Sipha maydis sensitivity to defences of Lolium multiflorum and its endophytic fungus Epichloë occultans
Background Plants possess a sophisticated immune system to defend from herbivores. These defence responses are regulated by plant hormones including salicylic acid (SA) and jasmonic acid (JA). Sometimes, plant defences can be complemented by the presence of symbiotic microorganisms. A remarkable example of this are grasses establishing symbiotic associations with Epichloë fungal endophytes. We studied the level of resistance provided by the grass’ defence hormones, and that provided by Epichloë fungal endophytes, against an introduced herbivore aphid. These fungi protect their hosts against herbivores by producing bioactive alkaloids. We hypothesized that either the presence of fungal endophytes or the induction of the plant salicylic acid (SA) defence pathway would enhance the level of resistance of the grass to the aphid. Methods Lolium multiflorum plants, with and without the fungal endophyte Epichloë occultans, were subjected to an exogenous application of SA followed by a challenge with the aphid, Sipha maydis. Results Our results indicate that neither the presence of E. occultans nor the induction of the plant’s SA pathway regulate S. maydis populations. However, endophyte-symbiotic plants may have been more tolerant to the aphid feeding because these plants produced more aboveground biomass. We suggest that this insect insensitivity could be explained by a combination between the ineffectiveness of the specific alkaloids produced by E. occultans in controlling S. maydis aphids and the capacity of this herbivore to deal with hormone-dependent defences of L. multiflorum.
Bastías et al. (2019) Sipha maydis sensitivity to defences of Lolium multiflorum and its endophytic fungus Epichloë occultans. PeerJ 7:e8257 https://doi.org/10.7717/peerj.8257
qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data
Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern medicine. We propose a new classification method based on a model where the data is marginally negative binomial but dependent, thereby incorporating the dependence known to be present between measurements from different genes. The method, called qtQDA, works by first performing a quantile transformation (qt) then applying Gaussian quadratic discriminant analysis (QDA) using regularized covariance matrix estimates. We show that qtQDA has excellent performance when applied to real data sets and has advantages over some existing approaches. An R package implementing the method is also available on https://github.com/goknurginer/qtQDA.
Koçhan et al. (2019) qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data. PeerJ 7:e8260 https://doi.org/10.7717/peerj.8260
Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics
Recent advances in statistical machine learning techniques have led to the creation of probabilistic programming frameworks. These frameworks enable probabilistic models to be rapidly prototyped and fit to data using scalable approximation methods such as variational inference. In this work, we explore the use of the Stan language for probabilistic programming in application to phylogenetic models. We show that many commonly used phylogenetic models including the general time reversible substitution model, rate heterogeneity among sites, and a range of coalescent models can be implemented using a probabilistic programming language. The posterior probability distributions obtained via the black box variational inference engine in Stan were compared to those obtained with reference implementations of Markov chain Monte Carlo (MCMC) for phylogenetic inference. We find that black box variational inference in Stan is less accurate than MCMC methods for phylogenetic models, but requires far less compute time. Finally, we evaluate a custom implementation of mean-field variational inference on the Jukes–Cantor substitution model and show that a specialized implementation of variational inference can be two orders of magnitude faster and more accurate than a general purpose probabilistic implementation.
Fourment et al. (2019) Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics. PeerJ 7:e8272 https://doi.org/10.7717/peerj.8272
A systematic review of the application of machine learning in the detection and classification of transposable elements
Background Transposable elements (TEs) constitute the most common repeated sequences in eukaryotic genomes. Recent studies demonstrated their deep impact on species diversity, adaptation to the environment and diseases. Although there are many conventional bioinformatics algorithms for detecting and classifying TEs, none have achieved reliable results on different types of TEs. Machine learning (ML) techniques can automatically extract hidden patterns and novel information from labeled or non-labeled data and have been applied to solving several scientific problems. Methodology We followed the Systematic Literature Review (SLR) process, applying the six stages of the review protocol from it, but added a previous stage, which aims to detect the need for a review. Then search equations were formulated and executed in several literature databases. Relevant publications were scanned and used to extract evidence to answer research questions. Results Several ML approaches have already been tested on other bioinformatics problems with promising results, yet there are few algorithms and architectures available in literature focused specifically on TEs, despite representing the majority of the nuclear DNA of many organisms. Only 35 articles were found and categorized as relevant in TE or related fields. Conclusions ML is a powerful tool that can be used to address many problems. Although ML techniques have been used widely in other biological tasks, their utilization in TE analyses is still limited. Following the SLR, it was possible to notice that the use of ML for TE analyses (detection and classification) is an open problem, and this new field of research is growing in interest.
