PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model
items: The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China
items: What are the probable predictors of urinary incontinence during pregnancy?
items: Further evidence of Chelonid herpesvirus 5 (ChHV5) latency: high levels of ChHV5 DNA detected in clinically healthy marine turtles
items: Medium-sized exotic prey create novel food webs: the case of predators and scavengers consuming lagomorphs
items: Competition-function tradeoffs in ectomycorrhizal fungi
items: Community shelter use in response to two benthic decapod predators in the Long Island Sound
items: Dropping behaviour of pea aphid nymphs increases their development time and reduces their reproductive capacity as adults
items: Development and characterization of novel microsatellite markers by Next Generation Sequencing for the blue and red shrimp Aristeus antennatus
items: Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase

A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model
type: item
type: AcademicArticle
description: Development of high-throughput technologies, such as Next-generation sequencing, allows thousands of experiments to be performed simultaneously while reducing resource requirement. Consequently, a massive amount of experiment data is now rapidly generated. Nevertheless, the data are not readily usable or meaningful until they are further analysed and interpreted. Due to the size of the data, a high performance computer (HPC) is required for the analysis and interpretation. However, the HPC is expensive and difficult to access. Other means were developed to allow researchers to acquire the power of HPC without a need to purchase and maintain one such as cloud computing services and grid computing system. In this study, we implemented grid computing in a computer training center environment using Berkeley Open Infrastructure for Network Computing (BOINC) as a job distributor and data manager combining all desktop computers to virtualize the HPC. Fifty desktop computers were used for setting up a grid system during the off-hours. In order to test the performance of the grid system, we adapted the Basic Local Alignment Search Tools (BLAST) to the BOINC system. Sequencing results from Illumina platform were aligned to the human genome database by BLAST on the grid system. The result and processing time were compared to those from a single desktop computer and HPC. The estimated durations of BLAST analysis for 4 million sequence reads on a desktop PC, HPC and the grid system were 568, 24 and 5 days, respectively. Thus, the grid implementation of BLAST by BOINC is an efficient alternative to the HPC for sequence alignment. The grid implementation by BOINC also helped tap unused computing resources during the off-hours and could be easily modified for other available bioinformatics software.
format: application/pdf
format: text/html
creator: Watthanai Pinthong
creator: Panya Muangruen
creator: Prapat Suriyaphol
creator: Dumrong Mairiang
subject: Bioinformatics
subject: Computational Science
description: doi:10.7717/peerj.2248
publisher: PeerJ Inc.
rights: © 2016 Pinthong et al.
abstract: Development of high-throughput technologies, such as Next-generation sequencing, allows thousands of experiments to be performed simultaneously while reducing resource requirement. Consequently, a massive amount of experiment data is now rapidly generated. Nevertheless, the data are not readily usable or meaningful until they are further analysed and interpreted. Due to the size of the data, a high performance computer (HPC) is required for the analysis and interpretation. However, the HPC is expensive and difficult to access. Other means were developed to allow researchers to acquire the power of HPC without a need to purchase and maintain one such as cloud computing services and grid computing system. In this study, we implemented grid computing in a computer training center environment using Berkeley Open Infrastructure for Network Computing (BOINC) as a job distributor and data manager combining all desktop computers to virtualize the HPC. Fifty desktop computers were used for setting up a grid system during the off-hours. In order to test the performance of the grid system, we adapted the Basic Local Alignment Search Tools (BLAST) to the BOINC system. Sequencing results from Illumina platform were aligned to the human genome database by BLAST on the grid system. The result and processing time were compared to those from a single desktop computer and HPC. The estimated durations of BLAST analysis for 4 million sequence reads on a desktop PC, HPC and the grid system were 568, 24 and 5 days, respectively. Thus, the grid implementation of BLAST by BOINC is an efficient alternative to the HPC for sequence alignment. The grid implementation by BOINC also helped tap unused computing resources during the off-hours and could be easily modified for other available bioinformatics software.
bibliographic citation: Pinthong et al. (2016) A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model. PeerJ 4:e2248 https://doi.org/10.7717/peerj.2248
date submitted: 2016-02-03
date accepted: 2016-06-22
issued: 2016-07-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pinthong
  given name: Watthanai
author list: Agent
  family name: Muangruen
  given name: Panya
author list: Agent
  family name: Suriyaphol
  given name: Prapat
author list: Agent
  family name: Mairiang
  given name: Dumrong
doi: 10.7717/peerj.2248
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-28
copyright: ©2016 Pinthong et al.
attribution name: Pinthong et al.

