PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Fungal infection, decline and persistence in the only obligate troglodytic Neotropical salamander
items: Site selection by geese in a suburban landscape
items: Dichocarpum hagiangense—a new species and an updated checklist of Ranunculaceae in Vietnam
items: Flavoured water consumption alters pharmacokinetic parameters and increases exposure of erlotinib and gefitinib in a preclinical study using Wistar rats
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

Fungal infection, decline and persistence in the only obligate troglodytic Neotropical salamander
type: item
type: AcademicArticle
description: The fungal pathogen Batrachochytrium dendrobatidis (Bd) is implicated in global mass die-offs and declines in amphibians. In Mesoamerica, the Bd epidemic wave hypothesis is supported by detection of Bd in historic museum specimens collected over the last century, yet the timing and impact of the early stages of the wave remain poorly understood. Chiropterotriton magnipes, the only obligate troglodytic Neotropical salamander, was abundant in its small range in the decade following its description in 1965, but subsequently disappeared from known localities and was not seen for 34 years. Its decline is roughly coincident with that of other populations of Neotropical salamanders associated with the invasion and spread of Bd. To determine the presence and infection intensity of Bd on C. magnipes and sympatric amphibian species (which are also Bd hosts), we used a noninvasive sampling technique and qPCR assay to detect Bd on museum specimens of C. magnipes collected from 1952 to 2012, and from extant populations of C. magnipes and sympatric species of amphibians. We also tested for the presence of the recently discovered Batrachochytrium salamandivorans (Bsal), another fungal chytridiomycete pathogen of salamanders, using a similar technique specific for Bsal. We did not detect Bd in populations of C. magnipes before 1969, while Bd was detected at low to moderate prevalence just prior to and during declines. This pattern is consistent with Bd-caused epizootics followed by host declines and extirpations described in other hosts. We did not detect Bsal in any extant population of C. magnipes. We obtained one of the earliest positive records of the fungus to date in Latin America, providing additional historical evidence consistent with the Bd epidemic wave hypothesis. Genotyping results show that at least one population is currently infected with the Global Panzootic Lineage of Bd, but our genotyping of the historical positive samples was unsuccessful. The lack of large sam…
format: application/pdf
format: text/html
creator: Mizraim Olivares-Miranda
creator: Vance T. Vredenburg
creator: Julio C. García-Sánchez
creator: Allison Q. Byrne
creator: Erica B. Rosenblum
creator: Sean M. Rovito
subject: Conservation Biology
subject: Molecular Biology
subject: Mycology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.9763
publisher: PeerJ Inc.
rights: © 2020 Olivares-Miranda et al.
abstract: The fungal pathogen Batrachochytrium dendrobatidis (Bd) is implicated in global mass die-offs and declines in amphibians. In Mesoamerica, the Bd epidemic wave hypothesis is supported by detection of Bd in historic museum specimens collected over the last century, yet the timing and impact of the early stages of the wave remain poorly understood. Chiropterotriton magnipes, the only obligate troglodytic Neotropical salamander, was abundant in its small range in the decade following its description in 1965, but subsequently disappeared from known localities and was not seen for 34 years. Its decline is roughly coincident with that of other populations of Neotropical salamanders associated with the invasion and spread of Bd. To determine the presence and infection intensity of Bd on C. magnipes and sympatric amphibian species (which are also Bd hosts), we used a noninvasive sampling technique and qPCR assay to detect Bd on museum specimens of C. magnipes collected from 1952 to 2012, and from extant populations of C. magnipes and sympatric species of amphibians. We also tested for the presence of the recently discovered Batrachochytrium salamandivorans (Bsal), another fungal chytridiomycete pathogen of salamanders, using a similar technique specific for Bsal. We did not detect Bd in populations of C. magnipes before 1969, while Bd was detected at low to moderate prevalence just prior to and during declines. This pattern is consistent with Bd-caused epizootics followed by host declines and extirpations described in other hosts. We did not detect Bsal in any extant population of C. magnipes. We obtained one of the earliest positive records of the fungus to date in Latin America, providing additional historical evidence consistent with the Bd epidemic wave hypothesis. Genotyping results show that at least one population is currently infected with the Global Panzootic Lineage of Bd, but our genotyping of the historical positive samples was unsuccessful. The lack of large sam…
bibliographic citation: Olivares-Miranda et al. (2020) Fungal infection, decline and persistence in the only obligate troglodytic Neotropical salamander. PeerJ 8:e9763 https://doi.org/10.7717/peerj.9763
date submitted: 2020-05-20
date accepted: 2020-07-28
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olivares-Miranda
  given name: Mizraim
author list: Agent
  family name: Vredenburg
  given name: Vance T.
