PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Variation in the skulls of Elgaria and Gerrhonotus (Anguidae, Gerrhonotinae) and implications for phylogenetics and fossil identification
items: Comparative anatomy of the middle ear in some lizard species with comments on the evolutionary changes within Squamata
items: Change in mental health, physical health, and social relationships during highly restrictive lockdown in the COVID-19 pandemic: evidence from Australia
items: Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz)
items: Alterations to arbuscular mycorrhizal fungal community composition is driven by warming at specific elevations
items: Influenza A virus infection in turkeys induces respiratory and enteric bacterial dysbiosis correlating with cytokine gene expression
items: Predicted distribution of a rare and understudied forest carnivore: Humboldt marten (Martes caurina humboldtensis)
items: Morphological observation and protein expression of fertile and abortive ovules in Castanea mollissima
items: The effects of genetic drift and genomic selection on differentiation and local adaptation of the introduced populations of Aedes albopictus in southern Russia
items: Leveraging the potential of nature to meet net zero greenhouse gas emissions in Washington State

Variation in the skulls of Elgaria and Gerrhonotus (Anguidae, Gerrhonotinae) and implications for phylogenetics and fossil identification
type: item
type: AcademicArticle
description: Background There are limited data on intra- and interspecific osteological variation for many squamate clades. Those data are relevant for phylogenetic analyses that use osteological characters and for apomorphic identifications of fossils. We investigate whether morphological features in the skulls of extant gerrhonotine lizards can be used to distinguish taxa at the species- and genus-level and assess whether newly discovered intra- and interspecific osteological variation alters the utility of previously reported apomorphic features. We examined skulls of species belonging to the gerrhonotine genera Elgaria and Gerrhonotus. These genera contain 17 extant species, but the cranial osteology of only a few species was previously examined. As a result, intra- and interspecific osteological variation of these gerrhonotines is poorly understood. Methods We employed high-resolution x-ray computed tomography (CT) to scan 25 alcohol-preserved specimens. We provide data on the skulls of all eight species of Elgaria, four for the first time, and five species of Gerrhonotus, three for the first time. We examined 3-D reconstructed skulls of the scanned specimens as well as dry, traditionally prepared skeletons (when they were available). Results We found that the purported diagnostic utility of many previously described morphological features is impacted because of substantial morphological variation between and within species. We present an assessment of osteological differences that may be useful to differentiate species of Elgaria and Gerrhonotus, many of which are present on isolated cranial elements commonly recovered as fossils, including the premaxilla, maxilla, parietal, pterygoid, prootic, dentary, and surangular. We demonstrate the importance of documenting patterns of osteological variation using large sample sizes, and the utility of examining disarticulated cranial elements of the squamate skull to identify diagnostic morphology. This study adds to a growing body …
format: application/pdf
format: text/html
creator: David T. Ledesma
creator: Simon G. Scarpetta
creator: Christopher J. Bell
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11602
publisher: PeerJ Inc.
rights: © 2021 Ledesma et al.
abstract: Background There are limited data on intra- and interspecific osteological variation for many squamate clades. Those data are relevant for phylogenetic analyses that use osteological characters and for apomorphic identifications of fossils. We investigate whether morphological features in the skulls of extant gerrhonotine lizards can be used to distinguish taxa at the species- and genus-level and assess whether newly discovered intra- and interspecific osteological variation alters the utility of previously reported apomorphic features. We examined skulls of species belonging to the gerrhonotine genera Elgaria and Gerrhonotus. These genera contain 17 extant species, but the cranial osteology of only a few species was previously examined. As a result, intra- and interspecific osteological variation of these gerrhonotines is poorly understood. Methods We employed high-resolution x-ray computed tomography (CT) to scan 25 alcohol-preserved specimens. We provide data on the skulls of all eight species of Elgaria, four for the first time, and five species of Gerrhonotus, three for the first time. We examined 3-D reconstructed skulls of the scanned specimens as well as dry, traditionally prepared skeletons (when they were available). Results We found that the purported diagnostic utility of many previously described morphological features is impacted because of substantial morphological variation between and within species. We present an assessment of osteological differences that may be useful to differentiate species of Elgaria and Gerrhonotus, many of which are present on isolated cranial elements commonly recovered as fossils, including the premaxilla, maxilla, parietal, pterygoid, prootic, dentary, and surangular. We demonstrate the importance of documenting patterns of osteological variation using large sample sizes, and the utility of examining disarticulated cranial elements of the squamate skull to identify diagnostic morphology. This study adds to a growing body …
bibliographic citation: Ledesma et al. (2021) Variation in the skulls of Elgaria and Gerrhonotus (Anguidae, Gerrhonotinae) and implications for phylogenetics and fossil identification. PeerJ 9:e11602 https://doi.org/10.7717/peerj.11602
date submitted: 2021-02-17
date accepted: 2021-05-21
issued: 2021-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ledesma
  given name: David T.
author list: Agent
  family name: Scarpetta
  given name: Simon G.
author list: Agent
  family name: Bell
  given name: Christopher J.
doi: 10.7717/peerj.11602
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-22
copyright: © 2021 Ledesma et al.
attribution name: Ledesma et al.

