation in economic games and whether cooperative or non-cooperative decisions occur more quickly. Here, we connect this work by exploring the relationship between decision time and cooperation in American versus Indian subjects. We use a series of dynamic social network experiments in which subjects play a repeated public goods game: 80 sessions for a total of 1,462 subjects (1,059 from the United States, 337 from India, and 66 from other countries) making 13,560 decisions. In the first round, where subjects do not know if connecting neighbors are cooperative, American subjects are highly cooperative and decide faster when cooperating than when defecting, whereas a majority of Indian subjects defect and Indians decide faster when defecting than when cooperating. Almost the same is true in later rounds where neighbors were previously cooperative (a cooperative environment) except decision time among Indian subjects. However, when connecting neighbors were previously not cooperative (a non-cooperative environment), a large majority of both American and Indian subjects defect, and defection is faster than cooperation among both sets of subjects. Our results imply the cultural background of subjects in their real life affects the speed of cooperation decision-making differentially in online social environments.
Tree mortality across biomes is promoted by drought intensity, lower wood density and higher specific leaf area
Feb 21, 2017   Ecology Letters
Greenwood S, Ruiz-Benito P, Martínez-Vilalta J, Lloret F, Kitzberger T, Allen CD, Fensham R, Laughlin DC, Kattge J, Bönisch G, Kraft NJ, Jump AS
Tree mortality across biomes is promoted by drought intensity, lower wood density and higher specific leaf area
Feb 21, 2017
Ecology Letters
UNASSIGNED: Drought events are increasing globally, and reports of consequent forest mortality are widespread. However, due to a lack of a quantitative global synthesis, it is still not clear whether drought-induced mortality rates differ among global biomes and whether functional traits influence the risk of drought-induced mortality. To address these uncertainties, we performed a global meta-analysis of 58 studies of drought-induced forest mortality. Mortality rates were modelled as a function of drought, temperature, biomes, phylogenetic and functional groups and functional traits. We identified a consistent global-scale response, where mortality increased with drought severity [log mortality (trees trees © 2017 John Wiley & Sons Ltd/CNRS.
Lamarck rises from his grave: parental environment-induced epigenetic inheritance in model organisms and humans
Feb 21, 2017   Biological Reviews Of The Cambridge Philosophical Society
Wang Y, Liu H, Sun Z
Lamarck rises from his grave: parental environment-induced epigenetic inheritance in model organisms and humans
Feb 21, 2017
Biological Reviews Of The Cambridge Philosophical Society
UNASSIGNED: Organisms can change their physiological/behavioural traits to adapt and survive in changed environments. However, whether these acquired traits can be inherited across generations through non-genetic alterations has been a topic of debate for over a century. Emerging evidence indicates that both ancestral and parental experiences, including nutrition, environmental toxins, nurturing behaviour, and social stress, can have powerful effects on the physiological, metabolic and cellular functions in an organism. In certain circumstances, these effects can be transmitted across several generations through epigenetic (i.e. non-DNA sequence-based rather than mutational) modifications. In this review, we summarize recent evidence on epigenetic inheritance from parental environment-induced developmental and physiological alterations in nematodes, fruit flies, zebrafish, rodents, and humans. The epigenetic modifications demonstrated to be both susceptible to modulation by environmental cues and heritable, including DNA methylation, histone modification, and small non-coding RNAs, are also summarized. We particularly focus on evidence that parental environment-induced epigenetic alterations are transmitted through both the maternal and paternal germlines and exert sex-specific effects. The thought-provoking data presented here raise fundamental questions about the mechanisms responsible for these phenomena. In particular, the means that define the specificity of the response to parental experience in the gamete epigenome and that direct the establishment of the specific epigenetic change in the developing embryos, as well as in specific tissues in the descendants, remain obscure and require elucidation. More precise epigenetic assessment at both the genome-wide level and single-cell resolution as well as strategies for breeding at relatively sensitive periods of development and manipulation aimed at specific epigenetic modification are imperative for identifying parental environment-induced epigenetic marks across generations. Considering their diverse epigenetic architectures, the conservation and prevalence of the mechanisms underlying epigenetic inheritance in non-mammals require further investigation in mammals. Interpretation of the consequences arising from epigenetic inheritance on organisms and a better understanding of the underlying mechanisms will provide insight into how gene-environment interactions shape developmental processes and physiological functions, which in turn may have wide-ranging implications for human health, and understanding biological adaptation and evolution. © 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.
Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
Feb 16, 2017   Proceedings. Biological Sciences
Dutoit L, Vijay N, Mugal CF, Bossu CM, Burri R, Wolf J, Ellegren H
Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
Feb 16, 2017
Proceedings. Biological Sciences
UNASSIGNED: Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird species-collared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman's © 2017 The Authors.
