Article added to library!
x
Pubchase is a service of protocols.io - free, open access, crowdsourced protocols repository. Explore protocols.
Sign in
Reset password
or connect with
Facebook
By signing in you are agreeing to our
Terms Of Service and Privacy Policy
Evolutionary Biology
Evidence for prehistoric origins of the G2019S mutation in the North African Berber population
Jul 20, 2017   PloS One
Ben El Haj R, Salmi A, Regragui W, Moussa A, Bouslam N, Tibar H, Benomar A, Yahyaoui M, Bouhouche A
Evidence for prehistoric origins of the G2019S mutation in the North African Berber population
Jul 20, 2017
PloS One
The most common cause of the monogenic form of Parkinson's disease known so far is the G2019S mutation of the leucine-rich repeat kinase 2 (LRRK2) gene. Its frequency varies greatly among ethnic groups and geographic regions ranging from less than 0.1% in Asia to 40% in North Africa. This mutation has three distinct haplotypes; haplotype 1 being the oldest and most common. Recent studies have dated haplotype 1 of the G2019S mutation to about 4000 years ago, but it remains controversial whether the mutation has a Near-Eastern or Moroccan-Berber ancestral origin. To decipher this evolutionary history, we genotyped 10 microsatellite markers spanning a region of 11.27 Mb in a total of 57 unrelated Moroccan PD patients carrying the G2019S mutation for which the Berber or Arab origin was established over 3 generations based on spoken language. We estimated the age of the most recent common ancestor for the 36 Arab-speaking and the 15 Berber-speaking G2019S carriers using the likelihood-based method with a mutation rate of 10-4. Data analysis suggests that the shortest haplotype originated in a patient of Berber ethnicity. The common founder was estimated to have lived 159 generations ago (95% CI 116-224) for Arab patients, and 200 generations ago (95% CI 123-348) for Berber patients. Then, 29 native North African males carrying the mutation were assessed for specific uniparental markers by sequencing the Y-chromosome (E-M81, E-M78, and M-267) and mitochondrial DNA (mtDNA) hypervariable regions (HV1 and HV2) to examine paternal and maternal contributions, respectively. Results showed that the autochthonous genetic component reached 76% for mtDNA (Eurasian and north African haplogroups) and 59% for the Y-chromosome (E-M81 and E-M78), suggesting that the G2019S mutation may have arisen in an autochthonous DNA pool. Therefore, we conclude that LRRK2 G2019S mutation most likely originated in a Berber founder who lived at least 5000 years ago (95% CI 3075-8700).
Early-life disruption of amphibian microbiota decreases later-life resistance to parasites
Jul 21, 2017   Nature Communications
Knutie SA, Wilkinson CL, Kohl KD, Rohr JR
Early-life disruption of amphibian microbiota decreases later-life resistance to parasites
Jul 21, 2017
Nature Communications
Changes in the early-life microbiota of hosts might affect infectious disease risk throughout life, if such disruptions during formative times alter immune system development. Here, we test whether an early-life disruption of host-associated microbiota affects later-life resistance to infections by manipulating the microbiota of tadpoles and challenging them with parasitic gut worms as adults. We find that tadpole bacterial diversity is negatively correlated with parasite establishment in adult frogs: adult frogs that had reduced bacterial diversity as tadpoles have three times more worms than adults without their microbiota manipulated as tadpoles. In contrast, adult bacterial diversity during parasite exposure is not correlated with parasite establishment in adult frogs. Thus, in this experimental setup, an early-life disruption of the microbiota has lasting reductions on host resistance to infections, which is possibly mediated by its effects on immune system development. Our results support the idea that preventing early-life disruption of host-associated microbiota might confer protection against diseases later in life.Early-life microbiota alterations can affect infection susceptibility later in life, in animal models. Here, Knutie et al. show that manipulating the microbiota of tadpoles leads to increased susceptibility to parasitic infection in adult frogs, in the absence of substantial changes in the adults' microbiota.
