PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Food safety in Thailand 4: comparison of pesticide residues found in three commonly consumed vegetables purchased from local markets and supermarkets in Thailand
items: Inferring extinction in North American and Hawaiian birds in the presence of sighting uncertainty
items: Parrotfish grazing ability: interspecific differences in relation to jaw-lever mechanics and relative weight of adductor mandibulae on an Okinawan coral reef
items: Development and characterization of 24 polymorphic microsatellite loci for the freshwater fish Ichthyoelephas longirostris (Characiformes: Prochilodontidae)
items: Cross-sectional study of expression of divalent metal transporter-1, transferrin, and hepcidin in blood of smelters who are occupationally exposed to manganese
items: Do beaver dams reduce habitat connectivity and salmon productivity in expansive river floodplains?
items: Screening microalgae isolated from urban storm- and wastewater systems as feedstock for biofuel
items: The inheritance of female colour polymorphism in Ischnura genei (Zygoptera: Coenagrionidae), with observations on melanism under laboratory conditions
items: Transcriptome analysis of colored calla lily (Zantedeschia rehmannii Engl.) by Illumina sequencing: de novo assembly, annotation and EST-SSR marker development
items: Stable isotope analysis (δ13C and δ15N) of soil nematodes from four feeding groups

Food safety in Thailand 4: comparison of pesticide residues found in three commonly consumed vegetables purchased from local markets and supermarkets in Thailand
type: item
type: AcademicArticle
description: Background The wide use of pesticides raises concerns on the health risks associated with pesticide exposure. For developing countries, like Thailand, pesticide monitoring program (in vegetables and fruits) and also the maximum residue limits (MRL) regulation have not been entirely implemented. The MRL is a product limit, not a safety limit. The MRL is the maximum concentration of a pesticide residue (expressed as mg/kg) recommended by the Codex Alimentarius Commission to be legally permitted in or on food commodities and animal feeds (Codex Alimentarius Commission, 2015; European Commission, 2015). MRLs are based on supervised residue trial data where the pesticide has been applied in accordance with GAP (Good Agricultural Practice). This study aims at providing comparison data on pesticide residues found in three commonly consumed vegetables (Chinese kale, pakchoi and morning glory) purchased from some local markets and supermarkets in Thailand. Methods These vegetables were randomly bought from local markets and supermarkets. Then they were analyzed for the content of 28 pesticides by using GC-MS/MS. Results Types of pesticides detected in the samples either from local markets or supermarkets were similar. The incidence of detected pesticides was 100% (local markets) and 99% (supermarkets) for the Chinese kale; 98% (local markets) and 100% (supermarkets) for the pakchoi; and 99% (local markets) and 97% (supermarkets) for the morning glory samples. The pesticides were detected exceeding their MRL at a rate of 48% (local markets) and 35% (supermarkets) for the Chinese kale; 71% (local markets) and 55% (supermarkets) for the pakchoi, and 42% (local markets) and 49% (supermarkets) for the morning glory. Discussion These rates are much higher than those seen in developed countries. It should be noted that these findings were assessed on basis of using criteria (such as MRL) obtained from developed countries. Our findings were also confined to these vegetables sold in …
format: application/pdf
format: text/html
creator: Sompon Wanwimolruk
creator: Kamonrat Phopin
creator: Somchai Boonpangrak
creator: Virapong Prachayasittikul
subject: Agricultural Science
subject: Environmental Sciences
subject: Food Science and Technology
subject: Nutrition
subject: Toxicology
description: doi:10.7717/peerj.2432
publisher: PeerJ Inc.
rights: © 2016 Wanwimolruk et al.
abstract: Background The wide use of pesticides raises concerns on the health risks associated with pesticide exposure. For developing countries, like Thailand, pesticide monitoring program (in vegetables and fruits) and also the maximum residue limits (MRL) regulation have not been entirely implemented. The MRL is a product limit, not a safety limit. The MRL is the maximum concentration of a pesticide residue (expressed as mg/kg) recommended by the Codex Alimentarius Commission to be legally permitted in or on food commodities and animal feeds (Codex Alimentarius Commission, 2015; European Commission, 2015). MRLs are based on supervised residue trial data where the pesticide has been applied in accordance with GAP (Good Agricultural Practice). This study aims at providing comparison data on pesticide residues found in three commonly consumed vegetables (Chinese kale, pakchoi and morning glory) purchased from some local markets and supermarkets in Thailand. Methods These vegetables were randomly bought from local markets and supermarkets. Then they were analyzed for the content of 28 pesticides by using GC-MS/MS. Results Types of pesticides detected in the samples either from local markets or supermarkets were similar. The incidence of detected pesticides was 100% (local markets) and 99% (supermarkets) for the Chinese kale; 98% (local markets) and 100% (supermarkets) for the pakchoi; and 99% (local markets) and 97% (supermarkets) for the morning glory samples. The pesticides were detected exceeding their MRL at a rate of 48% (local markets) and 35% (supermarkets) for the Chinese kale; 71% (local markets) and 55% (supermarkets) for the pakchoi, and 42% (local markets) and 49% (supermarkets) for the morning glory. Discussion These rates are much higher than those seen in developed countries. It should be noted that these findings were assessed on basis of using criteria (such as MRL) obtained from developed countries. Our findings were also confined to these vegetables sold in …
bibliographic citation: Wanwimolruk et al. (2016) Food safety in Thailand 4: comparison of pesticide residues found in three commonly consumed vegetables purchased from local markets and supermarkets in Thailand. PeerJ 4:e2432 https://doi.org/10.7717/peerj.2432
date submitted: 2016-04-01
date accepted: 2016-08-06
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wanwimolruk
  given name: Sompon
author list: Agent
  family name: Phopin
  given name: Kamonrat
author list: Agent
  family name: Boonpangrak
  given name: Somchai
author list: Agent
  family name: Prachayasittikul
  given name: Virapong
doi: 10.7717/peerj.2432
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Wanwimolruk et al.
