A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species
We present a new supertree method that enables rapid estimation of a summary tree on the scale of millions of leaves. This supertree method summarizes a collection of input phylogenies and an input taxonomy. We introduce formal goals and criteria for such a supertree to satisfy in order to transparently and justifiably represent the input trees. In addition to producing a supertree, our method computes annotations that describe which grouping in the input trees support and conflict with each group in the supertree. We compare our supertree construction method to a previously published supertree construction method by assessing their performance on input trees used to construct the Open Tree of Life version 4, and find that our method increases the number of displayed input splits from 35,518 to 39,639 and decreases the number of conflicting input splits from 2,760 to 1,357. The new supertree method also improves on the previous supertree construction method in that it produces no unsupported branches and avoids unnecessary polytomies. This pipeline is currently used by the Open Tree of Life project to produce all of the versions of project’s “synthetic tree” starting at version 5. This software pipeline is called “propinquity”. It relies heavily on “otcetera”—a set of C++ tools to perform most of the steps of the pipeline. All of the components are free software and are available on GitHub.
Redelings et al. (2017) A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species. PeerJ 5:e3058 https://doi.org/10.7717/peerj.3058
Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors
Bayesian phylogenetic methods integrating simultaneously morphological and stratigraphic information have been applied increasingly among paleontologists. Most of these studies have used Bayesian methods as an alternative to the widely-used parsimony analysis, to infer macroevolutionary patterns and relationships among species-level or higher taxa. Among recently introduced Bayesian methodologies, the Fossilized Birth-Death (FBD) model allows incorporation of hypotheses on ancestor-descendant relationships in phylogenetic analyses including fossil taxa. Here, the FBD model is used to infer the relationships among an ingroup formed exclusively by fossil individuals, i.e., dipnoan tooth plates from four localities in the Ain el Guettar Formation of Tunisia. Previous analyses of this sample compared the results of phylogenetic analysis using parsimony with stratigraphic methods, inferred a high diversity (five or more genera) in the Ain el Guettar Formation, and interpreted it as an artifact inflated by depositional factors. In the analysis performed here, the uncertainty on the chronostratigraphic relationships among the specimens was included among the prior settings. The results of the analysis confirm the referral of most of the specimens to the taxa Asiatoceratodus, Equinoxiodus, Lavocatodus and Neoceratodus, but reject those to Ceratodus and Ferganoceratodus. The resulting phylogeny constrained the evolution of the Tunisian sample exclusively in the Early Cretaceous, contrasting with the previous scenario inferred by the stratigraphically-calibrated topology resulting from parsimony analysis. The phylogenetic framework also suggests that (1) the sampled localities are laterally equivalent, (2) but three localities are restricted to the youngest part of the section; both results are in agreement with previous stratigraphic analyses of these localities. The FBD model of specimen-level units provides a novel tool for phylogenetic inference among fossils but also for independent tests of stratigraphic scenarios.
Cau (2017) Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors. PeerJ 5:e3055 https://doi.org/10.7717/peerj.3055
Digital reconstruction of the mandible of an adult Lesothosaurus diagnosticus with insight into the tooth replacement process and diet
Fragmentary caudal ends of the left and right mandible assigned to Lesothosaurus diagnosticus, an early ornithischian, was recently discovered in the continental red bed succession of the upper Elliot Formation (Lower Jurassic) at Likhoele Mountain (Mafeteng District) in Lesotho. Using micro-CT scanning, this mandible could be digitally reconstructed in 3D. The replacement teeth within the better preserved (left) dentary were visualised. The computed tomography dataset suggests asynchronous tooth replacement in an individual identified as an adult on the basis of bone histology. Clear evidence for systematic wear facets created by attrition is lacking. The two most heavily worn teeth are only apically truncated. Our observations of this specimen as well as others do not support the high level of dental wear expected from the semi-arid palaeoenvironment in which Lesothosaurus diagnosticus lived. Accordingly, a facultative omnivorous lifestyle, where seasonality determined the availability, quality, and abundance of food is suggested. This would have allowed for adaptability to episodes of increased environmental stress.