Northern Elephant Seals Memorize the Rhythm and Timbre of Their Rivals' Voices
Jul 24, 2017   Current Biology : CB
Mathevon N, Casey C, Reichmuth C, Charrier I
Northern Elephant Seals Memorize the Rhythm and Timbre of Their Rivals' Voices
Jul 24, 2017
Current Biology : CB
The evolutionary origin of rhythm perception, a cognitive ability essential to musicality, remains unresolved [1-5]. The ability to perceive and memorize rhythmic sounds is widely shared among humans [6] but seems rare among other mammals [7, 8]. Although the perception of temporal metrical patterns has been found in a few species, this ability has only been demonstrated through behavioral training [9] (but see [10] for an example of spontaneous tempo coordination in a bonobo), and there is no experimental evidence to indicate its biological function. Furthermore, there is no example of a non-human mammal able to remember and recognize auditory rhythmic patterns among a wide range of tempi. In the northern elephant seal Mirounga angustirostris, the calls of mature males comprise a rhythmic series of pulses, with the call of each individual characterized by its tempo and timbre; these individual vocal signatures are stable over years and across contexts [11]. Here, we report that northern elephant seal males routinely memorize and recognize the unique tempo and timbre of their rivals' voices and use this rhythmic information to individually identify competitors, which facilitates navigation within the social network of the rookery. By performing playbacks with natural and modified vocalizations, we show that males are sensitive to call rhythm disruption independently of modification of spectral features and that they use both temporal and spectral cues to identify familiar rivals. While spectral features of calls typically encode individual identity in mammalian vocalizations [12], this is the first example of this phenomenon involving sound rhythm. Copyright © 2017 Elsevier Ltd. All rights reserved.
Rhamnose-Containing Cell Wall Polymers Suppress Helical Plant Growth Independently of Microtubule Orientation
Jul 24, 2017   Current Biology : CB
Saffer AM, Carpita NC, Irish VF
Rhamnose-Containing Cell Wall Polymers Suppress Helical Plant Growth Independently of Microtubule Orientation
Jul 24, 2017
Current Biology : CB
Although specific organs in some plant species exhibit helical growth patterns of fixed or variable handedness, most plant organs are not helical. Here we report that mutations in Arabidopsis RHAMNOSE BIOSYNTHESIS 1 (RHM1) cause dramatic left-handed helical growth of petal epidermal cells, leading to left-handed twisted petals. rhm1 mutant roots also display left-handed growth. Furthermore, we find that RHM1 is required to promote epidermal cell expansion. RHM1 encodes a UDP-L-rhamnose synthase, and rhm1 mutations affect synthesis of the pectic polysaccharide rhamnogalacturonan-I. Unlike other mutants that exhibit helical growth of fixed handedness, the orientation of cortical microtubule arrays is unaltered in rhm1 mutants. Our findings reveal a novel source of left-handed plant growth caused by changes in cell wall composition that is independent of microtubule orientation. We propose that an important function of rhamnose-containing cell wall polymers is to suppress helical twisting of expanding plant cells. Copyright © 2017 Elsevier Ltd. All rights reserved.
Cophylogenetic signal is detectable in pollination interactions across ecological scales
Jul 22, 2017   Ecology
Hutchinson MC, Cagua EF, Stouffer DB
Cophylogenetic signal is detectable in pollination interactions across ecological scales
Jul 22, 2017
Ecology
That evolutionary history can influence the way that species interact is a basic tenet of evolutionary ecology. However, when the role of evolution in determining ecological interactions is investigated, focus typically centers on just one side of the interaction. A cophylogenetic signal-the congruence of evolutionary history across both sides of anecological interaction-extends these previous explorations and provides a more complete picture of how evolutionary patterns influence the way species interact. To date,cophylogenetic signal has most typically been studied in interactions that occur between fine taxonomic clades that show high intimacy. In this study, we took an alternative approach and made an exhaustive assessment of cophylogeny in pollination interactions To do so, we assessed the strength of cophylogenetic signal at four distinct scales of pollination interaction: (i) across plant-pollinator associations globally, (ii) in local pollination communities, (iii) within the modular structure of those communities, and (iv) in individual modules. We did so using a globally-distributed dataset comprised of 54 pollination networks, over 4000 species, and over 12,000 interactions. Within these data, we detected cophylogenetic signal at all four scales. Cophylogenetic signal was found at the level of plant-pollinator interactions on a global scale and in the majority of pollination communities. At the scale defined by the modular structure within those communities, however, we observed a much weaker cophylogenetic signal. Cophylogenetic signal was detectable in a significant proportion of individual modules and most typically when within-module phylogenetic diversity was low. In sum, the detection of cophylogenetic signal in pollination interactions across scales provides a new dimension to the story of how past evolution shapes extant pollinator-angiosperm interactions. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Population demography and heterozygosity-fitness correlations in natural guppy populations: an examination using sexually selected fitness traits
Jul 22, 2017   Molecular Ecology
