title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=802 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems link: https://peerj.com/articles/12458 last-modified: 2021-11-15 description: Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest. creator: Laurence J. Clarke creator: Leonie Suter creator: Bruce E. Deagle creator: Andrea M. Polanowski creator: Aleks Terauds creator: Glenn J. Johnstone creator: Jonathan S. Stark uri: https://doi.org/10.7717/peerj.12458 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Clarke et al. title: Heteropelta boboi n. gen., n. sp. an armored archosauriform (Reptilia: Archosauromorpha) from the Middle Triassic of Italy link: https://peerj.com/articles/12468 last-modified: 2021-11-15 description: Heteropelta boboi is a new archosauriform reptile from the upper Anisian of northeastern Italy represented by a fragment of dorsal armor with a row of neural arches of the dorsal vertebrae. The dorsal armor of the new taxon is composed of two columns of paramedian osteoderms and at least six columns of lateral osteoderms. Unlike other armored archosaurs, the osteoderms are imbricated with the posterior osteoderm overlapping the anterior one. The low neural arches bear small neural spines and long postzygapophyses. The osteoderms of the lateral columns increase in size and change in shape from the most medial to the most lateral columns. Among the Archosauriformes, only the non-archosaur proterochampsians Vancleavea campi, Litorosuchus somnii, and the doswelliids have dorsal armor comprised of more than two columns of osteoderms per side, but the morphology and arrangement of their osteoderms is unlike those of the new Italian taxon. A cladistic analysis of Archosauromorpha positions Heteropelta boboi as either a basal phytosaur or a basal suchian. However, a second cladistic analysis focused on armored archosaurs alternatively positions the new taxon as a basal archosauriform, basal suchian, basal loricatan or crocodylomorph. Better resolution of the phylogenetic relationships of Heteropelta boboi will likely be obtained only with the discovery of cranial and postcranial remains associated with its diagnostic armor elements. creator: Fabio Marco Dalla Vecchia uri: https://doi.org/10.7717/peerj.12468 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Dalla Vecchia title: Integrated population modelling reveals potential drivers of demography from partially aligned data: a case study of snowy plover declines under human stressors link: https://peerj.com/articles/12475 last-modified: 2021-11-15 description: Knowledge of demography is essential for understanding wildlife population dynamics and developing appropriate conservation plans. However, population survey and demographic data (e.g., capture-recapture) are not always aligned in space and time, hindering our ability to robustly estimate population size and demographic processes. Integrated population models (IPMs) can provide inference for population dynamics with poorly aligned but jointly analysed population and demographic data. In this study, we used an IPM to analyse partially aligned population and demographic data of a migratory shorebird species, the snowy plover (Charadrius nivosus). Snowy plover populations have declined dramatically during the last two decades, yet the demographic mechanisms and environmental drivers of these declines remain poorly understood, hindering development of appropriate conservation strategies. We analysed 21 years (1998–2018) of partially aligned population survey, nest survey, and capture-recapture-resight data in three snowy plover populations (i.e., Texas, New Mexico, Oklahoma) in the Southern Great Plains of the US. By using IPMs we aimed to achieve better precision while evaluating the effects of wetland habitat and climatic factors (minimum temperature, wind speed) on snowy plover demography. Our IPM provided reasonable precision for productivity measures even with missing data, but population and survival estimates had greater uncertainty in years without corresponding data. Our model also uncovered the complex relationships between wetland habitat, climate, and demography with reasonable precision. Wetland habitat had positive effects on snowy plover productivity (i.e., clutch size and clutch fate), indicating the importance of protecting wetland habitat under climate change and other human stressors for the conservation of this species. We also found a positive effect of minimum temperature on snowy plover productivity, indicating potential benefits of warmth during night on their population. Based on our results, we suggest prioritizing population and capture-recapture surveys for understanding population dynamics and underlying demographic processes when data collection is limited by time and/or financial resources. Our modelling approach can be used to allocate limited conservation resources for evidence-based decision-making. creator: Qing Zhao creator: Kristen Heath-Acre creator: Daniel Collins