PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Using historical dip net data to infer absence of flatwoods salamanders in stochastic environments
items: Rapid authenticity testing of artificially bred green turtles (Chelonia mydas) using microsatellite and mitochondrial DNA markers
items: Psychometric evaluation of an Italian custom 4-item short form of the PROMIS anxiety item bank in immune-mediated inflammatory diseases: an item response theory analysis
items: Polycaprolactone nanofibers as an adjuvant strategy for Tamoxifen release and their cytotoxicity on breast cancer cells
items: Land-use change influence soil quality parameters at an ecologically fragile area of YongDeng County of Gansu Province, China
items: Hierarchical drift diffusion modeling uncovers multisensory benefit in numerosity discrimination tasks
items: Age and lunar cycle predict harbor porpoise bycatch in the south-western Baltic Sea
items: Differences in insectivore bird diets in coffee agroecosystems driven by obligate or generalist guild, shade management, season, and year
items: Relatively low tooth replacement rate in a sauropod dinosaur from the Early Cretaceous Ruyang Basin of central China
items: In vitro induction and identification of polyploid Neolamarckia cadamba plants by colchicine treatment

Using historical dip net data to infer absence of flatwoods salamanders in stochastic environments
type: item
type: AcademicArticle
description: Local extinction and undetected presence are two very different biological phenomena, but they can be challenging to differentiate. Stochastic environments hamper the development of standardized monitoring schemes for wildlife, and make it more challenging to plan and evaluate the success of conservation efforts. To avoid reintroductions of species at risk that could jeopardize extant populations, managers attempting translocation events require a higher level of confidence that a failure to confirm presence represents a true absence. For many pond breeding amphibians, monitoring of the breeding population occurs indirectly through larval surveys. Larval development and successful recruitment only occurs after a sequence of appropriate environmental conditions, thus it is possible for a breeding population of adults to exist at a site but for detectability of the species to be functionally zero. We investigate how annual variability in detection influences long-term monitoring efforts of Reticulated Flatwoods Salamanders (Ambystoma bishopi) breeding in 29 wetlands in Florida. Using 8 years of historic dip net data, we simulate plausible monitoring scenarios that incorporate environmental stochasticity into estimates of detection probability. We found that annual variation in environmental conditions precluded a high degree of certainty in predicting site status for low-intensity monitoring schemes. Uncertainty was partly alleviated by increasing survey effort, but even at the highest level of sampling intensity assessed, multiple years of monitoring are required to confidently determine presence/absence at a site. Combined with assessments of habitat quality and landscape connectivity, our results can be used to identify sites suitable for reintroduction efforts. Our methodologies can be generally applied to increase the effectiveness of surveys for diverse organisms for which annual variability in detectability is known.
format: application/pdf
format: text/html
creator: George C. Brooks
creator: Carola A. Haas
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Freshwater Biology
subject: Population Biology
description: doi:10.7717/peerj.12388
publisher: PeerJ Inc.
rights: © 2021 Brooks and Haas
abstract: Local extinction and undetected presence are two very different biological phenomena, but they can be challenging to differentiate. Stochastic environments hamper the development of standardized monitoring schemes for wildlife, and make it more challenging to plan and evaluate the success of conservation efforts. To avoid reintroductions of species at risk that could jeopardize extant populations, managers attempting translocation events require a higher level of confidence that a failure to confirm presence represents a true absence. For many pond breeding amphibians, monitoring of the breeding population occurs indirectly through larval surveys. Larval development and successful recruitment only occurs after a sequence of appropriate environmental conditions, thus it is possible for a breeding population of adults to exist at a site but for detectability of the species to be functionally zero. We investigate how annual variability in detection influences long-term monitoring efforts of Reticulated Flatwoods Salamanders (Ambystoma bishopi) breeding in 29 wetlands in Florida. Using 8 years of historic dip net data, we simulate plausible monitoring scenarios that incorporate environmental stochasticity into estimates of detection probability. We found that annual variation in environmental conditions precluded a high degree of certainty in predicting site status for low-intensity monitoring schemes. Uncertainty was partly alleviated by increasing survey effort, but even at the highest level of sampling intensity assessed, multiple years of monitoring are required to confidently determine presence/absence at a site. Combined with assessments of habitat quality and landscape connectivity, our results can be used to identify sites suitable for reintroduction efforts. Our methodologies can be generally applied to increase the effectiveness of surveys for diverse organisms for which annual variability in detectability is known.
bibliographic citation: Brooks et al. (2021) Using historical dip net data to infer absence of flatwoods salamanders in stochastic environments. PeerJ 9:e12388 https://doi.org/10.7717/peerj.12388
date submitted: 2021-07-26
date accepted: 2021-10-04
issued: 2021-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brooks
  given name: George C.
author list: Agent
  family name: Haas
  given name: Carola A.
