PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Multi-gene phylogeny and divergence estimations for Evaniidae (Hymenoptera)
items: Spiders did not repeatedly gain, but repeatedly lost, foraging webs
items: Prehemodialysis arteriovenous access creation is associated with better cardiovascular outcomes in patients receiving hemodialysis: a population-based cohort study
items: A longitudinal study of the faecal microbiome and metabolome of periparturient mares
items: Density of intertidal barnacles along their full elevational range of distribution conforms to the abundant-centre hypothesis
items: Environmental modulation of the proteomic profiles from closely phylogenetically related populations of the red seaweed Plocamium brasiliense
items: Reproductive biology of little tunny Euthynnus alletteratus (Rafinesque, 1810) in the southwest Gulf of Mexico
items: Comparison of shallow-water seston among biogenic habitats on tidal flats
items: Prevalence of malocclusion and occlusal traits in the early mixed dentition in Shanghai, China
items: On the half-life of thiocyanate in the plasma of the marine fish Amphiprion ocellaris: implications for cyanide detection

Multi-gene phylogeny and divergence estimations for Evaniidae (Hymenoptera)
type: item
type: AcademicArticle
description: Ensign wasps (Hymenoptera: Evaniidae) develop as predators of cockroach eggs (Blattodea), have a wide distribution and exhibit numerous interesting biological phenomena. The taxonomy of this lineage has been the subject of several recent, intensive efforts, but the lineage lacked a robust phylogeny. In this paper we present a new phylogeny, based on increased taxonomic sampling and data from six molecular markers (mitochondrial 16S and COI, and nuclear markers 28S, RPS23, CAD, and AM2), the latter used for the first time in phylogenetic reconstruction. Our intent is to provide a robust phylogeny that will stabilize and facilitate revision of the higher-level classification. We also show the continued utility of molecular motifs, especially the presence of an intron in the RPS23 fragments of certain taxa, to diagnose evaniid clades and assist with taxonomic classification. Furthermore, we estimate divergence times among evaniid lineages for the first time, using multiple fossil calibrations. Evaniidae radiated primarily in the Early Cretaceous (134.1–141.1 Mya), with and most extant genera diverging near the K-T boundary. The estimated phylogeny reveals a more robust topology than previous efforts, with the recovery of more monophyletic taxa and better higher-level resolution. The results facilitate a change in ensign wasp taxonomy, with Parevania, and Papatuka, syn. nov. becoming junior synonyms of Zeuxevania, and Acanthinevania, syn. nov. being designated as junior synonym of Szepligetella. We transfer 30 species to Zeuxevania, either reestablishing past combinations or as new combinations. We also transfer 20 species from Acanthinevania to Szepligetella as new combinations.
format: application/pdf
format: text/html
creator: Barbara J. Sharanowski
creator: Leanne Peixoto
creator: Anamaria Dal Molin
creator: Andrew R. Deans
subject: Entomology
subject: Evolutionary Studies
subject: Taxonomy
description: doi:10.7717/peerj.6689
publisher: PeerJ Inc.
rights: © 2019 Sharanowski et al.
abstract: Ensign wasps (Hymenoptera: Evaniidae) develop as predators of cockroach eggs (Blattodea), have a wide distribution and exhibit numerous interesting biological phenomena. The taxonomy of this lineage has been the subject of several recent, intensive efforts, but the lineage lacked a robust phylogeny. In this paper we present a new phylogeny, based on increased taxonomic sampling and data from six molecular markers (mitochondrial 16S and COI, and nuclear markers 28S, RPS23, CAD, and AM2), the latter used for the first time in phylogenetic reconstruction. Our intent is to provide a robust phylogeny that will stabilize and facilitate revision of the higher-level classification. We also show the continued utility of molecular motifs, especially the presence of an intron in the RPS23 fragments of certain taxa, to diagnose evaniid clades and assist with taxonomic classification. Furthermore, we estimate divergence times among evaniid lineages for the first time, using multiple fossil calibrations. Evaniidae radiated primarily in the Early Cretaceous (134.1–141.1 Mya), with and most extant genera diverging near the K-T boundary. The estimated phylogeny reveals a more robust topology than previous efforts, with the recovery of more monophyletic taxa and better higher-level resolution. The results facilitate a change in ensign wasp taxonomy, with Parevania, and Papatuka, syn. nov. becoming junior synonyms of Zeuxevania, and Acanthinevania, syn. nov. being designated as junior synonym of Szepligetella. We transfer 30 species to Zeuxevania, either reestablishing past combinations or as new combinations. We also transfer 20 species from Acanthinevania to Szepligetella as new combinations.
bibliographic citation: Sharanowski et al. (2019) Multi-gene phylogeny and divergence estimations for Evaniidae (Hymenoptera). PeerJ 7:e6689 https://doi.org/10.7717/peerj.6689
date submitted: 2018-03-18
date accepted: 2019-02-24
issued: 2019-04-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sharanowski
  given name: Barbara J.
author list: Agent
  family name: Peixoto
  given name: Leanne
author list: Agent
  family name: Dal Molin
  given name: Anamaria
author list: Agent
  family name: Deans
  given name: Andrew R.
doi: 10.7717/peerj.6689
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-04
copyright: ©2019 Sharanowski et al.
attribution name: Sharanowski et al.

