title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=992 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Supraspecific units in correlative niche modeling improves the prediction of geographic potential of biological invasions link: https://peerj.com/articles/10454 last-modified: 2020-12-22 description: BackgroundBiological invasions rank among the most significant threats to biodiversity and ecosystems. Correlative ecological niche modeling is among the most frequently used tools with which to estimate potential distributions of invasive species. However, when areas accessible to the species across its native distribution do not represent the full spectrum of environmental conditions that the species can tolerate, correlative studies often underestimate fundamental niches.MethodsHere, we explore the utility of supraspecific modeling units to improve the predictive ability of models focused on biological invasions. Taking into account phylogenetic relationships in correlative ecological niche models, we studied the invasion patterns of three species (Aedes aegypti, Pterois volitans and Oreochromis mossambicus).ResultsUse of supraspecific modeling units improved the predictive ability of correlative niche models in anticipating potential distributions of three invasive species. We demonstrated that integrating data on closely related species allowed a more complete characterization of fundamental niches. This approach could be used to model species with invasive potential but that have not yet invaded new regions. creator: Sandra Castaño-Quintero creator: Jazmín Escobar-Luján creator: Luis Osorio-Olvera creator: A Townsend Peterson creator: Xavier Chiappa-Carrara creator: Enrique Martínez-Meyer creator: Carlos Yañez-Arenas uri: https://doi.org/10.7717/peerj.10454 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Castaño-Quintero et al. title: BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis link: https://peerj.com/articles/10469 last-modified: 2020-12-22 description: BackgroundRNA sequencing is an indispensable research tool used in a broad range of transcriptome analysis studies. The most common application of RNA Sequencing is differential expression analysis and it is used to determine genetic loci with distinct expression across different conditions. An emerging field called single-cell RNA sequencing is used for transcriptome profiling at the individual cell level. The standard protocols for both of these approaches include the processing of sequencing libraries and result in the generation of count matrices. An obstacle to these analyses and the acquisition of meaningful results is that they require programing expertise. Although some effort has been directed toward the development of user-friendly RNA-Seq analysis analysis tools, few have the flexibility to explore both Bulk and single-cell RNA sequencing.ImplementationBingleSeq was developed as an intuitive application that provides a user-friendly solution for the analysis of count matrices produced by both Bulk and Single-cell RNA-Seq experiments. This was achieved by building an interactive dashboard-like user interface which incorporates three state-of-the-art software packages for each type of the aforementioned analyses. Furthermore, BingleSeq includes additional features such as visualization techniques, extensive functional annotation analysis and rank-based consensus for differential gene analysis results. As a result, BingleSeq puts some of the best reviewed and most widely used packages and tools for RNA-Seq analyses at the fingertips of biologists with no programing experience.AvailabilityBingleSeq is as an easy-to-install R package available on GitHub at https://github.com/dbdimitrov/BingleSeq/. creator: Daniel Dimitrov creator: Quan Gu uri: https://doi.org/10.7717/peerj.10469 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Dimitrov and Gu title: Expression of the neurotrophic tyrosine kinase receptors, ntrk1 and ntrk2a, precedes expression of other ntrk genes in embryonic zebrafish link: https://peerj.com/articles/10479 last-modified: 2020-12-22 description: BackgroundThe neurotrophic tyrosine kinase receptor (Ntrk) gene family plays a critical role in the survival of somatosensory neurons. Most vertebrates have three Ntrk genes each of which encode a Trk receptor: TrkA, TrkB, or TrkC. The function of the Trk receptors is modulated by the p75 neurotrophin receptors (NTRs). Five ntrk genes and one p75 NTR