PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Expression differences in Aphidius ervi (Hymenoptera: Braconidae) females reared on different aphid host species
items: A systematic review of differential rate of use of the word “evolve” across fields
items: RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers
items: Implications of nutritional stress as nestling or fledgling on subsequent attractiveness and fecundity in zebra finches (Taeniopygia guttata)
items: Influence of CNTRENE® C100LM carbon nanotube material on the growth and regulation of Escherichia coli
items: Exposure to elevated sea-surface temperatures below the bleaching threshold impairs coral recovery and regeneration following injury
items: Inadequate thermal refuge constrains landscape habitability for a grassland bird species
items: Genomic evidence of bitter taste in snakes and phylogenetic analysis of bitter taste receptor genes in reptiles
items: Extended exposure to elevated temperature affects escape response behaviour in coral reef fishes
items: Shifting communities after­­ typhoon damage on an upper mesophotic reef in Okinawa, Japan

Expression differences in Aphidius ervi (Hymenoptera: Braconidae) females reared on different aphid host species
type: item
type: AcademicArticle
description: The molecular mechanisms that allow generalist parasitoids to exploit many, often very distinct hosts are practically unknown. The wasp Aphidius ervi, a generalist koinobiont parasitoid of aphids, was introduced from Europe into Chile in the late 1970s to control agriculturally important aphid species. A recent study showed significant differences in host preference and host acceptance (infectivity) depending on the host A. ervi were reared on. In contrast, no genetic differentiation between A. ervi populations parasitizing different aphid species and aphids of the same species reared on different host plants was found in Chile. Additionally, the same study did not find any fitness effects in A. ervi if offspring were reared on a different host as their mothers. Here, we determined the effect of aphid host species (Sitobion avenae versus Acyrthosiphon pisum reared on two different host plants alfalfa and pea) on the transcriptome of adult A. ervi females. We found a large number of differentially expressed genes (between host species: head: 2,765; body: 1,216; within the same aphid host species reared on different host plants: alfalfa versus pea: head 593; body 222). As expected, the transcriptomes from parasitoids reared on the same host species (pea aphid) but originating from different host plants (pea versus alfalfa) were more similar to each other than the transcriptomes of parasitoids reared on a different aphid host and host plant (head: 648 and 1,524 transcripts; body: 566 and 428 transcripts). We found several differentially expressed odorant binding proteins and olfactory receptor proteins in particular, when we compared parasitoids from different host species. Additionally, we found differentially expressed genes involved in neuronal growth and development as well as signaling pathways. These results point towards a significant rewiring of the transcriptome of A. ervi depending on aphid-plant complex where parasitoids develop, even if different biotypes o…
format: application/pdf
format: text/html
creator: Gabriel I. Ballesteros
creator: Jürgen Gadau
creator: Fabrice Legeai
creator: Angelica Gonzalez-Gonzalez
creator: Blas Lavandero
creator: Jean-Christophe Simon
creator: Christian C. Figueroa
subject: Animal Behavior
subject: Entomology
subject: Genomics
description: doi:10.7717/peerj.3640
publisher: PeerJ Inc.
rights: © 2017 Ballesteros et al.
abstract: The molecular mechanisms that allow generalist parasitoids to exploit many, often very distinct hosts are practically unknown. The wasp Aphidius ervi, a generalist koinobiont parasitoid of aphids, was introduced from Europe into Chile in the late 1970s to control agriculturally important aphid species. A recent study showed significant differences in host preference and host acceptance (infectivity) depending on the host A. ervi were reared on. In contrast, no genetic differentiation between A. ervi populations parasitizing different aphid species and aphids of the same species reared on different host plants was found in Chile. Additionally, the same study did not find any fitness effects in A. ervi if offspring were reared on a different host as their mothers. Here, we determined the effect of aphid host species (Sitobion avenae versus Acyrthosiphon pisum reared on two different host plants alfalfa and pea) on the transcriptome of adult A. ervi females. We found a large number of differentially expressed genes (between host species: head: 2,765; body: 1,216; within the same aphid host species reared on different host plants: alfalfa versus pea: head 593; body 222). As expected, the transcriptomes from parasitoids reared on the same host species (pea aphid) but originating from different host plants (pea versus alfalfa) were more similar to each other than the transcriptomes of parasitoids reared on a different aphid host and host plant (head: 648 and 1,524 transcripts; body: 566 and 428 transcripts). We found several differentially expressed odorant binding proteins and olfactory receptor proteins in particular, when we compared parasitoids from different host species. Additionally, we found differentially expressed genes involved in neuronal growth and development as well as signaling pathways. These results point towards a significant rewiring of the transcriptome of A. ervi depending on aphid-plant complex where parasitoids develop, even if different biotypes o…
bibliographic citation: Ballesteros et al. (2017) Expression differences in Aphidius ervi (Hymenoptera: Braconidae) females reared on different aphid host species. PeerJ 5:e3640 https://doi.org/10.7717/peerj.3640
date submitted: 2017-04-07
date accepted: 2017-07-12
issued: 2017-08-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ballesteros
  given name: Gabriel I.
author list: Agent
  family name: Gadau
  given name: Jürgen
author list: Agent
  family name: Legeai
  given name: Fabrice
author list: Agent
  family name: Gonzalez-Gonzalez
  given name: Angelica
author list: Agent
  family name: Lavandero
  given name: Blas
author list: Agent
  family name: Simon
  given name: Jean-Christophe
author list: Agent
  family name: Figueroa
  given name: Christian C.
doi: 10.7717/peerj.3640
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-21
copyright: ©2017 Ballesteros et al.
attribution name: Ballesteros et al.