Comparative anatomy of the middle ear in some lizard species with comments on the evolutionary changes within Squamata
type: item
type: AcademicArticle
description: The skeleton of the middle ear of lizards is composed of three anatomical elements: columella, extracolumella, and tympanic membrane, with some exceptions that show modifications of this anatomy. The main function of the middle ear is transforming sound waves into vibrations and transmitting these to the inner ear. Most middle ear studies mainly focus on its functional aspects, while few describe the anatomy in detail. In lizards, the morphology of the columella is highly conservative, while the extracolumella shows variation in its presence/absence, size, and the number of processes present on the structure. In this work, we used diaphanized and double-stained specimens of 38 species of lizards belonging to 24 genera to study the middle ear’s morphology in a comparative framework. Results presented here indicate more variation in the morphology of the extracolumella than previously known. This variation in the extracolumella is found mainly in the pars superior and anterior processes, while the pars inferior and the posterior process are more constant in morphology. We also provide new information about the shape of gekkotan extracolumella, including traits that are diagnostic for the iguanid and gekkonid middle ear types. The data collected in this study were combined with information from published descriptive works. The new data included here refers to the length of the columella relative to the extracolumella central axis length, the general structure of the extracolumella, and the presence of the internal process. These characters were included in ancestral reconstruction analysis using Bayesian and parsimony approaches. The results indicate high levels of homoplasy in the variation of the columella-extracolumella ratio, providing a better understanding of the ratio variation among lizards. Additionally, the presence of four processes in the extracolumella is the ancestral state for Gekkota, Pleurodonta, and Xantusiidae, and the absence of the internal process…
format: application/pdf
format: text/html
creator: Paola María Sánchez-Martínez
creator: Juan D. Daza
creator: Julio Mario Hoyos
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.11722
publisher: PeerJ Inc.
rights: © 2021 Sánchez-Martínez et al.
abstract: The skeleton of the middle ear of lizards is composed of three anatomical elements: columella, extracolumella, and tympanic membrane, with some exceptions that show modifications of this anatomy. The main function of the middle ear is transforming sound waves into vibrations and transmitting these to the inner ear. Most middle ear studies mainly focus on its functional aspects, while few describe the anatomy in detail. In lizards, the morphology of the columella is highly conservative, while the extracolumella shows variation in its presence/absence, size, and the number of processes present on the structure. In this work, we used diaphanized and double-stained specimens of 38 species of lizards belonging to 24 genera to study the middle ear’s morphology in a comparative framework. Results presented here indicate more variation in the morphology of the extracolumella than previously known. This variation in the extracolumella is found mainly in the pars superior and anterior processes, while the pars inferior and the posterior process are more constant in morphology. We also provide new information about the shape of gekkotan extracolumella, including traits that are diagnostic for the iguanid and gekkonid middle ear types. The data collected in this study were combined with information from published descriptive works. The new data included here refers to the length of the columella relative to the extracolumella central axis length, the general structure of the extracolumella, and the presence of the internal process. These characters were included in ancestral reconstruction analysis using Bayesian and parsimony approaches. The results indicate high levels of homoplasy in the variation of the columella-extracolumella ratio, providing a better understanding of the ratio variation among lizards. Additionally, the presence of four processes in the extracolumella is the ancestral state for Gekkota, Pleurodonta, and Xantusiidae, and the absence of the internal process…
bibliographic citation: Sánchez-Martínez et al. (2021) Comparative anatomy of the middle ear in some lizard species with comments on the evolutionary changes within Squamata. PeerJ 9:e11722 https://doi.org/10.7717/peerj.11722
date submitted: 2021-01-07
date accepted: 2021-06-14
issued: 2021-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sánchez-Martínez
  given name: Paola María
author list: Agent
  family name: Daza
  given name: Juan D.
author list: Agent
  family name: Hoyos
  given name: Julio Mario
doi: 10.7717/peerj.11722
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-22
copyright: © 2021 Sánchez-Martínez et al.
attribution name: Sánchez-Martínez et al.

Change in mental health, physical health, and social relationships during highly restrictive lockdown in the COVID-19 pandemic: evidence from Australia
type: item
type: AcademicArticle
description: Background A novel coronavirus first reported in Wuhan City in China in 2019 (COVID-19) developed into a global pandemic throughout 2020. Many countries around the world implemented strict social distancing policies to curb the spread of the virus. In this study we aimed to examine potential change in mental/physical health and social relationships during a highly restrictive COVID-19 lockdown period in Australia during April 2020. Methods Our survey (n = 1, 599) included questions about concerns, social behaviour, perceived change in relationship quality, social media use, frequency of exercise, physical health, and mental health during COVID-19 lockdown (April, 2020). Results When estimating their mental health for the previous year 13% of participants reported more negative than positive emotion, whereas this increased to 41% when participants reflected on their time during COVID-19 lockdown. A substantial proportion (39–54%) of participants reported deterioration in mental health, physical health, financial situation, and work productivity. However, most of these participants reported ’somewhat’ rather than ’a lot’ of deterioration, and many others reported ’no change’ (40–50%) or even ’improvement’ (6–17%). Even less impact was apparent for social relationships (68% reported ’no change’) as participants compensated for decreased face-to-face interaction via increased technology-mediated interaction. Conclusions The psychological toll of COVID-19 on Australians may not have been as large as other parts of the world with greater infection rates. Our findings highlight how technology-mediated communication can allow people to adequately maintain social relationships during an extreme lockdown event.
