PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Framework for community functioning: synthesis of stress gradient and resource partitioning concepts
items: Elevated serum osteoprotegerin may predict peripheral arterial disease after kidney transplantation: a single-center prospective cross-sectional study in Taiwan
items: Diverse responses of Symbiodinium types to menthol and DCMU treatment
items: Harnessing mtDNA variation to resolve ambiguity in ‘Redfish’ sold in Europe
items: Comparative study of Cd uptake and tolerance of two Italian ryegrass (Lolium multiflorum) cultivars
items: Growth of hybrid open access, 2009–2016
items: Effect of the environment on horizontal gene transfer between bacteria and archaea
items: Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?
items: A prospective study of the motivational and health dynamics of Internet Gaming Disorder
items: Unraveling the diversification history of grasshoppers belonging to the “Trimerotropis pallidipennis” (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes

Framework for community functioning: synthesis of stress gradient and resource partitioning concepts
type: item
type: AcademicArticle
description: To understand how communities function and generate abundance, I develop a framework integrating elements from the stress gradient and resource partitioning concepts. The framework suggests that guild abundance depends on environmental and spatial factors but also on inter-guild interactions (competitor or facilitator richness), which can alter the fundamental niche of constituent species in negative (competition) or positive direction (facilitation). Consequently, the environmental and spatial mechanisms driving guild abundance would differ across guilds and interaction modes. Using continental data on stream diatoms and physico-chemistry, the roles of these mechanisms were tested under three interaction modes—shared preference, distinct preference, and facilitative, whereby pairs of guilds exhibited, respectively, a dominance-tolerance tradeoff along a eutrophication gradient, specialization along a pH gradient, or a donor-recipient relationship along a nitrogen gradient. Representative of the shared preference mode were the motile (dominant) and low profile (tolerant) guilds, of the distinct preference mode—the acidophilous and alkaliphilous (low profile) guilds, and of the facilitative mode—nitrogen fixers (donors) and motile species (recipients). In each mode, the influences of environment, space (latitude and longitude), and competitor or facilitator richness on guild density were assessed by variance partitioning. Pure environment constrained most strongly the density of the dominant, the acidophilous, and the recipient guild in the shared preference, distinct preference, and facilitative mode, respectively, while spatial effects were important only for the low profile guild. Higher competitor richness was associated with lower density of the tolerant guild in the shared preference mode, both guilds in the distinct preference mode, and the donor guild in the facilitative mode. Conversely, recipient density in the facilitative mode increased with donor richnes…
format: application/pdf
format: text/html
creator: Sophia I. Passy
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Environmental Sciences
subject: Freshwater Biology
description: doi:10.7717/peerj.3885
publisher: PeerJ Inc.
rights: © 2017 Passy
abstract: To understand how communities function and generate abundance, I develop a framework integrating elements from the stress gradient and resource partitioning concepts. The framework suggests that guild abundance depends on environmental and spatial factors but also on inter-guild interactions (competitor or facilitator richness), which can alter the fundamental niche of constituent species in negative (competition) or positive direction (facilitation). Consequently, the environmental and spatial mechanisms driving guild abundance would differ across guilds and interaction modes. Using continental data on stream diatoms and physico-chemistry, the roles of these mechanisms were tested under three interaction modes—shared preference, distinct preference, and facilitative, whereby pairs of guilds exhibited, respectively, a dominance-tolerance tradeoff along a eutrophication gradient, specialization along a pH gradient, or a donor-recipient relationship along a nitrogen gradient. Representative of the shared preference mode were the motile (dominant) and low profile (tolerant) guilds, of the distinct preference mode—the acidophilous and alkaliphilous (low profile) guilds, and of the facilitative mode—nitrogen fixers (donors) and motile species (recipients). In each mode, the influences of environment, space (latitude and longitude), and competitor or facilitator richness on guild density were assessed by variance partitioning. Pure environment constrained most strongly the density of the dominant, the acidophilous, and the recipient guild in the shared preference, distinct preference, and facilitative mode, respectively, while spatial effects were important only for the low profile guild. Higher competitor richness was associated with lower density of the tolerant guild in the shared preference mode, both guilds in the distinct preference mode, and the donor guild in the facilitative mode. Conversely, recipient density in the facilitative mode increased with donor richnes…
bibliographic citation: Passy (2017) Framework for community functioning: synthesis of stress gradient and resource partitioning concepts. PeerJ 5:e3885 https://doi.org/10.7717/peerj.3885
date submitted: 2017-03-18
date accepted: 2017-09-13
issued: 2017-10-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Passy
  given name: Sophia I.