A systematic review of differential rate of use of the word “evolve” across fields
type: item
type: AcademicArticle
description: Background Although evolution is the driving force behind many of today’s major public health and agriculture issues, both journalists and scientific researchers often do not use the term “evolve” in discussions of these topics. Methods In a total of 1,066 articles and 716 papers selected from 25 US newspapers and 34 scientific journals, we assess usage of the word “evolve” and its substitute words in the contexts of cancer tumor drug resistance, HIV drug resistance, mosquito insecticide resistance, and weed pesticide resistance. Results We find significant differences in the use of “evolve” among fields and sources. “Evolve” is used most when discussing weed pesticide resistance (25.9% in newspapers, 52.4% in journals) and least when discussing cancer tumor drug resistance (3.9% in newspapers, 9.8% in journals). On average, scientific journals use “evolve” more often (22.2%) than newspapers (7.8%). Different types of journals (general science, general clinical, cancer specific, and drug resistance specific) show significantly different “evolve” usages when discussing cancer tumor drug resistance. Discussion We examine potential explanations of these findings, such as the relatively recent framing of cancer in evolutionary terms, before looking at consequences of low “evolve” usage and of differential “evolve” usage across fields. Use of the word “evolve” may not reflect current understanding of the problems we examine. However, given that our ability to tackle resistance issues relies upon accurate understandings of what causes and exacerbates resistance, use of the word “evolve” when called for may help us confront these issues in the future.
format: application/pdf
format: text/html
creator: Nina Singh
creator: Matthew T. Sit
creator: Marissa K. Schutte
creator: Gabriel E. Chan
creator: Jeyson E. Aldana
creator: Diana Cervantes
creator: Clyde H. Himmelstein
creator: Pamela J. Yeh
subject: Evolutionary Studies
subject: Public Health
subject: Science and Medical Education
subject: Science Policy
description: doi:10.7717/peerj.3639
publisher: PeerJ Inc.
rights: © 2017 Singh et al.
abstract: Background Although evolution is the driving force behind many of today’s major public health and agriculture issues, both journalists and scientific researchers often do not use the term “evolve” in discussions of these topics. Methods In a total of 1,066 articles and 716 papers selected from 25 US newspapers and 34 scientific journals, we assess usage of the word “evolve” and its substitute words in the contexts of cancer tumor drug resistance, HIV drug resistance, mosquito insecticide resistance, and weed pesticide resistance. Results We find significant differences in the use of “evolve” among fields and sources. “Evolve” is used most when discussing weed pesticide resistance (25.9% in newspapers, 52.4% in journals) and least when discussing cancer tumor drug resistance (3.9% in newspapers, 9.8% in journals). On average, scientific journals use “evolve” more often (22.2%) than newspapers (7.8%). Different types of journals (general science, general clinical, cancer specific, and drug resistance specific) show significantly different “evolve” usages when discussing cancer tumor drug resistance. Discussion We examine potential explanations of these findings, such as the relatively recent framing of cancer in evolutionary terms, before looking at consequences of low “evolve” usage and of differential “evolve” usage across fields. Use of the word “evolve” may not reflect current understanding of the problems we examine. However, given that our ability to tackle resistance issues relies upon accurate understandings of what causes and exacerbates resistance, use of the word “evolve” when called for may help us confront these issues in the future.
bibliographic citation: Singh et al. (2017) A systematic review of differential rate of use of the word “evolve” across fields. PeerJ 5:e3639 https://doi.org/10.7717/peerj.3639
date submitted: 2017-04-11
date accepted: 2017-07-12
issued: 2017-08-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Singh
  given name: Nina
author list: Agent
  family name: Sit
  given name: Matthew T.
author list: Agent
  family name: Schutte
  given name: Marissa K.
author list: Agent
  family name: Chan
  given name: Gabriel E.
author list: Agent
  family name: Aldana
  given name: Jeyson E.
author list: Agent
  family name: Cervantes
  given name: Diana
author list: Agent
  family name: Himmelstein
  given name: Clyde H.
author list: Agent
  family name: Yeh
  given name: Pamela J.
doi: 10.7717/peerj.3639
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-21
copyright: ©2017 Singh et al.
attribution name: Singh et al.

RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers
type: item
type: AcademicArticle
description: Identification of appropriate reference genes (RGs) is critical to accurate data interpretation in quantitative real-time PCR (qPCR) experiments. In this study, we have utilised next generation RNA sequencing (RNA-seq) to analyse the transcriptome of a panel of non-melanoma skin cancer lesions, identifying genes that are consistently expressed across all samples. Genes encoding ribosomal proteins were amongst the most stable in this dataset. Validation of this RNA-seq data was examined using qPCR to confirm the suitability of a set of highly stable genes for use as qPCR RGs. These genes will provide a valuable resource for the normalisation of qPCR data for the analysis of non-melanoma skin cancer.
format: application/pdf
format: text/html
creator: Van L.T. Hoang
creator: Lisa N. Tom
creator: Xiu-Cheng Quek
creator: Jean-Marie Tan
creator: Elizabeth J. Payne
creator: Lynlee L. Lin
creator: Sudipta Sinnya
creator: Anthony P. Raphael
creator: Duncan Lambie
creator: Ian H. Frazer
creator: Marcel E. Dinger
creator: H. Peter Soyer
creator: Tarl W. Prow
subject: Genomics
subject: Molecular Biology
subject: Dermatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.3631
publisher: PeerJ Inc.
rights: © 2017 Hoang et al.
abstract: Identification of appropriate reference genes (RGs) is critical to accurate data interpretation in quantitative real-time PCR (qPCR) experiments. In this study, we have utilised next generation RNA sequencing (RNA-seq) to analyse the transcriptome of a panel of non-melanoma skin cancer lesions, identifying genes that are consistently expressed across all samples. Genes encoding ribosomal proteins were amongst the most stable in this dataset. Validation of this RNA-seq data was examined using qPCR to confirm the suitability of a set of highly stable genes for use as qPCR RGs. These genes will provide a valuable resource for the normalisation of qPCR data for the analysis of non-melanoma skin cancer.
bibliographic citation: Hoang et al. (2017) RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers. PeerJ 5:e3631 https://doi.org/10.7717/peerj.3631
date submitted: 2016-06-24
date accepted: 2017-07-11
issued: 2017-08-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoang
  given name: Van L.T.
author list: Agent
  family name: Tom
  given name: Lisa N.
author list: Agent
  family name: Quek
  given name: Xiu-Cheng
author list: Agent
  family name: Tan
  given name: Jean-Marie
author list: Agent
  family name: Payne
  given name: Elizabeth J.
author list: Agent
  family name: Lin
  given name: Lynlee L.
author list: Agent
  family name: Sinnya
  given name: Sudipta
author list: Agent
  family name: Raphael
  given name: Anthony P.
author list: Agent
  family name: Lambie
  given name: Duncan
author list: Agent
  family name: Frazer
  given name: Ian H.
author list: Agent
  family name: Dinger
  given name: Marcel E.
author list: Agent
  family name: Soyer
  given name: H. Peter
author list: Agent
  family name: Prow
  given name: Tarl W.
doi: 10.7717/peerj.3631
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-21
copyright: ©2017 Hoang et al.
attribution name: Hoang et al.

Implications of nutritional stress as nestling or fledgling on subsequent attractiveness and fecundity in zebra finches (Taeniopygia guttata)
type: item
type: AcademicArticle
description: The conditions an organism experiences during early development can have profound and long lasting effects on its subsequent behavior, attractiveness, and life history decisions. Most previous studies have exposed individuals to different conditions throughout development until nutritional independence. Yet under natural conditions, individuals may experience limitations for much shorter periods due to transient environmental fluctuations. Here, we used zebra finches (Taeniopygia guttata) in captivity to determine if conditions experienced during distinctly different early developmental phases contribute differently to male and female attractiveness and subsequent reproduction. We conducted a breeding experiment in which offspring were exposed to food regimes with (a) low quality food provided only during the nestling period, (b) low quality food provided only during the fledgling period, or (c) high quality food throughout early development. We show that despite short-term effects on biometry and physiology, there were no effects on either male or female attractiveness, as tested in two-way mate choice free-flight aviary experiments. In a subsequent breeding experiment, the offspring from the initial experiment were allowed to breed themselves. The next generation offspring from mothers raised under lower quality nutrition as either nestling or fledging were lighter at hatching compared to offspring from mothers raised under higher quality nutrition whereas paternal early nutrition had no such effects. The lack of early developmental limitations on attractiveness suggests that attractiveness traits were not affected or that birds compensated for any such effects. Furthermore, maternal trans-generational effects of dietary restrictions emphasize the importance of role of limited periods of early developmental stress in the expression of environmentally determined fitness components.
format: application/pdf
format: text/html
creator: Mariam Honarmand
creator: E. Tobias Krause
creator: Marc Naguib
subject: Animal Behavior
description: doi:10.7717/peerj.3628
publisher: PeerJ Inc.
rights: © 2017 Honarmand et al.
