PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Transitional evolutionary forms in chasmosaurine ceratopsid dinosaurs: evidence from the Campanian of New Mexico
items: Assessment of methods used for 3-dimensional superimposition of craniofacial skeletal structures: a systematic review
items: Immune priming against bacteria in spiders and scorpions?
items: Profiling lysophosphatidic acid levels in plasma from head and neck cancer patients
items: Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection
items: Comparative study of gut microbiota in Tibetan wild asses (Equus kiang) and domestic donkeys (Equus asinus) on the Qinghai-Tibet plateau
items: Evidence of overfishing of geoduck clam Panopea globosa from a length-based stock assessment approach
items: Genome-wide sequence identification and expression analysis of ARF family in sugar beet (Beta vulgaris L.) under salinity stresses
items: A high-resolution growth series of Tyrannosaurus rex obtained from multiple lines of evidence
items: Bee diversity in secondary forests and coffee plantations in a transition between foothills and highlands in the Guatemalan Pacific Coast

Transitional evolutionary forms in chasmosaurine ceratopsid dinosaurs: evidence from the Campanian of New Mexico
type: item
type: AcademicArticle
description: Three new chasmosaurines from the Kirtland Formation (~75.0–73.4 Ma), New Mexico, form morphological and stratigraphic intermediates between Pentaceratops (~74.7–75 Ma, Fruitland Formation, New Mexico) and Anchiceratops (~72–71 Ma, Horseshoe Canyon Formation, Alberta). The new specimens exhibit gradual enclosure of the parietal embayment that characterizes Pentaceratops, providing support for the phylogenetic hypothesis that Pentaceratops and Anchiceratops are closely related. This stepwise change of morphologic characters observed in chasmosaurine taxa that do not overlap stratigraphically is supportive of evolution by anagenesis. Recently published hypotheses that place Pentaceratops and Anchiceratops into separate clades are not supported. This phylogenetic relationship demonstrates unrestricted movement of large-bodied taxa between hitherto purported northern and southern provinces in the late Campanian, weakening support for the hypothesis of extreme faunal provincialism in the Late Cretaceous Western Interior.
format: application/pdf
format: text/html
creator: Denver W. Fowler
creator: Elizabeth A. Freedman Fowler
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.9251
publisher: PeerJ Inc.
rights: © 2020 Fowler and Freedman Fowler
abstract: Three new chasmosaurines from the Kirtland Formation (~75.0–73.4 Ma), New Mexico, form morphological and stratigraphic intermediates between Pentaceratops (~74.7–75 Ma, Fruitland Formation, New Mexico) and Anchiceratops (~72–71 Ma, Horseshoe Canyon Formation, Alberta). The new specimens exhibit gradual enclosure of the parietal embayment that characterizes Pentaceratops, providing support for the phylogenetic hypothesis that Pentaceratops and Anchiceratops are closely related. This stepwise change of morphologic characters observed in chasmosaurine taxa that do not overlap stratigraphically is supportive of evolution by anagenesis. Recently published hypotheses that place Pentaceratops and Anchiceratops into separate clades are not supported. This phylogenetic relationship demonstrates unrestricted movement of large-bodied taxa between hitherto purported northern and southern provinces in the late Campanian, weakening support for the hypothesis of extreme faunal provincialism in the Late Cretaceous Western Interior.
bibliographic citation: Fowler et al. (2020) Transitional evolutionary forms in chasmosaurine ceratopsid dinosaurs: evidence from the Campanian of New Mexico. PeerJ 8:e9251 https://doi.org/10.7717/peerj.9251
date submitted: 2019-11-20
date accepted: 2020-05-07
issued: 2020-06-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fowler
  given name: Denver W.
author list: Agent
  family name: Freedman Fowler
  given name: Elizabeth A.
doi: 10.7717/peerj.9251
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-05
copyright: © 2020 Fowler and Freedman Fowler
attribution name: Fowler and Freedman Fowler

Assessment of methods used for 3-dimensional superimposition of craniofacial skeletal structures: a systematic review
type: item
type: AcademicArticle
description: Background So far, several techniques have been recommended for the assessment of craniofacial changes through skeletal tissue superimposition, but the evidence that supports them remains unexplored. The purpose of the present study is to assess the available literature on skeletal-tissue superimpositions of serial craniofacial CT or CBCT images used to detect morphological changes. Materials and Methods Medline (via Pubmed), EMBASE, Google Scholar, Cochrane Library, Open Grey and Grey Literature Report were searched (last search: 17.11.2019) using specific terms that fulfilled the requirements of each database in the context of the study aim. Hand searches were also performed. The outcomes of interest were the accuracy, precision, or agreement between skeletal-tissue superimposition techniques to assess changes in the morphology of craniofacial structures. Studies of any design with sample size ≥3 were assessed by two authors independently. The study protocol was registered in PROSPERO (ID: CRD42019143356). Results Out of 832 studies, fifteen met the eligibility criteria. From the 15 included studies, 12 have shown high total risk of bias, one low risk of bias, and two studies have shown unclear risk of bias. Thirteen out of the 15 studies showed high applicability concerns, two unclear and no study had low applicability concerns. There was high heterogeneity among studies regarding the type of participants, sample size, growth status, machines, acquisition parameters, superimposition techniques, assessment techniques and outcomes measured. Fourteen of them were performed on Cone Beam Computed Tomography (CBCT) and one on Computed Tomography (CT) derived 3D models. Most of the studies (eleven) used voxel-based registration, one landmark-based registration and three studies compared different registration techniques, which include the surface-based registration. Concerning the area of interest, nine studies focused on the anterior cranial base and certain facial str…
format: application/pdf
format: text/html
creator: Daniel Dinh-Phuc Mai
creator: Sven Stucki
creator: Nikolaos Gkantidis
subject: Dentistry
subject: Radiology and Medical Imaging
subject: Computational Science
description: doi:10.7717/peerj.9263
publisher: PeerJ Inc.