doi: 10.7717/peerj.3885
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-02
copyright: ©2017 Passy
attribution name: Passy

Elevated serum osteoprotegerin may predict peripheral arterial disease after kidney transplantation: a single-center prospective cross-sectional study in Taiwan
type: item
type: AcademicArticle
description: Background Osteoprotegerin (OPG) is a potential biomarker for severity and complications of cardiovascular diseases. Peripheral arterial disease (PAD) is associated with an increased risk of death in kidney transplantation (KT) patients. This prospective cross-sectional study evaluated the relationship between serum OPG and PAD in KT patients. Methods Seventy-four KT patients were enrolled for this PAD study. Fasting blood samples were obtained to measure serum OPG levels by using enzyme-linked immunosorbent assay kits. The ankle-brachial index (ABI) of less than 0.9 was applied for PAD diagnosis. Results Thirteen patients (17.6%) were diagnosed with PAD. Diabetes (P = 0.025), smoking (P = 0.010), and increased OPG levels (P = 0.001) were significantly more frequent in the PAD group. Multivariate logistic regression analysis showed that serum OPG (odds ratio [OR], 1.336; 95% CI [1.108–1.611]; P = 0.002) and diabetes (OR, 7.120; 95% CI [1.080–46.940]; P = 0.041) were independent predictors of PAD in KT patients. The area under the receiver operating characteristic (ROC) curve determined that the probability of a serum OPG level of 7.117 pg/L in predicting PAD in KT patients was 0.799 (95% CI [0.690–0.884]; P < 0.001). Discussion Exploration of reliable biomarkers for early identification of vascular risk is crucial for KT patients. Elevated serum OPG levels may predict PAD in KT patients with cutoff value of 7.117 pg/L.
format: application/pdf
format: text/html
creator: Yen-Cheng Chen
creator: Bang-Gee Hsu
creator: Ching-Chun Ho
creator: Chung-Jen Lee
creator: Ming-Che Lee
subject: Nephrology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.3847
publisher: PeerJ Inc.
rights: © 2017 Chen et al.
abstract: Background Osteoprotegerin (OPG) is a potential biomarker for severity and complications of cardiovascular diseases. Peripheral arterial disease (PAD) is associated with an increased risk of death in kidney transplantation (KT) patients. This prospective cross-sectional study evaluated the relationship between serum OPG and PAD in KT patients. Methods Seventy-four KT patients were enrolled for this PAD study. Fasting blood samples were obtained to measure serum OPG levels by using enzyme-linked immunosorbent assay kits. The ankle-brachial index (ABI) of less than 0.9 was applied for PAD diagnosis. Results Thirteen patients (17.6%) were diagnosed with PAD. Diabetes (P = 0.025), smoking (P = 0.010), and increased OPG levels (P = 0.001) were significantly more frequent in the PAD group. Multivariate logistic regression analysis showed that serum OPG (odds ratio [OR], 1.336; 95% CI [1.108–1.611]; P = 0.002) and diabetes (OR, 7.120; 95% CI [1.080–46.940]; P = 0.041) were independent predictors of PAD in KT patients. The area under the receiver operating characteristic (ROC) curve determined that the probability of a serum OPG level of 7.117 pg/L in predicting PAD in KT patients was 0.799 (95% CI [0.690–0.884]; P < 0.001). Discussion Exploration of reliable biomarkers for early identification of vascular risk is crucial for KT patients. Elevated serum OPG levels may predict PAD in KT patients with cutoff value of 7.117 pg/L.