abstract: The conditions an organism experiences during early development can have profound and long lasting effects on its subsequent behavior, attractiveness, and life history decisions. Most previous studies have exposed individuals to different conditions throughout development until nutritional independence. Yet under natural conditions, individuals may experience limitations for much shorter periods due to transient environmental fluctuations. Here, we used zebra finches (Taeniopygia guttata) in captivity to determine if conditions experienced during distinctly different early developmental phases contribute differently to male and female attractiveness and subsequent reproduction. We conducted a breeding experiment in which offspring were exposed to food regimes with (a) low quality food provided only during the nestling period, (b) low quality food provided only during the fledgling period, or (c) high quality food throughout early development. We show that despite short-term effects on biometry and physiology, there were no effects on either male or female attractiveness, as tested in two-way mate choice free-flight aviary experiments. In a subsequent breeding experiment, the offspring from the initial experiment were allowed to breed themselves. The next generation offspring from mothers raised under lower quality nutrition as either nestling or fledging were lighter at hatching compared to offspring from mothers raised under higher quality nutrition whereas paternal early nutrition had no such effects. The lack of early developmental limitations on attractiveness suggests that attractiveness traits were not affected or that birds compensated for any such effects. Furthermore, maternal trans-generational effects of dietary restrictions emphasize the importance of role of limited periods of early developmental stress in the expression of environmentally determined fitness components.
bibliographic citation: Honarmand et al. (2017) Implications of nutritional stress as nestling or fledgling on subsequent attractiveness and fecundity in zebra finches (Taeniopygia guttata). PeerJ 5:e3628 https://doi.org/10.7717/peerj.3628
date submitted: 2017-01-18
date accepted: 2017-07-10
issued: 2017-08-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Honarmand
  given name: Mariam
author list: Agent
  family name: Krause
  given name: E. Tobias
author list: Agent
  family name: Naguib
  given name: Marc
doi: 10.7717/peerj.3628
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-21
copyright: ©2017 Honarmand et al.
attribution name: Honarmand et al.

Influence of CNTRENE® C100LM carbon nanotube material on the growth and regulation of Escherichia coli
type: item
type: AcademicArticle
description: The growing use of carbon nanotubes (CNTs) in industrial and consumer products raises important questions about their environmental fate and impact on prokaryotes. In the environment, CNTs are exposed to a variety of conditions (e.g., UV light) that could lead to decomposition and changes in their chemical properties. Therefore, the potential cytotoxic effect of both pristine and artificially aged carboxyl functionalized CNTRENE® C100LM CNTmaterial at neutral and acidic conditions on Escherichia coli K12 was analyzed using a minimal inhibitory concentration (MIC) assay, which also allowed monitoring of non-lethal growth effects. However, there were no observable MIC or significant changes in growth behavior in E. coli K12 when exposed to pristine or aged CNTs. Exposure to pristine CNTRENE® C100LM CNT material did not appear to influence cell morphology or damage the cells when examined by electron microscopy. In addition, RNA sequencing revealed no observable regulatory changes in typical stress response pathways. This is surprising considering that previous studies have claimed high cytotoxicity of CNTs, including carboxyl functionalized single-walled CNTs, and suggest that other factors such as trace heavy metals or other impurities are likely responsible for many of the previously reported cytotoxicity in E. coli and possibly other microorganisms.
format: application/pdf
format: text/html
creator: Brittany Twibell
creator: Kalie Somerville
creator: Geoffrey Manani
creator: Molly Duszynski
creator: Adam Wanekaya
creator: Paul Schweiger
subject: Microbiology
subject: Toxicology
description: doi:10.7717/peerj.3721
publisher: PeerJ Inc.
rights: © 2017 Twibell et al.
abstract: The growing use of carbon nanotubes (CNTs) in industrial and consumer products raises important questions about their environmental fate and impact on prokaryotes. In the environment, CNTs are exposed to a variety of conditions (e.g., UV light) that could lead to decomposition and changes in their chemical properties. Therefore, the potential cytotoxic effect of both pristine and artificially aged carboxyl functionalized CNTRENE® C100LM CNTmaterial at neutral and acidic conditions on Escherichia coli K12 was analyzed using a minimal inhibitory concentration (MIC) assay, which also allowed monitoring of non-lethal growth effects. However, there were no observable MIC or significant changes in growth behavior in E. coli K12 when exposed to pristine or aged CNTs. Exposure to pristine CNTRENE® C100LM CNT material did not appear to influence cell morphology or damage the cells when examined by electron microscopy. In addition, RNA sequencing revealed no observable regulatory changes in typical stress response pathways. This is surprising considering that previous studies have claimed high cytotoxicity of CNTs, including carboxyl functionalized single-walled CNTs, and suggest that other factors such as trace heavy metals or other impurities are likely responsible for many of the previously reported cytotoxicity in E. coli and possibly other microorganisms.
bibliographic citation: Twibell et al. (2017) Influence of CNTRENE® C100LM carbon nanotube material on the growth and regulation of Escherichia coli. PeerJ 5:e3721 https://doi.org/10.7717/peerj.3721
date submitted: 2017-05-22
date accepted: 2017-07-31
issued: 2017-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Twibell
  given name: Brittany
author list: Agent
  family name: Somerville
  given name: Kalie
author list: Agent
  family name: Manani
  given name: Geoffrey
author list: Agent
  family name: Duszynski
  given name: Molly
author list: Agent
  family name: Wanekaya
  given name: Adam
author list: Agent
  family name: Schweiger
  given name: Paul
doi: 10.7717/peerj.3721
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-18
copyright: ©2017 Twibell et al.
attribution name: Twibell et al.

