PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Saccades and handedness interact to affect scene memory
items: Effects of sex and joint action on voluntary activation
items: A taxonomic reassessment of Piramys auffenbergi, a neglected turtle from the late Miocene of Piram Island, Gujarat, India
items: Intake of supplementary food during pregnancy and lactation and its association with child nutrition in Timor Leste
items: Do mothers also “manipulate” grandparental care?
items: Ecological divergence of burying beetles into the forest canopy
items: Greenhouse gas flux with reflooding of a drained salt marsh soil
items: Skin bacterial diversity is higher on lizards than sympatric frogs in tropical Australia
items: Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications
items: Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions

Saccades and handedness interact to affect scene memory
type: item
type: AcademicArticle
description: Repetitive saccades benefit memory when executed before retrieval, with greatest effects for episodic memory in consistent-handers. Questions remain including how saccades affect scene memory, an important visual component of episodic memory. The present study tested how repetitive saccades affect working and recognition memory for novel scenes. Handedness direction (left–right) and degree (strong/consistent vs. mixed/inconsistent) was measured by raw and absolute laterality quotients respectively from an 8-question handedness inventory completed by 111 adults. Each then performed either 30 s of repetitive horizontal saccades or fixation before or after tasks of scene working memory and scene recognition. Regression with criterion variables of overall percent correct accuracy and d-prime sensitivity showed that when saccades were made before working memory, there was better overall accuracy as a function of increased direction but not degree of handedness. Subjects who made saccades before working memory also performed worse during subsequent recognition memory, while subjects who fixated or made saccades after the working memory task performed better. Saccades made before recognition resulted in recognition accuracy that was better (Cohen’s d = 0.3729), but not significantly different from fixation before recognition. The results demonstrate saccades and handedness interact to affect scene memory with larger effects on encoding than recognition. Saccades before scene encoding in working memory are detrimental to short- and long-term memory, especially for those who are not consistently right-handed, while saccade execution before scene recognition does not appear to benefit recognition accuracy. The findings are discussed with respect to theories of interhemispheric interaction and control of visuospatial attention.
format: application/pdf
format: text/html
creator: Timothy M. Ellmore
creator: Bridget Mackin
creator: Kenneth Ng
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.5969
publisher: PeerJ Inc.
rights: © 2018 Ellmore et al.
abstract: Repetitive saccades benefit memory when executed before retrieval, with greatest effects for episodic memory in consistent-handers. Questions remain including how saccades affect scene memory, an important visual component of episodic memory. The present study tested how repetitive saccades affect working and recognition memory for novel scenes. Handedness direction (left–right) and degree (strong/consistent vs. mixed/inconsistent) was measured by raw and absolute laterality quotients respectively from an 8-question handedness inventory completed by 111 adults. Each then performed either 30 s of repetitive horizontal saccades or fixation before or after tasks of scene working memory and scene recognition. Regression with criterion variables of overall percent correct accuracy and d-prime sensitivity showed that when saccades were made before working memory, there was better overall accuracy as a function of increased direction but not degree of handedness. Subjects who made saccades before working memory also performed worse during subsequent recognition memory, while subjects who fixated or made saccades after the working memory task performed better. Saccades made before recognition resulted in recognition accuracy that was better (Cohen’s d = 0.3729), but not significantly different from fixation before recognition. The results demonstrate saccades and handedness interact to affect scene memory with larger effects on encoding than recognition. Saccades before scene encoding in working memory are detrimental to short- and long-term memory, especially for those who are not consistently right-handed, while saccade execution before scene recognition does not appear to benefit recognition accuracy. The findings are discussed with respect to theories of interhemispheric interaction and control of visuospatial attention.
bibliographic citation: Ellmore et al. (2018) Saccades and handedness interact to affect scene memory. PeerJ 6:e5969 https://doi.org/10.7717/peerj.5969
date submitted: 2018-06-26
date accepted: 2018-10-21
issued: 2018-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ellmore
  given name: Timothy M.
author list: Agent
  family name: Mackin
  given name: Bridget
author list: Agent
  family name: Ng
  given name: Kenneth
doi: 10.7717/peerj.5969
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-15
copyright: ©2018 Ellmore et al.
attribution name: Ellmore et al.

