PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing
items: An artificial neural network for automated behavioral state classification in rats
items: Plastic response of Medicago sativa L. root system traits and cold resistance to simulated rainfall events
items: Risk assessment of freezing injury during overwintering of wheat in the northern boundary of the Winter Wheat Region in China
items: CBF transcription factors involved in the cold response of Camellia japonica (Naidong)
items: High bycatch rates of manta and devil rays in the “small-scale” artisanal fisheries of Sri Lanka
items: Inter-element variation in the bone histology of Anteosaurus (Dinocephalia, Anteosauridae) from the Tapinocephalus Assemblage Zone of the Karoo Basin of South Africa
items: No adverse effect of a maternal high carbohydrate diet on their offspring, in rainbow trout (Oncorhynchus mykiss)
items: High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River
items: Whole-genome comparative analysis at the lineage/sublineage level discloses relationships between Mycobacterium tuberculosis genotype and clinical phenotype

Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing
type: item
type: AcademicArticle
description: Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydroidolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.
format: application/pdf
format: text/html
creator: Bastian Bentlage
creator: Allen G. Collins
subject: Evolutionary Studies
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12104
publisher: PeerJ Inc.
rights: © 2021 ©2021 Bentlage and Collins
abstract: Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydroidolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.
bibliographic citation: Bentlage et al. (2021) Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing. PeerJ 9:e12104 https://doi.org/10.7717/peerj.12104
date submitted: 2020-12-03
date accepted: 2021-08-11
issued: 2021-09-09
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Bentlage
  given name: Bastian
author list: Agent
  family name: Collins
  given name: Allen G.
doi: 10.7717/peerj.12104
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-09
copyright: ©2021 Bentlage and Collins
attribution name: ©2021 Bentlage and Collins

An artificial neural network for automated behavioral state classification in rats
type: item
type: AcademicArticle
description: Accurate behavioral state classification is critical for many research applications. Researchers typically rely upon manual identification of behavioral state through visual inspection of electrophysiological signals, but this approach is time intensive and subject to low inter-rater reliability. To overcome these limitations, a diverse set of algorithmic approaches have been put forth to automate the classification process. Recently, novel machine learning approaches have been detailed that produce rapid and highly accurate classifications. These approaches however, are often computationally expensive, require significant expertise to implement, and/or require proprietary software that limits broader adoption. Here we detail a novel artificial neural network that uses electrophysiological features to automatically classify behavioral state in rats with high accuracy, sensitivity, and specificity. Common parameters of interest to sleep scientists, including state-dependent power spectra and homeostatic non-REM slow wave activity, did not significantly differ when using this automated classifier as compared to manual scoring. Flexible options enable researchers to further increase classification accuracy through manual rescoring of a small subset of time intervals with low model prediction certainty or further decrease researcher time by generalizing trained networks across multiple recording days. The algorithm is fully open-source and coded within a popular, and freely available, software platform to increase access to this research tool and provide additional flexibility for future researchers. In sum, we have developed a readily implementable, efficient, and effective approach for automated behavioral state classification in rats.
format: application/pdf
format: text/html
creator: Jacob G. Ellen
creator: Michael B. Dash
subject: Animal Behavior
subject: Bioinformatics
subject: Neuroscience
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.12127
publisher: PeerJ Inc.
rights: © 2021 Ellen and Dash
abstract: Accurate behavioral state classification is critical for many research applications. Researchers typically rely upon manual identification of behavioral state through visual inspection of electrophysiological signals, but this approach is time intensive and subject to low inter-rater reliability. To overcome these limitations, a diverse set of algorithmic approaches have been put forth to automate the classification process. Recently, novel machine learning approaches have been detailed that produce rapid and highly accurate classifications. These approaches however, are often computationally expensive, require significant expertise to implement, and/or require proprietary software that limits broader adoption. Here we detail a novel artificial neural network that uses electrophysiological features to automatically classify behavioral state in rats with high accuracy, sensitivity, and specificity. Common parameters of interest to sleep scientists, including state-dependent power spectra and homeostatic non-REM slow wave activity, did not significantly differ when using this automated classifier as compared to manual scoring. Flexible options enable researchers to further increase classification accuracy through manual rescoring of a small subset of time intervals with low model prediction certainty or further decrease researcher time by generalizing trained networks across multiple recording days. The algorithm is fully open-source and coded within a popular, and freely available, software platform to increase access to this research tool and provide additional flexibility for future researchers. In sum, we have developed a readily implementable, efficient, and effective approach for automated behavioral state classification in rats.
bibliographic citation: Ellen et al. (2021) An artificial neural network for automated behavioral state classification in rats. PeerJ 9:e12127 https://doi.org/10.7717/peerj.12127
date submitted: 2021-06-03
date accepted: 2021-08-17
issued: 2021-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ellen
  given name: Jacob G.
