PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Social rank overrides environmental and community fluctuations in determining meat access by female chimpanzees in the Taï National Park, Côte d’Ivoire
items: High variability within pet foods prevents the identification of native species in pet cats’ diets using isotopic evaluation
items: Prehaustorial local resistance to coffee leaf rust in a Mexican cultivar involves expression of salicylic acid-responsive genes
items: The effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the transcriptome of aryl hydrocarbon receptor (AhR) knock-down porcine granulosa cells
items: Shifts in soil nutrient concentrations and C:N:P stoichiometry during long-term natural vegetation restoration
items: First record of Gyrosteus mirabilis (Actinopterygii, Chondrosteidae) from the Toarcian (Lower Jurassic) of the Baltic region
items: Florida manatees Trichechus manatus latirostris actively consume the sponge Chondrilla caribensis
items: CD86+/CD206+ tumor-associated macrophages predict prognosis of patients with intrahepatic cholangiocarcinoma
items: Predicting hedgehog mortality risks on British roads using habitat suitability modelling
items: Pseudolebinthus lunipterus sp. nov.: a striking deaf and mute new cricket from Malawi (Orthoptera, Gryllidae, Eneopterinae)

Social rank overrides environmental and community fluctuations in determining meat access by female chimpanzees in the Taï National Park, Côte d’Ivoire
type: item
type: AcademicArticle
description: Meat, long hypothesized as an important food source in human evolution, is still a substantial component of the modern human diet, with some humans relying entirely on meat during certain times of the year. Understanding the socio-ecological context leading to the successful acquisition and consumption of meat by chimpanzees (Pan troglodytes), our closest living relative, can provide insight into the emergence of this trait because humans and chimpanzees are unusual among primates in that they both (i) hunt mammalian prey, (ii) share meat with community members, and (iii) form long-term relationships and complex social hierarchies within their communities. However, females in both human hunter-gatherer societies as well as chimpanzee groups rarely hunt, instead typically accessing meat via males that share meat with group members. In general, female chimpanzee dominance rank affects feeding competition, but so far, the effect of female dominance rank on meat access found different results within and across studied chimpanzee groups. Here we contribute to the debate on how female rank influences meat access while controlling for several socio-ecological variables. Multivariate analyses of 773 separate meat-eating events collected over more than 25 years from two chimpanzee communities located in the Taï National Park, Côte d’Ivoire, were used to test the importance of female dominance rank for being present at, and for acquiring meat, during meat-eating events. We found that high-ranking females were more likely to be present during a meat-eating event and, in addition, were more likely to eat meat compared to the subordinates. These findings were robust to both large demographic changes (decrease of community size) and seasonal ecological changes (fruit abundance dynamics). In addition to social rank, we found that other female properties had a positive influence on presence to meat-eating events and access to meat given presence, including oestrus status, nursing o…
format: application/pdf
format: text/html
creator: Julia Riedel
creator: Leo Polansky
creator: Roman M. Wittig
creator: Christophe Boesch
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.8283
publisher: PeerJ Inc.
rights: © 2020 Riedel et al.
abstract: Meat, long hypothesized as an important food source in human evolution, is still a substantial component of the modern human diet, with some humans relying entirely on meat during certain times of the year. Understanding the socio-ecological context leading to the successful acquisition and consumption of meat by chimpanzees (Pan troglodytes), our closest living relative, can provide insight into the emergence of this trait because humans and chimpanzees are unusual among primates in that they both (i) hunt mammalian prey, (ii) share meat with community members, and (iii) form long-term relationships and complex social hierarchies within their communities. However, females in both human hunter-gatherer societies as well as chimpanzee groups rarely hunt, instead typically accessing meat via males that share meat with group members. In general, female chimpanzee dominance rank affects feeding competition, but so far, the effect of female dominance rank on meat access found different results within and across studied chimpanzee groups. Here we contribute to the debate on how female rank influences meat access while controlling for several socio-ecological variables. Multivariate analyses of 773 separate meat-eating events collected over more than 25 years from two chimpanzee communities located in the Taï National Park, Côte d’Ivoire, were used to test the importance of female dominance rank for being present at, and for acquiring meat, during meat-eating events. We found that high-ranking females were more likely to be present during a meat-eating event and, in addition, were more likely to eat meat compared to the subordinates. These findings were robust to both large demographic changes (decrease of community size) and seasonal ecological changes (fruit abundance dynamics). In addition to social rank, we found that other female properties had a positive influence on presence to meat-eating events and access to meat given presence, including oestrus status, nursing o…
bibliographic citation: Riedel et al. (2020) Social rank overrides environmental and community fluctuations in determining meat access by female chimpanzees in the Taï National Park, Côte d’Ivoire. PeerJ 8:e8283 https://doi.org/10.7717/peerj.8283
date submitted: 2019-04-08
date accepted: 2019-11-22
issued: 2020-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Riedel
  given name: Julia
author list: Agent
  family name: Polansky
  given name: Leo
author list: Agent
  family name: Wittig
  given name: Roman M.
author list: Agent
  family name: Boesch
  given name: Christophe
doi: 10.7717/peerj.8283
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-22
copyright: ©2020 Riedel et al.
attribution name: Riedel et al.

