PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The influence of socioeconomic factors on the densities of high-value cross-border species, the African elephant
items: A retrospective study detects a novel variant of porcine epidemic diarrhea virus in England in archived material from the year 2000
items: Post-reproductive parthenogenetic pea aphids (Acyrthosiphon pisum) are visually identifiable and disproportionately positioned distally to clonal colonies
items: Early evolution of polyisoprenol biosynthesis and the origin of cell walls
items: In silico study on anti-Chikungunya virus activity of hesperetin
items: Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae)
items: A 12-year record of intertidal barnacle recruitment in Atlantic Canada (2005–2016): relationships with sea surface temperature and phytoplankton abundance
items: Baseline reef health surveys at Bangka Island (North Sulawesi, Indonesia) reveal new threats
items: A single-nucleotide-polymorphism-based genotyping assay for simultaneous detection of different carbendazim-resistant genotypes in the Fusarium graminearum species complex
items: Spatial and temporal genetic homogeneity of the Monterey Spanish mackerel, Scomberomorus concolor, in the Gulf of California

The influence of socioeconomic factors on the densities of high-value cross-border species, the African elephant
type: item
type: AcademicArticle
description: Unprecedented poaching levels triggered by demand for ivory in Far East Asia are threatening the persistence of African elephant Loxodonta africana. Southern African countries make an important contribution to elephant conservation and could soon become the last stronghold of elephant conservation in Africa. While the ecological factors affecting elephant distribution and densities have extensively been accounted for, there is a need to understand which socioeconomic factors affect elephant numbers in order to prevent conflict over limited space and resources with humans. We used elephant count data from aerial surveys for seven years in a generalized linear model, which accounted for temporal correlation, to investigate the effect of six socioeconomic and ecological variables on the number of elephant at the country level in the Greater Mapungubwe Transfrontier Conservation Area (GMTFCA). Important factors in predicting elephant numbers were the proportion of total land surface under cultivation, human population density and the number of tourists visiting the country. Specifically, elephant numbers were higher where the proportion of total land surface under cultivation was the lowest; where population density was the lowest and where tourist numbers had increased over the years. Our results confirm that human disturbance is affecting elephant numbers, but highlight that the benefits provided by ecotourism could help enhance elephant conservation. While future studies should include larger areas and more detailed data at the site level, we stress that the development of coordinated legislation and policies to improve land-use planning are needed to reduce the impact of increasing human populations and agriculture on elephant.
format: application/pdf
format: text/html
creator: Sarah-Anne Jeanetta Selier
creator: Rob Slotow
creator: Enrico Di Minin
subject: Biogeography
subject: Biosphere Interactions
subject: Conservation Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.2581
publisher: PeerJ Inc.
rights: © 2016 Selier et al.
abstract: Unprecedented poaching levels triggered by demand for ivory in Far East Asia are threatening the persistence of African elephant Loxodonta africana. Southern African countries make an important contribution to elephant conservation and could soon become the last stronghold of elephant conservation in Africa. While the ecological factors affecting elephant distribution and densities have extensively been accounted for, there is a need to understand which socioeconomic factors affect elephant numbers in order to prevent conflict over limited space and resources with humans. We used elephant count data from aerial surveys for seven years in a generalized linear model, which accounted for temporal correlation, to investigate the effect of six socioeconomic and ecological variables on the number of elephant at the country level in the Greater Mapungubwe Transfrontier Conservation Area (GMTFCA). Important factors in predicting elephant numbers were the proportion of total land surface under cultivation, human population density and the number of tourists visiting the country. Specifically, elephant numbers were higher where the proportion of total land surface under cultivation was the lowest; where population density was the lowest and where tourist numbers had increased over the years. Our results confirm that human disturbance is affecting elephant numbers, but highlight that the benefits provided by ecotourism could help enhance elephant conservation. While future studies should include larger areas and more detailed data at the site level, we stress that the development of coordinated legislation and policies to improve land-use planning are needed to reduce the impact of increasing human populations and agriculture on elephant.
bibliographic citation: Selier et al. (2016) The influence of socioeconomic factors on the densities of high-value cross-border species, the African elephant. PeerJ 4:e2581 https://doi.org/10.7717/peerj.2581
date submitted: 2016-04-27
date accepted: 2016-09-18
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Selier
  given name: Sarah-Anne Jeanetta
author list: Agent
  family name: Slotow
  given name: Rob
author list: Agent
  family name: Di Minin
  given name: Enrico
doi: 10.7717/peerj.2581
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: © 2016 Selier et al.
attribution name: Selier et al.

