Wedge-tailed Shearwater (Ardenna pacifica) nesting success in human-dominated coastal environments
Many seabird populations are declining globally, but successful conservation efforts have led to population expansion of some species into human-dominated landscapes. Thus, there is an increased potential for direct human and seabird interactions for certain species in human-occupied areas, with nest-site characteristics potentially affecting the susceptibility of nests to human disturbance. We assessed the effect of human activity and nest-site characteristics on Wedge-tailed Shearwater (Ardenna pacifica, ʻuaʻu kani) nesting success at two breeding colonies, one with human exposure and one without, located in Kailua, Oʻahu, Hawaiʻi. Human activity was measured by recording the frequency of people who entered a 5 m buffer around each nest. Nests were checked every two to three days to monitor nest success. The effect of human activity and nest-site characteristics on nesting success was determined using a variety of combinations of variables within binomial logistic regression models and AICc model selection. Nest-site characteristics among nests at both sites and human activity at the human-exposed site did not show a significant effect on nesting success. Our results suggest Wedge-tailed Shearwaters may experience some tolerance of human activity immediately around their nests—as long as burrow collapse does not occur. Given the small sample sizes and a single season of data collection, additional studies are needed to better understand the effect of human disturbance on Wedge-tailed Shearwaters. Infrastructure, such as fencing and signage, may be effective at reducing human-caused nest failure and may allow humans and disturbance-tolerant seabird species to coexist in shared coastal environments.
Idle et al. (2021) Wedge-tailed Shearwater (Ardenna pacifica) nesting success in human-dominated coastal environments. PeerJ 9:e12096 https://doi.org/10.7717/peerj.12096
When size matters: the first comprehensive anatomical study of a species of “Condylocardiidae”, an extremely miniaturized bivalve
‘Miniaturization’ is a widespread phenomenon among the Metazoa. In the molluscan class Bivalvia, records of miniaturization are numerous. Among the Archiheterodonta, Warrana besnardi (Klappenbach, 1963) has attracted attention for its tiny size, which does not exceed 1.5 mm in shell length, and because it belongs to a group with limited anatomical information and often-debated status, the “Condylocardiidae” (which recent molecular studies place deeply nested within the family Carditidae). All species of Warrana Laseron, 1953 are small-bodied, and so miniaturization presumably occurred from a large-bodied ancestor within the Carditidae sensu lato. South American W. besnardi is here studied in detail. Its small size and the enlargement of the anterodorsal region during growth, reflects (and likely led) to infaunal habit, living as a burrowing bivalve that passively feeds on deposit particles entering the pallial cavity anteriorly. Mantle glands, previously reported as a common feature of other archiheterodonts, are missing in W. besnardi, but spongiform tissue in the antero-ventral portion of the mantle lobes presumably represents a blood sinus that might compensate for the great reduction of the ctenidia. Lecithotrophy is reported, with yolky oocytes bearing a thick non-cellular capsule layer; brooding was not observed, and it is here hypothesized that the extreme miniaturization, with the great reduction of ctenidia, is responsible for a shift in the reproductive mode of condylocardiids, contrasting with the commonly reported ovoviviparity of the carditids.