rights: © 2020 Mai et al.
abstract: Background So far, several techniques have been recommended for the assessment of craniofacial changes through skeletal tissue superimposition, but the evidence that supports them remains unexplored. The purpose of the present study is to assess the available literature on skeletal-tissue superimpositions of serial craniofacial CT or CBCT images used to detect morphological changes. Materials and Methods Medline (via Pubmed), EMBASE, Google Scholar, Cochrane Library, Open Grey and Grey Literature Report were searched (last search: 17.11.2019) using specific terms that fulfilled the requirements of each database in the context of the study aim. Hand searches were also performed. The outcomes of interest were the accuracy, precision, or agreement between skeletal-tissue superimposition techniques to assess changes in the morphology of craniofacial structures. Studies of any design with sample size ≥3 were assessed by two authors independently. The study protocol was registered in PROSPERO (ID: CRD42019143356). Results Out of 832 studies, fifteen met the eligibility criteria. From the 15 included studies, 12 have shown high total risk of bias, one low risk of bias, and two studies have shown unclear risk of bias. Thirteen out of the 15 studies showed high applicability concerns, two unclear and no study had low applicability concerns. There was high heterogeneity among studies regarding the type of participants, sample size, growth status, machines, acquisition parameters, superimposition techniques, assessment techniques and outcomes measured. Fourteen of them were performed on Cone Beam Computed Tomography (CBCT) and one on Computed Tomography (CT) derived 3D models. Most of the studies (eleven) used voxel-based registration, one landmark-based registration and three studies compared different registration techniques, which include the surface-based registration. Concerning the area of interest, nine studies focused on the anterior cranial base and certain facial str…
bibliographic citation: Mai et al. (2020) Assessment of methods used for 3-dimensional superimposition of craniofacial skeletal structures: a systematic review. PeerJ 8:e9263 https://doi.org/10.7717/peerj.9263
date submitted: 2020-03-09
date accepted: 2020-05-09
issued: 2020-06-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mai
  given name: Daniel Dinh-Phuc
author list: Agent
  family name: Stucki
  given name: Sven
author list: Agent
  family name: Gkantidis
  given name: Nikolaos
doi: 10.7717/peerj.9263
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-05
copyright: ©2020 Mai et al.
attribution name: Mai et al.

Immune priming against bacteria in spiders and scorpions?
type: item
type: AcademicArticle
description: Empirical evidence of immune priming in arthropods keeps growing, both at the within- and trans-generational level. The evidence comes mostly from work on insects and it remains unclear for some other arthropods whether exposure to a non-lethal dose of a pathogen provides protection during a second exposure with a lethal dose. A poorly investigated group are arachnids, with regard to the benefits of immune priming measured as improved survival. Here, we investigated immune priming in two arachnids: the wolf spider Lycosa cerrofloresiana and the scorpion Centruroides granosus. We injected a third of the individuals with lipopolysaccharides of Escherichia coli (LPS, an immune elicitor), another third were injected with the control solution (PBS) and the other third were kept naive. Four days after the first inoculations, we challenged half of the individuals of each group with an injection of a high dose of E. coli and the other half was treated with the control solution. For scorpions, individuals that were initially injected with PBS or LPS did not differ in their survival rates against the bacterial challenge. Individuals injected with LPS showed higher survival than that of naive individuals as evidence of immune priming. Individuals injected with PBS tended to show higher survival rates than naive individuals, but the difference was not significant—perhaps suggesting a general immune upregulation caused by the wounding done by the needle. For spiders, we did not observe evidence of priming, the bacterial challenge reduced the survival of naive, PBS and LPS individuals at similar rates. Moreover; for scorpions, we performed antibacterial assays of hemolymph samples from the three priming treatments (LPS, PBS and naive) and found that the three treatments reduced bacterial growth but without differences among treatments. As non-model organisms, with some unique differences in their immunological mechanisms as compared to the most studied arthropods (insects), arach…
format: application/pdf
format: text/html
creator: Dumas Gálvez
creator: Yostin Añino
creator: Carlos Vega
creator: Eleodoro Bonilla
subject: Ecology
subject: Entomology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.9285
publisher: PeerJ Inc.
rights: © 2020 Gálvez et al.