High variability within pet foods prevents the identification of native species in pet cats’ diets using isotopic evaluation
type: item
type: AcademicArticle
description: Domestic cats preying on wildlife is a frequent conservation concern but typical approaches for assessing impacts rely on owner reports of prey returned home, which can be biased by inaccurate reporting or by cats consuming prey instead of bringing it home. Isotopes offer an alternative way to quantify broad differences in animal diets. By obtaining samples of pet food from cat owners we predicted that we would have high power to identify cats feeding on wild birds or mammals, given that pet food is thought to have higher C isotope values, due to the pervasive use of corn and/or corn by-products as food ingredients, than native prey. We worked with citizen scientists to quantify the isotopes of 202 cat hair samples and 239 pet food samples from the US and UK. We also characterized the isotopes of 11 likely native prey species from the southeastern US and used mixing models to assess the diet of 47 cats from the same region. Variation in C and N isotope values for cat food was very high, even within the same brand/flavor, suggesting that pet food manufacturers use a wide range of ingredients, and that these may change over time. Cat food and cat hair from the UK had lower C values than the US, presumably reflecting differences in the amount of corn used in the food chains of the two countries. This high variation in pet food reduced our ability to classify cats as hunters of native prey, such that only 43% of the animals could be confidently assigned. If feral or free ranging cats were considered, this uncertainty would be even higher as pet food types would be unknown. Our results question the general assumption that anthropogenic foods always have high C isotope values, because of the high variability we documented within one product type (cat food) and between countries (US vs. UK), and emphasize the need to test a variety of standards before making conclusions from isotope ecology studies.
format: application/pdf
format: text/html
creator: Brandon W. McDonald
creator: Troi Perkins
creator: Robert R. Dunn
creator: Jennifer McDonald
creator: Holly Cole
creator: Robert S. Feranec
creator: Roland Kays
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.8337
publisher: PeerJ Inc.
rights: © 2020 McDonald et al.
abstract: Domestic cats preying on wildlife is a frequent conservation concern but typical approaches for assessing impacts rely on owner reports of prey returned home, which can be biased by inaccurate reporting or by cats consuming prey instead of bringing it home. Isotopes offer an alternative way to quantify broad differences in animal diets. By obtaining samples of pet food from cat owners we predicted that we would have high power to identify cats feeding on wild birds or mammals, given that pet food is thought to have higher C isotope values, due to the pervasive use of corn and/or corn by-products as food ingredients, than native prey. We worked with citizen scientists to quantify the isotopes of 202 cat hair samples and 239 pet food samples from the US and UK. We also characterized the isotopes of 11 likely native prey species from the southeastern US and used mixing models to assess the diet of 47 cats from the same region. Variation in C and N isotope values for cat food was very high, even within the same brand/flavor, suggesting that pet food manufacturers use a wide range of ingredients, and that these may change over time. Cat food and cat hair from the UK had lower C values than the US, presumably reflecting differences in the amount of corn used in the food chains of the two countries. This high variation in pet food reduced our ability to classify cats as hunters of native prey, such that only 43% of the animals could be confidently assigned. If feral or free ranging cats were considered, this uncertainty would be even higher as pet food types would be unknown. Our results question the general assumption that anthropogenic foods always have high C isotope values, because of the high variability we documented within one product type (cat food) and between countries (US vs. UK), and emphasize the need to test a variety of standards before making conclusions from isotope ecology studies.
bibliographic citation: McDonald et al. (2020) High variability within pet foods prevents the identification of native species in pet cats’ diets using isotopic evaluation. PeerJ 8:e8337 https://doi.org/10.7717/peerj.8337
date submitted: 2019-06-28
date accepted: 2019-12-03
issued: 2020-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McDonald
  given name: Brandon W.
author list: Agent
  family name: Perkins
  given name: Troi
author list: Agent
  family name: Dunn
  given name: Robert R.
author list: Agent
  family name: McDonald
  given name: Jennifer
author list: Agent
  family name: Cole
  given name: Holly
author list: Agent
  family name: Feranec
  given name: Robert S.
author list: Agent
  family name: Kays
  given name: Roland
doi: 10.7717/peerj.8337
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-22
copyright: ©2020 McDonald et al.
attribution name: McDonald et al.