Orozco-Arias et al. (2019) A systematic review of the application of machine learning in the detection and classification of transposable elements. PeerJ 7:e8311 https://doi.org/10.7717/peerj.8311
Comparison of diversity and composition of macrofungal species between intensive mushroom harvesting and non-harvesting areas in Oaxaca, Mexico
Wild edible mushrooms have been collected and consumed by human groups for centuries, and today they represent a relevant source of food and income for many rural families worldwide. Preserving these non-timber forest products is of great interest, and there is concern about the damage caused by intensive mushroom harvesting on macromycete communities. The aim of this study was to evaluate variation in diversity and composition of macromycete species between areas regularly used for mushroom harvesting and non-harvested areas in the Mixteca region of Oaxaca, Mexico, as well as to assess the influence of microclimatic and environmental factors on this variation. We selected two harvested and two non-harvested sites within the study area. In each one, we established 10 permanent plots of 10 m × 10 m where we sampled all the observed fruit bodies weekly from June to October 2017. We recorded a total of 856 individuals corresponding to 138 species, and 23 of these were identified as edible. Overall macromycete diversity, edible species diversity and composition were similar in Sites 1 (non-harvested) and 3 (harvested), and in Sites 2 (non-harvested) and 4 (harvested). Variation of diversity and species composition along the studied area was mainly related to microclimatic variables, while most environmental variables and variables related to vegetation structure similarly affected macromycete species in the four sites. Our results indicate that intensive harvesting of wild edible mushrooms is not affecting the diversity and distribution of macromycete species in our study area. Knowledge on the sustainability of mushroom harvesting practices can help improve current regulations regarding the management of these valuable non-timber forest products.
Ruiz-Almenara et al. (2019) Comparison of diversity and composition of macrofungal species between intensive mushroom harvesting and non-harvesting areas in Oaxaca, Mexico. PeerJ 7:e8325 https://doi.org/10.7717/peerj.8325
Ontogenetic and inter-elemental osteohistological variability in the leopard tortoise Stigmochelys pardalis
Testudines are a group of reptiles characterized by the presence of a shell covered by keratinous shields. Stigmochelys pardalis is the most widely distributed terrestrial testudine in southern Africa. Although relatively common with some life history traits being well known, the growth of this species has yet to be studied in any detail. The bone microanatomy of this clade differs from that found in other amniotes, where terrestrial species tend to display characteristics normally seen in aquatic species and vice versa. A detailed histological analysis of the limb bones of S. pardalis reveals extensive variation through ontogeny. Cortical bone becomes increasingly thicker through ontogeny and is finally resorbed in the late sub-adult stage, resulting in a thin cortex and a large infilled medullary cavity. The predominant bone tissues are parallel-fibred and lamellar-zonal for the forelimbs and hind limbs respectively. The oldest individual displayed an External Fundamental System indicating that the growth rate had decreased substantially by this stage. Variability is prevalent between the forelimb and hind limb as well as between early and late sub-adults Forelimb elements exhibit characteristics such as faster growing parallel-fibered bone tissue, slightly higher vascularization and a predominance of annuli over Lines of Arrested Growth (LAG) compared to the hind limb which exhibits poorly vascularized, slower growing lamellar-zonal bone interrupted by LAGs. These differences indicate that the forelimb grew more rapidly than the hind limb, possibly due to the method of locomotion seen in terrestrial species. The extensive bone resorption that occurs from the early sub-adult stage destroys much of the primary cortex and results in a significantly different ratio of inner and outer bone diameter (p = 3.59 × 10­−5; df = 28.04) as well as compactness (p = 2.91 × 10­−5; df = 31.27) between early and late sub-adults. The extensive bone resorption seen also destroys the ecological signal and infers an aquatic lifestyle for this species despite it being clearly terrestrial. This supports the results of other studies that have found that using bone microanatomy to determine lifestyle in testudines does not produce accurate results.