gene (ngfrb) have been discovered in zebrafish. To date, the expression of these genes in the initial stages of neuron specification have not been investigated.PurposeThe present work used whole mount in situ hybridization to analyze expression of the five ntrk genes and ngfrb in zebrafish at a timepoint when the first sensory neurons of the zebrafish body are being established (16.5 hpf). Because expression of multiple genes were not found at this time point, we also checked expression at 24 hpf to ensure the functionality of our six probes.ResultsAt 16.5 hpf, we found tissue specific expression of ntrk1 in cranial ganglia, and tissue specific expression of ntrk2a in cranial ganglia and in the spinal cord. Other genes analyzed at 16.5 hpf were either diffuse or not detected. At 24 hpf, we found expression of both ntrk1 and ntrk2a in the spinal cord as well as in multiple cranial ganglia, and we identified ngfrb expression in cranial ganglia at 24 hpf. ntrk2b, ntrk3a and ntrk3b were detected in the developing brain at 24 hpf.ConclusionThese data are the first to demonstrate that ntrk1 and ntrk2a are the initial neurotrophic tyrosine kinase receptors expressed in sensory neurons during the development of the zebrafish body, and the first to establish expression patterns of ngfrb during early zebrafish development. Our data indicate co-expression of ntrk1, ntrk2a and ngfrb, and we speculate that these overlapping patterns indicate relatedness of function. creator: Katie Hahn creator: Paul Manuel creator: Cortney Bouldin uri: https://doi.org/10.7717/peerj.10479 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hahn et al. title: The ecomorphology of the shell of extant turtles and its applications for fossil turtles link: https://peerj.com/articles/10490 last-modified: 2020-12-22 description: Turtles are a successful clade of reptiles that originated in the Late Triassic. The group adapted during its evolution to different types of environments, ranging from dry land to ponds, rivers, and the open ocean, and survived all Mesozoic and Cenozoic extinction events. The body of turtles is characterized by a shell, which has been hypothesized to have several biological roles, like protection, thermal and pH regulation, but also to be adapted in its shape to the ecology of the animal. However, only few studies have investigated the relationships between shell shape and ecology in a global context or clarified if shape can be used to diagnose habitat preferences in fossil representatives. Here, we assembled a three-dimensional dataset of 69 extant turtles and three fossils, in particular, the Late Triassic Proganochelys quenstedtii and Proterochersis robusta and the Late Jurassic Plesiochelys bigleri to test explicitly for a relationship between shell shape and ecology. 3D models were obtained using surface scanning and photogrammetry. The general shape of the shells was captured using geometric morphometrics. The habitat ecology of extant turtles was classified using the webbing of their forelimbs as a proxy. Principal component analysis (PCA) highlights much overlap between habitat groups. Discriminant analyses suggests significant differences between extant terrestrial turtles, extant fully aquatic (i.e., marine and riverine) turtles, and an unspecialized assemblage that includes extant turtles from all habitats, mostly freshwater aquatic forms. The paleoecology of the three fossil species cannot be determined with confidence, as all three fall within the unspecialized category, even if Plesiochelys bigleri plots closer to fully aquatic turtles, while the two Triassic species group closer to extant terrestrial forms. Although the shape of the shell of turtles indeed contains an ecological signal, it is overall too weak to uncover using shell shape in paleoecological studies, at least with the methods we selected. creator: Ilya Dziomber creator: Walter G. Joyce creator: Christian Foth uri: https://doi.org/10.7717/peerj.10490 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dziomber et al. title: SKP1-like protein, CrSKP1-e, interacts with pollen-specific F-box proteins and assembles into SCF-type E3 complex in ‘Wuzishatangju’ (Citrus reticulata Blanco) pollen link: https://peerj.com/articles/10578 last-modified: 2020-12-22 description: S-ribonuclease (S-RNase)-based self-incompatibility (SI) mechanisms have been extensively studied in Solanaceae, Rosaceae and Plantaginaceae. S-RNase-based SI is controlled