format: application/pdf
format: text/html
creator: Shane L. Rogers
creator: Travis Cruickshank
subject: Health Policy
subject: Infectious Diseases
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11767
publisher: PeerJ Inc.
rights: © 2021 Rogers and Cruickshank
abstract: Background A novel coronavirus first reported in Wuhan City in China in 2019 (COVID-19) developed into a global pandemic throughout 2020. Many countries around the world implemented strict social distancing policies to curb the spread of the virus. In this study we aimed to examine potential change in mental/physical health and social relationships during a highly restrictive COVID-19 lockdown period in Australia during April 2020. Methods Our survey (n = 1, 599) included questions about concerns, social behaviour, perceived change in relationship quality, social media use, frequency of exercise, physical health, and mental health during COVID-19 lockdown (April, 2020). Results When estimating their mental health for the previous year 13% of participants reported more negative than positive emotion, whereas this increased to 41% when participants reflected on their time during COVID-19 lockdown. A substantial proportion (39–54%) of participants reported deterioration in mental health, physical health, financial situation, and work productivity. However, most of these participants reported ’somewhat’ rather than ’a lot’ of deterioration, and many others reported ’no change’ (40–50%) or even ’improvement’ (6–17%). Even less impact was apparent for social relationships (68% reported ’no change’) as participants compensated for decreased face-to-face interaction via increased technology-mediated interaction. Conclusions The psychological toll of COVID-19 on Australians may not have been as large as other parts of the world with greater infection rates. Our findings highlight how technology-mediated communication can allow people to adequately maintain social relationships during an extreme lockdown event.
bibliographic citation: Rogers et al. (2021) Change in mental health, physical health, and social relationships during highly restrictive lockdown in the COVID-19 pandemic: evidence from Australia. PeerJ 9:e11767 https://doi.org/10.7717/peerj.11767
date submitted: 2021-02-12
date accepted: 2021-06-22
issued: 2021-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rogers
  given name: Shane L.
author list: Agent
  family name: Cruickshank
  given name: Travis
doi: 10.7717/peerj.11767
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-22
copyright: ©2021 Rogers and Cruickshank
attribution name: Rogers and Cruickshank

Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz)
type: item
type: AcademicArticle
description: Background The YABBY gene family is a family of small zinc finger transcription factors associated with plant morphogenesis, growth, and development. In particular, it is closely related to the development of polarity in the lateral organs of plants. Despite being studied extensively in many plant species, there is little information on genome-wide characterization of this gene family in Moso bamboo. Methods In the present study, we identified 16 PeYABBY genes, which were unequally distributed on 11 chromosomes, through genome-wide analysis of high-quality genome sequences of M oso bamboo by bioinformatics tools and biotechnological tools. Gene expression under hormone stress conditions was verified by quantitative real-time PCR (qRT-PCR) experiments. Results Based on peptide sequences and similarity of exon-intron structures, we classified the PeYABBY genes into four subfamilies. Analysis of putative cis-acting elements in promoters of these genes revealed that PeYABBYs contained a large number of hormone-responsive and stress-responsive elements. Expression analysis showed that they were expressed at a high level in Moso bamboo panicles, rhizomes, and leaves. Expression patterns of putative PeYABBY genes in different organs and hormone-treated were analyzed using RNA-seq data, results showed that some PeYABBY genes were responsive to gibberellin (GA) and abscisic acid (ABA), indicating that they may play an important role in plant hormone responses. Gene Ontology (GO) analyses of YABBY proteins indicated that they may be involved in many developmental processes, particularly high level of enrichment seen in plant leaf development. In summary, our results provide a comprehensive genome-wide study of the YABBY gene family in bamboos, which could be useful for further detailed studies of the function and evolution of the YABBY genes, and to provide a fundamental basis for the study of YABBY in Gramineae for resistance to stress and hormonal stress.
format: application/pdf
format: text/html
creator: Ruifang Ma
creator: Bin Huang
creator: Zhinuo Huang
creator: Zhijun Zhang
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.11780
publisher: PeerJ Inc.
rights: © 2021 Ma et al.
abstract: Background The YABBY gene family is a family of small zinc finger transcription factors associated with plant morphogenesis, growth, and development. In particular, it is closely related to the development of polarity in the lateral organs of plants. Despite being studied extensively in many plant species, there is little information on genome-wide characterization of this gene family in Moso bamboo. Methods In the present study, we identified 16 PeYABBY genes, which were unequally distributed on 11 chromosomes, through genome-wide analysis of high-quality genome sequences of M oso bamboo by bioinformatics tools and biotechnological tools. Gene expression under hormone stress conditions was verified by quantitative real-time PCR (qRT-PCR) experiments. Results Based on peptide sequences and similarity of exon-intron structures, we classified the PeYABBY genes into four subfamilies. Analysis of putative cis-acting elements in promoters of these genes revealed that PeYABBYs contained a large number of hormone-responsive and stress-responsive elements. Expression analysis showed that they were expressed at a high level in Moso bamboo panicles, rhizomes, and leaves. Expression patterns of putative PeYABBY genes in different organs and hormone-treated were analyzed using RNA-seq data, results showed that some PeYABBY genes were responsive to gibberellin (GA) and abscisic acid (ABA), indicating that they may play an important role in plant hormone responses. Gene Ontology (GO) analyses of YABBY proteins indicated that they may be involved in many developmental processes, particularly high level of enrichment seen in plant leaf development. In summary, our results provide a comprehensive genome-wide study of the YABBY gene family in bamboos, which could be useful for further detailed studies of the function and evolution of the YABBY genes, and to provide a fundamental basis for the study of YABBY in Gramineae for resistance to stress and hormonal stress.