creator: Warren Conway creator: Mitch D. Weegman uri: https://doi.org/10.7717/peerj.12475 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhao et al. title: Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution link: https://peerj.com/articles/12491 last-modified: 2021-11-15 description: BackgroundFlax (Linum usitatissimum) is an important crop for its seed oil and stem fiber. Really Interesting New Gene (RING) finger genes play essential roles in growth, development, and biotic and abiotic stress responses in plants. However, little is known about these genes in flax.MethodsHere, we performed a systematic genome-wide analysis to identify RING finger genes in flax.ResultsWe identified 587 RING domains in 574 proteins and classified them into RING-H2 (292), RING-HCa (181), RING-HCb (23), RING-v (53), RING-C2 (31), RING-D (2), RING-S/T (3), and RING-G (2). These proteins were further divided into 45 groups according to domain organization. These genes were located in 15 chromosomes and clustered into three clades according to their phylogenetic relationships. A total of 312 segmental duplicated gene pairs were inferred from 411 RING finger genes, indicating a major contribution of segmental duplications to the RING finger gene family expansion. The non-synonymous/synonymous substitution ratio of the segmentally duplicated gene pairs was less than 1, suggesting that the gene family was under negative selection since duplication. Further, most RING genes in flax were differentially expressed during seed development or in the shoot apex. This study provides useful information for further functional analysis of RING finger genes in flax and to develop gene-derived molecular markers in flax breeding. creator: Xianwen Meng creator: Jing Liu creator: Mingde Zhao uri: https://doi.org/10.7717/peerj.12491 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Meng et al. title: Morphological and molecular analyses of parasitic barnacles (Crustacea: Cirripedia: Rhizocephala) in Korea: preliminary data for the taxonomy and host ranges of Korean species link: https://peerj.com/articles/12281 last-modified: 2021-11-12 description: Morphological and molecular analyses of Korean rhizocephalan barnacle species were performed to examine their host ranges and taxonomy. Morphological examination and molecular analysis of mtDNA cox1, 16S, and nuclear 18S rRNA sequences revealed nine rhizocephalan species from three genera of the two families, Sacculinidae and Polyascidae. Phylogenetic analysis of molecular sequences revealed two new species candidates in the genus Parasacculina, and three Sacculina species (S. pilosella, S. pinnotherae, and S. imberbis) were transferred to the genus Parasacculina. Examination of host ranges revealed higher host specificity and lower infestation rates in Korean rhizocephalan species than rhizocephalans from other geographic regions. This is the first report of the taxonomy, species diversity, and host ranges of Korean parasitic rhizocephalan barnacles based on their morphological and molecular analyses. More information from extensive sampling of parasitic barnacles from a wide range of crustacean host species is necessary to fully understand their taxonomy, prevalence on decapod hosts, and phylogenetic relationships among major rhizocephalan taxa. creator: Jibom Jung creator: Ryuta Yoshida creator: Damin Lee creator: Joong-Ki Park uri: https://doi.org/10.7717/peerj.12281 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jung et al. title: Characteristics of solar radiation at Xiaotang, in the northern marginal zone of the Taklimakan Desert link: https://peerj.com/articles/12373 last-modified: 2021-11-12 description: The characteristics of solar radiation and the influence of sand and dust on solar radiation in the northern margin of Taklimakan Desert were analyzed using radiation observation data from 2018. The results showed that the annual total radiation, direct radiation, and scattered radiation at Xiaotang were 5,781.8, 2,337.9, and 3,323.8 MJ m−2, respectively. The maximum monthly total radiation, direct radiation, and scattered radiation were observed in July (679.8 MJ m−2), August (317.3 MJ m−2), and May (455.7 MJ m−2), respectively. The aerosol optical depth corresponded well with the scattered radiation, and the maximum value was in May. Further analysis showed a significant correlation between the total radiation and solar height angle under different weather conditions. Under the same solar height angle, total radiation was higher during clear days but lower on sandstorm days. Calculation of atmospheric transmittance showed that the average atmospheric transmittance on a clear day was 0.67; on sand-and-dust days, it was 0.46. When the atmospheric transmittance was 0.5, the increase in scattering radiation by aerosol in the air began to decrease. Probability analysis of radiation indicated the following probabilities of total radiation <500 W m−2 occurring on clear, floating-dust, blowing-sand, and sandstorm