Spiders did not repeatedly gain, but repeatedly lost, foraging webs
type: item
type: AcademicArticle
description: Much genomic-scale, especially transcriptomic, data on spider phylogeny has accumulated in the last few years. These data have recently been used to investigate the diverse architectures and the origin of spider webs, concluding that the ancestral spider spun no foraging web, that spider webs evolved de novo 10–14 times, and that the orb web evolved at least three times. These findings in fact result from a particular phylogenetic character coding strategy, specifically coding the absence of webs as logically equivalent, and homologous to, 10 other observable (i.e., not absent) web architectures. “Absence” of webs should be regarded as inapplicable data. To be analyzed properly by character optimization algorithms, it should be coded as “?” because these codes—or their equivalent—are handled differently by such algorithms. Additional problems include critical misspellings of taxon names from one analysis to the next (misspellings cause some optimization algorithms to drop terminals, which affects taxon sampling and results), and mistakes in spider natural history. In sum, the method causes character optimization algorithms to produce counter-intuitive results, and does not distinguish absence from secondary loss. Proper treatment of missing entries and corrected data instead imply that foraging webs are primitive for spiders and that webs have been lost ∼5–7 times, not gained 10–14 times. The orb web, specifically, may be homologous (originated only once) although lost 2–6 times.
format: application/pdf
format: text/html
creator: Jonathan A. Coddington
creator: Ingi Agnarsson
creator: Chris A. Hamilton
creator: Jason E. Bond
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6703
publisher: PeerJ Inc.
rights: © 2019 Coddington et al.
abstract: Much genomic-scale, especially transcriptomic, data on spider phylogeny has accumulated in the last few years. These data have recently been used to investigate the diverse architectures and the origin of spider webs, concluding that the ancestral spider spun no foraging web, that spider webs evolved de novo 10–14 times, and that the orb web evolved at least three times. These findings in fact result from a particular phylogenetic character coding strategy, specifically coding the absence of webs as logically equivalent, and homologous to, 10 other observable (i.e., not absent) web architectures. “Absence” of webs should be regarded as inapplicable data. To be analyzed properly by character optimization algorithms, it should be coded as “?” because these codes—or their equivalent—are handled differently by such algorithms. Additional problems include critical misspellings of taxon names from one analysis to the next (misspellings cause some optimization algorithms to drop terminals, which affects taxon sampling and results), and mistakes in spider natural history. In sum, the method causes character optimization algorithms to produce counter-intuitive results, and does not distinguish absence from secondary loss. Proper treatment of missing entries and corrected data instead imply that foraging webs are primitive for spiders and that webs have been lost ∼5–7 times, not gained 10–14 times. The orb web, specifically, may be homologous (originated only once) although lost 2–6 times.
bibliographic citation: Coddington et al. (2019) Spiders did not repeatedly gain, but repeatedly lost, foraging webs. PeerJ 7:e6703 https://doi.org/10.7717/peerj.6703
date submitted: 2018-11-12
date accepted: 2019-02-21
issued: 2019-04-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coddington
  given name: Jonathan A.
author list: Agent
  family name: Agnarsson
  given name: Ingi
author list: Agent
  family name: Hamilton
  given name: Chris A.
author list: Agent
  family name: Bond
  given name: Jason E.
doi: 10.7717/peerj.6703
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-04
copyright: ©2019 Coddington et al.
attribution name: Coddington et al.

Prehemodialysis arteriovenous access creation is associated with better cardiovascular outcomes in patients receiving hemodialysis: a population-based cohort study
type: item
type: AcademicArticle
description: Background Cardiovascular (CV) disease contributes to nearly half of the mortalities in patients with end-stage renal disease. Patients who received prehemodialysis arteriovenous access (pre-HD AVA) creation had divergent CV outcomes. Methods We conducted a population-based cohort study by recruiting incident patients receiving HD from 2001 to 2012 from the Taiwan National Health Insurance Research Database. Patients’ characteristics, comorbidities, and medicines were analyzed. The primary outcome of interest was major adverse cardiovascular events (MACEs), defined as hospitalization due to acute myocardial infarction, stroke, or congestive heart failure (CHF) occurring within the first year of HD. Secondary outcomes included MACE-related mortality and all-cause mortality in the same follow-up period. Results The patients in the pre-HD AVA group were younger, had a lower burden of underlying diseases, were more likely to use erythropoiesis-stimulating agents but less likely to use renin–angiotensin–aldosterone system blockers. The patients with pre-HD AVA creation had a marginally lower rate of MACEs but a significant 35% lower rate of CHF hospitalization than those without creation (adjusted hazard ratio (HR) 0.65, 95% confidence interval (CI) [0.48–0.88]). In addition, the pre-HD AVA group exhibited an insignificantly lower rate of MACE-related mortality but a significantly 52% lower rate of all-cause mortality than the non-pre-HD AVA group (adjusted HR 0.48, 95% CI [0.39–0.59]). Sensitivity analyses obtained consistent results. Conclusions Pre-HD AVA creation is associated with a lower rate of CHF hospitalization and overall death in the first year of dialysis.