Passos et al. (2021) When size matters: the first comprehensive anatomical study of a species of “Condylocardiidae”, an extremely miniaturized bivalve. PeerJ 9:e12108 https://doi.org/10.7717/peerj.12108
Anti-clustering in the national SARS-CoV-2 daily infection counts
The noise in daily infection counts of an epidemic should be super-Poissonian due to intrinsic epidemiological and administrative clustering. Here, we use this clustering to classify the official national SARS-CoV-2 daily infection counts and check for infection counts that are unusually anti-clustered. We adopt a one-parameter model of $\phi _i^{\prime}$ϕi′ infections per cluster, dividing any daily count ni into $n_i/ _i^{\prime}$ni/ϕi′ ‘clusters’, for ‘country’ i. We assume that ${n_i}/\phi _i^{\prime}$ni/ϕi′ on a given day j is drawn from a Poisson distribution whose mean is robustly estimated from the four neighbouring days, and calculate the inferred Poisson probability $P_{ij}^{\prime}$Pij′ of the observation. The $P_{ij}^{\prime}$Pij′ values should be uniformly distributed. We find the value $\phi_i$ϕi that minimises the Kolmogorov–Smirnov distance from a uniform distribution. We investigate the (ϕi, Ni) distribution, for total infection count Ni. We consider consecutive count sequences above a threshold of 50 daily infections. We find that most of the daily infection count sequences are inconsistent with a Poissonian model. Most are found to be consistent with the ϕi model. The 28-, 14- and 7-day least noisy sequences for several countries are best modelled as sub-Poissonian, suggesting a distinct epidemiological family. The 28-day least noisy sequence of Algeria has a preferred model that is strongly sub-Poissonian, with $\phi _i^{28} < 0.1$ϕi28<0.1 . Tajikistan, Turkey, Russia, Belarus, Albania, United Arab Emirates and Nicaragua have preferred models that are also sub-Poissonian, with $\phi _i^{28} < 0.5$ϕi28<0.5 . A statistically significant (Pτ < 0.05) correlation was found between the lack of media freedom in a country, as represented by a high Reporters sans frontieres Press Freedom Index (PFI2020), and the lack of statistical noise in the country’s daily counts. The ϕi model appears to be an effective detector of suspiciously low statistical noise in the national SARS-CoV-2 daily infection counts.
Roukema (2021) Anti-clustering in the national SARS-CoV-2 daily infection counts. PeerJ 9:e11856 https://doi.org/10.7717/peerj.11856
Genetic diversity and structure of one of the most endangered freshwater fish species in Mexico: Tlaloc hildebrandi (Miller, 1950) and recognition of its evolutionarily significant units
The endangered Chiapas killifish Tlaloc hildebrandi is an endemic freshwater species that lives in four subbasins of the Grijalva and Usumacinta basins, and one of the most geographically restricted species of the Produndulidae family. The species was originally described as endemic to springs in the high limestone plateau in San Cristóbal de Las Casas in the Río Amarillo subbasin (upper Grijalva basin). However, it was recently recorded in the Jataté and Tzaconejá subbasins in the upper Usumacinta basin, thereby expanding its known distribution range. The discovery of these populations is relevant not only for the conservation of the species but also for a better understanding of its evolutionary history. Currently, the scarce populations of T. hildebrandi, found in only a few localities in the Grijalva and Usumacinta basins, are fragmented and living under unfavorable conditions. Here, we analyzed three mitochondrial (mt-atp8&6 and mt-nd2) and one nuclear (nuc-s7) marker in order to assess the genetic diversity and population structure of T. hildebrandi. We found that, in comparison with other endangered freshwater fish species from Mexico, T. hildebrandi showed a lower level of genetic diversity (mt-nd2: h = 0.469, π = 0.0009; mt-atp8&6: h = 0.398, π = 0.001; and nuc-S7: h = 0.433, π = 0.001). Moreover, the analyzed populations exhibited a strong genetic structure in accordance with their geographic distribution, and can be placed into three genetic clusters: (1) Amarillo plus Chenhaló in the upper Grijalva basin, (2) Jataté, and (3) Tzaconejá, both in the upper Usumacinta basin. On the basis of our results, we propose the recognition of at least three evolutionarily significant units (ESUs) for the species and the urgent implementation of ex situ and in situ conservation and management efforts that consider the genetic background of the species.
Beltrán-López et al. (2021) Genetic diversity and structure of one of the most endangered freshwater fish species in Mexico: Tlaloc hildebrandi (Miller, 1950) and recognition of its evolutionarily significant units. PeerJ 9:e11952 https://doi.org/10.7717/peerj.11952
Low winter precipitation, but not warm autumns and springs, threatens mountain butterflies in middle-high mountains
Low-elevation mountains represent unique model systems to study species endangered by climate warming, such as subalpine and alpine species of butterflies. We aimed to test the effect of climate variables experienced by Erebia butterflies during their development on adult abundances and phenology, targeting the key climate factors determining the population dynamics of mountain insects. We analysed data from a long-term monitoring of adults of two subalpine and alpine butterfly species, Erebia epiphron and E. sudetica (Nymphalidae: Satyrinae) in the Jeseník Mts and Krkonoše Mts (Czech Republic). Our data revealed consistent patterns in their responses to climatic conditions. Lower precipitation (i.e., less snow cover) experienced by overwintering larvae decreases subsequent adult abundances. Conversely, warmer autumns and warmer and drier springs during the active larval phase increase adult abundances and lead to earlier onset and extended duration of the flight season. The population trends of these mountain butterflies are stable or even increasing. On the background of generally increasing temperatures within the mountain ranges, population stability indicates dynamic equilibrium of positive and detrimental consequences of climate warming among different life history stages. These contradictory effects warn against simplistic predictions of climate change consequences on mountain species based only on predicted increases in average temperature. Microclimate variability may facilitate the survival of mountain insect populations, however the availability of suitable habitats will strongly depend on the management of mountain grasslands.
