title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1935
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Genetic architecture of pollination syndrome transition between hummingbird-specialist and generalist species in the genus Rhytidophyllum (Gesneriaceae)
link: https://peerj.com/articles/1028
last-modified: 2015-06-18
description: Adaptation to pollinators is a key factor of diversification in angiosperms. The Caribbean sister genera Rhytidophyllum and Gesneria present an important diversification of floral characters. Most of their species can be divided in two major pollination syndromes. Large-open flowers with pale colours and great amount of nectar represent the generalist syndrome, while the hummingbird-specialist syndrome corresponds to red tubular flowers with a less important nectar volume. Repeated convergent evolution toward the generalist syndrome in this group suggests that such transitions rely on few genes of moderate to large effect. To test this hypothesis, we built a linkage map and performed a QTL detection for divergent pollination syndrome traits by crossing one specimen of the generalist species Rhytidophyllum auriculatum with one specimen of the hummingbird pollinated R. rupincola. Using geometric morphometrics and univariate traits measurements, we found that floral shape among the second-generation hybrids is correlated with morphological variation observed between generalist and hummingbird-specialist species at the genus level. The QTL analysis showed that colour and nectar volume variation between syndromes involve each one major QTL while floral shape has a more complex genetic basis and rely on few genes of moderate effect. Finally, we did not detect any genetic linkage between the QTLs underlying those traits. This genetic independence of traits could have facilitated evolution toward optimal syndromes.
creator: Hermine Alexandre
creator: Justine Vrignaud
creator: Brigitte Mangin
creator: Simon Joly
uri: https://doi.org/10.7717/peerj.1028
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Alexandre et al.

title: How reproducible are the measurements of leaf fluctuating asymmetry?
link: https://peerj.com/articles/1027
last-modified: 2015-06-18
description: Fluctuating asymmetry (FA) represents small, non-directional deviations from perfect symmetry in morphological characters. FA is generally assumed to increase in response to stress; therefore, FA is frequently used in ecological studies as an index of environmental or genetic stress experienced by an organism. The values of FA are usually small, and therefore the reliable detection of FA requires precise measurements. The reproducibility of fluctuating asymmetry (FA) was explored by comparing the results of measurements of scanned images of 100 leaves of downy birch (Betula pubescens) conducted by 31 volunteer scientists experienced in studying plant FA. The median values of FA varied significantly among the participants, from 0.000 to 0.074, and the coefficients of variation in FA for individual leaves ranged from 25% to 179%. The overall reproducibility of the results among the participants was rather low (0.074). Variation in instruments and methods used by the participants had little effect on the reported FA values, but the reproducibility of the measurements increased by 30% following exclusion of data provided by seven participants who had modified the suggested protocol for leaf measurements. The scientists working with plant FA are advised to pay utmost attention to adequate and detailed description of their data acquisition protocols in their forthcoming publications, because all characteristics of instruments and methods need to be controlled to increase the quality and reproducibility of the data. Whenever possible, the images of all measured objects and the results of primary measurements should be published as electronic appendices to scientific papers.
creator: Mikhail V. Kozlov
uri: https://doi.org/10.7717/peerj.1027
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kozlov

title: Global sensitivity analysis of a dynamic model for gene expression in Drosophila embryos
link: https://peerj.com/articles/1022
last-modified: 2015-06-18
description: It is well known that gene regulation is a tightly controlled process in early organismal development. However, the roles of key processes involved in this regulation, such as transcription and translation, are less well understood, and mathematical modeling approaches in this field are still in their infancy. In recent studies, biologists have taken precise measurements of protein and mRNA abundance to determine the relative contributions of key factors involved in regulating protein levels in mammalian cells. We now approach this question from a mathematical modeling perspective. In this study, we use a simple dynamic mathematical model that incorporates terms representing transcription, translation, mRNA and protein decay, and diffusion in an early Drosophila embryo. We perform global sensitivity analyses on this model using various different initial conditions and spatial and temporal outputs. Our results indicate that transcription and translation are often the key parameters to determine protein abundance. This observation is in close agreement with the experimental results from mammalian cells for various initial conditions at particular time points, suggesting that a simple dynamic model can capture the qualitative behavior of a gene. Additionally, we find that parameter sensitivites are temporally dynamic, illustrating the importance of conducting a thorough global sensitivity analysis across multiple time points when analyzing mathematical models of gene regulation.
creator: Gregory D. McCarthy
creator: Robert A. Drewell
creator: Jacqueline M. Dresch
uri: https://doi.org/10.7717/peerj.1022
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 McCarthy et al.