format: application/pdf
format: text/html
creator: Cheng-Chieh Yen
creator: Mei-Yin Liu
creator: Po-Wei Chen
creator: Peir-Haur Hung
creator: Tse-Hsuan Su
creator: Yueh-Han Hsu
subject: Cardiology
subject: Internal Medicine
subject: Nephrology
description: doi:10.7717/peerj.6680
publisher: PeerJ Inc.
rights: © 2019 Yen et al.
abstract: Background Cardiovascular (CV) disease contributes to nearly half of the mortalities in patients with end-stage renal disease. Patients who received prehemodialysis arteriovenous access (pre-HD AVA) creation had divergent CV outcomes. Methods We conducted a population-based cohort study by recruiting incident patients receiving HD from 2001 to 2012 from the Taiwan National Health Insurance Research Database. Patients’ characteristics, comorbidities, and medicines were analyzed. The primary outcome of interest was major adverse cardiovascular events (MACEs), defined as hospitalization due to acute myocardial infarction, stroke, or congestive heart failure (CHF) occurring within the first year of HD. Secondary outcomes included MACE-related mortality and all-cause mortality in the same follow-up period. Results The patients in the pre-HD AVA group were younger, had a lower burden of underlying diseases, were more likely to use erythropoiesis-stimulating agents but less likely to use renin–angiotensin–aldosterone system blockers. The patients with pre-HD AVA creation had a marginally lower rate of MACEs but a significant 35% lower rate of CHF hospitalization than those without creation (adjusted hazard ratio (HR) 0.65, 95% confidence interval (CI) [0.48–0.88]). In addition, the pre-HD AVA group exhibited an insignificantly lower rate of MACE-related mortality but a significantly 52% lower rate of all-cause mortality than the non-pre-HD AVA group (adjusted HR 0.48, 95% CI [0.39–0.59]). Sensitivity analyses obtained consistent results. Conclusions Pre-HD AVA creation is associated with a lower rate of CHF hospitalization and overall death in the first year of dialysis.
bibliographic citation: Yen et al. (2019) Prehemodialysis arteriovenous access creation is associated with better cardiovascular outcomes in patients receiving hemodialysis: a population-based cohort study. PeerJ 7:e6680 https://doi.org/10.7717/peerj.6680
date submitted: 2018-11-24
date accepted: 2019-02-21
issued: 2019-04-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yen
  given name: Cheng-Chieh
author list: Agent
  family name: Liu
  given name: Mei-Yin
author list: Agent
  family name: Chen
  given name: Po-Wei
author list: Agent
  family name: Hung
  given name: Peir-Haur
author list: Agent
  family name: Su
  given name: Tse-Hsuan
author list: Agent
  family name: Hsu
  given name: Yueh-Han
doi: 10.7717/peerj.6680
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-03
copyright: © 2019 Yen et al.
attribution name: Yen et al.

A longitudinal study of the faecal microbiome and metabolome of periparturient mares
type: item
type: AcademicArticle
description: Background Periparturient mares are at increased risk of colic including large colon volvulus, which has a high mortality rate. Alterations in colonic microbiota related to either physiological or management changes, or both, that occur at this time have been suggested as potential causes for increased colic risk in this population of horses. Although the effect of management changes on the horse faecal microbiota has been investigated, limited work has been conducted to investigate changes in faecal microbiota structure and function in the periparturient period. The objectives of the current study were to investigate temporal stability of the faecal microbiota and volatile organic compounds (VOCs) of the faecal metabolome in periparturient mares. Methods Faecal samples were collected weekly from five pregnant mares from 3 weeks pre-foaling to 7 weeks post-foaling. The microbiome data was generated by PCR amplification and sequencing of the V1–V2 regions of the bacterial 16S rRNA genes, while the VOC profile was characterised using headspace solid phase microextraction gas chromatography mass spectrometry. Results The mare faecal microbiota was relatively stable over the periparturient period and most variation was associated with individual mares. A small number of operational taxonomic units were found to be significantly differentially abundant between samples collected before and after foaling. A total of 98 VOCs were identified. The total number of VOCs did not vary significantly between individual mares, weeks of sample collection and feeds available to the mares. Three VOCs (decane, 2-pentylfuran, and oct-2-ene) showed significant increase overtime on linear mixed effects modelling analysis. These results suggest that the mare faecal microbiota is structurally and functionally stable during the periparturient period. The findings also suggest that if changes in the gut microbiota are related to development of colic postpartum, altered risk may be due to inher…
format: application/pdf
format: text/html
creator: Shebl E. Salem
creator: Rachael Hough
creator: Chris Probert
creator: Thomas W. Maddox
creator: Philipp Antczak
creator: Julian M. Ketley
creator: Nicola J. Williams
creator: Sarah J. Stoneham
creator: Debra C. Archer
subject: Ecology
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.6687
publisher: PeerJ Inc.
rights: © 2019 Salem et al.