Grueber CE, Fitzpatrick JL, Devigili A, Gasparini C, Ramnarine IW, Evans JP
Population demography and heterozygosity-fitness correlations in natural guppy populations: an examination using sexually selected fitness traits
Jul 22, 2017
Molecular Ecology
Heterozygosity-fitness correlations (HFCs) have been examined in a wide diversity of contexts, and the results are often used to infer the role of inbreeding in natural populations. Although population demography, reflected in population-level genetic parameters such as allelic diversity or identity disequilibrium, is expected to play a role in the emergence and detectability of HFCs, direct comparisons of variation in HFCs across many populations of the same species, with different genetic histories, are rare. Here, we examined the relationship between individual microsatellite heterozygosity and a range of sexually selected traits in 660 male guppies from 22 natural populations in Trinidad. Similar to previous studies, observed HFCs were weak overall. However, variation in HFCs among populations was high for some traits (although these variances were not statistically different from zero). Population-level genetic parameters, specifically genetic diversity levels (number of alleles, observed/expected heterozygosity) and measures of identity disequilibrium (g2 and heterozygosity-heterozygosity correlations) were not associated with variation in population-level HFCs. This latter result indicates that these metrics do not necessarily provide a reliable predictor of HFC effect sizes across populations. Importantly, diversity and identity disequilibrium statistics were not correlated, providing empirical evidence that these metrics capture different essential characteristics of populations. A complex genetic architecture likely underpins multiple fitness traits, including those associated with male fitness, which may have reduced our ability to detect HFCs in guppy populations. Further advances in this field would benefit from additional research to determine the demographic contexts in which HFCs are most likely to occur. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Detecting ancient co-dispersals and host shifts by double dating of host and parasite phylogenies: Application in proctophyllodid feather mites associated with passerine birds
Jul 22, 2017   Evolution; International Journal Of Organic Evolution
Klimov PB, Mironov SV, OConnor BM
Detecting ancient co-dispersals and host shifts by double dating of host and parasite phylogenies: Application in proctophyllodid feather mites associated with passerine birds
Jul 22, 2017
Evolution; International Journal Of Organic Evolution
Inferring co-phylogeographic events requires matching the timing of these events on both host and symbiont (e.g., parasites) phylogenies because divergences of hosts and their symbionts may not temporally coincide, and host switches may occur. We investigate a large radiation of birds (Passeriformes) and their permanent symbionts, the proctophyllodid feather mites (117 species from 116 bird species; 6 genes, 11,468 nt aligned) using two time-calibration strategies for mites: fossils only and host phylogeography only. Out of 10 putative co-phylogeographic events 4 agree in timing for both symbiont and host events being synchronous co-origins or co-dispersals; 3 were based on host shifts, but agree in timing being very close to the origin of modern hosts; 2 disagree; and 1 large basal mite split was seemingly independent from host phylogeography. Among these events was an ancient (21-25.3 Mya), synchronous co-dispersal from the Old World leading to the origin and diversifications of New World emberizoid passerids and their mites, the thraupis+quadratus species groups of Proctophyllodes. Our framework offers a more robust detection of host and symbiont co-phylogeographic events (as compared to host-symbiont reconciliation analysis and using host phylogeography for time-calibration) and provides independent data for testing alternative hypotheses on timing of host diversification and dispersal. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Microbiomarkers in inflammatory bowel diseases: caveats come with caviar
Jul 22, 2017   Gut
Sommer F, Rühlemann MC, Bang C, Höppner M, Rehman A,   . . . . . .   , Rupp J, Laudes M, Baines JF, Rosenstiel P, Franke A
Convergence and Divergence in a Long-Term Experiment with Bacteria
Jul 21, 2017   The American Naturalist
Lenski RE
Convergence and Divergence in a Long-Term Experiment with Bacteria
Jul 21, 2017
The American Naturalist
Suitably designed experiments offer the possibility of quantifying evolutionary convergence because the fraction of replicate populations that converge is known. Here I review an experiment with Escherichia coli, in which 12 populations were founded from the same ancestral strain and have evolved for almost 30 years and more than 65,000 generations under the same conditions. The tension between divergence and convergence has been a major focus of this experiment. I summarize analyses of competitive fitness, correlated responses to different environments, cell morphology, the capacity to use a previously untapped resource, mutation rates, genomic changes, and within-population polymorphisms. These analyses reveal convergence, divergence, and often a complicated mix thereof. Complications include concordance in the direction of evolutionary change with sustained quantitative variation among populations, and the potential for a given trait to exhibit divergence on one timescale and convergence on another. Despite these complications, which also occur in nature, experiments provide a powerful way to study evolutionary convergence based on analyzing replicate lineages that experience the same environment.