doi: 10.7717/peerj.12388
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-28
copyright: © 2021 Brooks and Haas
attribution name: Brooks and Haas

Rapid authenticity testing of artificially bred green turtles (Chelonia mydas) using microsatellite and mitochondrial DNA markers
type: item
type: AcademicArticle
description: Sea turtles are threatened by climate change and human activity, and their global populations continue to decline sharply. The Chinese government encourages artificial breeding of sea turtles to reduce the use of wild populations. However, artificial breeding of sea turtles is still fairly difficult, and some facilities may illegally purchase wild turtle eggs and then sell incubated turtles by marketing them as artificially bred turtles, which adds another threat to an already endangered species. Therefore, it is necessary to find a reliable method to distinguish the authenticity of artificially bred individuals. In this study, we investigated a turtle farm in southern China, that contained more than 400 green turtles, which were claimed to have been bred in captivity. Parentage testing of turtles from this farm was successfully conducted using two nuclear microsatellites combined with a mitochondrial D-loop DNA marker. Genetic matching of all 19 adults and randomly selected 16 juvenile turtles revealed that none of the juvenile turtles had a matching parent combination among the adult turtles. Therefore, we speculated that the green turtles in this farm were from the wild and that their origin of birth was mainly the Sulu Sea. The methods and molecular markers used in this study could be a reference for rapid authenticity testing of green turtles in future forensic enforcement and population management.
format: application/pdf
format: text/html
creator: Ting Zhang
creator: Liu Lin
creator: Daniel Gaillard
creator: Fang Chen
creator: Huaiqing Chen
creator: Meimei Li
creator: Shannan Wu
creator: Zhao Wang
creator: Haitao Shi
subject: Conservation Biology
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12410
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Sea turtles are threatened by climate change and human activity, and their global populations continue to decline sharply. The Chinese government encourages artificial breeding of sea turtles to reduce the use of wild populations. However, artificial breeding of sea turtles is still fairly difficult, and some facilities may illegally purchase wild turtle eggs and then sell incubated turtles by marketing them as artificially bred turtles, which adds another threat to an already endangered species. Therefore, it is necessary to find a reliable method to distinguish the authenticity of artificially bred individuals. In this study, we investigated a turtle farm in southern China, that contained more than 400 green turtles, which were claimed to have been bred in captivity. Parentage testing of turtles from this farm was successfully conducted using two nuclear microsatellites combined with a mitochondrial D-loop DNA marker. Genetic matching of all 19 adults and randomly selected 16 juvenile turtles revealed that none of the juvenile turtles had a matching parent combination among the adult turtles. Therefore, we speculated that the green turtles in this farm were from the wild and that their origin of birth was mainly the Sulu Sea. The methods and molecular markers used in this study could be a reference for rapid authenticity testing of green turtles in future forensic enforcement and population management.
bibliographic citation: Zhang et al. (2021) Rapid authenticity testing of artificially bred green turtles (Chelonia mydas) using microsatellite and mitochondrial DNA markers. PeerJ 9:e12410 https://doi.org/10.7717/peerj.12410
date submitted: 2021-04-23
date accepted: 2021-10-08
issued: 2021-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Ting
author list: Agent
  family name: Lin
  given name: Liu
author list: Agent
  family name: Gaillard
  given name: Daniel
author list: Agent
  family name: Chen
  given name: Fang
author list: Agent
  family name: Chen
  given name: Huaiqing
author list: Agent
  family name: Li
  given name: Meimei
author list: Agent
  family name: Wu
  given name: Shannan
author list: Agent
  family name: Wang
  given name: Zhao
author list: Agent
  family name: Shi
  given name: Haitao
doi: 10.7717/peerj.12410
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-28
copyright: ©2021 Zhang et al.
attribution name: Zhang et al.

Psychometric evaluation of an Italian custom 4-item short form of the PROMIS anxiety item bank in immune-mediated inflammatory diseases: an item response theory analysis
type: item
type: AcademicArticle
description: Background There has recently been growing interest in the roles of inflammation in contributing to the development of anxiety in people with immune-mediated inflammatory diseases (IMID). Patient-reported outcome measures can facilitate the assessment of physical and psychological functioning. The National Institutes of Health (NIH)’s Patient-Reported Outcomes Measurement Information System (PROMIS®) is a set of Patient-Reported Outcomes (PROs) that cover physical appearance, mental health, and social health. The PROMIS has been built through an Item Response Theory approach (IRT), a model-based measurement in which trait level estimates depend on both persons’ responses and on the properties of the items that were administered. The aim of this study is to test the psychometric properties of an Italian custom four-item Short Form of the PROMIS Anxiety item bank in a cohort of outpatients with IMIDs. Methods We selected four items from the Italian standard Short Form Anxiety 8a and administered them to consecutive outpatients affected by Inflammatory Bowel disease (n = 246), rheumatological (n = 100) and dermatological (n = 43) diseases, and healthy volunteers (n = 280). Data was analyzed through an Item Response Theory (IRT) analysis in order to evaluate the psychometric properties of the Italian adaptation of the PROMIS anxiety short form. Results Taken together, Confirmatory Factor Analysis and Exploratory Factor analysis suggest that the unidimensionality assumption of the instrument holds. The instrument has excellent reliability from a Classical Theory of Test (CTT) standpoint (Cronbach’s α = 0.93, McDonald’s ω = 0.92). The 2PL Graded Response Model (GRM) model provided showed a better goodness of fit as compared to the 1PL GRM model, and local independence assumption appears to be met overall. We did not find signs of differential item functioning (DIF) for age and gender, but evidence for uniform (but not non-uniform) DIF was found in three out of four items …
format: application/pdf
format: text/html
creator: Marco Tullio Liuzza
creator: Rocco Spagnuolo
creator: Gabriella Antonucci
creator: Rosa Daniela Grembiale
creator: Cristina Cosco
creator: Francesco Salvatore Iaquinta
creator: Vanessa Funari
creator: Stefano Dastoli
creator: Steven Nistico
creator: Patrizia Doldo
subject: Dermatology
subject: Gastroenterology and Hepatology
subject: Psychiatry and Psychology
subject: Public Health
subject: Rheumatology
description: doi:10.7717/peerj.12100
publisher: PeerJ Inc.