attribution name: Wanwimolruk et al.

Inferring extinction in North American and Hawaiian birds in the presence of sighting uncertainty
type: item
type: AcademicArticle
description: For most species the timing of extinction events is uncertain, occurring sometime after the last sighting. However, the sightings themselves may also be uncertain. Recently a number of methods have been developed that incorporate sighting uncertainty in the inference of extinction based on a series of sightings. Here we estimate the timing of extinction for 41 of 52 North American and Hawaiian bird taxa and populations, the results of which suggest all became extinct before 2009. By acknowledging sighting uncertainty it results in two opposite effects, one pushing the timing of extinction away from the last sighting and the other drawing the timing of extinction nearer to it. However, for 14 assessed taxa and populations the upper 95% bounds lie beyond the end of the observation period and therefore suggest the possibility of continued persistence. This has important implications for conservation decision-makers and potentially reduces the likelihood of Romeo’s Error.
format: application/pdf
format: text/html
creator: David L. Roberts
creator: Ivan Jarić
subject: Biodiversity
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.2426
publisher: PeerJ Inc.
rights: © 2016 Roberts and Jarić
abstract: For most species the timing of extinction events is uncertain, occurring sometime after the last sighting. However, the sightings themselves may also be uncertain. Recently a number of methods have been developed that incorporate sighting uncertainty in the inference of extinction based on a series of sightings. Here we estimate the timing of extinction for 41 of 52 North American and Hawaiian bird taxa and populations, the results of which suggest all became extinct before 2009. By acknowledging sighting uncertainty it results in two opposite effects, one pushing the timing of extinction away from the last sighting and the other drawing the timing of extinction nearer to it. However, for 14 assessed taxa and populations the upper 95% bounds lie beyond the end of the observation period and therefore suggest the possibility of continued persistence. This has important implications for conservation decision-makers and potentially reduces the likelihood of Romeo’s Error.
bibliographic citation: Roberts et al. (2016) Inferring extinction in North American and Hawaiian birds in the presence of sighting uncertainty. PeerJ 4:e2426 https://doi.org/10.7717/peerj.2426
date submitted: 2016-07-15
date accepted: 2016-08-11
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roberts
  given name: David L.
author list: Agent
  family name: Jarić
  given name: Ivan
doi: 10.7717/peerj.2426
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Roberts and Jarić
attribution name: Roberts and Jarić

Parrotfish grazing ability: interspecific differences in relation to jaw-lever mechanics and relative weight of adductor mandibulae on an Okinawan coral reef
type: item
type: AcademicArticle
description: Parrotfishes (family Labridae: Scarini) are regarded to have important roles for maintaining the ecosystem balance in coral reefs due to their removal of organic matter and calcic substrates by grazing. The purpose of the present study was to clarify the interspecific differences in grazing ability of five parrotfish species (Chlorurus sordidus, C. bowersi, Scarus rivulatus, S. niger and S. forsteni) in relation to interspecific differences in jaw-lever mechanics and the relative weight of the adductor mandibulae (muscles operating jaw closing). The grazing ability was calculated by using stomach contents (CaCO3 weight/organic matter weight) defined as the grazing ability index (GAI). There were significant interspecific differences in GAI (C. sordidus = C. bowersi > S. rivulatus > S. niger = S. forsteni). Teeth of C. sordidus and C. bowersi were protrusive-shape whereas teeth of S. rivulatus, S. niger and S. forsteni were flat-shape. C. sordidus and C. bowersihave jaw-lever mechanics producing a greater biting force and have a larger weight of adductor mandibulae. S. rivulatus has jaw-lever mechanics producing a greater biting force but a smaller weight of adductor mandibulae that produce an intermediate biting force. In contrast, S. niger and S. forsteni have jaw-lever mechanics producing a lesser biting force and have a smaller weight of adductor mandibulae. Feeding rates and foray size of S. rivulatus, S. niger and S. forsteni were greater than C. sordidus and C. bowersi. The degree in bioerosion (GAI × feeding rate) was the largest for S. rivulatusand the smallest for S. forsteni. The degree in bioerosion for C. sordidus was larger than S. niger whereas relatively equal between C. bowersi and S. niger. These results suggest that interspecific difference in GAI was explained by interspecific differences in teeth shape, jaw-lever mechanics and relative weight of adductor mandibulae. The interspecific difference in the degree of bioerosion suggests the importance …
format: application/pdf
format: text/html
creator: Atsushi Nanami
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.2425
publisher: PeerJ Inc.
