PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood
items: Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils
items: Ecomorphological characterization of murines and non-arvicoline cricetids (Rodentia) from south-western Europe since the latest Middle Miocene to the Mio-Pliocene boundary (MN 7/8–MN13)
items: Rootstock influence on iron uptake responses in Citrus leaves and their regulation under the Fe paradox effect
items: Filtering out parasites: sand crabs (Lepidopa benedicti) are infected by more parasites than sympatric mole crabs (Emerita benedicti)
items: Functional modularity in lake-dwelling characin fishes of Mexico
items: The Dark Cube: dark character profiles and OCEAN
items: Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?
items: Spontaneous reoccurrence of “scooping”, a wild tool-use behaviour, in naïve chimpanzees
items: Selected nutritional habits of teenagers associated with overweight and obesity

Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood
type: item
type: AcademicArticle
description: Background Melissococcus plutonius is an entomopathogenic bacterium that causes European foulbrood (EFB), a honeybee (Apis mellifera L.) disease that necessitates quarantine in some countries. In Czechia, positive evidence of EFB was absent for almost 40 years, until an outbreak in the Krkonose Mountains National Park in 2015. This occurrence of EFB gave us the opportunity to study the epizootiology of EFB by focusing on the microbiome of honeybee workers, which act as vectors of honeybee diseases within and between colonies. Methods The study included worker bees collected from brood combs of colonies (i) with no signs of EFB (EFB0), (ii) without clinical symptoms but located at an apiary showing clinical signs of EFB (EFB1), and (iii) with clinical symptoms of EFB (EFB2). In total, 49 samples from 27 honeybee colonies were included in the dataset evaluated in this study. Each biological sample consisted of 10 surface-sterilized worker bees processed for DNA extraction. All subjects were analyzed using conventional PCR and by metabarcoding analysis based on the 16S rRNA gene V1–V3 region, as performed through Illumina MiSeq amplicon sequencing. Results The bees from EFB2 colonies with clinical symptoms exhibited a 75-fold-higher incidence of M. plutonius than those from EFB1 asymptomatic colonies. Melissococcus plutonius was identified in all EFB1 colonies as well as in some of the control colonies. The proportions of Fructobacillus fructosus, Lactobacillus kunkeei, Gilliamella apicola, Frischella perrara, and Bifidobacterium coryneforme were higher in EFB2 than in EFB1, whereas Lactobacillus mellis was significantly higher in EFB2 than in EFB0. Snodgrassella alvi and L. melliventris, L. helsingborgensis and, L. kullabergensis exhibited higher proportion in EFB1 than in EFB2 and EFB0. The occurrence of Bartonella apis and Commensalibacter intestini were higher in EFB0 than in EFB2 and EFB1. Enterococcus faecalis incidence was highest in EFB2. Conclusions High-throu…
format: application/pdf
format: text/html
creator: Tomas Erban
creator: Ondrej Ledvinka
creator: Martin Kamler
creator: Bronislava Hortova
creator: Marta Nesvorna
creator: Jan Tyl
creator: Dalibor Titera
creator: Martin Markovic
creator: Jan Hubert
subject: Ecology
subject: Entomology
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.3816
publisher: PeerJ Inc.
rights: © 2017 Erban et al.
abstract: Background Melissococcus plutonius is an entomopathogenic bacterium that causes European foulbrood (EFB), a honeybee (Apis mellifera L.) disease that necessitates quarantine in some countries. In Czechia, positive evidence of EFB was absent for almost 40 years, until an outbreak in the Krkonose Mountains National Park in 2015. This occurrence of EFB gave us the opportunity to study the epizootiology of EFB by focusing on the microbiome of honeybee workers, which act as vectors of honeybee diseases within and between colonies. Methods The study included worker bees collected from brood combs of colonies (i) with no signs of EFB (EFB0), (ii) without clinical symptoms but located at an apiary showing clinical signs of EFB (EFB1), and (iii) with clinical symptoms of EFB (EFB2). In total, 49 samples from 27 honeybee colonies were included in the dataset evaluated in this study. Each biological sample consisted of 10 surface-sterilized worker bees processed for DNA extraction. All subjects were analyzed using conventional PCR and by metabarcoding analysis based on the 16S rRNA gene V1–V3 region, as performed through Illumina MiSeq amplicon sequencing. Results The bees from EFB2 colonies with clinical symptoms exhibited a 75-fold-higher incidence of M. plutonius than those from EFB1 asymptomatic colonies. Melissococcus plutonius was identified in all EFB1 colonies as well as in some of the control colonies. The proportions of Fructobacillus fructosus, Lactobacillus kunkeei, Gilliamella apicola, Frischella perrara, and Bifidobacterium coryneforme were higher in EFB2 than in EFB1, whereas Lactobacillus mellis was significantly higher in EFB2 than in EFB0. Snodgrassella alvi and L. melliventris, L. helsingborgensis and, L. kullabergensis exhibited higher proportion in EFB1 than in EFB2 and EFB0. The occurrence of Bartonella apis and Commensalibacter intestini were higher in EFB0 than in EFB2 and EFB1. Enterococcus faecalis incidence was highest in EFB2. Conclusions High-throu…
bibliographic citation: Erban et al. (2017) Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood. PeerJ 5:e3816 https://doi.org/10.7717/peerj.3816
date submitted: 2016-11-30
date accepted: 2017-08-26
issued: 2017-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Erban
  given name: Tomas
author list: Agent
  family name: Ledvinka
  given name: Ondrej
author list: Agent
  family name: Kamler
  given name: Martin
author list: Agent
  family name: Hortova
  given name: Bronislava
author list: Agent
  family name: Nesvorna
  given name: Marta
author list: Agent
  family name: Tyl
  given name: Jan
author list: Agent
  family name: Titera
  given name: Dalibor
author list: Agent
  family name: Markovic
  given name: Martin
author list: Agent
  family name: Hubert
  given name: Jan
doi: 10.7717/peerj.3816
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-25
copyright: ©2017 Erban et al.