Effects of sex and joint action on voluntary activation
type: item
type: AcademicArticle
description: The current study tested the hypothesis that voluntary activation during maximal voluntary contraction (MVC) conditionally depends on sex and joint action. Twenty-eight healthy adults (14 of each sex) performed knee extensor MVC and plantar flexor MVC at extended and flexed knee positions. Voluntary activation during MVC was assessed using a twitch interpolation technique. The voluntary activation during plantar flexor MVC at the extended knee position was significantly lower (P = 0.020, 95% confidence interval 1.4 to 14.6, Cohen’s d for between-subject design = 0.94) in women (88.3% ± 10.0%) than in men (96.2% ± 6.6%). In contrast, no significant sex differences were shown in the voluntary activation during knee extensor MVC (93.7% ± 5.9% (women) vs. 95.0% ± 3.9% (men)) and during plantar flexor MVC at the flexed knee position (90.4% ± 12.2% (women) vs. 96.8% ± 5.6% (men)). The voluntary activation during knee extensor MVC was significantly higher (P = 0.001, 95% confidence interval 2.1 to 8.8, Cohen’s d for within-subject design = 0.69) than that during plantar flexor MVC at the extended knee position in women, whereas the corresponding difference was not observed in men. The results revealed that the existence of sex difference in the voluntary activation during MVC depends on joint action and joint angle.
format: application/pdf
format: text/html
creator: Ryoichi Ema
creator: Momoka Suzuki
creator: Emi Kawaguchi
creator: Itaru Saito
creator: Ryota Akagi
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.5968
publisher: PeerJ Inc.
rights: © 2018 Ema et al.
abstract: The current study tested the hypothesis that voluntary activation during maximal voluntary contraction (MVC) conditionally depends on sex and joint action. Twenty-eight healthy adults (14 of each sex) performed knee extensor MVC and plantar flexor MVC at extended and flexed knee positions. Voluntary activation during MVC was assessed using a twitch interpolation technique. The voluntary activation during plantar flexor MVC at the extended knee position was significantly lower (P = 0.020, 95% confidence interval 1.4 to 14.6, Cohen’s d for between-subject design = 0.94) in women (88.3% ± 10.0%) than in men (96.2% ± 6.6%). In contrast, no significant sex differences were shown in the voluntary activation during knee extensor MVC (93.7% ± 5.9% (women) vs. 95.0% ± 3.9% (men)) and during plantar flexor MVC at the flexed knee position (90.4% ± 12.2% (women) vs. 96.8% ± 5.6% (men)). The voluntary activation during knee extensor MVC was significantly higher (P = 0.001, 95% confidence interval 2.1 to 8.8, Cohen’s d for within-subject design = 0.69) than that during plantar flexor MVC at the extended knee position in women, whereas the corresponding difference was not observed in men. The results revealed that the existence of sex difference in the voluntary activation during MVC depends on joint action and joint angle.
bibliographic citation: Ema et al. (2018) Effects of sex and joint action on voluntary activation. PeerJ 6:e5968 https://doi.org/10.7717/peerj.5968
date submitted: 2018-06-01
date accepted: 2018-10-19
issued: 2018-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ema
  given name: Ryoichi
author list: Agent
  family name: Suzuki
  given name: Momoka
author list: Agent
  family name: Kawaguchi
  given name: Emi
author list: Agent
  family name: Saito
  given name: Itaru
author list: Agent
  family name: Akagi
  given name: Ryota
doi: 10.7717/peerj.5968
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-15
copyright: ©2018 Ema et al.
attribution name: Ema et al.

A taxonomic reassessment of Piramys auffenbergi, a neglected turtle from the late Miocene of Piram Island, Gujarat, India
type: item
type: AcademicArticle
description: Background Piramys auffenbergi was described as an emydine turtle based on a well-preserved skull retrieved from late Miocene deposits exposed on Piram Island, India. The description and figures provided in the original publication are vague and do not support assignment to Emydinae. This taxon has mostly been ignored by subsequent authors. Material and Methods We reexamine the holotype specimen, provide an extensive description and diagnosis for Piramys auffenbergi, and include this taxon in a global character-taxon matrix for Pleurodira. Results The presence of a processus trochlearis pterygoidei conclusively shows pleurodiran affinities for Piramys auffenbergi. Inclusion of this taxon in a phylogenetic analysis retrieves it within Stereogenyini closely related to the Asian taxa Shweboemys pilgrimi and Brontochelys gaffneyi. Discussion Our reexamination of the holotype of Piramys auffenbergi confidently rejects the original assessment of this taxon as an emydine testudinoid and conclusively shows affinities with the pleurodiran clade Stereogenyini instead. Even though most taxa from this lineage are thought to be coastal turtles, all Asian stereogenyines were collected from continental deposits, suggesting a more diverse paleoecology for the group.
format: application/pdf
format: text/html
creator: Gabriel S. Ferreira
creator: Saswati Bandyopadhyay
creator: Walter G. Joyce
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.5938
publisher: PeerJ Inc.
