title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=659 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Diagnosis and potential invasion risk of Thrips parvispinus under current and future climate change scenarios link: https://peerj.com/articles/13868 last-modified: 2022-08-25 description: Background and ObjectiveInvasive thrips, Thrips parvispinus Karny recently reported in India, causing a widespread severe infestation in more than 0.4 million ha of chilli (Capsicum annum L.) growing areas. This species is native to Thailand and most prevalent in other South East Asian countries. Large scale cultivation of the major host plants (chilli and papaya), and favourable climatic conditions in India and other countries similar to native range of Thrips parvispinus expected to favour its further spread and establishment to new areas.Materials and MethodsThe present study was undertaken to confirm invasive thrips species identity through both morphological and molecular approaches and predict its potential invasion using the maximum entropy (MaxEnt) algorithm.ResultsThe model predicted species range in respect of discrimination of suitable and unsuitable areas for its occurrence both in current and future climatic scenarios. The model provided a good fit for species distribution with a high value of area under the curve (0.957). The jackknife test indicated annual mean temperature and precipitation were found to be the most important bioclimatic variable in determining the distribution of T. parvispinus. High suitability areas were predicted in the countries wherever its occurrence was reported with high discrimination ability of suitable and unsuitable areas. Key distinguishing morphological characters of T. parvispinus were illustrated through high-resolution scanning electron microscopic images.ConclusionThe identity of the thrips causing wide spread damage in chilli confirmed through morphological and molecular approaches. Key identifying characters were described through high resolution scanning electron microscopic images for accurate identification of the species. MaxEnt model identified high suitability regions for the potential establishment of T. parvispinus in India and other parts of the world. This study facilitates forecasting of further spread and also suggests imposing strict domestic quarantine measures to curtail its establishment in the new areas. creator: Timmanna Hulagappa creator: Gundappa Baradevanal creator: Shwetha Surpur creator: Devaramane Raghavendra creator: Sagar Doddachowdappa creator: Pathour R. Shashank creator: Kumaranag Kereyagalahalli Mallaiah creator: Jamuna Bedar uri: https://doi.org/10.7717/peerj.13868 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hn et al. title: Total evidence time-scaled phylogenetic and biogeographic models for the evolution of sea cows (Sirenia, Afrotheria) link: https://peerj.com/articles/13886 last-modified: 2022-08-25 description: Molecular phylogenetic studies that have included sirenians from the genera Trichechus, Dugong, and Hydrodamalis have resolved their interrelationships but have yielded divergence age estimates that are problematically discordant. The ages of these lineage splits have profound implications for how to interpret the sirenian fossil record—including clade membership, biogeographic patterns, and correlations with Earth history events. In an effort to address these issues, here we present a total evidence phylogenetic analysis of Sirenia that includes living and fossil species and applies Bayesian tip-dating methods to estimate their interrelationships and divergence times. In addition to extant sirenians, our dataset includes 56 fossil species from 106 dated localities and numerous afrotherian outgroup taxa. Genetic, morphological, temporal, and biogeographic data are assessed simultaneously to bring all available evidence to bear on sirenian phylogeny. The resulting time-tree is then used for Bayesian geocoordinates reconstruction analysis, which models ancestral geographic areas at splits throughout the phylogeny, thereby allowing us to infer the direction and timing of dispersals. Our results suggest that Pan-Sirenia arose in North Africa during the latest Paleocene and that the Eocene evolution of stem sirenians was primarily situated in the Tethyan realm. In the late Eocene, some lineages moved into more northern European latitudes, an area that became the source region for a key trans-Atlantic dispersal towards the Caribbean and northern-adjacent west Atlantic. This event led to the phylogenetic and biogeographic founding of crown Sirenia with the Dugongidae-Trichechidae split occurring at the Eocene-Oligocene boundary (~33.9 Ma), temporally coincident with the onset of dropping global sea levels and temperatures. This region became the nexus of sirenian diversification and supported taxonomically-rich dugongid communities until the earliest Pliocene. The Dugonginae-Hydrodamalinae split occurred near Florida during the early Miocene (~21.2 Ma) and was followed by a west-bound dispersal that gave rise to the