attribution name: Erban et al.

Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils
type: item
type: AcademicArticle
description: Alkaline saline soils, known also as “soda solonchaks”, represent a natural soda habitat which differs from soda lake sediments by higher aeration and lower humidity. The microbiology of soda soils, in contrast to the more intensively studied soda lakes, remains poorly explored. In this work we investigate the diversity of culturable aerobic haloalkalitolerant bacteria with various hydrolytic activities from soda soils at different locations in Central Asia, Africa, and North America. In total, 179 pure cultures were obtained by using media with various polymers at pH 10 and 0.6 M total Na+. According to the 16S rRNA gene sequence analysis, most of the isolates belonged to Firmicutes and Actinobacteria. Most isolates possessed multiple hydrolytic activities, including endoglucanase, xylanase, amylase and protease. The pH profiling of selected representatives of actinobacteria and endospore-forming bacteria showed, that the former were facultative alkaliphiles, while the latter were mostly obligate alkaliphiles. The hydrolases of selected representatives from both groups were active at a broad pH range from six to 11. Overall, this work demonstrates the presence of a rich hydrolytic bacterial community in soda soils which might be explored further for production of haloalkalistable hydrolases.
format: application/pdf
format: text/html
creator: Dimitry Y. Sorokin
creator: Tatiana V. Kolganova
creator: Tatiana V. Khijniak
creator: Brian E. Jones
creator: Ilya V. Kublanov
subject: Microbiology
description: doi:10.7717/peerj.3796
publisher: PeerJ Inc.
rights: © 2017 Sorokin et al.
abstract: Alkaline saline soils, known also as “soda solonchaks”, represent a natural soda habitat which differs from soda lake sediments by higher aeration and lower humidity. The microbiology of soda soils, in contrast to the more intensively studied soda lakes, remains poorly explored. In this work we investigate the diversity of culturable aerobic haloalkalitolerant bacteria with various hydrolytic activities from soda soils at different locations in Central Asia, Africa, and North America. In total, 179 pure cultures were obtained by using media with various polymers at pH 10 and 0.6 M total Na+. According to the 16S rRNA gene sequence analysis, most of the isolates belonged to Firmicutes and Actinobacteria. Most isolates possessed multiple hydrolytic activities, including endoglucanase, xylanase, amylase and protease. The pH profiling of selected representatives of actinobacteria and endospore-forming bacteria showed, that the former were facultative alkaliphiles, while the latter were mostly obligate alkaliphiles. The hydrolases of selected representatives from both groups were active at a broad pH range from six to 11. Overall, this work demonstrates the presence of a rich hydrolytic bacterial community in soda soils which might be explored further for production of haloalkalistable hydrolases.
bibliographic citation: Sorokin et al. (2017) Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils. PeerJ 5:e3796 https://doi.org/10.7717/peerj.3796
date submitted: 2017-06-09
date accepted: 2017-08-21
issued: 2017-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sorokin
  given name: Dimitry Y.
author list: Agent
  family name: Kolganova
  given name: Tatiana V.
author list: Agent
  family name: Khijniak
  given name: Tatiana V.
author list: Agent
  family name: Jones
  given name: Brian E.
author list: Agent
  family name: Kublanov
  given name: Ilya V.
doi: 10.7717/peerj.3796
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-25
copyright: ©2017 Sorokin et al.
attribution name: Sorokin et al.