author list: Agent
  family name: Dash
  given name: Michael B.
doi: 10.7717/peerj.12127
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-09
copyright: © 2021 Ellen and Dash
attribution name: Ellen and Dash

Plastic response of Medicago sativa L. root system traits and cold resistance to simulated rainfall events
type: item
type: AcademicArticle
description: Climate change (rainfall events and global warming) affects the survival of alfalfa (Medicago sativa L.) in winter. Appropriate water management can quickly reduce the mortality of alfalfa during winter. To determine how changes in water affect the cold resistance of alfalfa, we explored the root system traits under different rainfall events and the effects on cold resistance in three alfalfa cultivars. These were exposed to three simulated rainfall events (SRE) × two phases in a randomized complete block design with six replications. The three cultivars were WL168, WL353 and WL440, and the three SRE were irrigation once every second day (D2), every four days (D4) and every eight days (D8). There were two phases: before cold acclimation and after cold acclimation. Our results demonstrated that a period of exposure to low temperature was required for alfalfa to achieve maximum cold resistance. The root system tended toward herringbone branching under D8, compared with D2 and D4, and demonstrated greater root biomass, crown diameter, root volume, average link length and topological index. Nevertheless, D8 had less lateral root length, root surface area, specific root length, root forks and fractal dimensions. Greater root biomass and topological index were beneficial to cold resistance in alfalfa, while more lateral roots and root forks inhibited its ability to survive winter. Alfalfa roots had higher proline, soluble sugar and starch content in D8 than in D2 and D4. In contrast, there was lower malondialdehyde in D8, indicating that alfalfa had better cold resistance following a longer irrigation interval before winter. After examining root biomass, root system traits and physiological indexes we concluded that WL168 exhibited stronger cold resistance. Our results contribute to greater understanding of root and cold stress, consequently providing references for selection of cultivars and field water management to improve cold resistance of alfalfa in the context of c…
format: application/pdf
format: text/html
creator: Zhensong Li
creator: Liqiang Wan
creator: Shuo Li
creator: Xianglin Li
creator: Feng He
creator: Zongyong Tong
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.11962
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Climate change (rainfall events and global warming) affects the survival of alfalfa (Medicago sativa L.) in winter. Appropriate water management can quickly reduce the mortality of alfalfa during winter. To determine how changes in water affect the cold resistance of alfalfa, we explored the root system traits under different rainfall events and the effects on cold resistance in three alfalfa cultivars. These were exposed to three simulated rainfall events (SRE) × two phases in a randomized complete block design with six replications. The three cultivars were WL168, WL353 and WL440, and the three SRE were irrigation once every second day (D2), every four days (D4) and every eight days (D8). There were two phases: before cold acclimation and after cold acclimation. Our results demonstrated that a period of exposure to low temperature was required for alfalfa to achieve maximum cold resistance. The root system tended toward herringbone branching under D8, compared with D2 and D4, and demonstrated greater root biomass, crown diameter, root volume, average link length and topological index. Nevertheless, D8 had less lateral root length, root surface area, specific root length, root forks and fractal dimensions. Greater root biomass and topological index were beneficial to cold resistance in alfalfa, while more lateral roots and root forks inhibited its ability to survive winter. Alfalfa roots had higher proline, soluble sugar and starch content in D8 than in D2 and D4. In contrast, there was lower malondialdehyde in D8, indicating that alfalfa had better cold resistance following a longer irrigation interval before winter. After examining root biomass, root system traits and physiological indexes we concluded that WL168 exhibited stronger cold resistance. Our results contribute to greater understanding of root and cold stress, consequently providing references for selection of cultivars and field water management to improve cold resistance of alfalfa in the context of c…
bibliographic citation: Li et al. (2021) Plastic response of Medicago sativa L. root system traits and cold resistance to simulated rainfall events. PeerJ 9:e11962 https://doi.org/10.7717/peerj.11962
date submitted: 2021-03-25
date accepted: 2021-07-21
issued: 2021-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhensong
author list: Agent
  family name: Wan
  given name: Liqiang
author list: Agent
  family name: Li
  given name: Shuo
author list: Agent
  family name: Li
  given name: Xianglin
author list: Agent
  family name: He
  given name: Feng
author list: Agent
  family name: Tong
  given name: Zongyong
doi: 10.7717/peerj.11962
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-09
copyright: © 2021 Li et al.
attribution name: Li et al.