Pacific hydrodamalines. The late middle Miocene (~12.2 Ma) split of Dugong from all other dugongines also occurred near Florida and our analyses suggest that the Indo-Pacific distribution of modern dugongs is the result of a trans-Pacific dispersal. From at least the early Miocene, trichechid evolution was based entirely in South America, presumably within the Pebas Wetlands System. We infer that the eventual establishment of Amazon drainage into the South Atlantic allowed the dispersal of Trichechus out of South America no earlier than the mid-Pliocene. Our analyses provide a new temporal and biogeographic framework for understanding major events in sirenian evolution and their possible relationships to oceanographic and climatic changes. These hypotheses can be further tested with the recovery and integration of new fossil evidence. creator: Steven Heritage creator: Erik R. Seiffert uri: https://doi.org/10.7717/peerj.13886 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Heritage and Seiffert title: Phylogenetic position of the enigmatic genus Atherospio and description of Atherospio aestuarii sp. nov. (Annelida: Spionidae) from Japan link: https://peerj.com/articles/13909 last-modified: 2022-08-25 description: BackgroundThere are currently two species within the small enigmatic genus Atherospio Mackie & Duff, 1986, which belongs to the Pygospiopsis-Atherospio group in the family Spionidae Grube, 1850. The taxonomic relationship of the genus Atherospio with other spionid or spioniform genera is currently not well understood due to its unusual morphological characteristics.MethodsHere, we describe a new Atherospio species, Atherospio aestuariisp. nov., based on materials collected from three localities in Japan: Hirota Bay (Iwate Prefecture), Ago Bay (Mie Prefecture), and Yakushima Island (Kagoshima Prefecture). We have also evaluated the possible systematic position of this new species by conducting molecular phylogenetic analyses using the nuclear 18S, 28S, and mitochondrial 16S rRNA gene sequences.ResultsThe morphology of A. aestuariisp. nov. resembles that of A. disticha Mackie & Duff, 1986 and A. guillei (Laubier & Ramos, 1974) in having branchiae fused to the notopodial lamellae on a restricted number of segments from chaetiger 7, modified neurochaetae on chaetiger 5, and at least some bidentate neuropodial hooks with the secondary tooth below the main fang. The form and arrangement of the modified aristate neurochaetae in double vertical rows closely resemble those found on chaetigers 4 and 5 of A. disticha. The new species lacks the occipital antenna present in A. disticha. In this respect it resembles A. guillei, however, that species differs in having robust neuropodial spines on chaetiger 5 and peristomial papillae, and a preponderance of unidentate neurochaetae. Both A. guillei and the new species have slender needle-like notochaetae in their posteriormost chaetigers. Atherospio aestuariisp. nov. is distinguished from both congeneric species by its branchial and neuropodial hook distributions. The new species is also unique in that it was recorded at relatively shallow depths, which included intertidal zones. The results of our molecular phylogenetic analysis indicate that the new species was included in a clade that included the genera of the Polydora complex, Pygospio Claparède, 1863, Glandulospio Meißner, Bick, Guggolz, Götting, 2014, Spio Fabricius, 1785, Microspio Mesnil, 1896, Marenzelleria Mesnil, 1896, Rhynchospio Hartman, 1936, Scolelepis Blainville, 1828, Dispio Hartman, 1951, and Malacoceros Quatrefages, 1843 with robust statistical support. The new species formed a clade with Dispio and Scolelepis, however, statistical support for the node was not significant. creator: Hirokazu Abe creator: Kotaro Kan uri: https://doi.org/10.7717/peerj.13909 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Abe and Kan title: Association between changes in social capital and mental well-being among older people in China link: https://peerj.com/articles/13938 last-modified: 2022-08-25 description: BackgroundThe mental well-being of older people has become social concern under aging times in China. Social capital has been linked to mental well-being. Our aims were to explore how social capital and the state of mental well-being of older people were changing and what the relationship between them was.MethodsData were from six waves of the China Family Panel Studies that were conducted between 2010 and 2020, and a total of 1,055 participants aged 60 and over were included in the analysis. The Generalized Estimated Equation model (GEE) was used to clarify the long-term relationship, and to use GEE we first defined how time points were related, in other words, an appropriate working correlation structure was supposed to choose. Therefore, correlation coefficient between measurements at two time points was calculated to choose the exchange structure. All the analyses were performed in the statistical software Stata 15.0.ResultsThe mental well-being of older people has deteriorated over time, especially