rights: © 2021 Liuzza et al.
abstract: Background There has recently been growing interest in the roles of inflammation in contributing to the development of anxiety in people with immune-mediated inflammatory diseases (IMID). Patient-reported outcome measures can facilitate the assessment of physical and psychological functioning. The National Institutes of Health (NIH)’s Patient-Reported Outcomes Measurement Information System (PROMIS®) is a set of Patient-Reported Outcomes (PROs) that cover physical appearance, mental health, and social health. The PROMIS has been built through an Item Response Theory approach (IRT), a model-based measurement in which trait level estimates depend on both persons’ responses and on the properties of the items that were administered. The aim of this study is to test the psychometric properties of an Italian custom four-item Short Form of the PROMIS Anxiety item bank in a cohort of outpatients with IMIDs. Methods We selected four items from the Italian standard Short Form Anxiety 8a and administered them to consecutive outpatients affected by Inflammatory Bowel disease (n = 246), rheumatological (n = 100) and dermatological (n = 43) diseases, and healthy volunteers (n = 280). Data was analyzed through an Item Response Theory (IRT) analysis in order to evaluate the psychometric properties of the Italian adaptation of the PROMIS anxiety short form. Results Taken together, Confirmatory Factor Analysis and Exploratory Factor analysis suggest that the unidimensionality assumption of the instrument holds. The instrument has excellent reliability from a Classical Theory of Test (CTT) standpoint (Cronbach’s α = 0.93, McDonald’s ω = 0.92). The 2PL Graded Response Model (GRM) model provided showed a better goodness of fit as compared to the 1PL GRM model, and local independence assumption appears to be met overall. We did not find signs of differential item functioning (DIF) for age and gender, but evidence for uniform (but not non-uniform) DIF was found in three out of four items …
bibliographic citation: Liuzza et al. (2021) Psychometric evaluation of an Italian custom 4-item short form of the PROMIS anxiety item bank in immune-mediated inflammatory diseases: an item response theory analysis. PeerJ 9:e12100 https://doi.org/10.7717/peerj.12100
date submitted: 2020-05-29
date accepted: 2021-08-10
issued: 2021-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liuzza
  given name: Marco Tullio
author list: Agent
  family name: Spagnuolo
  given name: Rocco
author list: Agent
  family name: Antonucci
  given name: Gabriella
author list: Agent
  family name: Grembiale
  given name: Rosa Daniela
author list: Agent
  family name: Cosco
  given name: Cristina
author list: Agent
  family name: Iaquinta
  given name: Francesco Salvatore
author list: Agent
  family name: Funari
  given name: Vanessa
author list: Agent
  family name: Dastoli
  given name: Stefano
author list: Agent
  family name: Nistico
  given name: Steven
author list: Agent
  family name: Doldo
  given name: Patrizia
doi: 10.7717/peerj.12100
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-27
copyright: © 2021 Liuzza et al.
attribution name: Liuzza et al.

Polycaprolactone nanofibers as an adjuvant strategy for Tamoxifen release and their cytotoxicity on breast cancer cells
type: item
type: AcademicArticle
description: Breast cancer is the second leading cause of death in women, and tamoxifen citrate (TMX) is accepted widely for the treatment of hormone receptor–positive breast cancers. Several local drug-delivery systems, including nanofibers, have been developed for antitumor treatment. Nanofibers are biomaterials that mimic the natural extracellular matrix, and they have been used as controlled release devices because they enable highly efficient drug loading. The purpose of the present study was to develop polycaprolactone (PCL) nanofibers incorporating TMX for use in the treatment of breast tumors. Pristine PCL and PCL-TMX nanofibers were produced by electrospinning and characterized physiochemically using different techniques. In addition, an in vitro study of TMX release from the nanofibers was performed. The PCL-TMX nanofibers showed sustained TMX release up to 14 h, releasing 100% of the TMX. The Resazurin reduction assay was used to evaluate the TMX cytotoxicity on MCF-7 breast cancer cell line and PBMCs human. The PCL-TMX nanofiber was cytotoxic toPBMCs and MCF-7. Based on these results, the PCL-TMX nanofibers developed have potential as an alternative for local chronic TMX use for breast cancer treatment, however tissue tests must be done.