The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China
type: item
type: AcademicArticle
description: Many studies predict that climate change will cause species movement and turnover, but few have considered the effect of climate change on range fragmentation for current species and/or populations. We used MaxEnt to predict suitable habitat, fragmentation and turnover for 134 amphibian species in China under 40 future climate change scenarios spanning four pathways (RCP2.6, RCP4.5, RCP6 and RCP8.5) and two time periods (the 2050s and 2070s). Our results show that climate change may cause a major shift in spatial patterns of amphibian diversity. Amphibians in China would lose 20% of their original ranges on average; the distribution outside current ranges would increase by 15%. Suitable habitats for over 90% of species will be located in the north of their current range, for over 95% of species in higher altitudes (from currently 137–4,124 m to 286–4,396 m in the 2050s or 314–4,448 m in the 2070s), and for over 75% of species in the west of their current range. Also, our results predict two different general responses to the climate change: some species contract their ranges while moving westwards, southwards and to higher altitudes, while others expand their ranges. Finally, our analyses indicate that range dynamics and fragmentation are related, which means that the effects of climate change on Chinese amphibians might be two-folded.
format: application/pdf
format: text/html
creator: Ren-Yan Duan
creator: Xiao-Quan Kong
creator: Min-Yi Huang
creator: Sara Varela
creator: Xiang Ji
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.2185
publisher: PeerJ Inc.
rights: © 2016 Duan et al.
abstract: Many studies predict that climate change will cause species movement and turnover, but few have considered the effect of climate change on range fragmentation for current species and/or populations. We used MaxEnt to predict suitable habitat, fragmentation and turnover for 134 amphibian species in China under 40 future climate change scenarios spanning four pathways (RCP2.6, RCP4.5, RCP6 and RCP8.5) and two time periods (the 2050s and 2070s). Our results show that climate change may cause a major shift in spatial patterns of amphibian diversity. Amphibians in China would lose 20% of their original ranges on average; the distribution outside current ranges would increase by 15%. Suitable habitats for over 90% of species will be located in the north of their current range, for over 95% of species in higher altitudes (from currently 137–4,124 m to 286–4,396 m in the 2050s or 314–4,448 m in the 2070s), and for over 75% of species in the west of their current range. Also, our results predict two different general responses to the climate change: some species contract their ranges while moving westwards, southwards and to higher altitudes, while others expand their ranges. Finally, our analyses indicate that range dynamics and fragmentation are related, which means that the effects of climate change on Chinese amphibians might be two-folded.
bibliographic citation: Duan et al. (2016) The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China. PeerJ 4:e2185 https://doi.org/10.7717/peerj.2185
date submitted: 2016-01-25
date accepted: 2016-06-07
issued: 2016-07-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duan
  given name: Ren-Yan
author list: Agent
  family name: Kong
  given name: Xiao-Quan
author list: Agent
  family name: Huang
  given name: Min-Yi
author list: Agent
  family name: Varela
  given name: Sara
author list: Agent
  family name: Ji
  given name: Xiang
doi: 10.7717/peerj.2185
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-28
copyright: © 2016 Duan et al.
attribution name: Duan et al.

What are the probable predictors of urinary incontinence during pregnancy?