Epistasis Analysis Goes Genome-Wide
Feb 16, 2017   PLoS Genetics
Zhang J
Specificity of genome evolution in experimental populations of
Feb 16, 2017   Proceedings Of The National Academy Of Sciences Of The United States Of America
Deatherage DE, Kepner JL, Bennett AF, Lenski RE, Barrick JE
Specificity of genome evolution in experimental populations of
Feb 16, 2017
Proceedings Of The National Academy Of Sciences Of The United States Of America
UNASSIGNED: Isolated populations derived from a common ancestor are expected to diverge genetically and phenotypically as they adapt to different local environments. To examine this process, 30 populations of
Efficient inference of recent and ancestral recombination within bacterial populations
Feb 15, 2017   Molecular Biology And Evolution
Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen P
Towards a mechanistic foundation of evolutionary theory
Feb 15, 2017   ELife
Doebeli M, Ispolatov Y, Simon B
Towards a mechanistic foundation of evolutionary theory
Feb 15, 2017
ELife
UNASSIGNED: Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or mathematical descriptions of evolution. Instead, we propose that evolutionary birth-death processes, in which individuals give birth and die at ever-changing rates, should be the basis of evolutionary theory, because such processes capture the fundamental events that generate evolutionary dynamics. In evolutionary birth-death processes, fitness is at best a derived quantity, and owing to the potential complexity of such processes, there is no guarantee that there is a simple scalar, such as fitness, that would describe long-term evolutionary outcomes. We discuss how evolutionary birth-death processes can provide useful perspectives on a number of central issues in evolution.
The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish
Feb 17, 2017   BMC Genomics
Adrian-Kalchhauser I, Svensson O, Kutschera VE, Alm Rosenblad M, Pippel M, Winkler S, Schloissnig S, Blomberg A, Burkhardt-Holm P
The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish
Feb 17, 2017
BMC Genomics
BACKGROUND: Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb). RESULTS: During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4 kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19 kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies. CONCLUSIONS: Our results indicate that the round goby mitochondrial genome may contain novel features. Since mitochondrial genome organisation is tightly linked to energy metabolism, these features may be linked to its invasion success. Also, the unique tRNA arrangement among Ponto-Caspian gobies may be helpful in studying the evolution of this highly adaptive and invasive species group. Finally, we find that the phylogeny of gobiids can be further refined by the use of longer stretches of linked DNA sequence.
Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes
Feb 17, 2017   BMC Bioinformatics
Petersen M, Meusemann K, Donath A, Dowling D, Liu S, Peters RS, Podsiadlowski L, Vasilikopoulos A, Zhou X, Misof B, Niehuis O
Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes
Feb 17, 2017
BMC Bioinformatics
BACKGROUND: Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms' gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e.g., RNA sequencing). Here, identification of orthologous nucleotide or amino acid sequences can be achieved using a graph-based approach that maps nucleotide sequences to genes of known orthology. Existing implementations of this approach, however, suffer from algorithmic issues that may cause problems in downstream analyses. RESULTS: We present a new software pipeline, Orthograph, that addresses and solves the above problems and implements useful features for a wide range of comparative genomic and transcriptomic analyses. Orthograph applies a best reciprocal hit search strategy using profile hidden Markov models and maps nucleotide sequences to the globally best matching cluster of orthologous genes, thus enabling researchers to conveniently and reliably delineate orthologs and paralogs from transcriptomic and genomic sequence data. We demonstrate the performance of our approach on de novo-sequenced and assembled transcript libraries of 24 species of apoid wasps (Hymenoptera: Aculeata) as well as on published genomic datasets. CONCLUSION: With Orthograph, we implemented a best reciprocal hit approach to reference-based orthology prediction for coding nucleotide sequences such as RNAseq data. Orthograph is flexible, easy to use, open source and freely available at https://mptrsen.github.io/Orthograph . Additionally, we release 24 de novo-sequenced and assembled transcript libraries of apoid wasp species.
Demographics, epidemiology and the impact of vaccination campaigns in a measles-free world - Can elimination be maintained?
Feb 20, 2017   Vaccine
Prada JM, Metcalf CJ, Takahashi S, Lessler J, Tatem AJ, Ferrari M
Demographics, epidemiology and the impact of vaccination campaigns in a measles-free world - Can elimination be maintained?