format: application/pdf
format: text/html
creator: Ana D. Pinzón-García
creator: Ruben Sinisterra
creator: Maria Cortes
creator: Fredy Mesa
creator: Sandra Ramírez-Clavijo
subject: Biochemistry
subject: Bioengineering
subject: Biotechnology
subject: Drugs and Devices
description: doi:10.7717/peerj.12124
publisher: PeerJ Inc.
rights: © 2021 Pinzón-García et al.
abstract: Breast cancer is the second leading cause of death in women, and tamoxifen citrate (TMX) is accepted widely for the treatment of hormone receptor–positive breast cancers. Several local drug-delivery systems, including nanofibers, have been developed for antitumor treatment. Nanofibers are biomaterials that mimic the natural extracellular matrix, and they have been used as controlled release devices because they enable highly efficient drug loading. The purpose of the present study was to develop polycaprolactone (PCL) nanofibers incorporating TMX for use in the treatment of breast tumors. Pristine PCL and PCL-TMX nanofibers were produced by electrospinning and characterized physiochemically using different techniques. In addition, an in vitro study of TMX release from the nanofibers was performed. The PCL-TMX nanofibers showed sustained TMX release up to 14 h, releasing 100% of the TMX. The Resazurin reduction assay was used to evaluate the TMX cytotoxicity on MCF-7 breast cancer cell line and PBMCs human. The PCL-TMX nanofiber was cytotoxic toPBMCs and MCF-7. Based on these results, the PCL-TMX nanofibers developed have potential as an alternative for local chronic TMX use for breast cancer treatment, however tissue tests must be done.
bibliographic citation: Pinzón-García et al. (2021) Polycaprolactone nanofibers as an adjuvant strategy for Tamoxifen release and their cytotoxicity on breast cancer cells. PeerJ 9:e12124 https://doi.org/10.7717/peerj.12124
date submitted: 2020-12-28
date accepted: 2021-08-17
issued: 2021-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pinzón-García
  given name: Ana D.
author list: Agent
  family name: Sinisterra
  given name: Ruben
author list: Agent
  family name: Cortes
  given name: Maria
author list: Agent
  family name: Mesa
  given name: Fredy
author list: Agent
  family name: Ramírez-Clavijo
  given name: Sandra
doi: 10.7717/peerj.12124
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-27
copyright: ©2021 Pinzón-García et al.
attribution name: Pinzón-García et al.

Land-use change influence soil quality parameters at an ecologically fragile area of YongDeng County of Gansu Province, China
type: item
type: AcademicArticle
description: Dry ecosystems, despite their relative levels of aridity, are very diverse, and play a vital role in the livelihoods of many dryland inhabitants. It is therefore critical to investigate the relationship between land-use change and soil quality parameters to offer a scientific basis for optimizing land-use planning and improving soil quality status in dry ecosystems and ecologically vulnerable areas. This study, therefore, analyzed the physicochemical properties of soils in five different land-use types namely farmland, abandoned farmland, natural grassland, artificial lemon forest, and poplar woodland at YongDeng County. The soil quality status of the aforementioned land-use types was also evaluated through Principal component analysis. The results revealed that abandoned farmland and natural grassland recorded the highest average values of soil coarse particles of 24.0% and 23.4% respectively compared to the other land-use types. The highest average value (46.1%) of fine soil particles was recorded in poplar woodland followed by natural grassland (36.6%) and the average value of very fine soil particles was higher in farmland (40.8%) and artificial lemon woodland (38.3%) than in the other land-use types. The average value of clayey particles was highest in farmland (11.1%), followed by artificial lemon woodland (9.3%), and abandoned farmland (6.5%), then poplar woodland which recorded an average value of (4.2%). The average values of Soil water content, soil pH, soil electrical conductivity, and soil total nitrogen content were significantly higher in farmland compared to the other land-use types. Soil organic carbon content was significantly higher in abandoned farmland at (P < 0.03) and lemon woodland at (P < 0.01) than in farmlands, natural grasslands, and poplar stands. The soil quality indicators of the different land-use types were significantly correlated with each other. Among them, the correlation coefficient of each evaluation index was highest in poplar …
format: application/pdf
format: text/html
creator: Samuel Adingo
creator: Jie-Ru Yu
creator: Liu Xuelu
creator: Sun Jing
creator: Xiaodan Li
creator: Zhang Xiaoning
subject: Agricultural Science
subject: Soil Science
subject: Biogeochemistry
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.12246
publisher: PeerJ Inc.
rights: © 2021 Adingo et al.