Seed desiccation mechanisms co-opted for vegetative desiccation in the resurrection grass Oropetium thomeaum
Jul 21, 2017   Plant, Cell & Environment
VanBuren R, Wai J, Zhang Q, Song X, Edger PP, Bryant D, Michael TP, Mockler TC, Bartels D
Seed desiccation mechanisms co-opted for vegetative desiccation in the resurrection grass Oropetium thomeaum
Jul 21, 2017
Plant, Cell & Environment
Resurrection plants desiccate during periods of prolonged drought stress, then resume normal cellular metabolism upon water availability. Desiccation tolerance has multiple origins in flowering plants and it likely evolved through rewiring seed desiccation pathways. Oropetium thomaeum is an emerging model for extreme drought tolerance and its genome, which is the smallest among surveyed grasses, was recently sequenced. Combining RNA-seq, targeted metabolite analysis, and comparative genomics, we show evidence for co-option of seed specific pathways during vegetative desiccation. Desiccation related gene-coexpression clusters are enriched in functions related to seed development including several seed specific-transcription factors. Across the metabolic network, pathways involved in programed cell death inhibition, ABA signaling, and others are activated during dehydration. Oleosins and oil bodies that typically function in seed storage are highly abundant in desiccated leaves and may function for membrane stability and storage. Orthologs to seed-specific LEA proteins from rice and maize have neofunctionalized in Oropetium with high expression during desiccation. Accumulation of sucrose, raffinose, and stachyose in drying leaves mirrors sugar accumulation patterns in maturing seeds. Together, these results connect vegetative desiccation with existing seed desiccation and drought responsive pathways and provide some key candidate genes for engineering improved drought tolerance in crop plants. This article is protected by copyright. All rights reserved.
Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept
Jul 21, 2017   Frontiers In Microbiology
Duhaime MB, Solonenko N, Roux S, Verberkmoes NC, Wichels A, Sullivan MB
Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept
Jul 21, 2017
Frontiers In Microbiology
Viruses influence the ecology and evolutionary trajectory of microbial communities. Yet our understanding of their roles in ecosystems is limited by the paucity of model systems available for hypothesis generation and testing. Further, virology is limited by the lack of a broadly accepted conceptual framework to classify viral diversity into evolutionary and ecologically cohesive units. Here, we introduce genomes, structural proteomes, and quantitative host range data for eight Pseudoalteromonas phages isolated from Helgoland (North Sea, Germany) and use these data to advance a genome-based viral operational taxonomic unit (OTU) definition. These viruses represent five new genera and inform 498 unaffiliated or unannotated protein clusters (PCs) from global virus metagenomes. In a comparison of previously sequenced Pseudoalteromonas phage isolates (n = 7) and predicted prophages (n = 31), the eight phages are unique. They share a genus with only one other isolate, Pseudoalteromonas podophage RIO-1 (East Sea, South Korea) and two Pseudoalteromonas prophages. Mass-spectrometry of purified viral particles identified 12-20 structural proteins per phage. When combined with 3-D structural predictions, these data led to the functional characterization of five previously unidentified major capsid proteins. Protein functional predictions revealed mechanisms for hijacking host metabolism and resources. Further, they uncovered a hybrid sipho-myovirus that encodes genes for Mu-like infection rarely described in ocean systems. Finally, we used these data to evaluate a recently introduced definition for virus populations that requires members of the same population to have >95% average nucleotide identity across at least 80% of their genes. Using physiological traits and genomics, we proposed a conceptual model for a viral OTU definition that captures evolutionarily cohesive and ecologically distinct units. In this trait-based framework, sensitive hosts are considered viral niches, while host ranges and infection efficiencies are tracked as viral traits. Quantitative host range assays revealed conserved traits within virus OTUs that break down between OTUs, suggesting the defined units capture niche and fitness differentiation. Together these analyses provide a foundation for model system-based hypothesis testing that will improve our understanding of marine copiotrophs, as well as phage-host interactions on the ocean particles and aggregates where Pseudoalteromonas thrive.
A genomic glance through the fog of plasticity and diversification in Pocillopora
Jul 21, 2017   Scientific Reports
Johnston EC, Forsman ZH, Flot JF, Schmidt-Roach S, Pinzón JH, Knapp ISS, Toonen RJ
A genomic glance through the fog of plasticity and diversification in Pocillopora
Jul 21, 2017
Scientific Reports
Scleractinian corals of the genus Pocillopora (Lamarck, 1816) are notoriously difficult to identify morphologically with considerable debate on the degree to which phenotypic plasticity, introgressive hybridization and incomplete lineage sorting obscure well-defined taxonomic lineages. Here, we used RAD-seq to resolve the phylogenetic relationships among seven species of Pocillopora represented by 15 coral holobiont metagenomic libraries. We found strong concordance between the coral holobiont datasets, reads that mapped to the Pocillopora damicornis (Linnaeus, 1758) transcriptome, nearly complete mitochondrial genomes, 430 unlinked high-quality SNPs shared across all Pocillopora taxa, and a conspecificity matrix of the holobiont dataset. These datasets also show strong concordance with previously published clustering of the mitochondrial clades based on the mtDNA open reading frame (ORF). We resolve seven clear monophyletic groups, with no evidence for introgressive hybridization among any but the most recently derived sister species. In contrast, ribosomal and histone datasets, which are most commonly used in coral phylogenies to date, were less informative and contradictory to these other datasets. These data indicate that extant Pocillopora species diversified from a common ancestral lineage within the last ~3 million years. Key to this evolutionary success story may be the high phenotypic plasticity exhibited by Pocillopora species.