rights: © 2018 Ferreira et al.
abstract: Background Piramys auffenbergi was described as an emydine turtle based on a well-preserved skull retrieved from late Miocene deposits exposed on Piram Island, India. The description and figures provided in the original publication are vague and do not support assignment to Emydinae. This taxon has mostly been ignored by subsequent authors. Material and Methods We reexamine the holotype specimen, provide an extensive description and diagnosis for Piramys auffenbergi, and include this taxon in a global character-taxon matrix for Pleurodira. Results The presence of a processus trochlearis pterygoidei conclusively shows pleurodiran affinities for Piramys auffenbergi. Inclusion of this taxon in a phylogenetic analysis retrieves it within Stereogenyini closely related to the Asian taxa Shweboemys pilgrimi and Brontochelys gaffneyi. Discussion Our reexamination of the holotype of Piramys auffenbergi confidently rejects the original assessment of this taxon as an emydine testudinoid and conclusively shows affinities with the pleurodiran clade Stereogenyini instead. Even though most taxa from this lineage are thought to be coastal turtles, all Asian stereogenyines were collected from continental deposits, suggesting a more diverse paleoecology for the group.
bibliographic citation: Ferreira et al. (2018) A taxonomic reassessment of Piramys auffenbergi, a neglected turtle from the late Miocene of Piram Island, Gujarat, India. PeerJ 6:e5938 https://doi.org/10.7717/peerj.5938
date submitted: 2018-08-17
date accepted: 2018-10-15
issued: 2018-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferreira
  given name: Gabriel S.
author list: Agent
  family name: Bandyopadhyay
  given name: Saswati
author list: Agent
  family name: Joyce
  given name: Walter G.
doi: 10.7717/peerj.5938
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-15
copyright: © 2018 Ferreira et al.
attribution name: Ferreira et al.

Intake of supplementary food during pregnancy and lactation and its association with child nutrition in Timor Leste
type: item
type: AcademicArticle
description: Abstract There is little evidence on maternal consumption of supplementary food on nutritional status of children. The objectives of this study were to measure the prevalence and determinants of supplementary food intake during pregnancy and lactation, and their association with nutritional status of under-five children in Timor Leste. Methods Cross-sectional data from Timor Leste Demographic and Health Survey on 5,993 mother (15–49 years) child dyads (<5 years) were included in the analysis. Self-reported intake of supplementary food intake was the explanatory variable. Child’s nutritional status was assessed by stunting, wasting, and underweight and categorized according to WHO recommendations. Results The prevalence of taking supplementary food during pregnancy and lactation was, respectively, 29.1% (95% CI [27.2–31.0]) 31.0% (95% CI [29.1–33.0]), and that of taking iron supplement during pregnancy was close to three-fifths (63.1%, 95% CI [60.9–65.3]). The odds of taking supplementary food during pregnancy and lactation were lower among those in the younger age groups and higher among urban residents. Compared with mothers who had supplementary food during pregnancy and lactation, those did not have had respectively 1.36 (OR = 1.360, 95% CI [1.191–2.072]) and 1.15 times (OR = 1.152, 95% CI [1.019–1.754]) higher odds of having stunted, and 1.30 (OR = 1.307, 95% CI [1.108–1.853]) and 1.43 (OR = 1.426, 95% CI [1.140–1.863]) times higher odds of having underweight children. Those who had none of the supplements had respectively 1.67 (OR = 1.674, 95% CI [1.118–2.087]) and 1.63 (OR = 1.631, 95% CI [1.130–2.144]) times higher odds of having stunted and underweight children. Conclusion A great majority of the mothers in Timor Leste are not taking supplementary food during pregnancy and lactation. We found a positive relationship between supplementary food intake during pregnancy and lactation with stunting and wasting among under-five children.
format: application/pdf
format: text/html
creator: Sanni Yaya
creator: Ruoxi Wang
creator: Shangfeng Tang
creator: Bishwajit Ghose
subject: Global Health
subject: Nutrition
subject: Public Health
subject: Women's Health
description: doi:10.7717/peerj.5935
publisher: PeerJ Inc.
rights: © 2018 Yaya et al.