Feb 20, 2017
Vaccine
INTRODUCTION: All six WHO regions currently have goals for measles elimination by 2020. Measles vaccination is delivered via routine immunization programmes, which in most sub-Saharan African countries reach children around 9months of age, and supplementary immunization activities (SIAs), which target a wider age range at multi-annual intervals. In the absence of endemic measles circulation, the proportion of individuals susceptible to measles will gradually increase through accumulation of new unvaccinated individuals in each birth cohort, increasing the risk of an epidemic. The impact of SIAs and the financial investment they require, depend on coverage and target age range. MATERIALS AND METHODS: We evaluated the impact of target population age range for periodic SIAs, evaluating outcomes for two different levels of coverage, using a demographic and epidemiological model adapted to reflect populations in 4 sub-Saharan African countries. RESULTS: We found that a single SIA can maintain elimination over short time-scales, even with low routine coverage. However, maintaining elimination for more than a few years is difficult, even with large (high coverage/wide age range) recurrent SIAs, due to the build-up of susceptible individuals. Across the demographic and vaccination contexts investigated, expanding SIAs to target individuals over 10years did not significantly reduce outbreak risk. CONCLUSIONS: Elimination was not maintained in the contexts we evaluated without a second opportunity for vaccination. In the absence of an expanded routine program, SIAs provide a powerful option for providing this second dose. We show that a single high coverage SIA can deliver most key benefits in terms of maintaining elimination, with follow-up campaigns potentially requiring smaller investments. This makes post-campaign evaluation of coverage increasingly relevant to correctly assess future outbreak risk. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.
The complete mitochondrial genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 confirms evolutionary division within the fungal Phialocephala fortinii s.l. - Acephala appalanata species complex
Feb 20, 2017   Fungal Biology
Robicheau BM, Young AP, LaButti K, Grigoriev IV, Walker AK
The complete mitochondrial genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 confirms evolutionary division within the fungal Phialocephala fortinii s.l. - Acephala appalanata species complex
Feb 20, 2017
Fungal Biology
UNASSIGNED: Despite the recent surge in mitochondrial (mt) genome sequencing, Kingdom Fungi remains underrepresented with respect to mtDNA. We describe the mt genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 (Helotiales, Ascomycota). This strain is of interest to the Canadian forestry industry as it produces the anti-insectan compound rugulosin. Sequence was obtained from whole genome shotgun sequencing. Comparison to the only other published Phialocephala mt genome, Phialocephala subalpina, indicates that the suite of common mt genes - cox1-3, cob, nad1-6 and 4L, atp6, 8 and 9, as well as rrnL and rrnS - has retained an identical order. Nad4L remains one of the most conserved mitochondrial genes within Phialocephala. Members of the closely related Phialocephala fortinii s.l. - Acephala appalanata species complex (PAC) share too much sequence similarity to properly resolve lineages using ITS barcoding alone. Using P. scopiformis sequence as an outgroup, we determined ancestral gene states that help confirm clades within Phialocephala. Our results show: (1) the complete mt genome of P. scopiformis, representing the 10th complete mt genome for the order Helotiales (containing >3800 species), and (2) how large-scale genomic patterns, such as mitochondrial gene order, can be used to confirm lineages within fungal species complexes. Copyright © 2016 British Mycological Society. All rights reserved.
Maximising Synergy among Tropical Plant Systematists, Ecologists, and Evolutionary Biologists
Feb 18, 2017   Trends In Ecology & Evolution
Baker TR, Pennington RT, Dexter KG, Fine PV, Fortune-Hopkins H,   . . . . . .   , Kress WJ, Lehmann CE, Monteagudo A, Phillips OL, Vasquez R
Maximising Synergy among Tropical Plant Systematists, Ecologists, and Evolutionary Biologists
Feb 18, 2017
Trends In Ecology & Evolution
UNASSIGNED: Closer collaboration among ecologists, systematists, and evolutionary biologists working in tropical forests, centred on studies within long-term permanent plots, would be highly beneficial for their respective fields. With a key unifying theme of the importance of vouchered collection and precise identification of species, especially rare ones, we identify four priority areas where improving links between these communities could achieve significant progress in biodiversity and conservation science: (i) increasing the pace of species discovery; (ii) documenting species turnover across space and time; (iii) improving models of ecosystem change; and (iv) understanding the evolutionary assembly of communities and biomes. Copyright © 2017 Elsevier Ltd. All rights reserved.
Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes, and invertebrates
Feb 17, 2017   Science (New York, N.Y.)
Lamb JB, van de Water JA, Bourne DG, Altier C, Hein MY, Fiorenza EA, Abu N, Jompa J, Harvell CD
Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes, and invertebrates
Feb 17, 2017
Science (New York, N.Y.)
UNASSIGNED: Plants are important in urban environments for removing pathogens and improving water quality. Seagrass meadows are the most widespread coastal ecosystem on the planet. Although these plants are known to be associated with natural biocide production, they have not been evaluated for their ability to remove microbiological contamination. Using amplicon sequencing of the 16 Copyright © 2017, American Association for the Advancement of Science.
A phylogenetic transform enhances analysis of compositional microbiota data
Feb 15, 2017   ELife
Silverman JD, Washburne AD, Mukherjee S, David LA
A phylogenetic transform enhances analysis of compositional microbiota data
Feb 15, 2017
ELife
UNASSIGNED: Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, By decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities.

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