abstract: Dry ecosystems, despite their relative levels of aridity, are very diverse, and play a vital role in the livelihoods of many dryland inhabitants. It is therefore critical to investigate the relationship between land-use change and soil quality parameters to offer a scientific basis for optimizing land-use planning and improving soil quality status in dry ecosystems and ecologically vulnerable areas. This study, therefore, analyzed the physicochemical properties of soils in five different land-use types namely farmland, abandoned farmland, natural grassland, artificial lemon forest, and poplar woodland at YongDeng County. The soil quality status of the aforementioned land-use types was also evaluated through Principal component analysis. The results revealed that abandoned farmland and natural grassland recorded the highest average values of soil coarse particles of 24.0% and 23.4% respectively compared to the other land-use types. The highest average value (46.1%) of fine soil particles was recorded in poplar woodland followed by natural grassland (36.6%) and the average value of very fine soil particles was higher in farmland (40.8%) and artificial lemon woodland (38.3%) than in the other land-use types. The average value of clayey particles was highest in farmland (11.1%), followed by artificial lemon woodland (9.3%), and abandoned farmland (6.5%), then poplar woodland which recorded an average value of (4.2%). The average values of Soil water content, soil pH, soil electrical conductivity, and soil total nitrogen content were significantly higher in farmland compared to the other land-use types. Soil organic carbon content was significantly higher in abandoned farmland at (P < 0.03) and lemon woodland at (P < 0.01) than in farmlands, natural grasslands, and poplar stands. The soil quality indicators of the different land-use types were significantly correlated with each other. Among them, the correlation coefficient of each evaluation index was highest in poplar …
bibliographic citation: Adingo et al. (2021) Land-use change influence soil quality parameters at an ecologically fragile area of YongDeng County of Gansu Province, China. PeerJ 9:e12246 https://doi.org/10.7717/peerj.12246
date submitted: 2021-07-27
date accepted: 2021-09-13
issued: 2021-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adingo
  given name: Samuel
author list: Agent
  family name: Yu
  given name: Jie-Ru
author list: Agent
  family name: Xuelu
  given name: Liu
author list: Agent
  family name: Jing
  given name: Sun
author list: Agent
  family name: Li
  given name: Xiaodan
author list: Agent
  family name: Xiaoning
  given name: Zhang
doi: 10.7717/peerj.12246
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-27
copyright: ©2021 Adingo et al.
attribution name: Adingo et al.

Hierarchical drift diffusion modeling uncovers multisensory benefit in numerosity discrimination tasks
type: item
type: AcademicArticle
description: Studies of accuracy and reaction time in decision making often observe a speed-accuracy tradeoff, where either accuracy or reaction time is sacrificed for the other. While this effect may mask certain multisensory benefits in performance when accuracy and reaction time are separately measured, drift diffusion models (DDMs) are able to consider both simultaneously. However, drift diffusion models are often limited by large sample size requirements for reliable parameter estimation. One solution to this restriction is the use of hierarchical Bayesian estimation for DDM parameters. Here, we utilize hierarchical drift diffusion models (HDDMs) to reveal a multisensory advantage in auditory-visual numerosity discrimination tasks. By fitting this model with a modestly sized dataset, we also demonstrate that large sample sizes are not necessary for reliable parameter estimation.
format: application/pdf
format: text/html
creator: Edwin Chau
creator: Carolyn A. Murray
creator: Ladan Shams
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12273
publisher: PeerJ Inc.
rights: © 2021 Chau et al.
abstract: Studies of accuracy and reaction time in decision making often observe a speed-accuracy tradeoff, where either accuracy or reaction time is sacrificed for the other. While this effect may mask certain multisensory benefits in performance when accuracy and reaction time are separately measured, drift diffusion models (DDMs) are able to consider both simultaneously. However, drift diffusion models are often limited by large sample size requirements for reliable parameter estimation. One solution to this restriction is the use of hierarchical Bayesian estimation for DDM parameters. Here, we utilize hierarchical drift diffusion models (HDDMs) to reveal a multisensory advantage in auditory-visual numerosity discrimination tasks. By fitting this model with a modestly sized dataset, we also demonstrate that large sample sizes are not necessary for reliable parameter estimation.
bibliographic citation: Chau et al. (2021) Hierarchical drift diffusion modeling uncovers multisensory benefit in numerosity discrimination tasks. PeerJ 9:e12273 https://doi.org/10.7717/peerj.12273
date submitted: 2021-05-05
date accepted: 2021-09-19
issued: 2021-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chau
  given name: Edwin
author list: Agent
  family name: Murray
  given name: Carolyn A.
author list: Agent
  family name: Shams
  given name: Ladan
doi: 10.7717/peerj.12273
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-27
copyright: © 2021 Chau et al.
attribution name: Chau et al.

Age and lunar cycle predict harbor porpoise bycatch in the south-western Baltic Sea
type: item
type: AcademicArticle
description: The harbor porpoise, Phocoena phocoena, is the only cetacean regularly occurring in the Baltic Sea. During the last decades, several anthropogenic activities have affected porpoises in the Baltic region. Most notably is bycatch in static fishing gear, such as gill nets, which is the main human-induced cause of death in odontocetes. There is still considerable uncertainty about which factors influence the amount of bycatch. In the present study, we reviewed bycatch data collected from 1987 to 2016 from the south-western Baltic Sea. There was a significant difference in bycatch due to seasonality and region, and there was a higher bycatch rate in juveniles than in adults. The only abiotic factor associated with bycatch was the lunar cycle, with more animals bycaught during a full moon. These results improve our understanding of which biotic and abiotic factors are associated with bycatch of Baltic harbor porpoises, which can be used to strengthen conservation endeavors such as managing fishing efforts.
