title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1427 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Worldwide co-occurrence analysis of 17 species of the genus Brachypodium using data mining link: https://peerj.com/articles/6193 last-modified: 2019-01-14 description: The co-occurrence of plant species is a fundamental aspect of plant ecology that contributes to understanding ecological processes, including the establishment of ecological communities and its applications in biological conservation. A priori algorithms can be used to measure the co-occurrence of species in a spatial distribution given by coordinates. We used 17 species of the genus Brachypodium, downloaded from the Global Biodiversity Information Facility data repository or obtained from bibliographical sources, to test an algorithm with the spatial points process technique used by Silva et al. (2016), generating association rules for co-occurrence analysis. Brachypodium spp. has emerged as an effective model for monocot species, growing in different environments, latitudes, and elevations; thereby, representing a wide range of biotic and abiotic conditions that may be associated with adaptive natural genetic variation. We created seven datasets of two, three, four, six, seven, 15, and 17 species in order to test the algorithm with four different distances (1, 5, 10, and 20 km). Several measurements (support, confidence, lift, Chi-square, and p-value) were used to evaluate the quality of the results generated by the algorithm. No negative association rules were created in the datasets, while 95 positive co-occurrences rules were found for datasets with six, seven, 15, and 17 species. Using 20 km in the dataset with 17 species, we found 16 positive co-occurrences involving five species, suggesting that these species are coexisting. These findings are corroborated by the results obtained in the dataset with 15 species, where two species with broad range distributions present in the previous dataset are eliminated, obtaining seven positive co-occurrences. We found that B. sylvaticum has co-occurrence relations with several species, such as B. pinnatum, B. rupestre, B. retusum, and B. phoenicoides, due to its wide distribution in Europe, Asia, and north of Africa. We demonstrate the utility of the algorithm implemented for the analysis of co-occurrence of 17 species of the genus Brachypodium, agreeing with distributions existing in nature. Data mining has been applied in the field of biological sciences, where a great amount of complex and noisy data of unseen proportion has been generated in recent years. Particularly, ecological data analysis represents an opportunity to explore and comprehend biological systems with data mining and bioinformatics tools. creator: Simon Orozco-Arias creator: Ana María Núñez-Rincón creator: Reinel Tabares-Soto creator: Diana López-Álvarez uri: https://doi.org/10.7717/peerj.6193 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Orozco-Arias et al. title: Combining legacy data with new drone and DGPS mapping to identify the provenance of Plio-Pleistocene fossils from Bolt’s Farm, Cradle of Humankind (South Africa) link: https://peerj.com/articles/6202 last-modified: 2019-01-14 description: Bolt’s Farm is a Plio-Pleistocene fossil site located within the southwestern corner of the UNESCO Hominid Fossil Sites of South Africa World Heritage Site. The site is a complex of active caves and more than 20 palaeokarst deposits or pits, many of which were exposed through the action of lime mining in the early 20th century. The pits represent heavily eroded cave systems, and as such associating the palaeocave sediments within and between the pits is difficult, especially as little geochronological data exists. These pits and the associated lime miner’s rubble were first explored by palaeoanthropologists in the late 1930s, but as yet no hominin material has been recovered. The first systematic mapping was undertaken by Frank Peabody as part of the University of California Africa Expedition (UCAE) in 1947–1948. A redrawn version of the map was not published until 1991 by Basil Cooke and this has subsequently been used and modified by recent researchers. Renewed work in the 2000s used Cooke’s map to try and relocate the original fossil deposits. However, Peabody’s map does not include all the pits and caves, and thus in some cases this was successful, while in others previously sampled pits were inadvertently given new names. This was compounded by the fact that new fossil bearing deposits were discovered in this new phase, causing confusion in associating the 1940s fossils with the deposits from which they originated; as well as associating them with the recently excavated material. To address this, we have used a