Exposure to elevated sea-surface temperatures below the bleaching threshold impairs coral recovery and regeneration following injury
type: item
type: AcademicArticle
description: Elevated sea surface temperatures (SSTs) are linked to an increase in the frequency and severity of bleaching events due to temperatures exceeding corals’ upper thermal limits. The temperatures at which a breakdown of the coral-Symbiodinium endosymbiosis (coral bleaching) occurs are referred to as the upper thermal limits for the coral species. This breakdown of the endosymbiosis results in a reduction of corals’ nutritional uptake, growth, and tissue integrity. Periods of elevated sea surface temperature, thermal stress and coral bleaching are also linked to increased disease susceptibility and an increased frequency of storms which cause injury and physical damage to corals. Herein we aimed to determine the capacity of corals to regenerate and recover from injuries (removal of apical tips) sustained during periods of elevated sea surface temperatures which result in coral stress responses, but which do not result in coral bleaching (i.e., sub-bleaching thermal stress events). In this study, exposure of the species Acropora aspera to an elevated SST of 32 °C (2 °C below the bleaching threshold, 34 °C) was found to result in reduced fluorescence of green fluorescent protein (GFP), reduced skeletal calcification and a lack of branch regrowth at the site of injury, compared to corals maintained under ambient SST conditions (26 °C). Corals maintained under normal, ambient, sea surface temperatures expressed high GFP fluorescence at the injury site, underwent a rapid regeneration of the coral branch apical tip within 12 days of sustaining injury, and showed extensive regrowth of the coral skeleton. Taken together, our results have demonstrated that periods of sustained increased sea surface temperatures, below the corals’ bleaching threshold but above long-term summertime averages, impair coral recovery from damage, regardless of the onset or occurrence of coral bleaching.
format: application/pdf
format: text/html
creator: Joshua Louis Bonesso
creator: William Leggat
creator: Tracy Danielle Ainsworth
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.3719
publisher: PeerJ Inc.
rights: © 2017 Bonesso et al.
abstract: Elevated sea surface temperatures (SSTs) are linked to an increase in the frequency and severity of bleaching events due to temperatures exceeding corals’ upper thermal limits. The temperatures at which a breakdown of the coral-Symbiodinium endosymbiosis (coral bleaching) occurs are referred to as the upper thermal limits for the coral species. This breakdown of the endosymbiosis results in a reduction of corals’ nutritional uptake, growth, and tissue integrity. Periods of elevated sea surface temperature, thermal stress and coral bleaching are also linked to increased disease susceptibility and an increased frequency of storms which cause injury and physical damage to corals. Herein we aimed to determine the capacity of corals to regenerate and recover from injuries (removal of apical tips) sustained during periods of elevated sea surface temperatures which result in coral stress responses, but which do not result in coral bleaching (i.e., sub-bleaching thermal stress events). In this study, exposure of the species Acropora aspera to an elevated SST of 32 °C (2 °C below the bleaching threshold, 34 °C) was found to result in reduced fluorescence of green fluorescent protein (GFP), reduced skeletal calcification and a lack of branch regrowth at the site of injury, compared to corals maintained under ambient SST conditions (26 °C). Corals maintained under normal, ambient, sea surface temperatures expressed high GFP fluorescence at the injury site, underwent a rapid regeneration of the coral branch apical tip within 12 days of sustaining injury, and showed extensive regrowth of the coral skeleton. Taken together, our results have demonstrated that periods of sustained increased sea surface temperatures, below the corals’ bleaching threshold but above long-term summertime averages, impair coral recovery from damage, regardless of the onset or occurrence of coral bleaching.
bibliographic citation: Bonesso et al. (2017) Exposure to elevated sea-surface temperatures below the bleaching threshold impairs coral recovery and regeneration following injury. PeerJ 5:e3719 https://doi.org/10.7717/peerj.3719
date submitted: 2016-09-13
date accepted: 2017-07-29
issued: 2017-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bonesso
  given name: Joshua Louis
author list: Agent
  family name: Leggat
  given name: William
author list: Agent
  family name: Ainsworth
  given name: Tracy Danielle
doi: 10.7717/peerj.3719
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-18
copyright: ©2017 Bonesso et al.
attribution name: Bonesso et al.