Prehaustorial local resistance to coffee leaf rust in a Mexican cultivar involves expression of salicylic acid-responsive genes
type: item
type: AcademicArticle
description: Background In Mexico, coffee leaf rust (CLR) is the main disease that affects the Arabica coffee crop. In this study, the local response of two Mexican cultivars of Coffea arabica (Oro Azteca and Garnica) in the early stages of Hemileia vastatrix infection was evaluated. Methods We quantified the development of fungal structures in locally-infected leaf disks from both cultivars, using qRT-PCR to measure the relative expression of two pathogenesis recognition genes (CaNDR1 and CaNBS-LRR) and three genes associated with the salicylic acid (SA)-related pathway (CaNPR1, CaPR1, and CaPR5). Results Resistance of the cv. Oro Azteca was significantly higher than that of the cv. Garnica, with 8.2% and 53.3% haustorial detection, respectively. In addition, the non-race specific disease resistance gene (CaNDR1), a key gene for the pathogen recognition, as well as the genes associated with SA, CaNPR1, CaPR1, and CaPR5, presented an increased expression in response to infection by H. vastatrix in cv. Oro Azteca if comparing with cv. Garnica. Our results suggest that Oro Azteca’s defense mechanisms could involve early recognition of CLR by NDR1 and the subsequent activation of the SA signaling pathway.
format: application/pdf
format: text/html
creator: Edgar Couttolenc-Brenis
creator: Gloria L. Carrión
creator: Luc Villain
creator: Fernando Ortega-Escalona
creator: Daniel Ramírez-Martínez
creator: Martín Mata-Rosas
creator: Alfonso Méndez-Bravo
subject: Agricultural Science
subject: Molecular Biology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.8345
publisher: PeerJ Inc.
rights: © 2020 Couttolenc-Brenis et al.
abstract: Background In Mexico, coffee leaf rust (CLR) is the main disease that affects the Arabica coffee crop. In this study, the local response of two Mexican cultivars of Coffea arabica (Oro Azteca and Garnica) in the early stages of Hemileia vastatrix infection was evaluated. Methods We quantified the development of fungal structures in locally-infected leaf disks from both cultivars, using qRT-PCR to measure the relative expression of two pathogenesis recognition genes (CaNDR1 and CaNBS-LRR) and three genes associated with the salicylic acid (SA)-related pathway (CaNPR1, CaPR1, and CaPR5). Results Resistance of the cv. Oro Azteca was significantly higher than that of the cv. Garnica, with 8.2% and 53.3% haustorial detection, respectively. In addition, the non-race specific disease resistance gene (CaNDR1), a key gene for the pathogen recognition, as well as the genes associated with SA, CaNPR1, CaPR1, and CaPR5, presented an increased expression in response to infection by H. vastatrix in cv. Oro Azteca if comparing with cv. Garnica. Our results suggest that Oro Azteca’s defense mechanisms could involve early recognition of CLR by NDR1 and the subsequent activation of the SA signaling pathway.
bibliographic citation: Couttolenc-Brenis et al. (2020) Prehaustorial local resistance to coffee leaf rust in a Mexican cultivar involves expression of salicylic acid-responsive genes. PeerJ 8:e8345 https://doi.org/10.7717/peerj.8345
date submitted: 2019-02-05
date accepted: 2019-12-04
issued: 2020-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Couttolenc-Brenis
  given name: Edgar
author list: Agent
  family name: Carrión
  given name: Gloria L.
author list: Agent
  family name: Villain
  given name: Luc
author list: Agent
  family name: Ortega-Escalona
  given name: Fernando
author list: Agent
  family name: Ramírez-Martínez
  given name: Daniel
author list: Agent
  family name: Mata-Rosas
  given name: Martín
author list: Agent
  family name: Méndez-Bravo
  given name: Alfonso
doi: 10.7717/peerj.8345
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-22
copyright: ©2020 Couttolenc-Brenis et al.
attribution name: Couttolenc-Brenis et al.

The effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the transcriptome of aryl hydrocarbon receptor (AhR) knock-down porcine granulosa cells
type: item
type: AcademicArticle
description: Background 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a toxic man-made chemical, adversely affecting reproductive processes. The well-characterized canonical mechanism of TCDD action involves the activation of aryl hydrocarbon receptor (AhR) pathway, but AhR-independent mechanisms were also suggested. By applying RNA interference technology and Next Generation Sequencing (NGS) we aimed to identify genes involved in the mechanism of TCDD action in AhR knock-down porcine granulosa cells. Methods Porcine granulosa cells were transfected with small interfering RNAs targeting mRNA of AhR. After transfection, medium was exchanged and the AhR knock-down cells were treated with TCDD (100 nM) for 3, 12 or 24 h, total cellular RNA was isolated and designated for NGS. Following sequencing, differentially expressed genes (DEGs) were identified. To analyze functions and establish possible interactions of DEGs, the Gene Ontology (GO) database and the Search Tool for the Retrieval of Interacting Genes (STRING) database were used, respectively. Results The AhR gene expression level and protein abundance were significantly decreased after AhR-targeted siRNAs transfection of the cells. In TCDD-treated AhR knock-down cells we identified 360 differentially expressed genes (DEGs; P-adjusted < 0.05 and log2 fold change [log2FC] ≥ 1.0). The functional enrichment analysis of DEGs revealed that TCDD influenced the expression of genes involved, among other, in the metabolism of vitamin A, follicular development and oocyte maturation, proliferation and differentiation as well as inflammation, stress response, apoptosis and oncogenesis. The three-time point study demonstrated that TCDD-induced changes in the transcriptome of AhR knock-down porcine granulosa cells were especially pronounced during the early stages of the treatment (3 h). Conclusions TCDD affected the transcriptome of AhR knock-down porcine granulosa cells. The molecules involved in the AhR-independent action of TCDD were ind…
format: application/pdf
format: text/html
creator: Monika Ruszkowska
creator: Agnieszka Sadowska
creator: Anna Nynca
creator: Karina Orlowska
creator: Sylwia Swigonska
creator: Tomasz Molcan
creator: Lukasz Paukszto
creator: Jan P. Jastrzebski
creator: Renata E. Ciereszko
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.8371
publisher: PeerJ Inc.