author list: Agent
  family name: García-Sánchez
  given name: Julio C.
author list: Agent
  family name: Byrne
  given name: Allison Q.
author list: Agent
  family name: Rosenblum
  given name: Erica B.
author list: Agent
  family name: Rovito
  given name: Sean M.
doi: 10.7717/peerj.9763
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: © 2020 Olivares-Miranda et al.
attribution name: Olivares-Miranda et al.

Site selection by geese in a suburban landscape
type: item
type: AcademicArticle
description: Background In European and North American cities geese are among the most common and most visible large herbivores. As such, their presence and behaviour often conflict with the desires of the human residents. Fouling, noise, aggression and health concerns are all cited as reasons that there are “too many”. Lethal control is often used for population management; however, this raises questions about whether this is a sustainable strategy to resolve the conflict between humans and geese when, paradoxically, it is humans that are responsible for creating the habitat and often providing the food and protection of geese at other times. We hypothesise that the landscaping of suburban parks can be improved to decrease its attractiveness to geese and to reduce the opportunity for conflict between geese and humans. Methods Using observations collected over five years from a botanic garden situated in suburban Belgium and data from the whole of Flanders in Belgium, we examined landscape features that attract geese. These included the presence of islands in lakes, the distance from water, barriers to level flight and the size of exploited areas. The birds studied were the tadornine goose Alopochen aegyptiaca (L. 1766) (Egyptian goose) and the anserine geese, Branta canadensis (L. 1758) (Canada goose), Anser anser (L. 1758) (greylag goose) and Branta leucopsis (Bechstein, 1803) (barnacle goose). Landscape modification is a known method for altering goose behaviour, but there is little information on the power of such methods with which to inform managers and planners. Results Our results demonstrate that lakes with islands attract more than twice as many anserine geese than lakes without islands, but make little difference to Egyptian geese. Furthermore, flight barriers between grazing areas and lakes are an effective deterrent to geese using an area for feeding. Keeping grazing areas small and surrounded by trees reduces their attractiveness to geese. Conclusion The results su…
format: application/pdf
format: text/html
creator: Quentin J. Groom
creator: Tim Adriaens
creator: Claire Colsoulle
creator: Pauline Delhez
creator: Iris Van der Beeten
subject: Animal Behavior
subject: Biogeography
subject: Ecology
subject: Natural Resource Management
description: doi:10.7717/peerj.9846
publisher: PeerJ Inc.
rights: © 2020 Groom et al.
abstract: Background In European and North American cities geese are among the most common and most visible large herbivores. As such, their presence and behaviour often conflict with the desires of the human residents. Fouling, noise, aggression and health concerns are all cited as reasons that there are “too many”. Lethal control is often used for population management; however, this raises questions about whether this is a sustainable strategy to resolve the conflict between humans and geese when, paradoxically, it is humans that are responsible for creating the habitat and often providing the food and protection of geese at other times. We hypothesise that the landscaping of suburban parks can be improved to decrease its attractiveness to geese and to reduce the opportunity for conflict between geese and humans. Methods Using observations collected over five years from a botanic garden situated in suburban Belgium and data from the whole of Flanders in Belgium, we examined landscape features that attract geese. These included the presence of islands in lakes, the distance from water, barriers to level flight and the size of exploited areas. The birds studied were the tadornine goose Alopochen aegyptiaca (L. 1766) (Egyptian goose) and the anserine geese, Branta canadensis (L. 1758) (Canada goose), Anser anser (L. 1758) (greylag goose) and Branta leucopsis (Bechstein, 1803) (barnacle goose). Landscape modification is a known method for altering goose behaviour, but there is little information on the power of such methods with which to inform managers and planners. Results Our results demonstrate that lakes with islands attract more than twice as many anserine geese than lakes without islands, but make little difference to Egyptian geese. Furthermore, flight barriers between grazing areas and lakes are an effective deterrent to geese using an area for feeding. Keeping grazing areas small and surrounded by trees reduces their attractiveness to geese. Conclusion The results su…
bibliographic citation: Groom et al. (2020) Site selection by geese in a suburban landscape. PeerJ 8:e9846 https://doi.org/10.7717/peerj.9846
date submitted: 2020-01-21
date accepted: 2020-08-11
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Groom
  given name: Quentin J.
