title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1765 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest link: https://peerj.com/articles/2764 last-modified: 2016-12-22 description: IntroductionTheory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate), indirect gene flow and contemporary pollen dynamics in the understory herb Aphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios.MethodsTwelve populations of A. aurantiaca were sampled in large (4), medium (3), and small (5) forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28–30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population.ResultsDespite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (He = 0.61), weak genetic structure (Rst = 0.037), and slight inbreeding in small fragments. Effective population sizes (Ne) were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events were detected. Aphelandra aurantiaca shows a mixed mating system (tm = 0.81) and the outcrossing rate have not been affected by habitat fragmentation. A strong pollen pool structure was detected due to few effective pollen donors (Nep) and low distance pollen movement, pointing that most plants received pollen from close neighbors. Past demographic fluctuations may have affected the present population genetic structure as Bayesian coalescent analysis revealed the signature of past population expansion, possibly during warmer conditions after the last glacial maximum.DiscussionHabitat fragmentation has not increased genetic differentiation or reduced genetic diversity of A. aurantiaca despite dozens of generations since the onset of fragmentation in the region of Los Tuxtlas. Instead, past population expansion is compatible with the lack of observed genetic structure. The predicted negative effects of rainforest fragmentation on genetic diversity and population structure of A. aurantiaca seem to have been buffered owing to its large effective populations and long-distance dispersal events. In particular, its mixed-mating system, mostly of outcrossing, suggests high efficiency of pollinators promoting connectivity and reducing inbreeding. However, some results point that the effects of fragmentation are underway, as two small fragments showed higher membership probabilities to their population of origin, suggesting genetic isolation. Our findings underscore the importance of fragment size to maintain genetic connectivity across the landscape. creator: Pilar Suárez-Montes creator: Mariana Chávez-Pesqueira creator: Juan Núñez-Farfán uri: https://doi.org/10.7717/peerj.2764 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Suárez-Montes et al. title: Simplified large African carnivore density estimators from track indices link: https://peerj.com/articles/2662 last-modified: 2016-12-22 description: BackgroundThe range, population size and trend of large carnivores are important parameters to assess their status globally and to plan conservation strategies. One can use linear models to assess population size and trends of large carnivores from track-based surveys on suitable substrates. The conventional approach of a linear model with intercept may not intercept at zero, but may fit the data better than linear model through the origin. We assess whether a linear regression through the origin is more appropriate than a linear regression with intercept to model large African carnivore densities and track indices.MethodsWe did simple linear regression with intercept analysis and simple linear regression through the origin and used the confidence interval for ß in the linear model y = αx + ß, Standard Error of Estimate, Mean Squares Residual and Akaike Information Criteria to evaluate the models.ResultsThe Lion on Clay and Low Density on Sand models with intercept were not significant (P > 0.05). The other four models with intercept and the six models thorough origin were all significant (P < 0.05). The models using linear regression with intercept all included zero in the confidence interval for ß and the null hypothesis that ß = 0 could not be rejected. All models showed that the linear model through the origin provided a better fit than the linear model with intercept, as indicated by the Standard Error of Estimate and Mean Square Residuals. Akaike Information Criteria showed that linear models through the origin were better and that none of the linear models with intercept had substantial support.DiscussionOur results showed that linear regression through the origin is justified over the more typical linear regression with intercept for all models we tested. A general model can be used to estimate large carnivore densities from track densities across species and study areas. The formula observed track density = 3.26 × carnivore density can be used to estimate densities of large African carnivores using track counts on sandy substrates in areas where carnivore densities are 0.27 carnivores/100 km2 or higher. To improve the current models, we need independent data to validate the models and data to test for non-linear relationship between track indices and true density at low densities. creator: Christiaan W. Winterbach creator: Sam M. Ferreira creator: Paul J. Funston creator: Michael J. Somers uri: https://doi.org/10.7717/peerj.2662 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Winterbach et al. title: Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment link: https://peerj.com/articles/2812 last-modified: 2016-12-21 description: We developed a bio-inspired robot controller combining an artificial genome with an agent-based control system. The genome encodes a gene regulatory network (GRN) that is switched on by environmental cues and, following the rules of transcriptional regulation, provides output