bibliographic citation: Ma et al. (2021) Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz). PeerJ 9:e11780 https://doi.org/10.7717/peerj.11780
date submitted: 2021-03-31
date accepted: 2021-06-24
issued: 2021-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Ruifang
author list: Agent
  family name: Huang
  given name: Bin
author list: Agent
  family name: Huang
  given name: Zhinuo
author list: Agent
  family name: Zhang
  given name: Zhijun
doi: 10.7717/peerj.11780
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-22
copyright: ©2021 Ma et al.
attribution name: Ma et al.

Alterations to arbuscular mycorrhizal fungal community composition is driven by warming at specific elevations
type: item
type: AcademicArticle
description: Background Global warming can alter plant productivity, and community composition which has consequences for soil-plant associated microorganisms. Arbuscular mycorrhizal fungi (AMF) are distributed widely and form symbiotic relationships with more than 80% of vascular plants and play a key role in nutrient cycling processes at the ecosystem scale. Methods A simulated warming experiment at multiple elevations (3,000, 3,500, 3,800, and 4,170 m) was conducted utilizing an in-situ open-top chamber (OTC) for exploring the effect of global warming on AMF community structure in the Qinghai-Tibet Plateau (QTP). This region has been identified as one of the most sensitive areas to climatic changes. Soil DNA was extracted and sequenced using next the Mi-Seq platform for diversity profiling. Results AMF richness was higher under the simulated warming chamber, however this only occurred in the elevation of 3,500 m. Warming did not alter other AMF alpha diversity indices (e.g. Shannon, Ace, and Simpson evenness index). Glomus and Acaulospora were the dominate AMF genera as assessed through their relative abundance and occurrence in control and warming treatments at the different elevations. Conclusion Warming changed significantly AMF community. The effects of warming on AMF community structure varied depend on elevations. Moreover, the occurrences of AMF in different genera were also presented the different responses to warming in four elevations.
format: application/pdf
format: text/html
creator: Mei Yang
creator: Zhaoyong Shi
creator: Bede S. Mickan
creator: Mengge Zhang
creator: Libing Cao
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Mycology
subject: Soil Science
description: doi:10.7717/peerj.11792
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Background Global warming can alter plant productivity, and community composition which has consequences for soil-plant associated microorganisms. Arbuscular mycorrhizal fungi (AMF) are distributed widely and form symbiotic relationships with more than 80% of vascular plants and play a key role in nutrient cycling processes at the ecosystem scale. Methods A simulated warming experiment at multiple elevations (3,000, 3,500, 3,800, and 4,170 m) was conducted utilizing an in-situ open-top chamber (OTC) for exploring the effect of global warming on AMF community structure in the Qinghai-Tibet Plateau (QTP). This region has been identified as one of the most sensitive areas to climatic changes. Soil DNA was extracted and sequenced using next the Mi-Seq platform for diversity profiling. Results AMF richness was higher under the simulated warming chamber, however this only occurred in the elevation of 3,500 m. Warming did not alter other AMF alpha diversity indices (e.g. Shannon, Ace, and Simpson evenness index). Glomus and Acaulospora were the dominate AMF genera as assessed through their relative abundance and occurrence in control and warming treatments at the different elevations. Conclusion Warming changed significantly AMF community. The effects of warming on AMF community structure varied depend on elevations. Moreover, the occurrences of AMF in different genera were also presented the different responses to warming in four elevations.
bibliographic citation: Yang et al. (2021) Alterations to arbuscular mycorrhizal fungal community composition is driven by warming at specific elevations. PeerJ 9:e11792 https://doi.org/10.7717/peerj.11792
date submitted: 2021-01-26
date accepted: 2021-06-25
issued: 2021-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Mei
author list: Agent
  family name: Shi
  given name: Zhaoyong
author list: Agent
  family name: Mickan
  given name: Bede S.
author list: Agent
  family name: Zhang
  given name: Mengge
author list: Agent
  family name: Cao
  given name: Libing
doi: 10.7717/peerj.11792
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-22
copyright: © 2021 Yang et al.
attribution name: Yang et al.

