PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes
items: Low serum albumin and total lymphocyte count as predictors of 30 day hospital readmission in patients 65 years of age or older
items: Mammalian cycles: internally defined periods and interaction-driven amplitudes
items: A new species of Brachycephalus (Anura: Brachycephalidae) from the Quiriri mountain range of southern Brazil
items: Artificial light pollution increases nocturnal vigilance in peahens
items: A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications
items: Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway
items: Let’s be pals again: major systematic changes in Palaemonidae (Crustacea: Decapoda)
items: An enigmatic crocodyliform tooth from the bauxites of western Hungary suggests hidden mesoeucrocodylian diversity in the Early Cretaceous European archipelago
items: Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua)

A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes
type: item
type: AcademicArticle
description: Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7,609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK), Response Regulator (RR) and Histidine Phosphotranfer (HPt) domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances.
format: application/pdf
format: text/html
creator: Baldiri Salvado
creator: Ester Vilaprinyo
creator: Albert Sorribas
creator: Rui Alves
subject: Bioinformatics
subject: Computational Biology
subject: Mathematical Biology
subject: Synthetic Biology
description: doi:10.7717/peerj.1183
publisher: PeerJ Inc.
rights: © 2015 Salvado et al.
abstract: Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7,609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK), Response Regulator (RR) and Histidine Phosphotranfer (HPt) domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances.
bibliographic citation: Salvado et al. (2015) A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes. PeerJ 3:e1183 https://doi.org/10.7717/peerj.1183
date submitted: 2015-03-20
date accepted: 2015-07-23
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salvado
  given name: Baldiri
author list: Agent
  family name: Vilaprinyo
  given name: Ester
author list: Agent
  family name: Sorribas
  given name: Albert
author list: Agent
  family name: Alves
  given name: Rui
doi: 10.7717/peerj.1183
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Salvado et al.
attribution name: Salvado et al.

Low serum albumin and total lymphocyte count as predictors of 30 day hospital readmission in patients 65 years of age or older
type: item
type: AcademicArticle
description: Introduction. Hospital readmission within 30 days of discharge is a target for health care cost savings through the medicare Value Based Purchasing initiative. Because of this focus, hospitals and health systems are investing considerable resources into the identification of patients at risk of hospital readmission and designing interventions to reduce the rate of hospital readmission. Malnutrition is a known risk factor for hospital readmission. Materials and Methods. All medical patients 65 years of age or older discharged from Memorial Medical Center from January 1, 2012 to March 31, 2012 who had a determination of serum albumin level and total lymphocyte count on hospital admission were studied retrospectively. Admission serum albumin levels and total lymphocyte counts were used to classify the nutritional status of all patients in the study. Patients with a serum albumin less than 3.5 grams/dL and/or a TLC less than 1,500 cells per mm3 were classified as having protein energy malnutrition. The primary outcome investigated in this study was hospital readmission for any reason within 30 days of discharge. Results. The study population included 1,683 hospital discharges with an average age of 79 years. The majority of the patients were female (55.9%) and had a DRG weight of 1.22 (0.68). 219 patients (13%) were readmitted within 30 days of hospital discharge. Protein energy malnutrition was common in this population. Low albumin was found in 973 (58%) patients and a low TLC was found in 1,152 (68%) patients. Low albumin and low TLC was found in 709 (42%) of patients. Kaplan–Meier analysis shows any laboratory evidence of PEM is a significant (p < 0.001) predictor of hospital readmission. Low serum albumin (p < 0.001) and TLC (p = 0.018) show similar trends. Cox proportional-hazards regression analysis showed low serum albumin (Hazard Ratio 3.27, 95% CI [2.30–4.63]) and higher DRG weight (Hazard Ratio 1.19, 95% CI [1.03–1.38]) to be significant independent predictor…
format: application/pdf
format: text/html
creator: Robert Robinson
subject: Emergency and Critical Care
subject: Evidence Based Medicine
subject: Health Policy
subject: Hematology
subject: Internal Medicine
description: doi:10.7717/peerj.1181
publisher: PeerJ Inc.