title: Recent mobility of plastid encoded group II introns and twintrons in five strains of the unicellular red alga Porphyridium
link: https://peerj.com/articles/1017
last-modified: 2015-06-18
description: Group II introns are closely linked to eukaryote evolution because nuclear spliceosomal introns and the small RNAs associated with the spliceosome are thought to trace their ancient origins to these mobile elements. Therefore, elucidating how group II introns move, and how they lose mobility can potentially shed light on fundamental aspects of eukaryote biology. To this end, we studied five strains of the unicellular red alga Porphyridium purpureum that surprisingly contain 42 group II introns in their plastid genomes. We focused on a subset of these introns that encode mobility-conferring intron-encoded proteins (IEPs) and found them to be distributed among the strains in a lineage-specific manner. The reverse transcriptase and maturase domains were present in all lineages but the DNA endonuclease domain was deleted in vertically inherited introns, demonstrating a key step in the loss of mobility. P. purpureum plastid intron RNAs had a classic group IIB secondary structure despite variability in the DIII and DVI domains. We report for the first time the presence of twintrons (introns-within-introns, derived from the same mobile element) in Rhodophyta. The P. purpureum IEPs and their mobile introns provide a valuable model for the study of mobile retroelements in eukaryotes and offer promise for biotechnological applications.
creator: Marie-Mathilde Perrineau
creator: Dana C. Price
creator: Georg Mohr
creator: Debashish Bhattacharya
uri: https://doi.org/10.7717/peerj.1017
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Perrineau et al.

title: Leadership and management influences the outcome of wildlife reintroduction programs: findings from the Sea Eagle Recovery Project
link: https://peerj.com/articles/1012
last-modified: 2015-06-18
description: Wildlife reintroductions and translocations are statistically unlikely to succeed. Nevertheless, they remain a critical part of conservation because they are the only way to actively restore a species into a habitat from which it has been extirpated. Past efforts to improve these practices have attributed the low success rate to failures in the biological knowledge (e.g., ignorance of social behavior, poor release site selection), or to the inherent challenges of reinstating a species into an area where threats have already driven it to local extinction. Such research presumes that the only way to improve reintroduction outcomes is through improved biological knowledge. This emphasis on biological solutions may have caused researchers to overlook the potential influence of other factors on reintroduction outcomes. I employed a grounded theory approach to study the leadership and management of a successful reintroduction program (the Sea Eagle Recovery Project in Scotland, UK) and identify four critical managerial elements that I theorize may have contributed to the successful outcome of this 50-year reintroduction. These elements are: 1. Leadership & Management: Small, dedicated team of accessible experts who provide strong political and scientific advocacy (“champions”) for the project. 2. Hierarchy & Autonomy: Hierarchical management structure that nevertheless permits high individual autonomy. 3. Goals & Evaluation: Formalized goal-setting and regular, critical evaluation of the project’s progress toward those goals. 4. Adaptive Public Relations: Adaptive outreach campaigns that are open, transparent, inclusive (esp. linguistically), and culturally relevant.
creator: Alexandra E. Sutton
uri: https://doi.org/10.7717/peerj.1012
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Sutton

title: A new perspective on how humans assess their surroundings; derivation of head orientation and its role in ‘framing’ the environment
link: https://peerj.com/articles/908
last-modified: 2015-06-18
description: Understanding the way humans inform themselves about their environment is pivotal in helping explain our susceptibility to stimuli and how this modulates behaviour and movement patterns. We present a new device, the Human Interfaced Personal Observation Platform (HIPOP), which is a head-mounted (typically on a hat) unit that logs magnetometry and accelerometry data at high rates and, following appropriate calibration, can be used to determine the heading and pitch of the wearer’s head. We used this device on participants visiting a botanical garden and noted that although head pitch ranged between −80° and 60°, 25% confidence limits were restricted to an arc of about 25° with a tendency for the head to be pitched down (mean head pitch ranged between −43° and 0°). Mean rates of change of head pitch varied between −0.00187°/0.1 s and 0.00187°/0.1 s, markedly slower than rates of change of head heading which varied between −0.3141°/0.1 s and 0.01263°/0.1 s although frequency distributions of both parameters showed them to be symmetrical and monomodal. Overall, there was considerable variation in both head pitch and head heading, which highlighted the role that head orientation might play in exposing people to certain features of the environment. Thus, when used in tandem with accurate position-determining systems, the HIPOP can be used to determine how the head is orientated relative to gravity and geographic North and in relation to geographic position, presenting data on how the environment is being ‘framed’ by people in relation to environmental content.
creator: Gwendoline Ixia Wilson
creator: Mark D. Holton
creator: James Walker
creator: Mark W. Jones
creator: Ed Grundy
creator: Ian M. Davies
creator: David Clarke
creator: Adrian Luckman
creator: Nick Russill
creator: Vianney Wilson
creator: Rosie Plummer
creator: Rory P. Wilson
uri: https://doi.org/10.7717/peerj.908
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Wilson et al.