abstract: Empirical evidence of immune priming in arthropods keeps growing, both at the within- and trans-generational level. The evidence comes mostly from work on insects and it remains unclear for some other arthropods whether exposure to a non-lethal dose of a pathogen provides protection during a second exposure with a lethal dose. A poorly investigated group are arachnids, with regard to the benefits of immune priming measured as improved survival. Here, we investigated immune priming in two arachnids: the wolf spider Lycosa cerrofloresiana and the scorpion Centruroides granosus. We injected a third of the individuals with lipopolysaccharides of Escherichia coli (LPS, an immune elicitor), another third were injected with the control solution (PBS) and the other third were kept naive. Four days after the first inoculations, we challenged half of the individuals of each group with an injection of a high dose of E. coli and the other half was treated with the control solution. For scorpions, individuals that were initially injected with PBS or LPS did not differ in their survival rates against the bacterial challenge. Individuals injected with LPS showed higher survival than that of naive individuals as evidence of immune priming. Individuals injected with PBS tended to show higher survival rates than naive individuals, but the difference was not significant—perhaps suggesting a general immune upregulation caused by the wounding done by the needle. For spiders, we did not observe evidence of priming, the bacterial challenge reduced the survival of naive, PBS and LPS individuals at similar rates. Moreover; for scorpions, we performed antibacterial assays of hemolymph samples from the three priming treatments (LPS, PBS and naive) and found that the three treatments reduced bacterial growth but without differences among treatments. As non-model organisms, with some unique differences in their immunological mechanisms as compared to the most studied arthropods (insects), arach…
bibliographic citation: Gálvez et al. (2020) Immune priming against bacteria in spiders and scorpions?. PeerJ 8:e9285 https://doi.org/10.7717/peerj.9285
date submitted: 2020-02-20
date accepted: 2020-05-12
issued: 2020-06-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Gálvez
  given name: Dumas
author list: Agent
  family name: Añino
  given name: Yostin
author list: Agent
  family name: Vega
  given name: Carlos
author list: Agent
  family name: Bonilla
  given name: Eleodoro
doi: 10.7717/peerj.9285
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-05
copyright: ©2020 Gálvez et al.
attribution name: Gálvez et al.

Profiling lysophosphatidic acid levels in plasma from head and neck cancer patients
type: item
type: AcademicArticle
description: Head and neck squamous cell carcinoma (HNSCC) represents a significant world health problem, with approximately 600,000 new cases being diagnosed annually. The prognosis for patients with HNSCC is poor and, therefore, the identification of biomarkers for screening, diagnosis and prognostication would be clinically beneficial. A limited number of studies have used lipidomics to profile lipid species in the plasma of cancer patients. However, the profile and levels of lysophosphatidic acid (LPA) species have not been examined in HNSCC. In this study, a targeted lipidomics approach using liquid chromatography triple quadrupole mass spectrometry (LCMS/MS) was used to analyse the concentration of LPA (16:0 LPA, 18:0 LPA, 18:1 LPA, 18:2 LPA and 20:4 LPA) in the plasma of patients with oral squamous cell carcinoma (OSCC) and nasopharyngeal carcinoma (NPC), together with healthy controls. The levels of three LPA species (18:1 LPA, 18:2 LPA and 20:4 LPA) were significantly lower in the plasma of OSCC patients, whilst the concentrations of all five LPA species tested were significantly lower in plasma from NPC patients. Furthermore, the order of abundance of LPA species in plasma was different between the control and cancer groups, with 16:0 LPA, 18:0 LPA levels being more abundant in OSCC and NPC patients. Medium to strong correlations were observed using all pairs of LPA species and a clear separation of the normal and tumour groups was observed using PCA analysis. In summary, the results of this study showed that the levels of several LPA species in the plasma of patients with OSCC and NPC were lower than those from healthy individuals. Understanding these variations may provide novel insights into the role of LPA in these cancers.
format: application/pdf
format: text/html
creator: Mariati Abdul Rahman
creator: Didi Erwandi Mohamad Haron
creator: Robert J. Hollows
creator: Zuleen Delina Fasya Abdul Ghani
creator: Mustafa Ali Mohd
creator: Wen Lin Chai
creator: Ching Ching Ng
creator: Munn Sann Lye
creator: Saiful Anuar Karsani
creator: Lee Fah Yap
creator: Ian C. Paterson
subject: Biochemistry
subject: Oncology
description: doi:10.7717/peerj.9304
publisher: PeerJ Inc.
rights: © 2020 Abdul Rahman et al.