bibliographic citation: Chen et al. (2017) Elevated serum osteoprotegerin may predict peripheral arterial disease after kidney transplantation: a single-center prospective cross-sectional study in Taiwan. PeerJ 5:e3847 https://doi.org/10.7717/peerj.3847
date submitted: 2017-05-16
date accepted: 2017-09-02
issued: 2017-10-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yen-Cheng
author list: Agent
  family name: Hsu
  given name: Bang-Gee
author list: Agent
  family name: Ho
  given name: Ching-Chun
author list: Agent
  family name: Lee
  given name: Chung-Jen
author list: Agent
  family name: Lee
  given name: Ming-Che
doi: 10.7717/peerj.3847
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-02
copyright: ©2017 Chen et al.
attribution name: Chen et al.

Diverse responses of Symbiodinium types to menthol and DCMU treatment
type: item
type: AcademicArticle
description: To understand the mechanism of photosynthetic inhibition and generation of reactive oxygen species (ROS) in Symbiodinium types under stress, chemicals such as dichlorophenyl dimethylurea (DCMU) are widely used. Moreover, DCMU and recently menthol were used to generate aposymbiotic cnidarian hosts. While the effects of DCMU on Symbiodinium cells have been extensively studied, no studies have shown the mechanism behind menthol-induced coral bleaching. Moreover, no study has compared the effects of DCMU and menthol treatments on photosystem II (PSII) activity and generation of ROS in different Symbiodinium types. In this study, we utilized five freshly isolated Symbiodinium types (S. minutum (B1), S. goreaui (C1), C3, C15, and S. trenchii (D1a)) to compare the effects of DCMU and menthol treatments. Symbiodinium cells were exposed to DCMU and menthol at different concentrations for 4 h. Results showed that values of the 50% inhibitory concentration (IC50) for PSII inhibition were 0.72∼1.96 mM for menthol-treated cells compared to 29∼74 pM for DCMU-treated cells. Diverse responses of Symbiodinium types were displayed in terms of PSII tolerance to menthol (S. minutum > S. trenchii = C15 > C3 = S. goreaui), and also in the response curves. In contrast, responses were not so diverse when the different types were treated with DCMU. Three of five menthol-treated Symbiodinium types showed instant and significant ROS generation when PSII activity was inhibited, compared to no ROS being generated in DCMU-treated Symbiodinium types. Both results indicated that menthol inhibited Symbiodinium PSII activity through Symbiodinium type-dependent mechanisms, which were also distinct from those with DCMU treatment. This study further confirmed that photosynthetic functions Symbiodinium have diverse responses to stress even within the same clade.
format: application/pdf
format: text/html
creator: Jih-Terng Wang
creator: Shashank Keshavmurthy
creator: Tzu-Ying Chu
creator: Chaolun Allen Chen
subject: Environmental Impacts
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.3843
publisher: PeerJ Inc.
rights: © 2017 Wang et al.
abstract: To understand the mechanism of photosynthetic inhibition and generation of reactive oxygen species (ROS) in Symbiodinium types under stress, chemicals such as dichlorophenyl dimethylurea (DCMU) are widely used. Moreover, DCMU and recently menthol were used to generate aposymbiotic cnidarian hosts. While the effects of DCMU on Symbiodinium cells have been extensively studied, no studies have shown the mechanism behind menthol-induced coral bleaching. Moreover, no study has compared the effects of DCMU and menthol treatments on photosystem II (PSII) activity and generation of ROS in different Symbiodinium types. In this study, we utilized five freshly isolated Symbiodinium types (S. minutum (B1), S. goreaui (C1), C3, C15, and S. trenchii (D1a)) to compare the effects of DCMU and menthol treatments. Symbiodinium cells were exposed to DCMU and menthol at different concentrations for 4 h. Results showed that values of the 50% inhibitory concentration (IC50) for PSII inhibition were 0.72∼1.96 mM for menthol-treated cells compared to 29∼74 pM for DCMU-treated cells. Diverse responses of Symbiodinium types were displayed in terms of PSII tolerance to menthol (S. minutum > S. trenchii = C15 > C3 = S. goreaui), and also in the response curves. In contrast, responses were not so diverse when the different types were treated with DCMU. Three of five menthol-treated Symbiodinium types showed instant and significant ROS generation when PSII activity was inhibited, compared to no ROS being generated in DCMU-treated Symbiodinium types. Both results indicated that menthol inhibited Symbiodinium PSII activity through Symbiodinium type-dependent mechanisms, which were also distinct from those with DCMU treatment. This study further confirmed that photosynthetic functions Symbiodinium have diverse responses to stress even within the same clade.