Geographic Information System (GIS) to compare Peabody’s original map with subsequently published maps. This highlighted transcription errors between maps, most notably the location of Pit 23, an important palaeontological deposit given the recovery of well-preserved primate crania (Parapapio, Cercopithecoides) and partial skeletons of the extinct felid Dinofelis. We conducted the first drone and Differential Global Positioning System (DGPS) survey of Bolt’s Farm. Using legacy data, high-resolution aerial imagery, accurate DGPS survey and GIS, we relocate the original fossil deposits and propose a definitive and transparent naming strategy for Bolt’s Farm, based on the original UCAE Pit numbers. We provide datum points and a new comprehensive, georectified map to facilitate spatially accurate fossil collection for all future work. Additionally, we have collated recently published faunal data with historic fossil data to evaluate the biochronological potential of the various deposits. This suggests that the palaeocave deposits in different pits formed at different times with the occurrence of Equus in some pits implying ages of <2.3 Ma, whereas more primitive suids (Metridiochoerus) hint at a terminal Pliocene age for other deposits. This study highlights that Bolt’s Farm contains rare South African terminal Pliocene fossil deposits and creates a framework for future studies of the deposits and previously excavated material. creator: Tara R. Edwards creator: Brian J. Armstrong creator: Jessie Birkett-Rees creator: Alexander F. Blackwood creator: Andy I.R. Herries creator: Paul Penzo-Kajewski creator: Robyn Pickering creator: Justin W. Adams uri: https://doi.org/10.7717/peerj.6202 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Edwards et al. title: Using lidar to assess the development of structural diversity in forests undergoing passive rewilding in temperate Northern Europe link: https://peerj.com/articles/6219 last-modified: 2019-01-14 description: Forested areas are increasing across Europe, driven by both reforestation programs and farmland abandonment. While tree planting remains the standard reforestation strategy, there is increased interest in spontaneous regeneration as a cost-effective method with equal or potentially greater benefits. Furthermore, expanding areas of already established forests are left for passive rewilding to promote biodiversity conservation. Effective and objective methods are needed for monitoring and analyzing the development of forest structure under these management scenarios, with airborne laser scanning (lidar: light detection and ranging) being a promising methodology. Here, we assess the structural characteristics and development of unmanaged forests and 28- to 78-year old spontaneously regenerated forests on former agricultural land, relative to managed forests of similar age in Denmark, using 25 lidar-derived metrics in 10- and 30-m grid cells. We analyzed the lidar-derived cell values in a principal component analysis (PCA) and interpreted the axes ecologically, in conjunction with pairwise tests of median and variance of PCA-values for each forest. Spontaneously regenerated forest in general had increased structural heterogeneity compared to planted and managed forests. Furthermore, structural heterogeneity kept increasing in spontaneously regenerated forest across the maximal 78-year timespan investigated. Natural disturbances showed strong impacts on vegetation structure, leading to both structural homogeneity and heterogeneity. The results illustrate the utility of passive rewilding for generating structurally heterogeneous forested nature areas, and the utility of lidar surveys for monitoring and interpreting structural development of such forests. creator: Henrik Thers creator: Peder Klith Bøcher creator: Jens-Christian Svenning uri: https://doi.org/10.7717/peerj.6219 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Thers et al. title: Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments link: https://peerj.com/articles/6233 last-modified: 2019-01-14 description: BackgroundThe Streptococcus genus is relevant to both public health and food safety because of its ability to cause pathogenic infections. It is well-represented (>100 genomes) in publicly available databases. Streptococci are ubiquitous, with multiple sources of isolation, from human pathogens to dairy products. The Streptococcus genus has traditionally been classified by morphology, serum types, the 16S ribosomal RNA (rRNA) gene, and multi-locus sequence types subject to in-depth comparative genomic analysis.MethodsCore and pan-genomes described the genomic diversity of 108 strains belonging to 16 Streptococcus species. The core genome nucleotide diversity was calculated and compared to phylogenomic distances within the genus Streptococcus. The core genome was also used as a resource to recruit metagenomic fragment reads from streptococci dominated environments. A conventional 16S rRNA gene phylogeny reconstruction was used as a reference to compare the resulting dendrograms of average nucleotide identity (ANI) and genome similarity score (GSS) dendrograms.ResultsThe core genome, in this work, consists of 404 proteins that are shared by all 108 Streptococcus. The average identity of the pairwise compared core proteins decreases proportionally to GSS lower scores, across species. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). The GSS is a distance metric that can reflect evolutionary history comparing orthologous proteins. Additionally, GSS resulted in the most useful metric for genus and species comparisons, where ANI metrics failed due to false positives when comparing different species.DiscussionUnderstanding of genomic variability and species relatedness is the goal of tools like GSS, which makes use of the maximum pairwise shared orthologous sequences for its calculation. It allows for long evolutionary distances (above species) to be included because of the use of amino acid alignment scores, rather than nucleotides, and normalizing by positive matches. Newly sequenced species and strains could be easily placed into GSS dendrograms to infer overall genomic relatedness. The GSS is not restricted to ubiquitous conservancy of gene features; thus, it reflects the mosaic-structure and dynamism of gene acquisition and loss in bacterial genomes. creator: Hugo R. Barajas creator: Miguel F. Romero creator: Shamayim Martínez-Sánchez creator: Luis D. Alcaraz uri: https://doi.org/10.7717/peerj.6233 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Barajas et al. title: Method for the quantitative evaluation of ecosystem services in coastal regions link: https://peerj.com/articles/6234 last-modified: 2019-01-14 description: Wetlands, tidal flats, seaweed beds, and coral reefs are valuable not only as habitats for many species, but also as places where people interact with the sea. Unfortunately, these areas have declined in recent years, so environmental improvement projects to conserve and restore them are being carried out across the world. In this study, we propose a method for quantifying ecosystem services, that is, useful for the proper maintenance and management of artificial tidal flats, a type of environmental improvement project. With this method, a conceptual model of the relationship between each service and related environmental factors in natural and social systems was created, and the relationships between services and environmental factors were clarified. The state of the environmental factors affecting each service was quantified, and the state of those factors was reflected in the evaluation value of the service. As a result, the method can identify which environmental factors need to be improved and if the goal is to increase the value of the targeted tidal flat. The method demonstrates an effective approach in environmental conservation for the restoration and preservation of coastal areas. creator: Tomonari Okada creator: Yugo Mito creator: Erina Iseri creator: Toshiyuki Takahashi creator: Takanori Sugano creator: Yoshihiro B. Akiyama creator: Kenta Watanabe creator: Toko Tanaya creator: Hiroaki Sugino creator: Kanae Tokunaga creator: Takahiro Kubo creator: Tomohiro Kuwae uri: https://doi.org/10.7717/peerj.6234 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Okada et al. title: Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes link: https://peerj.com/articles/6245 last-modified: 2019-01-14 description: In molluscs, the shell secreted by mantle tissue during the biomineralization process is the first barrier against predators and mechanical damage. Changing environmental conditions, such as ocean acidification, influence shell strength and thus protection of the soft body within. Mussels are marine bivalves with important commercial and ecological value worldwide. Despite this importance, the proteins involved in the biomineralization and pigmentation processes in Mytilus spp. remain unclear, as does taxonomy of Mytilus taxa, though there have been many molecular studies. To further understanding in these areas, this study aimed to characterize and compare mantle transcriptomes of four mussel taxa using next generation sequencing. Mussels representing four taxa, were collected from several localities and RNA from mantle tissue was extracted. RNA sequences obtained were assembled, annotated and potential molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were identified. Candidate contigs putatively related to biomineralization and pigmentation processes were then selected