abstract: Background Periparturient mares are at increased risk of colic including large colon volvulus, which has a high mortality rate. Alterations in colonic microbiota related to either physiological or management changes, or both, that occur at this time have been suggested as potential causes for increased colic risk in this population of horses. Although the effect of management changes on the horse faecal microbiota has been investigated, limited work has been conducted to investigate changes in faecal microbiota structure and function in the periparturient period. The objectives of the current study were to investigate temporal stability of the faecal microbiota and volatile organic compounds (VOCs) of the faecal metabolome in periparturient mares. Methods Faecal samples were collected weekly from five pregnant mares from 3 weeks pre-foaling to 7 weeks post-foaling. The microbiome data was generated by PCR amplification and sequencing of the V1–V2 regions of the bacterial 16S rRNA genes, while the VOC profile was characterised using headspace solid phase microextraction gas chromatography mass spectrometry. Results The mare faecal microbiota was relatively stable over the periparturient period and most variation was associated with individual mares. A small number of operational taxonomic units were found to be significantly differentially abundant between samples collected before and after foaling. A total of 98 VOCs were identified. The total number of VOCs did not vary significantly between individual mares, weeks of sample collection and feeds available to the mares. Three VOCs (decane, 2-pentylfuran, and oct-2-ene) showed significant increase overtime on linear mixed effects modelling analysis. These results suggest that the mare faecal microbiota is structurally and functionally stable during the periparturient period. The findings also suggest that if changes in the gut microbiota are related to development of colic postpartum, altered risk may be due to inher…
bibliographic citation: Salem et al. (2019) A longitudinal study of the faecal microbiome and metabolome of periparturient mares. PeerJ 7:e6687 https://doi.org/10.7717/peerj.6687
date submitted: 2019-01-15
date accepted: 2019-02-26
issued: 2019-04-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salem
  given name: Shebl E.
author list: Agent
  family name: Hough
  given name: Rachael
author list: Agent
  family name: Probert
  given name: Chris
author list: Agent
  family name: Maddox
  given name: Thomas W.
author list: Agent
  family name: Antczak
  given name: Philipp
author list: Agent
  family name: Ketley
  given name: Julian M.
author list: Agent
  family name: Williams
  given name: Nicola J.
author list: Agent
  family name: Stoneham
  given name: Sarah J.
author list: Agent
  family name: Archer
  given name: Debra C.
doi: 10.7717/peerj.6687
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-03
copyright: © 2019 Salem et al.
attribution name: Salem et al.

Density of intertidal barnacles along their full elevational range of distribution conforms to the abundant-centre hypothesis
type: item
type: AcademicArticle
description: The abundant-centre hypothesis (ACH) predicts that the density of a species should peak at its distribution centre and decrease similarly towards distribution margins. The ACH has been deduced from a theory that postulates that environmental conditions should be most favourable for a species at the centre of its distribution. This idealised density pattern, however, has been supported by limited field studies, as natural patterns are often more complex. It is thus of interest to examine under what conditions compliance with the ACH could be favoured. Such conditions could be smooth environmental gradients with limited habitat patchiness throughout the distribution range of a species. Thus, we tested the ACH by measuring the density of an intertidal barnacle (Semibalanus balanoides) across its full vertical distribution range (from low to high elevations) on a rocky shore with similar substrate properties across elevations. To do a reliable test, we surveyed eight elevation zones applying an equal sampling effort in each zone. Average barnacle density conformed to the ACH, as it peaked at the middle of the vertical distribution range of this species. The same underlying theory predicts a similar unimodal pattern for maximum body size, but this trait was decoupled from density, as maximum barnacle size increased from low to high elevations. Overall, although the ACH is not a universal predictive tool as once envisioned, it may predict some cases well, as shown by this study. Therefore, the ACH should not be discarded completely, and its domain of application should be further evaluated.
format: application/pdf
format: text/html
creator: Ricardo A. Scrosati
creator: Matthew J. Freeman
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6719
publisher: PeerJ Inc.
rights: © 2019 Scrosati and Freeman
abstract: The abundant-centre hypothesis (ACH) predicts that the density of a species should peak at its distribution centre and decrease similarly towards distribution margins. The ACH has been deduced from a theory that postulates that environmental conditions should be most favourable for a species at the centre of its distribution. This idealised density pattern, however, has been supported by limited field studies, as natural patterns are often more complex. It is thus of interest to examine under what conditions compliance with the ACH could be favoured. Such conditions could be smooth environmental gradients with limited habitat patchiness throughout the distribution range of a species. Thus, we tested the ACH by measuring the density of an intertidal barnacle (Semibalanus balanoides) across its full vertical distribution range (from low to high elevations) on a rocky shore with similar substrate properties across elevations. To do a reliable test, we surveyed eight elevation zones applying an equal sampling effort in each zone. Average barnacle density conformed to the ACH, as it peaked at the middle of the vertical distribution range of this species. The same underlying theory predicts a similar unimodal pattern for maximum body size, but this trait was decoupled from density, as maximum barnacle size increased from low to high elevations. Overall, although the ACH is not a universal predictive tool as once envisioned, it may predict some cases well, as shown by this study. Therefore, the ACH should not be discarded completely, and its domain of application should be further evaluated.
bibliographic citation: Scrosati et al. (2019) Density of intertidal barnacles along their full elevational range of distribution conforms to the abundant-centre hypothesis. PeerJ 7:e6719 https://doi.org/10.7717/peerj.6719
date submitted: 2019-01-09
date accepted: 2019-03-04
issued: 2019-04-03
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: Freeman
  given name: Matthew J.