bibliographic citation: Wang et al. (2017) Diverse responses of Symbiodinium types to menthol and DCMU treatment. PeerJ 5:e3843 https://doi.org/10.7717/peerj.3843
date submitted: 2017-05-19
date accepted: 2017-09-02
issued: 2017-10-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jih-Terng
author list: Agent
  family name: Keshavmurthy
  given name: Shashank
author list: Agent
  family name: Chu
  given name: Tzu-Ying
author list: Agent
  family name: Chen
  given name: Chaolun Allen
doi: 10.7717/peerj.3843
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-02
copyright: ©2017 Wang et al.
attribution name: Wang et al.

Harnessing mtDNA variation to resolve ambiguity in ‘Redfish’ sold in Europe
type: item
type: AcademicArticle
description: Morphology-based identification of North Atlantic Sebastes has long been controversial and misidentification may produce misleading data, with cascading consequences that negatively affect fisheries management and seafood labelling. North Atlantic Sebastes comprises of four species, commonly known as ‘redfish’, but little is known about the number, identity and labelling accuracy of redfish species sold across Europe. We used a molecular approach to identify redfish species from ‘blind’ specimens to evaluate the performance of the Barcode of Life (BOLD) and Genbank databases, as well as carrying out a market product accuracy survey from retailers across Europe. The conventional BOLD approach proved ambiguous, and phylogenetic analysis based on mtDNA control region sequences provided a higher resolution for species identification. By sampling market products from four countries, we found the presence of two species of redfish (S. norvegicus and S. mentella) and one unidentified Pacific rockfish marketed in Europe. Furthermore, public databases revealed the existence of inaccurate reference sequences, likely stemming from species misidentification from previous studies, which currently hinders the efficacy of DNA methods for the identification of Sebastes market samples.
format: application/pdf
format: text/html
creator: Peter Shum
creator: Lauren Moore
creator: Christophe Pampoulie
creator: Cristina Di Muri
creator: Sara Vandamme
creator: Stefano Mariani
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Natural Resource Management
description: doi:10.7717/peerj.3746
publisher: PeerJ Inc.
rights: © 2017 Shum et al.
abstract: Morphology-based identification of North Atlantic Sebastes has long been controversial and misidentification may produce misleading data, with cascading consequences that negatively affect fisheries management and seafood labelling. North Atlantic Sebastes comprises of four species, commonly known as ‘redfish’, but little is known about the number, identity and labelling accuracy of redfish species sold across Europe. We used a molecular approach to identify redfish species from ‘blind’ specimens to evaluate the performance of the Barcode of Life (BOLD) and Genbank databases, as well as carrying out a market product accuracy survey from retailers across Europe. The conventional BOLD approach proved ambiguous, and phylogenetic analysis based on mtDNA control region sequences provided a higher resolution for species identification. By sampling market products from four countries, we found the presence of two species of redfish (S. norvegicus and S. mentella) and one unidentified Pacific rockfish marketed in Europe. Furthermore, public databases revealed the existence of inaccurate reference sequences, likely stemming from species misidentification from previous studies, which currently hinders the efficacy of DNA methods for the identification of Sebastes market samples.
bibliographic citation: Shum et al. (2017) Harnessing mtDNA variation to resolve ambiguity in ‘Redfish’ sold in Europe. PeerJ 5:e3746 https://doi.org/10.7717/peerj.3746
date submitted: 2017-04-11
date accepted: 2017-08-07
issued: 2017-10-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shum
  given name: Peter
author list: Agent
  family name: Moore
  given name: Lauren
author list: Agent
  family name: Pampoulie
  given name: Christophe
author list: Agent
  family name: Di Muri
  given name: Cristina
author list: Agent
  family name: Vandamme
  given name: Sara
author list: Agent
  family name: Mariani
  given name: Stefano
doi: 10.7717/peerj.3746
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-02
copyright: ©2017 Shum et al.
attribution name: Shum et al.