title: Were early pterosaurs inept terrestrial locomotors?
link: https://peerj.com/articles/1018
last-modified: 2015-06-16
description: Pterodactyloid pterosaurs are widely interpreted as terrestrially competent, erect-limbed quadrupeds, but the terrestrial capabilities of non-pterodactyloids are largely thought to have been poor. This is commonly justified by the absence of a non-pterodactyloid footprint record, suggestions that the expansive uropatagia common to early pterosaurs would restrict hindlimb motion in walking or running, and the presence of sprawling forelimbs in some species. Here, these arguments are re-visited and mostly found problematic. Restriction of limb mobility is not a problem faced by extant animals with extensive fight membranes, including species which routinely utilise terrestrial locomotion. The absence of non-pterodactyloid footprints is not necessarily tied to functional or biomechanical constraints. As with other fully terrestrial clades with poor ichnological records, biases in behaviour, preservation, sampling and interpretation likely contribute to the deficit of early pterosaur ichnites. Suggestions that non-pterodactyloids have slender, mechanically weak limbs are demonstrably countered by the proportionally long and robust limbs of many Triassic and Jurassic species. Novel assessments of pterosaur forelimb anatomies conflict with notions that all non-pterodactyloids were obligated to sprawling forelimb postures. Sprawling forelimbs seem appropriate for species with ventrally-restricted glenoid articulations (seemingly occurring in rhamphorhynchines and campylognathoidids). However, some early pterosaurs, such as Dimorphodon macronyx and wukongopterids, have glenoid arthrologies which are not ventrally restricted, and their distal humeri resemble those of pterodactyloids. It seems fully erect forelimb stances were possible in these pterosaurs, and may be probable given proposed correlation between pterodactyloid-like distal humeral morphology and forces incurred through erect forelimb postures. Further indications of terrestrial habits include antungual sesamoids, which occur in the manus and pes anatomy of many early pterosaur species, and only occur elsewhere in terrestrial reptiles, possibly developing through frequent interactions of large claws with firm substrates. It is argued that characteristics possibly associated with terrestriality are deeply nested within Pterosauria and not restricted to Pterodactyloidea as previously thought, and that pterodactyloid-like levels of terrestrial competency may have been possible in at least some early pterosaurs.
creator: Mark P. Witton
uri: https://doi.org/10.7717/peerj.1018
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Witton

title: Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY
link: https://peerj.com/articles/1026
last-modified: 2015-06-16
description: The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins are classified into six groups (V1–V6), based on three independent biological features—genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have fewer than 10 serpins, which expand into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA) possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2) of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, details of the phylogenetic history and genomic characteristics of vertebrate serpins are revisited.
creator: Abhishek Kumar
uri: https://doi.org/10.7717/peerj.1026
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kumar

title: GenomePeek—an online tool for prokaryotic genome and metagenome analysis
link: https://peerj.com/articles/1025
last-modified: 2015-06-16
description: As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.
creator: Katelyn McNair
creator: Robert A. Edwards
uri: https://doi.org/10.7717/peerj.1025
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 McNair and Edwards

title: Is grazing exclusion effective in restoring vegetation in degraded alpine grasslands in Tibet, China?
link: https://peerj.com/articles/1020
last-modified: 2015-06-16
description: Overgrazing is considered one of the key disturbance factors that results in alpine grassland degradation in Tibet. Grazing exclusion by fencing has been widely used as an approach to restore degraded grasslands in Tibet since 2004. Is the grazing exclusion management strategy effective for the vegetation restoration of degraded alpine grasslands? Three alpine grassland types were selected in Tibet to investigate the effect of grazing exclusion on plant community structure and biomass. Our results showed that species biodiversity indicators, including the Pielou evenness index, the Shannon–Wiener diversity index, and the Simpson dominance index, did not significantly change under grazing exclusion conditions. In contrast, the total vegetation cover, the mean vegetation height of the community, and the aboveground biomass were significantly higher in the grazing exclusion grasslands than in the free grazed grasslands. These results indicated that grazing exclusion is an effective measure for maintaining community stability and improving aboveground vegetation growth in alpine grasslands. However, the statistical analysis showed that the growing season precipitation (GSP) plays a more important role than grazing exclusion in which influence on vegetation in alpine grasslands. In addition, because the results of the present study come from short term (6–8 years) grazing exclusion, it is still uncertain whether these improvements will be continuable if grazing exclusion is continuously implemented. Therefore, the assessments of the ecological effects of the grazing exclusion management strategy on degraded alpine grasslands in Tibet still need long term continued research.
creator: Yan Yan
creator: Xuyang Lu
uri: https://doi.org/10.7717/peerj.1020
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Yan and Lu