Ecomorphological characterization of murines and non-arvicoline cricetids (Rodentia) from south-western Europe since the latest Middle Miocene to the Mio-Pliocene boundary (MN 7/8–MN13)
type: item
type: AcademicArticle
description: Rodents are the most speciose group of mammals and display a great ecological diversity. Despite the greater amount of ecomorphological information compiled for extant rodent species, studies usually lack of morphological data on dentition, which has led to difficulty in directly utilizing existing ecomorphological data of extant rodents for paleoecological reconstruction because teeth are the most common or often the only micromammal fossils. Here, we infer the environmental ranges of extinct rodent genera by extracting habitat information from extant relatives and linking it to extinct taxa based on the phenogram of the cluster analysis, in which variables are derived from the principal component analysis on outline shape of the upper first molars. This phenotypic “bracketing” approach is particularly useful in the study of the fossil record of small mammals, which is mostly represented by isolated teeth. As a case study, we utilize extinct genera of murines and non-arvicoline cricetids, ranging from the Iberoccitanian latest middle Miocene to the Mio-Pliocene boundary, and compare our results thoroughly with previous paleoecological reconstructions inferred by different methods. The resultant phenogram shows a predominance of ubiquitous genera among the Miocene taxa, and the presence of a few forest specialists in the two rodent groups (Murinae and Cricetidae), along with the absence of open environment specialists in either group of rodents. This appears to be related to the absence of enduring grassland biomes in the Iberian Peninsula during the late Miocene. High consistency between our result and previous studies suggests that this phenotypic “bracketing” approach is a very useful tool.
format: application/pdf
format: text/html
creator: Ana R. Gomez Cano
creator: Yuri Kimura
creator: Fernando Blanco
creator: Iris Menéndez
creator: María A. Álvarez-Sierra
creator: Manuel Hernández Fernández
subject: Ecology
subject: Paleontology
description: doi:10.7717/peerj.3646
publisher: PeerJ Inc.
rights: © 2017 Gomez Cano et al.
abstract: Rodents are the most speciose group of mammals and display a great ecological diversity. Despite the greater amount of ecomorphological information compiled for extant rodent species, studies usually lack of morphological data on dentition, which has led to difficulty in directly utilizing existing ecomorphological data of extant rodents for paleoecological reconstruction because teeth are the most common or often the only micromammal fossils. Here, we infer the environmental ranges of extinct rodent genera by extracting habitat information from extant relatives and linking it to extinct taxa based on the phenogram of the cluster analysis, in which variables are derived from the principal component analysis on outline shape of the upper first molars. This phenotypic “bracketing” approach is particularly useful in the study of the fossil record of small mammals, which is mostly represented by isolated teeth. As a case study, we utilize extinct genera of murines and non-arvicoline cricetids, ranging from the Iberoccitanian latest middle Miocene to the Mio-Pliocene boundary, and compare our results thoroughly with previous paleoecological reconstructions inferred by different methods. The resultant phenogram shows a predominance of ubiquitous genera among the Miocene taxa, and the presence of a few forest specialists in the two rodent groups (Murinae and Cricetidae), along with the absence of open environment specialists in either group of rodents. This appears to be related to the absence of enduring grassland biomes in the Iberian Peninsula during the late Miocene. High consistency between our result and previous studies suggests that this phenotypic “bracketing” approach is a very useful tool.
bibliographic citation: Gomez Cano et al. (2017) Ecomorphological characterization of murines and non-arvicoline cricetids (Rodentia) from south-western Europe since the latest Middle Miocene to the Mio-Pliocene boundary (MN 7/8–MN13). PeerJ 5:e3646 https://doi.org/10.7717/peerj.3646
date submitted: 2017-02-22
date accepted: 2017-07-13
issued: 2017-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gomez Cano
  given name: Ana R.
author list: Agent
  family name: Kimura
  given name: Yuri
author list: Agent
  family name: Blanco
  given name: Fernando
author list: Agent
  family name: Menéndez
  given name: Iris
author list: Agent
  family name: Álvarez-Sierra
  given name: María A.
author list: Agent
  family name: Hernández Fernández
  given name: Manuel
doi: 10.7717/peerj.3646
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-25
copyright: ©2017 Gomez Cano et al.
attribution name: Gomez Cano et al.