rights: © 2016 Nanami
abstract: Parrotfishes (family Labridae: Scarini) are regarded to have important roles for maintaining the ecosystem balance in coral reefs due to their removal of organic matter and calcic substrates by grazing. The purpose of the present study was to clarify the interspecific differences in grazing ability of five parrotfish species (Chlorurus sordidus, C. bowersi, Scarus rivulatus, S. niger and S. forsteni) in relation to interspecific differences in jaw-lever mechanics and the relative weight of the adductor mandibulae (muscles operating jaw closing). The grazing ability was calculated by using stomach contents (CaCO3 weight/organic matter weight) defined as the grazing ability index (GAI). There were significant interspecific differences in GAI (C. sordidus = C. bowersi > S. rivulatus > S. niger = S. forsteni). Teeth of C. sordidus and C. bowersi were protrusive-shape whereas teeth of S. rivulatus, S. niger and S. forsteni were flat-shape. C. sordidus and C. bowersihave jaw-lever mechanics producing a greater biting force and have a larger weight of adductor mandibulae. S. rivulatus has jaw-lever mechanics producing a greater biting force but a smaller weight of adductor mandibulae that produce an intermediate biting force. In contrast, S. niger and S. forsteni have jaw-lever mechanics producing a lesser biting force and have a smaller weight of adductor mandibulae. Feeding rates and foray size of S. rivulatus, S. niger and S. forsteni were greater than C. sordidus and C. bowersi. The degree in bioerosion (GAI × feeding rate) was the largest for S. rivulatusand the smallest for S. forsteni. The degree in bioerosion for C. sordidus was larger than S. niger whereas relatively equal between C. bowersi and S. niger. These results suggest that interspecific difference in GAI was explained by interspecific differences in teeth shape, jaw-lever mechanics and relative weight of adductor mandibulae. The interspecific difference in the degree of bioerosion suggests the importance …
bibliographic citation: Nanami (2016) Parrotfish grazing ability: interspecific differences in relation to jaw-lever mechanics and relative weight of adductor mandibulae on an Okinawan coral reef. PeerJ 4:e2425 https://doi.org/10.7717/peerj.2425
date submitted: 2016-05-17
date accepted: 2016-08-09
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nanami
  given name: Atsushi
doi: 10.7717/peerj.2425
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Nanami
attribution name: Nanami

Development and characterization of 24 polymorphic microsatellite loci for the freshwater fish Ichthyoelephas longirostris (Characiformes: Prochilodontidae)
type: item
type: AcademicArticle
description: The Neotropical freshwater fish Ichthyoelephas longirostris (Characiformes: prochilodontidae) is a short-distance migratory species endemic to Colombia. This study developed for the first time a set of 24 polymorphic microsatellite loci by using next-generation sequencing to explore the population genetics of this commercially exploited species. Nineteen of these loci were used to assess the genetic diversity and structure of 193 I. longirostris in three Colombian rivers of the Magdalena basin. Results showed that a single genetic stock circulates in the Cauca River, whereas other single different genetic stock is present in the rivers Samaná Norte and San Bartolomé-Magdalena. Additionally, I. longirostris was genetically different among and across rivers. This first insight about the population genetic structure of I. longirostris is crucial for monitoring the genetic diversity, the management and conservation of its populations, and complement the genetic studies in Prochilodontidae.
format: application/pdf
format: text/html
creator: Ricardo M. Landínez-García
creator: Edna J. Márquez
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.2419
publisher: PeerJ Inc.
rights: © 2016 Landínez-García and Márquez
abstract: The Neotropical freshwater fish Ichthyoelephas longirostris (Characiformes: prochilodontidae) is a short-distance migratory species endemic to Colombia. This study developed for the first time a set of 24 polymorphic microsatellite loci by using next-generation sequencing to explore the population genetics of this commercially exploited species. Nineteen of these loci were used to assess the genetic diversity and structure of 193 I. longirostris in three Colombian rivers of the Magdalena basin. Results showed that a single genetic stock circulates in the Cauca River, whereas other single different genetic stock is present in the rivers Samaná Norte and San Bartolomé-Magdalena. Additionally, I. longirostris was genetically different among and across rivers. This first insight about the population genetic structure of I. longirostris is crucial for monitoring the genetic diversity, the management and conservation of its populations, and complement the genetic studies in Prochilodontidae.
bibliographic citation: Landínez-García et al. (2016) Development and characterization of 24 polymorphic microsatellite loci for the freshwater fish Ichthyoelephas longirostris (Characiformes: Prochilodontidae). PeerJ 4:e2419 https://doi.org/10.7717/peerj.2419
date submitted: 2016-02-25
date accepted: 2016-08-06
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Landínez-García
  given name: Ricardo M.
