title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1477 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution link: https://peerj.com/articles/5549 last-modified: 2018-10-05 description: The number of amino acids that occupy a given protein site during evolution reflects the selective constraints operating on the site. This evolutionary variability is strongly influenced by the structural properties of the site in the native structure, and it is quantified either through sequence entropy or through substitution rates. However, while the sequence entropy only depends on the equilibrium frequencies of the amino acids, the substitution rate also depends on the exchangeability matrix that describes mutations in the mathematical model of the substitution process. Here we apply two variants of a mathematical model of protein evolution with selection for protein stability, both against unfolding and against misfolding. Exploiting the approximation of independent sites, these models allow computing site-specific substitution processes that satisfy global constraints on folding stability. We find that site-specific substitution rates do not depend only on the selective constraints acting on the site, quantified through its sequence entropy. In fact, polar sites evolve faster than hydrophobic sites even for equal sequence entropy, as a consequence of the fact that polar amino acids are characterized by higher mutational exchangeability than hydrophobic ones. Accordingly, the model predicts that more polar proteins tend to evolve faster. Nevertheless, these results change if we compare proteins that evolve under different mutation biases, such as orthologous proteins in different bacterial genomes. In this case, the substitution rates are faster in genomes that evolve under mutational bias that favor hydrophobic amino acids by preferentially incorporating the nucleotide Thymine that is more frequent in hydrophobic codons. This appearingly contradictory result arises because buried sites occupied by hydrophobic amino acids are characterized by larger selective factors that largely amplify the substitution rate between hydrophobic amino acids, while the selective factors of exposed sites have a weaker effect. Thus, changes in the mutational bias produce deep effects on the biophysical properties of the protein (hydrophobicity) and on its evolutionary properties (sequence entropy and substitution rate) at the same time. The program Prot_evol that implements the two site-specific substitution processes is freely available at https://ub.cbm.uam.es/prot_fold_evol/prot_fold_evol_soft_main.php#Prot_Evol. creator: María José Jiménez-Santos creator: Miguel Arenas creator: Ugo Bastolla uri: https://doi.org/10.7717/peerj.5549 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jiménez-Santos et al. title: Assessment of genomic changes in a CRISPR/Cas9 Phaeodactylum tricornutum mutant through whole genome resequencing link: https://peerj.com/articles/5507 last-modified: 2018-10-05 description: The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, co-opted from a bacterial defense natural mechanism, is the cutting edge technology to carry out genome editing in a revolutionary fashion. It has been shown to work in many different model organisms, from human to microbes, including two diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana. Transforming P. tricornutum by bacterial conjugation, we have performed CRISPR/Cas9-based mutagenesis delivering the nuclease as an episome; this allowed for avoiding unwanted perturbations due to random integration in the genome and for excluding the Cas9 activity when it was no longer required, reducing the probability of obtaining off-target mutations, a major drawback of the technology. Since there are no reports on off-target occurrence at the genome level in microalgae, we performed whole-genome Illumina sequencing and found a number of different unspecific changes in both the wild type and mutant strains, while we did not observe any preferential mutation in the genomic regions in which off-targets were predicted. Our results confirm that the CRISPR/Cas9 technology can be efficiently applied to diatoms, showing that the choice of the conjugation method is advantageous for minimizing unwanted changes in the genome of P. tricornutum. creator: Monia Teresa Russo creator: Riccardo Aiese Cigliano creator: Walter Sanseverino creator: Maria Immacolata Ferrante uri: https://doi.org/10.7717/peerj.5507 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Russo et al. title: A new limestone-dwelling species of Micryletta (Amphibia: Anura: Microhylidae) from northern Vietnam link: https://peerj.com/articles/5771 last-modified: 2018-10-04 description: We report on a new species of the genus Micryletta from limestone karst areas in northern Vietnam, which is described on the basis of molecular and morphological evidence. Micryletta nigromaculata sp. nov. is restricted to narrow areas of