rights: © 2015 Robinson
abstract: Introduction. Hospital readmission within 30 days of discharge is a target for health care cost savings through the medicare Value Based Purchasing initiative. Because of this focus, hospitals and health systems are investing considerable resources into the identification of patients at risk of hospital readmission and designing interventions to reduce the rate of hospital readmission. Malnutrition is a known risk factor for hospital readmission. Materials and Methods. All medical patients 65 years of age or older discharged from Memorial Medical Center from January 1, 2012 to March 31, 2012 who had a determination of serum albumin level and total lymphocyte count on hospital admission were studied retrospectively. Admission serum albumin levels and total lymphocyte counts were used to classify the nutritional status of all patients in the study. Patients with a serum albumin less than 3.5 grams/dL and/or a TLC less than 1,500 cells per mm3 were classified as having protein energy malnutrition. The primary outcome investigated in this study was hospital readmission for any reason within 30 days of discharge. Results. The study population included 1,683 hospital discharges with an average age of 79 years. The majority of the patients were female (55.9%) and had a DRG weight of 1.22 (0.68). 219 patients (13%) were readmitted within 30 days of hospital discharge. Protein energy malnutrition was common in this population. Low albumin was found in 973 (58%) patients and a low TLC was found in 1,152 (68%) patients. Low albumin and low TLC was found in 709 (42%) of patients. Kaplan–Meier analysis shows any laboratory evidence of PEM is a significant (p < 0.001) predictor of hospital readmission. Low serum albumin (p < 0.001) and TLC (p = 0.018) show similar trends. Cox proportional-hazards regression analysis showed low serum albumin (Hazard Ratio 3.27, 95% CI [2.30–4.63]) and higher DRG weight (Hazard Ratio 1.19, 95% CI [1.03–1.38]) to be significant independent predictor…
bibliographic citation: Robinson (2015) Low serum albumin and total lymphocyte count as predictors of 30 day hospital readmission in patients 65 years of age or older. PeerJ 3:e1181 https://doi.org/10.7717/peerj.1181
date submitted: 2015-06-18
date accepted: 2015-07-22
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Robinson
  given name: Robert
doi: 10.7717/peerj.1181
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Robinson
attribution name: Robinson

Mammalian cycles: internally defined periods and interaction-driven amplitudes
type: item
type: AcademicArticle
description: The cause of mammalian cycles—the rise and fall of populations over a predictable period of time—has remained controversial since these patterns were first observed over a century ago. In spite of extensive work on observable mammalian cycles, the field has remained divided upon what the true cause is, with a majority of opinions attributing it to either predation or to intra-species mechanisms. Here we unite the eigenperiod hypothesis, which describes an internal, maternal effect-based mechanism to explain the cycles’ periods with a recent generalization explaining the amplitude of snowshoe hare cycles in northwestern North America based on initial predator abundance. By explaining the period and the amplitude of the cycle with separate mechanisms, a unified and consistent view of the causation of cycles is reached. Based on our suggested theory, we forecast the next snowshoe hare cycle (predicted peak in 2016) to be of extraordinarily low amplitude.
format: application/pdf
format: text/html
creator: LR Ginzburg
creator: CJ Krebs
subject: Conservation Biology
subject: Ecology
subject: Mathematical Biology
subject: Zoology
description: doi:10.7717/peerj.1180
publisher: PeerJ Inc.
rights: © 2015 Ginzburg and Krebs
abstract: The cause of mammalian cycles—the rise and fall of populations over a predictable period of time—has remained controversial since these patterns were first observed over a century ago. In spite of extensive work on observable mammalian cycles, the field has remained divided upon what the true cause is, with a majority of opinions attributing it to either predation or to intra-species mechanisms. Here we unite the eigenperiod hypothesis, which describes an internal, maternal effect-based mechanism to explain the cycles’ periods with a recent generalization explaining the amplitude of snowshoe hare cycles in northwestern North America based on initial predator abundance. By explaining the period and the amplitude of the cycle with separate mechanisms, a unified and consistent view of the causation of cycles is reached. Based on our suggested theory, we forecast the next snowshoe hare cycle (predicted peak in 2016) to be of extraordinarily low amplitude.