rights: © 2020 Ruszkowska et al.
abstract: Background 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a toxic man-made chemical, adversely affecting reproductive processes. The well-characterized canonical mechanism of TCDD action involves the activation of aryl hydrocarbon receptor (AhR) pathway, but AhR-independent mechanisms were also suggested. By applying RNA interference technology and Next Generation Sequencing (NGS) we aimed to identify genes involved in the mechanism of TCDD action in AhR knock-down porcine granulosa cells. Methods Porcine granulosa cells were transfected with small interfering RNAs targeting mRNA of AhR. After transfection, medium was exchanged and the AhR knock-down cells were treated with TCDD (100 nM) for 3, 12 or 24 h, total cellular RNA was isolated and designated for NGS. Following sequencing, differentially expressed genes (DEGs) were identified. To analyze functions and establish possible interactions of DEGs, the Gene Ontology (GO) database and the Search Tool for the Retrieval of Interacting Genes (STRING) database were used, respectively. Results The AhR gene expression level and protein abundance were significantly decreased after AhR-targeted siRNAs transfection of the cells. In TCDD-treated AhR knock-down cells we identified 360 differentially expressed genes (DEGs; P-adjusted < 0.05 and log2 fold change [log2FC] ≥ 1.0). The functional enrichment analysis of DEGs revealed that TCDD influenced the expression of genes involved, among other, in the metabolism of vitamin A, follicular development and oocyte maturation, proliferation and differentiation as well as inflammation, stress response, apoptosis and oncogenesis. The three-time point study demonstrated that TCDD-induced changes in the transcriptome of AhR knock-down porcine granulosa cells were especially pronounced during the early stages of the treatment (3 h). Conclusions TCDD affected the transcriptome of AhR knock-down porcine granulosa cells. The molecules involved in the AhR-independent action of TCDD were ind…
bibliographic citation: Ruszkowska et al. (2020) The effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the transcriptome of aryl hydrocarbon receptor (AhR) knock-down porcine granulosa cells. PeerJ 8:e8371 https://doi.org/10.7717/peerj.8371
date submitted: 2019-08-23
date accepted: 2019-12-09
issued: 2020-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ruszkowska
  given name: Monika
author list: Agent
  family name: Sadowska
  given name: Agnieszka
author list: Agent
  family name: Nynca
  given name: Anna
author list: Agent
  family name: Orlowska
  given name: Karina
author list: Agent
  family name: Swigonska
  given name: Sylwia
author list: Agent
  family name: Molcan
  given name: Tomasz
author list: Agent
  family name: Paukszto
  given name: Lukasz
author list: Agent
  family name: Jastrzebski
  given name: Jan P.
author list: Agent
  family name: Ciereszko
  given name: Renata E.
doi: 10.7717/peerj.8371
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-22
copyright: ©2020 Ruszkowska et al.
attribution name: Ruszkowska et al.