doi: 10.7717/peerj.6719
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-03
copyright: © 2019 Scrosati and Freeman
attribution name: Scrosati and Freeman

Environmental modulation of the proteomic profiles from closely phylogenetically related populations of the red seaweed Plocamium brasiliense
type: item
type: AcademicArticle
description: The genus Plocamium encompasses seaweeds that are widely distributed throughout the world’s oceans, with Plocamium brasiliense found along the tropical and subtropical coasts of the Western Atlantic. This wide distribution can lead to structured populations due to environmental differences (e.g., light levels or temperature), restricted gene flow, and the presence of cryptic species. Abiotic variation can also affect gene expression, which consequently leads to differences in the seaweeds protein profile. This study aimed to analyze the genetic and proteomic profiles of P. brasiliense sampled in two geographically distinct sites on the coastline of Rio de Janeiro state, Brazil: Arraial do Cabo (P1) and Búzios (P2). The genetic profiles of macroalgal specimens from these two sites were indistinguishable as assessed by the markers UPA/23S, rbcL, and COI-5P; however, the protein profiles varied significantly between populations from the two sites. At both sites the ribulose-1,5-biphosphate carboxylase/oxygenase was the most abundant protein found in P. brasiliense specimens. The number of phycobiliproteins differed between both sites with the highest numbers being found at P1, possibly due to water depth. The differences in proteomic profiles of the two nearly identical populations of P. brasiliense suggest that environmental parameters such as light availability and desiccation might induce distinct protein expression, probably as a result of the phenotypic plasticity within this population of seaweed.
format: application/pdf
format: text/html
creator: Gabriela Calegario
creator: Lucas Freitas
creator: Eidy Santos
creator: Bruno Silva
creator: Louisi Oliveira
creator: Gizele Garcia
creator: Cláudia Omachi
creator: Renato Pereira
creator: Cristiane Thompson
creator: Fabiano Thompson
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.6469
publisher: PeerJ Inc.
rights: © 2019 Calegario et al.
abstract: The genus Plocamium encompasses seaweeds that are widely distributed throughout the world’s oceans, with Plocamium brasiliense found along the tropical and subtropical coasts of the Western Atlantic. This wide distribution can lead to structured populations due to environmental differences (e.g., light levels or temperature), restricted gene flow, and the presence of cryptic species. Abiotic variation can also affect gene expression, which consequently leads to differences in the seaweeds protein profile. This study aimed to analyze the genetic and proteomic profiles of P. brasiliense sampled in two geographically distinct sites on the coastline of Rio de Janeiro state, Brazil: Arraial do Cabo (P1) and Búzios (P2). The genetic profiles of macroalgal specimens from these two sites were indistinguishable as assessed by the markers UPA/23S, rbcL, and COI-5P; however, the protein profiles varied significantly between populations from the two sites. At both sites the ribulose-1,5-biphosphate carboxylase/oxygenase was the most abundant protein found in P. brasiliense specimens. The number of phycobiliproteins differed between both sites with the highest numbers being found at P1, possibly due to water depth. The differences in proteomic profiles of the two nearly identical populations of P. brasiliense suggest that environmental parameters such as light availability and desiccation might induce distinct protein expression, probably as a result of the phenotypic plasticity within this population of seaweed.
bibliographic citation: Calegario et al. (2019) Environmental modulation of the proteomic profiles from closely phylogenetically related populations of the red seaweed Plocamium brasiliense. PeerJ 7:e6469 https://doi.org/10.7717/peerj.6469
date submitted: 2018-10-02
date accepted: 2019-01-17
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Calegario
  given name: Gabriela
author list: Agent
  family name: Freitas
  given name: Lucas
author list: Agent
  family name: Santos
  given name: Eidy
author list: Agent
  family name: Silva
  given name: Bruno
author list: Agent
  family name: Oliveira
  given name: Louisi
author list: Agent
  family name: Garcia
  given name: Gizele
author list: Agent
  family name: Omachi
  given name: Cláudia
author list: Agent
  family name: Pereira
  given name: Renato
author list: Agent
  family name: Thompson
  given name: Cristiane
author list: Agent
  family name: Thompson
  given name: Fabiano
doi: 10.7717/peerj.6469
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: © 2019 Calegario et al.
attribution name: Calegario et al.

Reproductive biology of little tunny Euthynnus alletteratus (Rafinesque, 1810) in the southwest Gulf of Mexico
type: item
type: AcademicArticle
description: The aim of this study was to describe the reproductive dynamic of Euthynnus alletteratus in the southwest Gulf of Mexico. The annual variation of the volume fraction occupied by gametes and tissues in gonads were related with main body indexes, such as the gonadosomatic index (IG), the hepatosomatic index (IH), and the nutrition index (IN), and compared with the sea surface temperature. A total of 951 E. alletteratus individuals were sampled, where a sex ratio of 1:1 and a size interval strongly skewed towards organisms with a fork length (LF) of 36–40 cm were observed. The IG showed an increase from March to September with maximum values in April and July. Two clearly defined peaks were observed, and they were consistent with the histological analysis, where the percentage of ripe gametes predominated from April to September. The optimum thermal window for reproductive activity was from 24 to 28 °C. The size of first sex maturity was 34.35 cm of LF for males and 34.60 (LF) for females, without significant difference between sexes.