bibliographic citation: Ginzburg et al. (2015) Mammalian cycles: internally defined periods and interaction-driven amplitudes. PeerJ 3:e1180 https://doi.org/10.7717/peerj.1180
date submitted: 2015-06-03
date accepted: 2015-07-22
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ginzburg
  given name: LR
author list: Agent
  family name: Krebs
  given name: CJ
doi: 10.7717/peerj.1180
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Ginzburg and Krebs
attribution name: Ginzburg and Krebs

A new species of Brachycephalus (Anura: Brachycephalidae) from the Quiriri mountain range of southern Brazil
type: item
type: AcademicArticle
description: A new miniaturized toadled of the genus Brachycephalus (Anura: Brachycephalidae) is described from Serra do Quiriri in the municipality of Campo Alegre, Santa Catarina, southern Brazil. Specimens were collected from the leaf litter between from 1,263 and 1,318 m above sea level. The new species is distinguished from all its congeners by the combination of the following characters: snout–vent length 9.9–13.1 mm; skin on head and dorsum without dermal co-ossification; snout mucronate in dorsal view; dorsum rugose; general color brown, with a narrow orange vertebral stripe. The region where the new species is located is also shared with other endemic anuran species and has experienced strong anthropogenic impacts,suggesting that immediate actions should be taken to ensure their long-term preservation.
format: application/pdf
format: text/html
creator: Marcio R. Pie
creator: Luiz F. Ribeiro
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.1179
publisher: PeerJ Inc.
rights: © 2015 Pie and Ribeiro
abstract: A new miniaturized toadled of the genus Brachycephalus (Anura: Brachycephalidae) is described from Serra do Quiriri in the municipality of Campo Alegre, Santa Catarina, southern Brazil. Specimens were collected from the leaf litter between from 1,263 and 1,318 m above sea level. The new species is distinguished from all its congeners by the combination of the following characters: snout–vent length 9.9–13.1 mm; skin on head and dorsum without dermal co-ossification; snout mucronate in dorsal view; dorsum rugose; general color brown, with a narrow orange vertebral stripe. The region where the new species is located is also shared with other endemic anuran species and has experienced strong anthropogenic impacts,suggesting that immediate actions should be taken to ensure their long-term preservation.
bibliographic citation: Pie et al. (2015) A new species of Brachycephalus (Anura: Brachycephalidae) from the Quiriri mountain range of southern Brazil. PeerJ 3:e1179 https://doi.org/10.7717/peerj.1179
date submitted: 2015-06-04
date accepted: 2015-07-21
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pie
  given name: Marcio R.
author list: Agent
  family name: Ribeiro
  given name: Luiz F.
doi: 10.7717/peerj.1179
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Pie and Ribeiro
attribution name: Pie and Ribeiro

Artificial light pollution increases nocturnal vigilance in peahens
type: item
type: AcademicArticle
description: Artificial light pollution is drastically changing the sensory environments of animals. Even though many animals are now living in these changed environments, the effect light pollution has on animal behavior is poorly understood. We investigated the effect of light pollution on nocturnal vigilance in peahens (Pavo cristatus). Captive peahens were exposed to either artificial lighting or natural lighting at night. We employed a novel method to record their vigilance behavior by attaching accelerometers to their heads and continuously monitoring their large head movements. We found that light pollution significantly increases nocturnal vigilance in peahens. Furthermore, the birds faced a trade-off between vigilance and sleep at night: peahens that were more vigilant spent less time sleeping. Given the choice, peahens preferred to roost away from high levels of artificial lighting but showed no preference for roosting without artificial lighting or with low levels of artificial lighting. Our study demonstrates that light pollution can have a substantial impact on animal behavior that can potentially result in fitness consequences.
format: application/pdf
format: text/html
creator: Jessica L. Yorzinski
creator: Sarah Chisholm
creator: Sydney D Byerley
creator: Jeanee R. Coy
creator: Aisyah Aziz
creator: Jamie A. Wolf
creator: Amanda C. Gnerlich
subject: Animal Behavior
subject: Biosphere Interactions
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.1174
publisher: PeerJ Inc.