Sciscio et al. (2017) Digital reconstruction of the mandible of an adult Lesothosaurus diagnosticus with insight into the tooth replacement process and diet. PeerJ 5:e3054 https://doi.org/10.7717/peerj.3054
The impact of human development on individual health: a causal mediation analysis examining pathways through education and body mass index
Background The macro environment we live in projects what we can achieve and how we behave, and in turn, shapes our health in complex ways. Policymaking will benefit from insights into the mechanisms underlying how national socioeconomic context affects health. This study examined the impact of human development on individual health and the possible mediating roles of education and body mass index (BMI). Methods We analyzed World Health Survey data on 109,448 participants aged 25 or older from 42 low- and middle-income countries with augmented human development index (HDI) in 1990. We used principal components method to create a health score based on measures from eight health state domains, used years of schooling as education indicator and calculated BMI from self-reported height and weight. We used causal mediation analysis technique with random intercepts to account for the multilevel structure. Results Below a reference HDI level of 0.48, HDI was negatively associated with good health (total effect at HDI of 0.23: b = − 3.44, 95% CI [−6.39–−0.49] for males and b = − 5.16, 95% CI [−9.24,–−1.08] for females) but was positively associated with good health above this reference level (total effect at HDI of 0.75: b = 4.16, 95% CI [−0.33–8.66] for males and b = 6.62, 95% CI [0.85–12.38] for females). We found a small positive effect of HDI on health via education across reference HDI levels (b ranging from 0.24 to 0.29 for males and 0.40 to 0.49 for females) but not via pathways involving BMI only. Conclusion Human development has a non-linear effect on individual health, but the impact appears to be mainly through pathways other than education and BMI.
Wang et al. (2017) The impact of human development on individual health: a causal mediation analysis examining pathways through education and body mass index. PeerJ 5:e3053 https://doi.org/10.7717/peerj.3053
Effects of root exudates of woody species on the soil anti-erodibility in the rhizosphere in a karst region, China
Introduction Rhizospheres, the most active interfaces between plants and soils, play a central role in the long-term maintenance of the biosphere. The anti-erodibility of soils (AES) regulated by the root exudates is crucial to the soil stability in the rhizospheres. However, scientists still debate (1) the key organic matter of the root exudates affecting the AES and (2) the interspecific variation of these root exudates. Methods We used an incubation of soils to test the effects of the root exudates from eight woody plant species on the change in soil aggregation and identified the organic matter in these root exudates with gas chromatography-mass spectrometry (GC-MS) and biochemical methods. Furthermore, the relationships between the organic matter in the exudates and the AES in the rhizospheres of 34 additional tree species were analyzed. Results The water-stable aggregates of the soils incubated with the root exudates increased by 15%–50% on average compared with control samples. The interspecific differences were significant. The root exudates included hundreds of specific organic matter types; hydrocarbon, total sugar, total amino acids, and phenolic compounds were crucial to the AES. These organic matter types could explain approximately 20–75% of the variation in the total effect of the root exudates on the AES, which was quantified based on the aggregate status, degree of aggregation, dispersion ratio, and dispersion coefficient. Discussion The effects of the root exudates on the AES and the interspecific variation are as important as that of root density, litters, and vegetation covers. Many studies explored the effects of root density, litters, vegetation covers, and vegetation types on the AES, but little attention has been paid to the effects of the root exudates on the AES. Different plants secrete different relative contents of organic matter resulting in the variation of the effect of the root exudates on the AES. Our study quantified the causal relationships between the root exudates and the AES using modeling experiments in laboratory and field observations and indicated the interspecific variation of the AES and organic matter of the root exudates. Conclusions More organic compounds of the exudates related to the AES were recognized in this study. These results enhance the understanding of the soil stability at a slope and can be applied to ecosystem restoration.
Wang et al. (2017) Effects of root exudates of woody species on the soil anti-erodibility in the rhizosphere in a karst region, China. PeerJ 5:e3029 https://doi.org/10.7717/peerj.3029
Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda)
Background Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information. Methods Sequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements. Results We present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps, Callianassa ceramica and Trypaea australiensis, along with three caridean shrimps, Macrobrachium bullatum, Alpheus lobidens, and Caridina cf. nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders. Discussion Our findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.