Risk assessment of freezing injury during overwintering of wheat in the northern boundary of the Winter Wheat Region in China
type: item
type: AcademicArticle
description: Freezing injury is one of the main restriction factors for winter wheat production, especially in the northern part of the Winter Wheat Region in China. It is very important to assess the risk of winter wheat-freezing injury. However, most of the existing climate models are complex and cannot be widely used. In this study, Zunhua which is located in the northern boundary of Winter Wheat Region in China is selected as research region, based on the winter meteorological data of Zunhua from 1956 to 2016, seven freezing disaster-causing factors related to freezing injury were extracted to formulated the freezing injury index (FII) of wheat. Referring to the historical wheat-freezing injury in Zunhua and combining with the cold resistance identification data of the National Winter Wheat Variety Regional Test (NWWVRT), consistency between the FII and the actual freezing injury situation was tested. Furthermore, the occurrence law of freezing injury in Zunhua during the past 60 years was analyzed by Morlet wavelet analyze, and the risk of freezing injury in the short term was evaluated. Results showed that the FII can reflect the occurrence of winter wheat-freezing injury in Zunhua to a certain extent and had a significant linear correlation with the dead tiller rate of wheat (P = 0.014). The interannual variation of the FII in Zunhua also showed a significant downward trend (R2 = 0.7412). There are two cycles of freezing injury in 60 years, and it showed that there’s still exist a high risk in the short term. This study provides reference information for the rational use of meteorological data for winter wheat-freezing injury risk assessment.
format: application/pdf
format: text/html
creator: Jiahui Guo
creator: Xionghui Bai
creator: Weiping Shi
creator: Ruijie Li
creator: Xingyu Hao
creator: Hongfu Wang
creator: Zhiqiang Gao
creator: Jie Guo
creator: Wen Lin
subject: Agricultural Science
subject: Plant Science
subject: Climate Change Biology
subject: Ecohydrology
subject: Environmental Impacts
description: doi:10.7717/peerj.12154
publisher: PeerJ Inc.
rights: © 2021 Guo et al.
abstract: Freezing injury is one of the main restriction factors for winter wheat production, especially in the northern part of the Winter Wheat Region in China. It is very important to assess the risk of winter wheat-freezing injury. However, most of the existing climate models are complex and cannot be widely used. In this study, Zunhua which is located in the northern boundary of Winter Wheat Region in China is selected as research region, based on the winter meteorological data of Zunhua from 1956 to 2016, seven freezing disaster-causing factors related to freezing injury were extracted to formulated the freezing injury index (FII) of wheat. Referring to the historical wheat-freezing injury in Zunhua and combining with the cold resistance identification data of the National Winter Wheat Variety Regional Test (NWWVRT), consistency between the FII and the actual freezing injury situation was tested. Furthermore, the occurrence law of freezing injury in Zunhua during the past 60 years was analyzed by Morlet wavelet analyze, and the risk of freezing injury in the short term was evaluated. Results showed that the FII can reflect the occurrence of winter wheat-freezing injury in Zunhua to a certain extent and had a significant linear correlation with the dead tiller rate of wheat (P = 0.014). The interannual variation of the FII in Zunhua also showed a significant downward trend (R2 = 0.7412). There are two cycles of freezing injury in 60 years, and it showed that there’s still exist a high risk in the short term. This study provides reference information for the rational use of meteorological data for winter wheat-freezing injury risk assessment.
bibliographic citation: Guo et al. (2021) Risk assessment of freezing injury during overwintering of wheat in the northern boundary of the Winter Wheat Region in China. PeerJ 9:e12154 https://doi.org/10.7717/peerj.12154
date submitted: 2021-06-27
date accepted: 2021-08-24
issued: 2021-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Jiahui
author list: Agent
  family name: Bai
  given name: Xionghui
author list: Agent
  family name: Shi
  given name: Weiping
author list: Agent
  family name: Li
  given name: Ruijie
author list: Agent
  family name: Hao
  given name: Xingyu
author list: Agent
  family name: Wang
  given name: Hongfu
author list: Agent
  family name: Gao
  given name: Zhiqiang
author list: Agent
  family name: Guo
  given name: Jie
author list: Agent
  family name: Lin
  given name: Wen
doi: 10.7717/peerj.12154
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-09
copyright: ©2021 Guo et al.
attribution name: Guo et al.

CBF transcription factors involved in the cold response of Camellia japonica (Naidong)
type: item
type: AcademicArticle
description: CBFs belong to the ERF subfamily of the AP2 supergene family and often play an important role in the cold acclimation of temperate plants. However, the role of CBFs in Camellia japonica (Naidong), the only Camellia japonica population found in the temperate zones of China, remains unclear. It is very important to study the genetic composition of C. japonica (Naidong) to adapt to low temperature for Camellia species. Using full-length transcriptome data, we identified four CjCBF genes that respond to cold stress and analyzed their evolutionary relationships, domains, and expression patterns. The phylogeny of CBFs of 19 angiosperms divided the genes into three categories, and the four CjCBFs belong to a small subcluster. The strong response of CjCBF1 to cold treatment and its sustained high level of expression indicated that it plays an important role in the process of cold acclimation. A yeast two-hybrid assay revealed an interaction between CjCBF1, CjCBF2, and CjCBF5, and subcellular localization confirmed this finding. The expression of CjCBFs was tissue-specific: CBF1 was mainly expressed in leaves, and CBF3 was mainly expressed in stem. The responses of the four CjCBFs to drought and high temperature and the effect of light were also characterized. Our study provides new insight into the role of CBFs in the cold response in C. japonica (Naidong).