by two closely related genes, S-RNase and S-locus F-box (SLF), located at a polymorphic S-locus. In the SI system, the SCF-type (SKP1-CUL1-F-box-RBX1) complex functions as an E3 ubiquitin ligase complex for ubiquitination of non-self S-RNase. Pummelo (Citrus grandis) and several mandarin cultivars are suggested to utilize an S-RNase-based SI system. However, the molecular mechanism of the non-S-factors involved in the SI reaction is not straightforward in Citrus. To investigate the SCF-type E3 complex responsible for the SI reaction in mandarin, SLF, SKP1-like and CUL1 candidates potentially involved in the SI reaction of ‘Wuzishatangju’ (Citrus reticulata Blanco) were identified based on the genome-wide identification and expression analyses. Sixteen pollen-specific F-box genes (CrFBX1-CrFBX16), one pollen-specific SKP1-like gene (CrSKP1-e) and two CUL1 genes (CrCUL1A and CrCUL1B) were identified and cloned from ‘Wuzishatangju’. Yeast two-hybrid (Y2H) and in vitro binding assays showed that five CrFBX proteins could bind to CrSKP1-e, which is an ortholog of SSK1 (SLF-interacting-SKP1-like), a non-S-factor responsible for the SI reaction. Luciferase complementation imaging (LCI) and in vitro binding assays also showed that CrSKP1-e interacts with the N-terminal region of both CrCUL1A and CrCUL1B. These results indicate that CrSKP1-e may serve as a functional member of the SCF-type E3 ubiquitin ligase complex in ‘Wuzishatangju’. creator: Yi Ren creator: Qingzhu Hua creator: Jiayan Pan creator: Zhike Zhang creator: Jietang Zhao creator: Xinhua He creator: Yonghua Qin creator: Guibing Hu uri: https://doi.org/10.7717/peerj.10578 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ren et al. title: The effect of brewery spent grain application on biogas yields and kinetics in co-digestion with sewage sludge link: https://peerj.com/articles/10590 last-modified: 2020-12-22 description: The present study examines the effect of introducing dried brewery spent grain (BSG), known as the main solid by-product of the brewery industry on biogas yields and kinetics in co-digestion with sewage sludge (SS). The experiment was conducted in semi-continuous anaerobic reactors (supplied once a day) operating under mesophilic conditions (35°C) at different hydraulic retention times (HRT) of 18 and 20 d. In co-digestion runs, the BSG mass to the feed volume ratio was constant and maintained 1:10.The results indicated that the addition of BSG did not influence the biogas production, by comparison with SS mono-digestion (control run). At HRT of 18 d, in the co-digestion run, the average methane yield was 0.27 m3 kg/VSadded, while in the control run the higher value of 0.29 m3 kg/VSaddedwas observed. However, there was no difference in terms of statistical significance. At HRT of 20 d, the methane yield was 0.21 m3 kg/VSadded for both mono- and co-digestion runs. In the BSG presence, the decrease in kinetic constant values was observed. As compared to SS mono-digestion, reductions by 21 and 35% were found at HRT of 20 and 18 d, respectively. However, due to the supplementation of the feedstock with BSG rich in organic compounds, the significantly enhanced energy profits were achieved with the highest value of approx. 40% and related to the longer HRT of 20 d. Importantly, the mono- and co-digestion process proceeded in stable manner. Therefore, the anaerobic co-digestion of SS and BSG might be considered as a cost-effective solution that could contribute to the energy self-efficiency of wastewater treatment plants (WWTPs) and sustainable waste management for breweries. creator: Aleksandra Szaja creator: Agnieszka Montusiewicz creator: Magdalena Lebiocka creator: Marta Bis uri: https://doi.org/10.7717/peerj.10590 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Szaja et al. title: Diversification and selection pattern of CYP6B genes in Japanese Papilio butterflies and their association with host plant spectra link: https://peerj.com/articles/10625 last-modified: 2020-12-22 description: Herbivorous insects are thought to have evolved counteradaptations to conquer chemical defenses in their host plants in a stepwise co-evolutionary process. Papilio butterflies use CYP6B gene family members to metabolize furanocoumarins in their Rutaceae or Apiaceae host plants. CYP6Bs have functionally diverged among Papilio species to be able to metabolite diverse types of furanocoumarins in their host plants. In this study, we examined the