Shifts in soil nutrient concentrations and C:N:P stoichiometry during long-term natural vegetation restoration
type: item
type: AcademicArticle
description: Background Ecological stoichiometry (C:N:P ratios) in soil is an important indicator of the elemental balance in ecological interactions and processes. Long-term natural vegetation plays an important role in the accumulation and distribution of soil stoichiometry. However, information about the effects of long-term secondary forest succession on soil stoichiometry along a deep soil profile is still limited. Methods We selected Ziwuling secondary succession forest developed from farmland as the study area, investigated the concentrations and stoichiometry of soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) at a depth of 0–100 cm along a 90-year succession chronosequence, including farmland (control), grassland, shrub, early forest, and climax forest. Results SOC and TN concentrations significantly increased with increasing restoration age, whereas soil P concentration remained relatively stable across various successional stages. SOC and TN concentrations decreased with an increase in soil depth, exhibiting distinct soil nutrient “surface-aggregation” (high nutrients concentration in the top soil layer). The soil C:P and N:P ratios increased with an increase in restoration age, whereas the variation of the C:N ratio was small and relatively stable across vegetation succession. The nutrient limitation changed along with vegetation succession, transitioning from limited N in the earlier successional stages to limited P in the later successional stages. Conclusion Our results suggest that more nitrogen input should be applied to earlier succession stages, and more phosphorus input should be utilized in later succession stages in order to address limited availability of these elements. In general, natural vegetation restoration was an ecologically beneficial practice for the recovery of degraded soils in this area. The findings of this study strengthen our understanding of the changes of soil nutrient concentration and nutrient limitation after v…
format: application/pdf
format: text/html
creator: Rentian Ma
creator: Feinan Hu
creator: Jingfang Liu
creator: Chunli Wang
creator: Zilong Wang
creator: Gang Liu
creator: Shiwei Zhao
subject: Agricultural Science
subject: Ecology
subject: Soil Science
description: doi:10.7717/peerj.8382
publisher: PeerJ Inc.
rights: © 2020 Ma et al.
abstract: Background Ecological stoichiometry (C:N:P ratios) in soil is an important indicator of the elemental balance in ecological interactions and processes. Long-term natural vegetation plays an important role in the accumulation and distribution of soil stoichiometry. However, information about the effects of long-term secondary forest succession on soil stoichiometry along a deep soil profile is still limited. Methods We selected Ziwuling secondary succession forest developed from farmland as the study area, investigated the concentrations and stoichiometry of soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) at a depth of 0–100 cm along a 90-year succession chronosequence, including farmland (control), grassland, shrub, early forest, and climax forest. Results SOC and TN concentrations significantly increased with increasing restoration age, whereas soil P concentration remained relatively stable across various successional stages. SOC and TN concentrations decreased with an increase in soil depth, exhibiting distinct soil nutrient “surface-aggregation” (high nutrients concentration in the top soil layer). The soil C:P and N:P ratios increased with an increase in restoration age, whereas the variation of the C:N ratio was small and relatively stable across vegetation succession. The nutrient limitation changed along with vegetation succession, transitioning from limited N in the earlier successional stages to limited P in the later successional stages. Conclusion Our results suggest that more nitrogen input should be applied to earlier succession stages, and more phosphorus input should be utilized in later succession stages in order to address limited availability of these elements. In general, natural vegetation restoration was an ecologically beneficial practice for the recovery of degraded soils in this area. The findings of this study strengthen our understanding of the changes of soil nutrient concentration and nutrient limitation after v…
bibliographic citation: Ma et al. (2020) Shifts in soil nutrient concentrations and C:N:P stoichiometry during long-term natural vegetation restoration. PeerJ 8:e8382 https://doi.org/10.7717/peerj.8382
date submitted: 2019-06-14
date accepted: 2019-12-10
issued: 2020-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Rentian
author list: Agent
  family name: Hu
  given name: Feinan
author list: Agent
  family name: Liu
  given name: Jingfang
author list: Agent
  family name: Wang
  given name: Chunli
author list: Agent
  family name: Wang
  given name: Zilong
author list: Agent
  family name: Liu
  given name: Gang
author list: Agent
  family name: Zhao
  given name: Shiwei
doi: 10.7717/peerj.8382
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-22
copyright: ©2020 Ma et al.
attribution name: Ma et al.

First record of Gyrosteus mirabilis (Actinopterygii, Chondrosteidae) from the Toarcian (Lower Jurassic) of the Baltic region
type: item
type: AcademicArticle
description: An isolated hyomandibula from a lower Toarcian carbonate concretion of the Ahrensburg erratics assemblage (Schleswig-Holstein, northern Germany) represents the first record of a chondrosteid fish from the Lower Jurassic of the southwestern Baltic realm. Except for its smaller size, the specimen is morphologically indistinguishable from corresponding elements of Gyrosteus mirabilis from the Toarcian of Yorkshire, England. This find, which probably originates from the western Baltic basin between Bornholm Island (Denmark) and northeastern Germany, markedly expands the known range of this chondrosteid taxon across the northern part of the strait connecting the Boreal Sea with the Tethys Ocean during the Early Jurassic. For the first time the extension of the paleogeographic range of a chondrosteid species beyond its type area is documented, which can contribute to future studies of vertebrate faunal provincialism during the Lower Jurassic in Europe.
format: application/pdf
format: text/html
creator: Jahn J. Hornung
creator: Sven Sachs
subject: Biodiversity
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.8400
publisher: PeerJ Inc.