format: application/pdf
format: text/html
creator: Menglong Fan
creator: Rui Zhou
creator: Qinghua Liu
creator: Yingkun Sun
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12155
publisher: PeerJ Inc.
rights: © 2021 Fan et al.
abstract: CBFs belong to the ERF subfamily of the AP2 supergene family and often play an important role in the cold acclimation of temperate plants. However, the role of CBFs in Camellia japonica (Naidong), the only Camellia japonica population found in the temperate zones of China, remains unclear. It is very important to study the genetic composition of C. japonica (Naidong) to adapt to low temperature for Camellia species. Using full-length transcriptome data, we identified four CjCBF genes that respond to cold stress and analyzed their evolutionary relationships, domains, and expression patterns. The phylogeny of CBFs of 19 angiosperms divided the genes into three categories, and the four CjCBFs belong to a small subcluster. The strong response of CjCBF1 to cold treatment and its sustained high level of expression indicated that it plays an important role in the process of cold acclimation. A yeast two-hybrid assay revealed an interaction between CjCBF1, CjCBF2, and CjCBF5, and subcellular localization confirmed this finding. The expression of CjCBFs was tissue-specific: CBF1 was mainly expressed in leaves, and CBF3 was mainly expressed in stem. The responses of the four CjCBFs to drought and high temperature and the effect of light were also characterized. Our study provides new insight into the role of CBFs in the cold response in C. japonica (Naidong).
bibliographic citation: Fan et al. (2021) CBF transcription factors involved in the cold response of Camellia japonica (Naidong). PeerJ 9:e12155 https://doi.org/10.7717/peerj.12155
date submitted: 2021-04-14
date accepted: 2021-08-24
issued: 2021-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Menglong
author list: Agent
  family name: Zhou
  given name: Rui
author list: Agent
  family name: Liu
  given name: Qinghua
author list: Agent
  family name: Sun
  given name: Yingkun
doi: 10.7717/peerj.12155
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-09
copyright: ©2021 Fan et al.
attribution name: Fan et al.

High bycatch rates of manta and devil rays in the “small-scale” artisanal fisheries of Sri Lanka
type: item
type: AcademicArticle
description: Background Expanding fisheries in developing nations like Sri Lanka have a significant impact on threatened marine species such as elasmobranchs. Manta and devil (mobulid) rays have some of the most conservative life history strategies of any elasmobranch, and even low to moderate levels of bycatch from gillnet fisheries may lead to significant population declines. A lack of information on life history, demographics, population trends, and fisheries impacts hinders effective management measures for these species. Method We report on mobulid fishery landings over nine years between 2011 and 2020 across 38 landing sites in Sri Lanka. We collected data on catch numbers, body sizes, sex, and maturity status for five mobulid species. We used a Bayesian state-space model to estimate monthly country-wide catch rates and total annual landings of mobulid rays. We used catch curve analyses to estimate total mortality for Mobula mobular, and evaluated trends in recorded body sizes across the study period for M. mobular, M. birostris, M. tarapacana and M. thurstoni. Results We find that catch rates have declined an order of magnitude for all species across the study period, and that total annual captures of mobulid rays by the Sri Lankan artisanal fishing fleet exceed the estimated annual captures of mobulids in all global, industrial purse seine fisheries combined. Catch curve analyses suggest that M. mobular is being fished at rates far above the species’ intrinsic population growth rate, and the average sizes of all mobulids in the fishery except for M. birostris are declining. Collectively, these findings suggest overfishing of mobulid ray populations in the northern Indian Ocean by Sri Lankan artisanal fisheries. We recommend strengthening the management of these species through improved implementation of CITES, CMS, and regional fisheries management actions. In addition, we report on the demographic characteristics of mobulids landed in Sri Lanka and provide the first rec…
format: application/pdf
format: text/html
creator: Daniel Fernando
creator: Joshua D. Stewart
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
subject: Zoology
subject: Environmental Impacts
description: doi:10.7717/peerj.11994
publisher: PeerJ Inc.
