PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The selenium content of SEPP1 versus selenium requirements in vertebrates
items: Enhanced susceptibility to predation in corals of compromised condition
items: Dental peculiarities in the silvery mole-rat: an original model for studying the evolutionary and biological origins of continuous dental generation in mammals
items: An experimental study of rill sediment delivery in purple soil, using the volume-replacement method
items: Anatomy, feeding ecology, and ontogeny of a transitional baleen whale: a new genus and species of Eomysticetidae (Mammalia: Cetacea) from the Oligocene of New Zealand
items: A game theoretic analysis of research data sharing
items: The influence of finfish aquaculture on benthic fish and crustacean assemblages in Fitzgerald Bay, South Australia
items: The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems
items: Turbidity interferes with foraging success of visual but not chemosensory predators
items: Attitudes towards suicide attempts broadcast on social media: an exploratory study of Chinese microblogs

The selenium content of SEPP1 versus selenium requirements in vertebrates
type: item
type: AcademicArticle
description: Selenoprotein P (SEPP1) distributes selenium (Se) throughout the body via the circulatory system. For vertebrates, the Se content of SEPP1 varies from 7 to 18 Se atoms depending on the species, but the reason for this variation remains unclear. Herein we provide evidence that vertebrate SEPP1 Sec content correlates positively with Se requirements. As the Se content of full length SEPP1 is genetically determined, this presents a unique case where a nutrient requirement can be predicted based on genomic sequence information.
format: application/pdf
format: text/html
creator: Sam Penglase
creator: Kristin Hamre
creator: Ståle Ellingsen
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genomics
subject: Nutrition
subject: Ethical Issues
description: doi:10.7717/peerj.1244
publisher: PeerJ Inc.
rights: © 2015 Penglase et al.
abstract: Selenoprotein P (SEPP1) distributes selenium (Se) throughout the body via the circulatory system. For vertebrates, the Se content of SEPP1 varies from 7 to 18 Se atoms depending on the species, but the reason for this variation remains unclear. Herein we provide evidence that vertebrate SEPP1 Sec content correlates positively with Se requirements. As the Se content of full length SEPP1 is genetically determined, this presents a unique case where a nutrient requirement can be predicted based on genomic sequence information.
bibliographic citation: Penglase et al. (2015) The selenium content of SEPP1 versus selenium requirements in vertebrates. PeerJ 3:e1244 https://doi.org/10.7717/peerj.1244
date submitted: 2015-01-07
date accepted: 2015-08-25
issued: 2015-09-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Penglase
  given name: Sam
author list: Agent
  family name: Hamre
  given name: Kristin
author list: Agent
  family name: Ellingsen
  given name: Ståle
doi: 10.7717/peerj.1244
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-10
copyright: © 2015 Penglase et al.
attribution name: Penglase et al.

Enhanced susceptibility to predation in corals of compromised condition
type: item
type: AcademicArticle
description: The marine gastropod, Coralliophila abbreviata, is an obligate corallivore that causes substantial mortality in Caribbean Acropora spp. Considering the imperiled status of Acropora cervicornis and A. palmata, a better understanding of ecological interactions resulting in tissue loss may enable more effective conservation strategies. We examined differences in susceptibility of A. cervicornis to C. abbreviata predation based on coral tissue condition. Coral tissue condition was a strong determinant of snail prey choice, with snails preferring A. cervicornis fragments that were diseased or mechanically damaged over healthy fragments. In addition, snails always chose fragments undergoing active predation by another snail, while showing no preference for a non-feeding snail when compared with an undisturbed prey fragment. These results indicate that the condition of A. cervicornis prey influenced foraging behavior of C. abbreviata, creating a potential feedback that may exacerbate damage from predation in coral populations compromised by other types of disturbance.
format: application/pdf
format: text/html
creator: Allan J. Bright
creator: Caitlin M. Cameron
creator: Margaret W. Miller
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.1239
publisher: PeerJ Inc.
rights: © 2015
abstract: The marine gastropod, Coralliophila abbreviata, is an obligate corallivore that causes substantial mortality in Caribbean Acropora spp. Considering the imperiled status of Acropora cervicornis and A. palmata, a better understanding of ecological interactions resulting in tissue loss may enable more effective conservation strategies. We examined differences in susceptibility of A. cervicornis to C. abbreviata predation based on coral tissue condition. Coral tissue condition was a strong determinant of snail prey choice, with snails preferring A. cervicornis fragments that were diseased or mechanically damaged over healthy fragments. In addition, snails always chose fragments undergoing active predation by another snail, while showing no preference for a non-feeding snail when compared with an undisturbed prey fragment. These results indicate that the condition of A. cervicornis prey influenced foraging behavior of C. abbreviata, creating a potential feedback that may exacerbate damage from predation in coral populations compromised by other types of disturbance.