author list: Agent
  family name: Adriaens
  given name: Tim
author list: Agent
  family name: Colsoulle
  given name: Claire
author list: Agent
  family name: Delhez
  given name: Pauline
author list: Agent
  family name: Van der Beeten
  given name: Iris
doi: 10.7717/peerj.9846
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Groom et al.
attribution name: Groom et al.

Dichocarpum hagiangense—a new species and an updated checklist of Ranunculaceae in Vietnam
type: item
type: AcademicArticle
description: Dichocarpum hagiangense from Ha Giang province, northern Vietnam is described and illustrated. Diagnostic features of the new species are a short rhizomatous stem, (2–)3-foliolate or simple leaves, and pink-purple flowers. The described species is distinct from closely allied D. trifoliolatum in having longer sepals, shape and obcordate apex of petal limbs, shorter flower stem, number and tooth shape of basal leaves; it differs from D. basilare and D. carinatum in having stem leaf, retuse apex and longer of central leaflet, number and (2–)3-foliated (or simple) of leaf. With the support of molecular data, the new species was clearly distinguished from other species in the Dichocarpum group by eight autapomorphic characters in nrITS sequence. A key to all species of Dichocarpum is provided. We suggest the IUCN conservation status of D. hagiangense to be “Critically Endangered”. A newest checklist of the family Ranunculaceae in Vietnam is updated.
format: application/pdf
format: text/html
creator: Minh Ty Nguyen
creator: Ngoc Bon Trinh
creator: Thanh Thi Viet Tran
creator: Tran Duc Thanh
creator: Long Ke Phan
creator: Van The Pham
subject: Biodiversity
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.9874
publisher: PeerJ Inc.
rights: © 2020 Nguyen et al.
abstract: Dichocarpum hagiangense from Ha Giang province, northern Vietnam is described and illustrated. Diagnostic features of the new species are a short rhizomatous stem, (2–)3-foliolate or simple leaves, and pink-purple flowers. The described species is distinct from closely allied D. trifoliolatum in having longer sepals, shape and obcordate apex of petal limbs, shorter flower stem, number and tooth shape of basal leaves; it differs from D. basilare and D. carinatum in having stem leaf, retuse apex and longer of central leaflet, number and (2–)3-foliated (or simple) of leaf. With the support of molecular data, the new species was clearly distinguished from other species in the Dichocarpum group by eight autapomorphic characters in nrITS sequence. A key to all species of Dichocarpum is provided. We suggest the IUCN conservation status of D. hagiangense to be “Critically Endangered”. A newest checklist of the family Ranunculaceae in Vietnam is updated.
bibliographic citation: Nguyen et al. (2020) Dichocarpum hagiangense—a new species and an updated checklist of Ranunculaceae in Vietnam. PeerJ 8:e9874 https://doi.org/10.7717/peerj.9874
date submitted: 2020-02-14
date accepted: 2020-08-14
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nguyen
  given name: Minh Ty
author list: Agent
  family name: Trinh
  given name: Ngoc Bon
author list: Agent
  family name: Tran
  given name: Thanh Thi Viet
author list: Agent
  family name: Thanh
  given name: Tran Duc
author list: Agent
  family name: Phan
  given name: Long Ke
author list: Agent
  family name: Pham
  given name: Van The
doi: 10.7717/peerj.9874
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Nguyen et al.
attribution name: Nguyen et al.