author list: Agent
  family name: Márquez
  given name: Edna J.
doi: 10.7717/peerj.2419
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Landínez-García and Márquez
attribution name: Landínez-García and Márquez

Cross-sectional study of expression of divalent metal transporter-1, transferrin, and hepcidin in blood of smelters who are occupationally exposed to manganese
type: item
type: AcademicArticle
description: Background Manganese (Mn) is widely used in industries including the manufacture of Mn-iron (Fe) alloy. Occupational Mn overexposure causes manganism. Mn is known to affect Fe metabolism; this study was designed to test the hypothesis that workers exposed to Mn may have an altered expression of mRNAs encoding proteins in Fe metabolism. Methods Workers occupationally exposed to Mn (n = 71) from a Mn–Fe alloy factory and control workers without Mn-exposure (n = 48) from a pig-iron plant from Zunyi, China, were recruited for this study. Blood samples were collected into Trizol-containing tubes. Total RNA was isolated, purified, and subjected to real-time RT-PCR analysis. Metal concentrations were quantified by atomic absorption spectrophotometry. Results Working environment and genetic background of both groups were similar except for marked differences in airborne Mn concentrations (0.18 mg/m3 in Mn–Fe alloy factory vs. 0.0022 mg/m3 in pig-Fe plant), and in blood Mn levels (34.3 µg/L vs. 10.4 µg/L). Mn exposure caused a significant decrease in the expression of divalent metal transporter-1 (DMT1), transferrin (Tf) and hepcidin by 58.2%, 68.5% and 61.5%, respectively, as compared to controls, while the expression of transferrin receptor (TfR) was unaltered. Linear regression analysis revealed that expressions of DMT1, Tf and hepcidin were inversely correlated with the accumulative Mn exposure; the correlation coefficients (r) are −0.47, −0.54, and −0.49, respectively (p < 0.01). Conclusion The data suggest that occupational Mn exposure causes decreased expressions of DMT1, Tf and hepcidin in blood cells; the finding will help understand the mechanism underlying Mn exposure-associated alteration in Fe homeostasis among workers.
format: application/pdf
format: text/html
creator: Qiyuan Fan
creator: Yan Zhou
creator: Changyin Yu
creator: Jian Chen
creator: Xiujuan Shi
creator: Yanshu Zhang
creator: Wei Zheng
subject: Environmental Sciences
subject: Toxicology
subject: Public Health
description: doi:10.7717/peerj.2413
publisher: PeerJ Inc.
rights: © 2016 Fan et al.
abstract: Background Manganese (Mn) is widely used in industries including the manufacture of Mn-iron (Fe) alloy. Occupational Mn overexposure causes manganism. Mn is known to affect Fe metabolism; this study was designed to test the hypothesis that workers exposed to Mn may have an altered expression of mRNAs encoding proteins in Fe metabolism. Methods Workers occupationally exposed to Mn (n = 71) from a Mn–Fe alloy factory and control workers without Mn-exposure (n = 48) from a pig-iron plant from Zunyi, China, were recruited for this study. Blood samples were collected into Trizol-containing tubes. Total RNA was isolated, purified, and subjected to real-time RT-PCR analysis. Metal concentrations were quantified by atomic absorption spectrophotometry. Results Working environment and genetic background of both groups were similar except for marked differences in airborne Mn concentrations (0.18 mg/m3 in Mn–Fe alloy factory vs. 0.0022 mg/m3 in pig-Fe plant), and in blood Mn levels (34.3 µg/L vs. 10.4 µg/L). Mn exposure caused a significant decrease in the expression of divalent metal transporter-1 (DMT1), transferrin (Tf) and hepcidin by 58.2%, 68.5% and 61.5%, respectively, as compared to controls, while the expression of transferrin receptor (TfR) was unaltered. Linear regression analysis revealed that expressions of DMT1, Tf and hepcidin were inversely correlated with the accumulative Mn exposure; the correlation coefficients (r) are −0.47, −0.54, and −0.49, respectively (p < 0.01). Conclusion The data suggest that occupational Mn exposure causes decreased expressions of DMT1, Tf and hepcidin in blood cells; the finding will help understand the mechanism underlying Mn exposure-associated alteration in Fe homeostasis among workers.
bibliographic citation: Fan et al. (2016) Cross-sectional study of expression of divalent metal transporter-1, transferrin, and hepcidin in blood of smelters who are occupationally exposed to manganese. PeerJ 4:e2413 https://doi.org/10.7717/peerj.2413
date submitted: 2016-07-02
date accepted: 2016-08-04
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Qiyuan
author list: Agent
  family name: Zhou
  given name: Yan
author list: Agent
  family name: Yu
  given name: Changyin
author list: Agent
  family name: Chen
  given name: Jian
author list: Agent
  family name: Shi
  given name: Xiujuan
author list: Agent
  family name: Zhang
  given name: Yanshu
author list: Agent
  family name: Zheng
  given name: Wei
doi: 10.7717/peerj.2413
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Fan et al.
attribution name: Fan et al.