bibliographic citation: Bright et al. (2015) Enhanced susceptibility to predation in corals of compromised condition. PeerJ 3:e1239 https://doi.org/10.7717/peerj.1239
date submitted: 2015-07-03
date accepted: 2015-08-22
issued: 2015-09-10
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Bright
  given name: Allan J.
author list: Agent
  family name: Cameron
  given name: Caitlin M.
author list: Agent
  family name: Miller
  given name: Margaret W.
doi: 10.7717/peerj.1239
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-10

Dental peculiarities in the silvery mole-rat: an original model for studying the evolutionary and biological origins of continuous dental generation in mammals
type: item
type: AcademicArticle
description: Unravelling the evolutionary and developmental mechanisms that have impacted the mammalian dentition, since more than 200 Ma, is an intricate issue. Interestingly, a few mammal species, including the silvery mole-rat Heliophobius argenteocinereus, are able to replace their dentition by the addition of supernumerary molars at the back of jaw migrating then toward the front. The aim here was to demonstrate the potential interest of further studying this rodent in order to better understand the origins of continuous dental replacement in mammals, which could also provide interesting data concerning the evolution of limited dental generation occurring in first mammals. In the present study, we described the main stages of the dental eruptive sequence in the silvery mole-rat and the associated characteristics of horizontal replacement using X-ray microtomography. This was coupled to the investigation of other African mole-rats which have no dental replacement. This method permitted to establish evidence that the initial development of the dentition in Heliophobius is comparable to what it is observed in most of African mole-rats. This rodent first has premolars, but then identical additional molars, a mechanism convergent to manatees and the pygmy rock-wallaby. Evidence of continuous replacement and strong dental dynamics were also illustrated in Heliophobius, and stressed the need to deeply investigate these aspects for evolutionary, functional and developmental purposes. We also noticed that two groups of extinct non-mammalian synapsids convergently acquired this dental mechanism, but in a way differing from extant mammals. The discussion on the diverse evolutionary origins of horizontal dental replacement put emphasis on the necessity of focusing on biological parameters potentially involved in both continuous and limited developments of teeth in mammals. In that context, the silvery mole-rat could appear as the most appropriate candidate to do so.
format: application/pdf
format: text/html
creator: Helder Gomes Rodrigues
creator: Radim Šumbera
subject: Developmental Biology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.1233
publisher: PeerJ Inc.
rights: © 2015 Gomes Rodrigues and Šumbera
abstract: Unravelling the evolutionary and developmental mechanisms that have impacted the mammalian dentition, since more than 200 Ma, is an intricate issue. Interestingly, a few mammal species, including the silvery mole-rat Heliophobius argenteocinereus, are able to replace their dentition by the addition of supernumerary molars at the back of jaw migrating then toward the front. The aim here was to demonstrate the potential interest of further studying this rodent in order to better understand the origins of continuous dental replacement in mammals, which could also provide interesting data concerning the evolution of limited dental generation occurring in first mammals. In the present study, we described the main stages of the dental eruptive sequence in the silvery mole-rat and the associated characteristics of horizontal replacement using X-ray microtomography. This was coupled to the investigation of other African mole-rats which have no dental replacement. This method permitted to establish evidence that the initial development of the dentition in Heliophobius is comparable to what it is observed in most of African mole-rats. This rodent first has premolars, but then identical additional molars, a mechanism convergent to manatees and the pygmy rock-wallaby. Evidence of continuous replacement and strong dental dynamics were also illustrated in Heliophobius, and stressed the need to deeply investigate these aspects for evolutionary, functional and developmental purposes. We also noticed that two groups of extinct non-mammalian synapsids convergently acquired this dental mechanism, but in a way differing from extant mammals. The discussion on the diverse evolutionary origins of horizontal dental replacement put emphasis on the necessity of focusing on biological parameters potentially involved in both continuous and limited developments of teeth in mammals. In that context, the silvery mole-rat could appear as the most appropriate candidate to do so.