signals to actuators. Whereas the genome represents the full encoding of the transcriptional network, the agent-based system mimics the active regulatory network and signal transduction system also present in naturally occurring biological systems. Using such a design that separates the static from the conditionally active part of the gene regulatory network contributes to a better general adaptive behaviour. Here, we have explored the potential of our platform with respect to the evolution of adaptive behaviour, such as preying when food becomes scarce, in a complex and changing environment and show through simulations of swarm robots in an A-life environment that evolution of collective behaviour likely can be attributed to bio-inspired evolutionary processes acting at different levels, from the gene and the genome to the individual robot and robot population. creator: Yao Yao creator: Veronique Storme creator: Kathleen Marchal creator: Yves Van de Peer uri: https://doi.org/10.7717/peerj.2812 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yao et al. title: Floral development and vascularization help to explain merism evolution in Paepalanthus (Eriocaulaceae, Poales) link: https://peerj.com/articles/2811 last-modified: 2016-12-21 description: BackgroundFlowers in Eriocaulaceae, a monocot family that is highly diversified in Brazil, are generally trimerous, but dimerous flowers occur in Paepalanthus and a few other genera. The floral merism in an evolutionary context, however, is unclear. Paepalanthus encompasses significant morphological variation leading to a still unresolved infrageneric classification. Ontogenetic comparative studies of infrageneric groups in Paepalanthus and in Eriocaulaceae are lacking, albeit necessary to establish evolution of characters such as floral merism and their role as putative synapomorphies.MethodsWe studied the floral development and vascularization of eight species of Paepalanthus that belong to distinct clades in which dimery occurs, using light and scanning electron microscopies.ResultsFloral ontogeny in dimerous Paepalanthus shows lateral sepals emerging simultaneously and late-developing petals. The outer whorl of stamens is absent in all flowers examined here. The inner whorl of stamens becomes functional in staminate flowers and is reduced to staminodes in the pistillate ones. In pistillate flowers, vascular bundles reach the staminodes. Ovary vascularization shows ventral bundles in a commissural position reaching the synascidiate portion of the carpels. Three gynoecial patterns are described for the studied species: (1) gynoecium with a short style, two nectariferous branches and two long stigmatic branches, in most species; (2) gynoecium with a long style, two nectariferous branches and two short stigmatic branches, in P. echinoides; and (3) gynoecium with long style, absent nectariferous branches and two short stigmatic branches, in P. scleranthus.DiscussionFloral development of the studied species corroborates the hypothesis that the sepals of dimerous flowers of Paepalanthus correspond to the lateral sepals of trimerous flowers. The position and vascularization of floral parts also show that, during dimery evolution in Paepalanthus, a flower sector comprising the adaxial median sepal, a lateral petal, a lateral stamen and the adaxial median carpel was lost. In the staminate flower, the outer whorl of staminodes, previously reported by different authors, is correctly described as the apical portion of the petals and the pistillodes are reinterpreted as carpellodes. The occurrence of fused stigmatic branches and protected nectariferous carpellodes substantiates a close relationship between P. sect. Conodiscus and P. subg. Thelxinoë. Free stigmatic branches and exposed carpellodes substantiate a close relationship between P. sect. Diphyomene, P. sect. Eriocaulopsis and P. ser. Dimeri. Furthermore, the loss of nectariferous branches may have occurred later than the fusion of stigmatic branches in the clade that groups P. subg. Thelxinoë and P. sect. Conodiscus. creator: Arthur de Lima Silva creator: Marcelo Trovó creator: Alessandra Ike Coan uri: https://doi.org/10.7717/peerj.2811 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Silva et al. title: Cretaceous origin of dogwoods: an anatomically preserved Cornus (Cornaceae) fruit from the Campanian of Vancouver Island link: https://peerj.com/articles/2808 last-modified: 2016-12-21 description: BackgroundCornaceae consists of 58 species, all within the genus Cornus. The Cenozoic record of Cornus is extensive and well documented. Molecular divergence-time studies suggest that crown-group Cornus may have originated by the Late Cretaceous. However, there has been no formal report of Cornus from Cretaceous deposits. Here, we characterize a permineralized fossil fruit assignable to Cornus subg. Cornus from the Upper Cretaceous (Campanian) Shelter Point locality of Vancouver Island, British Columbia, Canada.MethodsSerial sections of the specimen were made using the cellulose acetate peel technique. Peels were mounted onto microscope slides and studied by light microscopy.ResultsThe fossil fruit consists of a tri-locular woody endocarp with dorsal germination valves. The locules are sub-triangular to ellipsoidal in transverse section and are separated by thin septa. Endocarp tissue consists of elongated and isodiametric sclereids and secretory cavities. Internal vascular tissue was not observed, but is interpreted to have been located along the outer periphery of the septa for some length, common in many cornalean taxa. There is one seed in each locule, one of which was found to have endosperm and a dicotyledonous embryo.DiscussionWoody endocarps with germination valves, without central