Antifungal treatment of wild amphibian populations caused a transient reduction in the prevalence of the fungal pathogen, Batrachochytrium dendrobatidis
Jul 21, 2017   Scientific Reports
Geiger CC, Bregnard C, Maluenda E, Voordouw MJ, Schmidt BR
Antifungal treatment of wild amphibian populations caused a transient reduction in the prevalence of the fungal pathogen, Batrachochytrium dendrobatidis
Jul 21, 2017
Scientific Reports
Emerging infectious diseases can drive host populations to extinction and are a major driver of biodiversity loss. Controlling diseases and mitigating their impacts is therefore a priority for conservation science and practice. Chytridiomycosis is a devastating disease of amphibians that is caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), and for which there is an urgent need to develop mitigation methods. We treated tadpoles of the common midwife toad (Alytes obstetricans) with antifungal agents using a capture-treat-release approach in the field. Antifungal treatment during the spring reduced the prevalence of Bd in the cohort of tadpoles that had overwintered and reduced transmission of Bd from this cohort to the uninfected young-of-the-year cohort. Unfortunately, the mitigation was only transient, and the antifungal treatment was unable to prevent the rapid spread of Bd through the young-of-the year cohort. During the winter, Bd prevalence reached 100% in both the control and treated ponds. In the following spring, no effects of treatment were detectable anymore. We conclude that the sporadic application of antifungal agents in the present study was not sufficient for the long-term and large-scale control of Bd in this amphibian system.
Haplotypes Phased from Population Transcriptomes Detecting Selection in the Initial Adaptation of Miscanthus lutarioriparius to Stressful Environments
Jul 20, 2017   The Plant Genome
Zhu CY, Liu W, Kang LF, Xu Q, Xing SL, Fan YY, Song ZH, Yan J, Li JQ, Sang T
Haplotypes Phased from Population Transcriptomes Detecting Selection in the Initial Adaptation of Miscanthus lutarioriparius to Stressful Environments
Jul 20, 2017
The Plant Genome
Adaptation is a characteristic that enhances the survival or reproduction of organisms; selection is the critical process leading to adaptive evolution. Therefore, detecting selection is important in studying evolutionary biology. Changes in allele frequency are fundamental to adaptive evolution. The allele frequency of entire genes at the genomic scale is more intensive and precise for analyzing selection effects, compared with simple sequence repeat and single nucleotide polymorphism (SNP) alleles from nuclear gene fragments. Here, we analyzed 29,094 SNPs derived from 80 individuals of 14 L. Liou ex S.L. Chen & Renvoize populations planted near their native habitat (Jiangxia, Hubei Province, JH) and a stressful environment (Qingyang, Gansu Province, QG) to detect selection during initial adaptation. The nucleotide diversity of over 60% of genes was decreased in QG compared with JH, suggesting that most genes were undergoing selection in the stressful environment. We explored a new approach based on haplotype data inferred from RNA-seq data to analyze the change in frequency between two sites and to detect selection signals. In total, 402 and 51 genes were found to be targets of positive and negative selection, respectively. Among these candidate genes, the enrichment of abiotic stress-response genes and photosynthesis-related genes might have been responsible for establishment in the stressful environment. This is the first study assessing the change in allele frequency at the genomic level during adaptation. The method in which allele frequency detects selection during initial adaptation using population RNA-seq data would be useful for developing evolutionary biology. Copyright © 2017 Crop Science Society of America.
New insights into the karyotype evolution of the free-living flatworm Macrostomum lignano (Platyhelminthes, Turbellaria)
Jul 21, 2017   Scientific Reports
Zadesenets KS, Schärer L, Rubtsov NB
New insights into the karyotype evolution of the free-living flatworm Macrostomum lignano (Platyhelminthes, Turbellaria)
Jul 21, 2017
Scientific Reports
The free-living flatworm Macrostomum lignano is a model organism for evolutionary and developmental biology studies. Recently, an unusual karyotypic diversity was revealed in this species. Specifically, worms are either 'normal' 2n = 8, or they are aneuploid with one or two additional large chromosome(s) (i.e. 2n = 9 or 2n = 10, respectively). Aneuploid worms did not show visible behavioral or morphological abnormalities and were successful in reproduction. In this study, we generated microdissected DNA probes from chromosome 1 (further called MLI1), chromosome 2 (MLI2), and a pair of similar-sized smaller chromosomes (MLI3, MLI4). FISH using these probes revealed that MLI1 consists of contiguous regions homologous to MLI2-MLI4, suggesting that MLI1 arose due to the whole genome duplication and subsequent fusion of one full chromosome set into one large metacentric chromosome. Therefore, one presumably full haploid genome was packed into MLI1, leading to hidden tetraploidy in the M. lignano genome. The study of Macrostomum sp. 8 - a sibling species of M. lignano - revealed that it usually has one additional pair of large chromosomes (2n = 10) showing a high homology to MLI1, thus suggesting hidden hexaploidy in its genome. Possible evolutionary scenarios for the emergence of the M. lignano and Macrostomum sp. 8 genomes are discussed.