format: application/pdf
format: text/html
creator: Roberto Cruz-Castán
creator: César Meiners-Mandujano
creator: David Macías
creator: Lourdes Jiménez-Badillo
creator: Sergio Curiel-Ramírez
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.6558
publisher: PeerJ Inc.
rights: © 2019 Cruz-Castán et al.
abstract: The aim of this study was to describe the reproductive dynamic of Euthynnus alletteratus in the southwest Gulf of Mexico. The annual variation of the volume fraction occupied by gametes and tissues in gonads were related with main body indexes, such as the gonadosomatic index (IG), the hepatosomatic index (IH), and the nutrition index (IN), and compared with the sea surface temperature. A total of 951 E. alletteratus individuals were sampled, where a sex ratio of 1:1 and a size interval strongly skewed towards organisms with a fork length (LF) of 36–40 cm were observed. The IG showed an increase from March to September with maximum values in April and July. Two clearly defined peaks were observed, and they were consistent with the histological analysis, where the percentage of ripe gametes predominated from April to September. The optimum thermal window for reproductive activity was from 24 to 28 °C. The size of first sex maturity was 34.35 cm of LF for males and 34.60 (LF) for females, without significant difference between sexes.
bibliographic citation: Cruz-Castán et al. (2019) Reproductive biology of little tunny Euthynnus alletteratus (Rafinesque, 1810) in the southwest Gulf of Mexico. PeerJ 7:e6558 https://doi.org/10.7717/peerj.6558
date submitted: 2018-12-31
date accepted: 2019-02-01
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cruz-Castán
  given name: Roberto
author list: Agent
  family name: Meiners-Mandujano
  given name: César
author list: Agent
  family name: Macías
  given name: David
author list: Agent
  family name: Jiménez-Badillo
  given name: Lourdes
author list: Agent
  family name: Curiel-Ramírez
  given name: Sergio
doi: 10.7717/peerj.6558
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: © 2019 Cruz-Castán et al.
attribution name: Cruz-Castán et al.

Comparison of shallow-water seston among biogenic habitats on tidal flats
type: item
type: AcademicArticle
description: Aquatic structure-formers have the potential to establish mosaics of seston in shallow water if they modify the relative amounts of deposition (or filtration) and resuspension of particles. By sampling surface water adjacent to Lagrangian drifters traveling 0.1 to 2 m above the bottom, we tested the modification of seston in water masses flowing over two biogenic marine species (native eelgrass, Zostera marina; introduced oysters, Crassostrea gigas) in comparison to unstructured tidal flats. Water properties were examined at five intertidal sites in Washington State, USA, each with 27 drifts (three drifts at different stages of the tidal cycle in each of three patches of three habitat types; drift distance 116 m (109SD), duration 24 min (15SD)). At the initiation of each drift, habitat differences in water properties were already apparent: chlorophyll-a and total suspended solid (TSS) concentrations were greater in structured habitats than bare, and TSS was also inversely related to water depth. Water flowed more slowly across eelgrass than other habitat types. As water flowed across each habitat type, TSS generally increased, especially in shallow water, but without habitat differences; chlorophyll-a in these surface-water samples showed no consistent change during drifts. At higher TSS concentrations, quality in terms of organic content declined, and this relationship was not habitat-specific. However, quality in terms of chlorophyll-a concentration increased with TSS, as well as being greater in water over eelgrass than over other habitat types. These results support widespread mobilization of seston in shallow water ebbing or flooding across Washington State’s tidal flats, especially as water passes into patches of biogenic species.
format: application/pdf
format: text/html
creator: Jennifer L. Ruesink
creator: Cinde R. Donoghue
creator: Micah J. Horwith
creator: Alexander T. Lowe
creator: Alan C. Trimble
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Ecohydrology
description: doi:10.7717/peerj.6616
publisher: PeerJ Inc.
rights: © 2019 Ruesink et al.
abstract: Aquatic structure-formers have the potential to establish mosaics of seston in shallow water if they modify the relative amounts of deposition (or filtration) and resuspension of particles. By sampling surface water adjacent to Lagrangian drifters traveling 0.1 to 2 m above the bottom, we tested the modification of seston in water masses flowing over two biogenic marine species (native eelgrass, Zostera marina; introduced oysters, Crassostrea gigas) in comparison to unstructured tidal flats. Water properties were examined at five intertidal sites in Washington State, USA, each with 27 drifts (three drifts at different stages of the tidal cycle in each of three patches of three habitat types; drift distance 116 m (109SD), duration 24 min (15SD)). At the initiation of each drift, habitat differences in water properties were already apparent: chlorophyll-a and total suspended solid (TSS) concentrations were greater in structured habitats than bare, and TSS was also inversely related to water depth. Water flowed more slowly across eelgrass than other habitat types. As water flowed across each habitat type, TSS generally increased, especially in shallow water, but without habitat differences; chlorophyll-a in these surface-water samples showed no consistent change during drifts. At higher TSS concentrations, quality in terms of organic content declined, and this relationship was not habitat-specific. However, quality in terms of chlorophyll-a concentration increased with TSS, as well as being greater in water over eelgrass than over other habitat types. These results support widespread mobilization of seston in shallow water ebbing or flooding across Washington State’s tidal flats, especially as water passes into patches of biogenic species.
bibliographic citation: Ruesink et al. (2019) Comparison of shallow-water seston among biogenic habitats on tidal flats. PeerJ 7:e6616 https://doi.org/10.7717/peerj.6616
date submitted: 2018-09-19
date accepted: 2019-02-11
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ruesink
  given name: Jennifer L.
author list: Agent
  family name: Donoghue
  given name: Cinde R.
author list: Agent
  family name: Horwith
  given name: Micah J.
author list: Agent
  family name: Lowe
  given name: Alexander T.
author list: Agent
  family name: Trimble
  given name: Alan C.
doi: 10.7717/peerj.6616
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: ©2019 Ruesink et al.
attribution name: Ruesink et al.