abstract: Head and neck squamous cell carcinoma (HNSCC) represents a significant world health problem, with approximately 600,000 new cases being diagnosed annually. The prognosis for patients with HNSCC is poor and, therefore, the identification of biomarkers for screening, diagnosis and prognostication would be clinically beneficial. A limited number of studies have used lipidomics to profile lipid species in the plasma of cancer patients. However, the profile and levels of lysophosphatidic acid (LPA) species have not been examined in HNSCC. In this study, a targeted lipidomics approach using liquid chromatography triple quadrupole mass spectrometry (LCMS/MS) was used to analyse the concentration of LPA (16:0 LPA, 18:0 LPA, 18:1 LPA, 18:2 LPA and 20:4 LPA) in the plasma of patients with oral squamous cell carcinoma (OSCC) and nasopharyngeal carcinoma (NPC), together with healthy controls. The levels of three LPA species (18:1 LPA, 18:2 LPA and 20:4 LPA) were significantly lower in the plasma of OSCC patients, whilst the concentrations of all five LPA species tested were significantly lower in plasma from NPC patients. Furthermore, the order of abundance of LPA species in plasma was different between the control and cancer groups, with 16:0 LPA, 18:0 LPA levels being more abundant in OSCC and NPC patients. Medium to strong correlations were observed using all pairs of LPA species and a clear separation of the normal and tumour groups was observed using PCA analysis. In summary, the results of this study showed that the levels of several LPA species in the plasma of patients with OSCC and NPC were lower than those from healthy individuals. Understanding these variations may provide novel insights into the role of LPA in these cancers.
bibliographic citation: Abdul Rahman et al. (2020) Profiling lysophosphatidic acid levels in plasma from head and neck cancer patients. PeerJ 8:e9304 https://doi.org/10.7717/peerj.9304
date submitted: 2020-02-18
date accepted: 2020-05-15
issued: 2020-06-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdul Rahman
  given name: Mariati
author list: Agent
  family name: Mohamad Haron
  given name: Didi Erwandi
author list: Agent
  family name: Hollows
  given name: Robert J.
author list: Agent
  family name: Abdul Ghani
  given name: Zuleen Delina Fasya
author list: Agent
  family name: Ali Mohd
  given name: Mustafa
author list: Agent
  family name: Chai
  given name: Wen Lin
author list: Agent
  family name: Ng
  given name: Ching Ching
author list: Agent
  family name: Lye
  given name: Munn Sann
author list: Agent
  family name: Karsani
  given name: Saiful Anuar
author list: Agent
  family name: Yap
  given name: Lee Fah
author list: Agent
  family name: Paterson
  given name: Ian C.
doi: 10.7717/peerj.9304
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-05
copyright: ©2020 Abdul Rahman et al.
attribution name: Abdul Rahman et al.

Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection
type: item
type: AcademicArticle
description: MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression found in more than 200 diverse organisms. Although it is still not fully established if RNA viruses could generate miRNAs, there are examples of miRNA like sequences from RNA viruses with regulatory functions. In the case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with viral replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA-based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Overall, 950 hairpin structured sequences were extracted from the virus genome and based on the prediction results, 29 of them could be precursor miRNAs. Targeting analysis showed that 30 viral mature miRNA-like sequences could target 1,367 different human genes. PANTHER gene function analysis results indicated that viral derived miRNA candidates could target various human genes involved in crucial cellular processes including transcription, metabolism, defense system and several signaling pathways such as Wnt and EGFR signalings. Protein class-based grouping of targeted human genes showed that host transcription might be one of the main targets of the virus since 96 genes involved in transcriptional processes were potential targets of predicted viral miRNAs. For instance, basal transcription machinery elements including several components of human mediator complex (MED1, MED9, MED12L, MED19), basal transcription factors such as TAF4, TAF5, TAF7L and site-specific transcription factors such as STAT1 were found to be targeted. In addition, many known human miRNAs appeared to be able to target viral genes involved in viral life cycle such as S, M, N, E proteins and ORF1ab, ORF3a, ORF8, ORF7a an…
format: application/pdf
format: text/html
creator: Müşerref Duygu Saçar Demirci
creator: Aysun Adan
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Virology
subject: Infectious Diseases
description: doi:10.7717/peerj.9369
publisher: PeerJ Inc.
