PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Influence of different types of sessile epibionts on the community structure of mobile invertebrates in an eelgrass bed
items: Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes
items: The prognostic value of tumor length to resectable esophageal squamous cell carcinoma: a retrospective study
items: Nest-site selection, reproductive ecology and shifts within core-use areas of Black-necked Cranes at the northern limit of the Tibetan Plateau
items: Investigation of Helicobacter pylori infection among symptomatic children in Hangzhou from 2007 to 2014: a retrospective study with 12,796 cases
items: An early geikiid dicynodont from the Tropidostoma Assemblage Zone (late Permian) of South Africa
items: In situ morphometric survey elucidates the evolutionary systematics of the Eurasian Himantoglossum clade (Orchidaceae: Orchidinae)
items: Identification of four potential predicting miRNA biomarkers for multiple myeloma from published datasets
items: Expanding our understanding of the trade in marine aquarium animals
items: Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy

Influence of different types of sessile epibionts on the community structure of mobile invertebrates in an eelgrass bed
type: item
type: AcademicArticle
description: Eelgrass (Zostera marina) beds are known to have high ecological and economical values within coastal ecosystems of the temperate northern hemisphere although their biodiversity and functions varied greatly from sites to sites. The variation in the biomass, abundance and diversity of mobile invertebrates in eelgrass beds has been examined in relation to various abiotic and biotic factors, such as water temperature, salinity, eelgrass biomass and epiphytic microalgae presence. However, the importance of sessile epibionts, such as macroalgae and calcific spirorbid polychaetes attached to eelgrass blades, has not been the focus of previous studies. In the present study, we examined the effects of three different sessile epibionts, namely, branched red algae, filamentous green algae, and calcific spirorbid polychaetes, on the biomass and diversity of mobile invertebrates in the eelgrass beds of Akkeshi in northeastern Japan. The relationships between seven abiotic and biotic variables including three types of epibionts, and biomass of 11 dominant mobile invertebrate species as well as three community-level variables (the total biomass of mobile invertebrates, species richness and the Shannon-Wiener species diversity index) were analyzed using a linear mixed model. Our results show that branched red algae are correlated with Pontogeneia rostrata, Lacuna spp., Nereis sp., Syllis sp. and the total biomass of mobile invertebrates, filamentous green algae with P. rostrata, Ansola angustata and the species diversity of mobile invertebrates, and spirorbid polychaetes with A. angustata, Lacuna spp., Siphonacmea oblongata, Syllis sp., the species richness and diversity of mobile invertebrates. The effect size of the epibionts was similar or even higher than that of abiotic and eelgrass factors on the total biomass of mobile invertebrates, species richness, species diversity and most of dominant invertebrate populations across the taxonomic groups. Consequently, epibiotic macroal…
format: application/pdf
format: text/html
creator: Kyosuke Momota
creator: Masahiro Nakaoka
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.2952
publisher: PeerJ Inc.
rights: © 2017 Momota and Nakaoka
abstract: Eelgrass (Zostera marina) beds are known to have high ecological and economical values within coastal ecosystems of the temperate northern hemisphere although their biodiversity and functions varied greatly from sites to sites. The variation in the biomass, abundance and diversity of mobile invertebrates in eelgrass beds has been examined in relation to various abiotic and biotic factors, such as water temperature, salinity, eelgrass biomass and epiphytic microalgae presence. However, the importance of sessile epibionts, such as macroalgae and calcific spirorbid polychaetes attached to eelgrass blades, has not been the focus of previous studies. In the present study, we examined the effects of three different sessile epibionts, namely, branched red algae, filamentous green algae, and calcific spirorbid polychaetes, on the biomass and diversity of mobile invertebrates in the eelgrass beds of Akkeshi in northeastern Japan. The relationships between seven abiotic and biotic variables including three types of epibionts, and biomass of 11 dominant mobile invertebrate species as well as three community-level variables (the total biomass of mobile invertebrates, species richness and the Shannon-Wiener species diversity index) were analyzed using a linear mixed model. Our results show that branched red algae are correlated with Pontogeneia rostrata, Lacuna spp., Nereis sp., Syllis sp. and the total biomass of mobile invertebrates, filamentous green algae with P. rostrata, Ansola angustata and the species diversity of mobile invertebrates, and spirorbid polychaetes with A. angustata, Lacuna spp., Siphonacmea oblongata, Syllis sp., the species richness and diversity of mobile invertebrates. The effect size of the epibionts was similar or even higher than that of abiotic and eelgrass factors on the total biomass of mobile invertebrates, species richness, species diversity and most of dominant invertebrate populations across the taxonomic groups. Consequently, epibiotic macroal…
bibliographic citation: Momota et al. (2017) Influence of different types of sessile epibionts on the community structure of mobile invertebrates in an eelgrass bed. PeerJ 5:e2952 https://doi.org/10.7717/peerj.2952
date submitted: 2016-11-11
date accepted: 2016-12-31
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Momota
  given name: Kyosuke
author list: Agent
  family name: Nakaoka
  given name: Masahiro
doi: 10.7717/peerj.2952
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Momota and Nakaoka
attribution name: Momota and Nakaoka

Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes
type: item
type: AcademicArticle
