PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops
items: Ancient divergence time estimates in Eutropis rugifera support the existence of Pleistocene barriers on the exposed Sunda Shelf
items: Inorganic, organic, and encapsulated minerals in vegetable meal based diets for Sparus aurata (Linnaeus, 1758)
items: Work-related stress, associated comorbidities and stress causes in French community pharmacies: a nationwide cross-sectional study
items: Constructing stage-structured matrix population models from life tables: comparison of methods
items: Species–specific crab predation on the hydrozoan clinging jellyfish Gonionemus sp. (Cnidaria, Hydrozoa), subsequent crab mortality, and possible ecological consequences
items: Indigenous Australian household structure: a simple data collection tool and implications for close contact transmission of communicable diseases
items: Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data
items: Erwinia amylovora psychrotrophic adaptations: evidence of pathogenic potential and survival at temperate and low environmental temperatures
items: Evaluation of genetic variability among “Early Mature” Juglans regia using microsatellite markers and morphological traits

Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops
type: item
type: AcademicArticle
description: Conservation biological control emphasizes natural and other non-crop vegetation as a source of natural enemies to focal crops. There is an unmet need for better methods to identify the types of vegetation that are optimal to support specific natural enemies that may colonize the crops. Here we explore the commonality of the spider assemblage—considering abundance and diversity (H)—in brassica crops with that of adjacent non-crop and non-brassica crop vegetation. We employ spatial-based multivariate ordination approaches, hierarchical clustering and spatial eigenvector analysis. The small-scale mixed cropping and high disturbance frequency of southern Chinese vegetation farming offered a setting to test the role of alternate vegetation for spider conservation. Our findings indicate that spider families differ markedly in occurrence with respect to vegetation type. Grassy field margins, non-crop vegetation, taro and sweetpotato harbour spider morphospecies and functional groups that are also present in brassica crops. In contrast, pumpkin and litchi contain spiders not found in brassicas, and so may have little benefit for conservation biological control services for brassicas. Our findings also illustrate the utility of advanced statistical approaches for identifying spatial relationships between natural enemies and the land uses most likely to offer alternative habitats for conservation biological control efforts that generates testable hypotheses for future studies.
format: application/pdf
format: text/html
creator: Hafiz Sohaib Ahmed Saqib
creator: Minsheng You
creator: Geoff M. Gurr
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
description: doi:10.7717/peerj.3795
publisher: PeerJ Inc.
rights: © 2017 Saqib et al.
abstract: Conservation biological control emphasizes natural and other non-crop vegetation as a source of natural enemies to focal crops. There is an unmet need for better methods to identify the types of vegetation that are optimal to support specific natural enemies that may colonize the crops. Here we explore the commonality of the spider assemblage—considering abundance and diversity (H)—in brassica crops with that of adjacent non-crop and non-brassica crop vegetation. We employ spatial-based multivariate ordination approaches, hierarchical clustering and spatial eigenvector analysis. The small-scale mixed cropping and high disturbance frequency of southern Chinese vegetation farming offered a setting to test the role of alternate vegetation for spider conservation. Our findings indicate that spider families differ markedly in occurrence with respect to vegetation type. Grassy field margins, non-crop vegetation, taro and sweetpotato harbour spider morphospecies and functional groups that are also present in brassica crops. In contrast, pumpkin and litchi contain spiders not found in brassicas, and so may have little benefit for conservation biological control services for brassicas. Our findings also illustrate the utility of advanced statistical approaches for identifying spatial relationships between natural enemies and the land uses most likely to offer alternative habitats for conservation biological control efforts that generates testable hypotheses for future studies.
bibliographic citation: Saqib et al. (2017) Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops. PeerJ 5:e3795 https://doi.org/10.7717/peerj.3795
date submitted: 2017-06-02
date accepted: 2017-08-18
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saqib
  given name: Hafiz Sohaib Ahmed
author list: Agent
  family name: You
  given name: Minsheng
author list: Agent
  family name: Gurr
  given name: Geoff M.
doi: 10.7717/peerj.3795
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Saqib et al.
attribution name: Saqib et al.

