PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The reuse of public datasets in the life sciences: potential risks and rewards
items: Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle
items: Species distribution modelling of Bryde’s whales, humpback whales, southern right whales, and sperm whales in the southern African region to inform their conservation in expanding economies
items: Quinquelaophonte enormis sp. nov., a new interstitial copepod (Harpacticoida: Laophontidae) from Korea
items: Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)
items: No Mow May lawns have higher pollinator richness and abundances: An engaged community provides floral resources for pollinators
items: A comparison of sex, morphology, physiology and behavior of black-capped chickadees trapped using two common capture methods
items: A laboratory comparison of the interactions between three plastic mulch types and 38 active substances found in pesticides
items: Nest-site selection and breeding success of passerines in the world’s southernmost forests
items: Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus)

The reuse of public datasets in the life sciences: potential risks and rewards
type: item
type: AcademicArticle
description: The ‘big data’ revolution has enabled novel types of analyses in the life sciences, facilitated by public sharing and reuse of datasets. Here, we review the prodigious potential of reusing publicly available datasets and the associated challenges, limitations and risks. Possible solutions to issues and research integrity considerations are also discussed. Due to the prominence, abundance and wide distribution of sequencing data, we focus on the reuse of publicly available sequence datasets. We define ‘successful reuse’ as the use of previously published data to enable novel scientific findings. By using selected examples of successful reuse from different disciplines, we illustrate the enormous potential of the practice, while acknowledging the respective limitations and risks. A checklist to determine the reuse value and potential of a particular dataset is also provided. The open discussion of data reuse and the establishment of this practice as a norm has the potential to benefit all stakeholders in the life sciences.
format: application/pdf
format: text/html
creator: Katharina Sielemann
creator: Alenka Hafner
creator: Boas Pucker
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Computational Science
subject: Data Science
description: doi:10.7717/peerj.9954
publisher: PeerJ Inc.
rights: © 2020 Sielemann et al.
abstract: The ‘big data’ revolution has enabled novel types of analyses in the life sciences, facilitated by public sharing and reuse of datasets. Here, we review the prodigious potential of reusing publicly available datasets and the associated challenges, limitations and risks. Possible solutions to issues and research integrity considerations are also discussed. Due to the prominence, abundance and wide distribution of sequencing data, we focus on the reuse of publicly available sequence datasets. We define ‘successful reuse’ as the use of previously published data to enable novel scientific findings. By using selected examples of successful reuse from different disciplines, we illustrate the enormous potential of the practice, while acknowledging the respective limitations and risks. A checklist to determine the reuse value and potential of a particular dataset is also provided. The open discussion of data reuse and the establishment of this practice as a norm has the potential to benefit all stakeholders in the life sciences.
bibliographic citation: Sielemann et al. (2020) The reuse of public datasets in the life sciences: potential risks and rewards. PeerJ 8:e9954 https://doi.org/10.7717/peerj.9954
date submitted: 2020-04-30
date accepted: 2020-08-25
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sielemann
  given name: Katharina
author list: Agent
  family name: Hafner
  given name: Alenka
author list: Agent
  family name: Pucker
  given name: Boas
doi: 10.7717/peerj.9954
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: © 2020 Sielemann et al.
attribution name: Sielemann et al.

Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle
type: item
type: AcademicArticle
description: The sheep is an economically important animal, and there is currently a major focus on improving its meat quality through breeding. There are variations in the growth regulation mechanisms of different sheep breeds, making fundamental research on skeletal muscle growth essential in understanding the regulation of (thus far) unknown genes. Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In this study, we used deep sequencing data from sheep longissimus dorsi (LD) muscles sampled at day 60, 90, and 120 of gestation, as well as at day 0 and 360 following birth, to identify and examine the lncRNA and miRNA temporal expression profiles that regulate sheep skeletal myogenesis. We stained LD muscles using histological sections to analyse the area and circumference of muscle fibers from the embryonic to postnatal development stages. Our results showed that embryonic skeletal muscle growth can be characterized by time. We obtained a total of 694 different lncRNAs and compared the differential expression between the E60 vs. E90, E90 vs. E120, E120 vs. D0, and D0 vs. D360 lncRNA and gene samples. Of the total 701 known sheep miRNAs we detected, the following showed a wide range of expression during the embryonic stage: miR-2387, miR-105, miR-767, miR-432, and miR-433. We propose that the detected lncRNA expression was time-specific during the gestational and postnatal stages. GO and KEGG analyses of the genes targeted by different miRNAs and lncRNAs revealed that these significantly enriched processes and pathways were consistent with skeletal muscle development over time across all sampled stages. We found four visual lncRNA–gene regulatory networks that can be used to explore the function of lncRNAs in sheep and may be valuable in helping improve muscle growth. This study also describes the function of several lncRNAs that interact with miRNAs to regu…
format: application/pdf
format: text/html
creator: Chao Yuan
creator: Ke Zhang
creator: Yaojing Yue
creator: Tingting Guo
creator: Jianbin Liu
creator: Chune Niu
creator: Xiaoping Sun
creator: Ruilin Feng
creator: Xiaolong Wang
creator: Bohui Yang
subject: Bioinformatics
subject: Developmental Biology
subject: Genetics
description: doi:10.7717/peerj.9957
publisher: PeerJ Inc.