Antarctic sea ice region as a source of biogenic organic nitrogen in aerosols
Jul 21, 2017   Scientific Reports
Dall'Osto M, Ovadnevaite J, Paglione M, Beddows DCS, Ceburnis D,   . . . . . .   , Decesari S, Cristina Facchini M, Harrison RM, O'Dowd C, Simó R
Antarctic sea ice region as a source of biogenic organic nitrogen in aerosols
Jul 21, 2017
Scientific Reports
Climate warming affects the development and distribution of sea ice, but at present the evidence of polar ecosystem feedbacks on climate through changes in the atmosphere is sparse. By means of synergistic atmospheric and oceanic measurements in the Southern Ocean near Antarctica, we present evidence that the microbiota of sea ice and sea ice-influenced ocean are a previously unknown significant source of atmospheric organic nitrogen, including low molecular weight alkyl-amines. Given the keystone role of nitrogen compounds in aerosol formation, growth and neutralization, our findings call for greater chemical and source diversity in the modelling efforts linking the marine ecosystem to aerosol-mediated climate effects in the Southern Ocean.
Genetic differentiation of the Schizothorax species complex (Cyprinidae) in the Nujiang River (upper Salween)
Jul 21, 2017   Scientific Reports
Chen W, Yue X, He S
Genetic differentiation of the Schizothorax species complex (Cyprinidae) in the Nujiang River (upper Salween)
Jul 21, 2017
Scientific Reports
Phenotypically diverse species from recently evolved groups always share allele/haplotype due to insufficient differentiation in the early process. In this study, we performed population genetics analyses using sequences from the mitochondrial cytochrome b gene, and two nuclear genes to investigate the genetic differentiation of the closely related Schizothorax species complex, comprising a group of alpine fish living in the Nujiang River. The results from both mtDNA and nDNA markers revealed relatively low but pronounced genetic differentiation among the three Schizothorax species, i.e., Schizothorax gongshanensis, S. lissolabiatus, and S. nukiangensis. However, haplotype sharing was frequently occurred among the three species. Divergence time estimation suggested the last glaciation on the Tibetan Plateau (0.075-0.01 Ma) might drive the divergence of the species complex. Gene flow might contribute to the haplotype sharing between S. gongshanensis and S. lissolabiatus, and between S. gongshanensis and S. nukiangensis, whereas retention of ancestral polymorphisms seemed to be a better explanation of the haplotype sharing between S. lissolabiatus and S. nukiangensis. In addition, S. lissolabiatus populations should obtain more protection in the future because of their low genetic diversity and habitat fragmentation. In summary, our study assesses genetic differentiation among the three closely related Schizothorax species and explores the possible driving forces for their differentiation.
Comparison of the protein-coding genomes of three deep-sea, sulfur-oxidising bacteria: "Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena
Jul 21, 2017   BMC Research Notes
McGill SE, Barker D
Comparison of the protein-coding genomes of three deep-sea, sulfur-oxidising bacteria: "Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena
Jul 21, 2017
BMC Research Notes
" Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena are all sulfur-oxidising bacteria found in deep-sea vent environments. Recent research suggests that the two symbiotic organisms, "Candidatus R. magnifica" and "Candidatus V. okutanii", may share common ancestry with the autonomously living species T. crunogena. We used comparative genomics to examine the genome-wide protein-coding content of all three species to explore their similarities. In particular, we used the OrthoMCL algorithm to sort proteins into groups of putative orthologs on the basis of sequence similarity. The OrthoMCL inflation parameter was tuned using biological criteria. Using the tuned value, OrthoMCL delimited 1070 protein groups. 63.5% of these groups contained one protein from each species. Two groups contained duplicate protein copies from all three species. 123 groups were unique to T. crunogena and ten groups included multiple copies of T. crunogena proteins but only single copies from the other species. "Candidatus R. magnifica" had one unique group, and had multiple copies in one group where the other species had a single copy. There were no groups unique to "Candidatus V. okutanii", and no groups in which there were multiple "Candidatus V. okutanii" proteins but only single proteins from the other species. Results align with previous suggestions that all three species share a common ancestor. However this is not definitive evidence to make taxonomic conclusions and the possibility of horizontal gene transfer was not investigated. Methodologically, the tuning of the OrthoMCL inflation parameter using biological criteria provides further methods to refine the OrthoMCL procedure.