description: A high-quality draft genome for Proctacanthus coquilletti (Insecta: Diptera: Asilidae) is presented along with transcriptomes for 16 Diptera species from five families: Asilidae, Apioceridae, Bombyliidae, Mydidae, and Tabanidae. Genome sequencing reveals that P. coquilletti has a genome size of approximately 210 Mbp and remarkably low heterozygosity (0.47%) and few repeats (15%). These characteristics helped produce a highly contiguous (N50 = 862 kbp) assembly, particularly given that only a single 2 × 250 bp PCR-free Illumina library was sequenced. A phylogenomic hypothesis is presented based on thousands of putative orthologs across the 16 transcriptomes. Phylogenetic relationships support the sister group relationship of Apioceridae + Mydidae to Asilidae. A time-calibrated phylogeny is also presented, with seven fossil calibration points, which suggests an older age of the split among Apioceridae, Asilidae, and Mydidae (158 mya) and Apioceridae and Mydidae (135 mya) than proposed in the AToL FlyTree project. Future studies will be able to take advantage of the resources presented here in order to produce large scale phylogenomic and evolutionary studies of assassin fly phylogeny, life histories, or venom. The bioinformatics tools and workflow presented here will be useful to others wishing to generate de novo genomic resources in species-rich taxa without a closely-related reference genome.
format: application/pdf
format: text/html
creator: Rebecca B. Dikow
creator: Paul B. Frandsen
creator: Mauren Turcatel
creator: Torsten Dikow
subject: Entomology
subject: Genomics
description: doi:10.7717/peerj.2951
publisher: PeerJ Inc.
rights: © 2017 Dikow et al.
abstract: A high-quality draft genome for Proctacanthus coquilletti (Insecta: Diptera: Asilidae) is presented along with transcriptomes for 16 Diptera species from five families: Asilidae, Apioceridae, Bombyliidae, Mydidae, and Tabanidae. Genome sequencing reveals that P. coquilletti has a genome size of approximately 210 Mbp and remarkably low heterozygosity (0.47%) and few repeats (15%). These characteristics helped produce a highly contiguous (N50 = 862 kbp) assembly, particularly given that only a single 2 × 250 bp PCR-free Illumina library was sequenced. A phylogenomic hypothesis is presented based on thousands of putative orthologs across the 16 transcriptomes. Phylogenetic relationships support the sister group relationship of Apioceridae + Mydidae to Asilidae. A time-calibrated phylogeny is also presented, with seven fossil calibration points, which suggests an older age of the split among Apioceridae, Asilidae, and Mydidae (158 mya) and Apioceridae and Mydidae (135 mya) than proposed in the AToL FlyTree project. Future studies will be able to take advantage of the resources presented here in order to produce large scale phylogenomic and evolutionary studies of assassin fly phylogeny, life histories, or venom. The bioinformatics tools and workflow presented here will be useful to others wishing to generate de novo genomic resources in species-rich taxa without a closely-related reference genome.
bibliographic citation: Dikow et al. (2017) Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes. PeerJ 5:e2951 https://doi.org/10.7717/peerj.2951
date submitted: 2016-10-25
date accepted: 2016-12-31
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dikow
  given name: Rebecca B.
author list: Agent
  family name: Frandsen
  given name: Paul B.
author list: Agent
  family name: Turcatel
  given name: Mauren
author list: Agent
  family name: Dikow
  given name: Torsten
doi: 10.7717/peerj.2951
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Dikow et al.
attribution name: Dikow et al.

The prognostic value of tumor length to resectable esophageal squamous cell carcinoma: a retrospective study
type: item
type: AcademicArticle
description: Background The current TNM classification system does not consider tumor length for patients with esophageal carcinoma (EC). This study explored the effect of tumor length, in addition to tumor depth and lymph node involvement, on survival in patients with esophageal squamous cell carcinoma (ESCC). Methods A total of 498 ESCC patients who underwent surgical resection as the primary treatment were selected in the retrospective study. Pathological details were collected, which included tumor type, TNM stage, differentiation. Other collected information were: the types of esophageal resection, ABO blood group, family history and demographic and lifestyle factors. A time-dependent receiver operating characteristic (ROC) curve and a regression tree for survival were used to identify the cut-off point of tumor length, which was 3 cm. Univariate and multivariate Cox proportional hazard regression models were used to identify the prognostic factors to ESCC. Results & Discussion The 1-, 3-, 5-year overall survival rates were found to be 82.5%, 55.6%, and 35.1%, respectively. Patients who had larger tumor length (>3 cm) had a higher risk for death than the rest patients. From the univariate Cox proportional hazards regression model, the overall survival rate was significantly influenced by the depth of the tumor and lymph node involvement (either as dummy or continuous variables), Sex, and tumor length. Using these four variables in the multivariate Cox proportional hazard regression model, we found that the overall survival was significantly influenced by all variables except Sex. Therefore, in addition to the depth of the tumor and lymph node involvement (as either dummy or continuous variables), the tumor length is also an independent prognostic factor for ESCC. The overall survival rate was higher in a group with smaller tumor length (≤3 cm) than those patients with larger tumor length (>3 cm), no matter what the tumor stage was. Conclusion The tumor length was found to b…
format: application/pdf
format: text/html
creator: Xiangwei Zhang
creator: Yang Wang
creator: Cheng Li
creator: Jing Helmersson
creator: Yuanzhu Jiang
creator: Guoyuan Ma
creator: Guanghui Wang
creator: Wei Dong
creator: Shaowei Sang
creator: Jiajun Du
subject: Oncology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.2943
publisher: PeerJ Inc.