rights: © 2020 Yuan et al.
abstract: The sheep is an economically important animal, and there is currently a major focus on improving its meat quality through breeding. There are variations in the growth regulation mechanisms of different sheep breeds, making fundamental research on skeletal muscle growth essential in understanding the regulation of (thus far) unknown genes. Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In this study, we used deep sequencing data from sheep longissimus dorsi (LD) muscles sampled at day 60, 90, and 120 of gestation, as well as at day 0 and 360 following birth, to identify and examine the lncRNA and miRNA temporal expression profiles that regulate sheep skeletal myogenesis. We stained LD muscles using histological sections to analyse the area and circumference of muscle fibers from the embryonic to postnatal development stages. Our results showed that embryonic skeletal muscle growth can be characterized by time. We obtained a total of 694 different lncRNAs and compared the differential expression between the E60 vs. E90, E90 vs. E120, E120 vs. D0, and D0 vs. D360 lncRNA and gene samples. Of the total 701 known sheep miRNAs we detected, the following showed a wide range of expression during the embryonic stage: miR-2387, miR-105, miR-767, miR-432, and miR-433. We propose that the detected lncRNA expression was time-specific during the gestational and postnatal stages. GO and KEGG analyses of the genes targeted by different miRNAs and lncRNAs revealed that these significantly enriched processes and pathways were consistent with skeletal muscle development over time across all sampled stages. We found four visual lncRNA–gene regulatory networks that can be used to explore the function of lncRNAs in sheep and may be valuable in helping improve muscle growth. This study also describes the function of several lncRNAs that interact with miRNAs to regu…
bibliographic citation: Yuan et al. (2020) Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle. PeerJ 8:e9957 https://doi.org/10.7717/peerj.9957
date submitted: 2019-11-22
date accepted: 2020-08-25
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Chao
author list: Agent
  family name: Zhang
  given name: Ke
author list: Agent
  family name: Yue
  given name: Yaojing
author list: Agent
  family name: Guo
  given name: Tingting
author list: Agent
  family name: Liu
  given name: Jianbin
author list: Agent
  family name: Niu
  given name: Chune
author list: Agent
  family name: Sun
  given name: Xiaoping
author list: Agent
  family name: Feng
  given name: Ruilin
author list: Agent
  family name: Wang
  given name: Xiaolong
author list: Agent
  family name: Yang
  given name: Bohui
doi: 10.7717/peerj.9957
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Yuan et al.
attribution name: Yuan et al.

Species distribution modelling of Bryde’s whales, humpback whales, southern right whales, and sperm whales in the southern African region to inform their conservation in expanding economies
type: item
type: AcademicArticle
description: In southern African waters, information about species distribution and habitat preferences of many cetacean species is limited, despite the recent economic growth that may affect them. We determined the relative importance of eight environmental variables (bathymetry, distance to shore, slope, chlorophyll-a, salinity, eastwards sea water velocity, northwards sea water velocity and sea surface temperature) as drivers of seasonal habitat preferences of Bryde’s whales (Balaenoptera brydei), humpback whales (Megaptera novaeangliae), southern right whales (Eubalaena australis) and sperm whales (Physeter macrocephalus). Using presence only data from multiple sources, we constructed predictive species distribution models (SDMs) consisting of ensembles of seven algorithms for these species during both summer and winter. Predicted distribution for all cetaceans was high in southern Africa and, in particular, within the South African Exclusive Economic Zone (EEZ). Predictive models indicated a more pronounced seasonal variation for humpback, sperm and southern right whales than for Bryde’s whales. Southern right whales occurred closer to shore during winter, humpback whales were more likely to occur along the east coast in winter and the west coast in summer, and sperm whales were more concentrated off the shelf in winter. Our study shows that ensemble models using historical, incidental and scientific data, in conjunction with modern environmental variables, can provide baseline knowledge on important environmental drivers of cetacean distribution for conservation purposes. Results of this study can further be used to help develop marine spatial plans and identify important marine mammal areas.