type: item
type: AcademicArticle
description: Objectives. The frequency, predisposing factors and impact of urinary incontinence (UI) on quality of life (QoL) during pregnancy were investigated. Materials and Method. A preliminary cross-sectional survey was studied among pregnant women between January and July of 2014. A total of 132 pregnant women were recruited using a questionnaire form for sociodemographic features, the Turkish version of the International Consultation on Incontinence-Short Form (ICIQ-SF), for the characteristics of UI and Wagner’s Quality of Life scale to assess impact on QoL. p < 0.05 was set significant. Results.Urinary incontinence was present in 56 out of 132 pregnant women (42.4%, UI-present group): mean age, 26.7 ± 5.4y(p = 0.780); median height, 160 cm (min–max: 153–176, p = 0.037); median BMI, 28.7 kg/m2(min–max: 22.4–50.0, p = 0.881); urine leakage occurred per week once (n = 18, 32.1%), twice or thrice (n = 8, 14.3%); per day few times (n = 14, 25%), once (n = 5, 8.9%) and always (n = 8, 14.3%) with mainly a small amount of urine leakage (n = 33, 58.9%) or a moderate (n = 4, 7.1%). There were statistically significant relationships between QoL scores and frequency of UI (p = 0.002) or amount of leakage (p = 0.002). Impact on QoL scores ranged from mild (n = 33, 58.9%), moderate (n = 4, 7.1%) to severe (n = 4, 7.1%) levels in daily life. UI impacted the daily life activities of women by making them less likely to undertake activities outside their homes (23.2%), by affecting their working performance and friendships (8.9%), their daily home activities (7.1%), their general health status (12.5%), their sexual relations (12.5%), by making them more nervous or anxious (10.7%) and by the need to wear pads or protectors (25%). ANOVA, Tukey, and Tamhane tests as the minimal important difference model yielded significant relevance between statistical analyses and clinical outcomes by using standard deviations (p = 0.001, 0.001 and 0.005 respectively). The following features favored the o…
format: application/pdf
format: text/html
creator: Nejat Demircan
creator: Ülkü Özmen
creator: Fürüzan Köktürk
creator: Hamdi Küçük
creator: Şevket Ata
creator: Müge Harma
creator: İnan İlker Arıkan
subject: Gynecology and Obstetrics
subject: Health Policy
subject: Nursing
subject: Urology
subject: Women's Health
description: doi:10.7717/peerj.2283
publisher: PeerJ Inc.
rights: © 2016 Demircan et al.
abstract: Objectives. The frequency, predisposing factors and impact of urinary incontinence (UI) on quality of life (QoL) during pregnancy were investigated. Materials and Method. A preliminary cross-sectional survey was studied among pregnant women between January and July of 2014. A total of 132 pregnant women were recruited using a questionnaire form for sociodemographic features, the Turkish version of the International Consultation on Incontinence-Short Form (ICIQ-SF), for the characteristics of UI and Wagner’s Quality of Life scale to assess impact on QoL. p < 0.05 was set significant. Results.Urinary incontinence was present in 56 out of 132 pregnant women (42.4%, UI-present group): mean age, 26.7 ± 5.4y(p = 0.780); median height, 160 cm (min–max: 153–176, p = 0.037); median BMI, 28.7 kg/m2(min–max: 22.4–50.0, p = 0.881); urine leakage occurred per week once (n = 18, 32.1%), twice or thrice (n = 8, 14.3%); per day few times (n = 14, 25%), once (n = 5, 8.9%) and always (n = 8, 14.3%) with mainly a small amount of urine leakage (n = 33, 58.9%) or a moderate (n = 4, 7.1%). There were statistically significant relationships between QoL scores and frequency of UI (p = 0.002) or amount of leakage (p = 0.002). Impact on QoL scores ranged from mild (n = 33, 58.9%), moderate (n = 4, 7.1%) to severe (n = 4, 7.1%) levels in daily life. UI impacted the daily life activities of women by making them less likely to undertake activities outside their homes (23.2%), by affecting their working performance and friendships (8.9%), their daily home activities (7.1%), their general health status (12.5%), their sexual relations (12.5%), by making them more nervous or anxious (10.7%) and by the need to wear pads or protectors (25%). ANOVA, Tukey, and Tamhane tests as the minimal important difference model yielded significant relevance between statistical analyses and clinical outcomes by using standard deviations (p = 0.001, 0.001 and 0.005 respectively). The following features favored the o…
bibliographic citation: Demircan et al. (2016) What are the probable predictors of urinary incontinence during pregnancy?. PeerJ 4:e2283 https://doi.org/10.7717/peerj.2283
date submitted: 2016-03-20
date accepted: 2016-07-03
issued: 2016-07-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Demircan
  given name: Nejat
author list: Agent
  family name: Özmen
  given name: Ülkü
author list: Agent
  family name: Köktürk
  given name: Fürüzan
author list: Agent
  family name: Küçük
  given name: Hamdi
author list: Agent
  family name: Ata
  given name: Şevket
author list: Agent
  family name: Harma
  given name: Müge
author list: Agent
  family name: Arıkan
  given name: İnan İlker
doi: 10.7717/peerj.2283
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-27
copyright: ©2016 Demircan et al.
attribution name: Demircan et al.