rights: © 2017 Zhang et al.
abstract: Background The current TNM classification system does not consider tumor length for patients with esophageal carcinoma (EC). This study explored the effect of tumor length, in addition to tumor depth and lymph node involvement, on survival in patients with esophageal squamous cell carcinoma (ESCC). Methods A total of 498 ESCC patients who underwent surgical resection as the primary treatment were selected in the retrospective study. Pathological details were collected, which included tumor type, TNM stage, differentiation. Other collected information were: the types of esophageal resection, ABO blood group, family history and demographic and lifestyle factors. A time-dependent receiver operating characteristic (ROC) curve and a regression tree for survival were used to identify the cut-off point of tumor length, which was 3 cm. Univariate and multivariate Cox proportional hazard regression models were used to identify the prognostic factors to ESCC. Results & Discussion The 1-, 3-, 5-year overall survival rates were found to be 82.5%, 55.6%, and 35.1%, respectively. Patients who had larger tumor length (>3 cm) had a higher risk for death than the rest patients. From the univariate Cox proportional hazards regression model, the overall survival rate was significantly influenced by the depth of the tumor and lymph node involvement (either as dummy or continuous variables), Sex, and tumor length. Using these four variables in the multivariate Cox proportional hazard regression model, we found that the overall survival was significantly influenced by all variables except Sex. Therefore, in addition to the depth of the tumor and lymph node involvement (as either dummy or continuous variables), the tumor length is also an independent prognostic factor for ESCC. The overall survival rate was higher in a group with smaller tumor length (≤3 cm) than those patients with larger tumor length (>3 cm), no matter what the tumor stage was. Conclusion The tumor length was found to b…
bibliographic citation: Zhang et al. (2017) The prognostic value of tumor length to resectable esophageal squamous cell carcinoma: a retrospective study. PeerJ 5:e2943 https://doi.org/10.7717/peerj.2943
date submitted: 2016-08-25
date accepted: 2016-12-28
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiangwei
author list: Agent
  family name: Wang
  given name: Yang
author list: Agent
  family name: Li
  given name: Cheng
author list: Agent
  family name: Helmersson
  given name: Jing
author list: Agent
  family name: Jiang
  given name: Yuanzhu
author list: Agent
  family name: Ma
  given name: Guoyuan
author list: Agent
  family name: Wang
  given name: Guanghui
author list: Agent
  family name: Dong
  given name: Wei
author list: Agent
  family name: Sang
  given name: Shaowei
author list: Agent
  family name: Du
  given name: Jiajun
doi: 10.7717/peerj.2943
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Zhang et al.
attribution name: Zhang et al.

Nest-site selection, reproductive ecology and shifts within core-use areas of Black-necked Cranes at the northern limit of the Tibetan Plateau
type: item
type: AcademicArticle
description: We investigated population dynamics, breeding pairs, breeding habitat selection, nest density, distance between neighboring nests, nest survival, reproductive success, and recruitment rate for Black-necked Cranes (BNC, Grus nigricollis) during 2013–2015 in Yanchiwan National Nature Reserve (YCW), Gansu, China. Numbers of BNC and breeding pairs remained relatively stable at around 140 individuals and 40 pairs. Recruitment rates ranged from 15.7% to 25.8%. The average nest distance was 718.66 ± 430.50 m (2013), 1064.51 ± 323.99 m (2014) and 534.99 ± 195.45 m (2015). Average nest survival rate, hatching success, and breeding success of all 29 nests were 65.56 ± 5.09%, 57.04 ± 6.12% and 32.78% ± 2.55. Water depth, water body area, and distance to land were positively related to nest survival, while disturbance level showed a negative relationship. However, nest site selection of BNC was determined by habitat type, disturbance and water depth. BNC often foraged in mudflats and freshwater marsh but seldom foraged in saline-alkali wet meadows due to food density and quantity in April, the month when BNC choose nest sites. Conservation strategies based on habitats should consider ecological factors that may not be well predicted by nest site selection. Shifts within core-use areas from satellite tracking of BNC demonstrated that maintaining populations demands that conservation areas are large enough to permit breeding BNC changes in space use. Our results are important for conservation management and provide quantitative reproductive data for this species.