Rootstock influence on iron uptake responses in Citrus leaves and their regulation under the Fe paradox effect
type: item
type: AcademicArticle
description: Background and aims This work evaluates the regulation of iron uptake responses in Citrus leaves and their involvement in the Fe paradox effect. Methods Experiments were performed in field-grown ‘Navelina’ trees grafted onto two Cleopatra mandarin × Poncirus trifoliata (L.) Raf. hybrids with different Fe-chlorosis symptoms: 030146 (non-chlorotic) and 030122 (chlorotic). Results Chlorotic leaves were smaller than non-chlorotic ones for both dry weight (DW) and area basis, and exhibited marked photosynthetic state affection, but reduced catalase and peroxidase enzymatic activities. Although both samples had a similar total Fe concentration on DW, it was lower in chlorotic leaves when expressed on an area basis. A similar pattern was observed for the total Fe concentration in the apoplast and cell sap and in active Fe (Fe2+) concentration. FRO2 gene expression and ferric chelate reductase (FC-R) activity were also lower in chlorotic samples, while HA1 and IRT1 were more induced. Despite similar apoplasmic pH, K+/Ca2+ was higher in chlorotic leaves, and both citrate and malate concentrations in total tissue and apoplast fluid were lower. Conclusion (1) The rootstock influences Fe acquisition system in the leaf; (2) the increased sensitivity to Fe-deficiency as revealed by chlorosis and decreased biomass, was correlated with lower FC-R activity and lower organic acid level in leaf cells, which could cause a decreased Fe mobility and trigger other Fe-stress responses in this organ to enhance acidification and Fe uptake inside cells; and (3) the chlorosis paradox phenomenon in citrus likely occurs as a combination of a marked FC-R activity impairment in the leaf and the strong growth inhibition in this organ.
format: application/pdf
format: text/html
creator: Mary-Rus Martinez-Cuenca
creator: Amparo Primo-Capella
creator: Ana Quiñones
creator: Almudena Bermejo
creator: Maria Angeles Forner-Giner
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.3553
publisher: PeerJ Inc.
rights: © 2017 Martinez-Cuenca et al.
abstract: Background and aims This work evaluates the regulation of iron uptake responses in Citrus leaves and their involvement in the Fe paradox effect. Methods Experiments were performed in field-grown ‘Navelina’ trees grafted onto two Cleopatra mandarin × Poncirus trifoliata (L.) Raf. hybrids with different Fe-chlorosis symptoms: 030146 (non-chlorotic) and 030122 (chlorotic). Results Chlorotic leaves were smaller than non-chlorotic ones for both dry weight (DW) and area basis, and exhibited marked photosynthetic state affection, but reduced catalase and peroxidase enzymatic activities. Although both samples had a similar total Fe concentration on DW, it was lower in chlorotic leaves when expressed on an area basis. A similar pattern was observed for the total Fe concentration in the apoplast and cell sap and in active Fe (Fe2+) concentration. FRO2 gene expression and ferric chelate reductase (FC-R) activity were also lower in chlorotic samples, while HA1 and IRT1 were more induced. Despite similar apoplasmic pH, K+/Ca2+ was higher in chlorotic leaves, and both citrate and malate concentrations in total tissue and apoplast fluid were lower. Conclusion (1) The rootstock influences Fe acquisition system in the leaf; (2) the increased sensitivity to Fe-deficiency as revealed by chlorosis and decreased biomass, was correlated with lower FC-R activity and lower organic acid level in leaf cells, which could cause a decreased Fe mobility and trigger other Fe-stress responses in this organ to enhance acidification and Fe uptake inside cells; and (3) the chlorosis paradox phenomenon in citrus likely occurs as a combination of a marked FC-R activity impairment in the leaf and the strong growth inhibition in this organ.
bibliographic citation: Martinez-Cuenca et al. (2017) Rootstock influence on iron uptake responses in Citrus leaves and their regulation under the Fe paradox effect. PeerJ 5:e3553 https://doi.org/10.7717/peerj.3553
date submitted: 2017-01-09
date accepted: 2017-06-16
issued: 2017-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martinez-Cuenca
  given name: Mary-Rus
author list: Agent
  family name: Primo-Capella
  given name: Amparo
author list: Agent
  family name: Quiñones
  given name: Ana
author list: Agent
  family name: Bermejo
  given name: Almudena
author list: Agent
  family name: Forner-Giner
  given name: Maria Angeles
doi: 10.7717/peerj.3553
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-25
copyright: © 2017 Martinez-Cuenca et al.
attribution name: Martinez-Cuenca et al.