Ancient divergence time estimates in Eutropis rugifera support the existence of Pleistocene barriers on the exposed Sunda Shelf
type: item
type: AcademicArticle
description: Episodic sea level changes that repeatedly exposed and inundated the Sunda Shelf characterize the Pleistocene. Available evidence points to a more xeric central Sunda Shelf during periods of low sea levels, and despite the broad land connections that persisted during this time, some organisms are assumed to have faced barriers to dispersal between land-masses on the Sunda Shelf. Eutropis rugifera is a secretive, forest adapted scincid lizard that ranges across the Sunda Shelf. In this study, we sequenced one mitochondrial (ND2) and four nuclear (BRCA1, BRCA2, RAG1, and MC1R) markers and generated a time-calibrated phylogeny in BEAST to test whether divergence times between Sundaic populations of E. rugifera occurred during Pleistocene sea-level changes, or if they predate the Pleistocene. We find that E. rugifera shows pre-Pleistocene divergences between populations on different Sundaic land-masses. The earliest divergence within E. rugifera separates the Philippine samples from the Sundaic samples approximately 16 Ma; the Philippine populations thus cannot be considered conspecific with Sundaic congeners. Sundaic populations diverged approximately 6 Ma, and populations within Borneo from Sabah and Sarawak separated approximately 4.5 Ma in the early Pliocene, followed by further cladogenesis in Sarawak through the Pleistocene. Divergence of peninsular Malaysian populations from the Mentawai Archipelago occurred approximately 5 Ma. Separation among island populations from the Mentawai Archipelago likely dates to the Pliocene/Pleistocene boundary approximately 3.5 Ma, and our samples from peninsular Malaysia appear to coalesce in the middle Pleistocene, about 1 Ma. Coupled with the monophyly of these populations, these divergence times suggest that despite consistent land-connections between these regions throughout the Pleistocene E. rugifera still faced barriers to dispersal, which may be a result of environmental shifts that accompanied the sea-level changes.
format: application/pdf
format: text/html
creator: Benjamin R. Karin
creator: Indraneil Das
creator: Todd R. Jackman
creator: Aaron M. Bauer
subject: Biogeography
subject: Evolutionary Studies
description: doi:10.7717/peerj.3762
publisher: PeerJ Inc.
rights: © 2017 Karin et al.
abstract: Episodic sea level changes that repeatedly exposed and inundated the Sunda Shelf characterize the Pleistocene. Available evidence points to a more xeric central Sunda Shelf during periods of low sea levels, and despite the broad land connections that persisted during this time, some organisms are assumed to have faced barriers to dispersal between land-masses on the Sunda Shelf. Eutropis rugifera is a secretive, forest adapted scincid lizard that ranges across the Sunda Shelf. In this study, we sequenced one mitochondrial (ND2) and four nuclear (BRCA1, BRCA2, RAG1, and MC1R) markers and generated a time-calibrated phylogeny in BEAST to test whether divergence times between Sundaic populations of E. rugifera occurred during Pleistocene sea-level changes, or if they predate the Pleistocene. We find that E. rugifera shows pre-Pleistocene divergences between populations on different Sundaic land-masses. The earliest divergence within E. rugifera separates the Philippine samples from the Sundaic samples approximately 16 Ma; the Philippine populations thus cannot be considered conspecific with Sundaic congeners. Sundaic populations diverged approximately 6 Ma, and populations within Borneo from Sabah and Sarawak separated approximately 4.5 Ma in the early Pliocene, followed by further cladogenesis in Sarawak through the Pleistocene. Divergence of peninsular Malaysian populations from the Mentawai Archipelago occurred approximately 5 Ma. Separation among island populations from the Mentawai Archipelago likely dates to the Pliocene/Pleistocene boundary approximately 3.5 Ma, and our samples from peninsular Malaysia appear to coalesce in the middle Pleistocene, about 1 Ma. Coupled with the monophyly of these populations, these divergence times suggest that despite consistent land-connections between these regions throughout the Pleistocene E. rugifera still faced barriers to dispersal, which may be a result of environmental shifts that accompanied the sea-level changes.