A retrospective study detects a novel variant of porcine epidemic diarrhea virus in England in archived material from the year 2000
type: item
type: AcademicArticle
description: Outbreaks of porcine epidemic diarrhea (PED) were first recorded in England in the 1970s and continued to be confirmed until 2002. Retrospective analysis of archived material from one of the last confirmed cases in England in the year 2000 demonstrates the previous existence of a very diverse PED virus strain. Following the outbreaks of PED in North America in 2013, there has been renewed interest in phylogenetic analysis of sequences from PEDV strains worldwide. There is a gap in the available sequence data between the mid 1980s and the mid 2000s. This work is an example of how this gap can be at least partially filled by the examination of archived material.
format: application/pdf
format: text/html
creator: Falko Steinbach
creator: Akbar Dastjerdi
creator: Julie Peake
creator: S. Anna La Rocca
creator: Frank P. Tobin
creator: Jean-Pierre Frossard
creator: Susanna Williamson
subject: Veterinary Medicine
subject: Virology
subject: Epidemiology
description: doi:10.7717/peerj.2564
publisher: PeerJ Inc.
rights: © 2016 Steinbach et al.
abstract: Outbreaks of porcine epidemic diarrhea (PED) were first recorded in England in the 1970s and continued to be confirmed until 2002. Retrospective analysis of archived material from one of the last confirmed cases in England in the year 2000 demonstrates the previous existence of a very diverse PED virus strain. Following the outbreaks of PED in North America in 2013, there has been renewed interest in phylogenetic analysis of sequences from PEDV strains worldwide. There is a gap in the available sequence data between the mid 1980s and the mid 2000s. This work is an example of how this gap can be at least partially filled by the examination of archived material.
bibliographic citation: Steinbach et al. (2016) A retrospective study detects a novel variant of porcine epidemic diarrhea virus in England in archived material from the year 2000. PeerJ 4:e2564 https://doi.org/10.7717/peerj.2564
date submitted: 2016-07-11
date accepted: 2016-09-13
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Steinbach
  given name: Falko
author list: Agent
  family name: Dastjerdi
  given name: Akbar
author list: Agent
  family name: Peake
  given name: Julie
author list: Agent
  family name: La Rocca
  given name: S. Anna
author list: Agent
  family name: Tobin
  given name: Frank P.
author list: Agent
  family name: Frossard
  given name: Jean-Pierre
author list: Agent
  family name: Williamson
  given name: Susanna
doi: 10.7717/peerj.2564
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Steinbach et al.
attribution name: Steinbach et al.

Post-reproductive parthenogenetic pea aphids (Acyrthosiphon pisum) are visually identifiable and disproportionately positioned distally to clonal colonies
type: item
type: AcademicArticle
description: The role of kin-selection in the evolution of post-reproductive life is controversial. While anthropological and demographic studies strongly suggest that humans and a few other species experience kin selection for significant post-reproductive survival, these results are necessarily correlational. Understanding could therefore be advanced by the development of a globally available, field and laboratory tractable experimental model of kin-selected post-reproductive survival. In only one invertebrate (Quadrartus yoshinomiyai, a gall-forming aphid endemic to Japan) have individuals too old to reproduce been shown to be both numerous in natural habitats and able to help close relatives survive or reproduce. Pea aphids, (Acyrthosiphon pisum), common, tractable organisms, frequently outlive their reproductive ages in laboratories, live in tight interacting groups that are often clonal, and therefore should be evaluated as potential model organisms for the study of adaptive post-reproductive life. The first major step in this process is to identify an optimal method for assessing if a parthenogenetic adult is post-reproductive. We evaluated three methods, relying respectively on isolation in clip cages, visual examination for embryonic eyespots, and dissection. In every case each method identified the same individuals as reproductive versus post-reproductive. While the clip-cage method requires a multi-day wait to produce data, and dissection is inevitably fatal, the eyespot method is quick (under one minute per individual) easy, and non-invasive. This method makes it possible to accurately assess the post-reproductive status of a large number of parthenogenetic pea aphids. We demonstrate the usefulness of the eyespot method in showing that while reproductively valuable adults tend to place themselves near the centers of clonal colonies, less valuable post-reproductive adults are more often at or beyond the edges of colonies. These encouraging early results provide both i…
format: application/pdf
format: text/html
creator: Erik T. Saberski
creator: Julia Daisy Diamond
creator: Nathaniel Fath Henneman
creator: Daniel A. Levitis
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.2631
publisher: PeerJ Inc.