Filtering out parasites: sand crabs (Lepidopa benedicti) are infected by more parasites than sympatric mole crabs (Emerita benedicti)
type: item
type: AcademicArticle
description: Two digging decapod crustaceans, the sand crab species Lepidopa benedicti and the mole crab species Emerita benedicti, both live in the swash zone of fine sand beaches. They were examined for two parasites that infect decapod crustaceans in the region, an unidentified nematode previously shown to infect L. benedicti, and cestode tapeworm larvae, Polypocephalus sp., previously shown to infect shrimp (Litopenaeus setiferus). Lepidopa benedicti were almost always infected with both parasite species, while E. benedicti were rarely infected with either parasite species. This difference in infection pattern suggests that tapeworms are ingested during sediment feeding in L. benedicti, which E. benedicti avoid by filter feeding. Larger L. benedicti had more Polypocephalus sp. larvae. The thoracic ganglia, which make up the largest proportion of neural tissue, contained the largest numbers of Polypocephalus sp. larvae. Intensity of Polypocephalus sp. infection was not correlated with how long L. benedicti remained above sand in behavioural tests, suggesting that Polypocephalus sp. do not manipulate the sand crabs in a way that facilitates trophic transmission of the parasite. Litopenaeus setiferus may be a primary host for Polypocephalus sp., and L. benedict may be a secondary, auxiliary host.
format: application/pdf
format: text/html
creator: Zen Faulkes
subject: Animal Behavior
subject: Marine Biology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.3852
publisher: PeerJ Inc.
rights: © 2017 Faulkes
abstract: Two digging decapod crustaceans, the sand crab species Lepidopa benedicti and the mole crab species Emerita benedicti, both live in the swash zone of fine sand beaches. They were examined for two parasites that infect decapod crustaceans in the region, an unidentified nematode previously shown to infect L. benedicti, and cestode tapeworm larvae, Polypocephalus sp., previously shown to infect shrimp (Litopenaeus setiferus). Lepidopa benedicti were almost always infected with both parasite species, while E. benedicti were rarely infected with either parasite species. This difference in infection pattern suggests that tapeworms are ingested during sediment feeding in L. benedicti, which E. benedicti avoid by filter feeding. Larger L. benedicti had more Polypocephalus sp. larvae. The thoracic ganglia, which make up the largest proportion of neural tissue, contained the largest numbers of Polypocephalus sp. larvae. Intensity of Polypocephalus sp. infection was not correlated with how long L. benedicti remained above sand in behavioural tests, suggesting that Polypocephalus sp. do not manipulate the sand crabs in a way that facilitates trophic transmission of the parasite. Litopenaeus setiferus may be a primary host for Polypocephalus sp., and L. benedict may be a secondary, auxiliary host.
bibliographic citation: Faulkes (2017) Filtering out parasites: sand crabs (Lepidopa benedicti) are infected by more parasites than sympatric mole crabs (Emerita benedicti). PeerJ 5:e3852 https://doi.org/10.7717/peerj.3852
date submitted: 2017-07-15
date accepted: 2017-09-05
issued: 2017-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Faulkes
  given name: Zen
doi: 10.7717/peerj.3852
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-22
copyright: ©2017 Faulkes
attribution name: Faulkes

Functional modularity in lake-dwelling characin fishes of Mexico
type: item
type: AcademicArticle
description: Modular evolution promotes evolutionary change, allowing independent variation across morphological units. Recent studies have shown that under contrasting ecological pressures, patterns of modularity could be related to divergent evolution. The main goal of the present study was to evaluate the presence of modular evolution in two sister lacustrine species, Astyanax aeneus and A. caballeroi, which are differentiated by their trophic habits. Two different datasets were analyzed: (1) skull X-rays from 73 specimens (35 A. aeneus and 38 A. caballeroi) to characterize skull variation patterns, considering both species and sex effects. For this dataset, three different modularity hypotheses were tested, previously supported in other lacustrine divergent species; (2) a complete body shape dataset was also tested for four modularity hypotheses, which included a total of 196 individuals (110 Astyanax aeneus and 86 A. caballeroi). Skull shape showed significant differences among species and sex (P < 0.001), where Astyanax caballeroi species showed an upwardly projected mandible and larger preorbital region. For the skull dataset, the modularity hypothesis ranked first included three partitioning modules. While for the complete body dataset the best ranked hypothesis included two modules (head vs the rest of the body), being significant only for A. caballeroi.
format: application/pdf
format: text/html
creator: Claudia Patricia Ornelas-García
creator: Amando Bautista
creator: Fabian Herder
creator: Ignacio Doadrio
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.3851
publisher: PeerJ Inc.
rights: © 2017 Ornelas-García et al.
abstract: Modular evolution promotes evolutionary change, allowing independent variation across morphological units. Recent studies have shown that under contrasting ecological pressures, patterns of modularity could be related to divergent evolution. The main goal of the present study was to evaluate the presence of modular evolution in two sister lacustrine species, Astyanax aeneus and A. caballeroi, which are differentiated by their trophic habits. Two different datasets were analyzed: (1) skull X-rays from 73 specimens (35 A. aeneus and 38 A. caballeroi) to characterize skull variation patterns, considering both species and sex effects. For this dataset, three different modularity hypotheses were tested, previously supported in other lacustrine divergent species; (2) a complete body shape dataset was also tested for four modularity hypotheses, which included a total of 196 individuals (110 Astyanax aeneus and 86 A. caballeroi). Skull shape showed significant differences among species and sex (P < 0.001), where Astyanax caballeroi species showed an upwardly projected mandible and larger preorbital region. For the skull dataset, the modularity hypothesis ranked first included three partitioning modules. While for the complete body dataset the best ranked hypothesis included two modules (head vs the rest of the body), being significant only for A. caballeroi.