Influenza A virus infection in turkeys induces respiratory and enteric bacterial dysbiosis correlating with cytokine gene expression
type: item
type: AcademicArticle
description: Turkey respiratory and gut microbiota play important roles in promoting health and production performance. Loss of microbiota homeostasis due to pathogen infection can worsen the disease or predispose the bird to infection by other pathogens. While turkeys are highly susceptible to influenza viruses of different origins, the impact of influenza virus infection on turkey gut and respiratory microbiota has not been demonstrated. In this study, we investigated the relationships between low pathogenicity avian influenza (LPAI) virus replication, cytokine gene expression, and respiratory and gut microbiota disruption in specific-pathogen-free turkeys. Differential replication of two LPAI H5N2 viruses paralleled the levels of clinical signs and cytokine gene expression. During active virus shedding, there was significant increase of ileal and nasal bacterial contents, which inversely corresponded with bacterial species diversity. Spearman’s correlation tests between bacterial abundance and local viral titers revealed that LPAI virus-induced dysbiosis was strongest in the nasal cavity followed by trachea, and weakest in the gut. Significant correlations were also observed between cytokine gene expression levels and relative abundances of several bacteria in tracheas of infected turkeys. For example, interferon γ/λ and interleukin-6 gene expression levels were correlated positively with Staphylococcus and Pseudomonas abundances, and negatively with Lactobacillus abundance. Overall, our data suggest a potential relationship where bacterial community diversity and enrichment or depletion of several bacterial genera in the gut and respiratory tract are dependent on the level of LPAI virus replication. Further work is needed to establish whether respiratory and enteric dysbiosis in LPAI virus-infected turkeys is a result of host immunological responses or other causes such as changes in nutritional uptake.
format: application/pdf
format: text/html
creator: John M. Ngunjiri
creator: Kara J.M. Taylor
creator: Hana Ji
creator: Michael C. Abundo
creator: Amir Ghorbani
creator: Mahesh KC
creator: Chang-Won Lee
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Virology
description: doi:10.7717/peerj.11806
publisher: PeerJ Inc.
rights: © 2021 Ngunjiri et al.
abstract: Turkey respiratory and gut microbiota play important roles in promoting health and production performance. Loss of microbiota homeostasis due to pathogen infection can worsen the disease or predispose the bird to infection by other pathogens. While turkeys are highly susceptible to influenza viruses of different origins, the impact of influenza virus infection on turkey gut and respiratory microbiota has not been demonstrated. In this study, we investigated the relationships between low pathogenicity avian influenza (LPAI) virus replication, cytokine gene expression, and respiratory and gut microbiota disruption in specific-pathogen-free turkeys. Differential replication of two LPAI H5N2 viruses paralleled the levels of clinical signs and cytokine gene expression. During active virus shedding, there was significant increase of ileal and nasal bacterial contents, which inversely corresponded with bacterial species diversity. Spearman’s correlation tests between bacterial abundance and local viral titers revealed that LPAI virus-induced dysbiosis was strongest in the nasal cavity followed by trachea, and weakest in the gut. Significant correlations were also observed between cytokine gene expression levels and relative abundances of several bacteria in tracheas of infected turkeys. For example, interferon γ/λ and interleukin-6 gene expression levels were correlated positively with Staphylococcus and Pseudomonas abundances, and negatively with Lactobacillus abundance. Overall, our data suggest a potential relationship where bacterial community diversity and enrichment or depletion of several bacterial genera in the gut and respiratory tract are dependent on the level of LPAI virus replication. Further work is needed to establish whether respiratory and enteric dysbiosis in LPAI virus-infected turkeys is a result of host immunological responses or other causes such as changes in nutritional uptake.
bibliographic citation: Ngunjiri et al. (2021) Influenza A virus infection in turkeys induces respiratory and enteric bacterial dysbiosis correlating with cytokine gene expression. PeerJ 9:e11806 https://doi.org/10.7717/peerj.11806
date submitted: 2021-02-17
date accepted: 2021-06-27
issued: 2021-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ngunjiri
  given name: John M.
author list: Agent
  family name: Taylor
  given name: Kara J.M.
author list: Agent
  family name: Ji
  given name: Hana
author list: Agent
  family name: Abundo
  given name: Michael C.
author list: Agent
  family name: Ghorbani
  given name: Amir
author list: Agent
  family name: KC
  given name: Mahesh
author list: Agent
  family name: Lee
  given name: Chang-Won
doi: 10.7717/peerj.11806
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-22
copyright: ©2021 Ngunjiri et al.
attribution name: Ngunjiri et al.

Predicted distribution of a rare and understudied forest carnivore: Humboldt marten (Martes caurina humboldtensis)
type: item
type: AcademicArticle
description: Background Many mammalian species have experienced range contractions. Following a reduction in distribution that has resulted in apparently small and disjunct populations, the Humboldt marten (Martes caurina humboldtensis) was recently designated as federally Threatened and state Endangered. This subspecies of Pacific marten occurring in coastal Oregon and northern California, also known as coastal martens, appear unlike martens that occur in snow-associated regions in that vegetation associations appear to differ widely between Humboldt marten populations. We expected current distributions represent realized niches, but estimating factors associated with long-term occurrence was challenging for this rare and little-known species. Here, we assessed the predicted contemporary distribution of Humboldt martens and interpret our findings as hypotheses correlated with the subspecies’ niche to inform strategic conservation actions. Methods We modeled Humboldt marten distribution using a maximum entropy (Maxent) approach. We spatially-thinned 10,229 marten locations collected from 1996–2020 by applying a minimum distance of 500-m between locations, resulting in 384 locations used to assess correlations of marten occurrence with biotic and abiotic variables. We independently optimized the spatial scale of each variable and focused development of model variables on biotic associations (e.g., hypothesized relationships with forest conditions), given that abiotic factors such as precipitation are largely static and not alterable within a management context. Results Humboldt marten locations were positively associated with increased shrub cover (salal (Gautheria shallon)), mast producing trees (e.g., tanoak, Notholithocarpus densiflorus), increased pine (Pinus sp.) proportion of total basal area, annual precipitation at home-range spatial scales, low and high amounts of canopy cover and slope, and cooler August temperatures. Unlike other recent literature, we found little evid…
format: application/pdf
format: text/html
creator: Katie M. Moriarty
creator: Joel Thompson
creator: Matthew Delheimer
creator: Brent R. Barry
creator: Mark Linnell
creator: Taal Levi
creator: Keith Hamm
creator: Desiree Early
creator: Holly Gamblin
creator: Micaela Szykman Gunther
creator: Jordan Ellison
creator: Janet S. Prevéy
creator: Jennifer Hartman
creator: Raymond Davis
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Natural Resource Management
subject: Population Biology
description: doi:10.7717/peerj.11670
publisher: PeerJ Inc.
