PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Predicting the effect of variants on splicing using Convolutional Neural Networks
items: Evaluation of psychological stress in scientific researchers during the 2019–2020 COVID-19 outbreak in China
items: Novel circulating protein biomarkers for thyroid cancer determined through data-independent acquisition mass spectrometry
items: Association between the number and size of intrapulmonary lymph nodes and chronic obstructive pulmonary disease severity
items: Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.)
items: Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships
items: A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genus Microhyla (Amphibia: Microhylidae)
items: The impact of short-term exposure to near shore stressors on the early life stages of the reef building coral Montipora capitata
items: A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains
items: Treating coral bleaching as weather: a framework to validate and optimize prediction skill

Predicting the effect of variants on splicing using Convolutional Neural Networks
type: item
type: AcademicArticle
description: Mutations that cause an error in the splicing of a messenger RNA (mRNA) can lead to diseases in humans. Various computational models have been developed to recognize the sequence pattern of the splice sites. In recent studies, Convolutional Neural Network (CNN) architectures were shown to outperform other existing models in predicting the splice sites. However, an insufficient effort has been put into extending the CNN model to predict the effect of the genomic variants on the splicing of mRNAs. This study proposes a framework to elaborate on the utility of CNNs to assess the effect of splice variants on the identification of potential disease-causing variants that disrupt the RNA splicing process. Five models, including three CNN-based and two non-CNN machine learning based, were trained and compared using two existing splice site datasets, Genome Wide Human splice sites (GWH) and a dataset provided at the Deep Learning and Artificial Intelligence winter school 2018 (DLAI). The donor sites were also used to test on the HSplice tool to evaluate the predictive models. To improve the effectiveness of predictive models, two datasets were combined. The CNN model with four convolutional layers showed the best splice site prediction performance with an AUPRC of 93.4% and 88.8% for donor and acceptor sites, respectively. The effects of variants on splicing were estimated by applying the best model on variant data from the ClinVar database. Based on the estimation, the framework could effectively differentiate pathogenic variants from the benign variants (p = 5.9 × 10−7). These promising results support that the proposed framework could be applied in future genetic studies to identify disease causing loci involving the splicing mechanism. The datasets and Python scripts used in this study are available on the GitHub repository at https://github.com/smiile8888/rna-splice-sites-recognition.
format: application/pdf
format: text/html
creator: Thanyathorn Thanapattheerakul
creator: Worrawat Engchuan
creator: Jonathan H. Chan
subject: Bioinformatics
subject: Computational Biology
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.9470
publisher: PeerJ Inc.
rights: © 2020 Thanapattheerakul et al.
abstract: Mutations that cause an error in the splicing of a messenger RNA (mRNA) can lead to diseases in humans. Various computational models have been developed to recognize the sequence pattern of the splice sites. In recent studies, Convolutional Neural Network (CNN) architectures were shown to outperform other existing models in predicting the splice sites. However, an insufficient effort has been put into extending the CNN model to predict the effect of the genomic variants on the splicing of mRNAs. This study proposes a framework to elaborate on the utility of CNNs to assess the effect of splice variants on the identification of potential disease-causing variants that disrupt the RNA splicing process. Five models, including three CNN-based and two non-CNN machine learning based, were trained and compared using two existing splice site datasets, Genome Wide Human splice sites (GWH) and a dataset provided at the Deep Learning and Artificial Intelligence winter school 2018 (DLAI). The donor sites were also used to test on the HSplice tool to evaluate the predictive models. To improve the effectiveness of predictive models, two datasets were combined. The CNN model with four convolutional layers showed the best splice site prediction performance with an AUPRC of 93.4% and 88.8% for donor and acceptor sites, respectively. The effects of variants on splicing were estimated by applying the best model on variant data from the ClinVar database. Based on the estimation, the framework could effectively differentiate pathogenic variants from the benign variants (p = 5.9 × 10−7). These promising results support that the proposed framework could be applied in future genetic studies to identify disease causing loci involving the splicing mechanism. The datasets and Python scripts used in this study are available on the GitHub repository at https://github.com/smiile8888/rna-splice-sites-recognition.
bibliographic citation: Thanapattheerakul et al. (2020) Predicting the effect of variants on splicing using Convolutional Neural Networks. PeerJ 8:e9470 https://doi.org/10.7717/peerj.9470
date submitted: 2019-11-25
date accepted: 2020-06-11
issued: 2020-07-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thanapattheerakul
  given name: Thanyathorn
author list: Agent
  family name: Engchuan
  given name: Worrawat
author list: Agent
  family name: Chan
  given name: Jonathan H.
doi: 10.7717/peerj.9470
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-06
copyright: ©2020 Thanapattheerakul et al.
attribution name: Thanapattheerakul et al.