bibliographic citation: Gomes Rodrigues et al. (2015) Dental peculiarities in the silvery mole-rat: an original model for studying the evolutionary and biological origins of continuous dental generation in mammals. PeerJ 3:e1233 https://doi.org/10.7717/peerj.1233
date submitted: 2015-05-24
date accepted: 2015-08-18
issued: 2015-09-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gomes Rodrigues
  given name: Helder
author list: Agent
  family name: Šumbera
  given name: Radim
doi: 10.7717/peerj.1233
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-10
copyright: © 2015 Gomes Rodrigues and Šumbera
attribution name: Gomes Rodrigues and Šumbera

An experimental study of rill sediment delivery in purple soil, using the volume-replacement method
type: item
type: AcademicArticle
description: Experimental studies provide a basis for understanding the mechanisms of rill erosion and can provide estimates for parameter values in physical models simulating the erosion process. In this study, we investigated sediment delivery during rill erosion in purple soil. We used the volume-replacement method to measure the volume of eroded soil and hence estimate the mass of eroded soil. A 12 m artificial rill was divided into the following sections: 0–0.5 m, 0.5–1 m, 1–2 m, 2–3 m, 3–4 m, 4–5 m, 5–6 m, 6–7 m, 7–8 m, 8–10 m, and 10–12 m. Erosion trials were conducted with three flow rates (2 L/min, 4 L/min, and 8 L/min) and five slope gradients (5°, 10°, 15°, 20°, and 25°). The eroded rill sections were refilled with water to measure the eroded volume in each section and subsequently calculate the eroded sediment mass. The cumulative sediment mass was used to compute the sediment concentration along the length of the rill. The results show that purple soil sediment concentration increases with rill length before eventually reaching a maximal value; that is, the rate of increase in sediment concentration is greatest at the rill inlet and then gradually slows. Steeper slopes and higher flow rates result in sediment concentration increasing more rapidly along the rill length and the maximum sediment concentration being reached at an earlier location in the rill. Slope gradient and flow rate both result in an increase in maximal sediment concentration and accumulated eroded amount. However, slope gradient has a greater influence on rill erosion than flow rate. The results and experimental method in this study may provide a reference for future rill-erosion experiments.
format: application/pdf
format: text/html
creator: Yuhan Huang
creator: Xiaoyan Chen
creator: Banglin Luo
creator: Linqiao Ding
creator: Chunming Gong
subject: Ecology
subject: Environmental Sciences
subject: Soil Science
description: doi:10.7717/peerj.1220
publisher: PeerJ Inc.
rights: © 2015 Huang et al.
abstract: Experimental studies provide a basis for understanding the mechanisms of rill erosion and can provide estimates for parameter values in physical models simulating the erosion process. In this study, we investigated sediment delivery during rill erosion in purple soil. We used the volume-replacement method to measure the volume of eroded soil and hence estimate the mass of eroded soil. A 12 m artificial rill was divided into the following sections: 0–0.5 m, 0.5–1 m, 1–2 m, 2–3 m, 3–4 m, 4–5 m, 5–6 m, 6–7 m, 7–8 m, 8–10 m, and 10–12 m. Erosion trials were conducted with three flow rates (2 L/min, 4 L/min, and 8 L/min) and five slope gradients (5°, 10°, 15°, 20°, and 25°). The eroded rill sections were refilled with water to measure the eroded volume in each section and subsequently calculate the eroded sediment mass. The cumulative sediment mass was used to compute the sediment concentration along the length of the rill. The results show that purple soil sediment concentration increases with rill length before eventually reaching a maximal value; that is, the rate of increase in sediment concentration is greatest at the rill inlet and then gradually slows. Steeper slopes and higher flow rates result in sediment concentration increasing more rapidly along the rill length and the maximum sediment concentration being reached at an earlier location in the rill. Slope gradient and flow rate both result in an increase in maximal sediment concentration and accumulated eroded amount. However, slope gradient has a greater influence on rill erosion than flow rate. The results and experimental method in this study may provide a reference for future rill-erosion experiments.
bibliographic citation: Huang et al. (2015) An experimental study of rill sediment delivery in purple soil, using the volume-replacement method. PeerJ 3:e1220 https://doi.org/10.7717/peerj.1220
date submitted: 2015-06-25
date accepted: 2015-08-07
issued: 2015-09-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Yuhan
author list: Agent
  family name: Chen
  given name: Xiaoyan
author list: Agent
  family name: Luo
  given name: Banglin
author list: Agent
  family name: Ding
  given name: Linqiao
author list: Agent
  family name: Gong
  given name: Chunming
doi: 10.7717/peerj.1220
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-10
copyright: © 2015 Huang et al.
attribution name: Huang et al.