abstract: Abstract There is little evidence on maternal consumption of supplementary food on nutritional status of children. The objectives of this study were to measure the prevalence and determinants of supplementary food intake during pregnancy and lactation, and their association with nutritional status of under-five children in Timor Leste. Methods Cross-sectional data from Timor Leste Demographic and Health Survey on 5,993 mother (15–49 years) child dyads (<5 years) were included in the analysis. Self-reported intake of supplementary food intake was the explanatory variable. Child’s nutritional status was assessed by stunting, wasting, and underweight and categorized according to WHO recommendations. Results The prevalence of taking supplementary food during pregnancy and lactation was, respectively, 29.1% (95% CI [27.2–31.0]) 31.0% (95% CI [29.1–33.0]), and that of taking iron supplement during pregnancy was close to three-fifths (63.1%, 95% CI [60.9–65.3]). The odds of taking supplementary food during pregnancy and lactation were lower among those in the younger age groups and higher among urban residents. Compared with mothers who had supplementary food during pregnancy and lactation, those did not have had respectively 1.36 (OR = 1.360, 95% CI [1.191–2.072]) and 1.15 times (OR = 1.152, 95% CI [1.019–1.754]) higher odds of having stunted, and 1.30 (OR = 1.307, 95% CI [1.108–1.853]) and 1.43 (OR = 1.426, 95% CI [1.140–1.863]) times higher odds of having underweight children. Those who had none of the supplements had respectively 1.67 (OR = 1.674, 95% CI [1.118–2.087]) and 1.63 (OR = 1.631, 95% CI [1.130–2.144]) times higher odds of having stunted and underweight children. Conclusion A great majority of the mothers in Timor Leste are not taking supplementary food during pregnancy and lactation. We found a positive relationship between supplementary food intake during pregnancy and lactation with stunting and wasting among under-five children.
bibliographic citation: Yaya et al. (2018) Intake of supplementary food during pregnancy and lactation and its association with child nutrition in Timor Leste. PeerJ 6:e5935 https://doi.org/10.7717/peerj.5935
date submitted: 2018-06-29
date accepted: 2018-10-15
issued: 2018-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yaya
  given name: Sanni
author list: Agent
  family name: Wang
  given name: Ruoxi
author list: Agent
  family name: Tang
  given name: Shangfeng
author list: Agent
  family name: Ghose
  given name: Bishwajit
doi: 10.7717/peerj.5935
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-15
copyright: © 2018 Yaya et al.
attribution name: Yaya et al.

Do mothers also “manipulate” grandparental care?
type: item
type: AcademicArticle
description: Paternity uncertainty has proven to be a robust ultimate hypothesis for predicting the higher investment in grandchildren observed among maternal grandparents compared to that of the paternal grandparents. Yet the proximate mechanisms for generating such preferred biases in grandparental investment remain unclear. Here we address two different questions for better understanding the proximate mechanisms leading to the observed bias in grandparental investments: (i) is there a larger emphasis on resemblance descriptions (between grandchildren and grandparent) among daughters than among sons, and (ii) do mothers really believe that their offspring more resemble their parents, that is, the children’s grandparents, than fathers do? From questioning grandparents, we find that daughters more often and more intensely than sons express opinions about grandchild–grandparent resemblance. Moreover, daughters also seem to believe that their children more resemble their grandmother than sons do. The latter is, however, not the case for beliefs about children’s resemblance to grandfathers. In sum, our results suggest that even in a population of Norwegians, strongly influenced by ideas concerning gender equality, there exist a sexual bias among parents in opinions and descriptions about grandchild–grandparent resemblance. This resemblance bias, which echoes that of mothers biasing resemblance descriptions of newborns to putative fathers, does not seem to represent a conscious manipulation. Yet it could be instrumental for influencing grandparental investments. We believe that a “manipulative mother hypothesis” might parsimoniously account for many of the results relating to biased alloparenting hitherto not entirely explained by “the paternity uncertainty hypothesis.”
format: application/pdf
format: text/html
creator: Mari V. Busch
creator: Sandra Olaisen
creator: Ina Jeanette Bruksås
creator: Ivar Folstad
subject: Evolutionary Studies
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.5924
publisher: PeerJ Inc.
rights: © 2018 Busch et al.
abstract: Paternity uncertainty has proven to be a robust ultimate hypothesis for predicting the higher investment in grandchildren observed among maternal grandparents compared to that of the paternal grandparents. Yet the proximate mechanisms for generating such preferred biases in grandparental investment remain unclear. Here we address two different questions for better understanding the proximate mechanisms leading to the observed bias in grandparental investments: (i) is there a larger emphasis on resemblance descriptions (between grandchildren and grandparent) among daughters than among sons, and (ii) do mothers really believe that their offspring more resemble their parents, that is, the children’s grandparents, than fathers do? From questioning grandparents, we find that daughters more often and more intensely than sons express opinions about grandchild–grandparent resemblance. Moreover, daughters also seem to believe that their children more resemble their grandmother than sons do. The latter is, however, not the case for beliefs about children’s resemblance to grandfathers. In sum, our results suggest that even in a population of Norwegians, strongly influenced by ideas concerning gender equality, there exist a sexual bias among parents in opinions and descriptions about grandchild–grandparent resemblance. This resemblance bias, which echoes that of mothers biasing resemblance descriptions of newborns to putative fathers, does not seem to represent a conscious manipulation. Yet it could be instrumental for influencing grandparental investments. We believe that a “manipulative mother hypothesis” might parsimoniously account for many of the results relating to biased alloparenting hitherto not entirely explained by “the paternity uncertainty hypothesis.”