rights: © 2021 Moriarty et al.
abstract: Background Many mammalian species have experienced range contractions. Following a reduction in distribution that has resulted in apparently small and disjunct populations, the Humboldt marten (Martes caurina humboldtensis) was recently designated as federally Threatened and state Endangered. This subspecies of Pacific marten occurring in coastal Oregon and northern California, also known as coastal martens, appear unlike martens that occur in snow-associated regions in that vegetation associations appear to differ widely between Humboldt marten populations. We expected current distributions represent realized niches, but estimating factors associated with long-term occurrence was challenging for this rare and little-known species. Here, we assessed the predicted contemporary distribution of Humboldt martens and interpret our findings as hypotheses correlated with the subspecies’ niche to inform strategic conservation actions. Methods We modeled Humboldt marten distribution using a maximum entropy (Maxent) approach. We spatially-thinned 10,229 marten locations collected from 1996–2020 by applying a minimum distance of 500-m between locations, resulting in 384 locations used to assess correlations of marten occurrence with biotic and abiotic variables. We independently optimized the spatial scale of each variable and focused development of model variables on biotic associations (e.g., hypothesized relationships with forest conditions), given that abiotic factors such as precipitation are largely static and not alterable within a management context. Results Humboldt marten locations were positively associated with increased shrub cover (salal (Gautheria shallon)), mast producing trees (e.g., tanoak, Notholithocarpus densiflorus), increased pine (Pinus sp.) proportion of total basal area, annual precipitation at home-range spatial scales, low and high amounts of canopy cover and slope, and cooler August temperatures. Unlike other recent literature, we found little evid…
bibliographic citation: Moriarty et al. (2021) Predicted distribution of a rare and understudied forest carnivore: Humboldt marten (Martes caurina humboldtensis). PeerJ 9:e11670 https://doi.org/10.7717/peerj.11670
date submitted: 2021-01-27
date accepted: 2021-06-03
issued: 2021-07-21
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Moriarty
  given name: Katie M.
author list: Agent
  family name: Thompson
  given name: Joel
author list: Agent
  family name: Delheimer
  given name: Matthew
author list: Agent
  family name: Barry
  given name: Brent R.
author list: Agent
  family name: Linnell
  given name: Mark
author list: Agent
  family name: Levi
  given name: Taal
author list: Agent
  family name: Hamm
  given name: Keith
author list: Agent
  family name: Early
  given name: Desiree
author list: Agent
  family name: Gamblin
  given name: Holly
author list: Agent
  family name: Szykman Gunther
  given name: Micaela
author list: Agent
  family name: Ellison
  given name: Jordan
author list: Agent
  family name: Prevéy
  given name: Janet S.
author list: Agent
  family name: Hartman
  given name: Jennifer
author list: Agent
  family name: Davis
  given name: Raymond
doi: 10.7717/peerj.11670
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-21
copyright: ©2021 Moriarty et al.
attribution name: Moriarty et al.

Morphological observation and protein expression of fertile and abortive ovules in Castanea mollissima
type: item
type: AcademicArticle
description: Chinese chestnuts (Castanea mollissima Blume.) contain 12–18 ovules in one ovary, but only one ovule develops into a seed, indicating a high ovule abortion rate. In this study, the Chinese chestnut ‘Huaihuang’ was used to explore the possible mechanisms of ovule abortion with respect to morphology and proteomics. The morphology and microstructure of abortive ovules were found to be considerably different from those of fertile ovules at 20 days after anthesis (20 DAA). The fertile ovules had completely formed tissues, such as the embryo sac, embryo and endosperm. By contrast, in the abortive ovules, there were no embryo sacs, and wide spaces between the integuments were observed, with few nucelli. Fluorescence labelling of the nuclei and transmission electron microscopy (TEM) observations showed that cells of abortive ovules were abnormally shaped and had thickened cell walls, folded cell membranes, condensed cytoplasm, ruptured nuclear membranes, degraded nucleoli and reduced mitochondria. The iTRAQ (isobaric tag for relative and absolute quantitation) results showed that in the abortive ovules, low levels of soluble protein with small molecular weights were found, and most of differently expressed proteins (DEPs) were related to protein synthesis, accumulation of active oxygen free radical, energy synthesis and so on. These DEPs might be associated with abnormal ovules formation.
format: application/pdf
format: text/html
creator: Bingshuai Du
creator: Qing Zhang
creator: Qingqin Cao
creator: Yu Xing
creator: Ling Qin
creator: Kefeng Fang
subject: Agricultural Science
subject: Bioinformatics
subject: Cell Biology
subject: Developmental Biology
subject: Plant Science
description: doi:10.7717/peerj.11756
publisher: PeerJ Inc.