Comparative study of Cd uptake and tolerance of two Italian ryegrass (Lolium multiflorum) cultivars
type: item
type: AcademicArticle
description: Cadmium (Cd) is one of the most toxic heavy metals and is difficult to be removed from contaminated soil and water. Italian ryegrass (Lolium multiflorum), as an energy crop, exhibits a valuable potential to develop Cd polluted sites due to its use as a biofuel rather than as food and forage. Previously, via a screening for Cd-tolerant ryegrass, the two most extreme cultivars (IdyII and Harukaze) with high and low Cd tolerance during seed germination, respectively, were selected. However, the underlying mechanism for Cd tolerance was not well investigated. In this study, we comparatively investigated the growth, physiological responses, and Cd uptake and translocation of IdyII and Harukaze when the seedlings were exposed to a Cd (0–100 μM) solution for 12 days. As expected, excess Cd inhibited seedling growth and was accompanied by an accumulation of malondialdehyde (MDA) and reduced photosynthetic pigments in both cultivars. The effects of Cd on the uptake and translocation of other nutrient elements (Zn, Fe, Mn and Mg) were dependent on Cd concentrations, cultivars, plant tissues and elements. Compared with Harukaze, IdyII exhibited better performance with less MDA and higher pigment content. Furthermore, IdyII was less efficient in Cd uptake and translocation compared to Harukaze, which might be explained by the higher non-protein thiols content in its roots. Taken together, our data indicate that IdyII is more tolerant than Harukaze, which partially resulted from the differences in Cd uptake and translocation.
format: application/pdf
format: text/html
creator: Zhigang Fang
creator: Laiqing Lou
creator: Zhenglan Tai
creator: Yufeng Wang
creator: Lei Yang
creator: Zhubing Hu
creator: Qingsheng Cai
subject: Plant Science
subject: Toxicology
subject: Biosphere Interactions
subject: Ecotoxicology
subject: Natural Resource Management
description: doi:10.7717/peerj.3621
publisher: PeerJ Inc.
rights: © 2017 Fang et al.
abstract: Cadmium (Cd) is one of the most toxic heavy metals and is difficult to be removed from contaminated soil and water. Italian ryegrass (Lolium multiflorum), as an energy crop, exhibits a valuable potential to develop Cd polluted sites due to its use as a biofuel rather than as food and forage. Previously, via a screening for Cd-tolerant ryegrass, the two most extreme cultivars (IdyII and Harukaze) with high and low Cd tolerance during seed germination, respectively, were selected. However, the underlying mechanism for Cd tolerance was not well investigated. In this study, we comparatively investigated the growth, physiological responses, and Cd uptake and translocation of IdyII and Harukaze when the seedlings were exposed to a Cd (0–100 μM) solution for 12 days. As expected, excess Cd inhibited seedling growth and was accompanied by an accumulation of malondialdehyde (MDA) and reduced photosynthetic pigments in both cultivars. The effects of Cd on the uptake and translocation of other nutrient elements (Zn, Fe, Mn and Mg) were dependent on Cd concentrations, cultivars, plant tissues and elements. Compared with Harukaze, IdyII exhibited better performance with less MDA and higher pigment content. Furthermore, IdyII was less efficient in Cd uptake and translocation compared to Harukaze, which might be explained by the higher non-protein thiols content in its roots. Taken together, our data indicate that IdyII is more tolerant than Harukaze, which partially resulted from the differences in Cd uptake and translocation.
bibliographic citation: Fang et al. (2017) Comparative study of Cd uptake and tolerance of two Italian ryegrass (Lolium multiflorum) cultivars. PeerJ 5:e3621 https://doi.org/10.7717/peerj.3621
date submitted: 2016-11-24
date accepted: 2017-07-07
issued: 2017-10-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fang
  given name: Zhigang
author list: Agent
  family name: Lou
  given name: Laiqing
author list: Agent
  family name: Tai
  given name: Zhenglan
author list: Agent
  family name: Wang
  given name: Yufeng
author list: Agent
  family name: Yang
  given name: Lei
author list: Agent
  family name: Hu
  given name: Zhubing
author list: Agent
  family name: Cai
  given name: Qingsheng
doi: 10.7717/peerj.3621
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-02
copyright: © 2017 Fang et al.
attribution name: Fang et al.