format: application/pdf
format: text/html
creator: Jean Purdon
creator: Fannie W. Shabangu
creator: Dawit Yemane
creator: Marc Pienaar
creator: Michael J. Somers
creator: Ken Findlay
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Environmental Impacts
description: doi:10.7717/peerj.9997
publisher: PeerJ Inc.
rights: © 2020 Purdon et al.
abstract: In southern African waters, information about species distribution and habitat preferences of many cetacean species is limited, despite the recent economic growth that may affect them. We determined the relative importance of eight environmental variables (bathymetry, distance to shore, slope, chlorophyll-a, salinity, eastwards sea water velocity, northwards sea water velocity and sea surface temperature) as drivers of seasonal habitat preferences of Bryde’s whales (Balaenoptera brydei), humpback whales (Megaptera novaeangliae), southern right whales (Eubalaena australis) and sperm whales (Physeter macrocephalus). Using presence only data from multiple sources, we constructed predictive species distribution models (SDMs) consisting of ensembles of seven algorithms for these species during both summer and winter. Predicted distribution for all cetaceans was high in southern Africa and, in particular, within the South African Exclusive Economic Zone (EEZ). Predictive models indicated a more pronounced seasonal variation for humpback, sperm and southern right whales than for Bryde’s whales. Southern right whales occurred closer to shore during winter, humpback whales were more likely to occur along the east coast in winter and the west coast in summer, and sperm whales were more concentrated off the shelf in winter. Our study shows that ensemble models using historical, incidental and scientific data, in conjunction with modern environmental variables, can provide baseline knowledge on important environmental drivers of cetacean distribution for conservation purposes. Results of this study can further be used to help develop marine spatial plans and identify important marine mammal areas.
bibliographic citation: Purdon et al. (2020) Species distribution modelling of Bryde’s whales, humpback whales, southern right whales, and sperm whales in the southern African region to inform their conservation in expanding economies. PeerJ 8:e9997 https://doi.org/10.7717/peerj.9997
date submitted: 2020-01-16
date accepted: 2020-08-28
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Purdon
  given name: Jean
author list: Agent
  family name: Shabangu
  given name: Fannie W.
author list: Agent
  family name: Yemane
  given name: Dawit
author list: Agent
  family name: Pienaar
  given name: Marc
author list: Agent
  family name: Somers
  given name: Michael J.
author list: Agent
  family name: Findlay
  given name: Ken
doi: 10.7717/peerj.9997
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Purdon et al.
attribution name: Purdon et al.

Quinquelaophonte enormis sp. nov., a new interstitial copepod (Harpacticoida: Laophontidae) from Korea
type: item
type: AcademicArticle
description: We collected an undescribed laophontid copepod from a coarse sand habitat on the east coast of Korea and named it Quinquelaophonte enormis sp. nov. We compared the detailed morphological characteristics of the new species with those of congeneric species. Among them, the new species shows a superficial resemblance to the Californian species Quinquelaophonte longifurcata Lang, 1965. However, the two species are easily distinguishable by the setation of the syncoxa on the maxilliped and the fourth swimming leg. The new species has the variable setation on the second to fourth swimming legs. The variations appear among individuals or between the left and right rami of a pair of legs in a single specimen. Although complex chaetotaxical polymorphism occur in this new species, we used myCOI and Cytb to confirm that the new species is not a species complex. Also, partial sequences of 18S and 28S ribosomal RNA genes were used to analyze the position of the new species within the family Laophontidae. The new speciesis the fourteenth Quinquelaophonte species in the world and the second species in Korea.
format: application/pdf
format: text/html
creator: Jaehyun Kim
creator: Eunjung Nam
creator: Wonchoel Lee
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10007
publisher: PeerJ Inc.
rights: © 2020 Kim et al.
abstract: We collected an undescribed laophontid copepod from a coarse sand habitat on the east coast of Korea and named it Quinquelaophonte enormis sp. nov. We compared the detailed morphological characteristics of the new species with those of congeneric species. Among them, the new species shows a superficial resemblance to the Californian species Quinquelaophonte longifurcata Lang, 1965. However, the two species are easily distinguishable by the setation of the syncoxa on the maxilliped and the fourth swimming leg. The new species has the variable setation on the second to fourth swimming legs. The variations appear among individuals or between the left and right rami of a pair of legs in a single specimen. Although complex chaetotaxical polymorphism occur in this new species, we used myCOI and Cytb to confirm that the new species is not a species complex. Also, partial sequences of 18S and 28S ribosomal RNA genes were used to analyze the position of the new species within the family Laophontidae. The new speciesis the fourteenth Quinquelaophonte species in the world and the second species in Korea.