bibliographic citation: Ornelas-García et al. (2017) Functional modularity in lake-dwelling characin fishes of Mexico. PeerJ 5:e3851 https://doi.org/10.7717/peerj.3851
date submitted: 2017-05-20
date accepted: 2017-09-05
issued: 2017-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ornelas-García
  given name: Claudia Patricia
author list: Agent
  family name: Bautista
  given name: Amando
author list: Agent
  family name: Herder
  given name: Fabian
author list: Agent
  family name: Doadrio
  given name: Ignacio
doi: 10.7717/peerj.3851
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-22
copyright: ©2017 Ornelas-García et al.
attribution name: Ornelas-García et al.

The Dark Cube: dark character profiles and OCEAN
type: item
type: AcademicArticle
description: Background The Big Five traits (i.e., openness, conscientiousness, extraversion, agreeableness, and neuroticism: OCEAN) have been suggested to provide a meaningful taxonomy for studying the Dark Triad: Machiavellianism, narcissism, and psychopathy. Nevertheless, current research consists of mixed and inconsistent associations between the Dark Triad and OCEAN. Here we used the Dark Cube (Garcia & Rosenberg, 2016), a model of malevolent character theoretically based on Cloninger’s biopsychosocial model of personality and in the assumption of a ternary structure of malevolent character. We use the dark cube profiles to investigate differences in OCEAN between individuals who differ in one dark character trait while holding the other two constant (i.e., conditional relationships). Method Participants (N = 330) responded to the Short Dark Triad Inventory and the Big Five Inventory and were grouped according to the eight possible combinations using their dark trait scores (M, high Machiavellianism; m, low Machiavellianism; N, high narcissism; n, low narcissism; P, high psychopathy; p, low psychopathy): MNP “maleficent”, MNp “manipulative narcissistic”, MnP “anti-social”, Mnp “Machiavellian”, mNP “psychopathic narcissistic”, mNp “narcissistic”, mnP “psychopathic”, and mnp “benevolent”. Results High narcissism-high extraversion and high psychopathy-low agreeableness were consistently associated across comparisons. The rest of the comparisons showed a complex interaction. For example, high Machiavellianism-high neuroticism only when both narcissism and psychopathy were low (Mnp vs. mnp), high narcissism-high conscientiousness only when both Machiavellianism and psychopathy were also high (MNP vs. MnP), and high psychopathy-high neuroticism only when Machiavellianism was low and narcissism was high (mNP vs. mNp). Conclusions We suggest that the Dark Cube is a useful tool in the investigation of a consistent Dark Triad Theory. This approach suggests that the only clear relatio…
format: application/pdf
format: text/html
creator: Danilo Garcia
creator: Fernando R. González Moraga
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3845
publisher: PeerJ Inc.
rights: © 2017 Garcia and González Moraga
abstract: Background The Big Five traits (i.e., openness, conscientiousness, extraversion, agreeableness, and neuroticism: OCEAN) have been suggested to provide a meaningful taxonomy for studying the Dark Triad: Machiavellianism, narcissism, and psychopathy. Nevertheless, current research consists of mixed and inconsistent associations between the Dark Triad and OCEAN. Here we used the Dark Cube (Garcia & Rosenberg, 2016), a model of malevolent character theoretically based on Cloninger’s biopsychosocial model of personality and in the assumption of a ternary structure of malevolent character. We use the dark cube profiles to investigate differences in OCEAN between individuals who differ in one dark character trait while holding the other two constant (i.e., conditional relationships). Method Participants (N = 330) responded to the Short Dark Triad Inventory and the Big Five Inventory and were grouped according to the eight possible combinations using their dark trait scores (M, high Machiavellianism; m, low Machiavellianism; N, high narcissism; n, low narcissism; P, high psychopathy; p, low psychopathy): MNP “maleficent”, MNp “manipulative narcissistic”, MnP “anti-social”, Mnp “Machiavellian”, mNP “psychopathic narcissistic”, mNp “narcissistic”, mnP “psychopathic”, and mnp “benevolent”. Results High narcissism-high extraversion and high psychopathy-low agreeableness were consistently associated across comparisons. The rest of the comparisons showed a complex interaction. For example, high Machiavellianism-high neuroticism only when both narcissism and psychopathy were low (Mnp vs. mnp), high narcissism-high conscientiousness only when both Machiavellianism and psychopathy were also high (MNP vs. MnP), and high psychopathy-high neuroticism only when Machiavellianism was low and narcissism was high (mNP vs. mNp). Conclusions We suggest that the Dark Cube is a useful tool in the investigation of a consistent Dark Triad Theory. This approach suggests that the only clear relatio…
bibliographic citation: Garcia et al. (2017) The Dark Cube: dark character profiles and OCEAN. PeerJ 5:e3845 https://doi.org/10.7717/peerj.3845
date submitted: 2016-07-19
date accepted: 2017-09-02
issued: 2017-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garcia
  given name: Danilo
author list: Agent
  family name: González Moraga
  given name: Fernando R.