Prevalence of malocclusion and occlusal traits in the early mixed dentition in Shanghai, China
type: item
type: AcademicArticle
description: Background Epidemiological data on malocclusion among Chinese children are scant. The aim of this study was to provide detailed information on the prevalence of malocclusion in early mixed dentition children in Shanghai, China. Methods A cross-sectional survey was conducted from September 2016 to April 2017, and 2,810 children aged 7- to 9- years were selected from 10 primary schools by cluster random sampling. Several occlusal parameters, including Angle molar relationship, overjet, overbite, open bite, anterior and posterior crossbite, midline displacement, scissors bite, and teeth crowding and spacing, were clinically registered by five calibrated orthodontic dentists. Results We found that 79.4% children presented one or more occlusal anomalies. Angle Class I, Class II and Class III molar relationship were recorded in 42.3%, 50.9% and 5.9% of the sample, respectively. The proportion of Class III increased from 5.0% at age 7 to 7.8% at age 9. In the sagittal plane, increased overjet >3 mm was observed in 40.8% subjects, while the prevalence of severe overjet (>8 mm), anterior edge-to-edge (zero overjet) and anterior crossbite were 5.2%, 8.1% and 10.5%, respectively. Vertically, deep overbite >2/3 overlap was found in 6.2% of the children and open bite in 4.3%. Boys exhibited a higher rate of overbite than girls. For the transversal occlusal anomalies, 36.1% of the children had a midline displacement, which was followed by posterior crossbite (2.6%) and scissors bite (1.0%). Teeth space discrepancies were also common anomalies and anterior crowding (>2 mm) affecting 28.4% of the children, while anterior spacing (>4 mm) affecting 9.5%. Girls showed a higher prevalence of anterior crowding and a lower frequency of teeth spacing than boys. Conclusions Our study demonstrated that malocclusion is prevalent among children in the early mixed dentition, and more health resources should be warranted to meet the challenge of prevention or early intervention of malocclusion.
format: application/pdf
format: text/html
creator: Xin Yu
creator: Hao Zhang
creator: Liangyan Sun
creator: Jie Pan
creator: Yuehua Liu
creator: Li Chen
subject: Dentistry
subject: Epidemiology
subject: Pediatrics
description: doi:10.7717/peerj.6630
publisher: PeerJ Inc.
rights: © 2019 Yu et al.
abstract: Background Epidemiological data on malocclusion among Chinese children are scant. The aim of this study was to provide detailed information on the prevalence of malocclusion in early mixed dentition children in Shanghai, China. Methods A cross-sectional survey was conducted from September 2016 to April 2017, and 2,810 children aged 7- to 9- years were selected from 10 primary schools by cluster random sampling. Several occlusal parameters, including Angle molar relationship, overjet, overbite, open bite, anterior and posterior crossbite, midline displacement, scissors bite, and teeth crowding and spacing, were clinically registered by five calibrated orthodontic dentists. Results We found that 79.4% children presented one or more occlusal anomalies. Angle Class I, Class II and Class III molar relationship were recorded in 42.3%, 50.9% and 5.9% of the sample, respectively. The proportion of Class III increased from 5.0% at age 7 to 7.8% at age 9. In the sagittal plane, increased overjet >3 mm was observed in 40.8% subjects, while the prevalence of severe overjet (>8 mm), anterior edge-to-edge (zero overjet) and anterior crossbite were 5.2%, 8.1% and 10.5%, respectively. Vertically, deep overbite >2/3 overlap was found in 6.2% of the children and open bite in 4.3%. Boys exhibited a higher rate of overbite than girls. For the transversal occlusal anomalies, 36.1% of the children had a midline displacement, which was followed by posterior crossbite (2.6%) and scissors bite (1.0%). Teeth space discrepancies were also common anomalies and anterior crowding (>2 mm) affecting 28.4% of the children, while anterior spacing (>4 mm) affecting 9.5%. Girls showed a higher prevalence of anterior crowding and a lower frequency of teeth spacing than boys. Conclusions Our study demonstrated that malocclusion is prevalent among children in the early mixed dentition, and more health resources should be warranted to meet the challenge of prevention or early intervention of malocclusion.
bibliographic citation: Yu et al. (2019) Prevalence of malocclusion and occlusal traits in the early mixed dentition in Shanghai, China. PeerJ 7:e6630 https://doi.org/10.7717/peerj.6630
date submitted: 2018-07-31
date accepted: 2019-02-15
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Xin
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: Sun
  given name: Liangyan
author list: Agent
  family name: Pan
  given name: Jie
author list: Agent
  family name: Liu
  given name: Yuehua
author list: Agent
  family name: Chen
  given name: Li
doi: 10.7717/peerj.6630
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: ©2019 Yu et al.
attribution name: Yu et al.