rights: © 2021 Fernando and Stewart
abstract: Background Expanding fisheries in developing nations like Sri Lanka have a significant impact on threatened marine species such as elasmobranchs. Manta and devil (mobulid) rays have some of the most conservative life history strategies of any elasmobranch, and even low to moderate levels of bycatch from gillnet fisheries may lead to significant population declines. A lack of information on life history, demographics, population trends, and fisheries impacts hinders effective management measures for these species. Method We report on mobulid fishery landings over nine years between 2011 and 2020 across 38 landing sites in Sri Lanka. We collected data on catch numbers, body sizes, sex, and maturity status for five mobulid species. We used a Bayesian state-space model to estimate monthly country-wide catch rates and total annual landings of mobulid rays. We used catch curve analyses to estimate total mortality for Mobula mobular, and evaluated trends in recorded body sizes across the study period for M. mobular, M. birostris, M. tarapacana and M. thurstoni. Results We find that catch rates have declined an order of magnitude for all species across the study period, and that total annual captures of mobulid rays by the Sri Lankan artisanal fishing fleet exceed the estimated annual captures of mobulids in all global, industrial purse seine fisheries combined. Catch curve analyses suggest that M. mobular is being fished at rates far above the species’ intrinsic population growth rate, and the average sizes of all mobulids in the fishery except for M. birostris are declining. Collectively, these findings suggest overfishing of mobulid ray populations in the northern Indian Ocean by Sri Lankan artisanal fisheries. We recommend strengthening the management of these species through improved implementation of CITES, CMS, and regional fisheries management actions. In addition, we report on the demographic characteristics of mobulids landed in Sri Lanka and provide the first rec…
bibliographic citation: Fernando et al. (2021) High bycatch rates of manta and devil rays in the “small-scale” artisanal fisheries of Sri Lanka. PeerJ 9:e11994 https://doi.org/10.7717/peerj.11994
date submitted: 2021-05-21
date accepted: 2021-07-27
issued: 2021-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fernando
  given name: Daniel
author list: Agent
  family name: Stewart
  given name: Joshua D.
doi: 10.7717/peerj.11994
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-08
copyright: ©2021 Fernando and Stewart
attribution name: Fernando and Stewart

Inter-element variation in the bone histology of Anteosaurus (Dinocephalia, Anteosauridae) from the Tapinocephalus Assemblage Zone of the Karoo Basin of South Africa
type: item
type: AcademicArticle
description: Despite its abundance in the Permian fossil record of South Africa, little is known about the life history of Anteosaurus. Here we examine the bone microstructure of multiple skeletal elements of Anteosaurus from the Tapinocephalus Assemblage Zone of the Karoo Basin. The bone histology of Anteosaurus magnificus reveals that the cortex is composed of highly vascularized, uninterrupted fibrolamellar bone tissue surrounding the inner spongy medullary region. However, the histology of two ribs and a previously described femur of another Anteosaurus taxon revealed an interrupted growth pattern with lines of arrested growth and peripheral rest lines occurring in the compacta, indicating periodic pauses in growth possibly linked to the slowing down of growth during maturity. Given that the fibula of the same individual has well-vascularised fibrolamellar bone tissue without any growth marks in the cortex; this suggests variation in skeletal growth. Based on our histological results, three growth dynamic stages are deduced for the genus Anteosaurus: (i) the earliest growth stage is represented by the predominance of highly vascularized, uninterrupted fibrolamellar bone tissue in the inner cortex, which suggests rapid periosteal bone deposition during early ontogeny; (ii) the next stage of growth shows periodic interruptions in the bone deposition as indicated by the deposition of lines of arrested growth; (iii) the third stage shows the development of lamellar bone tissue with rest lines in the peripheral part of the cortex suggesting a slowing down of growth prior to death. Most of the skeletal elements are characterized by thick bone walls, extensive secondary reconstruction and the complete infilling of the medullary cavity. However, the radius and a previously studied femur have open medullary cavities with struts of bony trabeculae. Based on histologic structures and comparisons with extant taxa, it is likely that Anteosaurus may have been more terrestrial as its osteo…
format: application/pdf
format: text/html
creator: Mohd Shafi Bhat
creator: Christen D. Shelton
creator: Anusuya Chinsamy
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.12082
publisher: PeerJ Inc.
rights: © 2021 Bhat et al.