rights: © 2020 Saçar Demirci and Adan
abstract: MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression found in more than 200 diverse organisms. Although it is still not fully established if RNA viruses could generate miRNAs, there are examples of miRNA like sequences from RNA viruses with regulatory functions. In the case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with viral replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA-based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Overall, 950 hairpin structured sequences were extracted from the virus genome and based on the prediction results, 29 of them could be precursor miRNAs. Targeting analysis showed that 30 viral mature miRNA-like sequences could target 1,367 different human genes. PANTHER gene function analysis results indicated that viral derived miRNA candidates could target various human genes involved in crucial cellular processes including transcription, metabolism, defense system and several signaling pathways such as Wnt and EGFR signalings. Protein class-based grouping of targeted human genes showed that host transcription might be one of the main targets of the virus since 96 genes involved in transcriptional processes were potential targets of predicted viral miRNAs. For instance, basal transcription machinery elements including several components of human mediator complex (MED1, MED9, MED12L, MED19), basal transcription factors such as TAF4, TAF5, TAF7L and site-specific transcription factors such as STAT1 were found to be targeted. In addition, many known human miRNAs appeared to be able to target viral genes involved in viral life cycle such as S, M, N, E proteins and ORF1ab, ORF3a, ORF8, ORF7a an…
bibliographic citation: Saçar Demirci et al. (2020) Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection. PeerJ 8:e9369 https://doi.org/10.7717/peerj.9369
date submitted: 2020-04-08
date accepted: 2020-05-26
issued: 2020-06-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saçar Demirci
  given name: Müşerref Duygu
author list: Agent
  family name: Adan
  given name: Aysun
doi: 10.7717/peerj.9369
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-05
copyright: © 2020 Saçar Demirci and Adan
attribution name: Saçar Demirci and Adan

Comparative study of gut microbiota in Tibetan wild asses (Equus kiang) and domestic donkeys (Equus asinus) on the Qinghai-Tibet plateau
type: item
type: AcademicArticle
description: Tibetan wild asses (Equus Kiang) are the only wild species of perissodactyls on the Qinghai-Tibet Plateau and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. Therefore, understanding the gut microbiota composition and function of wild asses can provide a theoretical for the situ conservation of wild animals in the future.In this study, we measured the dry matter digestion by the 4 molar hydrochloric acid (4N HCL) acid-insoluble ash method and analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA genes in V3–V4 regions. The results showed that the dry matter digestion in wild asses was significantly higher than in domestic donkeys (P < 0.05). No significant difference in alpha diversity was detected between these two groups. Beta diversity showed that the bacterial community structure of wild asses was acutely different from domestic donkeys. At the phylum level, the two dominant phyla Bacteroidetes and Firmicutes in wild asses were significantly higher than that in domestic donkeys. At the genus level, Ruminococcaceae_NK4A214, Phascolarctobacterium, Coprostanoligenes_group, Lachnospiraceae_XPB1014_group and Akkermansia in wild asses were significantly higher than in domestic donkeys. Moreover, statistical comparisons showed that 40 different metabolic pathways exhibited significant differences. Among them, 29 pathways had richer concentrations in wild asses than domestic donkeys, mainly included amino acid metabolism, carbohydrate metabolism, and energy metabolism. Of note, network analysis showed that wild asses harbored a relatively more complex bacterial network than domestic donkeys, possibly reflecting the specific niche adaption of gut bacterial communities through species interactions. The overall results indicated that wild asses have advantages over domestic donkeys in dry matter digestion, gut microbial community composition and function,…
format: application/pdf
format: text/html
creator: Hongjin Liu
creator: Xinquan Zhao
creator: Xueping Han
creator: Shixiao Xu
creator: Liang Zhao
creator: Linyong Hu
creator: Tianwei Xu
creator: Na Zhao
creator: Xiaoling Zhang
creator: Dongdong Chen
creator: Fuquan He
creator: Xin Chen
subject: Microbiology
subject: Zoology
subject: Nutrition
description: doi:10.7717/peerj.9032
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: Tibetan wild asses (Equus Kiang) are the only wild species of perissodactyls on the Qinghai-Tibet Plateau and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. Therefore, understanding the gut microbiota composition and function of wild asses can provide a theoretical for the situ conservation of wild animals in the future.In this study, we measured the dry matter digestion by the 4 molar hydrochloric acid (4N HCL) acid-insoluble ash method and analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA genes in V3–V4 regions. The results showed that the dry matter digestion in wild asses was significantly higher than in domestic donkeys (P < 0.05). No significant difference in alpha diversity was detected between these two groups. Beta diversity showed that the bacterial community structure of wild asses was acutely different from domestic donkeys. At the phylum level, the two dominant phyla Bacteroidetes and Firmicutes in wild asses were significantly higher than that in domestic donkeys. At the genus level, Ruminococcaceae_NK4A214, Phascolarctobacterium, Coprostanoligenes_group, Lachnospiraceae_XPB1014_group and Akkermansia in wild asses were significantly higher than in domestic donkeys. Moreover, statistical comparisons showed that 40 different metabolic pathways exhibited significant differences. Among them, 29 pathways had richer concentrations in wild asses than domestic donkeys, mainly included amino acid metabolism, carbohydrate metabolism, and energy metabolism. Of note, network analysis showed that wild asses harbored a relatively more complex bacterial network than domestic donkeys, possibly reflecting the specific niche adaption of gut bacterial communities through species interactions. The overall results indicated that wild asses have advantages over domestic donkeys in dry matter digestion, gut microbial community composition and function,…
bibliographic citation: Liu et al. (2020) Comparative study of gut microbiota in Tibetan wild asses (Equus kiang) and domestic donkeys (Equus asinus) on the Qinghai-Tibet plateau. PeerJ 8:e9032 https://doi.org/10.7717/peerj.9032
date submitted: 2020-01-08
date accepted: 2020-03-31
issued: 2020-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hongjin
author list: Agent
  family name: Zhao
  given name: Xinquan
author list: Agent
  family name: Han
  given name: Xueping
author list: Agent
  family name: Xu
  given name: Shixiao
author list: Agent
  family name: Zhao
  given name: Liang
author list: Agent
  family name: Hu
  given name: Linyong
author list: Agent
  family name: Xu
  given name: Tianwei
author list: Agent
  family name: Zhao
  given name: Na
author list: Agent
  family name: Zhang
  given name: Xiaoling
author list: Agent
  family name: Chen
  given name: Dongdong
author list: Agent
  family name: He
  given name: Fuquan
author list: Agent
  family name: Chen
  given name: Xin
doi: 10.7717/peerj.9032
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-04
copyright: ©2020 Liu et al.
attribution name: Liu et al.