Inadequate thermal refuge constrains landscape habitability for a grassland bird species
type: item
type: AcademicArticle
description: Ecologists have long recognized the influence that environmental conditions have on abundance and range extent of animal species. We used the northern bobwhite (Colinus virginianus; hereafter bobwhite) as a model species for studying how microclimates serve as refuge against severe weather conditions. This species serves as an indicator or umbrella species for other sensitive ground-nesting, grassland obligate species. We conducted a mensurative field experiment in the rolling plains of Texas, USA, a semi-arid ecosystem on the southwestern periphery of bobwhite range, to determine whether native bunch grasses, apparently suitable for bobwhite nesting, could reduce ambient temperature below levels harmful for eggs. During the nesting season, we compared temperature and relative humidity readings at daily heat maxima (i.e., the 3 h during each day with highest temperatures) during the nesting season over the course of two years at 63 suitable nest sites paired with 63 random locations (n = 126) using two sensors at ∼10 and ∼60 cm above ground level. Mean temperature at nest height was 2.3% cooler at nest sites (35.99 °C ± 0.07 SE) compared to random locations (36.81 °C ± 0.07 SE); at ambient height, nest sites were slightly cooler (32.78 °C ± 0.06 SE) than random location (32.99 °C ± 0.06 SE). Mean relative humidity at nest sites was greater at nest height (34.53% ± 0.112 SE) and ambient height (36.22% ± 0.10 SE) compared to random locations at nest (33.35% ± 0.12 SE) and ambient height (35.75% ± 0.10 SE). Based on these results, cover at sites that appear visually suitable for nesting by bobwhites and other ground nesting birds provided adequate thermal refuge in the rolling plains by maintaining cooler, moister microclimates than surrounding non-nesting locations. Post-hoc analyses of data revealed that habitat conditions surrounding suitable nest sites strongly influenced thermal suitability of the substrate. Given that eggs of bobwhites and probably other species …
format: application/pdf
format: text/html
creator: John M. Tomecek
creator: Brian L. Pierce
creator: Kelly S. Reyna
creator: Markus J. Peterson
subject: Agricultural Science
subject: Ecology
subject: Zoology
subject: Climate Change Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.3709
publisher: PeerJ Inc.
rights: © 2017 Tomecek et al.
abstract: Ecologists have long recognized the influence that environmental conditions have on abundance and range extent of animal species. We used the northern bobwhite (Colinus virginianus; hereafter bobwhite) as a model species for studying how microclimates serve as refuge against severe weather conditions. This species serves as an indicator or umbrella species for other sensitive ground-nesting, grassland obligate species. We conducted a mensurative field experiment in the rolling plains of Texas, USA, a semi-arid ecosystem on the southwestern periphery of bobwhite range, to determine whether native bunch grasses, apparently suitable for bobwhite nesting, could reduce ambient temperature below levels harmful for eggs. During the nesting season, we compared temperature and relative humidity readings at daily heat maxima (i.e., the 3 h during each day with highest temperatures) during the nesting season over the course of two years at 63 suitable nest sites paired with 63 random locations (n = 126) using two sensors at ∼10 and ∼60 cm above ground level. Mean temperature at nest height was 2.3% cooler at nest sites (35.99 °C ± 0.07 SE) compared to random locations (36.81 °C ± 0.07 SE); at ambient height, nest sites were slightly cooler (32.78 °C ± 0.06 SE) than random location (32.99 °C ± 0.06 SE). Mean relative humidity at nest sites was greater at nest height (34.53% ± 0.112 SE) and ambient height (36.22% ± 0.10 SE) compared to random locations at nest (33.35% ± 0.12 SE) and ambient height (35.75% ± 0.10 SE). Based on these results, cover at sites that appear visually suitable for nesting by bobwhites and other ground nesting birds provided adequate thermal refuge in the rolling plains by maintaining cooler, moister microclimates than surrounding non-nesting locations. Post-hoc analyses of data revealed that habitat conditions surrounding suitable nest sites strongly influenced thermal suitability of the substrate. Given that eggs of bobwhites and probably other species …
bibliographic citation: Tomecek et al. (2017) Inadequate thermal refuge constrains landscape habitability for a grassland bird species. PeerJ 5:e3709 https://doi.org/10.7717/peerj.3709
date submitted: 2017-04-11
date accepted: 2017-07-28
issued: 2017-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tomecek
  given name: John M.
author list: Agent
  family name: Pierce
  given name: Brian L.
author list: Agent
  family name: Reyna
  given name: Kelly S.
author list: Agent
  family name: Peterson
  given name: Markus J.
doi: 10.7717/peerj.3709
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-18
copyright: © 2017 Tomecek et al.
attribution name: Tomecek et al.