Further evidence of Chelonid herpesvirus 5 (ChHV5) latency: high levels of ChHV5 DNA detected in clinically healthy marine turtles
type: item
type: AcademicArticle
description: The Chelonid herpesvirus 5 (ChHV5) has been consistently associated with fibropapillomatosis (FP), a transmissible neoplastic disease of marine turtles. Whether ChHV5 plays a causal role remains debated, partly because while FP tumours have been clearly documented to contain high concentrations of ChHV5 DNA, recent PCR-based studies have demonstrated that large proportions of asymptomatic marine turtles are also carriers of ChHV5. We used a real-time PCR assay to quantify the levels of ChHV5 Glycoprotein B (gB) DNA in both tumour and non-tumour skin tissues, from clinically affected and healthy turtles drawn from distant ocean basins across four species. In agreement with previous studies, higher ratios of viral to host DNA were consistently observed in tumour versus non-tumour tissues in turtles with FP. Unexpectedly however, the levels of ChHV5 gB DNA in clinically healthy turtles were significantly higher than in non-tumour tissues from FP positive turtles. Thus, a large proportion of clinically healthy sea turtle populations worldwide across species carry ChHV5 gB DNA presumably through persistent latent infections. ChHV5 appears to be ubiquitous regardless of the animals’ clinical conditions. Hence, these results support the theory that ChHV5 is a near ubiquitous virus with latency characteristics requiring co-factors, possibly environmental or immune related, to induce FP.
format: application/pdf
format: text/html
creator: Alonzo Alfaro-Núñez
creator: Anders Miki Bojesen
creator: Mads F. Bertelsen
creator: Nathan Wales
creator: George H. Balazs
creator: M. Thomas P. Gilbert
subject: Conservation Biology
subject: Environmental Sciences
subject: Genetics
subject: Marine Biology
subject: Virology
description: doi:10.7717/peerj.2274
publisher: PeerJ Inc.
rights: © 2016 Alfaro-Núñez et al.
abstract: The Chelonid herpesvirus 5 (ChHV5) has been consistently associated with fibropapillomatosis (FP), a transmissible neoplastic disease of marine turtles. Whether ChHV5 plays a causal role remains debated, partly because while FP tumours have been clearly documented to contain high concentrations of ChHV5 DNA, recent PCR-based studies have demonstrated that large proportions of asymptomatic marine turtles are also carriers of ChHV5. We used a real-time PCR assay to quantify the levels of ChHV5 Glycoprotein B (gB) DNA in both tumour and non-tumour skin tissues, from clinically affected and healthy turtles drawn from distant ocean basins across four species. In agreement with previous studies, higher ratios of viral to host DNA were consistently observed in tumour versus non-tumour tissues in turtles with FP. Unexpectedly however, the levels of ChHV5 gB DNA in clinically healthy turtles were significantly higher than in non-tumour tissues from FP positive turtles. Thus, a large proportion of clinically healthy sea turtle populations worldwide across species carry ChHV5 gB DNA presumably through persistent latent infections. ChHV5 appears to be ubiquitous regardless of the animals’ clinical conditions. Hence, these results support the theory that ChHV5 is a near ubiquitous virus with latency characteristics requiring co-factors, possibly environmental or immune related, to induce FP.
bibliographic citation: Alfaro-Núñez et al. (2016) Further evidence of Chelonid herpesvirus 5 (ChHV5) latency: high levels of ChHV5 DNA detected in clinically healthy marine turtles. PeerJ 4:e2274 https://doi.org/10.7717/peerj.2274
date submitted: 2016-03-25
date accepted: 2016-06-29
issued: 2016-07-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alfaro-Núñez
  given name: Alonzo
author list: Agent
  family name: Bojesen
  given name: Anders Miki
author list: Agent
  family name: Bertelsen
  given name: Mads F.
author list: Agent
  family name: Wales
  given name: Nathan
author list: Agent
  family name: Balazs
  given name: George H.
author list: Agent
  family name: Gilbert
  given name: M. Thomas P.
doi: 10.7717/peerj.2274
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-27
copyright: ©2016 Alfaro-Núñez et al.
attribution name: Alfaro-Núñez et al.

Medium-sized exotic prey create novel food webs: the case of predators and scavengers consuming lagomorphs
type: item
type: AcademicArticle
description: Food web interactions are key to community structure. The introduction of species can be seen as an uncontrolled experiment of the addition of species. Introduced species lead to multiple changes, frequently threatening the native biodiversity. However, little is known about their direct effect on the upper level of the food web. In this study we review empirical data on the predator–prey relationship between the introduced lagomorphs and their consumers, and use meta-analytical tools to quantify the strength of their interactions. We expect that exotic lagomorphs will destabilize food webs, affect ecological processes and compromise the conservation of the invaded regions. We found 156 studies on the diet of 43 species of predators that consume lagomorphs as exotic preys in South America and Oceania. We found an average exotic lagomorphs-predator link of 20% which indicates a strong interaction, given that the average for the strongest links with native prey (when lagomorphs are not included in the predator diet) is about 24%. Additionally, this last link decreases to 17% when lagomorphs are present. When lagomorphs arrive in a new environment they may become the most important resource for predators, producing an unstable equilibrium in the novel food web. Any disruption of this interaction could have catastrophic consequences for the native diversity by directly impacting predators or indirectly impacting native preys by apparent competition. Eradication or any change in their abundances should be carefully considered in conservation actions since those will have great impacts on predator populations and ultimately in the whole communities.