Germline and reproductive tract effects intensify in male mice with successive generations of estrogenic exposure
Jul 20, 2017   PLoS Genetics
Horan TS, Marre A, Hassold T, Lawson C, Hunt PA
Germline and reproductive tract effects intensify in male mice with successive generations of estrogenic exposure
Jul 20, 2017
PLoS Genetics
The hypothesis that developmental estrogenic exposure induces a constellation of male reproductive tract abnormalities is supported by experimental and human evidence. Experimental data also suggest that some induced effects persist in descendants of exposed males. These multi- and transgenerational effects are assumed to result from epigenetic changes to the germline, but few studies have directly analyzed germ cells. Typically, studies of transgenerational effects have involved exposing one generation and monitoring effects in subsequent unexposed generations. This approach, however, has limited human relevance, since both the number and volume of estrogenic contaminants has increased steadily over time, intensifying rather than reducing or eliminating exposure. Using an outbred CD-1 mouse model, and a sensitive and quantitative marker of germline development, meiotic recombination, we tested the effect of successive generations of exposure on the testis. We targeted the germline during a narrow, perinatal window using oral exposure to the synthetic estrogen, ethinyl estradiol. A complex three generation exposure protocol allowed us to compare the effects of individual, paternal, and grandpaternal (ancestral) exposure. Our data indicate that multiple generations of exposure not only exacerbate germ cell exposure effects, but also increase the incidence and severity of reproductive tract abnormalities. Taken together, our data suggest that male sensitivity to environmental estrogens is increased by successive generations of exposure.
Birth and death of a protein
Jul 20, 2017   ELife
Clément J, de Massy B
Birth and death of a protein
Jul 20, 2017
ELife
The ways in which recombination sites are determined during meiosis are becoming clearer following a phylogenomic analysis for 225 different species.
Dynamics of genomic innovation in the unicellular ancestry of animals
Jul 20, 2017   ELife
Grau-Bové X, Torruella G, Donachie S, Suga H, Leonard G, Richards TA, Ruiz-Trillo I
Dynamics of genomic innovation in the unicellular ancestry of animals
Jul 20, 2017
ELife
Which genomic innovations underpinned the origin of multicellular animals is still an open debate. Here, we investigate this question by reconstructing the genome architecture and gene family diversity of ancestral premetazoans, aiming to date the emergence of animal-like traits. Our comparative analysis involves genomes from animals and their closest unicellular relatives (the Holozoa), including four new genomes: three Ichthyosporea and Corallochytrium limacisporum. Here we show that the earliest animals were shaped by dynamic changes in genome architecture before the emergence of multicellularity: an early burst of gene diversity in the ancestor of Holozoa, enriched in transcription factors and cell adhesion machinery, was followed by multiple and differently-timed episodes of synteny disruption, intron gain and genome expansions. Thus, the foundations of animal genome architecture were laid before the origin of complex multicellularity - highlighting the necessity of a unicellular perspective to understand early animal evolution.
SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)
Jul 20, 2017   Ecology And Evolution
Shultz AJ, Baker AJ, Hill GE, Nolan PM, Edwards SV
SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)
Jul 20, 2017
Ecology And Evolution
Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen-induced selection event. Using ddRADseq, we genotyped over 18,000 SNPs across the genome in native pre-epizootic western US birds, introduced birds from Hawaii and the eastern United States, post-epizootic eastern birds, and western birds sampled across a similar time span. We found 14% and 7% reductions in nucleotide diversity, respectively, in Hawaiian and pre-epizootic eastern birds relative to pre-epizootic western birds, as well as elevated levels of linkage disequilibrium and other signatures of founder events. Despite finding numerous significant frequency shifts (outlier loci) between pre-epizootic native and introduced populations, we found no signal of reduced genetic diversity, elevated linkage disequilibrium, or outlier loci as a result of the epizootic. Simulations demonstrate that the proportion of outliers associated with founder events could be explained by genetic drift. This rare view of genetic evolution across time in an invasive species provides direct evidence that demographic shifts like founder events have genetic consequences more widespread across the genome than natural selection.