format: application/pdf
format: text/html
creator: Dennis Brennecke
creator: Magnus Wahlberg
creator: Anita Gilles
creator: Ursula Siebert
subject: Animal Behavior
subject: Conservation Biology
subject: Marine Biology
subject: Zoology
subject: Environmental Impacts
description: doi:10.7717/peerj.12284
publisher: PeerJ Inc.
rights: © 2021 Brennecke et al.
abstract: The harbor porpoise, Phocoena phocoena, is the only cetacean regularly occurring in the Baltic Sea. During the last decades, several anthropogenic activities have affected porpoises in the Baltic region. Most notably is bycatch in static fishing gear, such as gill nets, which is the main human-induced cause of death in odontocetes. There is still considerable uncertainty about which factors influence the amount of bycatch. In the present study, we reviewed bycatch data collected from 1987 to 2016 from the south-western Baltic Sea. There was a significant difference in bycatch due to seasonality and region, and there was a higher bycatch rate in juveniles than in adults. The only abiotic factor associated with bycatch was the lunar cycle, with more animals bycaught during a full moon. These results improve our understanding of which biotic and abiotic factors are associated with bycatch of Baltic harbor porpoises, which can be used to strengthen conservation endeavors such as managing fishing efforts.
bibliographic citation: Brennecke et al. (2021) Age and lunar cycle predict harbor porpoise bycatch in the south-western Baltic Sea. PeerJ 9:e12284 https://doi.org/10.7717/peerj.12284
date submitted: 2021-03-10
date accepted: 2021-09-20
issued: 2021-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brennecke
  given name: Dennis
author list: Agent
  family name: Wahlberg
  given name: Magnus
author list: Agent
  family name: Gilles
  given name: Anita
author list: Agent
  family name: Siebert
  given name: Ursula
doi: 10.7717/peerj.12284
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-27
copyright: ©2021 Brennecke et al.
attribution name: Brennecke et al.

Differences in insectivore bird diets in coffee agroecosystems driven by obligate or generalist guild, shade management, season, and year
type: item
type: AcademicArticle
description: Neotropical shade-grown coffee systems are renowned for their potential to conserve avian biodiversity. Yet, little is known about food resources consumed by insectivorous birds in these systems, the extent of resource competition between resident and migratory birds, or how management of shade trees might influence diet selection. We identified arthropods in stomach contents from obligate and generalist insectivorous birds captured in mist-nets at five coffee farms in Chiapas, Mexico between 2001–2003. Overall stomach contents from 938 individuals revealed dietary differences resulting from changes in seasons, years, and foraging guilds. Of four species sampled across all management systems, Yellow-green Vireo (Vireo flavoviridis) prey differed depending on coffee shade management, consuming more ants in shaded monoculture than polyculture systems. Diets of obligate and generalist resident insectivores were 72% dissimilar with obligate insectivores consuming more Coleoptera and Araneae, and generalist insectivores consuming more Formicidae and other Hymenoptera. This suggests that obligate insectivores target more specialized prey whereas generalist insectivores rely on less favorable, chemically-defended prey found in clumped distributions. Our dataset provides important natural history data for many Nearctic-Neotropical migrants such as Tennessee Warbler (Leiothlypis peregrina; N = 163), Nashville Warbler (Leiothlypis ruficapilla; N = 69), and Swainson’s Thrush (Catharus ustulatus; N = 68) and tropical residents including Red-legged Honeycreepers (Cyanerpes cyaneus; N = 70) and Rufous-capped Warblers (Basileuterus rufifrons; N = 56). With declining arthropod populations worldwide, understanding the ecological interactions between obligate and generalist avian insectivores gives researchers the tools to evaluate community stability and inform conservation efforts.
format: application/pdf
format: text/html
creator: Julie A. Jedlicka
creator: Stacy M. Philpott
creator: Martha L. Baena
creator: Peter Bichier
creator: Thomas V. Dietsch
creator: Laney H. Nute
creator: Suzanne M. Langridge
creator: Ivette Perfecto
creator: Russell Greenberg
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.12296
publisher: PeerJ Inc.
rights: © 2021 Jedlicka et al.
abstract: Neotropical shade-grown coffee systems are renowned for their potential to conserve avian biodiversity. Yet, little is known about food resources consumed by insectivorous birds in these systems, the extent of resource competition between resident and migratory birds, or how management of shade trees might influence diet selection. We identified arthropods in stomach contents from obligate and generalist insectivorous birds captured in mist-nets at five coffee farms in Chiapas, Mexico between 2001–2003. Overall stomach contents from 938 individuals revealed dietary differences resulting from changes in seasons, years, and foraging guilds. Of four species sampled across all management systems, Yellow-green Vireo (Vireo flavoviridis) prey differed depending on coffee shade management, consuming more ants in shaded monoculture than polyculture systems. Diets of obligate and generalist resident insectivores were 72% dissimilar with obligate insectivores consuming more Coleoptera and Araneae, and generalist insectivores consuming more Formicidae and other Hymenoptera. This suggests that obligate insectivores target more specialized prey whereas generalist insectivores rely on less favorable, chemically-defended prey found in clumped distributions. Our dataset provides important natural history data for many Nearctic-Neotropical migrants such as Tennessee Warbler (Leiothlypis peregrina; N = 163), Nashville Warbler (Leiothlypis ruficapilla; N = 69), and Swainson’s Thrush (Catharus ustulatus; N = 68) and tropical residents including Red-legged Honeycreepers (Cyanerpes cyaneus; N = 70) and Rufous-capped Warblers (Basileuterus rufifrons; N = 56). With declining arthropod populations worldwide, understanding the ecological interactions between obligate and generalist avian insectivores gives researchers the tools to evaluate community stability and inform conservation efforts.