Evaluation of psychological stress in scientific researchers during the 2019–2020 COVID-19 outbreak in China
type: item
type: AcademicArticle
description: Background Beginning in December 2019, coronavirus disease 2019 (COVID-19) caused an outbreak of infectious pneumonia. The Chinese government introduced a series of grounding measures to prevent the spread of COVID-19. The living and working patterns of many scientific researchers also underwent significant changes during this period. Methods An opportunity sample (n = 251) was obtained in China using a questionnaire with 42 questions on scientific research progress and psychological stress during the COVID-19 epidemic. Results Of the 251 participants, 76.9% indicated that their research was affected by the COVID-19 outbreak, and participants who were affected by the outbreak had higher stress levels than those who were not affected. Participants who conducted COVID-19 research and indicated concern that they would fail to finish the research on time were more likely to indicate high levels of stress. Respondents indicated that extending deadlines (64.1%), receiving support from superiors for research (51.8%), and increasing benefits for researchers (51.0%) would likely relieve outbreak-related stress. Conclusion The COVID-19 outbreak had a major impact on the experiments of researchers in the life sciences, especially in basic and clinical medicine. It has also caused high levels of psychological stress in these populations. Measures should be taken to relieve psychological pressure on basic medical researchers and students who will soon complete their degrees (e.g., Master’s and PhD candidates in graduation years).
format: application/pdf
format: text/html
creator: Xueyan Zhang
creator: Xinyu Li
creator: Zhenxin Liao
creator: Mingyi Zhao
creator: Quan Zhuang
subject: Global Health
subject: Infectious Diseases
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.9497
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Background Beginning in December 2019, coronavirus disease 2019 (COVID-19) caused an outbreak of infectious pneumonia. The Chinese government introduced a series of grounding measures to prevent the spread of COVID-19. The living and working patterns of many scientific researchers also underwent significant changes during this period. Methods An opportunity sample (n = 251) was obtained in China using a questionnaire with 42 questions on scientific research progress and psychological stress during the COVID-19 epidemic. Results Of the 251 participants, 76.9% indicated that their research was affected by the COVID-19 outbreak, and participants who were affected by the outbreak had higher stress levels than those who were not affected. Participants who conducted COVID-19 research and indicated concern that they would fail to finish the research on time were more likely to indicate high levels of stress. Respondents indicated that extending deadlines (64.1%), receiving support from superiors for research (51.8%), and increasing benefits for researchers (51.0%) would likely relieve outbreak-related stress. Conclusion The COVID-19 outbreak had a major impact on the experiments of researchers in the life sciences, especially in basic and clinical medicine. It has also caused high levels of psychological stress in these populations. Measures should be taken to relieve psychological pressure on basic medical researchers and students who will soon complete their degrees (e.g., Master’s and PhD candidates in graduation years).
bibliographic citation: Zhang et al. (2020) Evaluation of psychological stress in scientific researchers during the 2019–2020 COVID-19 outbreak in China. PeerJ 8:e9497 https://doi.org/10.7717/peerj.9497
date submitted: 2020-03-12
date accepted: 2020-06-17
issued: 2020-07-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xueyan
author list: Agent
  family name: Li
  given name: Xinyu
author list: Agent
  family name: Liao
  given name: Zhenxin
author list: Agent
  family name: Zhao
  given name: Mingyi
author list: Agent
  family name: Zhuang
  given name: Quan
doi: 10.7717/peerj.9497
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-06
copyright: © 2020 Zhang et al.
attribution name: Zhang et al.

Novel circulating protein biomarkers for thyroid cancer determined through data-independent acquisition mass spectrometry
type: item
type: AcademicArticle
description: Background Distinguishing between different types of thyroid cancers (TC) remains challenging in clinical laboratories. As different tumor types require different clinical interventions, it is necessary to establish new methods for accurate diagnosis of TC. Methods Proteomic analysis of the human serum was performed through data-independent acquisition mass spectrometry for 29 patients with TC (stages I–IV): 13 cases of papillary TC (PTC), 10 cases of medullary TC (MTC), and six cases follicular TC (FTC). In addition, 15 patients with benign thyroid nodules (TNs) and 10 healthy controls (HCs) were included in this study. Subsequently, 17 differentially expressed proteins were identified in 291 patients with TC, including 247 with PTC, 38 with MTC, and six with FTC, and 69 patients with benign TNs and 176 with HC, using enzyme-linked immunosorbent assays. Results In total, 517 proteins were detected in the serum samples using an Orbitrap Q-Exactive-plus mass spectrometer. The amyloid beta A4 protein, apolipoprotein A-IV, gelsolin, contactin-1, gamma-glutamyl hydrolase, and complement factor H-related protein 1 (CFHR1) were selected for further analysis. The median serum CFHR1 levels were significantly higher in the MTC and FTC groups than in the PTC and control groups (P < 0.001). CFHR1 exhibited higher diagnostic performance in distinguishing patients with MTC from those with PTC (P < 0.001), with a sensitivity of 100.0%, specificity of 85.08%, area under the curve of 0.93, and detection cut-off of 0.92 ng/mL. Conclusion CFHR1 may serve as a novel biomarker to distinguish PTC from MTC with high sensitivity and specificity.