Anatomy, feeding ecology, and ontogeny of a transitional baleen whale: a new genus and species of Eomysticetidae (Mammalia: Cetacea) from the Oligocene of New Zealand
type: item
type: AcademicArticle
description: The Eocene history of cetacean evolution is now represented by the expansive fossil record of archaeocetes elucidating major morphofunctional shifts relating to the land to sea transition, but the change from archaeocetes to modern cetaceans is poorly established. New fossil material of the recently recognized family Eomysticetidae from the upper Oligocene Otekaike Limestone includes a new genus and species, Waharoa ruwhenua, represented by skulls and partial skeletons of an adult, juvenile, and a smaller juvenile. Ontogenetic status is confirmed by osteohistology of ribs. Waharoa ruwhenua is characterized by an elongate and narrow rostrum which retains vestigial alveoli and alveolar grooves. Palatal foramina and sulci are present only on the posterior half of the palate. The nasals are elongate, and the bony nares are positioned far anteriorly. Enormous temporal fossae are present adjacent to an elongate and narrow intertemporal region with a sharp sagittal crest. The earbones are characterized by retaining inner and outer posterior pedicles, lacking fused posterior processes, and retaining a separate accessory ossicle. Phylogenetic analysis supports inclusion of Waharoa ruwhenua within a monophyletic Eomysticetidae as the earliest diverging clade of toothless mysticetes. This eomysticetid clade also included Eomysticetus whitmorei, Micromysticetus rothauseni, Tohoraata raekohao, Tokarahia kauaeroa, Tokarahia lophocephalus, and Yamatocetus canaliculatus. Detailed study of ontogenetic change demonstrates postnatal elaboration of the sagittal and nuchal crests, elongation of the intertemporal region, inflation of the zygomatic processes, and an extreme proportional increase in rostral length. Tympanic bullae are nearly full sized during early postnatal ontogeny indicating precocial development of auditory structures, but do increase slightly in size. Positive allometry of the rostrum suggests an ontogenetic change in feeding ecology, from neonatal suckling to a more …
format: application/pdf
format: text/html
creator: Robert W. Boessenecker
creator: R. Ewan Fordyce
subject: Paleontology
description: doi:10.7717/peerj.1129
publisher: PeerJ Inc.
rights: © 2015 Boessenecker and Fordyce
abstract: The Eocene history of cetacean evolution is now represented by the expansive fossil record of archaeocetes elucidating major morphofunctional shifts relating to the land to sea transition, but the change from archaeocetes to modern cetaceans is poorly established. New fossil material of the recently recognized family Eomysticetidae from the upper Oligocene Otekaike Limestone includes a new genus and species, Waharoa ruwhenua, represented by skulls and partial skeletons of an adult, juvenile, and a smaller juvenile. Ontogenetic status is confirmed by osteohistology of ribs. Waharoa ruwhenua is characterized by an elongate and narrow rostrum which retains vestigial alveoli and alveolar grooves. Palatal foramina and sulci are present only on the posterior half of the palate. The nasals are elongate, and the bony nares are positioned far anteriorly. Enormous temporal fossae are present adjacent to an elongate and narrow intertemporal region with a sharp sagittal crest. The earbones are characterized by retaining inner and outer posterior pedicles, lacking fused posterior processes, and retaining a separate accessory ossicle. Phylogenetic analysis supports inclusion of Waharoa ruwhenua within a monophyletic Eomysticetidae as the earliest diverging clade of toothless mysticetes. This eomysticetid clade also included Eomysticetus whitmorei, Micromysticetus rothauseni, Tohoraata raekohao, Tokarahia kauaeroa, Tokarahia lophocephalus, and Yamatocetus canaliculatus. Detailed study of ontogenetic change demonstrates postnatal elaboration of the sagittal and nuchal crests, elongation of the intertemporal region, inflation of the zygomatic processes, and an extreme proportional increase in rostral length. Tympanic bullae are nearly full sized during early postnatal ontogeny indicating precocial development of auditory structures, but do increase slightly in size. Positive allometry of the rostrum suggests an ontogenetic change in feeding ecology, from neonatal suckling to a more …
bibliographic citation: Boessenecker et al. (2015) Anatomy, feeding ecology, and ontogeny of a transitional baleen whale: a new genus and species of Eomysticetidae (Mammalia: Cetacea) from the Oligocene of New Zealand. PeerJ 3:e1129 https://doi.org/10.7717/peerj.1129
date submitted: 2015-04-17
date accepted: 2015-07-05
issued: 2015-09-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boessenecker
  given name: Robert W.