diversification and selection patterns of CYP6B among nine Papilio species in Japan (eight Rutaceae specialists and one Apiaceae specialist) and their association with host plant spectra and furanocoumarin profiles. We compared host plant spectrum of eight Rutaceae feeding Papilio species and also performed a furanocoumarin profiling of their host plants. In addition, we reconstructed CYP6B gene phylogeny and performed selection analysis based on the transcriptome data of those nine Papilio species. Among Rutaceae-feeding Papilio species, host plant spectrum differences were correlated with their furanocoumarin profiles. However, all tested Papilio species had similar duplicated sets of CYP6B, with no apparent lineage-specific or host plant-specific pattern of CYP6B diversification. Selection analysis showed a signature of positive selection on a CYP6B branch. The positively selected sites located at predicted substrate recognition sites and we also found that these CYP6B genes were observed only in Rutaceae-feeding species. These findings indicate that most CYP6B diversification occurred in ancestral species of these Papilio species, possibly in association with specific host plant chemical defenses and subsequent gene loss due to host specialization. These processes would have shaped the complex diversification patterns of the CYP6B gene family in Papilio butterflies. Our results also show potentially important CYP6B clades among Papilio species which likely to have diverged functions and associated with host plant phytochemicals in ancestral Papilio species. creator: Ai Sato creator: Yu Okamura creator: Masashi Murakami uri: https://doi.org/10.7717/peerj.10625 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sato et al. title: Viscoelastic characteristics of the canine cranial cruciate ligament complex at slow strain rates link: https://peerj.com/articles/10635 last-modified: 2020-12-22 description: Ligaments including the cruciate ligaments support and transfer loads between bones applied to the knee joint organ. The functions of these ligaments can get compromised due to changes to their viscoelastic material properties. Currently there are discrepancies in the literature on the viscoelastic characteristics of knee ligaments which are thought to be due to tissue variability and different testing protocols.The aim of this study was to characterise the viscoelastic properties of healthy cranial cruciate ligaments (CCLs), from the canine knee (stifle) joint, with a focus on the toe region of the stress-strain properties where any alterations in the extracellular matrix which would affect viscoelastic properties would be seen. Six paired CCLs, from skeletally mature and disease-free Staffordshire bull terrier stifle joints were retrieved as a femur-CCL-tibia complex and mechanically tested under uniaxial cyclic loading up to 10 N at three strain rates, namely 0.1%, 1% and 10%/min, to assess the viscoelastic property of strain rate dependency. The effect of strain history was also investigated by subjecting contralateral CCLs to an ascending (0.1%, 1% and 10%/min) or descending (10%, 1% and 0.1%/min) strain rate protocol. The differences between strain rates were not statistically significant. However, hysteresis and recovery of ligament lengths showed some dependency on strain rate. Only hysteresis was affected by the test protocol and lower strain rates resulted in higher hysteresis and lower recovery. These findings could be explained by the slow process of uncrimping of collagen fibres and the contribution of proteoglycans in the ligament extracellular matrix to intra-fibrillar gliding, which results in more tissue elongations and higher energy dissipation. This study further expands our understanding of canine CCL behaviour, providing data for material models of femur-CCL-tibia complexes, and demonstrating the challenges for engineering complex biomaterials such as knee joint ligaments. creator: Rosti Readioff creator: Brendan Geraghty creator: Ahmed Elsheikh creator: Eithne Comerford uri: https://doi.org/10.7717/peerj.10635 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Readioff et al. title: Australia’s prehistoric ‘swamp king’: revision of the Plio-Pleistocene crocodylian genus Pallimnarchus de Vis, 1886 link: https://peerj.com/articles/10466 last-modified: 2020-12-21 description: The crocodylian fossil record from the Cenozoic of Australasia is notable for its rich taxonomic diversity, and