format: application/pdf
format: text/html
creator: Dandan Li
creator: Jie Wu
creator: Zhongjuan Liu
creator: Ling Qiu
creator: Yimin Zhang
subject: Bioinformatics
subject: Oncology
subject: Public Health
description: doi:10.7717/peerj.9507
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Background Distinguishing between different types of thyroid cancers (TC) remains challenging in clinical laboratories. As different tumor types require different clinical interventions, it is necessary to establish new methods for accurate diagnosis of TC. Methods Proteomic analysis of the human serum was performed through data-independent acquisition mass spectrometry for 29 patients with TC (stages I–IV): 13 cases of papillary TC (PTC), 10 cases of medullary TC (MTC), and six cases follicular TC (FTC). In addition, 15 patients with benign thyroid nodules (TNs) and 10 healthy controls (HCs) were included in this study. Subsequently, 17 differentially expressed proteins were identified in 291 patients with TC, including 247 with PTC, 38 with MTC, and six with FTC, and 69 patients with benign TNs and 176 with HC, using enzyme-linked immunosorbent assays. Results In total, 517 proteins were detected in the serum samples using an Orbitrap Q-Exactive-plus mass spectrometer. The amyloid beta A4 protein, apolipoprotein A-IV, gelsolin, contactin-1, gamma-glutamyl hydrolase, and complement factor H-related protein 1 (CFHR1) were selected for further analysis. The median serum CFHR1 levels were significantly higher in the MTC and FTC groups than in the PTC and control groups (P < 0.001). CFHR1 exhibited higher diagnostic performance in distinguishing patients with MTC from those with PTC (P < 0.001), with a sensitivity of 100.0%, specificity of 85.08%, area under the curve of 0.93, and detection cut-off of 0.92 ng/mL. Conclusion CFHR1 may serve as a novel biomarker to distinguish PTC from MTC with high sensitivity and specificity.
bibliographic citation: Li et al. (2020) Novel circulating protein biomarkers for thyroid cancer determined through data-independent acquisition mass spectrometry. PeerJ 8:e9507 https://doi.org/10.7717/peerj.9507
date submitted: 2020-01-10
date accepted: 2020-06-17
issued: 2020-07-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Dandan
author list: Agent
  family name: Wu
  given name: Jie
author list: Agent
  family name: Liu
  given name: Zhongjuan
author list: Agent
  family name: Qiu
  given name: Ling
author list: Agent
  family name: Zhang
  given name: Yimin
doi: 10.7717/peerj.9507
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-06
copyright: © 2020 Li et al.
attribution name: Li et al.

Association between the number and size of intrapulmonary lymph nodes and chronic obstructive pulmonary disease severity
type: item
type: AcademicArticle
description: Purpose One of the main pathophysiological mechanisms of chronic obstructive pulmonary disease is inflammation, which has been associated with lymphadenopathy. Intrapulmonary lymph nodes can be identified on CT as perifissural nodules (PFN). We investigated the association between the number and size of PFNs and measures of COPD severity. Materials and Methods CT images were obtained from COPDGene. 50 subjects were randomly selected per GOLD stage (0 to 4), GOLD-unclassified, and never-smoker groups and allocated to either “Healthy,” “Mild,” or “Moderate/severe” groups. 26/350 (7.4%) subjects had missing images and were excluded. Supported by computer-aided detection, a trained researcher prelocated non-calcified opacities larger than 3 mm in diameter. Included lung opacities were classified independently by two radiologists as either “PFN,” “not a PFN,” “calcified,” or “not a nodule”; disagreements were arbitrated by a third radiologist. Ordinal logistic regression was performed as the main statistical test. Results A total of 592 opacities were included in the observer study. A total of 163/592 classifications (27.5%) required arbitration. A total of 17/592 opacities (2.9%) were excluded from the analysis because they were not considered nodular, were calcified, or all three radiologists disagreed. A total of 366/575 accepted nodules (63.7%) were considered PFNs. A maximum of 10 PFNs were found in one image; 154/324 (47.5%) contained no PFNs. The number of PFNs per subject did not differ between COPD severity groups (p = 0.50). PFN short-axis diameter could significantly distinguish between the Mild and Moderate/severe groups, but not between the Healthy and Mild groups (p = 0.021). Conclusions There is no relationship between PFN count and COPD severity. There may be a weak trend of larger intrapulmonary lymph nodes among patients with more advanced stages of COPD.