bibliographic citation: Kim et al. (2020) Quinquelaophonte enormis sp. nov., a new interstitial copepod (Harpacticoida: Laophontidae) from Korea. PeerJ 8:e10007 https://doi.org/10.7717/peerj.10007
date submitted: 2020-06-17
date accepted: 2020-08-31
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Jaehyun
author list: Agent
  family name: Nam
  given name: Eunjung
author list: Agent
  family name: Lee
  given name: Wonchoel
doi: 10.7717/peerj.10007
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Kim et al.
attribution name: Kim et al.

Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)
type: item
type: AcademicArticle
description: Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 ERF genes (AcoERFs) were identified in pineapple genome, named from AcoERF1 to AcoERF74, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of AcoERFs, and the AcoERFs within the same group possess similar gene structures and motif compositions. Three genes (AcoERF71, AcoERF73 and AcoERF74) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and cis-elements analysis of ERF genes provided deep insight into the evolution and function of pineapple ERF genes. Furthermore, we analyzed the expression profiling of AcoERF in different tissues and developmental stages, and 22 AcoERF genes were expressed in all examined tissues, in which five genes (AcoERF13, AcoERF16, AcoERF31, AcoERF42, and AcoERF65) had high expression levels. Additionally, nine AcoERF genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple.
format: application/pdf
format: text/html
creator: Youmei Huang
creator: Yanhui Liu
creator: Man Zhang
creator: Mengnan Chai
creator: Qing He
creator: Bello Hassan Jakada
creator: Fangqian Chen
creator: Huihuang Chen
creator: Xingyue Jin
creator: Hanyang Cai
creator: Yuan Qin
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.10014
publisher: PeerJ Inc.
rights: © 2020 Huang et al.
abstract: Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 ERF genes (AcoERFs) were identified in pineapple genome, named from AcoERF1 to AcoERF74, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of AcoERFs, and the AcoERFs within the same group possess similar gene structures and motif compositions. Three genes (AcoERF71, AcoERF73 and AcoERF74) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and cis-elements analysis of ERF genes provided deep insight into the evolution and function of pineapple ERF genes. Furthermore, we analyzed the expression profiling of AcoERF in different tissues and developmental stages, and 22 AcoERF genes were expressed in all examined tissues, in which five genes (AcoERF13, AcoERF16, AcoERF31, AcoERF42, and AcoERF65) had high expression levels. Additionally, nine AcoERF genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple.
bibliographic citation: Huang et al. (2020) Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.). PeerJ 8:e10014 https://doi.org/10.7717/peerj.10014
date submitted: 2020-04-21
date accepted: 2020-09-01
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Youmei
author list: Agent
  family name: Liu
  given name: Yanhui
author list: Agent
  family name: Zhang
  given name: Man
author list: Agent
  family name: Chai
  given name: Mengnan
author list: Agent
  family name: He
  given name: Qing
author list: Agent
  family name: Jakada
  given name: Bello Hassan
author list: Agent
  family name: Chen
  given name: Fangqian
author list: Agent
  family name: Chen
  given name: Huihuang
author list: Agent
  family name: Jin
  given name: Xingyue
author list: Agent
  family name: Cai
  given name: Hanyang
author list: Agent
  family name: Qin
  given name: Yuan
doi: 10.7717/peerj.10014
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Huang et al.
attribution name: Huang et al.

No Mow May lawns have higher pollinator richness and abundances: An engaged community provides floral resources for pollinators
type: item
type: AcademicArticle
description: No Mow May is a community science initiative popularized in recent years that encourages property owners to limit their lawn mowing practices during the month of May. The goal of No Mow May is to provide early season foraging resources for pollinators that emerge in the spring, especially in urban landscapes when few floral resources are available. We worked with the city council of Appleton, Wisconsin, USA. to allow No Mow May to take place in May 2020. Four hundred and thirty-five property owners registered for No Mow May in Appleton. We measured floral and bee richness and abundance in the yards of a subset of homes (N = 20) located near regularly mowed urban parks (N = 15) at the end of the month. We found that homes that participated in No Mow May had more diverse and abundant flora than regularly mowed green spaces throughout the city. No Mow May homes had three times higher bee richness and five times higher bee abundances than frequently mowed greenspaces. Using generalized linear models, we found that the best predictor of bee richness was the size of the designated unmowed area, and the best predictors of bee abundances were the size of the unmowed area as well as floral richness. While our findings cannot conclusively attribute increases in bee abundances and richness to the No Mow May efforts, our data does show that bee pollinators make use of no mow spaces as key floral resources during early spring in the upper midwestern United States. A post-No Mow May survey revealed that the participants were keen to increase native floral resources in their yards, increase native bee nesting habitat, reduce mowing intensities, and limit herbicide, pesticide, and fertilizer applications to their lawns. The No Mow May initiative educated an engaged community on best practices to improve the conservation of urban pollinators in future years.