rights: © 2021 Du et al.
abstract: Chinese chestnuts (Castanea mollissima Blume.) contain 12–18 ovules in one ovary, but only one ovule develops into a seed, indicating a high ovule abortion rate. In this study, the Chinese chestnut ‘Huaihuang’ was used to explore the possible mechanisms of ovule abortion with respect to morphology and proteomics. The morphology and microstructure of abortive ovules were found to be considerably different from those of fertile ovules at 20 days after anthesis (20 DAA). The fertile ovules had completely formed tissues, such as the embryo sac, embryo and endosperm. By contrast, in the abortive ovules, there were no embryo sacs, and wide spaces between the integuments were observed, with few nucelli. Fluorescence labelling of the nuclei and transmission electron microscopy (TEM) observations showed that cells of abortive ovules were abnormally shaped and had thickened cell walls, folded cell membranes, condensed cytoplasm, ruptured nuclear membranes, degraded nucleoli and reduced mitochondria. The iTRAQ (isobaric tag for relative and absolute quantitation) results showed that in the abortive ovules, low levels of soluble protein with small molecular weights were found, and most of differently expressed proteins (DEPs) were related to protein synthesis, accumulation of active oxygen free radical, energy synthesis and so on. These DEPs might be associated with abnormal ovules formation.
bibliographic citation: Du et al. (2021) Morphological observation and protein expression of fertile and abortive ovules in Castanea mollissima. PeerJ 9:e11756 https://doi.org/10.7717/peerj.11756
date submitted: 2021-01-21
date accepted: 2021-06-21
issued: 2021-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Du
  given name: Bingshuai
author list: Agent
  family name: Zhang
  given name: Qing
author list: Agent
  family name: Cao
  given name: Qingqin
author list: Agent
  family name: Xing
  given name: Yu
author list: Agent
  family name: Qin
  given name: Ling
author list: Agent
  family name: Fang
  given name: Kefeng
doi: 10.7717/peerj.11756
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-21
copyright: © 2021 Du et al.
attribution name: Du et al.

The effects of genetic drift and genomic selection on differentiation and local adaptation of the introduced populations of Aedes albopictus in southern Russia
type: item
type: AcademicArticle
description: Background Asian tiger mosquito Aedes albopictus is an arbovirus vector that has spread from its native habitation areal in Southeast Asia throughout North and South Americas, Europe, and Africa. Ae. albopictus was first detected in the Southern Federal District of the Russian Federation in the subtropical town of Sochi in 2011. In subsequent years, this species has been described in the continental areas with more severe climate and lower winter temperatures. Methods Genomic analysis of pooled Ae. albopictus samples collected in the mosquito populations in the coastal and continental regions of the Krasnodar Krai was conducted to look for the genetic changes associated with the spread and potential cold adaptation in Ae. albopictus. Results The results of the phylogenetic analysis based on mitochondrial genomes corresponded well with the hypothesis that Ae. albopictus haplotype A1a2a1 was introduced into the region from a single source. Population analysis revealed the role of dispersal and genetic drift in the local adaptation of the Asian tiger mosquito. The absence of shared haplotypes between the samples and high fixation indices suggest that gene flow between samples was heavily restricted. Mitochondrial and genomic differentiation together with different distances between dispersal routes, natural and anthropogenic barriers and local effective population size reduction could lead to difficulties in local climatic adaptations due to reduced selection effectiveness. We have found genomic regions with selective sweep patterns which can be considered as having been affected by recent selection events. The genes located in these regions participate in neural protection, lipid conservation, and cuticle formation during diapause. These processes were shown to be important for cold adaptation in the previous transcriptomic and proteomic studies. However, the population history and relatively low coverage obtained in the present article could have negatively affect sw…
format: application/pdf
format: text/html
creator: Evgenii A. Konorov
creator: Vyacheslav Yurchenko
creator: Ivan Patraman
creator: Alexander Lukashev
creator: Nadezhda Oyun
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.11776
publisher: PeerJ Inc.
rights: © 2021 Konorov et al.
abstract: Background Asian tiger mosquito Aedes albopictus is an arbovirus vector that has spread from its native habitation areal in Southeast Asia throughout North and South Americas, Europe, and Africa. Ae. albopictus was first detected in the Southern Federal District of the Russian Federation in the subtropical town of Sochi in 2011. In subsequent years, this species has been described in the continental areas with more severe climate and lower winter temperatures. Methods Genomic analysis of pooled Ae. albopictus samples collected in the mosquito populations in the coastal and continental regions of the Krasnodar Krai was conducted to look for the genetic changes associated with the spread and potential cold adaptation in Ae. albopictus. Results The results of the phylogenetic analysis based on mitochondrial genomes corresponded well with the hypothesis that Ae. albopictus haplotype A1a2a1 was introduced into the region from a single source. Population analysis revealed the role of dispersal and genetic drift in the local adaptation of the Asian tiger mosquito. The absence of shared haplotypes between the samples and high fixation indices suggest that gene flow between samples was heavily restricted. Mitochondrial and genomic differentiation together with different distances between dispersal routes, natural and anthropogenic barriers and local effective population size reduction could lead to difficulties in local climatic adaptations due to reduced selection effectiveness. We have found genomic regions with selective sweep patterns which can be considered as having been affected by recent selection events. The genes located in these regions participate in neural protection, lipid conservation, and cuticle formation during diapause. These processes were shown to be important for cold adaptation in the previous transcriptomic and proteomic studies. However, the population history and relatively low coverage obtained in the present article could have negatively affect sw…
bibliographic citation: Konorov et al. (2021) The effects of genetic drift and genomic selection on differentiation and local adaptation of the introduced populations of Aedes albopictus in southern Russia. PeerJ 9:e11776 https://doi.org/10.7717/peerj.11776
date submitted: 2021-02-11
date accepted: 2021-06-23
issued: 2021-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Konorov
  given name: Evgenii A.