bibliographic citation: Jedlicka et al. (2021) Differences in insectivore bird diets in coffee agroecosystems driven by obligate or generalist guild, shade management, season, and year. PeerJ 9:e12296 https://doi.org/10.7717/peerj.12296
date submitted: 2021-06-10
date accepted: 2021-09-21
issued: 2021-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jedlicka
  given name: Julie A.
author list: Agent
  family name: Philpott
  given name: Stacy M.
author list: Agent
  family name: Baena
  given name: Martha L.
author list: Agent
  family name: Bichier
  given name: Peter
author list: Agent
  family name: Dietsch
  given name: Thomas V.
author list: Agent
  family name: Nute
  given name: Laney H.
author list: Agent
  family name: Langridge
  given name: Suzanne M.
author list: Agent
  family name: Perfecto
  given name: Ivette
author list: Agent
  family name: Greenberg
  given name: Russell
doi: 10.7717/peerj.12296
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-27
copyright: © 2021 Jedlicka et al.
attribution name: Jedlicka et al.

Relatively low tooth replacement rate in a sauropod dinosaur from the Early Cretaceous Ruyang Basin of central China
type: item
type: AcademicArticle
description: Tooth replacement rate is an important feature related to feeding mechanics and food choices for dinosaurs. However, only a few data points are available for sauropod dinosaurs, partially due to rarity of relevant fossil material. Four somphospondylan sauropod species have been recovered from the Lower Cretaceous Aptian–Albian Haoling Formation in the Ruyang Basin, Henan Province of central China, but no cranial material has been reported except for a single crown. Here we report the discovery of the rostral portion of a left dentary with replacement teeth in its first five alveoli. Comparative anatomical study shows the partial dentary can be assigned to a member of early diverging somphospondylans. The non-destructive tooth length-based approach to estimating tooth formation time and replacement rate is adopted here. The estimated tooth replacement rate is 76 days, faster than that of Brachiosaurus (83 days) and much lower than typical late diverging lithostrotian titanosaurians (20 days). Thus, this discovery adds an intermediate tooth replacement rate in the evolution of titanosauriform sauropods and supports the idea that evolution of tooth replacement rate is clade-specific. This discovery also provides more information to understand the Ruyang sauropod assemblage, which includes one of the most giant dinosaurs to have walked our Earth (Ruyangosaurus giganteus).
format: application/pdf
format: text/html
creator: Huali Chang
creator: Hai-Lu You
creator: Li Xu
creator: Waisum Ma
creator: Diansong Gao
creator: Songhai Jia
creator: Mengli Xia
creator: Jiming Zhang
creator: Yu Li
creator: Xirui Wang
creator: Di Liu
creator: Jie Li
creator: Jianhua Zhang
creator: Lili Yang
creator: Xuefang Wei
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.12361
publisher: PeerJ Inc.
rights: © 2021 Chang et al.
abstract: Tooth replacement rate is an important feature related to feeding mechanics and food choices for dinosaurs. However, only a few data points are available for sauropod dinosaurs, partially due to rarity of relevant fossil material. Four somphospondylan sauropod species have been recovered from the Lower Cretaceous Aptian–Albian Haoling Formation in the Ruyang Basin, Henan Province of central China, but no cranial material has been reported except for a single crown. Here we report the discovery of the rostral portion of a left dentary with replacement teeth in its first five alveoli. Comparative anatomical study shows the partial dentary can be assigned to a member of early diverging somphospondylans. The non-destructive tooth length-based approach to estimating tooth formation time and replacement rate is adopted here. The estimated tooth replacement rate is 76 days, faster than that of Brachiosaurus (83 days) and much lower than typical late diverging lithostrotian titanosaurians (20 days). Thus, this discovery adds an intermediate tooth replacement rate in the evolution of titanosauriform sauropods and supports the idea that evolution of tooth replacement rate is clade-specific. This discovery also provides more information to understand the Ruyang sauropod assemblage, which includes one of the most giant dinosaurs to have walked our Earth (Ruyangosaurus giganteus).
bibliographic citation: Chang et al. (2021) Relatively low tooth replacement rate in a sauropod dinosaur from the Early Cretaceous Ruyang Basin of central China. PeerJ 9:e12361 https://doi.org/10.7717/peerj.12361
date submitted: 2021-06-08
date accepted: 2021-09-30
issued: 2021-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chang
  given name: Huali
author list: Agent
  family name: You
  given name: Hai-Lu
author list: Agent
  family name: Xu
  given name: Li
author list: Agent
  family name: Ma
  given name: Waisum
author list: Agent
  family name: Gao
  given name: Diansong
author list: Agent
  family name: Jia
  given name: Songhai
author list: Agent
  family name: Xia
  given name: Mengli
author list: Agent
  family name: Zhang
  given name: Jiming
author list: Agent
  family name: Li
  given name: Yu
author list: Agent
  family name: Wang
  given name: Xirui
author list: Agent
  family name: Liu
  given name: Di
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Zhang
  given name: Jianhua
author list: Agent
  family name: Yang
  given name: Lili
author list: Agent
  family name: Wei
  given name: Xuefang
doi: 10.7717/peerj.12361
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-27
copyright: ©2021 Chang et al.
attribution name: Chang et al.