On the half-life of thiocyanate in the plasma of the marine fish Amphiprion ocellaris: implications for cyanide detection
type: item
type: AcademicArticle
description: The illegal practice of using cyanide (CN) as a stunning agent to collect fish for both the marine aquarium and live fish food trades has been used throughout the Indo-Pacific for over 50 years. CN fishing is destructive to all life forms within the coral reef ecosystems where it is used and is certainly one of many anthropogenic activities that have led to 95% of the reefs in the Indo-Pacific being labeled at risk for degradation and loss. A field-deployable test for detecting fish caught using CN would assist in combating the use of this destructive practice, however, no reliable and robust test exists. Further, there is little toxicokinetic data available on marine fish to support the development of such a test, yet such data is critical to establishing the concentration range and time scale over which such a test would be viable. This study presents the first direct measurement of the half-life of the metabolite thiocyanate (SCN) after pulsed exposure to CN in a marine fish. SCN was measured in the plasma of Amphiprion ocellaris after exposure to 50 ppm CN for three exposure times (20, 45, and 60 s) using HPLC-UV and a C30 column pre-treated with polyethylene glycol. Plasma SCN levels observed are dose-dependent, reflecting a longer time for conversion of CN to SCN as the dose of CN increases. SCN plasma levels reached a maximum concentration (1.2–2.3 ppm) 12–20 h after exposure to CN. The half-life for the elimination of SCN was 1.01 ± 0.26 days for 45 s exposure and 0.44 ± 0.15 days for 20 s exposure. Fish were also directly exposed to SCN (100 ppm for 11 days) and the observed half-life for SCN elimination was 0.35 ± 0.07 days. Plasma SCN levels did not return to control levels, even after 41 days when exposed to CN but did return to control levels after 48 days when exposed to SCN. The similar half-lives observed for CN and SCN exposure suggests that SCN exposure can be used as a proxy for measuring the rate of SCN elimination following CN exposure. In order…
format: application/pdf
format: text/html
creator: Nancy E. Breen
creator: J. Alexander Bonanno
creator: Sara Hunt
creator: Julia Grossman
creator: Jordan Brown
creator: Hannah Nolte
creator: Andrew L. Rhyne
subject: Conservation Biology
subject: Marine Biology
subject: Toxicology
subject: Ecotoxicology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.6644
publisher: PeerJ Inc.
rights: © 2019 Breen et al.
abstract: The illegal practice of using cyanide (CN) as a stunning agent to collect fish for both the marine aquarium and live fish food trades has been used throughout the Indo-Pacific for over 50 years. CN fishing is destructive to all life forms within the coral reef ecosystems where it is used and is certainly one of many anthropogenic activities that have led to 95% of the reefs in the Indo-Pacific being labeled at risk for degradation and loss. A field-deployable test for detecting fish caught using CN would assist in combating the use of this destructive practice, however, no reliable and robust test exists. Further, there is little toxicokinetic data available on marine fish to support the development of such a test, yet such data is critical to establishing the concentration range and time scale over which such a test would be viable. This study presents the first direct measurement of the half-life of the metabolite thiocyanate (SCN) after pulsed exposure to CN in a marine fish. SCN was measured in the plasma of Amphiprion ocellaris after exposure to 50 ppm CN for three exposure times (20, 45, and 60 s) using HPLC-UV and a C30 column pre-treated with polyethylene glycol. Plasma SCN levels observed are dose-dependent, reflecting a longer time for conversion of CN to SCN as the dose of CN increases. SCN plasma levels reached a maximum concentration (1.2–2.3 ppm) 12–20 h after exposure to CN. The half-life for the elimination of SCN was 1.01 ± 0.26 days for 45 s exposure and 0.44 ± 0.15 days for 20 s exposure. Fish were also directly exposed to SCN (100 ppm for 11 days) and the observed half-life for SCN elimination was 0.35 ± 0.07 days. Plasma SCN levels did not return to control levels, even after 41 days when exposed to CN but did return to control levels after 48 days when exposed to SCN. The similar half-lives observed for CN and SCN exposure suggests that SCN exposure can be used as a proxy for measuring the rate of SCN elimination following CN exposure. In order…
bibliographic citation: Breen et al. (2019) On the half-life of thiocyanate in the plasma of the marine fish Amphiprion ocellaris: implications for cyanide detection. PeerJ 7:e6644 https://doi.org/10.7717/peerj.6644
date submitted: 2018-10-18
date accepted: 2019-02-19
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Breen
  given name: Nancy E.
author list: Agent
  family name: Bonanno
  given name: J. Alexander
author list: Agent
  family name: Hunt
  given name: Sara
author list: Agent
  family name: Grossman
  given name: Julia
author list: Agent
  family name: Brown
  given name: Jordan
author list: Agent
  family name: Nolte
  given name: Hannah
author list: Agent
  family name: Rhyne
  given name: Andrew L.
doi: 10.7717/peerj.6644
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: © 2019 Breen et al.
attribution name: Breen et al.

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