format: application/pdf
format: text/html
creator: Lixun Zhang
creator: Bei An
creator: Meilin Shu
creator: Xiaojun Yang
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.2939
publisher: PeerJ Inc.
rights: © 2017 Zhang et al.
abstract: We investigated population dynamics, breeding pairs, breeding habitat selection, nest density, distance between neighboring nests, nest survival, reproductive success, and recruitment rate for Black-necked Cranes (BNC, Grus nigricollis) during 2013–2015 in Yanchiwan National Nature Reserve (YCW), Gansu, China. Numbers of BNC and breeding pairs remained relatively stable at around 140 individuals and 40 pairs. Recruitment rates ranged from 15.7% to 25.8%. The average nest distance was 718.66 ± 430.50 m (2013), 1064.51 ± 323.99 m (2014) and 534.99 ± 195.45 m (2015). Average nest survival rate, hatching success, and breeding success of all 29 nests were 65.56 ± 5.09%, 57.04 ± 6.12% and 32.78% ± 2.55. Water depth, water body area, and distance to land were positively related to nest survival, while disturbance level showed a negative relationship. However, nest site selection of BNC was determined by habitat type, disturbance and water depth. BNC often foraged in mudflats and freshwater marsh but seldom foraged in saline-alkali wet meadows due to food density and quantity in April, the month when BNC choose nest sites. Conservation strategies based on habitats should consider ecological factors that may not be well predicted by nest site selection. Shifts within core-use areas from satellite tracking of BNC demonstrated that maintaining populations demands that conservation areas are large enough to permit breeding BNC changes in space use. Our results are important for conservation management and provide quantitative reproductive data for this species.
bibliographic citation: Zhang et al. (2017) Nest-site selection, reproductive ecology and shifts within core-use areas of Black-necked Cranes at the northern limit of the Tibetan Plateau. PeerJ 5:e2939 https://doi.org/10.7717/peerj.2939
date submitted: 2016-08-15
date accepted: 2016-12-23
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Lixun
author list: Agent
  family name: An
  given name: Bei
author list: Agent
  family name: Shu
  given name: Meilin
author list: Agent
  family name: Yang
  given name: Xiaojun
doi: 10.7717/peerj.2939
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Zhang et al.
attribution name: Zhang et al.

Investigation of Helicobacter pylori infection among symptomatic children in Hangzhou from 2007 to 2014: a retrospective study with 12,796 cases
type: item
type: AcademicArticle
description: Background and Aim The infection of Helicobacter pylori (H. pylori) is acquired in childhood and the prevalence vary greatly in different countries and regions. The study aimed to investigate the characteristics of H. pylori infection among children with gastrointestinal symptoms in Hangzhou, a representative city of eastern China. Methods A systematic surveillance of H. pylori infection according to the 13C-urea breath test was conducted from January 2007 to December 2014 in the Children’s hospital, Zhejiang University School of Medicine. The demographic information and main symptoms of every subject were recorded. Results A total of 12,796 subjects were recruited and 18.6% children evaluated as H. pylori positive. The annual positive rates decreased from 2007 to 2014 (χ2 = 20.461, p < 0.01). The positive rates were 14.8%, 20.2% and 25.8% in 3–6, 7–11 and 12–17 years age group respectively, which increased with age (χ2 = 116.002, p < 0.01). And it was significantly higher in boys than girls (χ2 = 15.090, p < 0.01). Multivariate logistic regression identified possible risk factors for H. pylori infection. Age, gender, gastrointestinal symptoms and history of H. pylori infected family member were all significantly associated with H. pylori infection (all p < 0.05). Conclusions H. pylori infection rates in children with gastrointestinal symptoms were lower than most of those reported in mainland China. Further studies are required to determine the prevalence in the general population. Comprehensively understanding of the characteristics and the possible risk factors of H. pylori infection will be helpful to its management strategies in children in China.
format: application/pdf
format: text/html
creator: Xiaoli Shu
creator: Mingfang Ping
creator: Guofeng Yin
creator: Mizu Jiang
subject: Gastroenterology and Hepatology
subject: Pediatrics
description: doi:10.7717/peerj.2937
publisher: PeerJ Inc.
rights: © 2017 Shu et al.
abstract: Background and Aim The infection of Helicobacter pylori (H. pylori) is acquired in childhood and the prevalence vary greatly in different countries and regions. The study aimed to investigate the characteristics of H. pylori infection among children with gastrointestinal symptoms in Hangzhou, a representative city of eastern China. Methods A systematic surveillance of H. pylori infection according to the 13C-urea breath test was conducted from January 2007 to December 2014 in the Children’s hospital, Zhejiang University School of Medicine. The demographic information and main symptoms of every subject were recorded. Results A total of 12,796 subjects were recruited and 18.6% children evaluated as H. pylori positive. The annual positive rates decreased from 2007 to 2014 (χ2 = 20.461, p < 0.01). The positive rates were 14.8%, 20.2% and 25.8% in 3–6, 7–11 and 12–17 years age group respectively, which increased with age (χ2 = 116.002, p < 0.01). And it was significantly higher in boys than girls (χ2 = 15.090, p < 0.01). Multivariate logistic regression identified possible risk factors for H. pylori infection. Age, gender, gastrointestinal symptoms and history of H. pylori infected family member were all significantly associated with H. pylori infection (all p < 0.05). Conclusions H. pylori infection rates in children with gastrointestinal symptoms were lower than most of those reported in mainland China. Further studies are required to determine the prevalence in the general population. Comprehensively understanding of the characteristics and the possible risk factors of H. pylori infection will be helpful to its management strategies in children in China.