Evidence of overfishing of geoduck clam Panopea globosa from a length-based stock assessment approach
type: item
type: AcademicArticle
description: Stock assessment of the geoduck clam Panopea globosa in Mexico has been based on data-poor without consideration of the biological traits of the species, promoting a passive management strategy without biological reference points for its harvest and conservation, which results in limited advice regarding the sustainability of the fishery. The stock assessment was supported on an integrated catch-at-size assessment model. The model described the population changes, including recruitment, selectivity, fishing mortality, individual growth patterns and survival over time, providing management quantities for the geoduck clam fishery, such as biomass-at-length (total and vulnerable) and harvest rate-at-length. The results indicated overfishing of the geoduck clam population; the harvest rate exceeded the management tactics established for this fishery, even the individuals smaller than the minimum legal size (130 mm) were harvested. Thus, declines in the total biomass (from 3,262 to 1,130 t) and recruitment (representing an 86% decrease) were observed from 2010 to 2012. Although the results showed a recovery trend in recruitment and total biomass from 2014 to 2016, this trend may have been due to the spatial relocation of fishing mortality.
format: application/pdf
format: text/html
creator: Marlene A. Luquin-Covarrubias
creator: Enrique Morales-Bojórquez
creator: Juan A. García-Borbón
creator: Sergio Amezcua-Castro
creator: Sergio A. Pérez-Valencia
creator: Estefani Larios-Castro
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.9069
publisher: PeerJ Inc.
rights: © 2020 Luquin-Covarrubias et al.
abstract: Stock assessment of the geoduck clam Panopea globosa in Mexico has been based on data-poor without consideration of the biological traits of the species, promoting a passive management strategy without biological reference points for its harvest and conservation, which results in limited advice regarding the sustainability of the fishery. The stock assessment was supported on an integrated catch-at-size assessment model. The model described the population changes, including recruitment, selectivity, fishing mortality, individual growth patterns and survival over time, providing management quantities for the geoduck clam fishery, such as biomass-at-length (total and vulnerable) and harvest rate-at-length. The results indicated overfishing of the geoduck clam population; the harvest rate exceeded the management tactics established for this fishery, even the individuals smaller than the minimum legal size (130 mm) were harvested. Thus, declines in the total biomass (from 3,262 to 1,130 t) and recruitment (representing an 86% decrease) were observed from 2010 to 2012. Although the results showed a recovery trend in recruitment and total biomass from 2014 to 2016, this trend may have been due to the spatial relocation of fishing mortality.
bibliographic citation: Luquin-Covarrubias et al. (2020) Evidence of overfishing of geoduck clam Panopea globosa from a length-based stock assessment approach. PeerJ 8:e9069 https://doi.org/10.7717/peerj.9069
date submitted: 2019-10-16
date accepted: 2020-04-06
issued: 2020-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luquin-Covarrubias
  given name: Marlene A.
author list: Agent
  family name: Morales-Bojórquez
  given name: Enrique
author list: Agent
  family name: García-Borbón
  given name: Juan A.
author list: Agent
  family name: Amezcua-Castro
  given name: Sergio
author list: Agent
  family name: Pérez-Valencia
  given name: Sergio A.
author list: Agent
  family name: Larios-Castro
  given name: Estefani
doi: 10.7717/peerj.9069
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-04
copyright: ©2020 Luquin-Covarrubias et al.
attribution name: Luquin-Covarrubias et al.

Genome-wide sequence identification and expression analysis of ARF family in sugar beet (Beta vulgaris L.) under salinity stresses
type: item
type: AcademicArticle
description: Auxin response factor (ARF) proteins respond to biological and abiotic stresses and play important roles in regulating plant growth and development. In this study, based on the genome-wide database of sugar beet, 16 BvARF proteins were identified. A detailed investigation into the BvARF family is performed, including analysis of the conserved domains, chromosomal locations, phylogeny, exon-intron structure, conserved motifs, subcellular localization, gene ontology (GO) annotations and expression profiles of BvARF under salt-tolerant condition. The majority of BvARF proteins contain B3 domain, AUX_RESP domain and AUX/IAA domain and a few lacked of AUX/IAA domain. Phylogenetic analysis suggests that the 16 BvARF proteins are clustered into six groups. Expression profile analysis shows that most of these BvARF genes in sugar beet under salinity stress were up-regulated or down-regulated to varying degrees and nine of the BvARF genes changed significantly. They were thought to have a significant response to salinity stress. The current study provides basic information for the BvARF genes and will pave the way for further studies on the roles of BvARF genes in regulating sugar beet’s growth, development and responses to salinity stress.
format: application/pdf
format: text/html
creator: Jie Cui
creator: Xinyan Li
creator: Junliang Li
creator: Congyu Wang
creator: Dayou Cheng
creator: Cuihong Dai
subject: Agricultural Science
subject: Bioinformatics
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.9131
publisher: PeerJ Inc.