rights: © 2015 Yorzinski et al.
abstract: Artificial light pollution is drastically changing the sensory environments of animals. Even though many animals are now living in these changed environments, the effect light pollution has on animal behavior is poorly understood. We investigated the effect of light pollution on nocturnal vigilance in peahens (Pavo cristatus). Captive peahens were exposed to either artificial lighting or natural lighting at night. We employed a novel method to record their vigilance behavior by attaching accelerometers to their heads and continuously monitoring their large head movements. We found that light pollution significantly increases nocturnal vigilance in peahens. Furthermore, the birds faced a trade-off between vigilance and sleep at night: peahens that were more vigilant spent less time sleeping. Given the choice, peahens preferred to roost away from high levels of artificial lighting but showed no preference for roosting without artificial lighting or with low levels of artificial lighting. Our study demonstrates that light pollution can have a substantial impact on animal behavior that can potentially result in fitness consequences.
bibliographic citation: Yorzinski et al. (2015) Artificial light pollution increases nocturnal vigilance in peahens. PeerJ 3:e1174 https://doi.org/10.7717/peerj.1174
date submitted: 2015-07-08
date accepted: 2015-07-20
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yorzinski
  given name: Jessica L.
author list: Agent
  family name: Chisholm
  given name: Sarah
author list: Agent
  family name: Byerley
  given name: Sydney D
author list: Agent
  family name: Coy
  given name: Jeanee R.
author list: Agent
  family name: Aziz
  given name: Aisyah
author list: Agent
  family name: Wolf
  given name: Jamie A.
author list: Agent
  family name: Gnerlich
  given name: Amanda C.
doi: 10.7717/peerj.1174
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Yorzinski et al.
attribution name: Yorzinski et al.

A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications
type: item
type: AcademicArticle
description: Background. The Late Cretaceous is a keystone period to understand the origin and early radiation of Crocodylia, the group containing all extant lineages of crocodilians. Among the taxa described from the latest Cretaceous of Europe, the genus Allodaposuchus is one of the most common but also one of the most controversial. However, because of its fragmentary record, several issues regarding its phylogenetic emplacement and its ecology remain unsolved or unknown. The discovery of a single specimen attributed to Allodaposuchus, represented by both cranial and postcranial remains, from the Casa Fabà site (Tremp Basin, NE Spain) in the lower red unit of the Tremp Fm. (early Maastrichtian, Late Cretaceous) offers a unique opportunity to deepen in the phylogenetic relationships of the group and its ecological features. Methods. The specimen is described in detail, and CT scan of the skull is performed in order to study the endocranial morphology as well as paratympanic sinuses configuration. In addition, myological and phylogenetic analyses are also carried out on the specimen for to shed light in ecological and phylogenetic issues, respectively. Results. The specimen described herein represents a new species, Allodaposuchus hulki sp. nov., closely related to the Romanian A. precedens. The CT scan of the skull revealed an unexpected paratympanic sinuses configuration. Allosaposuchus hulki exhibits an “anterodorsal tympanic sinus” not observed in any other extant or extinct crocodilian. The caudal tympanic recesses are extremely enlarged, and the expanded quadratic sinus seems to be connected to the middle-ear channel. Phylogenetic analyses confirm the emplacement of the informal taxonomic group ‘Allodaposuchia’ at the base of Crocodylia, being considered the sister group of Borealosuchus and Planocraniidae. Discussion. Although this is a preliminary hypothesis, the unique paratympanic configuration displayed by A. hulki suggests that it could possess a high-specialized au…
format: application/pdf
format: text/html
creator: Alejandro Blanco
creator: Josep Fortuny
creator: Alba Vicente
creator: Àngel H. Luján
creator: Jordi Alexis García-Marçà
creator: Albert G. Sellés
subject: Animal Behavior
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.1171
publisher: PeerJ Inc.
rights: © 2015 Blanco et al.