we found that between 2014 and 2016, the mental well-being of older people plummeted. In addition, cognitive social capital was positively correlated with mental well-being, while structural social capital was inverse.ConclusionsPolicymakers are supposed to take into account the long-term impact of cognitive and structural social capital on the mental well-being of older people and to provide them with projects aimed at increasing cognitive social capital and turning the pressure of structural social capital into a source of happiness in life. creator: Huihui Wang creator: Jingni Zhang creator: Zhenfan Yu creator: Naifan Hu creator: Yurun Du creator: Xiaoxue He creator: Degong Pan creator: Lining Pu creator: Xue Zhang creator: Jiangping Li uri: https://doi.org/10.7717/peerj.13938 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Mental arithmetic modulates temporal variabilities of finger-tapping tasks in a tempo-dependent manner link: https://peerj.com/articles/13944 last-modified: 2022-08-25 description: BackgroundSeveral psychiatric diseases impair temporal processing. Temporal processing is thought to be based on two domains: supra-second intervals and sub-second intervals. Studies show that temporal processing in sub-second intervals is mainly an automated process. However, the brain functions involved in temporal processing at each time scale remain unclear. We hypothesized that temporal processing in supra-second intervals requires several brain areas, such as the ventrolateral prefrontal cortex, intraparietal sulcus (IPS), and inferior parietal lobe, corresponding to various cognitions in a time scale-dependent manner. We focused on a dual-task paradigm (DTP) involving simultaneous performance of cognitive and motor tasks, which is an effective method for screening psychomotor functions; we then designed a DTP comprising finger tapping at various tempi as the temporal processing task and two cognitive tasks (mental arithmetic and reading) that might affect temporal processing. We hoped to determine whether task-dependent interferences on temporal processing in supra-second intervals differed depending on the cognitive tasks involved.MethodsThe study included 30 participants with no history of neuromuscular disorders. Participants were asked to perform a DTP involving right index finger tapping at varying tempi (0.33, 0.5, 1, 2, 3, and 4 s inter-tapping intervals). Cognitive tasks comprised mental arithmetic (MA) involving three-digit addition, mental reading (MR) of three- to four-digit numbers, and a control (CTL) task without any cognitive loading. For comparison between tasks, we calculated the SDs of the inter-tapping intervals. Participants’ MA abilities in the three-digit addition task were evaluated.ResultsThe MA and MR tasks significantly increased the SDs of the inter-tapping intervals compared to those of the CTL task in 2–3 s and 3–4 s for the MA and MR tasks, respectively. Furthermore, SD peaks in the finger-tapping tasks involving MA were normalized by those in the CTL task, which were moderately correlated with the participants’ MA ability (r = 0.462, P = 0.010).DiscussionOur results established that DTP involving the temporal coordination of finger-tapping and cognitive tasks increased temporal variability in a task- and tempo-dependent manner. Based on the behavioral aspects, we believe that these modulations of temporal variability might result from the interaction between finger function, arithmetic processing, and temporal processing, especially during the “pre-semantic period”. Our findings may help in understanding the temporal processing deficits in various disorders such as dementia, Parkinson’s disease, and autism. creator: Shun Irie creator: Yoshiteru Watanabe creator: Atsumichi Tachibana creator: Nobuhiro Sakata uri: https://doi.org/10.7717/peerj.13944 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Irie et al. title: Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas link: https://peerj.com/articles/13954 last-modified: 2022-08-25 description: BackgroundThe fathead minnow (Pimephales promelas) is a model species for toxicological research. A high-quality genome reference sequence is available, and genomic methods are increasingly used in toxicological studies of the species. However, phylogenetic relationships within the genus remain incompletely known and little population-genomic data are available for fathead minnow despite the potential effects of genetic background on toxicological responses. On the other hand, a wealth of extant samples is stored in museum collections that in principle allow fine-scale analysis of contemporary and historical genetic variation.MethodsHere we use short-read shotgun resequencing to investigate sequence variation among and within Pimephales species. At the genus level, our objectives were to resolve phylogenetic relationships and identify genes with signatures of positive diversifying selection. At the species level, our objective was to evaluate the utility of archived-sample resequencing for detecting selective sweeps within