bibliographic citation: Shu et al. (2017) Investigation of Helicobacter pylori infection among symptomatic children in Hangzhou from 2007 to 2014: a retrospective study with 12,796 cases. PeerJ 5:e2937 https://doi.org/10.7717/peerj.2937
date submitted: 2016-08-15
date accepted: 2016-12-23
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shu
  given name: Xiaoli
author list: Agent
  family name: Ping
  given name: Mingfang
author list: Agent
  family name: Yin
  given name: Guofeng
author list: Agent
  family name: Jiang
  given name: Mizu
doi: 10.7717/peerj.2937
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Shu et al.
attribution name: Shu et al.

An early geikiid dicynodont from the Tropidostoma Assemblage Zone (late Permian) of South Africa
type: item
type: AcademicArticle
description: Based on specimens previously identified as Tropidostoma, a new taxon of dicynodont (Bulbasaurus phylloxyron gen. et sp. nov.) from the Karoo Basin of South Africa is described. Bulbasaurus is a medium-sized dicynodont (maximum dorsal skull length 16.0 cm) restricted to the Tropidostoma Assemblage Zone (early Lopingian) of the Beaufort Group. Bulbasaurus can be distinguished from Tropidostoma by an array of characters including the presence of a tall, sharp premaxillary ridge, large, rugose, nearly-confluent nasal bosses, a nasofrontal ridge, massive tusks, robust pterygoids, prominently twisted subtemporal bar, and absence of a distinct postfrontal. Inclusion of Bulbasaurus in a phylogenetic analysis of anomodont therapsids recovers it as a member of Geikiidae, a clade of otherwise later Permian dicynodonts such as Aulacephalodon and Pelanomodon. Bulbasaurus exhibits many of the characters typical of adult Aulacephalodon, but at substantially smaller skull size (these characters are absent in comparably-sized Aulacephalodon juveniles), suggesting that the evolution of typical geikiid morphology preceded gigantism in the clade. Bulbasaurus is the earliest known geikiid and the only member of the group known from the Tropidostoma Assemblage Zone; discovery of this taxon shortens a perplexing ghost lineage and indicates that abundant clades from the later Permian of South Africa (e.g., Geikiidae, Dicynodontoidea) may have originated as rare components of earlier Karoo assemblage zones.
format: application/pdf
format: text/html
creator: Christian F. Kammerer
creator: Roger M.H. Smith
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2913
publisher: PeerJ Inc.
rights: © 2017 Kammerer et al.
abstract: Based on specimens previously identified as Tropidostoma, a new taxon of dicynodont (Bulbasaurus phylloxyron gen. et sp. nov.) from the Karoo Basin of South Africa is described. Bulbasaurus is a medium-sized dicynodont (maximum dorsal skull length 16.0 cm) restricted to the Tropidostoma Assemblage Zone (early Lopingian) of the Beaufort Group. Bulbasaurus can be distinguished from Tropidostoma by an array of characters including the presence of a tall, sharp premaxillary ridge, large, rugose, nearly-confluent nasal bosses, a nasofrontal ridge, massive tusks, robust pterygoids, prominently twisted subtemporal bar, and absence of a distinct postfrontal. Inclusion of Bulbasaurus in a phylogenetic analysis of anomodont therapsids recovers it as a member of Geikiidae, a clade of otherwise later Permian dicynodonts such as Aulacephalodon and Pelanomodon. Bulbasaurus exhibits many of the characters typical of adult Aulacephalodon, but at substantially smaller skull size (these characters are absent in comparably-sized Aulacephalodon juveniles), suggesting that the evolution of typical geikiid morphology preceded gigantism in the clade. Bulbasaurus is the earliest known geikiid and the only member of the group known from the Tropidostoma Assemblage Zone; discovery of this taxon shortens a perplexing ghost lineage and indicates that abundant clades from the later Permian of South Africa (e.g., Geikiidae, Dicynodontoidea) may have originated as rare components of earlier Karoo assemblage zones.
bibliographic citation: Kammerer et al. (2017) An early geikiid dicynodont from the Tropidostoma Assemblage Zone (late Permian) of South Africa. PeerJ 5:e2913 https://doi.org/10.7717/peerj.2913
date submitted: 2016-10-14
date accepted: 2016-12-14
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kammerer
  given name: Christian F.
author list: Agent
  family name: Smith
  given name: Roger M.H.
doi: 10.7717/peerj.2913
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Kammerer et al.
attribution name: Kammerer et al.