format: application/pdf
format: text/html
creator: Anton Schreuder
creator: Colin Jacobs
creator: Ernst T. Scholten
creator: Mathias Prokop
creator: Bram van Ginneken
creator: David A. Lynch
creator: Cornelia M. Schaefer-Prokop
subject: Anatomy and Physiology
subject: Epidemiology
subject: Radiology and Medical Imaging
subject: Respiratory Medicine
description: doi:10.7717/peerj.9166
publisher: PeerJ Inc.
rights: © 2020 Schreuder et al.
abstract: Purpose One of the main pathophysiological mechanisms of chronic obstructive pulmonary disease is inflammation, which has been associated with lymphadenopathy. Intrapulmonary lymph nodes can be identified on CT as perifissural nodules (PFN). We investigated the association between the number and size of PFNs and measures of COPD severity. Materials and Methods CT images were obtained from COPDGene. 50 subjects were randomly selected per GOLD stage (0 to 4), GOLD-unclassified, and never-smoker groups and allocated to either “Healthy,” “Mild,” or “Moderate/severe” groups. 26/350 (7.4%) subjects had missing images and were excluded. Supported by computer-aided detection, a trained researcher prelocated non-calcified opacities larger than 3 mm in diameter. Included lung opacities were classified independently by two radiologists as either “PFN,” “not a PFN,” “calcified,” or “not a nodule”; disagreements were arbitrated by a third radiologist. Ordinal logistic regression was performed as the main statistical test. Results A total of 592 opacities were included in the observer study. A total of 163/592 classifications (27.5%) required arbitration. A total of 17/592 opacities (2.9%) were excluded from the analysis because they were not considered nodular, were calcified, or all three radiologists disagreed. A total of 366/575 accepted nodules (63.7%) were considered PFNs. A maximum of 10 PFNs were found in one image; 154/324 (47.5%) contained no PFNs. The number of PFNs per subject did not differ between COPD severity groups (p = 0.50). PFN short-axis diameter could significantly distinguish between the Mild and Moderate/severe groups, but not between the Healthy and Mild groups (p = 0.021). Conclusions There is no relationship between PFN count and COPD severity. There may be a weak trend of larger intrapulmonary lymph nodes among patients with more advanced stages of COPD.
bibliographic citation: Schreuder et al. (2020) Association between the number and size of intrapulmonary lymph nodes and chronic obstructive pulmonary disease severity. PeerJ 8:e9166 https://doi.org/10.7717/peerj.9166
date submitted: 2019-10-15
date accepted: 2020-04-19
issued: 2020-07-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schreuder
  given name: Anton
author list: Agent
  family name: Jacobs
  given name: Colin
author list: Agent
  family name: Scholten
  given name: Ernst T.
author list: Agent
  family name: Prokop
  given name: Mathias
author list: Agent
  family name: van Ginneken
  given name: Bram
author list: Agent
  family name: Lynch
  given name: David A.
author list: Agent
  family name: Schaefer-Prokop
  given name: Cornelia M.
doi: 10.7717/peerj.9166
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-03
copyright: ©2020 Schreuder et al.
attribution name: Schreuder et al.

Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.)
type: item
type: AcademicArticle
description: The basic helix-loop-helix (bHLH) transcription factors (TFs) have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya (Carica papaya L.) has been reported previously. Here, a total of 73 CpbHLHs were identified in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis. Almost all of the CpbHLHs in the same subfamily shared similar gene structures and protein motifs according to analysis of exon/intron organizations and motif compositions. The number of exons in CpbHLHs varied from one to 10 with an average of five. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter cis-element analysis revealed that most of the CpbHLHs contained cis-elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that CpbHLHs mainly functions in protein dimerization activity and DNA-binding, and most CpbHLHs were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some important candidate CpbHLHs that might be responsible for abiotic stress responses in papaya. These findings would lay a foundation for further investigate of the molecular functions of CpbHLHs.
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format: text/html
creator: Min Yang
creator: Chenping Zhou
creator: Hu Yang
creator: Ruibin Kuang
creator: Bingxiong Huang
creator: Yuerong Wei
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.9319
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: The basic helix-loop-helix (bHLH) transcription factors (TFs) have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya (Carica papaya L.) has been reported previously. Here, a total of 73 CpbHLHs were identified in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis. Almost all of the CpbHLHs in the same subfamily shared similar gene structures and protein motifs according to analysis of exon/intron organizations and motif compositions. The number of exons in CpbHLHs varied from one to 10 with an average of five. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter cis-element analysis revealed that most of the CpbHLHs contained cis-elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that CpbHLHs mainly functions in protein dimerization activity and DNA-binding, and most CpbHLHs were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some important candidate CpbHLHs that might be responsible for abiotic stress responses in papaya. These findings would lay a foundation for further investigate of the molecular functions of CpbHLHs.