days: 67.1%, 76.3%, 76.1%, and 91.8%, respectively. Dust had the greatest influence on direct radiation; the probabilities of direct radiation <200 W m−2occurring on clear, floating-dust, blowing-sand, and sandstorm days were 44.5%, 93.5%, 91.3%, and 100%, respectively, whereas those of scattered radiation <600 W m−2were 100%, 99.1%, 98.1%, and 100%, respectively. Therefore, the presence of dust in the air will reduce scattered radiation. creator: Lili Jin creator: Sasa Zhou creator: Qing He creator: Alim Abbas uri: https://doi.org/10.7717/peerj.12373 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jin et al. title: Exploring women’s oxytocin responses to interactions with their pet cats link: https://peerj.com/articles/12393 last-modified: 2021-11-12 description: BackgroundExtensive research has evaluated the involvement of the neuropeptide oxytocin (OT) in human social behaviors, including parent-infant relationships. Studies have investigated OT’s connection to human attachment to nonhuman animals, with the majority of the literature focusing on domestic dogs (Canis lupis familiaris). Utilizing what is known about OT and its role in maternal-infant and human-dog bonding, we apply these frameworks to the study of human-domestic cat (Felis catus) interactions.MethodsWe investigated changes in salivary OT levels in 30 U.S. women of reproductive age before and after two conditions: reading a book (control) and interacting with their pet cat. Participant and cat behavioral patterns during the cat interaction condition were also quantified to determine if differences in women’s OT concentrations were associated with specific human and cat behaviors.ResultsOur results revealed no changes in women’s OT levels during the cat interaction, relative to the control condition, and pre-cat interaction OT levels. However, differences in women’s OT concentrations were correlated with some human-cat interactions (e.g., positively with petting cat and cat approach initiation, negatively with cat agonistic behavior) but not all observed behaviors (e.g., use of gentle or baby voice) coded during human-cat interactions.DiscussionThis study is the first to explore women’s OT in response to interactions with their pet cat and has identified distinct human and cat behaviors that influence OT release in humans. creator: Elizabeth A. Johnson creator: Arianna Portillo creator: Nikki E. Bennett creator: Peter B. Gray uri: https://doi.org/10.7717/peerj.12393 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Johnson et al. title: Comparative plastomics of Amaryllidaceae: inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq. link: https://peerj.com/articles/12400 last-modified: 2021-11-12 description: Amaryllidaceae is a widespread and distinctive plant family contributing both food and ornamental plants. Here we present an initial survey of plastomes across the family and report on both structural rearrangements and gene losses. Most plastomes in the family are of similar gene arrangement and content however some taxa have shown gains in plastome length while in several taxa there is evidence of gene loss. Strumaria truncata shows a substantial loss of ndh family genes while three other taxa show loss of cemA, which has been reported only rarely. Our sparse sampling of the family has detected sufficient variation to suggest further sampling across the family could be a rich source of new information on plastome variation and evolution. creator: Kálmán Könyves creator: Jordan Bilsborrow creator: Maria D. Christodoulou creator: Alastair Culham creator: John David uri: https://doi.org/10.7717/peerj.12400 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Könyves et al. title: Treatment with sodium (S)-2-hydroxyglutarate prevents liver injury in an ischemia-reperfusion model in female Wistar rats link: https://peerj.com/articles/12426 last-modified: 2021-11-12 description: BackgroundIschemia-reperfusion (IR) injury is one of the leading causes of early graft dysfunction in liver transplantation. Techniques such as ischemic preconditioning protect the graft through the activation of the hypoxia-inducible factors (HIF), which are downregulated by the EGLN family of prolyl-4-hydroxylases, a potential biological target for the development of strategies based on pharmacological preconditioning. For that reason, this study aims to evaluate the effect of the EGLN inhibitor sodium (S)-2-hydroxyglutarate [(S)-2HG] on liver IR injury in Wistar rats.MethodsTwenty-eight female Wistar rats were divided into the following groups: sham (SH, n = 7), non-toxicity (HGTox, n = 7, 25 mg/kg of (S)-2HG, twice per day for two days), IR (n = 7, total liver ischemia: 20 minutes, reperfusion: 60 minutes), and (S)-2HG+IR (HGIR, n = 7, 25 mg/kg of (S)-2HG, twice per day for two days, total liver ischemia as the IR group). Serum ALT, AST, LDH, ALP, glucose, and total bilirubin were assessed. The concentrations of IL-1β, IL-6, TNF, malondialdehyde, superoxide dismutase, and glutathione