format: application/pdf
format: text/html
creator: Facundo Barbar
creator: Fernando Hiraldo
creator: Sergio A. Lambertucci
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
description: doi:10.7717/peerj.2273
publisher: PeerJ Inc.
rights: © 2016 Barbar et al.
abstract: Food web interactions are key to community structure. The introduction of species can be seen as an uncontrolled experiment of the addition of species. Introduced species lead to multiple changes, frequently threatening the native biodiversity. However, little is known about their direct effect on the upper level of the food web. In this study we review empirical data on the predator–prey relationship between the introduced lagomorphs and their consumers, and use meta-analytical tools to quantify the strength of their interactions. We expect that exotic lagomorphs will destabilize food webs, affect ecological processes and compromise the conservation of the invaded regions. We found 156 studies on the diet of 43 species of predators that consume lagomorphs as exotic preys in South America and Oceania. We found an average exotic lagomorphs-predator link of 20% which indicates a strong interaction, given that the average for the strongest links with native prey (when lagomorphs are not included in the predator diet) is about 24%. Additionally, this last link decreases to 17% when lagomorphs are present. When lagomorphs arrive in a new environment they may become the most important resource for predators, producing an unstable equilibrium in the novel food web. Any disruption of this interaction could have catastrophic consequences for the native diversity by directly impacting predators or indirectly impacting native preys by apparent competition. Eradication or any change in their abundances should be carefully considered in conservation actions since those will have great impacts on predator populations and ultimately in the whole communities.
bibliographic citation: Barbar et al. (2016) Medium-sized exotic prey create novel food webs: the case of predators and scavengers consuming lagomorphs. PeerJ 4:e2273 https://doi.org/10.7717/peerj.2273
date submitted: 2016-05-05
date accepted: 2016-06-29
issued: 2016-07-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barbar
  given name: Facundo
author list: Agent
  family name: Hiraldo
  given name: Fernando
author list: Agent
  family name: Lambertucci
  given name: Sergio A.
doi: 10.7717/peerj.2273
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-27
copyright: ©2016 Barbar et al.
attribution name: Barbar et al.

Competition-function tradeoffs in ectomycorrhizal fungi
type: item
type: AcademicArticle
description: Background. The extent to which ectomycorrhizal fungi mediate primary production, carbon storage, and nutrient remineralization in terrestrial ecosystems depends upon fungal community composition. However, the factors that govern community composition at the root system scale are not well understood. Here, we explore a potential tradeoff between ectomycorrhizal fungal competitive ability and enzymatic function. Methods. We grew Pinus muricata (Bishop Pine) seedlings in association with ectomycorrhizal fungi from three different genera in a fully factorial experimental design. We measured seedling growth responses, ectomycorrhizal abundance, and the root tip activity of five different extracellular enzymes involved in the mobilization of carbon and phosphorus. Results. We found an inverse relationship between competitiveness, quantified based on relative colonization levels, and enzymatic activity. Specifically, Thelephora terrestris, the dominant fungus, had the lowest enzyme activity levels, while Suillus pungens, the least dominant fungus, had the highest. Discussion. Our results identify a tradeoff between competition and function in ectomycorrhizal fungi, perhaps mediated by the competing energetic demands associated with competitive interactions and enzymatic production. These data suggest that mechanisms such as active partner maintenance by host trees may be important to maintaining “high-quality” ectomycorrhizal fungal partners in natural systems.
format: application/pdf
format: text/html
creator: Holly V. Moeller
creator: Kabir G. Peay
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.2270
publisher: PeerJ Inc.