vascular bundles, and with one seed per locule are characteristic of several families within the order Cornales. The interpreted vascular pattern and presence of secretory cavities indicates that the fossil fruit is assignable to Cornus subg. Cornus. Comparative analysis suggests that the fossil is most similar to Cornus piggae, a species described from the Paleocene of North Dakota. This fossil is the first evidence of crown-group Cornaceae from the Cretaceous and sheds light on both the plesiomorphic fruit characters and the timing of the initial diversification of the family and basal asterid lineage, Cornales. creator: Brian A. Atkinson creator: Ruth A. Stockey creator: Gar W. Rothwell uri: https://doi.org/10.7717/peerj.2808 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Atkinson et al. title: Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA link: https://peerj.com/articles/2807 last-modified: 2016-12-21 description: We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda, Arthropoda and Annelida were the most diverse. We found a marked heterogeneity at all scales, with important differences between layers of sediment and significant changes in community composition with zone (canyon vs slope), depth, and season. We compared the information obtained from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs per sample with DNA (ca. 20% and 40% increase, respectively). Both datasets showed overall similar spatial trends, but most groups had higher MOTU richness with the DNA template, while others, such as nematodes, were more diverse in the RNA dataset. We provide metabarcoding protocols and guidelines for biomonitoring of these key communities in order to generate information applicable to management efforts. creator: Magdalena Guardiola creator: Owen S. Wangensteen creator: Pierre Taberlet creator: Eric Coissac creator: María Jesús Uriz creator: Xavier Turon uri: https://doi.org/10.7717/peerj.2807 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Guardiola et al. title: Candidate pathogenicity islands in the genome of ‘Candidatus Rickettsiella isopodorum’, an intracellular bacterium infecting terrestrial isopod crustaceans link: https://peerj.com/articles/2806 last-modified: 2016-12-21 description: The bacterial genus Rickettsiellabelongs to the order Legionellales in the Gammaproteobacteria, and consists of several described species and pathotypes, most of which are considered to be intracellular pathogens infecting arthropods. Two members of this genus, R. grylliand R. isopodorum, are known to infect terrestrial isopod crustaceans. In this study, we assembled a draft genomic sequence for R. isopodorum, and performed a comparative genomic analysis with R. grylli. We found evidence for several candidate genomic island regions in R. isopodorum, none of which appear in the previously available R. grylli genome sequence.Furthermore, one of these genomic island candidates in R. isopodorum contained a gene that encodes a cytotoxin partially homologous to those found in Photorhabdus luminescensand Xenorhabdus nematophilus (Enterobacteriaceae), suggesting that horizontal gene transfer may have played a role in the evolution of pathogenicity in Rickettsiella. These results lay the groundwork for future studies on the mechanisms underlying pathogenesis in R. isopodorum, and this system may provide a good model for studying the evolution of host-microbe interactions in nature. creator: YaDong Wang creator: Christopher Chandler uri: https://doi.org/10.7717/peerj.2806 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang and Chandler title: Molecular phylogenetics, seed morphometrics, chromosome number evolution and systematics of European Elatine L. (Elatinaceae) species link: https://peerj.com/articles/2800 last-modified: 2016-12-21 description: The genus Elatine contains ca 25 species, all of which are small, herbaceous annuals distributed in ephemeral waters on both hemispheres. However, due to a high degree of morphological variability (as a consequence of their amphibious life-style), the taxonomy of this genus remains controversial. Thus, to fill this gap in knowledge, we present a detailed molecular phylogenetic study of this genus based on nuclear (rITS) and plastid (accD-psaI, psbJ-petA, ycf6-psbM-trnD) sequences using 27 samples from 13 species. On the basis of this phylogenetic analysis, we provide a solid phylogenetic background for the modern taxonomy of the European members of the genus. Traditionally accepted sections of this tree (i.e., Crypta and Elatinella) were found to be monophyletic; only E. borchoni—found to be a basal member of the genus—has to be excluded from the latter lineage to achieve monophyly. A number of taxonomic conclusions can also be drawn: E. hexandra, a high-ploid species, is most likely a stabilised hybrid between the main sections; E. campylosperma merits full species status based on both molecular and morphological evidence; E. gussonei is a more widespread and genetically diverse species with two main lineages; and the presence of the Asian E. ambigua in the European flora is questionable. The main lineages recovered in this analysis are also supported by a number of synapomorphic morphological characters as well as uniform chromosome counts. Based on all the evidence presented here, two new subsections within Elatinella are described: subsection Hydropipera consisting of the temperate species of the section, and subsection Macropodae including the Mediterranean species of the section. creator: Gábor Sramkó creator: Attila Molnár V. creator: János Pál Tóth creator: Levente Laczkó creator: Anna Kalinka creator: Orsolya Horváth creator: Lidia Skuza creator: Balázs András Lukács creator: Agnieszka Popiela uri: https://doi.org/10.7717/peerj.2800 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sramkó et al. title: The effect of cognitive training on the subjective perception of well-being in older adults link: https://peerj.com/articles/2785 last-modified: 2016-12-21 description: BackgroundThere is a growing number of studies indicating the major consequences of the subjective perception of well-being on mental health and healthcare use. However, most of the cognitive training research focuses more on the preservation of cognitive function than on the implications of the state of well-being. This secondary analysis of data from a randomised controlled trial investigated the effects of individualised television-based cognitive training on self-rated well-being using the WHO-5 index while considering gender and education as influencing factors. The effects of cognitive training were compared with leisure activities that the elderly could be engaged in to pass time.MethodsCognitively healthy participants aged 60 years or above screened using the Mini-Mental State Examination (MMSE) and Major Depression Inventory (MDI) were randomly allocated to a cognitive training group or to an active control group in a single-blind controlled two-group design and underwent 24 training sessions. Data acquired from the WHO-5 questionnaire administered before and after intervention were statistically analysed using a mixed design model for repeated measures. The effect of individualised cognitive training was compared with leisure activities while the impact of gender and education was explored using estimated marginal means.ResultsA total of 81 participants aged 67.9 ± 5.59 [60–84] without cognitive impairments and absent of depression symptoms underwent the study. Participants with leisure time activities declared significantly higher scores compared to participants with cognitive training M = 73.48 ± 2.88, 95% CI [67.74–79.22] vs M = 64.13 ± 3.034, 95% CI [58.09–70.17] WHO-5 score. Gender and education were found to moderate the effect of cognitive training on well-being when compared to leisure activities. Females engaged in leisure activities in the control group reported higher by M = 9.77 ± 5.4, 95% CI [−0.99–20.54] WHO-5 scores than females with the cognitive training regimen. Participants with high school education declared leisure activities to increase WHO-5 scores by M = 14.59 ± 5.39, 95% CI [3.85–25.34] compared to individualised cognitive training.DiscussionThe findings revealed that individualised cognitive training was not directly associated with improvements in well-being. Changes in the control group indicated that involvement in leisure time activities, in which participants were partly free to choose from, represented more favourable stimulation to a self-perceived sense of well-being than individualised cognitive training. Results also supported the fact that gender and education moderated the effect of cognitive training on well-being. Females and participants with high school education were found to be negatively impacted in well-being when performance connected with cognitive training was expected. creator: Vladimír Bureš creator: Pavel Čech creator: Jaroslava Mikulecká creator: Daniela Ponce creator: Kamil Kuca uri: https://doi.org/10.7717/peerj.2785 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bureš et al. title: Hairiness: the missing link between pollinators and pollination link: https://peerj.com/articles/2779 last-modified: 2016-12-21 description: BackgroundFunctional traits are the primary biotic component driving organism influence on ecosystem functions; in consequence, traits are widely used in ecological research. However, most animal trait-based studies use easy-to-measure characteristics of species that are at best only weakly associated with functions. Animal-mediated pollination is a key ecosystem function and is likely to be influenced by pollinator traits, but to date no one has identified functional traits that are simple to measure and have good predictive power.MethodsHere, we show that a simple, easy to measure trait (hairiness) can predict pollinator effectiveness with high accuracy. We used a novel image analysis method to calculate entropy values for insect body surfaces as a measure of hairiness. We evaluated the power of our method for predicting pollinator effectiveness by regressing pollinator hairiness (entropy) against single visit pollen deposition (SVD) and pollen loads on insects. We used linear models and AICC model selection to determine which body regions were the best predictors of SVD and pollen load.ResultsWe found that hairiness can be used as a robust proxy of SVD. The best models for predicting SVD for the flower species Brassica rapa and Actinidia deliciosa were hairiness on the face and thorax as predictors (R2 = 0.98 and 0.91 respectively). The best model for predicting pollen load for B. rapa was hairiness on the face (R2 = 0.81).DiscussionWe suggest that the match between pollinator body region hairiness and plant reproductive structure morphology is a powerful predictor of pollinator effectiveness. We show that pollinator hairiness is strongly linked to pollination—an important ecosystem function, and provide a rigorous and time-efficient method for measuring hairiness. Identifying and accurately measuring key traits that drive ecosystem processes is critical as global change increasingly alters ecological communities, and subsequently, ecosystem functions worldwide. creator: Jamie R. Stavert creator: Gustavo Liñán-Cembrano creator: Jacqueline R. Beggs creator: Brad G. Howlett creator: David E. Pattemore creator: Ignasi Bartomeus uri: https://doi.org/10.7717/peerj.2779 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Stavert et al.