In vitro induction and identification of polyploid Neolamarckia cadamba plants by colchicine treatment
type: item
type: AcademicArticle
description: Polyploidization has played a crucial role in plant breeding and crop improvement. However, studies on the polyploidization of tropical tree species are still very scarce in this region. This paper described the in vitro induction and identification of polyploid plants of Neolamarckia cadamba by colchicine treatment. N. cadamba belongs to the Rubiaceae family is a natural tetraploid plant with 44 chromosomes (2n = 4x = 44). Nodal segments were treated with colchicine (0.1%, 0.3% and 0.5%) for 24 h and 48 h before transferring to shoot regeneration medium. Flow cytometry (FCM) and chromosome count were employed to determine the ploidy level and chromosome number of the regenerants, respectively. Of 180 colchicine-treated nodal segments, 39, 14 and 22 were tetraploids, mixoploids and octoploids, respectively. The highest percentage of polyploidization (20% octoploids; 6.7% mixoploids) was observed after treated with 0.3% colchicine for 48 h. The DNA content of tetraploid (4C) and octoploid (8C) was 2.59 ± 0.09 pg and 5.35 ± 0.24 pg, respectively. Mixoploid plants are made up of mixed tetraploid and octoploid cells. Chromosome count confirmed that tetraploid cell has 44 chromosomes and colchicine-induced octoploid cell has 88 chromosomes. Both octoploids and mixoploids grew slower than tetraploids under in vitro conditions. Morphological characterizations showed that mixoploid and octoploid leaves had thicker leaf blades, thicker midrib, bigger stomata size, lower stomata density, higher SPAD value and smaller pith layer than tetraploids. This indicates that polyploidization has changed and resulted in traits that are predicted to increase photosynthetic capacity of N. cadamba. These novel polyploid plants could be valuable resources for advanced N. cadamba breeding programs to produce improved clones for planted forest development.
format: application/pdf
format: text/html
creator: Wee Hiang Eng
creator: Wei Seng Ho
creator: Kwong Hung Ling
subject: Agricultural Science
subject: Biotechnology
subject: Plant Science
description: doi:10.7717/peerj.12399
publisher: PeerJ Inc.
rights: © 2021 Eng et al.
abstract: Polyploidization has played a crucial role in plant breeding and crop improvement. However, studies on the polyploidization of tropical tree species are still very scarce in this region. This paper described the in vitro induction and identification of polyploid plants of Neolamarckia cadamba by colchicine treatment. N. cadamba belongs to the Rubiaceae family is a natural tetraploid plant with 44 chromosomes (2n = 4x = 44). Nodal segments were treated with colchicine (0.1%, 0.3% and 0.5%) for 24 h and 48 h before transferring to shoot regeneration medium. Flow cytometry (FCM) and chromosome count were employed to determine the ploidy level and chromosome number of the regenerants, respectively. Of 180 colchicine-treated nodal segments, 39, 14 and 22 were tetraploids, mixoploids and octoploids, respectively. The highest percentage of polyploidization (20% octoploids; 6.7% mixoploids) was observed after treated with 0.3% colchicine for 48 h. The DNA content of tetraploid (4C) and octoploid (8C) was 2.59 ± 0.09 pg and 5.35 ± 0.24 pg, respectively. Mixoploid plants are made up of mixed tetraploid and octoploid cells. Chromosome count confirmed that tetraploid cell has 44 chromosomes and colchicine-induced octoploid cell has 88 chromosomes. Both octoploids and mixoploids grew slower than tetraploids under in vitro conditions. Morphological characterizations showed that mixoploid and octoploid leaves had thicker leaf blades, thicker midrib, bigger stomata size, lower stomata density, higher SPAD value and smaller pith layer than tetraploids. This indicates that polyploidization has changed and resulted in traits that are predicted to increase photosynthetic capacity of N. cadamba. These novel polyploid plants could be valuable resources for advanced N. cadamba breeding programs to produce improved clones for planted forest development.
bibliographic citation: Eng et al. (2021) In vitro induction and identification of polyploid Neolamarckia cadamba plants by colchicine treatment. PeerJ 9:e12399 https://doi.org/10.7717/peerj.12399
date submitted: 2021-07-15
date accepted: 2021-10-06
issued: 2021-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eng
  given name: Wee Hiang
author list: Agent
  family name: Ho
  given name: Wei Seng
author list: Agent
  family name: Ling
  given name: Kwong Hung
doi: 10.7717/peerj.12399
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-27
copyright: ©2021 Eng et al.
attribution name: Eng et al.

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