author list: Agent
  family name: Fordyce
  given name: R. Ewan
doi: 10.7717/peerj.1129
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-10
copyright: © 2015 Boessenecker and Fordyce
attribution name: Boessenecker and Fordyce

A game theoretic analysis of research data sharing
type: item
type: AcademicArticle
description: While reusing research data has evident benefits for the scientific community as a whole, decisions to archive and share these data are primarily made by individual researchers. In this paper we analyse, within a game theoretical framework, how sharing and reuse of research data affect individuals who share or do not share their datasets. We construct a model in which there is a cost associated with sharing datasets whereas reusing such sets implies a benefit. In our calculations, conflicting interests appear for researchers. Individual researchers are always better off not sharing and omitting the sharing cost, at the same time both sharing and not sharing researchers are better off if (almost) all researchers share. Namely, the more researchers share, the more benefit can be gained by the reuse of those datasets. We simulated several policy measures to increase benefits for researchers sharing or reusing datasets. Results point out that, although policies should be able to increase the rate of sharing researchers, and increased discoverability and dataset quality could partly compensate for costs, a better measure would be to directly lower the cost for sharing, or even turn it into a (citation-) benefit. Making data available would in that case become the most profitable, and therefore stable, strategy. This means researchers would willingly make their datasets available, and arguably in the best possible way to enable reuse.
format: application/pdf
format: text/html
creator: Tessa E. Pronk
creator: Paulien H. Wiersma
creator: Anne van Weerden
creator: Feike Schieving
subject: Computational Biology
subject: Science Policy
description: doi:10.7717/peerj.1242
publisher: PeerJ Inc.
rights: © 2015 Pronk et al.
abstract: While reusing research data has evident benefits for the scientific community as a whole, decisions to archive and share these data are primarily made by individual researchers. In this paper we analyse, within a game theoretical framework, how sharing and reuse of research data affect individuals who share or do not share their datasets. We construct a model in which there is a cost associated with sharing datasets whereas reusing such sets implies a benefit. In our calculations, conflicting interests appear for researchers. Individual researchers are always better off not sharing and omitting the sharing cost, at the same time both sharing and not sharing researchers are better off if (almost) all researchers share. Namely, the more researchers share, the more benefit can be gained by the reuse of those datasets. We simulated several policy measures to increase benefits for researchers sharing or reusing datasets. Results point out that, although policies should be able to increase the rate of sharing researchers, and increased discoverability and dataset quality could partly compensate for costs, a better measure would be to directly lower the cost for sharing, or even turn it into a (citation-) benefit. Making data available would in that case become the most profitable, and therefore stable, strategy. This means researchers would willingly make their datasets available, and arguably in the best possible way to enable reuse.
bibliographic citation: Pronk et al. (2015) A game theoretic analysis of research data sharing. PeerJ 3:e1242 https://doi.org/10.7717/peerj.1242
date submitted: 2015-06-15
date accepted: 2015-08-24
issued: 2015-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pronk
  given name: Tessa E.
author list: Agent
  family name: Wiersma
  given name: Paulien H.
author list: Agent
  family name: van Weerden
  given name: Anne
author list: Agent
  family name: Schieving
  given name: Feike
doi: 10.7717/peerj.1242
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-08
copyright: © 2015 Pronk et al.
attribution name: Pronk et al.

The influence of finfish aquaculture on benthic fish and crustacean assemblages in Fitzgerald Bay, South Australia
type: item
type: AcademicArticle
description: The influence of sea-cage aquaculture on wildfish assemblages has received little attention outside of Europe. Sea-cage aquaculture of finfish is a major focus in South Australia, and while the main species farmed is southern bluefin tuna (Thunnus maccoyii), there is also an important yellowtail kingfish (Seriola lalandi) industry. Yellowtail kingfish aquaculture did not appear to have any local or regional effects on demersal assemblages (primarily fish, but also some crustaceans) surveyed by baited remote underwater video (BRUV) in Fitzgerald Bay. We did, however, detect small scale spatial variations in assemblages within the bay. The type of bait used strongly influenced the assemblage recorded, with significantly greater numbers of fish attracted to deployments where sardines were used as the bait to compared to those with no bait. The pelleted feed used by the aquaculture industry was just as attractive as sardines at one site, and intermediate between sardines and no bait at the other. There was significant temporal variability in assemblages at both farm sites and one control site, while the second control site was temporally stable (over the 9 weeks of the study). Overall, the results suggested that aquaculture was having little if any impact on the abundance and assemblage structure of the demersal macrofauna in Fitzgerald Bay.
format: application/pdf
format: text/html
creator: Jason E. Tanner
creator: Kane Williams
subject: Aquaculture, Fisheries and Fish Science
subject: Biosphere Interactions
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.1238
publisher: PeerJ Inc.