bibliographic citation: Yang et al. (2020) Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.). PeerJ 8:e9319 https://doi.org/10.7717/peerj.9319
date submitted: 2020-02-14
date accepted: 2020-05-17
issued: 2020-07-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Min
author list: Agent
  family name: Zhou
  given name: Chenping
author list: Agent
  family name: Yang
  given name: Hu
author list: Agent
  family name: Kuang
  given name: Ruibin
author list: Agent
  family name: Huang
  given name: Bingxiong
author list: Agent
  family name: Wei
  given name: Yuerong
doi: 10.7717/peerj.9319
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-03
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships
type: item
type: AcademicArticle
description: Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable results. These poorly resolved relationships may be the product of methodological shortcomings or of an evolutionary history that did not generate the signal traits needed for its eventual reconstruction. Relationships within the euteleost fish family Salmonidae have proven challenging to resolve in molecular phylogenetics studies in part due to ancestral autopolyploidy contributing to conflicting gene trees. We examine a sequence capture dataset from salmonids and use alternative strategies to accommodate the effects of gene tree conflict based on aspects of salmonid genome history and the multispecies coalescent. We investigate in detail three uncertain relationships: (1) subfamily branching, (2) monophyly of Coregonus and (3) placement of Parahucho. Coregoninae and Thymallinae are resolved as sister taxa, although conflicting topologies are found across analytical strategies. We find inconsistent and generally low support for the monophyly of Coregonus, including in results of analyses with the most extensive dataset and complex model. The most consistent placement of Parahucho is as sister lineage of Salmo.
format: application/pdf
format: text/html
creator: Matthew A. Campbell
creator: Thaddaeus J. Buser
creator: Michael E. Alfaro
creator: J. Andrés López
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Evolutionary Studies
description: doi:10.7717/peerj.9389
publisher: PeerJ Inc.
rights: © 2020 Campbell et al.
abstract: Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable results. These poorly resolved relationships may be the product of methodological shortcomings or of an evolutionary history that did not generate the signal traits needed for its eventual reconstruction. Relationships within the euteleost fish family Salmonidae have proven challenging to resolve in molecular phylogenetics studies in part due to ancestral autopolyploidy contributing to conflicting gene trees. We examine a sequence capture dataset from salmonids and use alternative strategies to accommodate the effects of gene tree conflict based on aspects of salmonid genome history and the multispecies coalescent. We investigate in detail three uncertain relationships: (1) subfamily branching, (2) monophyly of Coregonus and (3) placement of Parahucho. Coregoninae and Thymallinae are resolved as sister taxa, although conflicting topologies are found across analytical strategies. We find inconsistent and generally low support for the monophyly of Coregonus, including in results of analyses with the most extensive dataset and complex model. The most consistent placement of Parahucho is as sister lineage of Salmo.
bibliographic citation: Campbell et al. (2020) Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships. PeerJ 8:e9389 https://doi.org/10.7717/peerj.9389
date submitted: 2020-02-03
date accepted: 2020-05-28
issued: 2020-07-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Campbell
  given name: Matthew A.
author list: Agent
  family name: Buser
  given name: Thaddaeus J.
author list: Agent
  family name: Alfaro
  given name: Michael E.
author list: Agent
  family name: López
  given name: J. Andrés
doi: 10.7717/peerj.9389
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-03
copyright: © 2020 Campbell et al.
attribution name: Campbell et al.

A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genus Microhyla (Amphibia: Microhylidae)
type: item
type: AcademicArticle
description: Frogs of the genus Microhyla include some of the world’s smallest amphibians and represent the largest radiation of Asian microhylids, currently encompassing 50 species, distributed across the Oriental biogeographic region. The genus Microhyla remains one of the taxonomically most challenging groups of Asian frogs and was found to be paraphyletic with respect to large-sized fossorial Glyphoglossus. In this study we present a time-calibrated phylogeny for frogs in the genus Microhyla, and discuss taxonomy, historical biogeography, and morphological evolution of these frogs. Our updated phylogeny of the genus with nearly complete taxon sampling includes 48 nominal Microhyla species and several undescribed candidate species. Phylogenetic analyses of 3,207 bp of combined mtDNA and nuDNA data recovered three well-supported groups: the Glyphoglossus clade, Southeast Asian Microhyla II clade (includes M. annectens species group), and a diverse Microhyla I clade including all other species. Within the largest major clade of Microhyla are seven well-supported subclades that we identify as the M. achatina, M. fissipes, M. berdmorei, M. superciliaris, M. ornata, M. butleri, and M. palmipes species groups. The phylogenetic position of 12 poorly known Microhyla species is clarified for the first time. These phylogenetic results, along with molecular clock and ancestral area analyses, show the Microhyla—Glyphoglossus assemblage to have originated in Southeast Asia in the middle Eocene just after the first hypothesized land connections between the Indian Plate and the Asian mainland. While Glyphoglossus and Microhyla II remained within their ancestral ranges, Microhyla I expanded its distribution generally east to west, colonizing and diversifying through the Cenozoic. The Indian Subcontinent was colonized by members of five Microhyla species groups independently, starting with the end Oligocene—early Miocene that coincides with an onset of seasonally dry climates in South Asia. B…
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creator: Vladislav A. Gorin
creator: Evgeniya N. Solovyeva
creator: Mahmudul Hasan
creator: Hisanori Okamiya
creator: D.M.S. Suranjan Karunarathna
creator: Parinya Pawangkhanant
creator: Anslem de Silva
creator: Watinee Juthong
creator: Konstantin D. Milto
creator: Luan Thanh Nguyen
creator: Chatmongkon Suwannapoom
creator: Alexander Haas
creator: David P. Bickford
creator: Indraneil Das
creator: Nikolay A. Poyarkov
subject: Biodiversity
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9411
publisher: PeerJ Inc.