Genomic evidence of bitter taste in snakes and phylogenetic analysis of bitter taste receptor genes in reptiles
type: item
type: AcademicArticle
description: As nontraditional model organisms with extreme physiological and morphological phenotypes, snakes are believed to possess an inferior taste system. However, the bitter taste sensation is essential to distinguish the nutritious and poisonous food resources and the genomic evidence of bitter taste in snakes is largely scarce. To explore the genetic basis of the bitter taste of snakes and characterize the evolution of bitter taste receptor genes (Tas2rs) in reptiles, we identified Tas2r genes in 19 genomes (species) corresponding to three orders of non-avian reptiles. Our results indicated contractions of Tas2r gene repertoires in snakes, however dramatic gene expansions have occurred in lizards. Phylogenetic analysis of the Tas2rs with NJ and BI methods revealed that Tas2r genes of snake species formed two clades, whereas in lizards the Tas2r genes clustered into two monophyletic clades and four large clades. Evolutionary changes (birth and death) of intact Tas2r genes in reptiles were determined by reconciliation analysis. Additionally, the taste signaling pathway calcium homeostasis modulator 1 (Calhm1) gene of snakes was putatively functional, suggesting that snakes still possess bitter taste sensation. Furthermore, Phylogenetically Independent Contrasts (PIC) analyses reviewed a significant correlation between the number of Tas2r genes and the amount of potential toxins in reptilian diets, suggesting that insectivores such as some lizards may require more Tas2rs genes than omnivorous and carnivorous reptiles.
format: application/pdf
format: text/html
creator: Huaming Zhong
creator: Shuai Shang
creator: Xiaoyang Wu
creator: Jun Chen
creator: Wanchao Zhu
creator: Jiakuo Yan
creator: Haotian Li
creator: Honghai Zhang
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.3708
publisher: PeerJ Inc.
rights: © 2017 Zhong et al.
abstract: As nontraditional model organisms with extreme physiological and morphological phenotypes, snakes are believed to possess an inferior taste system. However, the bitter taste sensation is essential to distinguish the nutritious and poisonous food resources and the genomic evidence of bitter taste in snakes is largely scarce. To explore the genetic basis of the bitter taste of snakes and characterize the evolution of bitter taste receptor genes (Tas2rs) in reptiles, we identified Tas2r genes in 19 genomes (species) corresponding to three orders of non-avian reptiles. Our results indicated contractions of Tas2r gene repertoires in snakes, however dramatic gene expansions have occurred in lizards. Phylogenetic analysis of the Tas2rs with NJ and BI methods revealed that Tas2r genes of snake species formed two clades, whereas in lizards the Tas2r genes clustered into two monophyletic clades and four large clades. Evolutionary changes (birth and death) of intact Tas2r genes in reptiles were determined by reconciliation analysis. Additionally, the taste signaling pathway calcium homeostasis modulator 1 (Calhm1) gene of snakes was putatively functional, suggesting that snakes still possess bitter taste sensation. Furthermore, Phylogenetically Independent Contrasts (PIC) analyses reviewed a significant correlation between the number of Tas2r genes and the amount of potential toxins in reptilian diets, suggesting that insectivores such as some lizards may require more Tas2rs genes than omnivorous and carnivorous reptiles.
bibliographic citation: Zhong et al. (2017) Genomic evidence of bitter taste in snakes and phylogenetic analysis of bitter taste receptor genes in reptiles. PeerJ 5:e3708 https://doi.org/10.7717/peerj.3708
date submitted: 2017-03-19
date accepted: 2017-07-28
issued: 2017-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Huaming
author list: Agent
  family name: Shang
  given name: Shuai
author list: Agent
  family name: Wu
  given name: Xiaoyang
author list: Agent
  family name: Chen
  given name: Jun
author list: Agent
  family name: Zhu
  given name: Wanchao
author list: Agent
  family name: Yan
  given name: Jiakuo
author list: Agent
  family name: Li
  given name: Haotian
author list: Agent
  family name: Zhang
  given name: Honghai
doi: 10.7717/peerj.3708
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-18
copyright: ©2017 Zhong et al.
attribution name: Zhong et al.

Extended exposure to elevated temperature affects escape response behaviour in coral reef fishes
type: item
type: AcademicArticle
description: The threat of predation, and the prey’s response, are important drivers of community dynamics. Yet environmental temperature can have a significant effect on predation avoidance techniques such as fast-start performance observed in marine fishes. While it is known that temperature increases can influence performance and behaviour in the short-term, little is known about how species respond to extended exposure during development. We produced a startle response in two species of damselfish, the lemon damsel Pomacentrus moluccensis, and the Ambon damselfish Pomacentrus amboinensis, by the repeated use of a drop stimulus. We show that the length of thermal exposure of juveniles to elevated temperature significantly affects this escape responses. Short-term (4d) exposure to warmer temperature affected directionality and responsiveness for both species. After long-term (90d) exposure, only P. moluccensis showed beneficial plasticity, with directionality returning to control levels. Responsiveness also decreased in both species, possibly to compensate for higher temperatures. There was no effect of temperature or length of exposure on latency to react, maximum swimming speed, or escape distance suggesting that the physical ability to escape was maintained. Evidence suggests that elevated temperature may impact some fish species through its effect on the behavioural responses while under threat rather than having a direct influence on their physical ability to perform an effective escape response.