In situ morphometric survey elucidates the evolutionary systematics of the Eurasian Himantoglossum clade (Orchidaceae: Orchidinae)
type: item
type: AcademicArticle
description: Background and Aims The charismatic Himantoglossum s.l. clade of Eurasian orchids contains an unusually large proportion of taxa that are of controversial circumscriptions and considerable conservation concern. Whereas our previously published study addressed the molecular phylogenetics and phylogeography of every named taxon within the clade, here we use detailed morphometric data obtained from the same populations to compare genotypes with associated phenotypes, in order to better explore taxonomic circumscription and character evolution within the clade. Methods Between one and 12 plants found in 25 populations that encompassed the entire distribution of the Himantoglossum s.l. clade were measured in situ for 51 morphological characters. Results for 45 of those characters were subjected to detailed multivariate and univariate analyses. Key Results Multivariate analyses readily separate subgenus Barlia and subgenus Comperia from subgenus Himantoglossum, and also the early-divergent H. formosum from the less divergent remainder of subgenus Himantoglossum. The sequence of divergence of these four lineages is confidently resolved. Our experimental approach to morphometric character analysis demonstrates clearly that phenotypic evolution within Himantoglossum is unusually multi-dimensional. Conclusions Degrees of divergence between taxa shown by morphological analyses approximate those previously shown using molecular analyses. Himantoglossum s.l. is readily divisible into three subgenera. The three sections of subgenus Himantoglossum—hircinum, caprinum and formosum—are arrayed from west to east with only limited geographical overlap. At this taxonomic level, their juxtaposition combines with conflict between contrasting datasets to complicate attempts to distinguish between clinal variation and the discontinuities that by definition separate bona fide species. All taxa achieve allogamy via food deceit and have only weak pollinator specificity. Artificial crossing dem…
format: application/pdf
format: text/html
creator: Richard M. Bateman
creator: Attila Molnár V.
creator: Gábor Sramkó
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.2893
publisher: PeerJ Inc.
rights: © 2017 Bateman et al.
abstract: Background and Aims The charismatic Himantoglossum s.l. clade of Eurasian orchids contains an unusually large proportion of taxa that are of controversial circumscriptions and considerable conservation concern. Whereas our previously published study addressed the molecular phylogenetics and phylogeography of every named taxon within the clade, here we use detailed morphometric data obtained from the same populations to compare genotypes with associated phenotypes, in order to better explore taxonomic circumscription and character evolution within the clade. Methods Between one and 12 plants found in 25 populations that encompassed the entire distribution of the Himantoglossum s.l. clade were measured in situ for 51 morphological characters. Results for 45 of those characters were subjected to detailed multivariate and univariate analyses. Key Results Multivariate analyses readily separate subgenus Barlia and subgenus Comperia from subgenus Himantoglossum, and also the early-divergent H. formosum from the less divergent remainder of subgenus Himantoglossum. The sequence of divergence of these four lineages is confidently resolved. Our experimental approach to morphometric character analysis demonstrates clearly that phenotypic evolution within Himantoglossum is unusually multi-dimensional. Conclusions Degrees of divergence between taxa shown by morphological analyses approximate those previously shown using molecular analyses. Himantoglossum s.l. is readily divisible into three subgenera. The three sections of subgenus Himantoglossum—hircinum, caprinum and formosum—are arrayed from west to east with only limited geographical overlap. At this taxonomic level, their juxtaposition combines with conflict between contrasting datasets to complicate attempts to distinguish between clinal variation and the discontinuities that by definition separate bona fide species. All taxa achieve allogamy via food deceit and have only weak pollinator specificity. Artificial crossing dem…
bibliographic citation: Bateman et al. (2017) In situ morphometric survey elucidates the evolutionary systematics of the Eurasian Himantoglossum clade (Orchidaceae: Orchidinae). PeerJ 5:e2893 https://doi.org/10.7717/peerj.2893
date submitted: 2016-10-14
date accepted: 2016-12-09
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bateman
  given name: Richard M.
author list: Agent
  family name: Molnár V.
  given name: Attila
author list: Agent
  family name: Sramkó
  given name: Gábor
doi: 10.7717/peerj.2893
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Bateman et al.
attribution name: Bateman et al.