author list: Agent
  family name: Yurchenko
  given name: Vyacheslav
author list: Agent
  family name: Patraman
  given name: Ivan
author list: Agent
  family name: Lukashev
  given name: Alexander
author list: Agent
  family name: Oyun
  given name: Nadezhda
doi: 10.7717/peerj.11776
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-21
copyright: © 2021 Konorov et al.
attribution name: Konorov et al.

Leveraging the potential of nature to meet net zero greenhouse gas emissions in Washington State
type: item
type: AcademicArticle
description: The State of Washington, USA, has set a goal to reach net zero greenhouse gas emissions by 2050, the year around which the Intergovernmental Panel on Climate Change (IPCC) recommended we must limit global warming to 1.5 °C above that of pre-industrial times or face catastrophic changes. We employed existing approaches to calculate the potential for a suite of Natural Climate Solution (NCS) pathways to reduce Washington’s net emissions under three implementation scenarios: Limited, Moderate, and Ambitious. We found that NCS could reduce emissions between 4.3 and 8.8 MMT CO2eyr−1 in thirty-one years, accounting for 4% to 9% of the State’s net zero goal. These potential reductions largely rely on changing forest management practices on portions of private and public timber lands. We also mapped the distribution of each pathway’s Ambitious potential emissions reductions by county, revealing spatial clustering of high potential reductions in three regions closely tied to major business sectors: private industrial forestry in southwestern coastal forests, cropland agriculture in the Columbia Basin, and urban and rural development in the Puget Trough. Overall, potential emissions reductions are provided largely by a single pathway, Extended Timber Harvest Rotations, which mostly clusters in southwestern counties. However, mapping distribution of each of the other pathways reveals wider distribution of each pathway’s unique geographic relevance to support fair, just, and efficient deployment. Although the relative potential for a single pathway to contribute to statewide emissions reductions may be small, they could provide co-benefits to people, communities, economies, and nature for adaptation and resiliency across the state.
format: application/pdf
format: text/html
creator: James C. Robertson
creator: Kristina V. Randrup
creator: Emily R. Howe
creator: Michael J. Case
creator: Phillip S. Levin
subject: Ecosystem Science
subject: Coupled Natural and Human Systems
subject: Climate Change Biology
subject: Natural Resource Management
subject: Atmospheric Chemistry
description: doi:10.7717/peerj.11802
publisher: PeerJ Inc.
rights: © 2021 Robertson et al.
abstract: The State of Washington, USA, has set a goal to reach net zero greenhouse gas emissions by 2050, the year around which the Intergovernmental Panel on Climate Change (IPCC) recommended we must limit global warming to 1.5 °C above that of pre-industrial times or face catastrophic changes. We employed existing approaches to calculate the potential for a suite of Natural Climate Solution (NCS) pathways to reduce Washington’s net emissions under three implementation scenarios: Limited, Moderate, and Ambitious. We found that NCS could reduce emissions between 4.3 and 8.8 MMT CO2eyr−1 in thirty-one years, accounting for 4% to 9% of the State’s net zero goal. These potential reductions largely rely on changing forest management practices on portions of private and public timber lands. We also mapped the distribution of each pathway’s Ambitious potential emissions reductions by county, revealing spatial clustering of high potential reductions in three regions closely tied to major business sectors: private industrial forestry in southwestern coastal forests, cropland agriculture in the Columbia Basin, and urban and rural development in the Puget Trough. Overall, potential emissions reductions are provided largely by a single pathway, Extended Timber Harvest Rotations, which mostly clusters in southwestern counties. However, mapping distribution of each of the other pathways reveals wider distribution of each pathway’s unique geographic relevance to support fair, just, and efficient deployment. Although the relative potential for a single pathway to contribute to statewide emissions reductions may be small, they could provide co-benefits to people, communities, economies, and nature for adaptation and resiliency across the state.
bibliographic citation: Robertson et al. (2021) Leveraging the potential of nature to meet net zero greenhouse gas emissions in Washington State. PeerJ 9:e11802 https://doi.org/10.7717/peerj.11802
date submitted: 2021-03-30
date accepted: 2021-06-26
issued: 2021-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Robertson
  given name: James C.
author list: Agent
  family name: Randrup
  given name: Kristina V.
author list: Agent
  family name: Howe
  given name: Emily R.
author list: Agent
  family name: Case
  given name: Michael J.
author list: Agent
  family name: Levin
  given name: Phillip S.
doi: 10.7717/peerj.11802
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-21
copyright: ©2021 Robertson et al.
attribution name: Robertson et al.

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