format: application/pdf
format: text/html
creator: Israel Del Toro
creator: Relena R. Ribbons
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.10021
publisher: PeerJ Inc.
rights: © 2020 Del Toro et al.
abstract: No Mow May is a community science initiative popularized in recent years that encourages property owners to limit their lawn mowing practices during the month of May. The goal of No Mow May is to provide early season foraging resources for pollinators that emerge in the spring, especially in urban landscapes when few floral resources are available. We worked with the city council of Appleton, Wisconsin, USA. to allow No Mow May to take place in May 2020. Four hundred and thirty-five property owners registered for No Mow May in Appleton. We measured floral and bee richness and abundance in the yards of a subset of homes (N = 20) located near regularly mowed urban parks (N = 15) at the end of the month. We found that homes that participated in No Mow May had more diverse and abundant flora than regularly mowed green spaces throughout the city. No Mow May homes had three times higher bee richness and five times higher bee abundances than frequently mowed greenspaces. Using generalized linear models, we found that the best predictor of bee richness was the size of the designated unmowed area, and the best predictors of bee abundances were the size of the unmowed area as well as floral richness. While our findings cannot conclusively attribute increases in bee abundances and richness to the No Mow May efforts, our data does show that bee pollinators make use of no mow spaces as key floral resources during early spring in the upper midwestern United States. A post-No Mow May survey revealed that the participants were keen to increase native floral resources in their yards, increase native bee nesting habitat, reduce mowing intensities, and limit herbicide, pesticide, and fertilizer applications to their lawns. The No Mow May initiative educated an engaged community on best practices to improve the conservation of urban pollinators in future years.
bibliographic citation: Del Toro et al. (2020) No Mow May lawns have higher pollinator richness and abundances: An engaged community provides floral resources for pollinators. PeerJ 8:e10021 https://doi.org/10.7717/peerj.10021
date submitted: 2020-06-26
date accepted: 2020-09-02
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Del Toro
  given name: Israel
author list: Agent
  family name: Ribbons
  given name: Relena R.
doi: 10.7717/peerj.10021
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Del Toro and Ribbons
attribution name: Del Toro et al.

A comparison of sex, morphology, physiology and behavior of black-capped chickadees trapped using two common capture methods
type: item
type: AcademicArticle
description: Many biological studies require the capture of individuals for sampling, for example for measurement of morphological or physiological traits, or for marking individuals for later observations. Capture methods employed often vary both within and between studies, and these differing methods could be more or less effective in capture of different individuals based on their morphology or behavior. If individuals that are prone to capture by the selected method differ with respect to traits of interest, such sampling bias could generate misleading or simply inaccurate results. The selection of capture methods could introduce two different forms of sampling bias, with the individuals that are sampled differing from the population at large or with individuals sampled via one method differing from individuals that could be sampled using a different method. We investigated this latter form of sampling bias by comparing individual birds sampled using two common capture techniques. We caught free-ranging black-capped chickadees (Poecile atricapillus) using walk-in traps baited with seed and mist nets paired with playback of an audio stimulus (conspecific mobbing calls). We measured 18 traits that we expect might vary among birds that are trappable by these differing methods—one that targets birds that are food motivated and potentially less neophobic and another that targets birds that respond readily to a perceived predation risk. We found no differences in the sex, morphology, initial and stress-induced corticosterone concentrations, behavioral response to a novel object, or behavioral response to a predator between individuals captured by these two methods. Individual variation in the behavioral response to a novel object was greater among birds caught by mist nets, suggesting this method might provide a sample that better reflects population-level individual variation. We do not know if the birds caught by these two methods provide a representative sample of the populatio…
format: application/pdf
format: text/html
creator: Sara M. Burns
creator: Frances Bonier
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.10037
publisher: PeerJ Inc.