rights: © 2016 Moeller and Peay
abstract: Background. The extent to which ectomycorrhizal fungi mediate primary production, carbon storage, and nutrient remineralization in terrestrial ecosystems depends upon fungal community composition. However, the factors that govern community composition at the root system scale are not well understood. Here, we explore a potential tradeoff between ectomycorrhizal fungal competitive ability and enzymatic function. Methods. We grew Pinus muricata (Bishop Pine) seedlings in association with ectomycorrhizal fungi from three different genera in a fully factorial experimental design. We measured seedling growth responses, ectomycorrhizal abundance, and the root tip activity of five different extracellular enzymes involved in the mobilization of carbon and phosphorus. Results. We found an inverse relationship between competitiveness, quantified based on relative colonization levels, and enzymatic activity. Specifically, Thelephora terrestris, the dominant fungus, had the lowest enzyme activity levels, while Suillus pungens, the least dominant fungus, had the highest. Discussion. Our results identify a tradeoff between competition and function in ectomycorrhizal fungi, perhaps mediated by the competing energetic demands associated with competitive interactions and enzymatic production. These data suggest that mechanisms such as active partner maintenance by host trees may be important to maintaining “high-quality” ectomycorrhizal fungal partners in natural systems.
bibliographic citation: Moeller et al. (2016) Competition-function tradeoffs in ectomycorrhizal fungi. PeerJ 4:e2270 https://doi.org/10.7717/peerj.2270
date submitted: 2016-05-26
date accepted: 2016-06-29
issued: 2016-07-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moeller
  given name: Holly V.
author list: Agent
  family name: Peay
  given name: Kabir G.
doi: 10.7717/peerj.2270
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-27
copyright: ©2016 Moeller and Peay
attribution name: Moeller and Peay

Community shelter use in response to two benthic decapod predators in the Long Island Sound
type: item
type: AcademicArticle
description: To investigate community shelter effects of two invasive decapod species, Hemigrapsus sanguineus and Carcinus maenas, in the Long Island Sound (LIS), we deployed artificial shelters in the intertidal and immediate subtidal zones. These consisted of five groups during the summer: a control, a resident H. sanguineus male or female group, and a resident C. maenas male or female group. We quantified utilization of the shelters at 24 h by counting crabs and fish present. We found significant avoidance of H. sanguineus in the field by benthic hermit crabs (Pagurus spp.) and significant avoidance of C. maenas by the seaboard goby (Gobiosoma ginsburgi). The grubby (Myoxocephalus aenaeus) avoided neither treatment, probably since it tends to be a predator of invertebrates. H. sanguineus avoided C. maenas treatments, whereas C. maenas did not avoid any treatment. Seasonal deployments in the subtidal indicated cohabitation of a number of benthic species in the LIS, with peak shelter use corresponding with increased predation and likely reproductive activity in spring and summer for green crabs (C. maenas), hermit crabs (Pagurus spp.), seaboard gobies (G. ginsburgi), and grubbies (Myoxocephalus aenaeus).
format: application/pdf
format: text/html
creator: David M. Hudson
creator: Dugan Reagan
creator: Joseph F. Crivello
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.2265
publisher: PeerJ Inc.
rights: © 2016 Hudson et al.
abstract: To investigate community shelter effects of two invasive decapod species, Hemigrapsus sanguineus and Carcinus maenas, in the Long Island Sound (LIS), we deployed artificial shelters in the intertidal and immediate subtidal zones. These consisted of five groups during the summer: a control, a resident H. sanguineus male or female group, and a resident C. maenas male or female group. We quantified utilization of the shelters at 24 h by counting crabs and fish present. We found significant avoidance of H. sanguineus in the field by benthic hermit crabs (Pagurus spp.) and significant avoidance of C. maenas by the seaboard goby (Gobiosoma ginsburgi). The grubby (Myoxocephalus aenaeus) avoided neither treatment, probably since it tends to be a predator of invertebrates. H. sanguineus avoided C. maenas treatments, whereas C. maenas did not avoid any treatment. Seasonal deployments in the subtidal indicated cohabitation of a number of benthic species in the LIS, with peak shelter use corresponding with increased predation and likely reproductive activity in spring and summer for green crabs (C. maenas), hermit crabs (Pagurus spp.), seaboard gobies (G. ginsburgi), and grubbies (Myoxocephalus aenaeus).
bibliographic citation: Hudson et al. (2016) Community shelter use in response to two benthic decapod predators in the Long Island Sound. PeerJ 4:e2265 https://doi.org/10.7717/peerj.2265
date submitted: 2016-04-03
date accepted: 2016-06-27
issued: 2016-07-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hudson
  given name: David M.
author list: Agent
  family name: Reagan
  given name: Dugan
author list: Agent
  family name: Crivello
  given name: Joseph F.
doi: 10.7717/peerj.2265
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-27
copyright: © 2016 Hudson et al.
attribution name: Hudson et al.