abstract: Background. The Late Cretaceous is a keystone period to understand the origin and early radiation of Crocodylia, the group containing all extant lineages of crocodilians. Among the taxa described from the latest Cretaceous of Europe, the genus Allodaposuchus is one of the most common but also one of the most controversial. However, because of its fragmentary record, several issues regarding its phylogenetic emplacement and its ecology remain unsolved or unknown. The discovery of a single specimen attributed to Allodaposuchus, represented by both cranial and postcranial remains, from the Casa Fabà site (Tremp Basin, NE Spain) in the lower red unit of the Tremp Fm. (early Maastrichtian, Late Cretaceous) offers a unique opportunity to deepen in the phylogenetic relationships of the group and its ecological features. Methods. The specimen is described in detail, and CT scan of the skull is performed in order to study the endocranial morphology as well as paratympanic sinuses configuration. In addition, myological and phylogenetic analyses are also carried out on the specimen for to shed light in ecological and phylogenetic issues, respectively. Results. The specimen described herein represents a new species, Allodaposuchus hulki sp. nov., closely related to the Romanian A. precedens. The CT scan of the skull revealed an unexpected paratympanic sinuses configuration. Allosaposuchus hulki exhibits an “anterodorsal tympanic sinus” not observed in any other extant or extinct crocodilian. The caudal tympanic recesses are extremely enlarged, and the expanded quadratic sinus seems to be connected to the middle-ear channel. Phylogenetic analyses confirm the emplacement of the informal taxonomic group ‘Allodaposuchia’ at the base of Crocodylia, being considered the sister group of Borealosuchus and Planocraniidae. Discussion. Although this is a preliminary hypothesis, the unique paratympanic configuration displayed by A. hulki suggests that it could possess a high-specialized au…
bibliographic citation: Blanco et al. (2015) A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications. PeerJ 3:e1171 https://doi.org/10.7717/peerj.1171
date submitted: 2015-03-20
date accepted: 2015-07-20
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Blanco
  given name: Alejandro
author list: Agent
  family name: Fortuny
  given name: Josep
author list: Agent
  family name: Vicente
  given name: Alba
author list: Agent
  family name: Luján
  given name: Àngel H.
author list: Agent
  family name: García-Marçà
  given name: Jordi Alexis
author list: Agent
  family name: Sellés
  given name: Albert G.
doi: 10.7717/peerj.1171
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Blanco et al.
attribution name: Blanco et al.

Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway
type: item
type: AcademicArticle
description: Greylag goose populations are steadily increasing in north-western Europe. Although individuals breeding in the Netherlands have been considered mainly sedentary birds, those from Scandinavia or northern Germany fly towards their winter quarters, namely over France as far as Spain. This study aimed to determine the genetic structure of these birds, and to evaluate how goose populations mix. We used mitochondrial DNA and microsatellites from individuals distributed throughout the European Atlantic flyway, from breeding sites in Norway and the Netherlands to stopover and wintering sites in northern and south-western France. The mtDNA marker (CR1 D-Loop, 288 bp sequence, 144 ind.) showed 23 different haplotypes. The genetic distances amongst individuals sampled in Norway, northern France and the Netherlands were low (range 0.012–0.013). Individuals in south-western France showed a slightly higher genetic distance compared to all other sampling areas (ranges 0.018–0.022). The NJ tree does not show evidence of any single clades grouping together all individuals from the same geographic area. Besides, individuals from each site are found in different branches. Bayesian clustering procedures on 14 microsatellites (169 individuals) did not detect any geographically distinct cluster, and a high genetic admixture was recorded in all studied areas except for the individuals from the breeding sites in Norway, which were genetically very close. Estimation of migration rates through Bayesian inference confirms the scenario for the current mixing of goose populations.
format: application/pdf
format: text/html
creator: Irene Pellegrino
creator: Marco Cucco
creator: Arne Follestad
creator: Mathieu Boos
subject: Biodiversity
subject: Zoology
description: doi:10.7717/peerj.1161
publisher: PeerJ Inc.
rights: © 2015 Pellegrino et al.