Identification of four potential predicting miRNA biomarkers for multiple myeloma from published datasets
type: item
type: AcademicArticle
description: Background Multiple myeloma is a cancer which has a high occurrence rate and causes great injury to people worldwide. In recent years, many studies reported the effects of miRNA on the appearance of multiple myeloma. However, due to the differences of samples and sequencing platforms, a large number of inconsistent results have been generated among these studies, which limited the cure of multiple myeloma at the miRNA level. Methods We performed meta-analyses to identify the key miRNA biomarkers which could be applied on the treatment of multiple myeloma. The key miRNAs were determined by overlap comparisons of seven datasets in multiple myeloma. Then, the target genes for key miRNAs were predicted by the software TargetScan. Additionally, functional enrichments and binding TFs were investigated by DAVID database and Tfacts database, respectively. Results Firstly, comparing the normal tissues, 13 miRNAs were differently expressed miRNAs (DEMs) for at least three datasets. They were considered as key miRNAs, with 12 up-regulated (hsa-miR-106b, hsa-miR-125b, hsa-miR-130b, hsa-miR-138, hsa-miR-15b, hsa-miR-181a, hsa-miR-183, hsa-miR-191, hsa-miR-19a, hsa-miR-20a, hsa-miR-221 and hsa-miR-25) and one down-regulated (hsa-miR-223). Secondly, functional enrichment analyses indicated that target genes of the upregulated miRNAs were mainly transcript factors and enriched in transcription regulation. Besides, these genes were enriched in multiple pathways: the cancer signal pathway, insulin signal metabolic pathway, cell binding molecules, melanin generation, long-term regression and P53 signaling pathway. However, no significant enrichment was found for target genes of the down-regulated genes. Due to the distinct regulation function, four miRNAs (hsa-miR-19a has-miR-221 has-miR25 and has-miR223) were ascertained as the potential prognostic and diagnostic markers in MM. Thirdly, transcript factors analysis unveiled that there were 148 TFs and 60 TFs which bind target genes of…
format: application/pdf
format: text/html
creator: Tian Xiang
creator: Ai-Xin Hu
creator: Peng Sun
creator: Gao Liu
creator: Gang Liu
creator: Yan Xiao
subject: Genomics
subject: Dermatology
subject: Oncology
description: doi:10.7717/peerj.2831
publisher: PeerJ Inc.
rights: © 2017 Xiang et al.
abstract: Background Multiple myeloma is a cancer which has a high occurrence rate and causes great injury to people worldwide. In recent years, many studies reported the effects of miRNA on the appearance of multiple myeloma. However, due to the differences of samples and sequencing platforms, a large number of inconsistent results have been generated among these studies, which limited the cure of multiple myeloma at the miRNA level. Methods We performed meta-analyses to identify the key miRNA biomarkers which could be applied on the treatment of multiple myeloma. The key miRNAs were determined by overlap comparisons of seven datasets in multiple myeloma. Then, the target genes for key miRNAs were predicted by the software TargetScan. Additionally, functional enrichments and binding TFs were investigated by DAVID database and Tfacts database, respectively. Results Firstly, comparing the normal tissues, 13 miRNAs were differently expressed miRNAs (DEMs) for at least three datasets. They were considered as key miRNAs, with 12 up-regulated (hsa-miR-106b, hsa-miR-125b, hsa-miR-130b, hsa-miR-138, hsa-miR-15b, hsa-miR-181a, hsa-miR-183, hsa-miR-191, hsa-miR-19a, hsa-miR-20a, hsa-miR-221 and hsa-miR-25) and one down-regulated (hsa-miR-223). Secondly, functional enrichment analyses indicated that target genes of the upregulated miRNAs were mainly transcript factors and enriched in transcription regulation. Besides, these genes were enriched in multiple pathways: the cancer signal pathway, insulin signal metabolic pathway, cell binding molecules, melanin generation, long-term regression and P53 signaling pathway. However, no significant enrichment was found for target genes of the down-regulated genes. Due to the distinct regulation function, four miRNAs (hsa-miR-19a has-miR-221 has-miR25 and has-miR223) were ascertained as the potential prognostic and diagnostic markers in MM. Thirdly, transcript factors analysis unveiled that there were 148 TFs and 60 TFs which bind target genes of…
bibliographic citation: Xiang et al. (2017) Identification of four potential predicting miRNA biomarkers for multiple myeloma from published datasets. PeerJ 5:e2831 https://doi.org/10.7717/peerj.2831
date submitted: 2016-08-23
date accepted: 2016-11-24
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiang
  given name: Tian
author list: Agent
  family name: Hu
  given name: Ai-Xin
author list: Agent
  family name: Sun
  given name: Peng
author list: Agent
  family name: Liu
  given name: Gao
author list: Agent
  family name: Liu
  given name: Gang
author list: Agent
  family name: Xiao
  given name: Yan
doi: 10.7717/peerj.2831
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Xiang et al.
attribution name: Xiang et al.