doi: 10.7717/peerj.3845
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-22
copyright: ©2017 Garcia and González Moraga
attribution name: Garcia and González Moraga

Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?
type: item
type: AcademicArticle
description: The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.
format: application/pdf
format: text/html
creator: Manuel Pimentel
creator: Marcial Escudero
creator: Elvira Sahuquillo
creator: Miguel Ángel Minaya
creator: Pilar Catalán
subject: Biodiversity
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.3815
publisher: PeerJ Inc.
rights: © 2017 Pimentel et al.
abstract: The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.
bibliographic citation: Pimentel et al. (2017) Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?. PeerJ 5:e3815 https://doi.org/10.7717/peerj.3815
date submitted: 2017-06-27
date accepted: 2017-08-26
issued: 2017-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pimentel
  given name: Manuel
author list: Agent
  family name: Escudero
  given name: Marcial
author list: Agent
  family name: Sahuquillo
  given name: Elvira
author list: Agent
  family name: Minaya
  given name: Miguel Ángel
author list: Agent
  family name: Catalán
  given name: Pilar
doi: 10.7717/peerj.3815
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-22
copyright: ©2017 Pimentel et al.
attribution name: Pimentel et al.

Spontaneous reoccurrence of “scooping”, a wild tool-use behaviour, in naïve chimpanzees
type: item
type: AcademicArticle
description: Modern human technological culture depends on social learning. A widespread assumption for chimpanzee tool-use cultures is that they, too, are dependent on social learning. However, we provide evidence to suggest that individual learning, rather than social learning, is the driver behind determining the form of these behaviours within and across individuals. Low-fidelity social learning instead merely facilitates the reinnovation of these behaviours, and thus helps homogenise the behaviour across chimpanzees, creating the population-wide patterns observed in the wild (what here we call “socially mediated serial reinnovations”). This is the main prediction of the Zone of Latent Solutions (ZLS) hypothesis. This study directly tested the ZLS hypothesis on algae scooping, a wild chimpanzee tool-use behaviour. We provided naïve chimpanzees (n = 14, Mage = 31.33, SD = 10.09) with ecologically relevant materials of the wild behaviour but, crucially, without revealing any information on the behavioural form required to accomplish this task. This study found that naïve chimpanzees expressed the same behavioural form as their wild counterparts, suggesting that, as the ZLS theory predicts, individual learning is the driver behind the frequency of this behavioural form. As more behaviours are being found to be within chimpanzee’s ZLS, this hypothesis now provides a parsimonious explanation for chimpanzee tool cultures.
format: application/pdf
format: text/html
creator: Elisa Bandini
creator: Claudio Tennie
subject: Animal Behavior
subject: Evolutionary Studies
description: doi:10.7717/peerj.3814
publisher: PeerJ Inc.
rights: © 2017 Bandini and Tennie
abstract: Modern human technological culture depends on social learning. A widespread assumption for chimpanzee tool-use cultures is that they, too, are dependent on social learning. However, we provide evidence to suggest that individual learning, rather than social learning, is the driver behind determining the form of these behaviours within and across individuals. Low-fidelity social learning instead merely facilitates the reinnovation of these behaviours, and thus helps homogenise the behaviour across chimpanzees, creating the population-wide patterns observed in the wild (what here we call “socially mediated serial reinnovations”). This is the main prediction of the Zone of Latent Solutions (ZLS) hypothesis. This study directly tested the ZLS hypothesis on algae scooping, a wild chimpanzee tool-use behaviour. We provided naïve chimpanzees (n = 14, Mage = 31.33, SD = 10.09) with ecologically relevant materials of the wild behaviour but, crucially, without revealing any information on the behavioural form required to accomplish this task. This study found that naïve chimpanzees expressed the same behavioural form as their wild counterparts, suggesting that, as the ZLS theory predicts, individual learning is the driver behind the frequency of this behavioural form. As more behaviours are being found to be within chimpanzee’s ZLS, this hypothesis now provides a parsimonious explanation for chimpanzee tool cultures.