abstract: Greylag goose populations are steadily increasing in north-western Europe. Although individuals breeding in the Netherlands have been considered mainly sedentary birds, those from Scandinavia or northern Germany fly towards their winter quarters, namely over France as far as Spain. This study aimed to determine the genetic structure of these birds, and to evaluate how goose populations mix. We used mitochondrial DNA and microsatellites from individuals distributed throughout the European Atlantic flyway, from breeding sites in Norway and the Netherlands to stopover and wintering sites in northern and south-western France. The mtDNA marker (CR1 D-Loop, 288 bp sequence, 144 ind.) showed 23 different haplotypes. The genetic distances amongst individuals sampled in Norway, northern France and the Netherlands were low (range 0.012–0.013). Individuals in south-western France showed a slightly higher genetic distance compared to all other sampling areas (ranges 0.018–0.022). The NJ tree does not show evidence of any single clades grouping together all individuals from the same geographic area. Besides, individuals from each site are found in different branches. Bayesian clustering procedures on 14 microsatellites (169 individuals) did not detect any geographically distinct cluster, and a high genetic admixture was recorded in all studied areas except for the individuals from the breeding sites in Norway, which were genetically very close. Estimation of migration rates through Bayesian inference confirms the scenario for the current mixing of goose populations.
bibliographic citation: Pellegrino et al. (2015) Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway. PeerJ 3:e1161 https://doi.org/10.7717/peerj.1161
date submitted: 2015-04-07
date accepted: 2015-07-17
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pellegrino
  given name: Irene
author list: Agent
  family name: Cucco
  given name: Marco
author list: Agent
  family name: Follestad
  given name: Arne
author list: Agent
  family name: Boos
  given name: Mathieu
doi: 10.7717/peerj.1161
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Pellegrino et al.
attribution name: Pellegrino et al.

Let’s be pals again: major systematic changes in Palaemonidae (Crustacea: Decapoda)
type: item
type: AcademicArticle
description: In recent years the systematic position of genera in the shrimp families Gnathophyllidae and Hymenoceridae has been under debate, with phylogenetic studies suggesting the families are not real family level units. Here, we review the molecular evidence as well as the morphological characters used to distinguish both families, leading to the conclusion that neither family is valid. Further, we studied the structural details of the single morphological character which distinguishes the two subfamilies (Palaemoninae, Pontoniinae) in Palaemonidae, as well as their phylogenetic relationship. As the supposed character distinction plainly does not hold true and supported by the phylogenetic results, the recognition of subfamilies in Palaemonidae is not warranted. As a consequence, all three supra-generic taxa (Gnathophyllidae, Hymenoceridae, Pontoniinae) are thus herein formally synonymised with Palaemonidae.
format: application/pdf
format: text/html
creator: Sammy De Grave
creator: Charles H.J.M. Fransen
creator: Timothy J. Page
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.1167
publisher: PeerJ Inc.
rights: © 2015 De Grave et al.
abstract: In recent years the systematic position of genera in the shrimp families Gnathophyllidae and Hymenoceridae has been under debate, with phylogenetic studies suggesting the families are not real family level units. Here, we review the molecular evidence as well as the morphological characters used to distinguish both families, leading to the conclusion that neither family is valid. Further, we studied the structural details of the single morphological character which distinguishes the two subfamilies (Palaemoninae, Pontoniinae) in Palaemonidae, as well as their phylogenetic relationship. As the supposed character distinction plainly does not hold true and supported by the phylogenetic results, the recognition of subfamilies in Palaemonidae is not warranted. As a consequence, all three supra-generic taxa (Gnathophyllidae, Hymenoceridae, Pontoniinae) are thus herein formally synonymised with Palaemonidae.
bibliographic citation: De Grave et al. (2015) Let’s be pals again: major systematic changes in Palaemonidae (Crustacea: Decapoda). PeerJ 3:e1167 https://doi.org/10.7717/peerj.1167
date submitted: 2015-06-26
date accepted: 2015-07-18
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Grave
  given name: Sammy
author list: Agent
  family name: Fransen
  given name: Charles H.J.M.
author list: Agent
  family name: Page
  given name: Timothy J.
doi: 10.7717/peerj.1167
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 De Grave et al.
attribution name: De Grave et al.