abstract: Despite its abundance in the Permian fossil record of South Africa, little is known about the life history of Anteosaurus. Here we examine the bone microstructure of multiple skeletal elements of Anteosaurus from the Tapinocephalus Assemblage Zone of the Karoo Basin. The bone histology of Anteosaurus magnificus reveals that the cortex is composed of highly vascularized, uninterrupted fibrolamellar bone tissue surrounding the inner spongy medullary region. However, the histology of two ribs and a previously described femur of another Anteosaurus taxon revealed an interrupted growth pattern with lines of arrested growth and peripheral rest lines occurring in the compacta, indicating periodic pauses in growth possibly linked to the slowing down of growth during maturity. Given that the fibula of the same individual has well-vascularised fibrolamellar bone tissue without any growth marks in the cortex; this suggests variation in skeletal growth. Based on our histological results, three growth dynamic stages are deduced for the genus Anteosaurus: (i) the earliest growth stage is represented by the predominance of highly vascularized, uninterrupted fibrolamellar bone tissue in the inner cortex, which suggests rapid periosteal bone deposition during early ontogeny; (ii) the next stage of growth shows periodic interruptions in the bone deposition as indicated by the deposition of lines of arrested growth; (iii) the third stage shows the development of lamellar bone tissue with rest lines in the peripheral part of the cortex suggesting a slowing down of growth prior to death. Most of the skeletal elements are characterized by thick bone walls, extensive secondary reconstruction and the complete infilling of the medullary cavity. However, the radius and a previously studied femur have open medullary cavities with struts of bony trabeculae. Based on histologic structures and comparisons with extant taxa, it is likely that Anteosaurus may have been more terrestrial as its osteo…
bibliographic citation: Bhat et al. (2021) Inter-element variation in the bone histology of Anteosaurus (Dinocephalia, Anteosauridae) from the Tapinocephalus Assemblage Zone of the Karoo Basin of South Africa. PeerJ 9:e12082 https://doi.org/10.7717/peerj.12082
date submitted: 2021-04-01
date accepted: 2021-08-07
issued: 2021-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bhat
  given name: Mohd Shafi
author list: Agent
  family name: Shelton
  given name: Christen D.
author list: Agent
  family name: Chinsamy
  given name: Anusuya
doi: 10.7717/peerj.12082
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-08
copyright: © 2021 Bhat et al.
attribution name: Bhat et al.

No adverse effect of a maternal high carbohydrate diet on their offspring, in rainbow trout (Oncorhynchus mykiss)
type: item
type: AcademicArticle
description: In order to develop a sustainable salmonid aquaculture, it is essential to continue to reduce the use of the protein-rich fishmeal. One promising solution to do so is the use of plant-derived carbohydrates in diet destined to broodstock. However, in mammals, the reduction of protein content (replaced by carbohydrates) in parental diet is known to have strong adverse effects on offspring phenotypes and metabolism. For the first time, the effect of a paternal and a maternal high carbohydrate-low protein diet was assessed on progeny at long term in the rainbow trout. A 30% protein diminution in both males and females broodstock diet during 10 month and 5 months, respectively, did not trigger adverse consequences on their offspring. At the molecular level, offspring transcriptomes were not significantly altered, emphasizing no effect on metabolism. Tenuous differences in the biochemical composition of the liver and the viscera were observed. The recorded effects remained in the normal range of value and accordingly offspring growth were not negatively affected over the long term. Overall, we demonstrated here that a 30% protein diminution during gametogenesis is feasible, confirming the possibility to increase the proportion of plant-derived carbohydrates in female broodstock diets to replace fishmeal proteins.
format: application/pdf
format: text/html
creator: Therese Callet
creator: Hongyan Li
creator: Anne Surget
creator: Frederic Terrier
creator: Franck Sandres
creator: Anthony Lanuque
creator: Stephane Panserat
creator: Lucie Marandel
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12102
publisher: PeerJ Inc.
rights: © 2021 Callet et al.
abstract: In order to develop a sustainable salmonid aquaculture, it is essential to continue to reduce the use of the protein-rich fishmeal. One promising solution to do so is the use of plant-derived carbohydrates in diet destined to broodstock. However, in mammals, the reduction of protein content (replaced by carbohydrates) in parental diet is known to have strong adverse effects on offspring phenotypes and metabolism. For the first time, the effect of a paternal and a maternal high carbohydrate-low protein diet was assessed on progeny at long term in the rainbow trout. A 30% protein diminution in both males and females broodstock diet during 10 month and 5 months, respectively, did not trigger adverse consequences on their offspring. At the molecular level, offspring transcriptomes were not significantly altered, emphasizing no effect on metabolism. Tenuous differences in the biochemical composition of the liver and the viscera were observed. The recorded effects remained in the normal range of value and accordingly offspring growth were not negatively affected over the long term. Overall, we demonstrated here that a 30% protein diminution during gametogenesis is feasible, confirming the possibility to increase the proportion of plant-derived carbohydrates in female broodstock diets to replace fishmeal proteins.
bibliographic citation: Callet et al. (2021) No adverse effect of a maternal high carbohydrate diet on their offspring, in rainbow trout (Oncorhynchus mykiss). PeerJ 9:e12102 https://doi.org/10.7717/peerj.12102
date submitted: 2021-05-11
date accepted: 2021-08-11
issued: 2021-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Callet
  given name: Therese
author list: Agent
  family name: Li
  given name: Hongyan
author list: Agent
  family name: Surget
  given name: Anne
author list: Agent
  family name: Terrier
  given name: Frederic
author list: Agent
  family name: Sandres
  given name: Franck
author list: Agent
  family name: Lanuque
  given name: Anthony
author list: Agent
  family name: Panserat
  given name: Stephane
author list: Agent
  family name: Marandel
  given name: Lucie
doi: 10.7717/peerj.12102
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-08
copyright: ©2021 Callet et al.
attribution name: Callet et al.