rights: © 2020 Gorin et al.
abstract: Frogs of the genus Microhyla include some of the world’s smallest amphibians and represent the largest radiation of Asian microhylids, currently encompassing 50 species, distributed across the Oriental biogeographic region. The genus Microhyla remains one of the taxonomically most challenging groups of Asian frogs and was found to be paraphyletic with respect to large-sized fossorial Glyphoglossus. In this study we present a time-calibrated phylogeny for frogs in the genus Microhyla, and discuss taxonomy, historical biogeography, and morphological evolution of these frogs. Our updated phylogeny of the genus with nearly complete taxon sampling includes 48 nominal Microhyla species and several undescribed candidate species. Phylogenetic analyses of 3,207 bp of combined mtDNA and nuDNA data recovered three well-supported groups: the Glyphoglossus clade, Southeast Asian Microhyla II clade (includes M. annectens species group), and a diverse Microhyla I clade including all other species. Within the largest major clade of Microhyla are seven well-supported subclades that we identify as the M. achatina, M. fissipes, M. berdmorei, M. superciliaris, M. ornata, M. butleri, and M. palmipes species groups. The phylogenetic position of 12 poorly known Microhyla species is clarified for the first time. These phylogenetic results, along with molecular clock and ancestral area analyses, show the Microhyla—Glyphoglossus assemblage to have originated in Southeast Asia in the middle Eocene just after the first hypothesized land connections between the Indian Plate and the Asian mainland. While Glyphoglossus and Microhyla II remained within their ancestral ranges, Microhyla I expanded its distribution generally east to west, colonizing and diversifying through the Cenozoic. The Indian Subcontinent was colonized by members of five Microhyla species groups independently, starting with the end Oligocene—early Miocene that coincides with an onset of seasonally dry climates in South Asia. B…
bibliographic citation: Gorin et al. (2020) A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genus Microhyla (Amphibia: Microhylidae). PeerJ 8:e9411 https://doi.org/10.7717/peerj.9411
date submitted: 2020-02-27
date accepted: 2020-06-03
issued: 2020-07-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gorin
  given name: Vladislav A.
author list: Agent
  family name: Solovyeva
  given name: Evgeniya N.
author list: Agent
  family name: Hasan
  given name: Mahmudul
author list: Agent
  family name: Okamiya
  given name: Hisanori
author list: Agent
  family name: Karunarathna
  given name: D.M.S. Suranjan
author list: Agent
  family name: Pawangkhanant
  given name: Parinya
author list: Agent
  family name: de Silva
  given name: Anslem
author list: Agent
  family name: Juthong
  given name: Watinee
author list: Agent
  family name: Milto
  given name: Konstantin D.
author list: Agent
  family name: Nguyen
  given name: Luan Thanh
author list: Agent
  family name: Suwannapoom
  given name: Chatmongkon
author list: Agent
  family name: Haas
  given name: Alexander
author list: Agent
  family name: Bickford
  given name: David P.
author list: Agent
  family name: Das
  given name: Indraneil
author list: Agent
  family name: Poyarkov
  given name: Nikolay A.
doi: 10.7717/peerj.9411
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-03
copyright: © 2020 Gorin et al.
attribution name: Gorin et al.