rights: © 2016 Saberski et al.
abstract: The role of kin-selection in the evolution of post-reproductive life is controversial. While anthropological and demographic studies strongly suggest that humans and a few other species experience kin selection for significant post-reproductive survival, these results are necessarily correlational. Understanding could therefore be advanced by the development of a globally available, field and laboratory tractable experimental model of kin-selected post-reproductive survival. In only one invertebrate (Quadrartus yoshinomiyai, a gall-forming aphid endemic to Japan) have individuals too old to reproduce been shown to be both numerous in natural habitats and able to help close relatives survive or reproduce. Pea aphids, (Acyrthosiphon pisum), common, tractable organisms, frequently outlive their reproductive ages in laboratories, live in tight interacting groups that are often clonal, and therefore should be evaluated as potential model organisms for the study of adaptive post-reproductive life. The first major step in this process is to identify an optimal method for assessing if a parthenogenetic adult is post-reproductive. We evaluated three methods, relying respectively on isolation in clip cages, visual examination for embryonic eyespots, and dissection. In every case each method identified the same individuals as reproductive versus post-reproductive. While the clip-cage method requires a multi-day wait to produce data, and dissection is inevitably fatal, the eyespot method is quick (under one minute per individual) easy, and non-invasive. This method makes it possible to accurately assess the post-reproductive status of a large number of parthenogenetic pea aphids. We demonstrate the usefulness of the eyespot method in showing that while reproductively valuable adults tend to place themselves near the centers of clonal colonies, less valuable post-reproductive adults are more often at or beyond the edges of colonies. These encouraging early results provide both i…
bibliographic citation: Saberski et al. (2016) Post-reproductive parthenogenetic pea aphids (Acyrthosiphon pisum) are visually identifiable and disproportionately positioned distally to clonal colonies. PeerJ 4:e2631 https://doi.org/10.7717/peerj.2631
date submitted: 2016-04-07
date accepted: 2016-09-29
issued: 2016-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saberski
  given name: Erik T.
author list: Agent
  family name: Diamond
  given name: Julia Daisy
author list: Agent
  family name: Henneman
  given name: Nathaniel Fath
author list: Agent
  family name: Levitis
  given name: Daniel A.
doi: 10.7717/peerj.2631
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-26
copyright: © 2016 Saberski et al.
attribution name: Saberski et al.

Early evolution of polyisoprenol biosynthesis and the origin of cell walls
type: item
type: AcademicArticle
description: After being a matter of hot debate for years, the presence of lipid membranes in the last common ancestor of extant organisms (i.e., the cenancestor) now begins to be generally accepted. By contrast, cenancestral cell walls have attracted less attention, probably owing to the large diversity of cell walls that exist in the three domains of life. Many prokaryotic cell walls, however, are synthesized using glycosylation pathways with similar polyisoprenol lipid carriers and topology (i.e., orientation across the cell membranes). Here, we provide the first systematic phylogenomic report on the polyisoprenol biosynthesis pathways in the three domains of life. This study shows that, whereas the last steps of the polyisoprenol biosynthesis are unique to the respective domain of life of which they are characteristic, the enzymes required for basic unsaturated polyisoprenol synthesis can be traced back to the respective last common ancestor of each of the three domains of life. As a result, regardless of the topology of the tree of life that may be considered, the most parsimonious hypothesis is that these enzymes were inherited in modern lineages from the cenancestor. This observation supports the presence of an enzymatic mechanism to synthesize unsaturated polyisoprenols in the cenancestor and, since these molecules are notorious lipid carriers in glycosylation pathways involved in the synthesis of a wide diversity of prokaryotic cell walls, it provides the first indirect evidence of the existence of a hypothetical unknown cell wall synthesis mechanism in the cenancestor.
format: application/pdf
format: text/html
creator: Jonathan Lombard
subject: Biochemistry
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.2626
publisher: PeerJ Inc.