subtropical forests covering karst massifs in Cat Ba National Park (Hai Phong Province) and Cuc Phuong National Park (Ninh Binh Province) at elevations of 90–150 m a.s.l. In the phylogenetic analyses, the new species is unambiguously positioned as a sister lineage to all remaining species of Micryletta. We also discuss genealogical relationships and taxonomic problems within the genus Micryletta, provide molecular evidence for the validity of M. erythropoda and discuss the taxonomic status of M. steinegeri. We suggest the new species should be considered as Endangered (B1ab(iii), EN) following the IUCN’s Red List categories. A discussion on herpetofaunal diversity and conservation in threatened limestone karst massifs in Southeast Asia is provided. creator: Nikolay A. Poyarkov creator: Tan Van Nguyen creator: Tang Van Duong creator: Vladislav A. Gorin creator: Jian-Huan Yang uri: https://doi.org/10.7717/peerj.5771 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Poyarkov et al. title: Relationships between neuropsychological and antisaccade measures in multiple sclerosis patients link: https://peerj.com/articles/5737 last-modified: 2018-10-04 description: BackgroundThe Stroop test is frequently used to assess deficits in inhibitory control in people with multiple sclerosis (MS). This test has limitations and antisaccade eye movements, that also measure inhibitory control, may be an alternative to Stroop.ObjectivesThe aim of this study was twofold: (i) to investigate if the performance in the antisaccade task is altered in patients with MS and (ii) to investigate the correlation between performances in neuropsychological tests, the Stroop test and the antisaccade task.MethodsWe measured antisaccades (AS) parameters with an infrared eye tracker (SMIRED 250 Hz) using a standard AS paradigm. A total of 38 subjects diagnosed with MS and 38 age and gender matched controls participated in this study. Neuropsychological measures were obtained from the MS group.ResultsPatients with MS have higher error rates and prolonged latency than controls in the antisaccade task. There was a consistent association between the Stroop performance and AS latency. Stroop performance but not AS latency was associated with other neuropsychological measures in which the MS group showed deficits.ConclusionsOur findings suggest that AS may be a selective and independent measure to investigate inhibitory control in patients with MS. More studies are necessary to confirm our results and to describe brain correlates associated with impaired performance in the antisaccade task in people diagnosed with MS. creator: Marisa Borges Ferreira creator: Paulo Alexandre Pereira creator: Marta Parreira creator: Ines Sousa creator: José Figueiredo creator: João José Cerqueira creator: Antonio Filipe Macedo uri: https://doi.org/10.7717/peerj.5737 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ferreira et al. title: An automated, high-throughput method for standardizing image color profiles to improve image-based plant phenotyping link: https://peerj.com/articles/5727 last-modified: 2018-10-04 description: High-throughput phenotyping has emerged as a powerful method for studying plant biology. Large image-based datasets are generated and analyzed with automated image analysis pipelines. A major challenge associated with these analyses is variation in image quality that can inadvertently bias results. Images are made up of tuples of data called pixels, which consist of R, G, and B values, arranged in a grid. Many factors, for example image brightness, can influence the quality of the image that is captured. These factors alter the values of the pixels within images and consequently can bias the data and downstream analyses. Here, we provide an automated method to adjust an image-based dataset so that brightness, contrast, and color profile is standardized. The correction method is a collection of linear models that adjusts pixel tuples based on a reference panel of colors. We apply this technique to a set of images taken in a high-throughput imaging facility and successfully detect variance within the image dataset. In this case, variation resulted from temperature-dependent light intensity throughout the experiment. Using this correction method, we were able to standardize images throughout the dataset, and we show that this correction enhanced our ability to accurately quantify morphological measurements within each image. We implement this technique in a high-throughput pipeline available with this paper, and it is also implemented in PlantCV. creator: Jeffrey C. Berry creator: Noah Fahlgren creator: Alexandria A. Pokorny creator: Rebecca S. Bart creator: Kira M. Veley uri: https://doi.org/10.7717/peerj.5727 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Berry et al. title: Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances link: https://peerj.com/articles/5710 last-modified: 2018-10-04 description: BackgroundMangroves are important