fathead minnow, applied to a population introduced to the San Juan River of the southwestern United States sometime prior to 1950.ResultsWe recovered well-supported but discordant phylogenetic topologies for nuclear and mitochondrial sequences that we hypothesize arose from mitochondrial transfer among species. The nuclear tree supported bluntnose minnow (P. notatus) as sister to fathead minnow, with the slim minnow (P. tenellus) and bullhead minnow (P. vigilax) more closely related to each other. Using multiple methods, we identified 11 genes that have diversified under positive selection within the genus. Within the San Juan River population, we identified selective-sweep regions overlapping several sets of related genes, including both genes that encode the giant sarcomere protein titin and the two genes encoding the MTORC1 complex, a key metabolic regulator. We also observed elevated polymorphism and reduced differentation among populations (FST) in genomic regions containing certain immune-gene clusters, similar to what has been reported in other taxa. Collectively, our data clarify evolutionary relationships and selective pressures within the genus and establish museum archives as a fruitful resource for characterizing genomic variation. We anticipate that large-scale resequencing will enable the detection of genetic variants associated with environmental toxicants such as heavy metals, high salinity, estrogens, and agrichemicals, which could be exploited as efficient biomarkers of exposure in natural populations. creator: Katy E. Klymus creator: Robert A. Hrabik creator: Nathan L. Thompson creator: Robert S. Cornman uri: https://doi.org/10.7717/peerj.13954 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2022 Klymus et al. title: Heterochronies and allometries in the evolution of the hominid cranium: a morphometric approach using classical anthropometric variables link: https://peerj.com/articles/13991 last-modified: 2022-08-25 description: This article studies the evolutionary change of allometries in the relative size of the two main cranial modules (neurocranium and splanchnocranium) in the five living hominid species and a diverse sample of extinct hominins. We use six standard craniometric variables as proxies for the length, width and height of each cranial module. Factor analysis and two-block partial least squares (2B-PLS) show that the great apes and modern humans share a pervasive negative ontogenetic allometry in the neurocranium and a positive one in the splanchnocranium. This developmental constraint makes it possible to interpret the cranial heterochronies in terms of ontogenetic scaling processes (i.e., extensions or truncations of the ancestral ontogenetic trajectory) and lateral transpositions (i.e., parallel translations of the entire trajectory starting from a different shape for a given cranial size). We hypothesize that ontogenetic scaling is the main evolutionary modality in the australopithecines while in the species of Homo it is also necessary to apply transpositions. Both types of processes are coordinated in Homo, which result in an evolutionary trend toward an increase in brain size and in the degree of paedomorphosis from the earliest habilines. creator: Juan Antonio Pérez-Claros creator: Paul Palmqvist uri: https://doi.org/10.7717/peerj.13991 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pérez-Claros and Palmqvist title: Energy demands in high-intensity intermittent taekwondo specific exercises link: https://peerj.com/articles/13654 last-modified: 2022-08-24 description: BackgroundTaekwondo is an intermittent Olympic combat sport, which shows an aerobic predominance in matches and high participation of alactic metabolism for actions that determine competitive success. However, there is no information on energetic contribution systems in different high-intensity intermittent exercises for metabolic conditioning with specific movements. The study aimed to measure the physiological demands, mainly the energy expenditure, in taekwondo-specific high-intensity intermittent exercises (HIIE).MethodsThis study recruited ten male black belt athletes with a mean age of 20.2 ± 4 years, body mass of 62.8 ± 10.5 kg and height of 170.6 ± 7.8 cm, and total practice time of 11.8 ± 5.4 years. Subjects performed an incremental specific test and three different HIIE protocols on nonconsecutive days, and all comprised three 2-min rounds and 1 min of recovery between rounds. Heart rate, oxygen consumption, and blood lactate were measured. Energetic expenditure of aerobic, alactic, and lactic metabolisms was estimated through oxygen consumption, excess post-exercise oxygen consumption, and peak blood lactate after each round.ResultsFor the mean of the three rounds, the TKDtest100 resulted in higher absolute and relative contribution from the aerobic metabolism (52.4 ± 4%; p = 0.01) and lower than the 35:5 relative alactic contribution (48.7 ± 5.4%; p = 0.03).ConclusionThe mean of the three rounds for 35:5 and 15:10:5 presented similar absolute and relative contributions of aerobic