Botha et al. (2019) Ontogenetic and inter-elemental osteohistological variability in the leopard tortoise Stigmochelys pardalis. PeerJ 7:e8030 https://doi.org/10.7717/peerj.8030
Exploring snake occurrence records: Spatial biases and marginal gains from accessible social media
A species’ distribution provides fundamental information on: climatic niche, biogeography, and conservation status. Species distribution models often use occurrence records from biodiversity databases, subject to spatial and taxonomic biases. Deficiencies in occurrence data can lead to incomplete species distribution estimates. We can incorporate other data sources to supplement occurrence datasets. The general public is creating (via GPS-enabled cameras to photograph wildlife) incidental occurrence records that may present an opportunity to improve species distribution models. We investigated (1) occurrence data of a cryptic group of animals: non-marine snakes, in a biodiversity database (Global Biodiversity Information Facility (GBIF)) and determined (2) whether incidental occurrence records extracted from geo-tagged social media images (Flickr) could improve distribution models for 18 tropical snake species. We provide R code to search for and extract data from images using Flickr’s API. We show the biodiversity database’s 302,386 records disproportionately originate from North America, Europe and Oceania (250,063, 82.7%), with substantial gaps in tropical areas that host the highest snake diversity. North America, Europe and Oceania averaged several hundred records per species; whereas Asia, Africa and South America averaged less than 35 per species. Occurrence density showed similar patterns; Asia, Africa and South America have roughly ten-fold fewer records per 100 km2than other regions. Social media provided 44,687 potential records. However, including them in distribution models only marginally impacted niche estimations; niche overlap indices were consistently over 0.9. Similarly, we show negligible differences in Maxent model performance between models trained using GBIF-only and Flickr-supplemented datasets. Model performance appeared dependent on species, rather than number of occurrences or training dataset. We suggest that for tropical snakes, accessible social media currently fails to deliver appreciable benefits for estimating species distributions; but due to the variation between species and the rapid growth in social media data, may still be worth considering in future contexts.
Marshall et al. (2019) Exploring snake occurrence records: Spatial biases and marginal gains from accessible social media. PeerJ 7:e8059 https://doi.org/10.7717/peerj.8059
Expression of extraocular opsin genes and light-dependent basal activity of blind cavefish
Background Animals living in well-lit environments utilize optical stimuli for detecting visual information, regulating the homeostatic pacemaker, and controlling patterns of body pigmentation. In contrast, many subterranean animal species without optical stimuli have evolved regressed binocular eyes and body pigmentation. Interestingly, some fossorial and cave-dwelling animals with regressed eyes still respond to light. These light-dependent responses may be simply evolutionary residuals or they may be adaptive, where negative phototaxis provides avoidance of predator-rich surface environments. However, the relationship between these non-ocular light responses and the underlying light-sensing Opsin proteins has not been fully elucidated. Methods To highlight the potential functions of opsins in a blind subterranean animal, we used the Mexican cave tetra to investigate opsin gene expression in the eyes and several brain regions of both surface and cave-dwelling adults. We performed database surveys, expression analyses by quantitative reverse transcription PCR (RT-qPCR), and light-dependent locomotor activity analysis using pinealectomized fish, one of the high-opsin expressing organs of cavefish. Results Based on conservative criteria, we identified 33 opsin genes in the cavefish genome. Surveys of available RNAseq data found 26 of these expressed in the surface fish eye as compared to 24 expressed in cavefish extraocular tissues, 20 of which were expressed in the brain. RT-qPCR of 26 opsins in surface and cavefish eye and brain tissues showed the highest opsin-expressing tissue in cavefish was the pineal organ, which expressed exo-rhodopsin at 72.7% of the expression levels in surface fish pineal. However, a pinealectomy resulted in no change to the light-dependent locomotor activity in juvenile cavefish and surface fish. Therefore, we conclude that, after 20,000 or more years of evolution in darkness, cavefish light-dependent basal activity is regulated by a non-pineal extraocular organ.
