PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Wedge-tailed Shearwater (Ardenna pacifica) nesting success in human-dominated coastal environments
items: When size matters: the first comprehensive anatomical study of a species of “Condylocardiidae”, an extremely miniaturized bivalve
items: Anti-clustering in the national SARS-CoV-2 daily infection counts
items: 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
items: Low winter precipitation, but not warm autumns and springs, threatens mountain butterflies in middle-high mountains
items: The stability of soil organic carbon across topographies in a tropical rainforest
items: Stereotyped whistles in southern resident killer whales
items: SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization
items: Differential regulation of antioxidant enzymes in Frankliniella occidentalis (Thysanoptera: Thripidae) exposed to thermal stress
items: Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation

Wedge-tailed Shearwater (Ardenna pacifica) nesting success in human-dominated coastal environments
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Jessica L. Idle
creator: Chad J. Wilhite
creator: Kristen C. Harmon
creator: Brooke Friswold
creator: Melissa R. Price
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.12096
publisher: PeerJ Inc.
rights: © 2021 Idle et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2020-09-14
date accepted: 2021-08-10
issued: 2021-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Idle
  given name: Jessica L.
author list: Agent
  family name: Wilhite
  given name: Chad J.
author list: Agent
  family name: Harmon
  given name: Kristen C.
author list: Agent
  family name: Friswold
  given name: Brooke
author list: Agent
  family name: Price
  given name: Melissa R.
doi: 10.7717/peerj.12096
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-30
copyright: ©2021 Idle et al.
attribution name: Idle et al.

When size matters: the first comprehensive anatomical study of a species of “Condylocardiidae”, an extremely miniaturized bivalve
type: item
type: AcademicArticle
description: ‘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.
format: application/pdf
format: text/html
creator: Flávio Dias Passos
creator: Alan Rodrigo Batistão
creator: Rüdiger Bieler
subject: Biodiversity
subject: Marine Biology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.12108
publisher: PeerJ Inc.
rights: © 2021 Passos et al.
abstract: ‘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.
bibliographic citation: 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
date submitted: 2021-03-29
date accepted: 2021-08-12
issued: 2021-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Passos
  given name: Flávio Dias
author list: Agent
  family name: Batistão
  given name: Alan Rodrigo
author list: Agent
  family name: Bieler
  given name: Rüdiger
doi: 10.7717/peerj.12108
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-30
copyright: © 2021 Passos et al.
attribution name: Passos et al.

Anti-clustering in the national SARS-CoV-2 daily infection counts
type: item
type: AcademicArticle
description: 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 i…
format: application/pdf
format: text/html
creator: Boudewijn F. Roukema
subject: Epidemiology
subject: Infectious Diseases
subject: Statistics
subject: Data Science
description: doi:10.7717/peerj.11856
publisher: PeerJ Inc.
rights: © 2021 Roukema
abstract: 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 i…
bibliographic citation: Roukema (2021) Anti-clustering in the national SARS-CoV-2 daily infection counts. PeerJ 9:e11856 https://doi.org/10.7717/peerj.11856
date submitted: 2021-01-26
date accepted: 2021-07-04
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roukema
  given name: Boudewijn F.
doi: 10.7717/peerj.11856
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: © 2021 Roukema
attribution name: Roukema

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
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Rosa G. Beltrán-López
creator: Alfonso A. González-Díaz
creator: Miriam Soria-Barreto
creator: Marco Antonio Garduño-Sánchez
creator: Carmela Xochitla-Castrejón
creator: Rocío Rodiles-Hernández
creator: Claudia Patricia Ornelas-García
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.11952
publisher: PeerJ Inc.
rights: © 2021 Beltrán-López et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2021-01-08
date accepted: 2021-07-20
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beltrán-López
  given name: Rosa G.
author list: Agent
  family name: González-Díaz
  given name: Alfonso A.
author list: Agent
  family name: Soria-Barreto
  given name: Miriam
author list: Agent
  family name: Garduño-Sánchez
  given name: Marco Antonio
author list: Agent
  family name: Xochitla-Castrejón
  given name: Carmela
author list: Agent
  family name: Rodiles-Hernández
  given name: Rocío
author list: Agent
  family name: Ornelas-García
  given name: Claudia Patricia
doi: 10.7717/peerj.11952
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: © 2021 Beltrán-López et al.
attribution name: Beltrán-López et al.

Low winter precipitation, but not warm autumns and springs, threatens mountain butterflies in middle-high mountains
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Martin Konvicka
creator: Tomas Kuras
creator: Jana Liparova
creator: Vit Slezak
creator: Dita Horázná
creator: Jan Klečka
creator: Irena Kleckova
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.12021
publisher: PeerJ Inc.
rights: © 2021 Konvicka et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2021-05-25
date accepted: 2021-07-29
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Konvicka
  given name: Martin
author list: Agent
  family name: Kuras
  given name: Tomas
author list: Agent
  family name: Liparova
  given name: Jana
author list: Agent
  family name: Slezak
  given name: Vit
author list: Agent
  family name: Horázná
  given name: Dita
author list: Agent
  family name: Klečka
  given name: Jan
author list: Agent
  family name: Kleckova
  given name: Irena
doi: 10.7717/peerj.12021
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: © 2021 Konvicka et al.
attribution name: Konvicka et al.