Do beaver dams reduce habitat connectivity and salmon productivity in expansive river floodplains?
type: item
type: AcademicArticle
description: Beaver have expanded in their native habitats throughout the northern hemisphere in recent decades following reductions in trapping and reintroduction efforts. Beaver have the potential to strongly influence salmon populations in the side channels of large alluvial rivers by building dams that create pond complexes. Pond habitat may improve salmon productivity or the presence of dams may reduce productivity if dams limit habitat connectivity and inhibit fish passage. Our intent in this paper is to contrast the habitat use and production of juvenile salmon on expansive floodplains of two geomorphically similar salmon rivers: the Kol River in Kamchatka, Russia (no beavers) and the Kwethluk River in Alaska (abundant beavers), and thereby provide a case study on how beavers may influence salmonids in large floodplain rivers. We examined important rearing habitats in each floodplain, including springbrooks, beaver ponds, beaver-influenced springbrooks, and shallow shorelines of the river channel. Juvenile coho salmon dominated fish assemblages in all habitats in both rivers but other species were present. Salmon density was similar in all habitat types in the Kol, but in the Kwethluk coho and Chinook densities were 3–12× lower in mid- and late-successional beaver ponds than in springbrook and main channel habitats. In the Kol, coho condition (length: weight ratios) was similar among habitats, but Chinook condition was highest in orthofluvial springbrooks. In the Kwethluk, Chinook condition was similar among habitats, but coho condition was lowest in main channel versus other habitats (0.89 vs. 0.99–1.10). Densities of juvenile salmon were extremely low in beaver ponds located behind numerous dams in the orthofluvial zone of the Kwethluk River floodplain, whereas juvenile salmon were abundant in habitats throughout the entire floodplain in the Kol River. If beavers were not present on the Kwethluk, floodplain habitats would be fully interconnected and theoretically could …
format: application/pdf
format: text/html
creator: Rachel L. Malison
creator: Kirill V. Kuzishchin
creator: Jack A. Stanford
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
description: doi:10.7717/peerj.2403
publisher: PeerJ Inc.
rights: © 2016 Malison et al.
abstract: Beaver have expanded in their native habitats throughout the northern hemisphere in recent decades following reductions in trapping and reintroduction efforts. Beaver have the potential to strongly influence salmon populations in the side channels of large alluvial rivers by building dams that create pond complexes. Pond habitat may improve salmon productivity or the presence of dams may reduce productivity if dams limit habitat connectivity and inhibit fish passage. Our intent in this paper is to contrast the habitat use and production of juvenile salmon on expansive floodplains of two geomorphically similar salmon rivers: the Kol River in Kamchatka, Russia (no beavers) and the Kwethluk River in Alaska (abundant beavers), and thereby provide a case study on how beavers may influence salmonids in large floodplain rivers. We examined important rearing habitats in each floodplain, including springbrooks, beaver ponds, beaver-influenced springbrooks, and shallow shorelines of the river channel. Juvenile coho salmon dominated fish assemblages in all habitats in both rivers but other species were present. Salmon density was similar in all habitat types in the Kol, but in the Kwethluk coho and Chinook densities were 3–12× lower in mid- and late-successional beaver ponds than in springbrook and main channel habitats. In the Kol, coho condition (length: weight ratios) was similar among habitats, but Chinook condition was highest in orthofluvial springbrooks. In the Kwethluk, Chinook condition was similar among habitats, but coho condition was lowest in main channel versus other habitats (0.89 vs. 0.99–1.10). Densities of juvenile salmon were extremely low in beaver ponds located behind numerous dams in the orthofluvial zone of the Kwethluk River floodplain, whereas juvenile salmon were abundant in habitats throughout the entire floodplain in the Kol River. If beavers were not present on the Kwethluk, floodplain habitats would be fully interconnected and theoretically could …
bibliographic citation: Malison et al. (2016) Do beaver dams reduce habitat connectivity and salmon productivity in expansive river floodplains?. PeerJ 4:e2403 https://doi.org/10.7717/peerj.2403
date submitted: 2015-11-23
date accepted: 2016-08-03
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malison
  given name: Rachel L.
author list: Agent
  family name: Kuzishchin
  given name: Kirill V.
author list: Agent
  family name: Stanford
  given name: Jack A.
doi: 10.7717/peerj.2403
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Malison et al.
attribution name: Malison et al.

Screening microalgae isolated from urban storm- and wastewater systems as feedstock for biofuel
type: item
type: AcademicArticle
description: Exploiting microalgae as feedstock for biofuel production is a growing field of research and application, but there remain challenges related to industrial viability and economic sustainability. A solution to the water requirements of industrial-scale production is the use of wastewater as a growth medium. Considering the variable quality and contaminant loads of wastewater, algal feedstock would need to have broad tolerance and resilience to fluctuating wastewater conditions during growth. As a first step in targeting strains for growth in wastewater, our study isolated microalgae from wastewater habitats, including urban stormwater-ponds and a municipal wastewater-treatment system, to assess growth, fatty acids and metal tolerance under standardized conditions. Stormwater ponds in particular have widely fluctuating conditions and metal loads, so microalgae from this type of environment may have desirable traits for growth in wastewater. Forty-three algal strains were isolated in total, including several strains from natural habitats. All strains, with the exception of one cyanobacterial strain, are members of the Chlorophyta, including several taxa commonly targeted for biofuel production. Isolates were identified using taxonomic and 18S rRNA sequence methods, and the fastest growing strains with ideal fatty acid profiles for biodiesel production included Scenedesmus and Desmodesmus species (Growth rate (d−1) > 1). All isolates in a small, but diverse taxonomic group of test-strains were tolerant of copper at wastewater-relevant concentrations. Overall, more than half of the isolated strains, particularly those from stormwater ponds, show promise as candidates for biofuel feedstock.