The impact of short-term exposure to near shore stressors on the early life stages of the reef building coral Montipora capitata
type: item
type: AcademicArticle
description: Successful reproduction and survival are crucial to the continuation and resilience of corals globally. As reef waters warm due to climate change, episodic largescale tropical storms are becoming more frequent, drastically altering the near shore water quality for short periods of time. Therefore, it is critical that we understand the effects warming waters, fresh water input, and run-off have on sexual reproduction of coral. To better understand the effects of these near shore stressors on Hawaiian coral, laboratory experiments were conducted at the Institute of Marine Biology to determine the independent effects of suspended sediment concentrations (100 mg l−1 and 200 mg l−1), lowered salinity (28‰), and elevated temperature (31 °C) on the successful fertilization, larval survival, and settlement of the scleractinian coral Montipora capitata. In the present study, early developmental stages of coral were exposed to one of three near shore stressors for a period of 24 h and the immediate (fertilization) and latent effects (larval survival and settlement) were observed and measured. Fertilization success and settlement were not affected by any of the treatments; however, larval survival was negatively affected by all of the treatments by 50% or greater (p > 0.05). These data show that early life stages of M. capitata may be impacted by near shore stressors associated with warming and more frequent storm events.
format: application/pdf
format: text/html
creator: Claire V.A. Lager
creator: Mary Hagedorn
creator: Kuʻulei S. Rodgers
creator: Paul L. Jokiel
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.9415
publisher: PeerJ Inc.
rights: © 2020 Lager et al.
abstract: Successful reproduction and survival are crucial to the continuation and resilience of corals globally. As reef waters warm due to climate change, episodic largescale tropical storms are becoming more frequent, drastically altering the near shore water quality for short periods of time. Therefore, it is critical that we understand the effects warming waters, fresh water input, and run-off have on sexual reproduction of coral. To better understand the effects of these near shore stressors on Hawaiian coral, laboratory experiments were conducted at the Institute of Marine Biology to determine the independent effects of suspended sediment concentrations (100 mg l−1 and 200 mg l−1), lowered salinity (28‰), and elevated temperature (31 °C) on the successful fertilization, larval survival, and settlement of the scleractinian coral Montipora capitata. In the present study, early developmental stages of coral were exposed to one of three near shore stressors for a period of 24 h and the immediate (fertilization) and latent effects (larval survival and settlement) were observed and measured. Fertilization success and settlement were not affected by any of the treatments; however, larval survival was negatively affected by all of the treatments by 50% or greater (p > 0.05). These data show that early life stages of M. capitata may be impacted by near shore stressors associated with warming and more frequent storm events.
bibliographic citation: Lager et al. (2020) The impact of short-term exposure to near shore stressors on the early life stages of the reef building coral Montipora capitata. PeerJ 8:e9415 https://doi.org/10.7717/peerj.9415
date submitted: 2019-11-20
date accepted: 2020-06-03
issued: 2020-07-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lager
  given name: Claire V.A.
author list: Agent
  family name: Hagedorn
  given name: Mary
author list: Agent
  family name: S. Rodgers
  given name: Kuʻulei
author list: Agent
  family name: Jokiel
  given name: Paul L.
doi: 10.7717/peerj.9415
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-03
copyright: ©2020 Lager et al.
attribution name: Lager et al.

A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains
type: item
type: AcademicArticle
description: Background Chrysanthemum boreale Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental and medicinal importance. We characterized and compared the chloroplast genomes of three C. boreale strains. These were collected from different geographic regions of Korea and varied in floral morphology. Methods The chloroplast genomes were obtained by next-generation sequencing techniques, assembled de novo, annotated, and compared with one another. Phylogenetic analysis placed them within the Anthemideae tribe. Results The sizes of the complete chloroplast genomes of the C. boreale strains were 151,012 bp (strain 121002), 151,098 bp (strain IT232531) and 151,010 bp (strain IT301358). Each genome contained 80 unique protein-coding genes, 4 rRNA genes and 29 tRNA genes. Comparative analyses revealed a high degree of conservation in the overall sequence, gene content, gene order and GC content among the strains. We identified 298 single nucleotide polymorphisms (SNPs) and 106 insertions/deletions (indels) in the chloroplast genomes. These variations were more abundant in non-coding regions than in coding regions. Long dispersed repeats and simple sequence repeats were present in both coding and noncoding regions, with greater frequency in the latter. Regardless of their location, these repeats can be used for molecular marker development. Phylogenetic analysis revealed the evolutionary relationship of the species in the Anthemideae tribe. The three complete chloroplast genomes will be valuable genetic resources for studying the population genetics and evolutionary relationships of Asteraceae species.
format: application/pdf
format: text/html
creator: Swati Tyagi
creator: Jae-A Jung
creator: Jung Sun Kim
creator: So Youn Won
subject: Agricultural Science
subject: Genomics
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.9448
publisher: PeerJ Inc.
rights: © 2020 Tyagi et al.