rights: © 2020 Hornung and Sachs
abstract: An isolated hyomandibula from a lower Toarcian carbonate concretion of the Ahrensburg erratics assemblage (Schleswig-Holstein, northern Germany) represents the first record of a chondrosteid fish from the Lower Jurassic of the southwestern Baltic realm. Except for its smaller size, the specimen is morphologically indistinguishable from corresponding elements of Gyrosteus mirabilis from the Toarcian of Yorkshire, England. This find, which probably originates from the western Baltic basin between Bornholm Island (Denmark) and northeastern Germany, markedly expands the known range of this chondrosteid taxon across the northern part of the strait connecting the Boreal Sea with the Tethys Ocean during the Early Jurassic. For the first time the extension of the paleogeographic range of a chondrosteid species beyond its type area is documented, which can contribute to future studies of vertebrate faunal provincialism during the Lower Jurassic in Europe.
bibliographic citation: Hornung et al. (2020) First record of Gyrosteus mirabilis (Actinopterygii, Chondrosteidae) from the Toarcian (Lower Jurassic) of the Baltic region. PeerJ 8:e8400 https://doi.org/10.7717/peerj.8400
date submitted: 2019-09-27
date accepted: 2019-12-16
issued: 2020-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hornung
  given name: Jahn J.
author list: Agent
  family name: Sachs
  given name: Sven
doi: 10.7717/peerj.8400
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-22
copyright: © 2020 Hornung and Sachs
attribution name: Hornung and Sachs

Florida manatees Trichechus manatus latirostris actively consume the sponge Chondrilla caribensis
type: item
type: AcademicArticle
description: The Florida manatee (Trichechus manatus latirostris Linnaeus 1758) actively selects and consumes the “chicken-liver” sponge Chondrilla caribensis. Manatees ate over 10% of C. caribensis on a sample dock, mostly from pylons that received no direct sunlight. Since manatees reportedly eat mostly seagrasses and algae, it was thought that the chlorophyll-a content of the symbiotic cyanobacteria in C. caribensis might be correlated to the amount eaten; however the correlation was not significant (P > 0.05). C. caribensis has variable chemical defenses and round spherasters (spicules), but these do not appear to be effective deterrents to predation by manatees. This is the first direct evidence that manatees actively seek out and consume a sponge.
format: application/pdf
format: text/html
creator: William Fitt
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.8443
publisher: PeerJ Inc.
rights: © 2020 Fitt
abstract: The Florida manatee (Trichechus manatus latirostris Linnaeus 1758) actively selects and consumes the “chicken-liver” sponge Chondrilla caribensis. Manatees ate over 10% of C. caribensis on a sample dock, mostly from pylons that received no direct sunlight. Since manatees reportedly eat mostly seagrasses and algae, it was thought that the chlorophyll-a content of the symbiotic cyanobacteria in C. caribensis might be correlated to the amount eaten; however the correlation was not significant (P > 0.05). C. caribensis has variable chemical defenses and round spherasters (spicules), but these do not appear to be effective deterrents to predation by manatees. This is the first direct evidence that manatees actively seek out and consume a sponge.
bibliographic citation: Fitt (2020) Florida manatees Trichechus manatus latirostris actively consume the sponge Chondrilla caribensis. PeerJ 8:e8443 https://doi.org/10.7717/peerj.8443
date submitted: 2019-08-15
date accepted: 2019-12-20
issued: 2020-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fitt
  given name: William
doi: 10.7717/peerj.8443
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-22
copyright: ©2020 Fitt
attribution name: Fitt

CD86+/CD206+ tumor-associated macrophages predict prognosis of patients with intrahepatic cholangiocarcinoma
type: item
type: AcademicArticle
description: Background As the main cellular ingredients of tumor microenvironment, tumor-associated macrophages (TAMs) play a vital role in tumor development and progression. Recent studies have suggested that TAMs are sensitive and specific prognostic factors in numerous cancers. The primary purpose of this study is to determine the prognostic significance of TAMs in intrahepatic cholangiocarcinoma (ICC). Methods Immunohistochemical staining of CD68, CD86 and CD206 were performed in tissue microarrays containing 322 patients, who underwent surgical resection and were pathologically diagnosed with ICC. The prognostic value of CD68, CD86 and CD206 were evaluated by Kaplan–Meier analysis (log-rank test) and nomogram models. Results We demonstrated that the CD86+/CD206+ TAMs model was an independent prognostic index for ICC patients. Patients with low CD86+ TAMs and high CD206+ TAMs infiltration had a markedly worse prognosis and increased risk of post-operative recurrence when compared to high CD86+ TAMs and low CD206+ TAMs intratumoral infiltration. Furthermore, subgroup analysis indicated that the CD86+/CD206+ TAMs model predicted prognosis of ICC patients more powerfully than single macrophage immunomarker. Interestingly, the CD86+/CD206+ TAMs model could further distinguish prognosis of CA-199 negative ICC patients, who were generally presumed to have a more favorable outcome. In order to further perfect the prognostic value of the CD86+/CD206+ TAMs model, we constructed and validated a postoperative nomogram to predict overall survival and recurrence-free survival time in ICC patients. Conclusions These findings indicate that the CD86+/CD206+ TAMs model possess potential value as a novel prognostic indicator for ICC patients.