rights: © 2015 Tanner and Williams
abstract: The influence of sea-cage aquaculture on wildfish assemblages has received little attention outside of Europe. Sea-cage aquaculture of finfish is a major focus in South Australia, and while the main species farmed is southern bluefin tuna (Thunnus maccoyii), there is also an important yellowtail kingfish (Seriola lalandi) industry. Yellowtail kingfish aquaculture did not appear to have any local or regional effects on demersal assemblages (primarily fish, but also some crustaceans) surveyed by baited remote underwater video (BRUV) in Fitzgerald Bay. We did, however, detect small scale spatial variations in assemblages within the bay. The type of bait used strongly influenced the assemblage recorded, with significantly greater numbers of fish attracted to deployments where sardines were used as the bait to compared to those with no bait. The pelleted feed used by the aquaculture industry was just as attractive as sardines at one site, and intermediate between sardines and no bait at the other. There was significant temporal variability in assemblages at both farm sites and one control site, while the second control site was temporally stable (over the 9 weeks of the study). Overall, the results suggested that aquaculture was having little if any impact on the abundance and assemblage structure of the demersal macrofauna in Fitzgerald Bay.
bibliographic citation: Tanner et al. (2015) The influence of finfish aquaculture on benthic fish and crustacean assemblages in Fitzgerald Bay, South Australia. PeerJ 3:e1238 https://doi.org/10.7717/peerj.1238
date submitted: 2015-04-27
date accepted: 2015-08-22
issued: 2015-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tanner
  given name: Jason E.
author list: Agent
  family name: Williams
  given name: Kane
doi: 10.7717/peerj.1238
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-08
copyright: © 2015 Tanner and Williams
attribution name: Tanner and Williams

The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems
type: item
type: AcademicArticle
description: The terrestrial cycling of Si is thought to have a large influence on the terrestrial and marine primary production, as well as the coupled biogeochemical cycles of Si and C. Biomineralization of silica is widespread among terrestrial eukaryotes such as plants, soil diatoms, freshwater sponges, silicifying flagellates and testate amoebae. Two major groups of testate (shelled) amoebae, arcellinids and euglyphids, produce their own silica particles to construct shells. The two are unrelated phylogenetically and acquired biomineralizing capabilities independently. Hyalosphenids, a group within arcellinids, are predators of euglyphids. We demonstrate that hyalosphenids can construct shells using silica scales mineralized by the euglyphids. Parsimony analyses of the current hyalosphenid phylogeny indicate that the ability to “steal” euglyphid scales is most likely ancestral in hyalosphenids, implying that euglyphids should be older than hyalosphenids. However, exactly when euglyphids arose is uncertain. Current fossil record contains unambiguous euglyphid fossils that are as old as 50 million years, but older fossils are scarce and difficult to interpret. Poor taxon sampling of euglyphids has also prevented the development of molecular clocks. Here, we present a novel molecular clock reconstruction for arcellinids and consider the uncertainties due to various previously used calibration points. The new molecular clock puts the origin of hyalosphenids in the early Carboniferous (∼370 mya). Notably, this estimate coincides with the widespread colonization of land by Si-accumulating plants, suggesting possible links between the evolution of Arcellinid testate amoebae and the expansion of terrestrial habitats rich in organic matter and bioavailable Si.
format: application/pdf
format: text/html
creator: Daniel J.G. Lahr
creator: Tanja Bosak
creator: Enrique Lara
creator: Edward A.D. Mitchell
subject: Biochemistry
subject: Biodiversity
subject: Evolutionary Studies
subject: Microbiology
subject: Paleontology
description: doi:10.7717/peerj.1234
publisher: PeerJ Inc.
rights: © 2015 Lahr et al.
abstract: The terrestrial cycling of Si is thought to have a large influence on the terrestrial and marine primary production, as well as the coupled biogeochemical cycles of Si and C. Biomineralization of silica is widespread among terrestrial eukaryotes such as plants, soil diatoms, freshwater sponges, silicifying flagellates and testate amoebae. Two major groups of testate (shelled) amoebae, arcellinids and euglyphids, produce their own silica particles to construct shells. The two are unrelated phylogenetically and acquired biomineralizing capabilities independently. Hyalosphenids, a group within arcellinids, are predators of euglyphids. We demonstrate that hyalosphenids can construct shells using silica scales mineralized by the euglyphids. Parsimony analyses of the current hyalosphenid phylogeny indicate that the ability to “steal” euglyphid scales is most likely ancestral in hyalosphenids, implying that euglyphids should be older than hyalosphenids. However, exactly when euglyphids arose is uncertain. Current fossil record contains unambiguous euglyphid fossils that are as old as 50 million years, but older fossils are scarce and difficult to interpret. Poor taxon sampling of euglyphids has also prevented the development of molecular clocks. Here, we present a novel molecular clock reconstruction for arcellinids and consider the uncertainties due to various previously used calibration points. The new molecular clock puts the origin of hyalosphenids in the early Carboniferous (∼370 mya). Notably, this estimate coincides with the widespread colonization of land by Si-accumulating plants, suggesting possible links between the evolution of Arcellinid testate amoebae and the expansion of terrestrial habitats rich in organic matter and bioavailable Si.
bibliographic citation: Lahr et al. (2015) The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems. PeerJ 3:e1234 https://doi.org/10.7717/peerj.1234
date submitted: 2015-05-29
date accepted: 2015-08-19
issued: 2015-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lahr
  given name: Daniel J.G.
author list: Agent
  family name: Bosak
  given name: Tanja
author list: Agent
  family name: Lara
  given name: Enrique
author list: Agent
  family name: Mitchell
  given name: Edward A.D.
doi: 10.7717/peerj.1234
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-08
copyright: © 2015 Lahr et al.
attribution name: Lahr et al.

Turbidity interferes with foraging success of visual but not chemosensory predators
type: item
type: AcademicArticle
description: Predation can significantly affect prey populations and communities, but predator effects can be attenuated when abiotic conditions interfere with foraging activities. In estuarine communities, turbidity can affect species richness and abundance and is changing in many areas because of coastal development. Many fish species are less efficient foragers in turbid waters, and previous research revealed that in elevated turbidity, fish are less abundant whereas crabs and shrimp are more abundant. We hypothesized that turbidity altered predatory interactions in estuaries by interfering with visually-foraging predators and prey but not with organisms relying on chemoreception. We measured the effects of turbidity on the predation rates of two model predators: a visual predator (pinfish, Lagodon rhomboides) and a chemosensory predator (blue crabs, Callinectes sapidus) in clear and turbid water (0 and ∼100 nephelometric turbidity units). Feeding assays were conducted with two prey items, mud crabs (Panopeus spp.) that rely heavily on chemoreception to detect predators, and brown shrimp (Farfantepenaus aztecus) that use both chemical and visual cues for predator detection. Because turbidity reduced pinfish foraging on both mud crabs and shrimp, the changes in predation rates are likely driven by turbidity attenuating fish foraging ability and not by affecting prey vulnerability to fish consumers. Blue crab foraging was unaffected by turbidity, and blue crabs were able to successfully consume nearly all mud crab and shrimp prey. Turbidity can influence predator–prey interactions by reducing the feeding efficiency of visual predators, providing a competitive advantage to chemosensory predators, and altering top-down control in food webs.
format: application/pdf
format: text/html
creator: Jessica Lunt
creator: Delbert L. Smee
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.1212
publisher: PeerJ Inc.
rights: © 2015 Lunt and Smee
abstract: Predation can significantly affect prey populations and communities, but predator effects can be attenuated when abiotic conditions interfere with foraging activities. In estuarine communities, turbidity can affect species richness and abundance and is changing in many areas because of coastal development. Many fish species are less efficient foragers in turbid waters, and previous research revealed that in elevated turbidity, fish are less abundant whereas crabs and shrimp are more abundant. We hypothesized that turbidity altered predatory interactions in estuaries by interfering with visually-foraging predators and prey but not with organisms relying on chemoreception. We measured the effects of turbidity on the predation rates of two model predators: a visual predator (pinfish, Lagodon rhomboides) and a chemosensory predator (blue crabs, Callinectes sapidus) in clear and turbid water (0 and ∼100 nephelometric turbidity units). Feeding assays were conducted with two prey items, mud crabs (Panopeus spp.) that rely heavily on chemoreception to detect predators, and brown shrimp (Farfantepenaus aztecus) that use both chemical and visual cues for predator detection. Because turbidity reduced pinfish foraging on both mud crabs and shrimp, the changes in predation rates are likely driven by turbidity attenuating fish foraging ability and not by affecting prey vulnerability to fish consumers. Blue crab foraging was unaffected by turbidity, and blue crabs were able to successfully consume nearly all mud crab and shrimp prey. Turbidity can influence predator–prey interactions by reducing the feeding efficiency of visual predators, providing a competitive advantage to chemosensory predators, and altering top-down control in food webs.
bibliographic citation: Lunt et al. (2015) Turbidity interferes with foraging success of visual but not chemosensory predators. PeerJ 3:e1212 https://doi.org/10.7717/peerj.1212
date submitted: 2015-05-13
date accepted: 2015-08-05
issued: 2015-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lunt
  given name: Jessica
author list: Agent
  family name: Smee
  given name: Delbert L.
doi: 10.7717/peerj.1212
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-08
copyright: © 2015 Lunt and Smee
attribution name: Lunt and Smee

Attitudes towards suicide attempts broadcast on social media: an exploratory study of Chinese microblogs
type: item
type: AcademicArticle
description: Introduction. Broadcasting a suicide attempt on social media has become a public health concern in many countries, particularly in China. In these cases, social media users are likely to be the first to witness the suicide attempt, and their attitudes may determine their likelihood of joining rescue efforts. This paper examines Chinese social media (Weibo) users’ attitudes towards suicide attempts broadcast on Weibo. Methods. A total of 4,969 Weibo posts were selected from a customised Weibo User Pool which consisted of 1.06 million active users. The selected posts were then independently coded by two researchers using a coding framework that assessed: (a) Themes, (b) General attitudes, (c) Stigmatising attitudes, (d) Perceived motivations, and (e) Desired responses. Results and Discussion. More than one third of Weibo posts were coded as “stigmatising” (35%). Among these, 22%, 16%, and 15% of posts were coded as “deceitful,” “pathetic,” and “stupid,” respectively. Among the posts which reflected different types of perceived motivations, 57% of posts were coded as “seeking attention.” Among the posts which reflected desired responses, 37% were “not saving” and 28% were “encouraging suicide.” Furthermore, among the posts with negative desired responses (i.e., “not saving” and “encouraging suicide”), 57% and 17% of them were related to different types of stigmatising attitudes and perceived motivations, respectively. Specifically, 29% and 26% of posts reflecting both stigmatising attitudes and negative desired responses were coded as “deceitful” and “pathetic,” respectively, while 66% of posts reflecting both perceived motivations, and negative desired responses were coded as “seeking attention.” Very few posts “promoted literacy” (2%) or “provided resources” (8%). Gender differences existed in multiple categories. Conclusions. This paper confirms the need for stigma reduction campaigns for Chinese social media users to improve their attitudes towards those who broadc…
format: application/pdf
format: text/html
creator: Ang Li
creator: Xiaoxiao Huang
creator: Bibo Hao
creator: Bridianne O’Dea
creator: Helen Christensen
creator: Tingshao Zhu
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.1209
publisher: PeerJ Inc.
rights: © 2015 Li et al.
abstract: Introduction. Broadcasting a suicide attempt on social media has become a public health concern in many countries, particularly in China. In these cases, social media users are likely to be the first to witness the suicide attempt, and their attitudes may determine their likelihood of joining rescue efforts. This paper examines Chinese social media (Weibo) users’ attitudes towards suicide attempts broadcast on Weibo. Methods. A total of 4,969 Weibo posts were selected from a customised Weibo User Pool which consisted of 1.06 million active users. The selected posts were then independently coded by two researchers using a coding framework that assessed: (a) Themes, (b) General attitudes, (c) Stigmatising attitudes, (d) Perceived motivations, and (e) Desired responses. Results and Discussion. More than one third of Weibo posts were coded as “stigmatising” (35%). Among these, 22%, 16%, and 15% of posts were coded as “deceitful,” “pathetic,” and “stupid,” respectively. Among the posts which reflected different types of perceived motivations, 57% of posts were coded as “seeking attention.” Among the posts which reflected desired responses, 37% were “not saving” and 28% were “encouraging suicide.” Furthermore, among the posts with negative desired responses (i.e., “not saving” and “encouraging suicide”), 57% and 17% of them were related to different types of stigmatising attitudes and perceived motivations, respectively. Specifically, 29% and 26% of posts reflecting both stigmatising attitudes and negative desired responses were coded as “deceitful” and “pathetic,” respectively, while 66% of posts reflecting both perceived motivations, and negative desired responses were coded as “seeking attention.” Very few posts “promoted literacy” (2%) or “provided resources” (8%). Gender differences existed in multiple categories. Conclusions. This paper confirms the need for stigma reduction campaigns for Chinese social media users to improve their attitudes towards those who broadc…
bibliographic citation: Li et al. (2015) Attitudes towards suicide attempts broadcast on social media: an exploratory study of Chinese microblogs. PeerJ 3:e1209 https://doi.org/10.7717/peerj.1209
date submitted: 2015-05-28
date accepted: 2015-08-03
issued: 2015-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Ang
author list: Agent
  family name: Huang
  given name: Xiaoxiao
author list: Agent
  family name: Hao
  given name: Bibo
author list: Agent
  family name: O’Dea
  given name: Bridianne
author list: Agent
  family name: Christensen
  given name: Helen
author list: Agent
  family name: Zhu
  given name: Tingshao
doi: 10.7717/peerj.1209
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-08
copyright: © 2015 Li et al.
attribution name: Li et al.

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