Simon et al. (2019) Expression of extraocular opsin genes and light-dependent basal activity of blind cavefish. PeerJ 7:e8148 https://doi.org/10.7717/peerj.8148
Social information affects Canada goose alert and escape responses to vehicle approach: implications for animal–vehicle collisions
Background Animal–vehicle collisions represent substantial sources of mortality for a variety of taxa and can pose hazards to property and human health. But there is comparatively little information available on escape responses by free-ranging animals to vehicle approach versus predators/humans. Methods We examined responses (alert distance and flight-initiation distance) of focal Canada geese (Branta canadensis maxima) to vehicle approach (15.6 m·s−1) in a semi-natural setting and given full opportunity to escape. We manipulated the direction of the vehicle approach (direct versus tangential) and availability of social information about the vehicle approach (companion group visually exposed or not to the vehicle). Results We found that both categorical factors interacted to affect alert and escape behaviors. Focal geese used mostly personal information to become alert to the vehicle under high risk scenarios (direct approach), but they combined personal and social information to become alert in low risk scenarios (tangential approach). Additionally, when social information was not available from the companion group, focal birds escaped at greater distances under direct compared to tangential approaches. However, when the companion group could see the vehicle approaching, focal birds escaped at similar distances irrespective of vehicle direction. Finally, geese showed a greater tendency to take flight when the vehicle approached directly, as opposed to a side step or walking away from the vehicle. Conclusions We suggest that the perception of risk to vehicle approach (likely versus unlikely collision) is weighted by the availability of social information in the group; a phenomenon not described before in the context of animal–vehicle interactions. Notably, when social information is available, the effects of heightened risk associated with a direct approach might be reduced, leading to the animal delaying the escape, which could ultimately increase the chances of a collision. Also, information on a priori escape distances required for surviving a vehicle approach (based on species behavior and vehicle approach speeds) can inform planning, such as location of designated cover or safe areas. Future studies should assess how information from vehicle approach flows within a flock, including aspects of vehicle speed and size, metrics that affect escape decision-making.
Blackwell et al. (2019) Social information affects Canada goose alert and escape responses to vehicle approach: implications for animal–vehicle collisions. PeerJ 7:e8164 https://doi.org/10.7717/peerj.8164
The interplay between movement, morphology and dispersal in Tetrahymena ciliates
Understanding how and why individual movement translates into dispersal between populations is a long-term goal in ecology. Movement is broadly defined as ‘any change in the spatial location of an individual’, whereas dispersal is more narrowly defined as a movement that may lead to gene flow. Because the former may create the condition for the latter, behavioural decisions that lead to dispersal may be detectable in underlying movement behaviour. In addition, dispersing individuals also have specific sets of morphological and behavioural traits that help them coping with the costs of movement and dispersal, and traits that mitigate costs should be under selection and evolve if they have a genetic basis. Here, we experimentally study the relationships between movement behaviour, morphology and dispersal across 44 genotypes of the actively dispersing unicellular, aquatic model organism Tetrahymena thermophila. We used two-patch populations to quantify individual movement trajectories, as well as activity, morphology and dispersal rate. First, we studied variation in movement behaviour among and within genotypes (i.e. between dispersers and residents) and tested whether this variation can be explained by morphology. Then, we addressed how much the dispersal rate is driven by differences in the underlying movement behaviour. Genotypes revealed clear differences in terms of movement speed and linearity. We also detected marked movement differences between resident and dispersing individuals, mediated by the genotype. Movement variation was partly explained by morphological properties such as cell size and shape, with larger cells consistently showing higher movement speed and higher linearity. Genetic differences in activity and movement were positively related to the observed dispersal and jointly explained 47% of the variation in dispersal rate. Our study shows that a detailed understanding of the interplay between morphology, movement and dispersal may have potential to improve dispersal predictions over broader spatio-temporal scales.
Pennekamp et al. (2019) The interplay between movement, morphology and dispersal in Tetrahymena ciliates. PeerJ 7:e8197 https://doi.org/10.7717/peerj.8197