format: application/pdf
format: text/html
creator: Dalong Sun
creator: Tiancheng Luo
creator: Pingping Dong
creator: Ningping Zhang
creator: Jing Chen
creator: Shuncai Zhang
creator: Longzi Liu
creator: Ling Dong
creator: Si Zhang
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.8458
publisher: PeerJ Inc.
rights: © 2020 Sun et al.
abstract: Background As the main cellular ingredients of tumor microenvironment, tumor-associated macrophages (TAMs) play a vital role in tumor development and progression. Recent studies have suggested that TAMs are sensitive and specific prognostic factors in numerous cancers. The primary purpose of this study is to determine the prognostic significance of TAMs in intrahepatic cholangiocarcinoma (ICC). Methods Immunohistochemical staining of CD68, CD86 and CD206 were performed in tissue microarrays containing 322 patients, who underwent surgical resection and were pathologically diagnosed with ICC. The prognostic value of CD68, CD86 and CD206 were evaluated by Kaplan–Meier analysis (log-rank test) and nomogram models. Results We demonstrated that the CD86+/CD206+ TAMs model was an independent prognostic index for ICC patients. Patients with low CD86+ TAMs and high CD206+ TAMs infiltration had a markedly worse prognosis and increased risk of post-operative recurrence when compared to high CD86+ TAMs and low CD206+ TAMs intratumoral infiltration. Furthermore, subgroup analysis indicated that the CD86+/CD206+ TAMs model predicted prognosis of ICC patients more powerfully than single macrophage immunomarker. Interestingly, the CD86+/CD206+ TAMs model could further distinguish prognosis of CA-199 negative ICC patients, who were generally presumed to have a more favorable outcome. In order to further perfect the prognostic value of the CD86+/CD206+ TAMs model, we constructed and validated a postoperative nomogram to predict overall survival and recurrence-free survival time in ICC patients. Conclusions These findings indicate that the CD86+/CD206+ TAMs model possess potential value as a novel prognostic indicator for ICC patients.
bibliographic citation: Sun et al. (2020) CD86+/CD206+ tumor-associated macrophages predict prognosis of patients with intrahepatic cholangiocarcinoma. PeerJ 8:e8458 https://doi.org/10.7717/peerj.8458
date submitted: 2019-05-06
date accepted: 2019-12-24
issued: 2020-01-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Dalong
author list: Agent
  family name: Luo
  given name: Tiancheng
author list: Agent
  family name: Dong
  given name: Pingping
author list: Agent
  family name: Zhang
  given name: Ningping
author list: Agent
  family name: Chen
  given name: Jing
author list: Agent
  family name: Zhang
  given name: Shuncai
author list: Agent
  family name: Liu
  given name: Longzi
author list: Agent
  family name: Dong
  given name: Ling
author list: Agent
  family name: Zhang
  given name: Si
doi: 10.7717/peerj.8458
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-22
copyright: © 2020 Sun et al.
attribution name: Sun et al.

Predicting hedgehog mortality risks on British roads using habitat suitability modelling
type: item
type: AcademicArticle
description: Road vehicle collisions are likely to be an important contributory factor in the decline of the European hedgehog (Erinaceus europaeus) in Britain. Here, a collaborative roadkill dataset collected from multiple projects across Britain was used to assess when, where and why hedgehog roadkill are more likely to occur. Seasonal trends were assessed using a Generalized Additive Model. There were few casualties in winter—the hibernation season for hedgehogs—with a gradual increase from February that reached a peak in July before declining thereafter. A sequential multi-level Habitat Suitability Modelling (HSM) framework was then used to identify areas showing a high probability of hedgehog roadkill occurrence throughout the entire British road network (∼400,000 km) based on multi-scale environmental determinants. The HSM predicted that grassland and urban habitat coverage were important in predicting the probability of roadkill at a national scale. Probabilities peaked at approximately 50% urban cover at a one km scale and increased linearly with grassland cover (improved and rough grassland). Areas predicted to experience high probabilities of hedgehog roadkill occurrence were therefore in urban and suburban environments, that is, where a mix of urban and grassland habitats occur. These areas covered 9% of the total British road network. In combination with information on the frequency with which particular locations have hedgehog road casualties, the framework can help to identify priority areas for mitigation measures.
format: application/pdf
format: text/html
creator: Patrick G.R. Wright
creator: Frazer G. Coomber
creator: Chloe C. Bellamy
creator: Sarah E. Perkins
creator: Fiona Mathews
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Environmental Impacts
description: doi:10.7717/peerj.8154
publisher: PeerJ Inc.
rights: © 2019 Wright et al.