Expanding our understanding of the trade in marine aquarium animals
type: item
type: AcademicArticle
description: The trade of live marine animals for home and public aquaria has grown into a major global industry. Millions of marine fishes and invertebrates are removed from coral reefs and associated habitats each year. The majority are imported into the United States, with the remainder sent to Europe, Japan, and a handful of other countries. Despite the recent growth and diversification of the aquarium trade, to date, data collection is not mandatory, and hence comprehensive information on species volume and diversity is lacking. This lack of information makes it impossible to study trade pathways. Without species-specific volume and diversity data, it is unclear how importing and exporting governments can oversee this industry effectively or how sustainability should be encouraged. To expand our knowledge and understanding of the trade, and to effectively communicate this new understanding, we introduce the publically-available Marine Aquarium Biodiversity and Trade Flow online database (https://www.aquariumtradedata.org/). This tool was created to communicate the volume and diversity of marine fishes and/or invertebrates imported into the US over three complete years (2008, 2009, and 2011) and three partial years (2000, 2004, 2005). To create this tool, invoices pertaining to shipments of live marine fishes and invertebrates were scanned and analyzed for species name, species quantities, country of origin, port of entry, and city of import destination. Here we focus on the analysis of the later three years of data and also produce an estimate for the entirety of 2000, 2004, and 2005. The three-year aggregate totals (2008, 2009, 2011) indicate that just under 2,300 fish and 725 invertebrate species were imported into the US cumulatively, although just under 1,800 fish and 550 invertebrate species were traded annually. Overall, the total number of live marine animals decreased between 2008 and 2011. In 2008, 2009, and 2011, the total number of individual fish (8.2, 7.3, and …
format: application/pdf
format: text/html
creator: Andrew L. Rhyne
creator: Michael F. Tlusty
creator: Joseph T. Szczebak
creator: Robert J. Holmberg
subject: Marine Biology
subject: Natural Resource Management
subject: Science Policy
description: doi:10.7717/peerj.2949
publisher: PeerJ Inc.
rights: © 2017 Rhyne et al.
abstract: The trade of live marine animals for home and public aquaria has grown into a major global industry. Millions of marine fishes and invertebrates are removed from coral reefs and associated habitats each year. The majority are imported into the United States, with the remainder sent to Europe, Japan, and a handful of other countries. Despite the recent growth and diversification of the aquarium trade, to date, data collection is not mandatory, and hence comprehensive information on species volume and diversity is lacking. This lack of information makes it impossible to study trade pathways. Without species-specific volume and diversity data, it is unclear how importing and exporting governments can oversee this industry effectively or how sustainability should be encouraged. To expand our knowledge and understanding of the trade, and to effectively communicate this new understanding, we introduce the publically-available Marine Aquarium Biodiversity and Trade Flow online database (https://www.aquariumtradedata.org/). This tool was created to communicate the volume and diversity of marine fishes and/or invertebrates imported into the US over three complete years (2008, 2009, and 2011) and three partial years (2000, 2004, 2005). To create this tool, invoices pertaining to shipments of live marine fishes and invertebrates were scanned and analyzed for species name, species quantities, country of origin, port of entry, and city of import destination. Here we focus on the analysis of the later three years of data and also produce an estimate for the entirety of 2000, 2004, and 2005. The three-year aggregate totals (2008, 2009, 2011) indicate that just under 2,300 fish and 725 invertebrate species were imported into the US cumulatively, although just under 1,800 fish and 550 invertebrate species were traded annually. Overall, the total number of live marine animals decreased between 2008 and 2011. In 2008, 2009, and 2011, the total number of individual fish (8.2, 7.3, and …
bibliographic citation: Rhyne et al. (2017) Expanding our understanding of the trade in marine aquarium animals. PeerJ 5:e2949 https://doi.org/10.7717/peerj.2949
date submitted: 2015-06-12
date accepted: 2016-12-30
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rhyne
  given name: Andrew L.
author list: Agent
  family name: Tlusty
  given name: Michael F.
author list: Agent
  family name: Szczebak
  given name: Joseph T.
author list: Agent
  family name: Holmberg
  given name: Robert J.
doi: 10.7717/peerj.2949
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Rhyne et al.
attribution name: Rhyne et al.

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy
type: item
type: AcademicArticle
description: The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.
format: application/pdf
format: text/html
creator: William J. Brazelton
creator: Christopher N. Thornton
creator: Alex Hyer
creator: Katrina I. Twing
creator: August A. Longino
creator: Susan Q. Lang
creator: Marvin D. Lilley
creator: Gretchen L. Früh-Green
creator: Matthew O. Schrenk
subject: Biosphere Interactions
subject: Ecology
subject: Environmental Sciences
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.2945
publisher: PeerJ Inc.
rights: © 2017 Brazelton et al.
abstract: The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.
bibliographic citation: Brazelton et al. (2017) Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy. PeerJ 5:e2945 https://doi.org/10.7717/peerj.2945
date submitted: 2016-07-22
date accepted: 2016-12-27
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brazelton
  given name: William J.
author list: Agent
  family name: Thornton
  given name: Christopher N.
author list: Agent
  family name: Hyer
  given name: Alex
author list: Agent
  family name: Twing
  given name: Katrina I.
author list: Agent
  family name: Longino
  given name: August A.
author list: Agent
  family name: Lang
  given name: Susan Q.
author list: Agent
  family name: Lilley
  given name: Marvin D.
author list: Agent
  family name: Früh-Green
  given name: Gretchen L.
author list: Agent
  family name: Schrenk
  given name: Matthew O.
doi: 10.7717/peerj.2945
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Brazelton et al.
attribution name: Brazelton et al.

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