is primarily represented by members of the clade Mekosuchinae. Reports of crocodylian fossils from Australia date back to the late nineteenth century. In 1886, Charles Walter de Vis proposed the name Pallimnarchus pollens for crocodylian fossils from southeast Queensland—the first binomen given to an extinct crocodylian taxon from Australia. Pallimnarchus has come to be regarded as a large, broad-snouted crocodylian from Australia’s Plio-Pleistocene, and numerous specimens, few of which are sufficiently complete, have been assigned to it by several authors throughout the twentieth century. In the late 1990s, the genus was expanded to include a second species, Pallimnarchus gracilis. Unfortunately, the original syntype series described as Pallimnarchus pollens is very fragmentary and derives from more than one taxon, while a large part of the subsequently selected lectotype specimen is missing. Because descriptions and illustrations of the complete lectotype do not reveal any autapomorphic features, we propose that Pallimnarchus pollens should be regarded as a nomen dubium. Following this decision, the fossil material previously referred to Pallimnarchus is of uncertain taxonomic placement. A partial skull, formerly assigned to Pallimnarchus pollens and known as ‘Geoff Vincent’s specimen’, possesses many features of diagnostic value and is therefore used as basis to erect a new genus and species—Paludirex vincenti gen. et sp. nov. A comprehensive description is given for the osteology of ‘Geoff Vincent’s specimen’ as well as aspects of its palaeoneurology, the latter being a first for an extinct Australian crocodyliform. The newly named genus is characterized by a unique combination of premaxillary features such as a distinctive arching of the anterior alveolar processes of the premaxillae, a peculiar arrangement of the first two premaxillary alveoli and a large size disparity between the 3rd and 4th premaxillary alveoli. These features presently allow formal recognition of two species within the genus, Paludirex vincenti and Paludirex gracilis comb. nov., with the former having comparatively more robust rostral proportions than the latter. The Paludirex vincenti holotype comes from the Pliocene Chinchilla Sand of the Darling Downs, south-eastern Queensland, whereas the material assigned to Paludirex gracilis is from the Pleistocene of Terrace Site Local Fauna, Riversleigh, northwest Queensland. Phylogenetic analyses recover Paludirex vincenti as a mekosuchine, although further cladistic assessments are needed to better understand the relationships within the clade. creator: Jorgo Ristevski creator: Adam M. Yates creator: Gilbert J. Price creator: Ralph E. Molnar creator: Vera Weisbecker creator: Steven W. Salisbury uri: https://doi.org/10.7717/peerj.10466 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ristevski et al. title: The Aichi Biodiversity Targets: achievements for marine conservation and priorities beyond 2020 link: https://peerj.com/articles/9743 last-modified: 2020-12-21 description: In 2010 the Conference of the Parties (COP) for the Convention on Biological Diversity revised and updated a Strategic Plan for Biodiversity 2011–2020, which included the Aichi Biodiversity Targets. Here a group of early career researchers mentored by senior scientists, convened as part of the 4th World Conference on Marine Biodiversity, reflects on the accomplishments and shortfalls under four of the Aichi Targets considered highly relevant to marine conservation: target 6 (sustainable fisheries), 11 (protection measures), 15 (ecosystem restoration and resilience) and 19 (knowledge, science and technology). We conclude that although progress has been made towards the targets, these have not been fully achieved for the marine environment by the 2020 deadline. The progress made, however, lays the foundations for further work beyond 2020 to work towards the 2050 Vision for Biodiversity. We identify key priorities that must be addressed to better enable marine biodiversity conservation efforts moving forward. creator: Hannah Carr creator: Marina Abas creator: Loubna Boutahar creator: Olivia N. Caretti creator: Wing Yan Chan creator: Abbie S.A. Chapman creator: Sarah N. de Mendonça creator: Abigail Engleman creator: Filippo Ferrario creator: Kayelyn R. Simmons creator: Jana Verdura creator: Anna Zivian uri: https://doi.org/10.7717/peerj.9743 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Carr et al.