Konvicka et al. (2021) Low winter precipitation, but not warm autumns and springs, threatens mountain butterflies in middle-high mountains. PeerJ 9:e12021 https://doi.org/10.7717/peerj.12021
The stability of soil organic carbon across topographies in a tropical rainforest
Mechanisms of soil organic carbon (SOC) stability are still unclear in forest ecosystems. In order to unveil the influences of topography on the SOC stability, a 60ha dynamic plot of a tropical montane rainforest was selected in Jianfengling, in Hainan Island, China and soil was sampled from 60 quadrats. The chemical fractions of the SOC were detected with 13C CPMAS/NMR and path analyses explore the mechanisms of SOC stability in different topographies. The chemical fractions of the SOC comprised alkyl carbon > O-alkyl carbon > carboxyl carbon > aromatic carbon. The decomposition index (DI) values were greater than 1 in the different topographies, with an average DI value was 1.29, which indicated that the SOC in the study area was stable. Flat and top areas (together named RF) had more favorable nutrients and silt contents compared with steep and slight steep areas (together named RS). The influencing factors of SOC stability varied across the topographies, where SOC, soil moisture (SM) and ammoniacal nitrogen (NH4+-N, AN) were the main influencing factors in the RF, while SM and AN were the main factors in the RS. Greater SOC and AN strengthened the SOC stability, while higher soil moisture lowered SOC stability. The inertia index was higher in the RS than the RF areas, indicating that local topography significantly affects SOC content and SOC stability by changing soil environmental factors. Topography cannot be neglected in considering SOC stability and future C budgets.
Jiang et al. (2021) The stability of soil organic carbon across topographies in a tropical rainforest. PeerJ 9:e12057 https://doi.org/10.7717/peerj.12057
Stereotyped whistles in southern resident killer whales
The endangered Southern Resident killer whales (Orcinus orca) of the northeast Pacific region use two main types of vocal signals to communicate: discrete calls and whistles. Despite being one of the most-studied cetacean populations in the world, whistles have not been as heavily analyzed due to their relatively low occurrence compared to discrete calls. The aim of the current study is to further investigate the whistle repertoire and characteristics of the Southern Resident killer whale population. Acoustic data were collected between 2006–2007 and 2015–2017 in the waters around San Juan Island, Washington State, USA from boats and from shore. A total of 228 whistles were extracted and analyzed with 53.5% of them found to be stereotyped. Three of the four stereotyped whistles identified by a previous study using recordings from 1979–1982 were still occurring, demonstrating that whistles are stable vocalizations for a period of more than 35 years. The presence of three new stereotyped whistles was also documented. These results demonstrate that whistles share the longevity and vocal tradition of discrete calls, and warrant further study as a key element of Southern Resident killer whale communication and cultural transmission.
Souhaut et al. (2021) Stereotyped whistles in southern resident killer whales. PeerJ 9:e12085 https://doi.org/10.7717/peerj.12085
SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization
Single-cell RNA-sequencing is a rapidly evolving technology that enables us to understand biological processes at unprecedented resolution. Single-cell expression analysis requires a complex data processing pipeline, and the pipeline is divided into two main parts: The quantification part, which converts the sequence information into gene-cell matrix data; the analysis part, which analyzes the matrix data using statistics and/or machine learning techniques. In the analysis part, unsupervised cell clustering plays an important role in identifying cell types and discovering cell diversity and subpopulations. Identified cell clusters are also used for subsequent analysis, such as finding differentially expressed genes and inferring cell trajectories. However, single-cell clustering using gene expression profiles shows different results depending on the quantification methods. Clustering results are greatly affected by the quantification method used in the upstream process. In other words, even if the original RNA-sequence data is the same, gene expression profiles processed by different quantification methods will produce different clusters. In this article, we propose a robust and highly accurate clustering method based on joint non-negative matrix factorization (joint-NMF) by utilizing the information from multiple gene expression profiles quantified using different methods from the same RNA-sequence data. Our joint-NMF can extract common factors among multiple gene expression profiles by applying each NMF under the constraint that one of the factorized matrices is shared among multiple NMFs. The joint-NMF determines more robust and accurate cell clustering results by leveraging multiple quantification methods compared to conventional clustering methods, which use only a single gene expression profile. Additionally, we showed the usefulness of discovering marker genes with the extracted features using our method.