Flavoured water consumption alters pharmacokinetic parameters and increases exposure of erlotinib and gefitinib in a preclinical study using Wistar rats
type: item
type: AcademicArticle
description: Background Erlotinib (ERL) and Gefitinib (GEF) are considered first line therapy for the management of non-small cell lung carcinoma (NSCLC). Like other tyrosine kinase inhibitors (TKIs), ERL and GEF are mainly metabolized by the cytochrome P450 (CYP450) CYP3A4 isoform and are substrates for transporter proteins with marked inter-/intra-individual pharmacokinetic (PK) variability. Therefore, ERL and GEF are candidates for drug-drug and food-drug interactions with a consequent effect on drug exposure and/or drug-related toxicities. In recent years, the consumption of flavoured water (FW) has gained in popularity. Among multiple ingredients, fruit extracts, which might constitute bioactive flavonoids, can possess an inhibitory effect on the CYP450 enzymes or transporter proteins. Therefore, in this study we investigated the effects of different types of FW on the PK parameters of ERL and GEF in Wistar rats. Methods ERL and GEF PK parameters in different groups of rats after four weeks consumption of different flavours of FW, namely berry, peach, lime, and pineapple, were determined from plasma drug concentrations using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS). Results Data indicated that tested FWs altered the PK parameters of both ERL and GEF differently. Lime water had the highest impact on most of ERL and GEF PK parameters, with a significant increase in Cmax (95% for ERL, 58% for GEF), AUC0–48 (111% for ERL, 203% for GEF), and AUC0–∞ (200% for ERL, 203% for GEF), along with a significant decrease in the apparent oral clearance of both drugs (65% for ERL, 67% for GEF). The order by which FW affected the PK parameters for ERL and GEF was as follows: lime > pineapple > berry > peach. Conclusion The present study indicates that drinking FW could be of significance in rats receiving ERL or GEF. Our results indicate that the alteration in PKs was mostly recorded with lime, resulting in an enhanced bioavailability, and reduced apparen…
format: application/pdf
format: text/html
creator: Aliyah Almomen
creator: Hadir M. Maher
creator: Nourah Z. Alzoman
creator: Shereen M. Shehata
creator: Amal Alsubaie
subject: Toxicology
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.9881
publisher: PeerJ Inc.
rights: © 2020 Almomen et al.
abstract: Background Erlotinib (ERL) and Gefitinib (GEF) are considered first line therapy for the management of non-small cell lung carcinoma (NSCLC). Like other tyrosine kinase inhibitors (TKIs), ERL and GEF are mainly metabolized by the cytochrome P450 (CYP450) CYP3A4 isoform and are substrates for transporter proteins with marked inter-/intra-individual pharmacokinetic (PK) variability. Therefore, ERL and GEF are candidates for drug-drug and food-drug interactions with a consequent effect on drug exposure and/or drug-related toxicities. In recent years, the consumption of flavoured water (FW) has gained in popularity. Among multiple ingredients, fruit extracts, which might constitute bioactive flavonoids, can possess an inhibitory effect on the CYP450 enzymes or transporter proteins. Therefore, in this study we investigated the effects of different types of FW on the PK parameters of ERL and GEF in Wistar rats. Methods ERL and GEF PK parameters in different groups of rats after four weeks consumption of different flavours of FW, namely berry, peach, lime, and pineapple, were determined from plasma drug concentrations using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS). Results Data indicated that tested FWs altered the PK parameters of both ERL and GEF differently. Lime water had the highest impact on most of ERL and GEF PK parameters, with a significant increase in Cmax (95% for ERL, 58% for GEF), AUC0–48 (111% for ERL, 203% for GEF), and AUC0–∞ (200% for ERL, 203% for GEF), along with a significant decrease in the apparent oral clearance of both drugs (65% for ERL, 67% for GEF). The order by which FW affected the PK parameters for ERL and GEF was as follows: lime > pineapple > berry > peach. Conclusion The present study indicates that drinking FW could be of significance in rats receiving ERL or GEF. Our results indicate that the alteration in PKs was mostly recorded with lime, resulting in an enhanced bioavailability, and reduced apparen…
bibliographic citation: Almomen et al. (2020) Flavoured water consumption alters pharmacokinetic parameters and increases exposure of erlotinib and gefitinib in a preclinical study using Wistar rats. PeerJ 8:e9881 https://doi.org/10.7717/peerj.9881
date submitted: 2019-11-18
date accepted: 2020-08-15
issued: 2020-09-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Almomen
  given name: Aliyah
author list: Agent
  family name: Maher
  given name: Hadir M.
author list: Agent
  family name: Alzoman
  given name: Nourah Z.
author list: Agent
  family name: Shehata
  given name: Shereen M.
author list: Agent
  family name: Alsubaie
  given name: Amal
doi: 10.7717/peerj.9881
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-22
copyright: ©2020 Almomen et al.
attribution name: Almomen et al.

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.

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