abstract: Background Chrysanthemum boreale Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental and medicinal importance. We characterized and compared the chloroplast genomes of three C. boreale strains. These were collected from different geographic regions of Korea and varied in floral morphology. Methods The chloroplast genomes were obtained by next-generation sequencing techniques, assembled de novo, annotated, and compared with one another. Phylogenetic analysis placed them within the Anthemideae tribe. Results The sizes of the complete chloroplast genomes of the C. boreale strains were 151,012 bp (strain 121002), 151,098 bp (strain IT232531) and 151,010 bp (strain IT301358). Each genome contained 80 unique protein-coding genes, 4 rRNA genes and 29 tRNA genes. Comparative analyses revealed a high degree of conservation in the overall sequence, gene content, gene order and GC content among the strains. We identified 298 single nucleotide polymorphisms (SNPs) and 106 insertions/deletions (indels) in the chloroplast genomes. These variations were more abundant in non-coding regions than in coding regions. Long dispersed repeats and simple sequence repeats were present in both coding and noncoding regions, with greater frequency in the latter. Regardless of their location, these repeats can be used for molecular marker development. Phylogenetic analysis revealed the evolutionary relationship of the species in the Anthemideae tribe. The three complete chloroplast genomes will be valuable genetic resources for studying the population genetics and evolutionary relationships of Asteraceae species.
bibliographic citation: Tyagi et al. (2020) A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains. PeerJ 8:e9448 https://doi.org/10.7717/peerj.9448
date submitted: 2020-03-13
date accepted: 2020-06-09
issued: 2020-07-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tyagi
  given name: Swati
author list: Agent
  family name: Jung
  given name: Jae-A
author list: Agent
  family name: Kim
  given name: Jung Sun
author list: Agent
  family name: Won
  given name: So Youn
doi: 10.7717/peerj.9448
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-03
copyright: © 2020 Tyagi et al.
attribution name: Tyagi et al.

Treating coral bleaching as weather: a framework to validate and optimize prediction skill
type: item
type: AcademicArticle
description: Few coral reefs remain unscathed by mass bleaching over the past several decades, and much of the coral reef science conducted today relates in some way to the causes, consequences, or recovery pathways of bleaching events. Most studies portray a simple cause and effect relationship between anomalously high summer temperatures and bleaching, which is understandable given that bleaching rarely occurs outside these unusually warm times. However, the statistical skill with which temperature captures bleaching is hampered by many “false alarms”, times when temperatures reached nominal bleaching levels, but bleaching did not occur. While these false alarms are often not included in global bleaching assessments, they offer valuable opportunities to improve predictive skill, and therefore understanding, of coral bleaching events. Here, I show how a statistical framework adopted from weather forecasting can optimize bleaching predictions and validate which environmental factors play a role in bleaching susceptibility. Removing the 1 °C above the maximum monthly mean cutoff in the typical degree heating weeks (DHW) definition, adjusting the DHW window from 12 to 9 weeks, using regional-specific DHW thresholds, and including an El Niño threshold already improves the model skill by 45%. Most importantly, this framework enables hypothesis testing of other factors or metrics that may improve our ability to forecast coral bleaching events.
format: application/pdf
format: text/html
creator: Thomas M. DeCarlo
subject: Conservation Biology
subject: Marine Biology
subject: Zoology
subject: Climate Change Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.9449
publisher: PeerJ Inc.
rights: © 2020 DeCarlo
abstract: Few coral reefs remain unscathed by mass bleaching over the past several decades, and much of the coral reef science conducted today relates in some way to the causes, consequences, or recovery pathways of bleaching events. Most studies portray a simple cause and effect relationship between anomalously high summer temperatures and bleaching, which is understandable given that bleaching rarely occurs outside these unusually warm times. However, the statistical skill with which temperature captures bleaching is hampered by many “false alarms”, times when temperatures reached nominal bleaching levels, but bleaching did not occur. While these false alarms are often not included in global bleaching assessments, they offer valuable opportunities to improve predictive skill, and therefore understanding, of coral bleaching events. Here, I show how a statistical framework adopted from weather forecasting can optimize bleaching predictions and validate which environmental factors play a role in bleaching susceptibility. Removing the 1 °C above the maximum monthly mean cutoff in the typical degree heating weeks (DHW) definition, adjusting the DHW window from 12 to 9 weeks, using regional-specific DHW thresholds, and including an El Niño threshold already improves the model skill by 45%. Most importantly, this framework enables hypothesis testing of other factors or metrics that may improve our ability to forecast coral bleaching events.
bibliographic citation: DeCarlo (2020) Treating coral bleaching as weather: a framework to validate and optimize prediction skill. PeerJ 8:e9449 https://doi.org/10.7717/peerj.9449
date submitted: 2020-05-05
date accepted: 2020-06-09
issued: 2020-07-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: DeCarlo
  given name: Thomas M.
doi: 10.7717/peerj.9449
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-03
copyright: ©2020 DeCarlo
attribution name: DeCarlo

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