Preliminary placement and new records of an overlooked Amazonian tree, Christiana mennegae (Malvaceae)
Christiana mennegae is a phylogenetically enigmatic taxon and represents a case in point of a species whose presence escaped the radar of the Amazon lists and the Brazilian Flora project. Here we expand its distribution by adding new records from Peru and overlooked ones from Brazil. To investigate its phylogenetic placement in the Brownlowioideae, part of the rbcL gene of the plastid and the intergenic ITS2 region were sequenced. Macro- and micro-morphological investigation of features of C. mennegae using SEM of foliar, flower, fruit and seed structures are presented. A lectotype for the name is designated here. The morphology of trichomes revealed five types of trichomes ranging from glandular to branched and unbranched and we also report stomata on the seed surface for the first time in Brownlowioideae. Christiana mennegae and C. africana were recovered as sister species in the phylogenetic analysis, albeit with low to moderate support, and more species of this and closely related genera must be sampled and analyzed in order to obtain a clearer picture of the group’s affinities and relationships. We provide an update of its conservation status from Vulnerable to Least Concern. We also highlight the need for investment in the digitization of biological collections, botanical capacity building at the local level and the importance of the availability of online literature to speed the study of Amazonian plant diversity.
Barbosa-Silva et al. (2021) Preliminary placement and new records of an overlooked Amazonian tree, Christiana mennegae (Malvaceae). PeerJ 9:e12244 https://doi.org/10.7717/peerj.12244
Virus-derived sequences from the transcriptomes of two snail vectors of schistosomiasis, Biomphalaria pfeifferi and Bulinus globosus from Kenya
Schistosomiasis, which infects more than 230 million people, is vectored by freshwater snails. We identified viral sequences in the transcriptomes of Biomphalaria pfeifferi (BP) and Bulinus globosus (BuG), two of the world’s most important schistosomiasis vectors in Africa. Sequences from 26 snails generated using Illumina Hi-Seq or 454 sequencing were assembled using Trinity and CAP3 and putative virus sequences were identified using a bioinformatics pipeline. Phylogenetic analyses were performed using viral RNA-dependent RNA polymerase and coat protein sequences to establish relatedness between virus sequences identified and those of known viruses. Viral sequences were identified from the entire snail holobiont, including symbionts, ingested material and organisms passively associated with the snails. Sequences derived from more than 17 different viruses were found including five near full-length genomes, most of which were small RNA viruses with positive sense RNA genomes (i.e., picorna-like viruses) and some of which are likely derived from adherent or ingested diatoms. Based on phylogenetic analysis, five of these viruses (including BPV2 and BuGV2) along with four Biomphalaria glabrata viruses reported previously, cluster with known invertebrate viruses and are putative viruses of snails. The presence of RNA sequences derived from four of these novel viruses in samples was confirmed. Identification of the genome sequences of candidate snail viruses provides a first step toward characterization of additional gastropod viruses, including from species of biomedical significance.
Liu et al. (2021) Virus-derived sequences from the transcriptomes of two snail vectors of schistosomiasis, Biomphalaria pfeifferi and Bulinus globosus from Kenya. PeerJ 9:e12290 https://doi.org/10.7717/peerj.12290
Fighting SARS-CoV-2 with green seaweed Ulva sp. extract: extraction protocol predetermines crude ulvan extract anti-SARS-CoV-2 inhibition properties in in vitro Vero-E6 cells assay
Due to the global COVID-19 pandemic, there is a need to screen for novel compounds with antiviral activity against SARS-COV-2. Here we compared chemical composition and the in vitro anti- SARS-COV-2 activity of two different Ulva sp. crude ulvan extracts: one obtained by an HCl-based and another one by ammonium oxalate-based (AOx) extraction protocols. The composition of the crude extracts was analyzed and their antiviral activity was assessed in a cytopathic effect reduction assay using Vero E6 cells. We show that the extraction protocols have a significant impact on the chemical composition, anti- SARS-COV-2 activity, and cytotoxicity of these ulvan extracts. The ulvan extract based on the AOx protocol had a higher average molecular weight, higher charge, and 11.3-fold higher antiviral activity than HCl-based extract. Our results strongly suggest that further bioassay-guided investigation into bioactivity of compounds found in Ulva sp. ulvan extracts could lead to the discovery of novel anti-SARS-CoV-2 antivirals.