High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River
type: item
type: AcademicArticle
description: Tamarix is a dominant species in the Tarim River Basin, the longest inland river in China. Tamarix plays an important role in the ecological restoration of this region. In this study, to investigate the soil bacterial community diversity in Tamarix shrubs, we collected soil samples from the inside and edge of the canopy and the edge of nebkhas and non-nebkhas Tamarix shrubs located near the Yingsu section in the lower reaches of Tarim River. High throughput sequencing technology was employed to discern the composition and function of soil bacterial communities in nebkhas and non-nebkhas Tamarix shrubs. Besides, the physicochemical properties of soil and the spatial distribution characteristics of soil bacteria and their correlation were analyzed. The outcomes of this analysis demonstrated that different parts of Tamarix shrubs had significantly different effects on soil pH, total K (TK), available K (AK), ammonium N (NH4+), and available P (AP) values (P < 0.05), but not on soil moisture (SWC), total salt (TDS), electrical conductivity (EC), organic matter (OM), total N (TN), total P (TP), and nitrate N (NO3−) values. The soil bacterial communities identified in Tamarix shrubs were categorized into two kingdoms, 71 phyla, 161 classes, 345 orders, 473 families, and 702 genera. Halobacterota, unidentified bacteria, and Proteobacteria were found to be dominant phyla. The correlation between the soil physicochemical factors and soil bacterial community was analyzed, and as per the outcomes OM, AK, AP, EC, and NH4+ were found to primarily affect the structure of the soil bacterial community. SWC, TK and pH were positively correlated with each other, but negatively correlated with other soil factors. At the phyla level, a significantly positive correlation was observed between the Halobacterota and AP, OM as well as Bacteroidota and AK (P < 0.01), but a significantly negative correlation was observed between the Chloroflexi and AK, EC (P < 0.01). The PICRUSt software was …
format: application/pdf
format: text/html
creator: Fangnan Xiao
creator: Yuanyuan Li
creator: Guifang Li
creator: Yaling He
creator: Xinhua Lv
creator: Li Zhuang
creator: Xiaozhen Pu
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.12105
publisher: PeerJ Inc.
rights: © 2021 Xiao et al.
abstract: Tamarix is a dominant species in the Tarim River Basin, the longest inland river in China. Tamarix plays an important role in the ecological restoration of this region. In this study, to investigate the soil bacterial community diversity in Tamarix shrubs, we collected soil samples from the inside and edge of the canopy and the edge of nebkhas and non-nebkhas Tamarix shrubs located near the Yingsu section in the lower reaches of Tarim River. High throughput sequencing technology was employed to discern the composition and function of soil bacterial communities in nebkhas and non-nebkhas Tamarix shrubs. Besides, the physicochemical properties of soil and the spatial distribution characteristics of soil bacteria and their correlation were analyzed. The outcomes of this analysis demonstrated that different parts of Tamarix shrubs had significantly different effects on soil pH, total K (TK), available K (AK), ammonium N (NH4+), and available P (AP) values (P < 0.05), but not on soil moisture (SWC), total salt (TDS), electrical conductivity (EC), organic matter (OM), total N (TN), total P (TP), and nitrate N (NO3−) values. The soil bacterial communities identified in Tamarix shrubs were categorized into two kingdoms, 71 phyla, 161 classes, 345 orders, 473 families, and 702 genera. Halobacterota, unidentified bacteria, and Proteobacteria were found to be dominant phyla. The correlation between the soil physicochemical factors and soil bacterial community was analyzed, and as per the outcomes OM, AK, AP, EC, and NH4+ were found to primarily affect the structure of the soil bacterial community. SWC, TK and pH were positively correlated with each other, but negatively correlated with other soil factors. At the phyla level, a significantly positive correlation was observed between the Halobacterota and AP, OM as well as Bacteroidota and AK (P < 0.01), but a significantly negative correlation was observed between the Chloroflexi and AK, EC (P < 0.01). The PICRUSt software was …
bibliographic citation: Xiao et al. (2021) High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River. PeerJ 9:e12105 https://doi.org/10.7717/peerj.12105
date submitted: 2021-05-10
date accepted: 2021-08-11
issued: 2021-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Fangnan
author list: Agent
  family name: Li
  given name: Yuanyuan
author list: Agent
  family name: Li
  given name: Guifang
author list: Agent
  family name: He
  given name: Yaling
author list: Agent
  family name: Lv
  given name: Xinhua
author list: Agent
  family name: Zhuang
  given name: Li
author list: Agent
  family name: Pu
  given name: Xiaozhen
doi: 10.7717/peerj.12105
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-08
copyright: © 2021 Xiao et al.
attribution name: Xiao et al.