abstract: Road vehicle collisions are likely to be an important contributory factor in the decline of the European hedgehog (Erinaceus europaeus) in Britain. Here, a collaborative roadkill dataset collected from multiple projects across Britain was used to assess when, where and why hedgehog roadkill are more likely to occur. Seasonal trends were assessed using a Generalized Additive Model. There were few casualties in winter—the hibernation season for hedgehogs—with a gradual increase from February that reached a peak in July before declining thereafter. A sequential multi-level Habitat Suitability Modelling (HSM) framework was then used to identify areas showing a high probability of hedgehog roadkill occurrence throughout the entire British road network (∼400,000 km) based on multi-scale environmental determinants. The HSM predicted that grassland and urban habitat coverage were important in predicting the probability of roadkill at a national scale. Probabilities peaked at approximately 50% urban cover at a one km scale and increased linearly with grassland cover (improved and rough grassland). Areas predicted to experience high probabilities of hedgehog roadkill occurrence were therefore in urban and suburban environments, that is, where a mix of urban and grassland habitats occur. These areas covered 9% of the total British road network. In combination with information on the frequency with which particular locations have hedgehog road casualties, the framework can help to identify priority areas for mitigation measures.
bibliographic citation: Wright et al. (2020) Predicting hedgehog mortality risks on British roads using habitat suitability modelling. PeerJ 7:e8154 https://doi.org/10.7717/peerj.8154
date submitted: 2019-07-12
date accepted: 2019-11-04
issued: 2020-01-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wright
  given name: Patrick G.R.
author list: Agent
  family name: Coomber
  given name: Frazer G.
author list: Agent
  family name: Bellamy
  given name: Chloe C.
author list: Agent
  family name: Perkins
  given name: Sarah E.
author list: Agent
  family name: Mathews
  given name: Fiona
doi: 10.7717/peerj.8154
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-21
copyright: © 2019 Wright et al.
attribution name: Wright et al.

Pseudolebinthus lunipterus sp. nov.: a striking deaf and mute new cricket from Malawi (Orthoptera, Gryllidae, Eneopterinae)
type: item
type: AcademicArticle
description: This article presents an intriguing new cricket species of the tribe Xenogryllini discovered in Northern Malawi. This is the first case of mute and deaf species in the subfamily Eneopterinae; it shows no stridulatory apparatus on short male forewings and no tympana on either side of fore tibiae in both sexes. We introduce the new species and its complete mitogenome and assess phylogenetic relationships based on molecular data obtained from next-generation sequencing genome skimming method. Phylogenetic analyses place the new species within the genus Pseudolebinthus in Xenogryllini, as the sister species of Pseudolebinthus gorochovi Robillard. We describe Pseudolebinthus lunipterus sp. nov., provide illustrations of main morphology, male and female genitalia, photographs of living specimens and information about habitat and update the identification key for species of genus Pseudolebinthus. We discuss the differences between the new species and related taxa and the striking loss of acoustic communication in this cricket.
format: application/pdf
format: text/html
creator: Karen Salazar
creator: Raymond J. Murphy
creator: Marion Guillaume
creator: Romain Nattier
creator: Tony Robillard
subject: Entomology
subject: Evolutionary Studies
subject: Taxonomy
description: doi:10.7717/peerj.8204
publisher: PeerJ Inc.
rights: © 2020 Salazar et al.
abstract: This article presents an intriguing new cricket species of the tribe Xenogryllini discovered in Northern Malawi. This is the first case of mute and deaf species in the subfamily Eneopterinae; it shows no stridulatory apparatus on short male forewings and no tympana on either side of fore tibiae in both sexes. We introduce the new species and its complete mitogenome and assess phylogenetic relationships based on molecular data obtained from next-generation sequencing genome skimming method. Phylogenetic analyses place the new species within the genus Pseudolebinthus in Xenogryllini, as the sister species of Pseudolebinthus gorochovi Robillard. We describe Pseudolebinthus lunipterus sp. nov., provide illustrations of main morphology, male and female genitalia, photographs of living specimens and information about habitat and update the identification key for species of genus Pseudolebinthus. We discuss the differences between the new species and related taxa and the striking loss of acoustic communication in this cricket.
bibliographic citation: Salazar et al. (2020) Pseudolebinthus lunipterus sp. nov.: a striking deaf and mute new cricket from Malawi (Orthoptera, Gryllidae, Eneopterinae). PeerJ 8:e8204 https://doi.org/10.7717/peerj.8204
date submitted: 2019-09-27
date accepted: 2019-11-13
issued: 2020-01-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salazar
  given name: Karen
author list: Agent
  family name: Murphy
  given name: Raymond J.
author list: Agent
  family name: Guillaume
  given name: Marion
author list: Agent
  family name: Nattier
  given name: Romain
author list: Agent
  family name: Robillard
  given name: Tony
doi: 10.7717/peerj.8204
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-21
copyright: © 2020 Salazar et al.
attribution name: Salazar et al.

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