rights: © 2020 Burns and Bonier
abstract: Many biological studies require the capture of individuals for sampling, for example for measurement of morphological or physiological traits, or for marking individuals for later observations. Capture methods employed often vary both within and between studies, and these differing methods could be more or less effective in capture of different individuals based on their morphology or behavior. If individuals that are prone to capture by the selected method differ with respect to traits of interest, such sampling bias could generate misleading or simply inaccurate results. The selection of capture methods could introduce two different forms of sampling bias, with the individuals that are sampled differing from the population at large or with individuals sampled via one method differing from individuals that could be sampled using a different method. We investigated this latter form of sampling bias by comparing individual birds sampled using two common capture techniques. We caught free-ranging black-capped chickadees (Poecile atricapillus) using walk-in traps baited with seed and mist nets paired with playback of an audio stimulus (conspecific mobbing calls). We measured 18 traits that we expect might vary among birds that are trappable by these differing methods—one that targets birds that are food motivated and potentially less neophobic and another that targets birds that respond readily to a perceived predation risk. We found no differences in the sex, morphology, initial and stress-induced corticosterone concentrations, behavioral response to a novel object, or behavioral response to a predator between individuals captured by these two methods. Individual variation in the behavioral response to a novel object was greater among birds caught by mist nets, suggesting this method might provide a sample that better reflects population-level individual variation. We do not know if the birds caught by these two methods provide a representative sample of the populatio…
bibliographic citation: Burns et al. (2020) A comparison of sex, morphology, physiology and behavior of black-capped chickadees trapped using two common capture methods. PeerJ 8:e10037 https://doi.org/10.7717/peerj.10037
date submitted: 2020-03-04
date accepted: 2020-09-03
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Burns
  given name: Sara M.
author list: Agent
  family name: Bonier
  given name: Frances
doi: 10.7717/peerj.10037
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: © 2020 Burns and Bonier
attribution name: Burns and Bonier

A laboratory comparison of the interactions between three plastic mulch types and 38 active substances found in pesticides
type: item
type: AcademicArticle
description: Background In semi-arid regions, the use of plastic mulch and pesticides in conventional agriculture is nearly ubiquitous. Although the sorption of pesticides on Low Density Polyethylene (LDPE) has been previously studied, no data are available for other plastics such as Pro-oxidant Additive Containing (PAC) plastics or “biodegradable” (Bio) plastics. The aim of this research was to measure the sorption pattern of active substances from pesticides on LDPE, PAC and Bio plastic mulches and to compare the decay of the active substances in the presence and absence of plastic debris. Methods For this purpose, 38 active substances from 17 insecticides, 15 fungicides and six herbicides commonly applied with plastic mulching in South-east Spain were incubated with a 3 × 3 cm2 piece of plastic mulch (LDPE, PAC and Bio). The incubation was done in a solution of 10% acetonitrile and 90% distilled water at 35 °C for 15 days in the dark. The Quick Easy Cheap Effective Rugged Safe approach was adapted to extract the pesticides. Results The sorption behavior depended on both the pesticide and the plastic mulch type. On average, the sorption percentage was ~23% on LDPE and PAC and ~50% on Bio. The decay of active substances in the presence of plastic was ~30% lesser than the decay of active substances in solution alone. This study is the first attempt at assessing the behavior of a diversity of plastic mulches and pesticides to further define research needs.
format: application/pdf
format: text/html
creator: Nicolas Beriot
creator: Paul Zomer
creator: Raul Zornoza
creator: Violette Geissen
subject: Agricultural Science
subject: Soil Science
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
subject: Green Chemistry
description: doi:10.7717/peerj.9876
publisher: PeerJ Inc.
rights: © 2020 Beriot et al.
abstract: Background In semi-arid regions, the use of plastic mulch and pesticides in conventional agriculture is nearly ubiquitous. Although the sorption of pesticides on Low Density Polyethylene (LDPE) has been previously studied, no data are available for other plastics such as Pro-oxidant Additive Containing (PAC) plastics or “biodegradable” (Bio) plastics. The aim of this research was to measure the sorption pattern of active substances from pesticides on LDPE, PAC and Bio plastic mulches and to compare the decay of the active substances in the presence and absence of plastic debris. Methods For this purpose, 38 active substances from 17 insecticides, 15 fungicides and six herbicides commonly applied with plastic mulching in South-east Spain were incubated with a 3 × 3 cm2 piece of plastic mulch (LDPE, PAC and Bio). The incubation was done in a solution of 10% acetonitrile and 90% distilled water at 35 °C for 15 days in the dark. The Quick Easy Cheap Effective Rugged Safe approach was adapted to extract the pesticides. Results The sorption behavior depended on both the pesticide and the plastic mulch type. On average, the sorption percentage was ~23% on LDPE and PAC and ~50% on Bio. The decay of active substances in the presence of plastic was ~30% lesser than the decay of active substances in solution alone. This study is the first attempt at assessing the behavior of a diversity of plastic mulches and pesticides to further define research needs.