Whole-genome comparative analysis at the lineage/sublineage level discloses relationships between Mycobacterium tuberculosis genotype and clinical phenotype
type: item
type: AcademicArticle
description: Background Human tuberculosis (TB) caused by members of the Mycobacterium tuberculosis complex (MTBC) is the main cause of death among infectious diseases worldwide. Pulmonary TB (PTB) is the most common clinical phenotype of the disease, but some patients develop an extrapulmonary (EPTB) phenotype in which any organ or tissue can be affected. MTBC species include nine phylogenetic lineages, with some appearing globally and others being geographically restricted. EPTB can or not have pulmonary involvement, challenging its diagnosis when lungs are not implicated, thus causing an inadequate treatment. Finding evidence of a specific M. tuberculosis genetic background associated with EPTB is epidemiologically relevant due to the virulent and multidrug-resistant strains isolated from such cases. Until now, the studies conducted to establish associations between M. tuberculosis lineages and PTB/EPTB phenotypes have shown inconsistent results, which are attributed to the strain predominance from specific M. tuberculosis lineages/sublineages in the samples analyzed and the use of low-resolution phylogenetic tools that have impaired sublineage discrimination abilities. The present work elucidates the relationships between the MTBC strain lineages/sublineages and the clinical phenotypes of the disease as well as the antibiotic resistance of the strains. Methods To avoid biases, we retrieved the raw genomic reads (RGRs) of all (n = 245) the M. tuberculosis strains worldwide causing EPTB available in databases and an equally representative sample of the RGRs (n = 245) of PTB strains. A multiple alignment was constructed, and a robust maximum likelihood phylogeny based on single-nucleotide polymorphisms was generated, allowing effective strain lineage/sublineage assignment. Results A significant Odds Ratio (OR range: 1.8–8.1) association was found between EPTB and the 1.1.1, 1.2.1, 4.1.2.1 and ancestral Beijing sublineages. Additionally, a significant association between PTB wit…
format: application/pdf
format: text/html
creator: Andrea Monserrat Negrete-Paz
creator: Gerardo Vázquez-Marrufo
creator: Ma. Soledad Vázquez-Garcidueñas
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.12128
publisher: PeerJ Inc.
rights: © 2021 Negrete-Paz et al.
abstract: Background Human tuberculosis (TB) caused by members of the Mycobacterium tuberculosis complex (MTBC) is the main cause of death among infectious diseases worldwide. Pulmonary TB (PTB) is the most common clinical phenotype of the disease, but some patients develop an extrapulmonary (EPTB) phenotype in which any organ or tissue can be affected. MTBC species include nine phylogenetic lineages, with some appearing globally and others being geographically restricted. EPTB can or not have pulmonary involvement, challenging its diagnosis when lungs are not implicated, thus causing an inadequate treatment. Finding evidence of a specific M. tuberculosis genetic background associated with EPTB is epidemiologically relevant due to the virulent and multidrug-resistant strains isolated from such cases. Until now, the studies conducted to establish associations between M. tuberculosis lineages and PTB/EPTB phenotypes have shown inconsistent results, which are attributed to the strain predominance from specific M. tuberculosis lineages/sublineages in the samples analyzed and the use of low-resolution phylogenetic tools that have impaired sublineage discrimination abilities. The present work elucidates the relationships between the MTBC strain lineages/sublineages and the clinical phenotypes of the disease as well as the antibiotic resistance of the strains. Methods To avoid biases, we retrieved the raw genomic reads (RGRs) of all (n = 245) the M. tuberculosis strains worldwide causing EPTB available in databases and an equally representative sample of the RGRs (n = 245) of PTB strains. A multiple alignment was constructed, and a robust maximum likelihood phylogeny based on single-nucleotide polymorphisms was generated, allowing effective strain lineage/sublineage assignment. Results A significant Odds Ratio (OR range: 1.8–8.1) association was found between EPTB and the 1.1.1, 1.2.1, 4.1.2.1 and ancestral Beijing sublineages. Additionally, a significant association between PTB wit…
bibliographic citation: Negrete-Paz et al. (2021) Whole-genome comparative analysis at the lineage/sublineage level discloses relationships between Mycobacterium tuberculosis genotype and clinical phenotype. PeerJ 9:e12128 https://doi.org/10.7717/peerj.12128
date submitted: 2021-05-10
date accepted: 2021-08-17
issued: 2021-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Negrete-Paz
  given name: Andrea Monserrat
author list: Agent
  family name: Vázquez-Marrufo
  given name: Gerardo
author list: Agent
  family name: Vázquez-Garcidueñas
  given name: Ma. Soledad
doi: 10.7717/peerj.12128
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-08
copyright: ©2021 Negrete-Paz et al.
attribution name: Negrete-Paz et al.

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