rights: © 2016 Lombard
abstract: After being a matter of hot debate for years, the presence of lipid membranes in the last common ancestor of extant organisms (i.e., the cenancestor) now begins to be generally accepted. By contrast, cenancestral cell walls have attracted less attention, probably owing to the large diversity of cell walls that exist in the three domains of life. Many prokaryotic cell walls, however, are synthesized using glycosylation pathways with similar polyisoprenol lipid carriers and topology (i.e., orientation across the cell membranes). Here, we provide the first systematic phylogenomic report on the polyisoprenol biosynthesis pathways in the three domains of life. This study shows that, whereas the last steps of the polyisoprenol biosynthesis are unique to the respective domain of life of which they are characteristic, the enzymes required for basic unsaturated polyisoprenol synthesis can be traced back to the respective last common ancestor of each of the three domains of life. As a result, regardless of the topology of the tree of life that may be considered, the most parsimonious hypothesis is that these enzymes were inherited in modern lineages from the cenancestor. This observation supports the presence of an enzymatic mechanism to synthesize unsaturated polyisoprenols in the cenancestor and, since these molecules are notorious lipid carriers in glycosylation pathways involved in the synthesis of a wide diversity of prokaryotic cell walls, it provides the first indirect evidence of the existence of a hypothetical unknown cell wall synthesis mechanism in the cenancestor.
bibliographic citation: Lombard (2016) Early evolution of polyisoprenol biosynthesis and the origin of cell walls. PeerJ 4:e2626 https://doi.org/10.7717/peerj.2626
date submitted: 2016-06-11
date accepted: 2016-09-27
issued: 2016-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lombard
  given name: Jonathan
doi: 10.7717/peerj.2626
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-26
copyright: ©2016 Lombard
attribution name: Lombard

In silico study on anti-Chikungunya virus activity of hesperetin
type: item
type: AcademicArticle
description: Background The re-emerging, Aedes spp. transmitted Chikungunya virus (CHIKV) has recently caused large outbreaks in a wide geographical distribution of the world including countries in Europe and America. Though fatalities associated with this self-remitting disease were rarely reported, quality of patients’ lives have been severely diminished by polyarthralgia recurrence. Neither effective antiviral treatment nor vaccines are available for CHIKV. Our previous in vitro screening showed that hesperetin, a bioflavonoid exhibits inhibitory effect on the virus intracellular replication. Here, we present a study using the computational approach to identify possible target proteins for future mechanistic studies of hesperetin. Methods 3D structures of CHIKV nsP2 (3TRK) and nsP3 (3GPG) were retrieved from Protein Data Bank (PDB), whereas nsP1, nsP4 and cellular factor SPK2 were modeled using Iterative Threading Assembly Refinement (I-TASSER) server based on respective amino acids sequence. We performed molecular docking on hesperetin against all four CHIKV non-structural proteins and SPK2. Proteins preparation and subsequent molecular docking were performed using Discovery Studio 2.5 and AutoDock Vina 1.5.6. The Lipinski’s values of the ligand were computed and compared with the available data from PubChem. Two non-structural proteins with crystal structures 3GPG and 3TRK in complexed with hesperetin, demonstrated favorable free energy of binding from the docking study, were further explored using molecular dynamics (MD) simulations. Results We observed that hesperetin interacts with different types of proteins involving hydrogen bonds, pi-pi effects, pi-cation bonding and pi-sigma interactions with varying binding energies. Among all five tested proteins, our compound has the highest binding affinity with 3GPG at −8.5 kcal/mol. The ligand used in this study also matches the Lipinski’s rule of five in addition to exhibiting closely similar properties with that of in PubChe…
format: application/pdf
format: text/html
creator: Adrian Oo
creator: Pouya Hassandarvish
creator: Sek Peng Chin
creator: Vannajan Sanghiran Lee
creator: Sazaly Abu Bakar
creator: Keivan Zandi
subject: Computational Biology
subject: Microbiology
subject: Virology
subject: Infectious Diseases
subject: Computational Science
description: doi:10.7717/peerj.2602
publisher: PeerJ Inc.
rights: © 2016 Oo et al.