format: application/pdf
format: text/html
creator: Donald T. Warren
creator: Jennifer M. Donelson
creator: Mark I. McCormick
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.3652
publisher: PeerJ Inc.
rights: © 2017 Warren et al.
abstract: The threat of predation, and the prey’s response, are important drivers of community dynamics. Yet environmental temperature can have a significant effect on predation avoidance techniques such as fast-start performance observed in marine fishes. While it is known that temperature increases can influence performance and behaviour in the short-term, little is known about how species respond to extended exposure during development. We produced a startle response in two species of damselfish, the lemon damsel Pomacentrus moluccensis, and the Ambon damselfish Pomacentrus amboinensis, by the repeated use of a drop stimulus. We show that the length of thermal exposure of juveniles to elevated temperature significantly affects this escape responses. Short-term (4d) exposure to warmer temperature affected directionality and responsiveness for both species. After long-term (90d) exposure, only P. moluccensis showed beneficial plasticity, with directionality returning to control levels. Responsiveness also decreased in both species, possibly to compensate for higher temperatures. There was no effect of temperature or length of exposure on latency to react, maximum swimming speed, or escape distance suggesting that the physical ability to escape was maintained. Evidence suggests that elevated temperature may impact some fish species through its effect on the behavioural responses while under threat rather than having a direct influence on their physical ability to perform an effective escape response.
bibliographic citation: Warren et al. (2017) Extended exposure to elevated temperature affects escape response behaviour in coral reef fishes. PeerJ 5:e3652 https://doi.org/10.7717/peerj.3652
date submitted: 2016-11-13
date accepted: 2017-07-14
issued: 2017-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Warren
  given name: Donald T.
author list: Agent
  family name: Donelson
  given name: Jennifer M.
author list: Agent
  family name: McCormick
  given name: Mark I.
doi: 10.7717/peerj.3652
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-18
copyright: ©2017 Warren et al.
attribution name: Warren et al.

Shifting communities after­­ typhoon damage on an upper mesophotic reef in Okinawa, Japan
type: item
type: AcademicArticle
description: Very few studies have been conducted on the long-term effects of typhoon damage on mesophotic coral reefs. This study investigates the long-term community dynamics of damage from Typhoon 17 (Jelawat) in 2012 on the coral community of the upper mesophotic Ryugu Reef in Okinawa, Japan. A shift from foliose to bushy coral morphologies between December 2012 and August 2015 was documented, especially on the area of the reef that was previously recorded to be poor in scleractinian genera diversity and dominated by foliose corals. Comparatively, an area with higher diversity of scleractinian coral genera was observed to be less affected by typhoon damage with more stable community structure due to less change in dominant coral morphologies. Despite some changes in the composition of dominant genera, the generally high coverage of the mesophotic coral community is facilitating the recovery of Ryugu Reef after typhoon damage.
format: application/pdf
format: text/html
creator: Kristine N. White
creator: David K. Weinstein
creator: Taku Ohara
creator: Vianney Denis
creator: Javier Montenegro
creator: James D. Reimer
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Biosphere Interactions
subject: Natural Resource Management
description: doi:10.7717/peerj.3573
publisher: PeerJ Inc.
rights: © 2017 White et al.
abstract: Very few studies have been conducted on the long-term effects of typhoon damage on mesophotic coral reefs. This study investigates the long-term community dynamics of damage from Typhoon 17 (Jelawat) in 2012 on the coral community of the upper mesophotic Ryugu Reef in Okinawa, Japan. A shift from foliose to bushy coral morphologies between December 2012 and August 2015 was documented, especially on the area of the reef that was previously recorded to be poor in scleractinian genera diversity and dominated by foliose corals. Comparatively, an area with higher diversity of scleractinian coral genera was observed to be less affected by typhoon damage with more stable community structure due to less change in dominant coral morphologies. Despite some changes in the composition of dominant genera, the generally high coverage of the mesophotic coral community is facilitating the recovery of Ryugu Reef after typhoon damage.
bibliographic citation: White et al. (2017) Shifting communities after­­ typhoon damage on an upper mesophotic reef in Okinawa, Japan. PeerJ 5:e3573 https://doi.org/10.7717/peerj.3573
date submitted: 2017-03-26
date accepted: 2017-06-22
issued: 2017-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: White
  given name: Kristine N.
author list: Agent
  family name: Weinstein
  given name: David K.
author list: Agent
  family name: Ohara
  given name: Taku
author list: Agent
  family name: Denis
  given name: Vianney
author list: Agent
  family name: Montenegro
  given name: Javier
author list: Agent
  family name: Reimer
  given name: James D.
doi: 10.7717/peerj.3573
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-18
copyright: ©2017 White et al.
attribution name: White et al.

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