bibliographic citation: Busch et al. (2018) Do mothers also “manipulate” grandparental care?. PeerJ 6:e5924 https://doi.org/10.7717/peerj.5924
date submitted: 2018-08-23
date accepted: 2018-10-14
issued: 2018-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Busch
  given name: Mari V.
author list: Agent
  family name: Olaisen
  given name: Sandra
author list: Agent
  family name: Bruksås
  given name: Ina Jeanette
author list: Agent
  family name: Folstad
  given name: Ivar
doi: 10.7717/peerj.5924
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-15
copyright: © 2018 Busch et al.
attribution name: Busch et al.

Ecological divergence of burying beetles into the forest canopy
type: item
type: AcademicArticle
description: Closely related species with overlapping geographic ranges encounter a significant challenge: they share many ecological traits and preferences but must partition resources to coexist. In Ontario, potentially eleven species of carrion beetles (Coleoptera: Silphidae) live together and require vertebrate carrion for reproduction. Their reliance on an ephemeral and uncommon resource that is unpredictable in space and time is thought to create intense intra- and interspecific competition. Evidence suggests that burying beetle species reduce competition by partitioning carrion for breeding across different habitats, temperatures, and seasons. Here, we test predictions of an alternative axis for partitioning carrion: vertical partitioning between the ground and forest canopy. We conducted a survey of carrion beetles from May to July 2016 at the Queen’s University Biological Station across 50 randomly generated points using baited lethal traps at zero and six metres. Ground traps yielded more species and individuals compared to those in the canopy, and the number of individuals and species caught increased through the season in both trap types. Ground and canopy traps were accurately distinguished by the presence or absence of three species: ground traps contained more Nicrophorus orbicollis and Necrophila americana, while canopy traps contained more Nicrophorus pustulatus. We trapped 253 N. pustulatus in the canopy, but only 60 on the ground. N. pustulatus is thought to be rare across its geographic range, but our results suggest it is uniquely common in canopy habitats, demonstrating a vertical partitioning of habitat and resources. Our results are consistent with N. pustulatus having diverged into canopy habitats as a strategy to coexist with closely related sympatric species when competing for similar resources. We still, however, do not know the traits that allow N. pustulatus to flourish in the canopy, exactly how N. pustulatus uses canopy resources for breeding, or …
format: application/pdf
format: text/html
creator: Jillian D. Wettlaufer
creator: Kevin W. Burke
creator: Adam Schizkoske
creator: David V. Beresford
creator: Paul R. Martin
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
description: doi:10.7717/peerj.5829
publisher: PeerJ Inc.
rights: © 2018 Wettlaufer et al.
abstract: Closely related species with overlapping geographic ranges encounter a significant challenge: they share many ecological traits and preferences but must partition resources to coexist. In Ontario, potentially eleven species of carrion beetles (Coleoptera: Silphidae) live together and require vertebrate carrion for reproduction. Their reliance on an ephemeral and uncommon resource that is unpredictable in space and time is thought to create intense intra- and interspecific competition. Evidence suggests that burying beetle species reduce competition by partitioning carrion for breeding across different habitats, temperatures, and seasons. Here, we test predictions of an alternative axis for partitioning carrion: vertical partitioning between the ground and forest canopy. We conducted a survey of carrion beetles from May to July 2016 at the Queen’s University Biological Station across 50 randomly generated points using baited lethal traps at zero and six metres. Ground traps yielded more species and individuals compared to those in the canopy, and the number of individuals and species caught increased through the season in both trap types. Ground and canopy traps were accurately distinguished by the presence or absence of three species: ground traps contained more Nicrophorus orbicollis and Necrophila americana, while canopy traps contained more Nicrophorus pustulatus. We trapped 253 N. pustulatus in the canopy, but only 60 on the ground. N. pustulatus is thought to be rare across its geographic range, but our results suggest it is uniquely common in canopy habitats, demonstrating a vertical partitioning of habitat and resources. Our results are consistent with N. pustulatus having diverged into canopy habitats as a strategy to coexist with closely related sympatric species when competing for similar resources. We still, however, do not know the traits that allow N. pustulatus to flourish in the canopy, exactly how N. pustulatus uses canopy resources for breeding, or …
bibliographic citation: Wettlaufer et al. (2018) Ecological divergence of burying beetles into the forest canopy. PeerJ 6:e5829 https://doi.org/10.7717/peerj.5829
date submitted: 2017-12-01
date accepted: 2018-09-26
issued: 2018-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wettlaufer
  given name: Jillian D.