Tan et al. (2017) Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda). PeerJ 5:e2982 https://doi.org/10.7717/peerj.2982
Indomethacin reproducibly induces metamorphosis in Cassiopea xamachana scyphistomae
Cassiopea xamachana jellyfish are an attractive model system to study metamorphosis and/or cnidarian–dinoflagellate symbiosis due to the ease of cultivation of their planula larvae and scyphistomae through their asexual cycle, in which the latter can bud new larvae and continue the cycle without differentiation into ephyrae. Then, a subsequent induction of metamorphosis and full differentiation into ephyrae is believed to occur when the symbionts are acquired by the scyphistomae. Although strobilation induction and differentiation into ephyrae can be accomplished in various ways, a controlled, reproducible metamorphosis induction has not been reported. Such controlled metamorphosis induction is necessary for an ensured synchronicity and reproducibility of biological, biochemical, and molecular analyses. For this purpose, we tested if differentiation could be pharmacologically stimulated as in Aurelia aurita, by the metamorphic inducers thyroxine, KI, NaI, Lugol’s iodine, H2O2, indomethacin, or retinol. We found reproducibly induced strobilation by 50 μM indomethacin after six days of exposure, and 10–25 μM after 7 days. Strobilation under optimal conditions reached 80–100% with subsequent ephyrae release after exposure. Thyroxine yielded inconsistent results as it caused strobilation occasionally, while all other chemicals had no effect. Thus, indomethacin can be used as a convenient tool for assessment of biological phenomena through a controlled metamorphic process in C. xamachana scyphistomae.
Cabrales-Arellano et al. (2017) Indomethacin reproducibly induces metamorphosis in Cassiopea xamachana scyphistomae. PeerJ 5:e2979 https://doi.org/10.7717/peerj.2979
LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks
One of the main challenges of the post-genomic era is the understanding of how gene expression is controlled. Changes in gene expression lay behind diverse biological phenomena such as development, disease and the adaptation to different environmental conditions. Despite the availability of well-established methods to identify these changes, tools to discern how gene regulation is orchestrated are still required. The regulation of gene expression is usually depicted as a Gene Regulatory Network (GRN) where changes in the network structure (i.e., network topology) represent adjustments of gene regulation. Like other networks, GRNs are composed of basic building blocks; small induced subgraphs called graphlets. Here we present LoTo, a novel method that using Graphlet Based Metrics (GBMs) identifies topological variations between different states of a GRN. Under our approach, different states of a GRN are analyzed to determine the types of graphlet formed by all triplets of nodes in the network. Subsequently, graphlets occurring in a state of the network are compared to those formed by the same three nodes in another version of the network. Once the comparisons are performed, LoTo applies metrics from binary classification problems calculated on the existence and absence of graphlets to assess the topological similarity between both network states. Experiments performed on randomized networks demonstrate that GBMs are more sensitive to topological variation than the same metrics calculated on single edges. Additional comparisons with other common metrics demonstrate that our GBMs are capable to identify nodes whose local topology changes between different states of the network. Notably, due to the explicit use of graphlets, LoTo captures topological variations that are disregarded by other approaches. LoTo is freely available as an online web server at http://dlab.cl/loto.
Martin et al. (2017) LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks. PeerJ 5:e3052 https://doi.org/10.7717/peerj.3052
Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana
Background The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an “African” CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide. Methods We first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients attending Buruli ulcer treatment centres in Ghana, three non-African ST88s and 15 other MRSA lineages. Results We show that Ghanaian ST88 forms a discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content analysis identified five distinct genomic regions enriched among ST88 isolates compared with the other S. aureus lineages. The Ghanaian ST88 isolates had only 658 core genome SNPs and there was no correlation between phylogeny and geography, suggesting the recent spread of this clone. The lineage was also resistant to multiple classes of antibiotics including β-lactams, tetracycline and chloramphenicol. Discussion This study reveals that S. aureus ST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana. The study highlights the capacity of small snapshot genomic studies to provide actionable public health information in resource limited settings. To our knowledge this is the first genomic assessment of the ST88 CA-MRSA clone.
Kpeli et al. (2017) Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana. PeerJ 5:e3047 https://doi.org/10.7717/peerj.3047
An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples
Background Salmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar, brown trout Salmo trutta, brook trout Salvelinus fontinalis, and lake trout Salvelinus namaycush. In contrast, other salmonids are endangered in their native settings. Methods Here we have developed a method to identify salmonid species directly from water samples, focusing on the Iberian Peninsula as a case study. We have designed nested Salmonidae-specific primers within the 16S rDNA region. From these primers and a PCR-RFLP procedure the target species can be unequivocally identified from DNA extracted from water samples. Results The method was validated in aquarium experiments and in the field with water from watersheds with known salmonid populations. Finally, the method was applied to obtain a global view of the Salmonidae community in Nalón River (north coast of Spain). Discussion This new powerful, very sensitive (identifying the species down to 10 pg DNA/ml water) and economical tool can be applied for monitoring the presence of salmonids in a variety of situations, from checking upstream colonization after removal of river barriers to monitoring potential escapes from fish farms.
Clusa et al. (2017) An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples. PeerJ 5:e3045 https://doi.org/10.7717/peerj.3045