bibliographic citation: Bandini et al. (2017) Spontaneous reoccurrence of “scooping”, a wild tool-use behaviour, in naïve chimpanzees. PeerJ 5:e3814 https://doi.org/10.7717/peerj.3814
date submitted: 2017-04-04
date accepted: 2017-08-26
issued: 2017-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bandini
  given name: Elisa
author list: Agent
  family name: Tennie
  given name: Claudio
doi: 10.7717/peerj.3814
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-22
copyright: ©2017 Bandini and Tennie
attribution name: Bandini and Tennie

Selected nutritional habits of teenagers associated with overweight and obesity
type: item
type: AcademicArticle
description: Introduction A balanced diet is at the heart of healthy growth and development of children and youth, whereas inappropriate eating habits considerably influence the incidence of disorders connected with nutrition, including overweight and obesity. This paper aims at studying nutritional factors of 18-year-old secondary school youth in the urban environment and their effect on the incidence of overweight and obesity. Materials and methods The survey was conducted among 1,999 secondary school students chosen at random. The research tool consisted an original survey questionnaire. The measurements of respondents’ height and body mass provided data for calculating the body mass index. Results and conclusion The percentage of youth with deficient body mass was estimated at 8.4%. The percentage of normal weight students in the surveyed group was estimated at 77.6%. Overweight and obesity characterized 14.0% of the total number. As many as 21.8% of overweight and obese respondents would eat one or two meals as opposed to 16.8% of normal weight students. Three-fourths of the surveyed students would eat breakfast regardless of their nutritional habits. Lunch is eaten by 52.9% of normal weight 18-year-olds and 46.1% of overweight and obese students. The analysis of mealtimes suggests that overweight and obese students would have their breakfast and dinner at later hours than the rest of the surveyed. More than half of the participating students failed to eat lunch (53.9%), and one in four students within this group resigned from supper. Girls would eat fruit and vegetables more frequently than boys several times a day. The percentage of persons in the surveyed groups who would eat fast foods on a daily basis was similar regardless of their nutritional status. Sweetened carbonated beverages would be drunk more often by overweight and obese boys (81.2%) as compared with boys with proper body mass (75.8%). The same type of beverages would be popular with two-thirds of girls, and…
format: application/pdf
format: text/html
creator: Magdalena Zalewska
creator: Elżbieta Maciorkowska
subject: Nutrition
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.3681
publisher: PeerJ Inc.
rights: © 2017 Zalewska and Maciorkowska
abstract: Introduction A balanced diet is at the heart of healthy growth and development of children and youth, whereas inappropriate eating habits considerably influence the incidence of disorders connected with nutrition, including overweight and obesity. This paper aims at studying nutritional factors of 18-year-old secondary school youth in the urban environment and their effect on the incidence of overweight and obesity. Materials and methods The survey was conducted among 1,999 secondary school students chosen at random. The research tool consisted an original survey questionnaire. The measurements of respondents’ height and body mass provided data for calculating the body mass index. Results and conclusion The percentage of youth with deficient body mass was estimated at 8.4%. The percentage of normal weight students in the surveyed group was estimated at 77.6%. Overweight and obesity characterized 14.0% of the total number. As many as 21.8% of overweight and obese respondents would eat one or two meals as opposed to 16.8% of normal weight students. Three-fourths of the surveyed students would eat breakfast regardless of their nutritional habits. Lunch is eaten by 52.9% of normal weight 18-year-olds and 46.1% of overweight and obese students. The analysis of mealtimes suggests that overweight and obese students would have their breakfast and dinner at later hours than the rest of the surveyed. More than half of the participating students failed to eat lunch (53.9%), and one in four students within this group resigned from supper. Girls would eat fruit and vegetables more frequently than boys several times a day. The percentage of persons in the surveyed groups who would eat fast foods on a daily basis was similar regardless of their nutritional status. Sweetened carbonated beverages would be drunk more often by overweight and obese boys (81.2%) as compared with boys with proper body mass (75.8%). The same type of beverages would be popular with two-thirds of girls, and…
bibliographic citation: Zalewska et al. (2017) Selected nutritional habits of teenagers associated with overweight and obesity. PeerJ 5:e3681 https://doi.org/10.7717/peerj.3681
date submitted: 2017-01-13
date accepted: 2017-07-22
issued: 2017-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zalewska
  given name: Magdalena
author list: Agent
  family name: Maciorkowska
  given name: Elżbieta
doi: 10.7717/peerj.3681
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-22
copyright: © 2017 Zalewska and Maciorkowska
attribution name: Zalewska and Maciorkowska

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