format: application/pdf
format: text/html
creator: Rebecca Massimi
creator: Andrea E. Kirkwood
subject: Biotechnology
subject: Genetics
subject: Microbiology
subject: Taxonomy
subject: Toxicology
description: doi:10.7717/peerj.2396
publisher: PeerJ Inc.
rights: © 2016 Massimi & Kirkwood
abstract: Exploiting microalgae as feedstock for biofuel production is a growing field of research and application, but there remain challenges related to industrial viability and economic sustainability. A solution to the water requirements of industrial-scale production is the use of wastewater as a growth medium. Considering the variable quality and contaminant loads of wastewater, algal feedstock would need to have broad tolerance and resilience to fluctuating wastewater conditions during growth. As a first step in targeting strains for growth in wastewater, our study isolated microalgae from wastewater habitats, including urban stormwater-ponds and a municipal wastewater-treatment system, to assess growth, fatty acids and metal tolerance under standardized conditions. Stormwater ponds in particular have widely fluctuating conditions and metal loads, so microalgae from this type of environment may have desirable traits for growth in wastewater. Forty-three algal strains were isolated in total, including several strains from natural habitats. All strains, with the exception of one cyanobacterial strain, are members of the Chlorophyta, including several taxa commonly targeted for biofuel production. Isolates were identified using taxonomic and 18S rRNA sequence methods, and the fastest growing strains with ideal fatty acid profiles for biodiesel production included Scenedesmus and Desmodesmus species (Growth rate (d−1) > 1). All isolates in a small, but diverse taxonomic group of test-strains were tolerant of copper at wastewater-relevant concentrations. Overall, more than half of the isolated strains, particularly those from stormwater ponds, show promise as candidates for biofuel feedstock.
bibliographic citation: Massimi et al. (2016) Screening microalgae isolated from urban storm- and wastewater systems as feedstock for biofuel. PeerJ 4:e2396 https://doi.org/10.7717/peerj.2396
date submitted: 2016-06-01
date accepted: 2016-08-02
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Massimi
  given name: Rebecca
author list: Agent
  family name: Kirkwood
  given name: Andrea E.
doi: 10.7717/peerj.2396
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: © 2016 Massimi & Kirkwood
attribution name: Massimi & Kirkwood

The inheritance of female colour polymorphism in Ischnura genei (Zygoptera: Coenagrionidae), with observations on melanism under laboratory conditions
type: item
type: AcademicArticle
description: Current research on female colour polymorphism in Ischnura damselflies suggests that a balanced fitness trade-off between morphotypes contributes to the maintenance of polymorphism inside populations. The genetic inheritance system constitutes a key factor to understand morph fluctuation and fitness. Ischnura genei, an endemic species of some Mediterranean islands, has three female colour morphs, including one androchrome (male-coloured) and two gynochromes. In this study, we reared two generations of I. genei under laboratory conditions and tested male behavioural responses to female colour morphs in the field. We recorded ontogenetic colour changes and studied morph frequency in three populations from Sardinia (Italy). Morph frequencies of laboratory crosses can be explained by a model based on an autosomal locus with three alleles and sex-restricted expression, except for one crossing of 42 families with unexpected offspring. The allelic dominance relationship was androchrome > infuscans > aurantiaca. Old individuals reared in the laboratory exhibited different levels of melanism in variable extent depending on sex and morph. Results of model presentations indicate a male preference for gynochrome females and the lack of recognition of androchromes as potential mates. Aurantiaca females were the most frequent morph in the field (63–87%). Further studies in other populations and islands are needed to understand the maintenance of this polymorphism.
format: application/pdf
format: text/html
creator: Iago Sanmartín-Villar
creator: Adolfo Cordero-Rivera
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Genetics
description: doi:10.7717/peerj.2380
publisher: PeerJ Inc.