abstract: Background The re-emerging, Aedes spp. transmitted Chikungunya virus (CHIKV) has recently caused large outbreaks in a wide geographical distribution of the world including countries in Europe and America. Though fatalities associated with this self-remitting disease were rarely reported, quality of patients’ lives have been severely diminished by polyarthralgia recurrence. Neither effective antiviral treatment nor vaccines are available for CHIKV. Our previous in vitro screening showed that hesperetin, a bioflavonoid exhibits inhibitory effect on the virus intracellular replication. Here, we present a study using the computational approach to identify possible target proteins for future mechanistic studies of hesperetin. Methods 3D structures of CHIKV nsP2 (3TRK) and nsP3 (3GPG) were retrieved from Protein Data Bank (PDB), whereas nsP1, nsP4 and cellular factor SPK2 were modeled using Iterative Threading Assembly Refinement (I-TASSER) server based on respective amino acids sequence. We performed molecular docking on hesperetin against all four CHIKV non-structural proteins and SPK2. Proteins preparation and subsequent molecular docking were performed using Discovery Studio 2.5 and AutoDock Vina 1.5.6. The Lipinski’s values of the ligand were computed and compared with the available data from PubChem. Two non-structural proteins with crystal structures 3GPG and 3TRK in complexed with hesperetin, demonstrated favorable free energy of binding from the docking study, were further explored using molecular dynamics (MD) simulations. Results We observed that hesperetin interacts with different types of proteins involving hydrogen bonds, pi-pi effects, pi-cation bonding and pi-sigma interactions with varying binding energies. Among all five tested proteins, our compound has the highest binding affinity with 3GPG at −8.5 kcal/mol. The ligand used in this study also matches the Lipinski’s rule of five in addition to exhibiting closely similar properties with that of in PubChe…
bibliographic citation: Oo et al. (2016) In silico study on anti-Chikungunya virus activity of hesperetin. PeerJ 4:e2602 https://doi.org/10.7717/peerj.2602
date submitted: 2016-05-30
date accepted: 2016-09-23
issued: 2016-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oo
  given name: Adrian
author list: Agent
  family name: Hassandarvish
  given name: Pouya
author list: Agent
  family name: Chin
  given name: Sek Peng
author list: Agent
  family name: Lee
  given name: Vannajan Sanghiran
author list: Agent
  family name: Abu Bakar
  given name: Sazaly
author list: Agent
  family name: Zandi
  given name: Keivan
doi: 10.7717/peerj.2602
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-26
copyright: © 2016 Oo et al.
attribution name: Oo et al.

Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae)
type: item
type: AcademicArticle
description: Background The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum. Methods The Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed. Results The 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispers…
format: application/pdf
format: text/html
creator: Jean-Simon Brouard
creator: Monique Turmel
creator: Christian Otis
creator: Claude Lemieux
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.2627
publisher: PeerJ Inc.
rights: © 2016 Brouard et al.
abstract: Background The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum. Methods The Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed. Results The 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispers…
bibliographic citation: Brouard et al. (2016) Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae). PeerJ 4:e2627 https://doi.org/10.7717/peerj.2627
date submitted: 2016-07-18
date accepted: 2016-09-29
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brouard
  given name: Jean-Simon
author list: Agent
  family name: Turmel
  given name: Monique
author list: Agent
  family name: Otis
  given name: Christian
author list: Agent
  family name: Lemieux
  given name: Claude
doi: 10.7717/peerj.2627
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: ©2016 Brouard et al.
attribution name: Brouard et al.

A 12-year record of intertidal barnacle recruitment in Atlantic Canada (2005–2016): relationships with sea surface temperature and phytoplankton abundance
type: item
type: AcademicArticle
description: On the Gulf of St. Lawrence coast of Nova Scotia (Canada), recruitment of the barnacle Semibalanus balanoides occurs in May and June. Every year in June between 2005 and 2016, we recorded recruit density for this barnacle at the same wave-exposed rocky intertidal location on this coast. During these 12 years, mean recruit density was lowest in 2015 (198 recruits dm−2) and highest in 2007 (969 recruits dm−2). The highest recruit density observed in a single quadrat was 1,457 recruits dm−2 (in 2011) and the lowest was 34 recruits dm−2 (in 2015). Most barnacle recruits appear during May, which suggests that most pelagic larvae (which develop over 5–6 weeks before benthic settlement) are in the water column in April. An AICc-based model selection approach identified sea surface temperature (SST) in April and the abundance of phytoplankton (food for barnacle larvae, measured as chlorophyll-a concentration –Chl-a–) in April as good explanatory variables. Together, April SST and April Chl-a explained 51% of the observed interannual variation in recruit density, with an overall positive influence. April SST was positively related to March–April air temperature (AT). April Chl-a was negatively related to the April ratio between the number of days with onshore winds (which blow from phytoplankton-limited offshore waters) and the number of days with alongshore winds (phytoplankton is more abundant on coastal waters). Therefore, this study suggests that climatic processes affecting April SST and April Chl-a indirectly influence intertidal barnacle recruitment by influencing larval performance.