Early evolution of radial glial cells in Bilateria
Jul 20, 2017   Proceedings. Biological Sciences
Helm C, Karl A, Beckers P, Kaul-Strehlow S, Ulbricht E, Kourtesis I, Kuhrt H, Hausen H, Bartolomaeus T, Reichenbach A, Bleidorn C
Early evolution of radial glial cells in Bilateria
Jul 20, 2017
Proceedings. Biological Sciences
Bilaterians usually possess a central nervous system, composed of neurons and supportive cells called glial cells. Whereas neuronal cells are highly comparable in all these animals, glial cells apparently differ, and in deuterostomes, radial glial cells are found. These particular secretory glial cells may represent the archetype of all (macro) glial cells and have not been reported from protostomes so far. This has caused controversial discussions of whether glial cells represent a homologous bilaterian characteristic or whether they (and thus, centralized nervous systems) evolved convergently in the two main clades of bilaterians. By using histology, transmission electron microscopy, immunolabelling and whole-mount in situ hybridization, we show here that protostomes also possess radial glia-like cells, which are very likely to be homologous to those of deuterostomes. Moreover, our antibody staining indicates that the secretory character of radial glial cells is maintained throughout their various evolutionary adaptations. This implies an early evolution of radial glial cells in the last common ancestor of Protostomia and Deuterostomia. Furthermore, it suggests that an intraepidermal nervous system-composed of sensory cells, neurons and radial glial cells-was probably the plesiomorphic condition in the bilaterian ancestor. © 2017 The Authors.
Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice
Jul 20, 2017   Genome Biology
Harkins CP, Pichon B, Doumith M, Parkhill J, Westh H, Tomasz A, de Lencastre H, Bentley SD, Kearns AM, Holden MTG
Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice
Jul 20, 2017
Genome Biology
The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the emergence of resistant strains. Methicillin-resistant Staphylococcus aureus (MRSA) was first observed in 1960, less than one year after the introduction of this second generation beta-lactam antibiotic into clinical practice. Epidemiological evidence has always suggested that resistance arose around this period, when the mecA gene encoding methicillin resistance carried on an SCCmec element, was horizontally transferred to an intrinsically sensitive strain of S. aureus. Whole genome sequencing a collection of the first MRSA isolates allows us to reconstruct the evolutionary history of the archetypal MRSA. We apply Bayesian phylogenetic reconstruction to infer the time point at which this early MRSA lineage arose and when SCCmec was acquired. MRSA emerged in the mid-1940s, following the acquisition of an ancestral type I SCCmec element, some 14 years before the first therapeutic use of methicillin. Methicillin use was not the original driving factor in the evolution of MRSA as previously thought. Rather it was the widespread use of first generation beta-lactams such as penicillin in the years prior to the introduction of methicillin, which selected for S. aureus strains carrying the mecA determinant. Crucially this highlights how new drugs, introduced to circumvent known resistance mechanisms, can be rendered ineffective by unrecognised adaptations in the bacterial population due to the historic selective landscape created by the widespread use of other antibiotics.
A G326E substitution in the glutamate-gated chloride channel 3 (GluCl3) of the two-spotted spider mite Tetranychus urticae abolishes the agonistic activity of macrocyclic lactones
Jul 24, 2017   Pest Management Science
Mermans C, Dermauw W, Geibel S, Van Leeuwen T
A G326E substitution in the glutamate-gated chloride channel 3 (GluCl3) of the two-spotted spider mite Tetranychus urticae abolishes the agonistic activity of macrocyclic lactones
Jul 24, 2017
Pest Management Science
The macrocyclic lactones abamectin and milbemectin are frequently used to control phytophagous mites such as Tetranychus urticae. Consequently, resistance has developed and was genetically linked with substitutions in the glutamate-gated chloride channel (GluCl) subunits TuGluCl1 and TuGluCl3. Here, we functionally validated a G326E substitution in TuGluCl3 by functional expression in Xenopus laevis oocytes followed by two-electrode voltage-clamp electrophysiology. Homomeric wild-type and mutated GluCl3 were successfully expressed. L-glutamic-acid-induced currents exhibited a rapid onset equal in both channels and EC50 for glutamate was in the micromolar range (384.2 μM and 292.7 μM, respectively). Abamectin and milbemycin A4 elicited sustained currents in wild-type GluCl3 channels, but the G326E substitution completely abolished the agonistic activity of macrocyclic lactones. A target-site mutation in GluCl3 contributes to avermectin resistance in T. urticae. However, given the multitude of channel genes and the potential additive or synergistic effects of mutations, to what extent mutations determine the often extremely strong resistance phenotype in the field deserves further study. This article is protected by copyright. All rights reserved.

The link you entered does not seem to be valid

Please make sure the link points to nature.com contains a valid shared_access_token

Downloading PDF to your library...

Uploading PDF...

PDF uploading

Delete tag: