PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The highly toxic and cryptogenic clinging jellyfish Gonionemus sp. (Hydrozoa, Limnomedusae) on the Swedish west coast
items: Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons
items: The interactive effect of herbivory, nutrient enrichment and mucilage on shallow rocky macroalgal communities
items: Using GIS to examine biogeographic and macroevolutionary patterns in some late Paleozoic cephalopods from the North American Midcontinent Sea
items: Conspecific coprophagy stimulates normal development in a germ-free model invertebrate
items: Plant diversity is closely related to the density of zokor mounds in three alpine rangelands on the Tibetan Plateau
items: Automated pupillometry to detect command following in neurological patients: a proof-of-concept study
items: Large-scale insect outbreak homogenizes the spatial structure of ectomycorrhizal fungal communities
items: Species delimitation of the Dermacentor ticks based on phylogenetic clustering and niche modeling
items: Use of aerial thermography to reduce mortality of roe deer fawns before harvest

The highly toxic and cryptogenic clinging jellyfish Gonionemus sp. (Hydrozoa, Limnomedusae) on the Swedish west coast
type: item
type: AcademicArticle
description: The clinging jellyfish Gonionemus sp. is a small hydromedusa species known historically from the Swedish west coast but not reported in recent times. This species is thought to be native to the northwest Pacific where it is notorious for causing severe stings in humans and is considered invasive or cryptogenic elsewhere. This year, unlike in the past, severe stings in swimmers making contact with Gonionemus sp. medusae occurred in Swedish waters from a sheltered eelgrass bed in the inner Skagerrak archipelago. To the best of our knowledge, this is only the second sting record of Gonionemus sp. from the Northeast Atlantic—with the first record occurring off the Belgian coast in the 1970s. Stinging Gonionemus sp. medusae have also been recently reported from the northwestern Atlantic coast, where, like on the Swedish coast, stings were not reported in the past. We analyzed sea surface temperature data from the past 30 years and show that 2018 had an exceptionally cold spring followed by an exceptionally hot summer. It is suggested that the 2018 temperature anomalies contributed to the Swedish outbreak. An analysis of mitochondrial COI sequences showed that Swedish medusae belong to the same clade as those from toxic populations in the Sea of Japan and northwest Atlantic. Gonionemus sp. is particularly prone to human-mediated dispersal and we suggest that it is possible that this year’s outbreak is the result of anthropogenic factors either through a climate-driven northward range shift or an introduction via shipping activity. We examined medusa growth rates and details of medusa morphology including nematocysts. Two types of penetrating nematocysts: euryteles and b-mastigophores were observed, suggesting that Gonionemus sp. medusae are able to feed on hard-bodied organisms like copepods and cladocerans. Given the now-regular occurrence and regional spread of Gonionemus sp. in the northwest Atlantic, it seems likely that outbreaks in Sweden will continue. More informa…
format: application/pdf
format: text/html
creator: Annette F. Govindarajan
creator: Björn Källström
creator: Erik Selander
creator: Carina Östman
creator: Thomas G. Dahlgren
subject: Biodiversity
subject: Biogeography
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6883
publisher: PeerJ Inc.
rights: © 2019 Govindarajan et al.
abstract: The clinging jellyfish Gonionemus sp. is a small hydromedusa species known historically from the Swedish west coast but not reported in recent times. This species is thought to be native to the northwest Pacific where it is notorious for causing severe stings in humans and is considered invasive or cryptogenic elsewhere. This year, unlike in the past, severe stings in swimmers making contact with Gonionemus sp. medusae occurred in Swedish waters from a sheltered eelgrass bed in the inner Skagerrak archipelago. To the best of our knowledge, this is only the second sting record of Gonionemus sp. from the Northeast Atlantic—with the first record occurring off the Belgian coast in the 1970s. Stinging Gonionemus sp. medusae have also been recently reported from the northwestern Atlantic coast, where, like on the Swedish coast, stings were not reported in the past. We analyzed sea surface temperature data from the past 30 years and show that 2018 had an exceptionally cold spring followed by an exceptionally hot summer. It is suggested that the 2018 temperature anomalies contributed to the Swedish outbreak. An analysis of mitochondrial COI sequences showed that Swedish medusae belong to the same clade as those from toxic populations in the Sea of Japan and northwest Atlantic. Gonionemus sp. is particularly prone to human-mediated dispersal and we suggest that it is possible that this year’s outbreak is the result of anthropogenic factors either through a climate-driven northward range shift or an introduction via shipping activity. We examined medusa growth rates and details of medusa morphology including nematocysts. Two types of penetrating nematocysts: euryteles and b-mastigophores were observed, suggesting that Gonionemus sp. medusae are able to feed on hard-bodied organisms like copepods and cladocerans. Given the now-regular occurrence and regional spread of Gonionemus sp. in the northwest Atlantic, it seems likely that outbreaks in Sweden will continue. More informa…
bibliographic citation: Govindarajan et al. (2019) The highly toxic and cryptogenic clinging jellyfish Gonionemus sp. (Hydrozoa, Limnomedusae) on the Swedish west coast. PeerJ 7:e6883 https://doi.org/10.7717/peerj.6883
date submitted: 2019-01-18
date accepted: 2019-04-01
issued: 2019-05-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Govindarajan
  given name: Annette F.
author list: Agent
  family name: Källström
  given name: Björn
author list: Agent
  family name: Selander
  given name: Erik
author list: Agent
  family name: Östman
  given name: Carina
author list: Agent
  family name: Dahlgren
  given name: Thomas G.
doi: 10.7717/peerj.6883
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-13
copyright: © 2019 Govindarajan et al.
attribution name: Govindarajan et al.

Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons
type: item
type: AcademicArticle
description: High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and tested a dual-index sequence library preparation method that pools and simultaneously sequences multiple Symbiodiniaceae gene amplicons per sample for in-depth biodiversity assessments. The rationale for this approach was to allow the metabarcoding of multiple genes without extra costs associated with additional single amplicon dual indexing and library preparations. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three pooled gene amplicons investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. The pooled Symbiodiniaceae multi-gene metabarcoding approach described here is readily scalable, offering considerable analytical cost savings while providing sufficient phylogenetic information and sequence coverage.
format: application/pdf
format: text/html
creator: Xavier Pochon
creator: Patricia Wecker
creator: Michael Stat
creator: Véronique Berteaux-Lecellier
creator: Gaël Lecellier
subject: Biodiversity
subject: Biotechnology
subject: Ecology
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.6898
publisher: PeerJ Inc.
rights: © 2019 Pochon et al.
abstract: High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and tested a dual-index sequence library preparation method that pools and simultaneously sequences multiple Symbiodiniaceae gene amplicons per sample for in-depth biodiversity assessments. The rationale for this approach was to allow the metabarcoding of multiple genes without extra costs associated with additional single amplicon dual indexing and library preparations. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three pooled gene amplicons investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. The pooled Symbiodiniaceae multi-gene metabarcoding approach described here is readily scalable, offering considerable analytical cost savings while providing sufficient phylogenetic information and sequence coverage.
bibliographic citation: Pochon et al. (2019) Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons. PeerJ 7:e6898 https://doi.org/10.7717/peerj.6898
date submitted: 2019-01-14
date accepted: 2019-04-02
issued: 2019-05-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pochon
  given name: Xavier
author list: Agent
  family name: Wecker
  given name: Patricia
author list: Agent
  family name: Stat
  given name: Michael
author list: Agent
  family name: Berteaux-Lecellier
  given name: Véronique
author list: Agent
  family name: Lecellier
  given name: Gaël
doi: 10.7717/peerj.6898
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-13
copyright: © 2019 Pochon et al.
attribution name: Pochon et al.

The interactive effect of herbivory, nutrient enrichment and mucilage on shallow rocky macroalgal communities
type: item
type: AcademicArticle
description: This paper focuses on the interactive short and long-term effect of three different stressors on a macroalgal assemblage. Three stressors are considered: herbivory, nutrients and mucilage. The experiment was conducted in Tavolara Punta Coda Cavallo Marine Protected Area (Mediterranean Sea) during a bloom of the benthic mucilage-producing microalga Chrysophaeum taylorii (Pelagophyceae); this microalga is recently spreading in the Mediterranean Sea. On a rocky substratum, 36 plots 20 × 20 cm in size were prepared. Factorial combinations of three experimental treatments were applied in triplicate, including three grazing levels crossed with two nutrient enrichment and two mucilage removal treatments. Significant differences were observed among treatments 8 weeks later, at the end of summer. In particular, dark filamentous algae were more abundant in all enriched plots, especially where mucilage and macroalgae had been removed; a higher percent cover of crustose coralline algae was instead observed where nutrients had been increased and no grazing pressure acted. Furthermore, the abundance of Dictyota spp. and Laurencia spp. was significantly higher in enriched mucilage-free plots where the grazing pressure was null or low. However, the effects of the treatments on the overall assemblage of the macroalgal community were not long persistent (36 weeks later). These results illustrate the capacity of a shallow-water macroalgal community to quickly recover from the simultaneous impacts of herbivory, nutrient enrichment, and mucilage.
format: application/pdf
format: text/html
creator: Sarah Caronni
creator: Chiara Calabretti
creator: Sandra Citterio
creator: Maria Anna Delaria
creator: Rodolfo Gentili
creator: Giovanni Macri
creator: Chiara Montagnani
creator: Augusto Navone
creator: Pieraugusto Panzalis
creator: Giulia Piazza
creator: Giulia Ceccherelli
subject: Ecology
subject: Marine Biology
subject: Plant Science
subject: Environmental Impacts
description: doi:10.7717/peerj.6908
publisher: PeerJ Inc.
rights: © 2019 Caronni et al.
abstract: This paper focuses on the interactive short and long-term effect of three different stressors on a macroalgal assemblage. Three stressors are considered: herbivory, nutrients and mucilage. The experiment was conducted in Tavolara Punta Coda Cavallo Marine Protected Area (Mediterranean Sea) during a bloom of the benthic mucilage-producing microalga Chrysophaeum taylorii (Pelagophyceae); this microalga is recently spreading in the Mediterranean Sea. On a rocky substratum, 36 plots 20 × 20 cm in size were prepared. Factorial combinations of three experimental treatments were applied in triplicate, including three grazing levels crossed with two nutrient enrichment and two mucilage removal treatments. Significant differences were observed among treatments 8 weeks later, at the end of summer. In particular, dark filamentous algae were more abundant in all enriched plots, especially where mucilage and macroalgae had been removed; a higher percent cover of crustose coralline algae was instead observed where nutrients had been increased and no grazing pressure acted. Furthermore, the abundance of Dictyota spp. and Laurencia spp. was significantly higher in enriched mucilage-free plots where the grazing pressure was null or low. However, the effects of the treatments on the overall assemblage of the macroalgal community were not long persistent (36 weeks later). These results illustrate the capacity of a shallow-water macroalgal community to quickly recover from the simultaneous impacts of herbivory, nutrient enrichment, and mucilage.
bibliographic citation: Caronni et al. (2019) The interactive effect of herbivory, nutrient enrichment and mucilage on shallow rocky macroalgal communities. PeerJ 7:e6908 https://doi.org/10.7717/peerj.6908
date submitted: 2018-02-28
date accepted: 2019-04-04
issued: 2019-05-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caronni
  given name: Sarah
author list: Agent
  family name: Calabretti
  given name: Chiara
author list: Agent
  family name: Citterio
  given name: Sandra
author list: Agent
  family name: Delaria
  given name: Maria Anna
author list: Agent
  family name: Gentili
  given name: Rodolfo
author list: Agent
  family name: Macri
  given name: Giovanni
author list: Agent
  family name: Montagnani
  given name: Chiara
author list: Agent
  family name: Navone
  given name: Augusto
author list: Agent
  family name: Panzalis
  given name: Pieraugusto
author list: Agent
  family name: Piazza
  given name: Giulia
author list: Agent
  family name: Ceccherelli
  given name: Giulia
doi: 10.7717/peerj.6908
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-13
copyright: ©2019 Caronni et al.
attribution name: Caronni et al.

Using GIS to examine biogeographic and macroevolutionary patterns in some late Paleozoic cephalopods from the North American Midcontinent Sea
type: item
type: AcademicArticle
description: Geographic range is an important macroevolutionary parameter frequently considered in paleontological studies as species’ distributions and range sizes are determined by a variety of biotic and abiotic factors well known to affect the differential birth and death of species. Thus, considering how distributions and range sizes fluctuate over time can provide important insight into evolutionary dynamics. This study uses Geographic Information Systems (GIS) and analyses of evolutionary rates to examine how in some species within the Cephalopoda, an important pelagic clade, geographic range size and rates of speciation and extinction changed throughout the Pennsylvanian and early Permian in the North American Midcontinent Sea. This period is particularly interesting for biogeographic and evolutionary studies because it is characterized by repetitive interglacial-glacial cycles, a global transition from an icehouse to a greenhouse climate during the Late Paleozoic Ice Age, and decelerated macroevolutionary dynamics, i.e. low speciation and extinction rates. The analyses presented herein indicate that cephalopod species diversity was not completely static and actually fluctuated throughout the Pennsylvanian and early Permian, matching findings from other studies. However, contrary to some other studies, the mean geographic ranges of cephalopod species did not change significantly through time, despite numerous climate oscillations; further, geographic range size did not correlate with rates of speciation and extinction. These results suggest that pelagic organisms may have responded differently to late Paleozoic climate changes than benthic organisms, although additional consideration of this issue is needed. Finally, these results indicate that, at least in the case of cephalopods, macroevolution during the late Paleozoic was more dynamic than previously characterized, and patterns may have varied across different clades during this interval.
format: application/pdf
format: text/html
creator: Kayla M. Kolis
creator: Bruce S. Lieberman
subject: Biogeography
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.6910
publisher: PeerJ Inc.
rights: © 2019 Kolis and Lieberman
abstract: Geographic range is an important macroevolutionary parameter frequently considered in paleontological studies as species’ distributions and range sizes are determined by a variety of biotic and abiotic factors well known to affect the differential birth and death of species. Thus, considering how distributions and range sizes fluctuate over time can provide important insight into evolutionary dynamics. This study uses Geographic Information Systems (GIS) and analyses of evolutionary rates to examine how in some species within the Cephalopoda, an important pelagic clade, geographic range size and rates of speciation and extinction changed throughout the Pennsylvanian and early Permian in the North American Midcontinent Sea. This period is particularly interesting for biogeographic and evolutionary studies because it is characterized by repetitive interglacial-glacial cycles, a global transition from an icehouse to a greenhouse climate during the Late Paleozoic Ice Age, and decelerated macroevolutionary dynamics, i.e. low speciation and extinction rates. The analyses presented herein indicate that cephalopod species diversity was not completely static and actually fluctuated throughout the Pennsylvanian and early Permian, matching findings from other studies. However, contrary to some other studies, the mean geographic ranges of cephalopod species did not change significantly through time, despite numerous climate oscillations; further, geographic range size did not correlate with rates of speciation and extinction. These results suggest that pelagic organisms may have responded differently to late Paleozoic climate changes than benthic organisms, although additional consideration of this issue is needed. Finally, these results indicate that, at least in the case of cephalopods, macroevolution during the late Paleozoic was more dynamic than previously characterized, and patterns may have varied across different clades during this interval.
bibliographic citation: Kolis et al. (2019) Using GIS to examine biogeographic and macroevolutionary patterns in some late Paleozoic cephalopods from the North American Midcontinent Sea. PeerJ 7:e6910 https://doi.org/10.7717/peerj.6910
date submitted: 2018-09-17
date accepted: 2019-03-23
issued: 2019-05-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kolis
  given name: Kayla M.
author list: Agent
  family name: Lieberman
  given name: Bruce S.
doi: 10.7717/peerj.6910
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-13
copyright: ©2019 Kolis and Lieberman
attribution name: Kolis and Lieberman

Conspecific coprophagy stimulates normal development in a germ-free model invertebrate
type: item
type: AcademicArticle
description: Microbial assemblages residing within and on animal gastric tissues contribute to various host beneficial processes that include diet accessibility and nutrient provisioning, and we sought to examine the degree to which intergenerational and community-acquired gut bacteria impact development in a tractable germ-free (GF) invertebrate model system. Coprophagy is a common behavior in cockroaches and termites that provides access to both nutrients and the primary means by which juveniles are inoculated with beneficial gut bacteria. This hypothesis was tested in the American cockroach (Periplaneta americana) by interfering with this means of acquiring gut bacteria, which resulted in GF insects that exhibited prolonged growth rates and gut tissue dysmorphias relative to wild-type (WT) P. americana. Conventionalization of GF P. americana via consumption of frass (feces) from conspecifics and siblings reared under non-sterile conditions resulted in colonization of P. americana gut tissues by a diverse microbial community and a significant (p < 0.05) recovery of WT level growth and hindgut tissue development phenotypes. These data suggest that coprophagy is essential for normal gut tissue and organismal development by introducing beneficial gut bacteria to P. americana, and that the GF P. americana model system is a useful system for examining how gut bacteria impact host outcomes.
format: application/pdf
format: text/html
creator: Benjamin C. Jahnes
creator: Madeline Herrmann
creator: Zakee L. Sabree
subject: Entomology
subject: Microbiology
description: doi:10.7717/peerj.6914
publisher: PeerJ Inc.
rights: © 2019 Jahnes et al.
abstract: Microbial assemblages residing within and on animal gastric tissues contribute to various host beneficial processes that include diet accessibility and nutrient provisioning, and we sought to examine the degree to which intergenerational and community-acquired gut bacteria impact development in a tractable germ-free (GF) invertebrate model system. Coprophagy is a common behavior in cockroaches and termites that provides access to both nutrients and the primary means by which juveniles are inoculated with beneficial gut bacteria. This hypothesis was tested in the American cockroach (Periplaneta americana) by interfering with this means of acquiring gut bacteria, which resulted in GF insects that exhibited prolonged growth rates and gut tissue dysmorphias relative to wild-type (WT) P. americana. Conventionalization of GF P. americana via consumption of frass (feces) from conspecifics and siblings reared under non-sterile conditions resulted in colonization of P. americana gut tissues by a diverse microbial community and a significant (p < 0.05) recovery of WT level growth and hindgut tissue development phenotypes. These data suggest that coprophagy is essential for normal gut tissue and organismal development by introducing beneficial gut bacteria to P. americana, and that the GF P. americana model system is a useful system for examining how gut bacteria impact host outcomes.
bibliographic citation: Jahnes et al. (2019) Conspecific coprophagy stimulates normal development in a germ-free model invertebrate. PeerJ 7:e6914 https://doi.org/10.7717/peerj.6914
date submitted: 2018-12-19
date accepted: 2019-04-05
issued: 2019-05-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jahnes
  given name: Benjamin C.
author list: Agent
  family name: Herrmann
  given name: Madeline
author list: Agent
  family name: Sabree
  given name: Zakee L.
doi: 10.7717/peerj.6914
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-13
copyright: © 2019 Jahnes et al.
attribution name: Jahnes et al.

Plant diversity is closely related to the density of zokor mounds in three alpine rangelands on the Tibetan Plateau
type: item
type: AcademicArticle
description: Background Plateau zokor (Myospalax baileyi) is a subterranean rodent endemic to the Tibetan Plateau. This species has been generally viewed as a pest in China due to the competition for food with livestock and also causing soil erosion. As a result, plateau zokor has been the target of widespread poisoning or trapping campaigns designed to control or eliminate it since 1970s. But there is little research on the effect of plateau zokor on plant diversity in alpine rangelands. Therefore, objectively evaluating the positive effects of the plateau zokors disturbance on their living environment and plant communities is of great significance to understand the function of plateau zokor in alpine ecosystem. Methods Here, we selected three rangelands (alpine meadow, alpine steppe and alpine shrub meadow) in which plateau zokors are typically distributed on the Tibetan Plateau, and five zokor mound density gradients were selected in each rangeland type to study the effects of the mounds on soil moisture and temperature related to plant species diversity. Results The results showed that, with the mound density increasing, the soil temperature decreased significantly in all three rangeland types, and the soil moisture significantly increased in all three rangeland types. In the alpine meadow, both the plant diversity and cumulative species richness increased significantly with increasing mound density. The increase in broad-leaved forbs is the main reason for the increase of plant diversity in the alpine meadow disturbed by zokor mounds. In the alpine steppe, the plant diversity decreased significantly with increasing mound density, while the cumulative species richness initially decreased and then increased. In the alpine shrub meadow, the plant diversity first increased and then decreased with increasing mound density as did the cumulative species richness. In conclusion, plateau zokor mounds dominated the distribution of soil moisture and temperature and significantly affec…
format: application/pdf
format: text/html
creator: Yujie Niu
creator: Jianwei Zhou
creator: Siwei Yang
creator: Bin Chu
creator: Huimin Zhu
creator: Bo Zhang
creator: Qiangen Fang
creator: Zhuangsheng Tang
creator: Limin Hua
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Biosphere Interactions
subject: Natural Resource Management
description: doi:10.7717/peerj.6921
publisher: PeerJ Inc.
rights: © 2019 Niu et al.
abstract: Background Plateau zokor (Myospalax baileyi) is a subterranean rodent endemic to the Tibetan Plateau. This species has been generally viewed as a pest in China due to the competition for food with livestock and also causing soil erosion. As a result, plateau zokor has been the target of widespread poisoning or trapping campaigns designed to control or eliminate it since 1970s. But there is little research on the effect of plateau zokor on plant diversity in alpine rangelands. Therefore, objectively evaluating the positive effects of the plateau zokors disturbance on their living environment and plant communities is of great significance to understand the function of plateau zokor in alpine ecosystem. Methods Here, we selected three rangelands (alpine meadow, alpine steppe and alpine shrub meadow) in which plateau zokors are typically distributed on the Tibetan Plateau, and five zokor mound density gradients were selected in each rangeland type to study the effects of the mounds on soil moisture and temperature related to plant species diversity. Results The results showed that, with the mound density increasing, the soil temperature decreased significantly in all three rangeland types, and the soil moisture significantly increased in all three rangeland types. In the alpine meadow, both the plant diversity and cumulative species richness increased significantly with increasing mound density. The increase in broad-leaved forbs is the main reason for the increase of plant diversity in the alpine meadow disturbed by zokor mounds. In the alpine steppe, the plant diversity decreased significantly with increasing mound density, while the cumulative species richness initially decreased and then increased. In the alpine shrub meadow, the plant diversity first increased and then decreased with increasing mound density as did the cumulative species richness. In conclusion, plateau zokor mounds dominated the distribution of soil moisture and temperature and significantly affec…
bibliographic citation: Niu et al. (2019) Plant diversity is closely related to the density of zokor mounds in three alpine rangelands on the Tibetan Plateau. PeerJ 7:e6921 https://doi.org/10.7717/peerj.6921
date submitted: 2019-02-07
date accepted: 2019-04-08
issued: 2019-05-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niu
  given name: Yujie
author list: Agent
  family name: Zhou
  given name: Jianwei
author list: Agent
  family name: Yang
  given name: Siwei
author list: Agent
  family name: Chu
  given name: Bin
author list: Agent
  family name: Zhu
  given name: Huimin
author list: Agent
  family name: Zhang
  given name: Bo
author list: Agent
  family name: Fang
  given name: Qiangen
author list: Agent
  family name: Tang
  given name: Zhuangsheng
author list: Agent
  family name: Hua
  given name: Limin
doi: 10.7717/peerj.6921
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-13
copyright: © 2019 Niu et al.
attribution name: Niu et al.

Automated pupillometry to detect command following in neurological patients: a proof-of-concept study
type: item
type: AcademicArticle
description: Background Levels of consciousness in patients with acute and chronic brain injury are notoriously underestimated. Paradigms based on electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) may detect covert consciousness in clinically unresponsive patients but are subject to logistical challenges and the need for advanced statistical analysis. Methods To assess the feasibility of automated pupillometry for the detection of command following, we enrolled 20 healthy volunteers and 48 patients with a wide range of neurological disorders, including seven patients in the intensive care unit (ICU), who were asked to engage in mental arithmetic. Results Fourteen of 20 (70%) healthy volunteers and 17 of 43 (39.5%) neurological patients, including 1 in the ICU, fulfilled prespecified criteria for command following by showing pupillary dilations during ≥4 of five arithmetic tasks. None of the five sedated and unconscious ICU patients passed this threshold. Conclusions Automated pupillometry combined with mental arithmetic appears to be a promising paradigm for the detection of covert consciousness in people with brain injury. We plan to build on this study by focusing on non-communicating ICU patients in whom the level of consciousness is unknown. If some of these patients show reproducible pupillary dilation during mental arithmetic, this would suggest that the present paradigm can reveal covert consciousness in unresponsive patients in whom standard investigations have failed to detect signs of consciousness.
format: application/pdf
format: text/html
creator: Alexandra Vassilieva
creator: Markus Harboe Olsen
creator: Costanza Peinkhofer
creator: Gitte Moos Knudsen
creator: Daniel Kondziella
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Cognitive Disorders
subject: Emergency and Critical Care
subject: Neurology
description: doi:10.7717/peerj.6929
publisher: PeerJ Inc.
rights: © 2019 Vassilieva et al.
abstract: Background Levels of consciousness in patients with acute and chronic brain injury are notoriously underestimated. Paradigms based on electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) may detect covert consciousness in clinically unresponsive patients but are subject to logistical challenges and the need for advanced statistical analysis. Methods To assess the feasibility of automated pupillometry for the detection of command following, we enrolled 20 healthy volunteers and 48 patients with a wide range of neurological disorders, including seven patients in the intensive care unit (ICU), who were asked to engage in mental arithmetic. Results Fourteen of 20 (70%) healthy volunteers and 17 of 43 (39.5%) neurological patients, including 1 in the ICU, fulfilled prespecified criteria for command following by showing pupillary dilations during ≥4 of five arithmetic tasks. None of the five sedated and unconscious ICU patients passed this threshold. Conclusions Automated pupillometry combined with mental arithmetic appears to be a promising paradigm for the detection of covert consciousness in people with brain injury. We plan to build on this study by focusing on non-communicating ICU patients in whom the level of consciousness is unknown. If some of these patients show reproducible pupillary dilation during mental arithmetic, this would suggest that the present paradigm can reveal covert consciousness in unresponsive patients in whom standard investigations have failed to detect signs of consciousness.
bibliographic citation: Vassilieva et al. (2019) Automated pupillometry to detect command following in neurological patients: a proof-of-concept study. PeerJ 7:e6929 https://doi.org/10.7717/peerj.6929
date submitted: 2019-01-22
date accepted: 2019-04-09
issued: 2019-05-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vassilieva
  given name: Alexandra
author list: Agent
  family name: Olsen
  given name: Markus Harboe
author list: Agent
  family name: Peinkhofer
  given name: Costanza
author list: Agent
  family name: Knudsen
  given name: Gitte Moos
author list: Agent
  family name: Kondziella
  given name: Daniel
doi: 10.7717/peerj.6929
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-13
copyright: ©2019 Vassilieva et al.
attribution name: Vassilieva et al.

Large-scale insect outbreak homogenizes the spatial structure of ectomycorrhizal fungal communities
type: item
type: AcademicArticle
description: Ectomycorrhizal fungi (plant symbionts) are diverse and exist within spatially variable communities that play fundamental roles in the functioning of terrestrial ecosystems. However, the underlying ecological mechanisms that maintain and regulate the spatial structuring of ectomycorrhizal fungal communities are both complex and remain poorly understood. Here, we use a gradient of mountain pine beetle (Dendroctonus ponderosae) induced tree mortality across eleven stands in lodgepole pine (Pinus contorta) forests of western Canada to investigate: (i) the degree to which spatial structure varies within this fungal group, and (ii) how these patterns may be driven by the relative importance of tree mortality from changes in understory plant diversity, productivity and fine root biomass following tree death. We found that the homogeneity of the ectomycorrhizal fungal community increased with increasing tree death, aboveground understory productivity and diversity. Whereas, the independent effect of fine root biomass, which declined along the same gradient of tree mortality, increased the heterogeneity of the ectomycorrhizal fungal community. Together, our results demonstrate that large-scale biotic disturbance homogenizes the spatial patterns of ectomycorrhizal fungal communities.
format: application/pdf
format: text/html
creator: Gregory J. Pec
creator: James F. Cahill, Jr.
subject: Ecology
subject: Mycology
description: doi:10.7717/peerj.6895
publisher: PeerJ Inc.
rights: © 2019 Pec and Cahill
abstract: Ectomycorrhizal fungi (plant symbionts) are diverse and exist within spatially variable communities that play fundamental roles in the functioning of terrestrial ecosystems. However, the underlying ecological mechanisms that maintain and regulate the spatial structuring of ectomycorrhizal fungal communities are both complex and remain poorly understood. Here, we use a gradient of mountain pine beetle (Dendroctonus ponderosae) induced tree mortality across eleven stands in lodgepole pine (Pinus contorta) forests of western Canada to investigate: (i) the degree to which spatial structure varies within this fungal group, and (ii) how these patterns may be driven by the relative importance of tree mortality from changes in understory plant diversity, productivity and fine root biomass following tree death. We found that the homogeneity of the ectomycorrhizal fungal community increased with increasing tree death, aboveground understory productivity and diversity. Whereas, the independent effect of fine root biomass, which declined along the same gradient of tree mortality, increased the heterogeneity of the ectomycorrhizal fungal community. Together, our results demonstrate that large-scale biotic disturbance homogenizes the spatial patterns of ectomycorrhizal fungal communities.
bibliographic citation: Pec et al. (2019) Large-scale insect outbreak homogenizes the spatial structure of ectomycorrhizal fungal communities. PeerJ 7:e6895 https://doi.org/10.7717/peerj.6895
date submitted: 2018-11-16
date accepted: 2019-04-02
issued: 2019-05-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pec
  given name: Gregory J.
author list: Agent
  family name: Cahill, Jr.
  given name: James F.
doi: 10.7717/peerj.6895
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-10
copyright: ©2019 Pec and Cahill
attribution name: Pec and Cahill

Species delimitation of the Dermacentor ticks based on phylogenetic clustering and niche modeling
type: item
type: AcademicArticle
description: Three species belonging to the genus Dermacentor (Acari: Ixodidae), D. marginatus, D. nuttalli and D. silvarum are well known as vectors for a great variety of infection pathogens. All three of them are host ticks, which are very similar in morphology characteristics, life cycle, seasonal variation and ecological conditions, making it difficult to distinguish the three species. In the present study, these three species were delimitated based on molecular data and ecological niche. The molecular analysis showed that the three species can be distinguished by COI and ITS2 sequences. We created future potential distribution maps for the three species under climate changes with MaxEnt, which highlighted the different levels of the suitable habitats for each tick species. In addition, niche comparisons among the three species in Dermacentor were conducted, and the analysis suggested that niche overlap was relatively high with D. nuttalli and D. silvarum compared to the other species pairs, which was consistent with the molecular data. Niche equivalency and similarity test confirmed that these Dermacentor species were closely related but distinct species. In conclusion, delimitation of these three species within Dermacentor was supported by molecular phylogeny and quantitative ecological space. This study will provide deep insights into the biology, ecology, and diversification processes within Dermacentor species, and for the development of effective control for ticks.
format: application/pdf
format: text/html
creator: Fang Wang
creator: Duo Wang
creator: Ge Guo
creator: Yonghong Hu
creator: Jiufeng Wei
creator: Jingze Liu
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6911
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Three species belonging to the genus Dermacentor (Acari: Ixodidae), D. marginatus, D. nuttalli and D. silvarum are well known as vectors for a great variety of infection pathogens. All three of them are host ticks, which are very similar in morphology characteristics, life cycle, seasonal variation and ecological conditions, making it difficult to distinguish the three species. In the present study, these three species were delimitated based on molecular data and ecological niche. The molecular analysis showed that the three species can be distinguished by COI and ITS2 sequences. We created future potential distribution maps for the three species under climate changes with MaxEnt, which highlighted the different levels of the suitable habitats for each tick species. In addition, niche comparisons among the three species in Dermacentor were conducted, and the analysis suggested that niche overlap was relatively high with D. nuttalli and D. silvarum compared to the other species pairs, which was consistent with the molecular data. Niche equivalency and similarity test confirmed that these Dermacentor species were closely related but distinct species. In conclusion, delimitation of these three species within Dermacentor was supported by molecular phylogeny and quantitative ecological space. This study will provide deep insights into the biology, ecology, and diversification processes within Dermacentor species, and for the development of effective control for ticks.