format: application/pdf
format: text/html
creator: Ricardo A. Scrosati
creator: Julius A. Ellrich
subject: Aquaculture, Fisheries and Fish Science
subject: Climate Change Biology
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.2623
publisher: PeerJ Inc.
rights: © 2016 Scrosati & Ellrich
abstract: On the Gulf of St. Lawrence coast of Nova Scotia (Canada), recruitment of the barnacle Semibalanus balanoides occurs in May and June. Every year in June between 2005 and 2016, we recorded recruit density for this barnacle at the same wave-exposed rocky intertidal location on this coast. During these 12 years, mean recruit density was lowest in 2015 (198 recruits dm−2) and highest in 2007 (969 recruits dm−2). The highest recruit density observed in a single quadrat was 1,457 recruits dm−2 (in 2011) and the lowest was 34 recruits dm−2 (in 2015). Most barnacle recruits appear during May, which suggests that most pelagic larvae (which develop over 5–6 weeks before benthic settlement) are in the water column in April. An AICc-based model selection approach identified sea surface temperature (SST) in April and the abundance of phytoplankton (food for barnacle larvae, measured as chlorophyll-a concentration –Chl-a–) in April as good explanatory variables. Together, April SST and April Chl-a explained 51% of the observed interannual variation in recruit density, with an overall positive influence. April SST was positively related to March–April air temperature (AT). April Chl-a was negatively related to the April ratio between the number of days with onshore winds (which blow from phytoplankton-limited offshore waters) and the number of days with alongshore winds (phytoplankton is more abundant on coastal waters). Therefore, this study suggests that climatic processes affecting April SST and April Chl-a indirectly influence intertidal barnacle recruitment by influencing larval performance.
bibliographic citation: Scrosati et al. (2016) A 12-year record of intertidal barnacle recruitment in Atlantic Canada (2005–2016): relationships with sea surface temperature and phytoplankton abundance. PeerJ 4:e2623 https://doi.org/10.7717/peerj.2623
date submitted: 2016-08-17
date accepted: 2016-09-27
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scrosati
  given name: Ricardo A.
author list: Agent
  family name: Ellrich
  given name: Julius A.
doi: 10.7717/peerj.2623
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: © 2016 Scrosati and Ellrich
attribution name: Scrosati & Ellrich

Baseline reef health surveys at Bangka Island (North Sulawesi, Indonesia) reveal new threats
type: item
type: AcademicArticle
description: Worldwide coral reef decline appears to be accompanied by an increase in the spread of hard coral diseases. However, whether this is the result of increased direct and indirect human disturbances and/or an increase in natural stresses remains poorly understood. The provision of baseline surveys for monitoring coral health status lays the foundations to assess the effects of any such anthropogenic and/or natural effects on reefs. Therefore, the objectives of this present study were to provide a coral health baseline in a poorly studied area, and to investigate possible correlations between coral health and the level of anthropogenic and natural disturbances. During the survey period, we recorded 20 different types of coral diseases and other compromised health statuses. The most abundant were cases of coral bleaching, followed by skeletal deformations caused by pyrgomatid barnacles, damage caused by fish bites, general pigmentation response and galls caused by cryptochirid crabs. Instances of colonies affected by skeletal eroding bands, and sedimentation damage increased in correlation to the level of bio-chemical disturbance and/or proximity to villages. Moreover, galls caused by cryptochirid crabs appeared more abundant at sites affected by blast fishing and close to a newly opened metal mine. Interestingly, in the investigated area the percentage of corals showing signs of ‘common’ diseases such as black band disease, brown band disease, white syndrome and skeletal eroding band disease were relatively low. Nevertheless, the relatively high occurrence of less common signs of compromised coral-related reef health, including the aggressive overgrowth by sponges, deserves further investigation. Although diseases appear relatively low at the current time, this area may be at the tipping point and an increase in activities such as mining may irredeemably compromise reef health.
format: application/pdf
format: text/html
creator: Massimo Ponti
creator: Francesca Fratangeli
creator: Nicolò Dondi
creator: Marco Segre Reinach
creator: Clara Serra
creator: Michael J. Sweet
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.2614
publisher: PeerJ Inc.
rights: © 2016 Ponti et al.