coastal ecosystems known for high photosynthetic productivity and the ability to support marine food chains through supply of dissolved carbon or particular organic matter. Most of the carbon found in mangroves is produced by its vegetation and is decomposed in root associated sediment. This process involves a tight interaction between microbial populations, litter chemical composition, and environmental parameters. Here, we study the complex interactions found during litter decomposition in mangroves by applying network analysis to metagenomic data.MethodsLeaves of three species of mangrove trees typically found in the southeast of Brazil (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) were collected in separate litter bags and left on three different mangroves for 60 days. These leaves were subsequently used for metagenome sequencing using Ion Torrent technology. Sequences were annotated in MG-RAST and used for network construction using MENAp.ResultsThe most common phyla were Proteobacteria (classes Gamma and Alphaproteobacteria) followed by Firmicutes (Clostridia and Bacilli). The most abundant protein clusters were associated with the metabolism of carbohydrates, amino acids, and proteins. Non-metric multidimensional scaling of the metagenomic data indicated that substrate (i.e., tree species) did not significantly select for a specific community. Both networks exhibited scale-free characteristics and small world structure due to the low mean shortest path length and high average clustering coefficient. These networks also had a low number of hub nodes most of which were module hubs.DiscussionThis study demonstrates that under different environmental pressures (i.e., plant species or mangrove location) the microbial community associated with the decaying material forms a robust and stable network. creator: Rodrigo G. Taketani creator: Marta A. Moitinho creator: Tim H. Mauchline creator: Itamar S. Melo uri: https://doi.org/10.7717/peerj.5710 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Taketani et al. title: Predicting academic career outcomes by predoctoral publication record link: https://peerj.com/articles/5707 last-modified: 2018-10-04 description: BackgroundFor students entering a science PhD program, a tenure-track faculty research position is often perceived as the ideal long-term goal. A relatively small percentage of individuals ultimately achieve this goal, however, with the vast majority of PhD recipients ultimately finding employment in industry or government positions. Given the disparity between academic career ambitions and outcomes, it is useful to understand factors that may predict those outcomes. Toward this goal, the current study examined employment status of PhD graduates from biomedical sciences programs at the University of Colorado Anschutz Medical Campus (CU AMC) and related this to metrics of predoctoral publication records, as well as to other potentially important factors, such as sex and time-since-degree, to determine if these measures could predict career outcomes.MethodsDemographic information (name, PhD program, graduation date, sex) of CU AMC biomedical sciences PhD graduates between 2000 and 2015 was obtained from University records. Career outcomes (academic faculty vs. non-faculty) and predoctoral publication records (number and impact factors of first-author and non-first-author publications) were obtained via publicly available information. Relationships between predoctoral publication record and career outcomes were investigated by (a) comparing faculty vs. non-faculty publication metrics, using t-tests, and (b) investigating the ability of predoctoral publication record, sex, and time-since-degree to predict career outcomes, using logistic regression.ResultsSignificant faculty vs. non-faculty differences were observed in months since graduation (p < 0.001), first-author publication number (p = 0.001), average first-author impact factor (p = 0.006), and highest first-author impact factor (p = 0.004). With sex and months since graduation as predictors of career outcome, the logistic regression model was significant (p < 0.001), with both being male and having more months since graduation predicting career status. First-author related publication metrics (number of publications, average impact factor, highest impact factor) all significantly improved model fit (χ2 < 0.05 for all) and were all significant predictors of faculty status (p < 0.05 for all). Non-first-author publication metrics did not significantly improve model fit or predict faculty status.DiscussionResults suggest that while sex and months since graduation also predict career outcomes, a strong predoctoral first-author publication record may increase likelihood of obtaining an academic faculty research position. Compared to non-faculty, individuals employed in faculty positions produced more predoctoral first-author publications, with these being in journals with higher impact