An enigmatic crocodyliform tooth from the bauxites of western Hungary suggests hidden mesoeucrocodylian diversity in the Early Cretaceous European archipelago
type: item
type: AcademicArticle
description: Background. The Cretaceous of southern Europe was characterized by an archipelago setting with faunas of mixed composition of endemic, Laurasian and Gondwanan elements. However, little is known about the relative timing of these faunal influences. The Lower Cretaceous of East-Central Europe holds a great promise for understanding the biogeographic history of Cretaceous European biotas because of the former proximity of the area to Gondwana (as part of the Apulian microcontinent). However, East-Central European vertebrates are typically poorly known from this time period. Here, we report on a ziphodont crocodyliform tooth discovered in the Lower Cretaceous (Albian) Alsópere Bauxite Formation of Olaszfalu, western Hungary. Methods. The morphology of the tooth is described and compared with that of other similar Cretaceous crocodyliforms. Results. Based on the triangular, slightly distally curved, constricted and labiolingually flattened crown, the small, subequal-sized true serrations on the carinae mesially and distally, the longitudinal fluting labially, and the extended shelves along the carinae lingually the tooth is most similar to some peirosaurid, non-baurusuchian sebecosuchian, and uruguaysuchid notosuchians. In addition, the paralligatorid Wannchampsus also possesses similar anterior teeth, thus the Hungarian tooth is referred here to Mesoeucrocodylia indet. Discussion. Supposing a notosuchian affinity, this tooth is the earliest occurrence of the group in Europe and one of the earliest in Laurasia. In case of a paralligatorid relationship the Hungarian tooth would represent their first European record, further expanding their cosmopolitan distribution. In any case, the ziphodont tooth from the Albian bauxite deposit of western Hungary belongs to a group still unknown from the Early Cretaceous European archipelago and therefore implies a hidden diversity of crocodyliforms in the area.
format: application/pdf
format: text/html
creator: Attila Ősi
creator: Márton Rabi
creator: László Makádi
subject: Paleontology
description: doi:10.7717/peerj.1160
publisher: PeerJ Inc.
rights: © 2015 Ősi et al.
abstract: Background. The Cretaceous of southern Europe was characterized by an archipelago setting with faunas of mixed composition of endemic, Laurasian and Gondwanan elements. However, little is known about the relative timing of these faunal influences. The Lower Cretaceous of East-Central Europe holds a great promise for understanding the biogeographic history of Cretaceous European biotas because of the former proximity of the area to Gondwana (as part of the Apulian microcontinent). However, East-Central European vertebrates are typically poorly known from this time period. Here, we report on a ziphodont crocodyliform tooth discovered in the Lower Cretaceous (Albian) Alsópere Bauxite Formation of Olaszfalu, western Hungary. Methods. The morphology of the tooth is described and compared with that of other similar Cretaceous crocodyliforms. Results. Based on the triangular, slightly distally curved, constricted and labiolingually flattened crown, the small, subequal-sized true serrations on the carinae mesially and distally, the longitudinal fluting labially, and the extended shelves along the carinae lingually the tooth is most similar to some peirosaurid, non-baurusuchian sebecosuchian, and uruguaysuchid notosuchians. In addition, the paralligatorid Wannchampsus also possesses similar anterior teeth, thus the Hungarian tooth is referred here to Mesoeucrocodylia indet. Discussion. Supposing a notosuchian affinity, this tooth is the earliest occurrence of the group in Europe and one of the earliest in Laurasia. In case of a paralligatorid relationship the Hungarian tooth would represent their first European record, further expanding their cosmopolitan distribution. In any case, the ziphodont tooth from the Albian bauxite deposit of western Hungary belongs to a group still unknown from the Early Cretaceous European archipelago and therefore implies a hidden diversity of crocodyliforms in the area.
bibliographic citation: Ősi et al. (2015) An enigmatic crocodyliform tooth from the bauxites of western Hungary suggests hidden mesoeucrocodylian diversity in the Early Cretaceous European archipelago. PeerJ 3:e1160 https://doi.org/10.7717/peerj.1160
date submitted: 2015-03-25
date accepted: 2015-07-17
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ősi
  given name: Attila
author list: Agent
  family name: Rabi
  given name: Márton
author list: Agent
  family name: Makádi
  given name: László
doi: 10.7717/peerj.1160
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Ősi et al.
attribution name: Ősi et al.

Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua)
type: item
type: AcademicArticle
description: The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) turfgrass. Anthracnose disease is geographically widespread throughout the world and highly destructive to cool-season turfgrasses, with infections by C. cereale resulting in extensive turf loss. Comprehensive research aimed at controlling turfgrass anthracnose has been performed in the field, but knowledge of the causal organism and its basic biology is still needed. In particular, the lack of a reliable greenhouse-based inoculation protocol performed under controlled environmental conditions is an obstacle to the study of C. cereale and anthracnose disease. Our objective was to develop a consistent and reproducible inoculation protocol for the two major genetic lineages of C. cereale. By adapting previously successful field-based protocols and combining with components of existing inoculation procedures, the method we developed consistently produced C. cereale infection on two susceptible P. annua biotypes. Approximately 7 to 10 days post-inoculation, plants exhibited chlorosis and thinning consistent with anthracnose disease symptomology. Morphological inspection of inoculated plants revealed visual signs of the fungus (appressoria and acervuli), although acervuli were not always present. After stringent surface sterilization of inoculated host tissue, C. cereale was consistently re-isolated from symptomatic tissue. Real-time PCR detection analysis based on the Apn2 marker confirmed the presence of the pathogen in host tissue, with both lineages of C. cereale detected from all inoculated plants. When a humidifier was not used, no infection developed for any biotypes or fungal isolates tested. The inoculation protocol described here marks significant progress for in planta studies of C. cereale, and will enable scientifically reproducible investigations of the biology, infectivity and lifestyle of this important grass pathogen.
format: application/pdf
format: text/html
creator: Lisa A. Beirn
creator: Ruying Wang
creator: Bruce B. Clarke
creator: Jo Anne Crouch
subject: Agricultural Science
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.1153
publisher: PeerJ Inc.
rights: © 2015
abstract: The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) turfgrass. Anthracnose disease is geographically widespread throughout the world and highly destructive to cool-season turfgrasses, with infections by C. cereale resulting in extensive turf loss. Comprehensive research aimed at controlling turfgrass anthracnose has been performed in the field, but knowledge of the causal organism and its basic biology is still needed. In particular, the lack of a reliable greenhouse-based inoculation protocol performed under controlled environmental conditions is an obstacle to the study of C. cereale and anthracnose disease. Our objective was to develop a consistent and reproducible inoculation protocol for the two major genetic lineages of C. cereale. By adapting previously successful field-based protocols and combining with components of existing inoculation procedures, the method we developed consistently produced C. cereale infection on two susceptible P. annua biotypes. Approximately 7 to 10 days post-inoculation, plants exhibited chlorosis and thinning consistent with anthracnose disease symptomology. Morphological inspection of inoculated plants revealed visual signs of the fungus (appressoria and acervuli), although acervuli were not always present. After stringent surface sterilization of inoculated host tissue, C. cereale was consistently re-isolated from symptomatic tissue. Real-time PCR detection analysis based on the Apn2 marker confirmed the presence of the pathogen in host tissue, with both lineages of C. cereale detected from all inoculated plants. When a humidifier was not used, no infection developed for any biotypes or fungal isolates tested. The inoculation protocol described here marks significant progress for in planta studies of C. cereale, and will enable scientifically reproducible investigations of the biology, infectivity and lifestyle of this important grass pathogen.
bibliographic citation: Beirn et al. (2015) Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua). PeerJ 3:e1153 https://doi.org/10.7717/peerj.1153
date submitted: 2015-04-14
date accepted: 2015-07-14
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Beirn
  given name: Lisa A.
author list: Agent
  family name: Wang
  given name: Ruying
author list: Agent
  family name: Clarke
  given name: Bruce B.
author list: Agent
  family name: Crouch
  given name: Jo Anne
doi: 10.7717/peerj.1153
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13

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