Dropping behaviour of pea aphid nymphs increases their development time and reduces their reproductive capacity as adults
type: item
type: AcademicArticle
description: Background. Many aphid species, including the pea aphid Acyrthosiphon pisum, exhibit a behaviour where they drop or fall from their host plant, a commonly used strategy to avoid predation, parasitism or physical disturbance. We hypothesised that there was a physiological non-consumptive cost due to such dropping behaviour because aphids would expend energy re-establishing themselves on a host plant and also lose feeding time. Methods. We evaluated this non-consumptive cost by determining the development time and reproductive potential of pea aphids that whilst developing as nymphs had regularly dropped to the ground following dislodgment from their host plant. Using a microcosm approach, in a replicated and balanced laboratory experiment, we caused aphid dropping behaviour by tapping the plants on which they were feeding. Results. The results demonstrated that disturbance by dropping behaviour increased nymphal development time and reduced their subsequent reproductive capacity as adults. Discussion. We conclude that dropping behaviour had a strong negative effect on the development of nymphs and their subsequent reproductive capacity. This implies that the physiological cost of such a behaviour choice is substantial, and that such avoidance strategies require a trade-off which reduces the capacity of a population to increase.
format: application/pdf
format: text/html
creator: Barbara Agabiti
creator: Roxanne J. Wassenaar
creator: Linton Winder
subject: Agricultural Science
subject: Animal Behavior
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.2236
publisher: PeerJ Inc.
rights: © 2016 Agabiti et al.
abstract: Background. Many aphid species, including the pea aphid Acyrthosiphon pisum, exhibit a behaviour where they drop or fall from their host plant, a commonly used strategy to avoid predation, parasitism or physical disturbance. We hypothesised that there was a physiological non-consumptive cost due to such dropping behaviour because aphids would expend energy re-establishing themselves on a host plant and also lose feeding time. Methods. We evaluated this non-consumptive cost by determining the development time and reproductive potential of pea aphids that whilst developing as nymphs had regularly dropped to the ground following dislodgment from their host plant. Using a microcosm approach, in a replicated and balanced laboratory experiment, we caused aphid dropping behaviour by tapping the plants on which they were feeding. Results. The results demonstrated that disturbance by dropping behaviour increased nymphal development time and reduced their subsequent reproductive capacity as adults. Discussion. We conclude that dropping behaviour had a strong negative effect on the development of nymphs and their subsequent reproductive capacity. This implies that the physiological cost of such a behaviour choice is substantial, and that such avoidance strategies require a trade-off which reduces the capacity of a population to increase.
bibliographic citation: Agabiti et al. (2016) Dropping behaviour of pea aphid nymphs increases their development time and reduces their reproductive capacity as adults. PeerJ 4:e2236 https://doi.org/10.7717/peerj.2236
date submitted: 2016-04-04
date accepted: 2016-06-20
issued: 2016-07-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Agabiti
  given name: Barbara
author list: Agent
  family name: Wassenaar
  given name: Roxanne J.
author list: Agent
  family name: Winder
  given name: Linton
doi: 10.7717/peerj.2236
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-27
copyright: ©2016 Agabiti et al.
attribution name: Agabiti et al.

Development and characterization of novel microsatellite markers by Next Generation Sequencing for the blue and red shrimp Aristeus antennatus
type: item
type: AcademicArticle
description: The blue and red shrimp, Aristeus antennatus, is a commercially important crustacean, in the Mediterranean Sea, which has been listed as a priority species for fishery management. Hypervariable microsatellite markers could be a useful tool to identify genetic stocks among geographically close fishing grounds. Potential microsatellite markers (97) identified from next-generation sequencing of an individual shrimp using a 454 GS Junior Pyrosequencer were tested on a preliminary panel of 15 individuals representing the four worldwide genetic stocks of the species from which 35 polymorphic loci were identified and used to characterize an additional 20 individuals from the Western Mediterranean Sea. In the Western Mediterranean sample, 32 out of 35 were polymorphic loci and the number of alleles per locus ranged from 2 to 14 and expected heterozygosity ranged from 0.050 to 0.968. No linkage disequilibrium was detected, indicating the independence of the loci. These novel microsatellites provide additional tools to address questions relating to genetic diversity, parentage studies and connectivity patterns of A. antennatus populations and help develop effective strategies to ensure long-term sustainability of this resource.