abstract: Worldwide coral reef decline appears to be accompanied by an increase in the spread of hard coral diseases. However, whether this is the result of increased direct and indirect human disturbances and/or an increase in natural stresses remains poorly understood. The provision of baseline surveys for monitoring coral health status lays the foundations to assess the effects of any such anthropogenic and/or natural effects on reefs. Therefore, the objectives of this present study were to provide a coral health baseline in a poorly studied area, and to investigate possible correlations between coral health and the level of anthropogenic and natural disturbances. During the survey period, we recorded 20 different types of coral diseases and other compromised health statuses. The most abundant were cases of coral bleaching, followed by skeletal deformations caused by pyrgomatid barnacles, damage caused by fish bites, general pigmentation response and galls caused by cryptochirid crabs. Instances of colonies affected by skeletal eroding bands, and sedimentation damage increased in correlation to the level of bio-chemical disturbance and/or proximity to villages. Moreover, galls caused by cryptochirid crabs appeared more abundant at sites affected by blast fishing and close to a newly opened metal mine. Interestingly, in the investigated area the percentage of corals showing signs of ‘common’ diseases such as black band disease, brown band disease, white syndrome and skeletal eroding band disease were relatively low. Nevertheless, the relatively high occurrence of less common signs of compromised coral-related reef health, including the aggressive overgrowth by sponges, deserves further investigation. Although diseases appear relatively low at the current time, this area may be at the tipping point and an increase in activities such as mining may irredeemably compromise reef health.
bibliographic citation: Ponti et al. (2016) Baseline reef health surveys at Bangka Island (North Sulawesi, Indonesia) reveal new threats. PeerJ 4:e2614 https://doi.org/10.7717/peerj.2614
date submitted: 2016-06-08
date accepted: 2016-09-27
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ponti
  given name: Massimo
author list: Agent
  family name: Fratangeli
  given name: Francesca
author list: Agent
  family name: Dondi
  given name: Nicolò
author list: Agent
  family name: Segre Reinach
  given name: Marco
author list: Agent
  family name: Serra
  given name: Clara
author list: Agent
  family name: Sweet
  given name: Michael J.
doi: 10.7717/peerj.2614
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: ©2016 Ponti et al.
attribution name: Ponti et al.

A single-nucleotide-polymorphism-based genotyping assay for simultaneous detection of different carbendazim-resistant genotypes in the Fusarium graminearum species complex
type: item
type: AcademicArticle
description: The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium graminearum species complex (FGSC) is becoming a serious problem in the control of Fusarium head blight in China. The resistance is caused by point mutations in the β2-tubulingene. So far, five resistant genotypes (F167Y, E198Q, E198L, E198K and F200Y) have been reported in the field. To establish a high-throughput method for rapid detection of all the five mutations simultaneously, an efficient single-nucleotide-polymorphism-based genotyping method was developed based on the Luminex xMAP system. One pair of amplification primers and five allele specific primer extension probes were designed and optimized to specially distinguish the different genotypes within one single reaction. This method has good extensibility and can be combined with previous reported probes to form a highly integrated tool for species, trichothecene chemotype and MBC resistance detection. Using this method, carbendazim resistant FGSC isolates from Jiangsu, Anhui and Sichuan Province in China were identified. High and moderate frequencies of resistance were observed in Jiangsu and Anhui Province, respectively. Carbendazim resistance in F. asiaticum is only observed in the 3ADON genotype. Overall, our method proved to be useful for early detection of MBC resistance in the field and the result aids in the choice of fungicide type.
format: application/pdf
format: text/html
creator: Hao Zhang
creator: Balázs Brankovics
creator: Theo A.J. van der Lee
creator: Cees Waalwijk
creator: Anne A.D. van Diepeningen
creator: Jin Xu
creator: Jingsheng Xu
creator: Wanquan Chen
creator: Jie Feng
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.2609
publisher: PeerJ Inc.
rights: © 2016 Zhang et al.