Growth of hybrid open access, 2009–2016
type: item
type: AcademicArticle
description: Hybrid Open Access is an intermediate form of OA, where authors pay scholarly publishers to make articles freely accessible within journals, in which reading the content otherwise requires a subscription or pay-per-view. Major scholarly publishers have in recent years started providing the hybrid option for the vast majority of their journals. Since the uptake usually has been low per journal and scattered over thousands of journals, it has been very difficult to obtain an overview of how common hybrid articles are. This study, using the results of earlier studies as well as a variety of methods, measures the evolution of hybrid OA over time. The number of journals offering the hybrid option has increased from around 2,000 in 2009 to almost 10,000 in 2016. The number of individual articles has in the same period grown from an estimated 8,000 in 2009 to 45,000 in 2016. The growth in article numbers has clearly increased since 2014, after some major research funders in Europe started to introduce new centralized payment schemes for the article processing charges (APCs).
format: application/pdf
format: text/html
creator: Bo-Christer Björk
subject: Science Policy
description: doi:10.7717/peerj.3878
publisher: PeerJ Inc.
rights: © 2017 Björk
abstract: Hybrid Open Access is an intermediate form of OA, where authors pay scholarly publishers to make articles freely accessible within journals, in which reading the content otherwise requires a subscription or pay-per-view. Major scholarly publishers have in recent years started providing the hybrid option for the vast majority of their journals. Since the uptake usually has been low per journal and scattered over thousands of journals, it has been very difficult to obtain an overview of how common hybrid articles are. This study, using the results of earlier studies as well as a variety of methods, measures the evolution of hybrid OA over time. The number of journals offering the hybrid option has increased from around 2,000 in 2009 to almost 10,000 in 2016. The number of individual articles has in the same period grown from an estimated 8,000 in 2009 to 45,000 in 2016. The growth in article numbers has clearly increased since 2014, after some major research funders in Europe started to introduce new centralized payment schemes for the article processing charges (APCs).
bibliographic citation: Björk (2017) Growth of hybrid open access, 2009–2016. PeerJ 5:e3878 https://doi.org/10.7717/peerj.3878
date submitted: 2017-07-04
date accepted: 2017-09-12
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Björk
  given name: Bo-Christer
doi: 10.7717/peerj.3878
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Björk
attribution name: Björk

Effect of the environment on horizontal gene transfer between bacteria and archaea
type: item
type: AcademicArticle
description: Background Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted). Results We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids. Conclusions Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the a…
format: application/pdf
format: text/html
creator: Clara A. Fuchsman
creator: Roy Eric Collins
creator: Gabrielle Rocap
creator: William J. Brazelton
subject: Environmental Sciences
subject: Genomics
subject: Microbiology
subject: Natural Resource Management
description: doi:10.7717/peerj.3865
publisher: PeerJ Inc.
rights: © 2017 Fuchsman et al.
abstract: Background Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted). Results We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids. Conclusions Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the a…
bibliographic citation: Fuchsman et al. (2017) Effect of the environment on horizontal gene transfer between bacteria and archaea. PeerJ 5:e3865 https://doi.org/10.7717/peerj.3865
date submitted: 2017-04-06
date accepted: 2017-09-08
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fuchsman
  given name: Clara A.
author list: Agent
  family name: Collins
  given name: Roy Eric
author list: Agent
  family name: Rocap
  given name: Gabrielle
author list: Agent
  family name: Brazelton
  given name: William J.
doi: 10.7717/peerj.3865
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Fuchsman et al.
attribution name: Fuchsman et al.

Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?
type: item
type: AcademicArticle
description: Background Fragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus. Methods We sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA), we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i) Isolation by Distance (IBD) as null model, (ii) Least-cost Path (LCP) where genetic distances between patch pairs increase with cost-weighted distances, and (iii) Isolation by Resistance (IBR) where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk. Results We found low values of nucleotide diversity (π) for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST) ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05), with shortest least-cost paths traced through native forest and arborescent shrublands. Discussion In this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that connectivity between fu…
format: application/pdf
format: text/html
creator: Daniela Lazo-Cancino
creator: Selim S. Musleh
creator: Cristian E. Hernandez
creator: Eduardo Palma
creator: Enrique Rodriguez-Serrano
subject: Biodiversity
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.3842
publisher: PeerJ Inc.
rights: © 2017 Lazo-Cancino et al.
abstract: Background Fragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus. Methods We sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA), we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i) Isolation by Distance (IBD) as null model, (ii) Least-cost Path (LCP) where genetic distances between patch pairs increase with cost-weighted distances, and (iii) Isolation by Resistance (IBR) where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk. Results We found low values of nucleotide diversity (π) for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST) ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05), with shortest least-cost paths traced through native forest and arborescent shrublands. Discussion In this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that connectivity between fu…
bibliographic citation: Lazo-Cancino et al. (2017) Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?. PeerJ 5:e3842 https://doi.org/10.7717/peerj.3842
date submitted: 2017-03-29
date accepted: 2017-09-01
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lazo-Cancino
  given name: Daniela
author list: Agent
  family name: Musleh
  given name: Selim S.
author list: Agent
  family name: Hernandez
  given name: Cristian E.
author list: Agent
  family name: Palma
  given name: Eduardo
author list: Agent
  family name: Rodriguez-Serrano
  given name: Enrique
doi: 10.7717/peerj.3842
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Lazo-Cancino et al.
attribution name: Lazo-Cancino et al.

A prospective study of the motivational and health dynamics of Internet Gaming Disorder
type: item
type: AcademicArticle
description: The American Psychiatric Association has identified Internet Gaming Disorder (IGD) as a potential psychiatric condition and called for research to investigate its etiology, stability, and impacts on health and behavior. The present study recruited 5,777 American adults and applied self-determination theory to examine how motivational factors influence, and are influenced by, IGD and health across a six month period. Following a preregistered analysis plan, results confirmed our hypotheses that IGD criteria are moderately stable and that they and basic psychological need satisfaction have a reciprocal relationship over time. Results also showed need satisfaction promoted health and served as a protective factor against IGD. Contrary to what was hypothesized, results provided no evidence directly linking IGD to health over time. Exploratory analyses suggested that IGD may have indirect effects on health by way of its impact on basic needs. Implications are discussed in terms of existing gaming addiction and motivational frameworks.
format: application/pdf
format: text/html
creator: Netta Weinstein
creator: Andrew K. Przybylski
creator: Kou Murayama
subject: Human-Computer Interaction
subject: Psychiatry and Psychology
subject: Science Policy
description: doi:10.7717/peerj.3838
publisher: PeerJ Inc.
rights: © 2017 Weinstein et al.
abstract: The American Psychiatric Association has identified Internet Gaming Disorder (IGD) as a potential psychiatric condition and called for research to investigate its etiology, stability, and impacts on health and behavior. The present study recruited 5,777 American adults and applied self-determination theory to examine how motivational factors influence, and are influenced by, IGD and health across a six month period. Following a preregistered analysis plan, results confirmed our hypotheses that IGD criteria are moderately stable and that they and basic psychological need satisfaction have a reciprocal relationship over time. Results also showed need satisfaction promoted health and served as a protective factor against IGD. Contrary to what was hypothesized, results provided no evidence directly linking IGD to health over time. Exploratory analyses suggested that IGD may have indirect effects on health by way of its impact on basic needs. Implications are discussed in terms of existing gaming addiction and motivational frameworks.
bibliographic citation: Weinstein et al. (2017) A prospective study of the motivational and health dynamics of Internet Gaming Disorder. PeerJ 5:e3838 https://doi.org/10.7717/peerj.3838
date submitted: 2017-07-07
date accepted: 2017-09-01
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weinstein
  given name: Netta
author list: Agent
  family name: Przybylski
  given name: Andrew K.
author list: Agent
  family name: Murayama
  given name: Kou
doi: 10.7717/peerj.3838
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Weinstein et al.
attribution name: Weinstein et al.