Shiga et al. (2021) SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization. PeerJ 9:e12087 https://doi.org/10.7717/peerj.12087
Differential regulation of antioxidant enzymes in Frankliniella occidentalis (Thysanoptera: Thripidae) exposed to thermal stress
Frankliniella occidentalis is an invasive insect pest that incites damage to ornamental and agronomic crops on a global scale. In this study, the effects of temperature on gene expression and enzyme activity were studied for superoxide dismutase (SOD), peroxidase (POD), and glutathione-S-transferase (GST) in F. occidentalis. SOD, POD and GST enzyme activity increased significantly at 35–37 °C but declined as the temperature increased to 41 °C. In a time course study at 35 °C, SOD, POD and GST activities were significantly elevated at 0.5, 1 and 2 h in comparison to the control at 26 °C. Expression patterns were evaluated for the three antioxidant genes under high and low temperature stress. In a time course study at –4 °C, SOD, POD and GST expression peaked at 1 h and declined at 2 h of exposure. In contrast, when transcription was monitored at 35 °C, expression was lowest at 1 h and increased at 2 h. The results provide data that will be useful in deciphering the role of antioxidant enzymes in the adaptation of F. occidentalis to climate change.
Yuan et al. (2021) Differential regulation of antioxidant enzymes in Frankliniella occidentalis (Thysanoptera: Thripidae) exposed to thermal stress. PeerJ 9:e12089 https://doi.org/10.7717/peerj.12089
Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation
Stromal cell-derived factor-1 (SDF-1) and Exendin-4 (EX-4) play beneficial roles in promoting periodontal ligament stem cells (PDLSCs) osteogenic differentiation, while the detailed mechanism has not been clarified. In this study, we aimed to evaluate the biological mechanism of SDF-1 and EX-4 alone or synergistic application in regulating PDLSCs differentiation by RNA-sequencing (RNA-seq). A total of 110, 116 and 109 differentially expressed genes (DEGs) were generated in osteogenic medium induced PDLSCs treated by SDF-1, EX-4, and SDF-1+EX-4, respectively. The DEGs in SDF-1 group were enriched in signal transduction related signaling pathways; the DEGs in EX-4 group were enriched in metabolism and biosynthesis-related pathways; and the DEGs generated in SDF-1+EX-4 group were mainly enriched in RNA polymerase II transcription, cell differentiation, chromatin organization, protein phosphorylation pathways. Based on Venn analysis, a total of 37 specific DEGs were identified in SDF-1+EX-4 group, which were mainly enriched in negative regulation of autophagy and cellular component disassembly signaling pathways. Short time-series expression miner (STEM) analysis grouped all expressed genes of PDLSCs into 49 clusters according to the dynamic expression patterns and 25 genes, including NRSN2, CHD9, TUBA1A, distributed in 10 gene clusters in SDF-1+EX-4 treated PDLSCs were significantly up-regulated compared with the SDF-1 and EX-4 alone groups. The gene set enrichment analysis indicated that SDF-1 could amplify the role of EX-4 in regulating varied signaling pathways, such as type II diabetes mellitus and insulin signaling pathways; while EX-4 could aggravate the effect of SDF-1 on PDLSCs biological roles via regulating primary immunodeficiency, tight junction signaling pathways. In summary, our study confirmed that SDF-1 and EX-4 combined application could enhance PDLSCs biological activity and promote PDLSCs osteogenic differentiation by regulating the metabolism, biosynthesis and immune-related signaling pathways.
Kang et al. (2021) Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation. PeerJ 9:e12091 https://doi.org/10.7717/peerj.12091