bibliographic citation: Beriot et al. (2020) A laboratory comparison of the interactions between three plastic mulch types and 38 active substances found in pesticides. PeerJ 8:e9876 https://doi.org/10.7717/peerj.9876
date submitted: 2020-02-26
date accepted: 2020-08-14
issued: 2020-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beriot
  given name: Nicolas
author list: Agent
  family name: Zomer
  given name: Paul
author list: Agent
  family name: Zornoza
  given name: Raul
author list: Agent
  family name: Geissen
  given name: Violette
doi: 10.7717/peerj.9876
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-21
copyright: © 2020 Beriot et al.
attribution name: Beriot et al.

Nest-site selection and breeding success of passerines in the world’s southernmost forests
type: item
type: AcademicArticle
description: Background Birds can maximize their reproductive success through careful selection of nest-sites. The ‘total-foliage’ hypothesis predicts that nests concealed in vegetation should have higher survival. We propose an additional hypothesis, the ‘predator proximity’ hypothesis, which states that nests placed farther from predators would have higher survival. We examined these hypotheses in the world’s southernmost forests of Navarino Island, in the Cape Horn Biosphere reserve, Chile (55°S). This island has been free of mammalian ground predators until recently, and forest passerines have been subject to depredation only by diurnal and nocturnal raptors. Methods During three breeding seasons (2014–2017), we monitored 104 nests for the five most abundant open-cup forest-dwelling passerines (Elaenia albiceps, Zonotrichia capensis, Phrygilus patagonicus, Turdus falcklandii, and Anairetes parulus). We identified nest predators using camera traps and assessed whether habitat characteristics affected nest-site selection and survival. Results Nest predation was the main cause of nest failure (71% of failed nests). Milvago chimango was the most common predator, depredating 13 (87%) of the 15 nests where we could identify a predator. By contrast, the recently introduced mammal Neovison vison, the only ground predator, depredated one nest (7%). Species selected nest-sites with more understory cover and taller understory, which according to the total-foliage hypothesis would provide more concealment against both avian and mammal predators. However, these variables negatively influenced nest survival. The apparent disconnect between selecting nest-sites to avoid predation and the actual risk of predation could be due to recent changes in the predator assemblage driven by an increased abundance of native M. chimango associated with urban development, and/or the introduction of exotic mammalian ground predators to this island. These predator assemblage changes could have resulted in …
format: application/pdf
format: text/html
creator: Rocío Fernanda Jara
creator: Ramiro Daniel Crego
creator: Michael David Samuel
creator: Ricardo Rozzi
creator: Jaime Enrique Jiménez
subject: Animal Behavior
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.9892
publisher: PeerJ Inc.
rights: © 2020 Jara et al.
abstract: Background Birds can maximize their reproductive success through careful selection of nest-sites. The ‘total-foliage’ hypothesis predicts that nests concealed in vegetation should have higher survival. We propose an additional hypothesis, the ‘predator proximity’ hypothesis, which states that nests placed farther from predators would have higher survival. We examined these hypotheses in the world’s southernmost forests of Navarino Island, in the Cape Horn Biosphere reserve, Chile (55°S). This island has been free of mammalian ground predators until recently, and forest passerines have been subject to depredation only by diurnal and nocturnal raptors. Methods During three breeding seasons (2014–2017), we monitored 104 nests for the five most abundant open-cup forest-dwelling passerines (Elaenia albiceps, Zonotrichia capensis, Phrygilus patagonicus, Turdus falcklandii, and Anairetes parulus). We identified nest predators using camera traps and assessed whether habitat characteristics affected nest-site selection and survival. Results Nest predation was the main cause of nest failure (71% of failed nests). Milvago chimango was the most common predator, depredating 13 (87%) of the 15 nests where we could identify a predator. By contrast, the recently introduced mammal Neovison vison, the only ground predator, depredated one nest (7%). Species selected nest-sites with more understory cover and taller understory, which according to the total-foliage hypothesis would provide more concealment against both avian and mammal predators. However, these variables negatively influenced nest survival. The apparent disconnect between selecting nest-sites to avoid predation and the actual risk of predation could be due to recent changes in the predator assemblage driven by an increased abundance of native M. chimango associated with urban development, and/or the introduction of exotic mammalian ground predators to this island. These predator assemblage changes could have resulted in …
bibliographic citation: Jara et al. (2020) Nest-site selection and breeding success of passerines in the world’s southernmost forests. PeerJ 8:e9892 https://doi.org/10.7717/peerj.9892
date submitted: 2020-02-05
date accepted: 2020-08-17
issued: 2020-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jara
  given name: Rocío Fernanda
author list: Agent
  family name: Crego
  given name: Ramiro Daniel
author list: Agent
  family name: Samuel
  given name: Michael David
author list: Agent
  family name: Rozzi
  given name: Ricardo
author list: Agent
  family name: Jiménez
  given name: Jaime Enrique
doi: 10.7717/peerj.9892
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-21
copyright: ©2020 Jara et al.