author list: Agent
  family name: Burke
  given name: Kevin W.
author list: Agent
  family name: Schizkoske
  given name: Adam
author list: Agent
  family name: Beresford
  given name: David V.
author list: Agent
  family name: Martin
  given name: Paul R.
doi: 10.7717/peerj.5829
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-15
copyright: © 2018 Wettlaufer et al.
attribution name: Wettlaufer et al.

Greenhouse gas flux with reflooding of a drained salt marsh soil
type: item
type: AcademicArticle
description: Salt marshes are highly effective carbon (C) sinks and bury more C per square meter annually than any other ecosystem. Reclamation and anthropogenic impacts, however, have resulted in extensive losses of salt marshes. Carbon credits can be generated and sold by restoring marshes, but only if C sequestration and net reductions in greenhouse gases (GHG) are reliably quantified. Restored marshes, however, may exhibit different patterns of GHG emissions than natural marshes and it is possible that they could temporarily become sources of N2O even in the usually N-limited estuarine environment. Research on short-term GHG flux following salt marsh restoration is limited to studies of two restored marshes which examined GHG flux more than six months after the return of tidal flooding. Here we report on a laboratory experiment in which soil cores collected from a drained agricultural marsh on the St. Lawrence Estuary were flooded with estuary water. Gas flux measurements immediately after flooding revealed small increases in N2O and CH4, but a large decline in CO2 yielding, from a climatic perspective, a net cooling effect over the observation period. In addition to restoring the land’s capacity to sequester C once a marsh develops, returning tidal flooding thus appears to have the added benefit of stemming large ongoing C losses. With more than 400 km2 of undeveloped dykeland, Eastern Canada is well positioned to restore large sections of marsh and contribute to reducing atmospheric CO2 concentrations.
format: application/pdf
format: text/html
creator: Jan T. Wollenberg
creator: Asim Biswas
creator: Gail L. Chmura
subject: Ecosystem Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.5659
publisher: PeerJ Inc.
rights: © 2018 Wollenberg et al.
abstract: Salt marshes are highly effective carbon (C) sinks and bury more C per square meter annually than any other ecosystem. Reclamation and anthropogenic impacts, however, have resulted in extensive losses of salt marshes. Carbon credits can be generated and sold by restoring marshes, but only if C sequestration and net reductions in greenhouse gases (GHG) are reliably quantified. Restored marshes, however, may exhibit different patterns of GHG emissions than natural marshes and it is possible that they could temporarily become sources of N2O even in the usually N-limited estuarine environment. Research on short-term GHG flux following salt marsh restoration is limited to studies of two restored marshes which examined GHG flux more than six months after the return of tidal flooding. Here we report on a laboratory experiment in which soil cores collected from a drained agricultural marsh on the St. Lawrence Estuary were flooded with estuary water. Gas flux measurements immediately after flooding revealed small increases in N2O and CH4, but a large decline in CO2 yielding, from a climatic perspective, a net cooling effect over the observation period. In addition to restoring the land’s capacity to sequester C once a marsh develops, returning tidal flooding thus appears to have the added benefit of stemming large ongoing C losses. With more than 400 km2 of undeveloped dykeland, Eastern Canada is well positioned to restore large sections of marsh and contribute to reducing atmospheric CO2 concentrations.
bibliographic citation: Wollenberg et al. (2018) Greenhouse gas flux with reflooding of a drained salt marsh soil. PeerJ 6:e5659 https://doi.org/10.7717/peerj.5659
date submitted: 2018-03-07
date accepted: 2018-08-29
issued: 2018-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wollenberg
  given name: Jan T.
author list: Agent
  family name: Biswas
  given name: Asim
author list: Agent
  family name: Chmura
  given name: Gail L.
doi: 10.7717/peerj.5659
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-15
copyright: ©2018 Wollenberg et al.
attribution name: Wollenberg et al.