Unraveling the diversification history of grasshoppers belonging to the “Trimerotropis pallidipennis” (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes
type: item
type: AcademicArticle
description: The Andean Mountain range has been recognized as one of the biodiversity hotspots of the world. The proposed mechanisms for such species diversification, among others, are due to the elevation processes occurring during the Miocene and the intensive glacial action during the Pleistocene. In this study we investigated the diversification history of the grasshopper Trimerotropis pallidipennis species complex which shows a particularly wide latitudinal and altitudinal distribution range across the northern, central and southern Andes in South America. Many genetic lineages of this complex have been so far discovered, making it an excellent model to investigate the role of the central Andes Mountains together with climatic fluctuations as drivers of speciation. Phylogenetics, biogeographic and molecular clock analyses using a multi-locus dataset revealed that in Peru there are at least two, and possibly four genetic lineages. Two different stocks originated from a common ancestor from North/Central America—would have dispersed toward southern latitudes favored by the closure of the Panama Isthmus giving rise to two lineages, the coastal and mountain lineages, which still coexist in Peru (i.e., T. pallidipennis and T. andeana). Subsequent vicariant and dispersal events continued the differentiation process, giving rise to three to six genetic lineages (i.e., clades) detected in this study, which were geographically restricted to locations dispersed over the central Andes Mountains in South America. Our results provide another interesting example of “island diversification” motored by the topography plus unstable climatic conditions during the Pleistocene, pointing out the presence of a hotspot of diversification in the Andean region of Peru.
format: application/pdf
format: text/html
creator: Noelia Verónica Guzmán
creator: Silvia Mónica Pietrokovsky
creator: Maria Marta Cigliano
creator: Viviana Andrea Confalonieri
subject: Entomology
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.3835
publisher: PeerJ Inc.
rights: © 2017 Guzmán et al.
abstract: The Andean Mountain range has been recognized as one of the biodiversity hotspots of the world. The proposed mechanisms for such species diversification, among others, are due to the elevation processes occurring during the Miocene and the intensive glacial action during the Pleistocene. In this study we investigated the diversification history of the grasshopper Trimerotropis pallidipennis species complex which shows a particularly wide latitudinal and altitudinal distribution range across the northern, central and southern Andes in South America. Many genetic lineages of this complex have been so far discovered, making it an excellent model to investigate the role of the central Andes Mountains together with climatic fluctuations as drivers of speciation. Phylogenetics, biogeographic and molecular clock analyses using a multi-locus dataset revealed that in Peru there are at least two, and possibly four genetic lineages. Two different stocks originated from a common ancestor from North/Central America—would have dispersed toward southern latitudes favored by the closure of the Panama Isthmus giving rise to two lineages, the coastal and mountain lineages, which still coexist in Peru (i.e., T. pallidipennis and T. andeana). Subsequent vicariant and dispersal events continued the differentiation process, giving rise to three to six genetic lineages (i.e., clades) detected in this study, which were geographically restricted to locations dispersed over the central Andes Mountains in South America. Our results provide another interesting example of “island diversification” motored by the topography plus unstable climatic conditions during the Pleistocene, pointing out the presence of a hotspot of diversification in the Andean region of Peru.
bibliographic citation: Guzmán et al. (2017) Unraveling the diversification history of grasshoppers belonging to the “Trimerotropis pallidipennis” (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes. PeerJ 5:e3835 https://doi.org/10.7717/peerj.3835
date submitted: 2017-06-29
date accepted: 2017-08-30
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guzmán
  given name: Noelia Verónica
author list: Agent
  family name: Pietrokovsky
  given name: Silvia Mónica
author list: Agent
  family name: Cigliano
  given name: Maria Marta
author list: Agent
  family name: Confalonieri
  given name: Viviana Andrea
doi: 10.7717/peerj.3835
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Guzmán et al.
attribution name: Guzmán et al.

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