attribution name: Jara et al.

Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus)
type: item
type: AcademicArticle
description: Limestone karsts of Southeast Asia can harbor high levels of endemism, but are highly fragmented, increasingly threatened, and their biodiversity is often poorly studied. This is true of the Padawan Limestone Area of Sarawak, Malaysia, home to the endemic Artocarpus annulatus, the closest known wild relative of two important and underutilized fruit tree crops, jackfruit (A. heterophyllus) and cempedak (A. integer). Identifying and conserving crop wild relatives is critical for the conservation of crop genetic diversity and breeding. In 2016 and 2017, five A. annulatus populations were located, and leaf material, locality information, and demographic data were collected. Microsatellite markers were used to assess genetic diversity and structure among populations, and to compare levels of genetic diversity to closely related congeneric species. Results indicate no evidence of inbreeding in A. annulatus, and there is no genetic structure among the five populations. However, diversity measures trended lower in seedlings compared to mature trees, suggesting allelic diversity may be under threat in the youngest generation of plants. Also, genetic diversity is lower in A. annulatus compared to closely related congeners. The present study provides a baseline estimate of A. annulatus genetic diversity that can be used for comparison in future studies and to other species in the unique limestone karst ecosystems. Considerations for in situ and ex situ conservation approaches are discussed.
format: application/pdf
format: text/html
creator: Leta Dickinson
creator: Hilary Noble
creator: Elliot Gardner
creator: Aida Shafreena Ahmad Puad
creator: Wan Nuur Fatiha Wan Zakaria
creator: Nyree J.C. Zerega
subject: Biodiversity
subject: Genetics
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.9897
publisher: PeerJ Inc.
rights: © 2020 Dickinson et al.
abstract: Limestone karsts of Southeast Asia can harbor high levels of endemism, but are highly fragmented, increasingly threatened, and their biodiversity is often poorly studied. This is true of the Padawan Limestone Area of Sarawak, Malaysia, home to the endemic Artocarpus annulatus, the closest known wild relative of two important and underutilized fruit tree crops, jackfruit (A. heterophyllus) and cempedak (A. integer). Identifying and conserving crop wild relatives is critical for the conservation of crop genetic diversity and breeding. In 2016 and 2017, five A. annulatus populations were located, and leaf material, locality information, and demographic data were collected. Microsatellite markers were used to assess genetic diversity and structure among populations, and to compare levels of genetic diversity to closely related congeneric species. Results indicate no evidence of inbreeding in A. annulatus, and there is no genetic structure among the five populations. However, diversity measures trended lower in seedlings compared to mature trees, suggesting allelic diversity may be under threat in the youngest generation of plants. Also, genetic diversity is lower in A. annulatus compared to closely related congeners. The present study provides a baseline estimate of A. annulatus genetic diversity that can be used for comparison in future studies and to other species in the unique limestone karst ecosystems. Considerations for in situ and ex situ conservation approaches are discussed.
bibliographic citation: Dickinson et al. (2020) Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus). PeerJ 8:e9897 https://doi.org/10.7717/peerj.9897
date submitted: 2020-02-24
date accepted: 2020-08-17
issued: 2020-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dickinson
  given name: Leta
author list: Agent
  family name: Noble
  given name: Hilary
author list: Agent
  family name: Gardner
  given name: Elliot
author list: Agent
  family name: Puad
  given name: Aida Shafreena Ahmad
author list: Agent
  family name: Zakaria
  given name: Wan Nuur Fatiha Wan
author list: Agent
  family name: Zerega
  given name: Nyree J.C.
doi: 10.7717/peerj.9897
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-21
copyright: ©2020 Dickinson et al.
attribution name: Dickinson et al.

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