and alactic metabolisms, whereas the TKDtest100 was a predominantly aerobic activity. We emphasize that aerobic metabolism was predominant from the second round in the 15:10:5 and 100%TKDtest protocols and in the last round of the 35:5 protocol. creator: Charles Bartel creator: Victor S. Coswig creator: Gabriel V. Protzen creator: Fabricio B. Del Vecchio uri: https://doi.org/10.7717/peerj.13654 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bartel et al. title: Changes and response mechanism of sugar and organic acids in fruits under water deficit stress link: https://peerj.com/articles/13691 last-modified: 2022-08-24 description: The content and the ratio of soluble sugars and organic acids in fruits are significant indicators for fruit quality. They are affected by multiple environmental factors, in which water-deficient is the most concern. Previous studies found that the content of soluble sugars and organic acids in fruit displayed great differences under varied water stress. It is important to clarify the mechanism of such difference and to provide researchers with systematic knowledge about the response to drought stress and the mechanism of sugar and acid changes in fruits, so that they can better carry out the study of fruit quality under drought stress. Therefore, the researchers studied dozens of research articles about the content of soluble sugar and organic acid, the activity of related metabolic enzymes, and the expression of related metabolic genes in fruits under water stress, and the stress response of plants to water stress. We found that after plants perceived and transmitted the signal of water deficit, the expression of genes related to the metabolism of soluble sugars and organic acids changed. It was then affected the synthesis of metabolic enzymes and changed their metabolic rate, ultimately leading to changes in soluble sugar and organic acid content. Based on the literature review, we described the pathway diagrams of sugar metabolism, organic acid metabolism, mainly malic acid, tartaric acid, and citric acid metabolism, and of the response to drought stress. From many aspects including plants’ perception of water stress signal, signal conversion and transmission, induced gene expression, the changes in soluble sugar and the enzyme activities of organic acids, as well as the final sugar and acid content in fruits, this thesis summarized previous studies on the influence of water stress on soluble sugars and the metabolism of organic acids in fruits. creator: Wei-Feng Ma creator: Yan-Biao Li creator: Guo-Jie Nai creator: Guo-Ping Liang creator: Zong-Huan Ma creator: Bai-Hong Chen creator: Juan Mao uri: https://doi.org/10.7717/peerj.13691 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ma et al. title: Identifying sources of variation in parasite aggregation link: https://peerj.com/articles/13763 last-modified: 2022-08-24 description: Aggregation of macroparasites among hosts is a near-universal pattern, and has important consequences for the stability of host-parasite associations and the impacts of disease. Identifying which potential drivers are contributing to levels of aggregation observed in parasite-host associations is challenging, particularly for observational studies. We apply beta regressions in a Bayesian framework to determine predictors of aggregation, quantified using Poulin’s index of discrepancy (D), for 13 species of parasites infecting Icelandic Rock Ptarmigan (Lagopus muta) collected over 12 years. 1,140 ptarmigan were collected using sampling protocols maximizing consistency of sample sizes and of composition of host ages and sexes represented across years from 2006–2017. Parasite species, taxonomic group (insect, mite, coccidian, or nematode), and whether the parasite was an ecto- or endoparasite were tested as predictors of aggregation, either alone or by modulating an effect of parasite mean abundance on D. Parasite species was an important predictor of aggregation in models. Despite variation in D across samples and years, relatively consistent aggregation was demonstrated for each specific host-parasite association, but not for broader taxonomic groups, after taking sample mean abundance into account. Furthermore, sample mean abundance was consistently and inversely related to aggregation among the nine ectoparasites, however no relationship between mean abundance and aggregation was observed among the four endoparasites. We discuss sources of variation in observed aggregation, sources both statistical and biological in nature, and show that aggregation is predictable, and distinguishable, among infecting species. We propose explanations for observed patterns and call for the review and re-analysis of parasite and other symbiont distributions using beta regression to identify important drivers of aggregation—both broad and association-specific. creator: André Morrill creator: Ólafur K. Nielsen creator: Karl Skírnisson creator: Mark R. Forbes uri: https://doi.org/10.7717/peerj.13763 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Morrill et al.