rights: © 2016 Sanmartín-Villar and Cordero-Rivera
abstract: Current research on female colour polymorphism in Ischnura damselflies suggests that a balanced fitness trade-off between morphotypes contributes to the maintenance of polymorphism inside populations. The genetic inheritance system constitutes a key factor to understand morph fluctuation and fitness. Ischnura genei, an endemic species of some Mediterranean islands, has three female colour morphs, including one androchrome (male-coloured) and two gynochromes. In this study, we reared two generations of I. genei under laboratory conditions and tested male behavioural responses to female colour morphs in the field. We recorded ontogenetic colour changes and studied morph frequency in three populations from Sardinia (Italy). Morph frequencies of laboratory crosses can be explained by a model based on an autosomal locus with three alleles and sex-restricted expression, except for one crossing of 42 families with unexpected offspring. The allelic dominance relationship was androchrome > infuscans > aurantiaca. Old individuals reared in the laboratory exhibited different levels of melanism in variable extent depending on sex and morph. Results of model presentations indicate a male preference for gynochrome females and the lack of recognition of androchromes as potential mates. Aurantiaca females were the most frequent morph in the field (63–87%). Further studies in other populations and islands are needed to understand the maintenance of this polymorphism.
bibliographic citation: Sanmartín-Villar et al. (2016) The inheritance of female colour polymorphism in Ischnura genei (Zygoptera: Coenagrionidae), with observations on melanism under laboratory conditions . PeerJ 4:e2380 https://doi.org/10.7717/peerj.2380
date submitted: 2016-05-17
date accepted: 2016-07-29
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sanmartín-Villar
  given name: Iago
author list: Agent
  family name: Cordero-Rivera
  given name: Adolfo
doi: 10.7717/peerj.2380
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Sanmartín-Villar and Cordero-Rivera
attribution name: Sanmartín-Villar and Cordero-Rivera

Transcriptome analysis of colored calla lily (Zantedeschia rehmannii Engl.) by Illumina sequencing: de novo assembly, annotation and EST-SSR marker development
type: item
type: AcademicArticle
description: Colored calla lily is the short name for the species or hybrids in section Aestivae of genus Zantedeschia. It is currently one of the most popular flower plants in the world due to its beautiful flower spathe and long postharvest life. However, little genomic information and few molecular markers are available for its genetic improvement. Here, de novo transcriptome sequencing was performed to produce large transcript sequences for Z. rehmannii cv. ‘Rehmannii’ using an Illumina HiSeq 2000 instrument. More than 59.9 million cDNA sequence reads were obtained and assembled into 39,298 unigenes with an average length of 1,038 bp. Among these, 21,077 unigenes showed significant similarity to protein sequences in the non-redundant protein database (Nr) and in the Swiss-Prot, Gene Ontology (GO), Cluster of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, a total of 117 unique transcripts were then defined that might regulate the flower spathe development of colored calla lily. Additionally, 9,933 simple sequence repeats (SSRs) and 7,162 single nucleotide polymorphisms (SNPs) were identified as putative molecular markers. High-quality primers for 200 SSR loci were designed and selected, of which 58 amplified reproducible amplicons were polymorphic among 21 accessions of colored calla lily. The sequence information and molecular markers in the present study will provide valuable resources for genetic diversity analysis, germplasm characterization and marker-assisted selection in the genus Zantedeschia.
format: application/pdf
format: text/html
creator: Zunzheng Wei
creator: Zhenzhen Sun
creator: Binbin Cui
creator: Qixiang Zhang
creator: Min Xiong
creator: Xian Wang
creator: Di Zhou
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.2378
publisher: PeerJ Inc.
rights: © 2016 Wei et al.
abstract: Colored calla lily is the short name for the species or hybrids in section Aestivae of genus Zantedeschia. It is currently one of the most popular flower plants in the world due to its beautiful flower spathe and long postharvest life. However, little genomic information and few molecular markers are available for its genetic improvement. Here, de novo transcriptome sequencing was performed to produce large transcript sequences for Z. rehmannii cv. ‘Rehmannii’ using an Illumina HiSeq 2000 instrument. More than 59.9 million cDNA sequence reads were obtained and assembled into 39,298 unigenes with an average length of 1,038 bp. Among these, 21,077 unigenes showed significant similarity to protein sequences in the non-redundant protein database (Nr) and in the Swiss-Prot, Gene Ontology (GO), Cluster of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, a total of 117 unique transcripts were then defined that might regulate the flower spathe development of colored calla lily. Additionally, 9,933 simple sequence repeats (SSRs) and 7,162 single nucleotide polymorphisms (SNPs) were identified as putative molecular markers. High-quality primers for 200 SSR loci were designed and selected, of which 58 amplified reproducible amplicons were polymorphic among 21 accessions of colored calla lily. The sequence information and molecular markers in the present study will provide valuable resources for genetic diversity analysis, germplasm characterization and marker-assisted selection in the genus Zantedeschia.
bibliographic citation: Wei et al. (2016) Transcriptome analysis of colored calla lily (Zantedeschia rehmannii Engl.) by Illumina sequencing: de novo assembly, annotation and EST-SSR marker development. PeerJ 4:e2378 https://doi.org/10.7717/peerj.2378
date submitted: 2016-04-23
date accepted: 2016-07-29
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Zunzheng
author list: Agent
  family name: Sun
  given name: Zhenzhen
author list: Agent
  family name: Cui
  given name: Binbin
author list: Agent
  family name: Zhang
  given name: Qixiang
author list: Agent
  family name: Xiong
  given name: Min
author list: Agent
  family name: Wang
  given name: Xian
author list: Agent
  family name: Zhou
  given name: Di
doi: 10.7717/peerj.2378
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Wei et al.
attribution name: Wei et al.