and several transcripts were chosen for phylogenetic analyses from the Bivalvia class. Transcriptome comparisons between Mytilus taxa, including gene ontology (GO) enrichment analysis and orthologues identification were performed. Of assembled contigs, 46.57%, 37.28% and 17.53% were annotated using NCBI NR, GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Potential SSRs (483) and SNPs (1,497) were identified. Results presented a total of 1,292 contigs putatively involved in biomineralization and melanogenesis. Phylogenetic analyses of α-carbonic anhydrase, chitinase and tyrosinase revealed complex evolutionary history and diversity of these genes, which may be a result of duplication events or adaptation to different environments in mussels and other bivalves. Enrichment analyses revealed GO terms associated with pH and thermal response in Mytilus edulis from the North Sea and M. galloprovincialis from the Mediterranean Sea. The phylogenetic analysis within the genus Mytilus revealed M. californianus and M. coruscus to be genetically more distant from the other taxa: M. trossulus, M. edulis, M. chilensis and M. galloprovincialis. This work represents the first mantle transcriptome comparison between Mytilus taxa and provides contigs putatively involved in biomineralization. creator: Magdalena Malachowicz creator: Roman Wenne uri: https://doi.org/10.7717/peerj.6245 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Malachowicz and Wenne title: Effect of agricultural land-use change on ant dominance hierarchy and food preferences in a temperate oak forest link: https://peerj.com/articles/6255 last-modified: 2019-01-14 description: BackgroundThe discovery-dominance trade-off is the inverse relationship between the ability of a species to discover resources and the species’ dominance of those resources; a paradigm used to explain species coexistence in ant communities dependent on similar resources. However, factors such as stress (e.g., temperature) or disturbance (e.g., removal of biomass) associated with the change in land use, can modify this trade-off. Here, we aimed to determine the potential effects of land use change on dominance hierarchy, food preferences and on the discovery-dominance trade-off.MethodsAn experiment with baits was used to investigate the dominance hierarchies of ant communities in a temperate mountain habitat in central Mexico. We evaluated the dominance index (DI), food preferences and discovery-dominance trade-offs of ants inhabiting two types of vegetation: a native oak forest and agricultural land resulting from agricultural land use and grazing.ResultsThe ant communities in both environments were comprised of three species of ants (Monomorium minimum, Myrmica mexicana, and Camponotus picipes pilosulus), four morphospecies (Pheidole sp.1 and Pheidole sp.2, Temnothorax sp. and Lasius sp.) and one genus (Formica spp.). All Formicidae showed values of intermediate to low DI, and this factor did not seem to be influenced by the change in land use. Ants in the modified vegetation (i.e., agricultural land) were found to be numerically greater. Overall, a higher number of visits were registered to the tuna bait, although the duration of foraging events to the honey baits was longer. However, foraging times were dependent on the species considered: the generalized Myrmicinae, M. minimum, the ant species with highest DI, foraged for longer periods of time in the agricultural land and on the tuna bait. Meanwhile, the cold-climate specialist Formica spp., with a lower DI, foraged for longer periods of time in the oak (although not significant) and on the honey bait. We found little evidence of the discovery-dominance trade-off; instead, we found considerable diversity in the strategies used by the different species to access resources. This range of strategies is well represented by the generalized Myrmicinae M. minimum, the cold-climate specialists Formica spp. and Temnothorax sp., and the rare species, as the cold climate specialist Lasius sp. (insinuators).ConclusionsOur evaluation shows that transformation of the original habitat does not appear to affect the hierarchical dominance of the ant communities, but it does affect their food preferences. Species with higher DI values such as the generalized Myrmicinae are more skilled at resource acquisition in modified habitats. Our results suggest that change in land use promotes an increase in the diversity of foraging strategies used by different ant species. This diversity may contribute to resource partitioning which favors coexistence. creator: Citlalli Castillo-Guevara creator: Mariana Cuautle creator: Carlos Lara creator: Brenda Juárez-Juárez uri: https://doi.org/10.7717/peerj.6255 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Castillo-Guevara et al. title: Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics link: https://peerj.com/articles/6258 last-modified: 2019-01-14 description: A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml−1, chloramphenicol 0–24 μg ml−1, and vancomycin 0–24 μg ml−1). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment. creator: Deric R. Learman creator: Zahra Ahmad creator: Allison Brookshier creator: Michael W. Henson creator: Victoria Hewitt creator: Amanda Lis creator: Cody Morrison creator: Autumn Robinson creator: Emily Todaro creator: Ethan Wologo creator: Sydney Wynne creator: Elizabeth W. Alm creator: Peter S. Kourtev uri: https://doi.org/10.7717/peerj.6258 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Learman et al. title: Variation in wild pea (Pisum sativum subsp. elatius) seed dormancy and its relationship to the environment and seed coat traits link: https://peerj.com/articles/6263 last-modified: 2019-01-14 description: BackgroundSeed germination is one of the earliest key events in the plant life cycle. The timing of transition from seed to seedling is an important developmental stage determining the survival of individuals that influences the status of populations and species. Because of wide geographical distribution and occurrence in diverse habitats, wild pea (Pisum sativum subsp. elatius) offers an excellent model to study physical type of seed dormancy in an ecological context. This study addresses the gap in knowledge of association between the seed dormancy, seed properties and environmental factors, experimentally testing oscillating temperature as dormancy release clue.MethodsSeeds of 97 pea accessions were subjected to two germination treatments (oscillating temperatures of 25/15 °C and 35/15 °C) over 28 days. Germination pattern was described using B-spline coefficients that aggregate both final germination and germination speed. Relationships between germination pattern and environmental conditions at the site of origin (soil and bioclimatic variables extracted from WorldClim 2.0 and SoilGrids databases) were studied using principal component analysis, redundancy analysis and ecological niche modelling. Seeds were analyzed for the seed coat thickness, seed morphology, weight and content of proanthocyanidins (PA).ResultsSeed total germination ranged from 0% to 100%. Cluster analysis of germination patterns of seeds under two temperature treatments differentiated the accessions into three groups: (1) non-dormant (28 accessions, mean germination of 92%), (2) dormant at both treatments (29 acc., 15%) and (3) responsive to increasing temperature range (41 acc., with germination change from 15 to 80%). Seed coat thickness differed between groups with dormant and responsive accessions having thicker testa (median 138 and 140 µm) than non-dormant ones (median 84 mm). The total PA content showed to be higher in the seed coat of dormant (mean 2.18 mg g−1) than those of non-dormant (mean 1.77 mg g−1) and responsive accessions (mean 1.87 mg g−1). Each soil and bioclimatic variable and also germination responsivity (representing synthetic variable characterizing germination pattern of seeds) was spatially clustered. However, only one environmental variable (BIO7, i.e., annual temperature range) was significantly related to germination responsivity. Non-dormant and responsive accessions covered almost whole range of BIO7 while dormant accessions are found in the environment with higher annual temperature, smaller temperature variation, seasonality and milder winter. Ecological niche modelling showed a more localized potential distribution of dormant group. Seed dormancy in the wild pea might be part of a bet-hedging mechanism for areas of the Mediterranean basin with more unpredictable water availability in an otherwise seasonal environment. This study provides the framework for analysis of environmental aspects of physical seed dormancy. creator: Iveta Hradilová creator: Martin Duchoslav creator: Jan Brus creator: Vilém Pechanec creator: Miroslav Hýbl creator: Pavel Kopecký creator: Lucie Smržová creator: Nikola Štefelová creator: Tadeáš Vaclávek creator: Michael Bariotakis creator: Jitka Machalová creator: Karel Hron creator: Stergios Pirintsos creator: Petr Smýkal uri: https://doi.org/10.7717/peerj.6263 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hradilová et al. title: The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties link: https://peerj.com/articles/6147 last-modified: 2019-01-11 description: Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties. creator: Shu-Hong Wu creator: Bing-Hong Huang creator: Jian Gao creator: Siqi Wang creator: Pei-Chun Liao uri: https://doi.org/10.7717/peerj.6147 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wu et al.