bibliographic citation: Wang et al. (2019) Species delimitation of the Dermacentor ticks based on phylogenetic clustering and niche modeling. PeerJ 7:e6911 https://doi.org/10.7717/peerj.6911
date submitted: 2019-02-07
date accepted: 2019-04-05
issued: 2019-05-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Fang
author list: Agent
  family name: Wang
  given name: Duo
author list: Agent
  family name: Guo
  given name: Ge
author list: Agent
  family name: Hu
  given name: Yonghong
author list: Agent
  family name: Wei
  given name: Jiufeng
author list: Agent
  family name: Liu
  given name: Jingze
doi: 10.7717/peerj.6911
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-10
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Use of aerial thermography to reduce mortality of roe deer fawns before harvest
type: item
type: AcademicArticle
description: In agricultural landscape, there are thousands of young wild animals killed every year. Their deaths are caused mostly by agricultural fieldworks during spring harvest. Among the affected animals there are also fawns of roe deer (Capreolus capreolus), which react to danger by pressing themselves against the ground in order to be protected from predators. There were various methods tested in the past aimed at decreasing roe deer mortality caused by agriculture machinery with varied levels of success. This contribution presents technology that documents the possibility of searching for fawns with a thermal imaging device carried by an unmanned aerial vehicles (UAV). The results are based on field research that estimated the ideal height of flight being ±40 meters above ground. If the climatic conditions are favourable, it is possible to monitor and mark fawn locations using GPS coordinates in an area of about 14 ha in 25 minutes, which is the average flight time of UAV on one battery charge. The thermo-camera is very reliable in finding fawns in early morning hours (4 to 6 a.m.) when there is the highest temperature contrast between the searched object and its surroundings. The main limiting factors are climatic conditions and the short time span in which the thermo-camera can be used. If the basic requirements are met, the rate of successful fawn detection can be even up to 100%. An undisputed advantage of this method is the possibility of involvement of local gamekeepers. Thus the agricultural fieldworks are not interrupted.
format: application/pdf
format: text/html
creator: Jan Cukor
creator: Jan Bartoška
creator: Jan Rohla
creator: Jan Sova
creator: Antonín Machálek
subject: Agricultural Science
subject: Ethical Issues
description: doi:10.7717/peerj.6923
publisher: PeerJ Inc.
rights: © 2019 Cukor et al.
abstract: In agricultural landscape, there are thousands of young wild animals killed every year. Their deaths are caused mostly by agricultural fieldworks during spring harvest. Among the affected animals there are also fawns of roe deer (Capreolus capreolus), which react to danger by pressing themselves against the ground in order to be protected from predators. There were various methods tested in the past aimed at decreasing roe deer mortality caused by agriculture machinery with varied levels of success. This contribution presents technology that documents the possibility of searching for fawns with a thermal imaging device carried by an unmanned aerial vehicles (UAV). The results are based on field research that estimated the ideal height of flight being ±40 meters above ground. If the climatic conditions are favourable, it is possible to monitor and mark fawn locations using GPS coordinates in an area of about 14 ha in 25 minutes, which is the average flight time of UAV on one battery charge. The thermo-camera is very reliable in finding fawns in early morning hours (4 to 6 a.m.) when there is the highest temperature contrast between the searched object and its surroundings. The main limiting factors are climatic conditions and the short time span in which the thermo-camera can be used. If the basic requirements are met, the rate of successful fawn detection can be even up to 100%. An undisputed advantage of this method is the possibility of involvement of local gamekeepers. Thus the agricultural fieldworks are not interrupted.
bibliographic citation: Cukor et al. (2019) Use of aerial thermography to reduce mortality of roe deer fawns before harvest. PeerJ 7:e6923 https://doi.org/10.7717/peerj.6923
date submitted: 2019-01-02
date accepted: 2019-04-06
issued: 2019-05-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cukor
  given name: Jan
author list: Agent
  family name: Bartoška
  given name: Jan
author list: Agent
  family name: Rohla
  given name: Jan
author list: Agent
  family name: Sova
  given name: Jan
author list: Agent
  family name: Machálek
  given name: Antonín
doi: 10.7717/peerj.6923
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-10
copyright: ©2019 Cukor et al.
attribution name: Cukor et al.

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