Skin bacterial diversity is higher on lizards than sympatric frogs in tropical Australia
type: item
type: AcademicArticle
description: Animal skin acts as a barrier between the organism and its environment and provides the first line of defense against invading pathogens. Thus, skin surfaces harbor communities of microbes that are interacting with both the host and its environment. Amphibian skin bacteria form distinct communities closely tied to their host species, but few studies have compared bacterial communities between amphibians and other, non-amphibian sympatric animals. Notably, skin microbes on reptiles have gained little attention. We used next-generation sequencing technology to describe bacterial communities on the skin of three lizard species and compared them to bacteria on six cohabiting frog species in the Northern Territory of Australia. We found bacterial communities had higher richness and diversity on lizards than frogs, with different community composition between reptiles and amphibians and among species. Core bacteria on the three lizard species overlapped by over 100 operational taxonomic units. The bacterial communities were similar within species of frogs and lizards, but the communities tended to be more similar between lizard species than between frog species and when comparing lizards with frogs. The diverse bacteria found on lizards invites further questions on how and how well reptiles interact with microorganisms through their scaly skin.
format: application/pdf
format: text/html
creator: Chava L. Weitzman
creator: Karen Gibb
creator: Keith Christian
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.5960
publisher: PeerJ Inc.
rights: © 2018 Weitzman et al.
abstract: Animal skin acts as a barrier between the organism and its environment and provides the first line of defense against invading pathogens. Thus, skin surfaces harbor communities of microbes that are interacting with both the host and its environment. Amphibian skin bacteria form distinct communities closely tied to their host species, but few studies have compared bacterial communities between amphibians and other, non-amphibian sympatric animals. Notably, skin microbes on reptiles have gained little attention. We used next-generation sequencing technology to describe bacterial communities on the skin of three lizard species and compared them to bacteria on six cohabiting frog species in the Northern Territory of Australia. We found bacterial communities had higher richness and diversity on lizards than frogs, with different community composition between reptiles and amphibians and among species. Core bacteria on the three lizard species overlapped by over 100 operational taxonomic units. The bacterial communities were similar within species of frogs and lizards, but the communities tended to be more similar between lizard species than between frog species and when comparing lizards with frogs. The diverse bacteria found on lizards invites further questions on how and how well reptiles interact with microorganisms through their scaly skin.
bibliographic citation: Weitzman et al. (2018) Skin bacterial diversity is higher on lizards than sympatric frogs in tropical Australia. PeerJ 6:e5960 https://doi.org/10.7717/peerj.5960
date submitted: 2018-06-05
date accepted: 2018-10-18
issued: 2018-11-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weitzman
  given name: Chava L.
author list: Agent
  family name: Gibb
  given name: Karen
author list: Agent
  family name: Christian
  given name: Keith
doi: 10.7717/peerj.5960
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-14
copyright: ©2018 Weitzman et al.
attribution name: Weitzman et al.

Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications
type: item
type: AcademicArticle
description: The owlflies (Family Ascalaphidae) belong to the Neuroptera but are often mistaken as dragonflies because of morphological characters. To date, only three mitochondrial genomes of Ascalaphidae, namely Libelloides macaronius; Ascaloptynx appendiculatus; Ascalohybris subjacens, are published in GenBank, meaning that they are greatly under-represented in comparison with the 430 described species reported in this family. In this study, we sequenced and described the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae). The total length of the S. longialata mitogenome was 15,911 bp, which is the longest known to date among the available family members of Ascalaphidae. However, the size of each gene was similar to the other three Ascalaphidae species. The S. longialata mitogenome included a transposition of tRNACys and tRNATrp genes and formed an unusual gene arrangement tRNACys-tRNATrp-tRNATyr (CWY). It is likely that the transposition occurred by a duplication of both genes followed by random loss of partial duplicated genes. The nucleotide composition of the S. longialata mitogenome was as follows: A = 41.0%, T = 33.8%, C = 15.5%, G = 9.7%. Both Bayesian inference and ML analyses strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.
format: application/pdf
format: text/html
creator: Xin-Yan Gao
creator: Yin-Yin Cai
creator: Dan-Na Yu
creator: Kenneth B. Storey
creator: Jia-Yong Zhang
subject: Entomology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.5914
publisher: PeerJ Inc.
rights: © 2018 Gao et al.