The stability of soil organic carbon across topographies in a tropical rainforest
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Yamin Jiang
creator: Huai Yang
creator: Qiu Yang
creator: Wenjie Liu
creator: Zhaolei Li
creator: Wei Mao
creator: Xu Wang
creator: Zhenghong Tan
subject: Ecology
subject: Soil Science
subject: Climate Change Biology
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.12057
publisher: PeerJ Inc.
rights: © 2021 Jiang et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2021-04-21
date accepted: 2021-08-04
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Yamin
author list: Agent
  family name: Yang
  given name: Huai
author list: Agent
  family name: Yang
  given name: Qiu
author list: Agent
  family name: Liu
  given name: Wenjie
author list: Agent
  family name: Li
  given name: Zhaolei
author list: Agent
  family name: Mao
  given name: Wei
author list: Agent
  family name: Wang
  given name: Xu
author list: Agent
  family name: Tan
  given name: Zhenghong
doi: 10.7717/peerj.12057
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: ©2021 Jiang et al.
attribution name: Jiang et al.

Stereotyped whistles in southern resident killer whales
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Marie Souhaut
creator: Monika W. Shields
subject: Animal Behavior
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12085
publisher: PeerJ Inc.
rights: © 2021 Souhaut and Shields
abstract: 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.
bibliographic citation: Souhaut et al. (2021) Stereotyped whistles in southern resident killer whales. PeerJ 9:e12085 https://doi.org/10.7717/peerj.12085
date submitted: 2021-06-23
date accepted: 2021-08-07
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Souhaut
  given name: Marie
author list: Agent
  family name: Shields
  given name: Monika W.
doi: 10.7717/peerj.12085
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: ©2021 Souhaut and Shields
attribution name: Souhaut and Shields

SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Mikio Shiga
creator: Shigeto Seno
creator: Makoto Onizuka
creator: Hideo Matsuda
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Computational Science
description: doi:10.7717/peerj.12087
publisher: PeerJ Inc.
rights: © 2021 Shiga et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2021-03-10
date accepted: 2021-08-07
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shiga
  given name: Mikio
author list: Agent
  family name: Seno
  given name: Shigeto
author list: Agent
  family name: Onizuka
  given name: Makoto
author list: Agent
  family name: Matsuda
  given name: Hideo
doi: 10.7717/peerj.12087
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: ©2021 Shiga et al.
attribution name: Shiga et al.

Differential regulation of antioxidant enzymes in Frankliniella occidentalis (Thysanoptera: Thripidae) exposed to thermal stress
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Jia-Wen Yuan
creator: Yutao Zheng
creator: Ya-Wen Chang
creator: Jing Bai
creator: Jing Qin
creator: Yu-Zhou Du
subject: Agricultural Science
subject: Entomology
subject: Molecular Biology
description: doi:10.7717/peerj.12089
publisher: PeerJ Inc.
rights: © 2021 Yuan et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2021-03-03
date accepted: 2021-08-08
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Jia-Wen
author list: Agent
  family name: Zheng
  given name: Yutao
author list: Agent
  family name: Chang
  given name: Ya-Wen
author list: Agent
  family name: Bai
  given name: Jing
author list: Agent
  family name: Qin
  given name: Jing
author list: Agent
  family name: Du
  given name: Yu-Zhou
doi: 10.7717/peerj.12089
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: © 2021 Yuan et al.
attribution name: Yuan et al.

Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation
type: item
type: AcademicArticle
description: 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, biosy…
format: application/pdf
format: text/html
creator: Wenyan Kang
creator: Lingqian Du
creator: Qianyu Liang
creator: Rui Zhang
creator: Chunxu Lv
creator: Shaohua Ge
subject: Biochemistry
subject: Cell Biology
subject: Developmental Biology
subject: Molecular Biology
subject: Dentistry
description: doi:10.7717/peerj.12091
publisher: PeerJ Inc.
rights: © 2021 Kang et al.
abstract: 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, biosy…
bibliographic citation: 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
date submitted: 2021-04-29
date accepted: 2021-08-09
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kang
  given name: Wenyan
author list: Agent
  family name: Du
  given name: Lingqian
author list: Agent
  family name: Liang
  given name: Qianyu
author list: Agent
  family name: Zhang
  given name: Rui
author list: Agent
  family name: Lv
  given name: Chunxu
author list: Agent
  family name: Ge
  given name: Shaohua
doi: 10.7717/peerj.12091
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: ©2021 Kang et al.
attribution name: Kang et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359