format: application/pdf
format: text/html
creator: Sandra Heras
creator: Laia Planella
creator: Ilaria Caldarazzo
creator: Manuel Vera
creator: José-Luis García-Marín
creator: Maria Ines Roldán
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.2200
publisher: PeerJ Inc.
rights: © 2016 Heras et al.
abstract: The blue and red shrimp, Aristeus antennatus, is a commercially important crustacean, in the Mediterranean Sea, which has been listed as a priority species for fishery management. Hypervariable microsatellite markers could be a useful tool to identify genetic stocks among geographically close fishing grounds. Potential microsatellite markers (97) identified from next-generation sequencing of an individual shrimp using a 454 GS Junior Pyrosequencer were tested on a preliminary panel of 15 individuals representing the four worldwide genetic stocks of the species from which 35 polymorphic loci were identified and used to characterize an additional 20 individuals from the Western Mediterranean Sea. In the Western Mediterranean sample, 32 out of 35 were polymorphic loci and the number of alleles per locus ranged from 2 to 14 and expected heterozygosity ranged from 0.050 to 0.968. No linkage disequilibrium was detected, indicating the independence of the loci. These novel microsatellites provide additional tools to address questions relating to genetic diversity, parentage studies and connectivity patterns of A. antennatus populations and help develop effective strategies to ensure long-term sustainability of this resource.
bibliographic citation: Heras et al. (2016) Development and characterization of novel microsatellite markers by Next Generation Sequencing for the blue and red shrimp Aristeus antennatus. PeerJ 4:e2200 https://doi.org/10.7717/peerj.2200
date submitted: 2016-02-29
date accepted: 2016-06-10
issued: 2016-07-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heras
  given name: Sandra
author list: Agent
  family name: Planella
  given name: Laia
author list: Agent
  family name: Caldarazzo
  given name: Ilaria
author list: Agent
  family name: Vera
  given name: Manuel
author list: Agent
  family name: García-Marín
  given name: José-Luis
author list: Agent
  family name: Roldán
  given name: Maria Ines
doi: 10.7717/peerj.2200
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-27
copyright: ©2016 Heras et al.
attribution name: Heras et al.

Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase
type: item
type: AcademicArticle
description: The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an RNA-dependent RNA polymerase (RdRp) gene, we found that a tandem duplication occurred after the divergence of potato and its wild relatives among other Solanum plants. The duplicated sequence crosses the intron-exon boundary of the first intron and the second exon. A new intron was detected at this duplicated region, and it includes a small previously exonic segment of the upstream copy of the duplicated sequence and the intronic segment of the downstream copy of the duplicated sequence. The donor site of this new intron was directly obtained from the small previously exonic segment. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3′ splicing site, two putative exonic splicing enhancers, and the GC contents differed between the intron and exon. In the widely cited model of intron gain by tandem genomic duplication, the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. Our results illustrate that the tandem duplication model of intron gain should be diverse in terms of obtaining the proper splicing signals.
format: application/pdf
format: text/html
creator: Ming-Yue Ma
creator: Xin-Ran Lan
creator: Deng-Ke Niu
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.2272
publisher: PeerJ Inc.
rights: © 2016 Ma et al.
abstract: The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an RNA-dependent RNA polymerase (RdRp) gene, we found that a tandem duplication occurred after the divergence of potato and its wild relatives among other Solanum plants. The duplicated sequence crosses the intron-exon boundary of the first intron and the second exon. A new intron was detected at this duplicated region, and it includes a small previously exonic segment of the upstream copy of the duplicated sequence and the intronic segment of the downstream copy of the duplicated sequence. The donor site of this new intron was directly obtained from the small previously exonic segment. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3′ splicing site, two putative exonic splicing enhancers, and the GC contents differed between the intron and exon. In the widely cited model of intron gain by tandem genomic duplication, the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. Our results illustrate that the tandem duplication model of intron gain should be diverse in terms of obtaining the proper splicing signals.
bibliographic citation: Ma et al. (2016) Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PeerJ 4:e2272 https://doi.org/10.7717/peerj.2272
date submitted: 2015-10-16
date accepted: 2016-06-29
issued: 2016-07-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Ming-Yue
author list: Agent
  family name: Lan
  given name: Xin-Ran
author list: Agent
  family name: Niu
  given name: Deng-Ke
doi: 10.7717/peerj.2272
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-26
copyright: © 2016 Ma et al.
attribution name: Ma et al.

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