abstract: The owlflies (Family Ascalaphidae) belong to the Neuroptera but are often mistaken as dragonflies because of morphological characters. To date, only three mitochondrial genomes of Ascalaphidae, namely Libelloides macaronius; Ascaloptynx appendiculatus; Ascalohybris subjacens, are published in GenBank, meaning that they are greatly under-represented in comparison with the 430 described species reported in this family. In this study, we sequenced and described the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae). The total length of the S. longialata mitogenome was 15,911 bp, which is the longest known to date among the available family members of Ascalaphidae. However, the size of each gene was similar to the other three Ascalaphidae species. The S. longialata mitogenome included a transposition of tRNACys and tRNATrp genes and formed an unusual gene arrangement tRNACys-tRNATrp-tRNATyr (CWY). It is likely that the transposition occurred by a duplication of both genes followed by random loss of partial duplicated genes. The nucleotide composition of the S. longialata mitogenome was as follows: A = 41.0%, T = 33.8%, C = 15.5%, G = 9.7%. Both Bayesian inference and ML analyses strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.
bibliographic citation: Gao et al. (2018) Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications. PeerJ 6:e5914 https://doi.org/10.7717/peerj.5914
date submitted: 2018-06-08
date accepted: 2018-10-10
issued: 2018-11-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Xin-Yan
author list: Agent
  family name: Cai
  given name: Yin-Yin
author list: Agent
  family name: Yu
  given name: Dan-Na
author list: Agent
  family name: Storey
  given name: Kenneth B.
author list: Agent
  family name: Zhang
  given name: Jia-Yong
doi: 10.7717/peerj.5914
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-14
copyright: © 2018 Gao et al.
attribution name: Gao et al.

Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions
type: item
type: AcademicArticle
description: Scorpions have evolved a variety of toxins with a plethora of biological targets, but characterizing their evolution has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships grounded in modern, genome-scale datasets. Disagreements over scorpion higher-level systematics have also incurred challenges to previous interpretations of venom families as ancestral or derived. To redress these gaps, we assessed the phylogenomic relationships of scorpions using the most comprehensive taxonomic sampling to date. We surveyed genomic resources for the incidence of calcins (a type of calcium channel toxin), which were previously known only from 16 scorpion species. Here, we show that calcins are diverse, but phylogenetically restricted only to parvorder Iurida, one of the two basal branches of scorpions. The other branch of scorpions, Buthida, bear the related LKTx toxins (absent in Iurida), but lack calcins entirely. Analysis of sequences and molecular models demonstrates remarkable phylogenetic inertia within both calcins and LKTx genes. These results provide the first synapomorphies (shared derived traits) for the recently redefined clades Buthida and Iurida, constituting the only known case of such traits defined from the morphology of molecules.
format: application/pdf
format: text/html
creator: Carlos E. Santibáñez-López
creator: Ricardo Kriebel
creator: Jesús A. Ballesteros
creator: Nathaniel Rush
creator: Zachary Witter
creator: John Williams
creator: Daniel A. Janies
creator: Prashant P. Sharma
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.5902
publisher: PeerJ Inc.
rights: © 2018 Santibáñez-López et al.
abstract: Scorpions have evolved a variety of toxins with a plethora of biological targets, but characterizing their evolution has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships grounded in modern, genome-scale datasets. Disagreements over scorpion higher-level systematics have also incurred challenges to previous interpretations of venom families as ancestral or derived. To redress these gaps, we assessed the phylogenomic relationships of scorpions using the most comprehensive taxonomic sampling to date. We surveyed genomic resources for the incidence of calcins (a type of calcium channel toxin), which were previously known only from 16 scorpion species. Here, we show that calcins are diverse, but phylogenetically restricted only to parvorder Iurida, one of the two basal branches of scorpions. The other branch of scorpions, Buthida, bear the related LKTx toxins (absent in Iurida), but lack calcins entirely. Analysis of sequences and molecular models demonstrates remarkable phylogenetic inertia within both calcins and LKTx genes. These results provide the first synapomorphies (shared derived traits) for the recently redefined clades Buthida and Iurida, constituting the only known case of such traits defined from the morphology of molecules.
bibliographic citation: Santibáñez-López et al. (2018) Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions. PeerJ 6:e5902 https://doi.org/10.7717/peerj.5902
date submitted: 2018-08-09
date accepted: 2018-10-09
issued: 2018-11-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santibáñez-López
  given name: Carlos E.
author list: Agent
  family name: Kriebel
  given name: Ricardo
author list: Agent
  family name: Ballesteros
  given name: Jesús A.
author list: Agent
  family name: Rush
  given name: Nathaniel
author list: Agent
  family name: Witter
  given name: Zachary
author list: Agent
  family name: Williams
  given name: John
author list: Agent
  family name: Janies
  given name: Daniel A.
author list: Agent
  family name: Sharma
  given name: Prashant P.
doi: 10.7717/peerj.5902
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-14
copyright: © 2018 Santibáñez-López et al.
attribution name: Santibáñez-López et al.

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