peroxidase were measured in liver tissue, as well as the expression of Hmox1, Vegfa, and Pdk1, determined by RT-qPCR. Sections of liver tissue were evaluated histologically, assessing the severity of necrosis, sinusoidal congestion, and cytoplasmatic vacuolization.ResultsThe administration of (S)-2HG did not cause any alteration in the assessed biochemical markers compared to SH. Preconditioning with (S)-2HG significantly ameliorated IR injury in the HGIR group, decreasing the serum activities of ALT, AST, and LDH, and the tissue concentrations of IL-1β and IL-6 compared to the IR group. IR injury decreased serum glucose compared to SH. There were no differences in the other biomarkers assessed. The treatment with (S)-2HG tended to decrease the severity of hepatocyte necrosis and sinusoidal congestion compared to the IR group. The administration of (S)-2HG did not affect the expression of Hmox1 but decreased the expression of both Vegfa and Pdk1 compared to the SH group, suggesting that the HIF-1 pathway is not involved in its mechanism of hepatoprotection. In conclusion, (S)-2HG showed a hepatoprotective effect, decreasing the levels of liver injury and inflammation biomarkers, without evidence of the involvement of the HIF-1 pathway. No hepatotoxic effect was observed at the tested dose. creator: Eduardo Cienfuegos-Pecina creator: Diana P. Moreno-Peña creator: Liliana Torres-González creator: Diana Raquel Rodríguez-Rodríguez creator: Diana Garza-Villarreal creator: Oscar H. Mendoza-Hernández creator: Raul Alejandro Flores-Cantú creator: Brenda Alejandra Samaniego Sáenz creator: Gabriela Alarcon-Galvan creator: Linda E. Muñoz-Espinosa creator: Tannya R. Ibarra-Rivera creator: Alma L. Saucedo creator: Paula Cordero-Pérez uri: https://doi.org/10.7717/peerj.12426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cienfuegos-Pecina et al. title: Conserved molecular signatures in the spike protein provide evidence indicating the origin of SARS-CoV-2 and a Pangolin-CoV (MP789) by recombination(s) between specific lineages of Sarbecoviruses link: https://peerj.com/articles/12434 last-modified: 2021-11-12 description: Both SARS-CoV-2 and SARS coronaviruses (CoVs) are members of the subgenus Sarbecovirus. To understand the origin of SARS-CoV-2, sequences for the spike and nucleocapsid proteins from sarbecoviruses were analyzed to identify molecular markers consisting of conserved inserts or deletions (termed CSIs) that are specific for either a particular clade of Sarbecovirus or are commonly shared by two or more clades of these viruses. Three novel CSIs in the N-terminal domain (NTD) of the spike protein S1-subunit (S1-NTD) are uniquely shared by SARS-CoV-2, Bat-CoV-RaTG13 and most pangolin CoVs (SARS-CoV-2r clade). Three other sarbecoviruses viz. bat-CoVZXC21, -CoVZC45 and -PrC31 (forming CoVZC/PrC31 clade), and a pangolin-CoV_MP789 also contain related CSIs in the same positions. In contrast to the S1-NTD, both SARS and SARS-CoV-2r viruses contain two large CSIs in the S1-C-terminal domain (S1-CTD) that are absent in the CoVZC/PrC31 clade. One of these CSIs, consisting of a 12 aa insert, is also present in the RShSTT clade (Cambodia-CoV strains). Sequence similarity studies show that the S1-NTD of SARS-CoV-2r viruses is most similar to the CoVZC/PrC31 clade, whereas their S1-CTD exhibits highest similarity to the RShSTT- (and the SARS-related) CoVs. Results from the shared presence of CSIs and sequence similarity studies on different CoV lineages support the inference that the SARS-CoV-2r cluster of viruses has originated by a genetic recombination between the S1-NTD of the CoVZC/PrC31 clade of CoVs and the S1-CTD of RShSTT/SARS viruses, respectively. We also present compelling evidence, based on the shared presence of CSIs and sequence similarity studies, that the pangolin-CoV_MP789, whose receptor-binding domain is most similar to the SARS-CoV-2 virus, has resulted from another independent recombination event involving the S1-NTD of the CoVZC/PrC31 CoVs and the S1-CTD of an unidentified SARS-CoV-2r related virus. The SARS-CoV-2 virus involved in this latter recombination event is postulated to be most similar to the SARS-CoV-2. Several other CSIs reported here are specific for other clusters of sarbecoviruses including a clade consisting of bat-SARS-CoVs (BM48-31/BGR/2008 and SARS_BtKY72). Structural mapping studies show that the identified CSIs form distinct loops/patches on the surface of the spike protein. It is hypothesized that these novel loops/patches on the spike protein, through their interactions with other host components, should play important roles in the biology/pathology of SARS-CoV-2 virus. Lastly, the CSIs specific for different clades of sarbecoviruses including SARS-CoV-2r clade provide novel means for the identification of these viruses and other potential applications. creator: Bijendra Khadka creator: Radhey S. Gupta uri: https://doi.org/10.7717/peerj.12434 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Khadka and Gupta