Stable isotope analysis (δ13C and δ15N) of soil nematodes from four feeding groups
type: item
type: AcademicArticle
description: Soil nematode feeding groups are a long-established trophic categorisation largely based on morphology and are used in ecological indices to monitor and analyse the biological state of soils. Stable isotope ratio analysis (13C/12C and 15N/14N, expressed as δ13C and δ15N) has provided verification of, and novel insights into, the feeding ecology of soil animals such as earthworms and mites. However, isotopic studies of soil nematodes have been limited to date as conventional stable isotope ratio analysis needs impractically large numbers of nematodes (up to 1,000) to achieve required minimum sample weights (typically >100 µg C and N). Here, micro-sample near-conventional elemental analysis–isotopic ratio mass spectrometry (μEA–IRMS) of C and N using microgram samples (typically 20 µg dry weight), was employed to compare the trophic position of selected soil nematode taxa from four feeding groups: predators (Anatonchus and Mononchus), bacterial feeders (Plectus and Rhabditis), omnivores (Aporcelaimidae and Qudsianematidae) and plant feeder (Rotylenchus). Free-living nematodes were collected from conventionally and organically managed arable soils. As few as 15 nematodes, for omnivores and predators, were sufficient to reach the 20 µg dry weight target. There was no significant difference in δ15N (p = 0.290) or δ13C (p = 0.706) between conventional and organic agronomic treatments but, within treatments, there was a significant difference in N and C stable isotope ratios between the plant feeder, Rotylenchus (δ15N = 1.08 to 3.22 mUr‰, δ13C = –29.58 to –27.87 mUr) and all other groups. There was an average difference of 9.62 mUr in δ15N between the plant feeder and the predator group (δ15N = 9.89 to 12.79 mUr, δ13C = –27.04 to –25.51 mUr). Isotopic niche widths were calculated as Bayesian derived standard ellipse areas and were smallest for the plant feeder (1.37 mUr2) and the predators (1.73 mUr2), but largest for omnivores (3.83 mUr2). These data may reflect more pref…
format: application/pdf
format: text/html
creator: Carol Melody
creator: Bryan Griffiths
creator: Jens Dyckmans
creator: Olaf Schmidt
subject: Agricultural Science
subject: Ecology
subject: Environmental Sciences
subject: Soil Science
subject: Zoology
description: doi:10.7717/peerj.2372
publisher: PeerJ Inc.
rights: © 2016 Melody et al.
abstract: Soil nematode feeding groups are a long-established trophic categorisation largely based on morphology and are used in ecological indices to monitor and analyse the biological state of soils. Stable isotope ratio analysis (13C/12C and 15N/14N, expressed as δ13C and δ15N) has provided verification of, and novel insights into, the feeding ecology of soil animals such as earthworms and mites. However, isotopic studies of soil nematodes have been limited to date as conventional stable isotope ratio analysis needs impractically large numbers of nematodes (up to 1,000) to achieve required minimum sample weights (typically >100 µg C and N). Here, micro-sample near-conventional elemental analysis–isotopic ratio mass spectrometry (μEA–IRMS) of C and N using microgram samples (typically 20 µg dry weight), was employed to compare the trophic position of selected soil nematode taxa from four feeding groups: predators (Anatonchus and Mononchus), bacterial feeders (Plectus and Rhabditis), omnivores (Aporcelaimidae and Qudsianematidae) and plant feeder (Rotylenchus). Free-living nematodes were collected from conventionally and organically managed arable soils. As few as 15 nematodes, for omnivores and predators, were sufficient to reach the 20 µg dry weight target. There was no significant difference in δ15N (p = 0.290) or δ13C (p = 0.706) between conventional and organic agronomic treatments but, within treatments, there was a significant difference in N and C stable isotope ratios between the plant feeder, Rotylenchus (δ15N = 1.08 to 3.22 mUr‰, δ13C = –29.58 to –27.87 mUr) and all other groups. There was an average difference of 9.62 mUr in δ15N between the plant feeder and the predator group (δ15N = 9.89 to 12.79 mUr, δ13C = –27.04 to –25.51 mUr). Isotopic niche widths were calculated as Bayesian derived standard ellipse areas and were smallest for the plant feeder (1.37 mUr2) and the predators (1.73 mUr2), but largest for omnivores (3.83 mUr2). These data may reflect more pref…
bibliographic citation: Melody et al. (2016) Stable isotope analysis (δ13C and δ15N) of soil nematodes from four feeding groups. PeerJ 4:e2372 https://doi.org/10.7717/peerj.2372
date submitted: 2015-12-28
date accepted: 2016-07-26
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Melody
  given name: Carol
author list: Agent
  family name: Griffiths
  given name: Bryan
author list: Agent
  family name: Dyckmans
  given name: Jens
author list: Agent
  family name: Schmidt
  given name: Olaf
doi: 10.7717/peerj.2372
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Melody et al.
attribution name: Melody et al.

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