factors. Furthermore, first-author publication record, sex, and months since graduation were significant predictors of faculty status. creator: Jason R. Tregellas creator: Jason Smucny creator: Donald C. Rojas creator: Kristina T. Legget uri: https://doi.org/10.7717/peerj.5707 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Tregellas et al. title: A new species of the odorous frog genus Odorrana (Amphibia, Anura, Ranidae) from southwestern China link: https://peerj.com/articles/5695 last-modified: 2018-10-04 description: The genus Odorrana is widely distributed in the mountains of East and Southeastern Asia. An increasing number of new species in the genus have been recognized especially in the last decade. Phylogenetic studies of the O. schmackeri species complex with wide distributional range also revealed several cryptic species. Here, we describe a new species in the species complex from Guizhou Province of China. Phylogenetic analyses based on mitochondrial DNA indicated the new species as a monophyly clustered into the Odorrana clade and sister to O. schmackeri, and nuclear DNA also indicated it as an independent lineage separated from its related species. Morphologically, the new species can be distinguished from its congeners based on a combination of the following characters: (1) having smaller body size in males (snout-vent length (SVL) <43.3 mm); (2) head longer than wide; (3) dorsolateral folds absent; (4) tympanum of males large and distinct, tympanum diameter twice as long as width of distal phalanx of finger III; (5) two metacarpal tubercles; (6) relative finger lengths: II < I < IV < III; (7) tibiotarsal articulation reaching to the level between eye to nostril when leg stretched forward; (8) disks on digits with circum-marginal grooves; (9) toes fully webbed to disks; (10) the first subarticular tubercle on fingers weak; (11) having white pectoral spinules, paired subgular vocal sacs located at corners of throat, light yellow nuptial pad on the first finger in males. creator: Shize Li creator: Ning Xu creator: Jingcai Lv creator: Jianping Jiang creator: Gang Wei creator: Bin Wang uri: https://doi.org/10.7717/peerj.5695 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Li et al. title: Effects of mangrove removal on benthic organisms in the Siangshan Wetland in Hsinchu, Taiwan link: https://peerj.com/articles/5670 last-modified: 2018-10-04 description: Mangrove degradation is a well-documented trend, but the spread of mangroves within the Siangshan Wetland in Hsinchu, Taiwan, runs contrary to that trend. The spread of mangroves changes the structure and functions of habitats for benthic organisms, causes infilling of estuaries and flooding and creates breeding grounds for small black mosquitoes. A large-scale mangrove-removal project was undertaken by the Hsinchu City Government from October 2015 to March 2016. They also investigated the consequences of mangrove removal on benthic organisms and adjacent habitats from October 2015 to September 2016, and the density, species count, Shannon–Wiener index (H′), and Pielou’s evenness index (J′) of the mangrove and non-mangrove regions were compared. In this study, we used satellite telemetry images to monitor fluctuations in mangrove density from 2006 to 2016. The non-mangrove region exhibited more variations than the mangrove region. After mangrove removal, species returned to their original habitats and noteworthy biological values significantly increased in the mangrove regions. This study presents evidence to argue that mangrove removal benefits benthic organisms. The results indicate that mangrove removal can be an appropriate habitat rehabilitation strategy for benthic organisms. The ecological findings of this study can inform coastal managers or other officials who seek to steward mangrove biomass. creator: Yu-Chi Chen creator: Ta-Jen Chu creator: Ju-Der Wei creator: Chun-Han Shih uri: https://doi.org/10.7717/peerj.5670 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chen et al. title: Conceptual and empirical advances in Neotropical biodiversity research link: https://peerj.com/articles/5644 last-modified: 2018-10-04 description: The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of “trans-disciplinary biogeography,” which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow’s ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life. creator: Alexandre Antonelli creator: María Ariza creator: James Albert creator: Tobias Andermann creator: Josué Azevedo creator: Christine Bacon creator: Søren Faurby creator: Thais Guedes creator: Carina Hoorn creator: Lúcia G. Lohmann creator: Pável Matos-Maraví creator: Camila D. Ritter creator: Isabel Sanmartín creator: Daniele Silvestro creator: Marcelo Tejedor creator: Hans ter Steege creator: Hanna Tuomisto creator: Fernanda P. Werneck creator: Alexander Zizka creator: Scott V. Edwards uri: https://doi.org/10.7717/peerj.5644 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Antonelli et al.