rights: © 2020 Cui et al.
abstract: Auxin response factor (ARF) proteins respond to biological and abiotic stresses and play important roles in regulating plant growth and development. In this study, based on the genome-wide database of sugar beet, 16 BvARF proteins were identified. A detailed investigation into the BvARF family is performed, including analysis of the conserved domains, chromosomal locations, phylogeny, exon-intron structure, conserved motifs, subcellular localization, gene ontology (GO) annotations and expression profiles of BvARF under salt-tolerant condition. The majority of BvARF proteins contain B3 domain, AUX_RESP domain and AUX/IAA domain and a few lacked of AUX/IAA domain. Phylogenetic analysis suggests that the 16 BvARF proteins are clustered into six groups. Expression profile analysis shows that most of these BvARF genes in sugar beet under salinity stress were up-regulated or down-regulated to varying degrees and nine of the BvARF genes changed significantly. They were thought to have a significant response to salinity stress. The current study provides basic information for the BvARF genes and will pave the way for further studies on the roles of BvARF genes in regulating sugar beet’s growth, development and responses to salinity stress.
bibliographic citation: Cui et al. (2020) Genome-wide sequence identification and expression analysis of ARF family in sugar beet (Beta vulgaris L.) under salinity stresses. PeerJ 8:e9131 https://doi.org/10.7717/peerj.9131
date submitted: 2019-05-14
date accepted: 2020-04-14
issued: 2020-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cui
  given name: Jie
author list: Agent
  family name: Li
  given name: Xinyan
author list: Agent
  family name: Li
  given name: Junliang
author list: Agent
  family name: Wang
  given name: Congyu
author list: Agent
  family name: Cheng
  given name: Dayou
author list: Agent
  family name: Dai
  given name: Cuihong
doi: 10.7717/peerj.9131
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-04
copyright: ©2020 Cui et al.
attribution name: Cui et al.

A high-resolution growth series of Tyrannosaurus rex obtained from multiple lines of evidence
type: item
type: AcademicArticle
description: Background During the growth of complex multicellular organisms, chronological age, size and morphology change together in a hierarchical and coordinated pattern. Among extinct species, the growth of Tyrannosaurus rex has received repeated attention through quantitative analyses of relative maturity and chronological age. Its growth series shows an extreme transformation from shallow skulls in juveniles to deep skulls in adults along with a reduction in tooth count, and its growth curve shows that T. rex had a high growth rate in contrast to its closest relatives. However, separately, these sets of data provide an incomplete picture of the congruence between age, size, and relative maturity in this exemplar species. The goal of this work is to analyze these data sets together using cladistic analysis to produce a single hypothesis of growth that includes all of the relevant data. Methods The three axes of growth were analyzed together using cladistic analysis, based on a data set of 1,850 morphological characters and 44 specimens. The analysis was run in TNT v.1.5 under a New Technology search followed by a Traditional search. Correlation tests were run in IBM SPSS Statistics v. 24.0.0.0. Results An initial analysis that included all of the specimens recovered 50 multiple most parsimonious ontograms a series of analyses identified 13 wildcard specimens. An analysis run without the wildcard specimens recovered a single most parsimonious tree (i.e., ontogram) of 3,053 steps. The ontogram is composed of 21 growth stages, and all but the first and third are supported by unambiguously optimized synontomorphies. T. rex ontogeny can be divided into five discrete growth categories that are diagnosed by chronological age, morphology, and, in part, size (uninformative among adults). The topology shows that the transition from shallow to deep skull shape occurred between 13 and 15 years of age, and the size of the immediate relatives of T. rex was exceeded between its 15th and…
format: application/pdf
format: text/html
creator: Thomas D. Carr
subject: Developmental Biology
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9192
publisher: PeerJ Inc.
rights: © 2020 Carr
abstract: Background During the growth of complex multicellular organisms, chronological age, size and morphology change together in a hierarchical and coordinated pattern. Among extinct species, the growth of Tyrannosaurus rex has received repeated attention through quantitative analyses of relative maturity and chronological age. Its growth series shows an extreme transformation from shallow skulls in juveniles to deep skulls in adults along with a reduction in tooth count, and its growth curve shows that T. rex had a high growth rate in contrast to its closest relatives. However, separately, these sets of data provide an incomplete picture of the congruence between age, size, and relative maturity in this exemplar species. The goal of this work is to analyze these data sets together using cladistic analysis to produce a single hypothesis of growth that includes all of the relevant data. Methods The three axes of growth were analyzed together using cladistic analysis, based on a data set of 1,850 morphological characters and 44 specimens. The analysis was run in TNT v.1.5 under a New Technology search followed by a Traditional search. Correlation tests were run in IBM SPSS Statistics v. 24.0.0.0. Results An initial analysis that included all of the specimens recovered 50 multiple most parsimonious ontograms a series of analyses identified 13 wildcard specimens. An analysis run without the wildcard specimens recovered a single most parsimonious tree (i.e., ontogram) of 3,053 steps. The ontogram is composed of 21 growth stages, and all but the first and third are supported by unambiguously optimized synontomorphies. T. rex ontogeny can be divided into five discrete growth categories that are diagnosed by chronological age, morphology, and, in part, size (uninformative among adults). The topology shows that the transition from shallow to deep skull shape occurred between 13 and 15 years of age, and the size of the immediate relatives of T. rex was exceeded between its 15th and…
bibliographic citation: Carr (2020) A high-resolution growth series of Tyrannosaurus rex obtained from multiple lines of evidence. PeerJ 8:e9192 https://doi.org/10.7717/peerj.9192
date submitted: 2019-12-04
date accepted: 2020-04-24
issued: 2020-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carr
  given name: Thomas D.