abstract: The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium graminearum species complex (FGSC) is becoming a serious problem in the control of Fusarium head blight in China. The resistance is caused by point mutations in the β2-tubulingene. So far, five resistant genotypes (F167Y, E198Q, E198L, E198K and F200Y) have been reported in the field. To establish a high-throughput method for rapid detection of all the five mutations simultaneously, an efficient single-nucleotide-polymorphism-based genotyping method was developed based on the Luminex xMAP system. One pair of amplification primers and five allele specific primer extension probes were designed and optimized to specially distinguish the different genotypes within one single reaction. This method has good extensibility and can be combined with previous reported probes to form a highly integrated tool for species, trichothecene chemotype and MBC resistance detection. Using this method, carbendazim resistant FGSC isolates from Jiangsu, Anhui and Sichuan Province in China were identified. High and moderate frequencies of resistance were observed in Jiangsu and Anhui Province, respectively. Carbendazim resistance in F. asiaticum is only observed in the 3ADON genotype. Overall, our method proved to be useful for early detection of MBC resistance in the field and the result aids in the choice of fungicide type.
bibliographic citation: Zhang et al. (2016) A single-nucleotide-polymorphism-based genotyping assay for simultaneous detection of different carbendazim-resistant genotypes in the Fusarium graminearum species complex. PeerJ 4:e2609 https://doi.org/10.7717/peerj.2609
date submitted: 2016-05-06
date accepted: 2016-09-25
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: Brankovics
  given name: Balázs
author list: Agent
  family name: van der Lee
  given name: Theo A.J.
author list: Agent
  family name: Waalwijk
  given name: Cees
author list: Agent
  family name: van Diepeningen
  given name: Anne A.D.
author list: Agent
  family name: Xu
  given name: Jin
author list: Agent
  family name: Xu
  given name: Jingsheng
author list: Agent
  family name: Chen
  given name: Wanquan
author list: Agent
  family name: Feng
  given name: Jie
doi: 10.7717/peerj.2609
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: ©2016 Zhang et al.
attribution name: Zhang et al.

Spatial and temporal genetic homogeneity of the Monterey Spanish mackerel, Scomberomorus concolor, in the Gulf of California
type: item
type: AcademicArticle
description: The genetic homogeneity of the Monterey Spanish mackerel Scomberomorus concolor population in the Gulf of California was confirmed using nine nuclear microsatellite loci in combination with mitochondrial cytochrome b gene sequences. Samples were collected from the upper and central Gulf areas, representing the two main biogeographical regions of the Gulf. The analyses support the existence of a single panmictic population of S. concolor inhabiting the Gulf of California which in terms of fishery management represents a single genetic stock. Additionally, the contemporary effective population size estimated for the S. concolor population (Ne = 3056.9) was high and similar to another pelagic species. The gene flow seems to be bidirectional between the upper and central Gulf, which coincides with the seasonal movements between both regions related to spawning and feeding activities. A population expansion event was detected, which agrees with a colonization-expansion hypothesis of the S. concolor population in the Gulf.
format: application/pdf
format: text/html
creator: Erika Magallón-Gayón
creator: Pindaro Diaz-Jaimes
creator: Manuel Uribe-Alcocer
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Conservation Biology
subject: Genetics
description: doi:10.7717/peerj.2583
publisher: PeerJ Inc.
rights: © 2016 Magallón-Gayón et al.
abstract: The genetic homogeneity of the Monterey Spanish mackerel Scomberomorus concolor population in the Gulf of California was confirmed using nine nuclear microsatellite loci in combination with mitochondrial cytochrome b gene sequences. Samples were collected from the upper and central Gulf areas, representing the two main biogeographical regions of the Gulf. The analyses support the existence of a single panmictic population of S. concolor inhabiting the Gulf of California which in terms of fishery management represents a single genetic stock. Additionally, the contemporary effective population size estimated for the S. concolor population (Ne = 3056.9) was high and similar to another pelagic species. The gene flow seems to be bidirectional between the upper and central Gulf, which coincides with the seasonal movements between both regions related to spawning and feeding activities. A population expansion event was detected, which agrees with a colonization-expansion hypothesis of the S. concolor population in the Gulf.
bibliographic citation: Magallón-Gayón et al. (2016) Spatial and temporal genetic homogeneity of the Monterey Spanish mackerel, Scomberomorus concolor, in the Gulf of California. PeerJ 4:e2583 https://doi.org/10.7717/peerj.2583
date submitted: 2016-04-15
date accepted: 2016-09-17
issued: 2016-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Magallón-Gayón
  given name: Erika
author list: Agent
  family name: Diaz-Jaimes
  given name: Pindaro
author list: Agent
  family name: Uribe-Alcocer
  given name: Manuel
doi: 10.7717/peerj.2583
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-25
copyright: ©2016 Magallón-Gayón et al.
attribution name: Magallón-Gayón et al.

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