Shefer et al. (2021) Fighting SARS-CoV-2 with green seaweed Ulva sp. extract: extraction protocol predetermines crude ulvan extract anti-SARS-CoV-2 inhibition properties in in vitro Vero-E6 cells assay. PeerJ 9:e12398 https://doi.org/10.7717/peerj.12398
Can harbor seals (Phoca vitulina) discriminate familiar conspecific calls after long periods of separation?
The ability to discriminate between familiar and unfamiliar calls may play a key role in pinnipeds’ communication and survival, as in the case of mother-pup interactions. Vocal discrimination abilities have been suggested to be more developed in pinniped species with the highest selective pressure such as the otariids; yet, in some group-living phocids, such as harbor seals (Phoca vitulina), mothers are also able to recognize their pup’s voice. Conspecifics’ vocal recognition in pups has never been investigated; however, the repeated interaction occurring between pups within the breeding season suggests that long-term vocal discrimination may occur. Here we explored this hypothesis by presenting three rehabilitated seal pups with playbacks of vocalizations from unfamiliar or familiar pups. It is uncommon for seals to come into rehabilitation for a second time in their lifespan, and this study took advantage of these rare cases. A simple visual inspection of the data plots seemed to show more reactions, and of longer duration, in response to familiar as compared to unfamiliar playbacks in two out of three pups. However, statistical analyses revealed no significant difference between the experimental conditions. We also found no significant asymmetry in orientation (left vs. right) towards familiar and unfamiliar sounds. While statistics do not support the hypothesis of an established ability to discriminate familiar vocalizations from unfamiliar ones in harbor seal pups, further investigations with a larger sample size are needed to confirm or refute this hypothesis.
Varola et al. (2021) Can harbor seals (Phoca vitulina) discriminate familiar conspecific calls after long periods of separation?. PeerJ 9:e12431 https://doi.org/10.7717/peerj.12431
Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems
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.
Clarke et al. (2021) Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems. PeerJ 9:e12458 https://doi.org/10.7717/peerj.12458
Heteropelta boboi n. gen., n. sp. an armored archosauriform (Reptilia: Archosauromorpha) from the Middle Triassic of Italy
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.
Dalla Vecchia (2021) Heteropelta boboi n. gen., n. sp. an armored archosauriform (Reptilia: Archosauromorpha) from the Middle Triassic of Italy. PeerJ 9:e12468 https://doi.org/10.7717/peerj.12468
Integrated population modelling reveals potential drivers of demography from partially aligned data: a case study of snowy plover declines under human stressors
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.
Zhao et al. (2021) Integrated population modelling reveals potential drivers of demography from partially aligned data: a case study of snowy plover declines under human stressors. PeerJ 9:e12475 https://doi.org/10.7717/peerj.12475
Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution
Background Flax (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. Methods Here, we performed a systematic genome-wide analysis to identify RING finger genes in flax. Results We 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.
Meng et al. (2021) Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution. PeerJ 9:e12491 https://doi.org/10.7717/peerj.12491
Morphological and molecular analyses of parasitic barnacles (Crustacea: Cirripedia: Rhizocephala) in Korea: preliminary data for the taxonomy and host ranges of Korean species
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.
Jung et al. (2021) Morphological and molecular analyses of parasitic barnacles (Crustacea: Cirripedia: Rhizocephala) in Korea: preliminary data for the taxonomy and host ranges of Korean species. PeerJ 9:e12281 https://doi.org/10.7717/peerj.12281
Characteristics of solar radiation at Xiaotang, in the northern marginal zone of the Taklimakan Desert
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.
Spatial and Geographic Information Science
Jin et al. (2021) Characteristics of solar radiation at Xiaotang, in the northern marginal zone of the Taklimakan Desert. PeerJ 9:e12373 https://doi.org/10.7717/peerj.12373