doi: 10.7717/peerj.9192
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-04
copyright: © 2020 Carr
attribution name: Carr

Bee diversity in secondary forests and coffee plantations in a transition between foothills and highlands in the Guatemalan Pacific Coast
type: item
type: AcademicArticle
description: Background Although conservation of pristine habitats is recognized in many countries as crucial for maintaining pollinator diversity, the contribution of secondary forest conservation is poorly recognized in the Latin American context, such as in Guatemala. San Lucas Tolimán (SLT) is a high-quality coffee production region from the Atitlan Province, which has the second highest deciduous forest cover in Guatemala and pristine forest is prioritized for conservation. In contrast, secondary forest protection is undetermined, since these forests are normally removed or strongly affected by coffee farming practices. This situation may affect the diversity of native pollinators, mainly bees, which usually rely on the secondary forest for food resources. Methods We conducted a study to investigate the importance of secondary forests around the SLT coffee plantations (Coffea arabica L.) for pollinators. We compared bee diversity (richness, abundance and composition) in secondary forests of different age and coffee plantations with diverse farming techniques. Being the first study of pollinators in Guatemalan coffee plantations, we also recorded data for an entire year (2013–2014) in order to describe bee seasonality. Results We found significant differences in bee diversity between the coffee plantations and secondary forests, particularly early secondary forests showed higher bee abundances but diversity indices were similar between different vegetation type plots. In the early dry season, secondary forests showed the greatest native bee diversity. During the late dry season, when the coffee was flowering, honey bees were dominant in the same plots. This study provides important management insights to support the conservation of pollinators, since our results offer guidelines to improve coffee production by increasing native pollinator diversity.
format: application/pdf
format: text/html
creator: Gabriela Armas-Quiñonez
creator: Ricardo Ayala-Barajas
creator: Carlos Avendaño-Mendoza
creator: Roberto Lindig-Cisneros
creator: Ek del-Val
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Natural Resource Management
description: doi:10.7717/peerj.9257
publisher: PeerJ Inc.
rights: © 2020 Armas-Quiñonez et al.
abstract: Background Although conservation of pristine habitats is recognized in many countries as crucial for maintaining pollinator diversity, the contribution of secondary forest conservation is poorly recognized in the Latin American context, such as in Guatemala. San Lucas Tolimán (SLT) is a high-quality coffee production region from the Atitlan Province, which has the second highest deciduous forest cover in Guatemala and pristine forest is prioritized for conservation. In contrast, secondary forest protection is undetermined, since these forests are normally removed or strongly affected by coffee farming practices. This situation may affect the diversity of native pollinators, mainly bees, which usually rely on the secondary forest for food resources. Methods We conducted a study to investigate the importance of secondary forests around the SLT coffee plantations (Coffea arabica L.) for pollinators. We compared bee diversity (richness, abundance and composition) in secondary forests of different age and coffee plantations with diverse farming techniques. Being the first study of pollinators in Guatemalan coffee plantations, we also recorded data for an entire year (2013–2014) in order to describe bee seasonality. Results We found significant differences in bee diversity between the coffee plantations and secondary forests, particularly early secondary forests showed higher bee abundances but diversity indices were similar between different vegetation type plots. In the early dry season, secondary forests showed the greatest native bee diversity. During the late dry season, when the coffee was flowering, honey bees were dominant in the same plots. This study provides important management insights to support the conservation of pollinators, since our results offer guidelines to improve coffee production by increasing native pollinator diversity.
bibliographic citation: Armas-Quiñonez et al. (2020) Bee diversity in secondary forests and coffee plantations in a transition between foothills and highlands in the Guatemalan Pacific Coast. PeerJ 8:e9257 https://doi.org/10.7717/peerj.9257
date submitted: 2020-02-25
date accepted: 2020-05-08
issued: 2020-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Armas-Quiñonez
  given name: Gabriela
author list: Agent
  family name: Ayala-Barajas
  given name: Ricardo
author list: Agent
  family name: Avendaño-Mendoza
  given name: Carlos
author list: Agent
  family name: Lindig-Cisneros
  given name: Roberto
author list: Agent
  family name: del-Val
  given name: Ek
doi: 10.7717/peerj.9257
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-04
copyright: © 2020 Armas-Quiñonez et al.
attribution name: Armas-Quiñonez et al.

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