bibliographic citation: Karin et al. (2017) Ancient divergence time estimates in Eutropis rugifera support the existence of Pleistocene barriers on the exposed Sunda Shelf. PeerJ 5:e3762 https://doi.org/10.7717/peerj.3762
date submitted: 2017-07-10
date accepted: 2017-08-15
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karin
  given name: Benjamin R.
author list: Agent
  family name: Das
  given name: Indraneil
author list: Agent
  family name: Jackman
  given name: Todd R.
author list: Agent
  family name: Bauer
  given name: Aaron M.
doi: 10.7717/peerj.3762
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Karin et al.
attribution name: Karin et al.

Inorganic, organic, and encapsulated minerals in vegetable meal based diets for Sparus aurata (Linnaeus, 1758)
type: item
type: AcademicArticle
description: Substituting fishmeal (FM) with vegetable meal (VM) can markedly affect the mineral composition of feeds, and may require additional mineral supplementation. Their bioavailability and optimal supplementation levels depend also on the form of delivery of minerals. The aim of the study was to determine the effect of different delivery forms of three major trace elements (Zn, Mn and Se) in a marine teleost. Gilthead sea bream juveniles of 22.5 g were fed a VM-based diet for 12 weeks that was either not supplemented with these minerals or supplemented with inorganic, organic, or encapsulated inorganic forms of minerals in triplicate and compared to a FM-based diet. Our results showed that mineral delivery form significantly affected the biochemical composition and morphology of posterior vertebrae. Supplementation of VM-based diets with inorganic forms of the target minerals significantly promoted growth, increased the vertebral weight and content of ash and Zn, enhanced bone mineralization and affected the vertebral shape. Conversely, encapsulation of inorganic minerals reduced fish growth and vertebral mineral content, whereas supplementation of organic minerals, enhanced bone osteogenesis by upregulating bone morphogenetic protein 2 (bmp2) gene and produced vertebrae with a larger length in relation to height. Furthermore, organic mineral forms of delivery downregulated the expression of oxidative stress related genes, such as Cu/Zn superoxide dismutase (Cu/Zn sod) and glutathione peroxidase 1 (gpx-1), suggesting thus that dietary minerals supplemented in the organic form could be reasonably considered more effective than the inorganic and encapsulated forms of supply.
format: application/pdf
format: text/html
creator: David Domínguez
creator: Simona Rimoldi
creator: Lidia E. Robaina
creator: Silvia Torrecillas
creator: Genciana Terova
creator: María J. Zamorano
creator: Vasileios Karalazos
creator: Kristin Hamre
creator: Marisol Izquierdo
subject: Aquaculture, Fisheries and Fish Science
subject: Nutrition
description: doi:10.7717/peerj.3710
publisher: PeerJ Inc.
rights: © 2017 Domínguez et al.
abstract: Substituting fishmeal (FM) with vegetable meal (VM) can markedly affect the mineral composition of feeds, and may require additional mineral supplementation. Their bioavailability and optimal supplementation levels depend also on the form of delivery of minerals. The aim of the study was to determine the effect of different delivery forms of three major trace elements (Zn, Mn and Se) in a marine teleost. Gilthead sea bream juveniles of 22.5 g were fed a VM-based diet for 12 weeks that was either not supplemented with these minerals or supplemented with inorganic, organic, or encapsulated inorganic forms of minerals in triplicate and compared to a FM-based diet. Our results showed that mineral delivery form significantly affected the biochemical composition and morphology of posterior vertebrae. Supplementation of VM-based diets with inorganic forms of the target minerals significantly promoted growth, increased the vertebral weight and content of ash and Zn, enhanced bone mineralization and affected the vertebral shape. Conversely, encapsulation of inorganic minerals reduced fish growth and vertebral mineral content, whereas supplementation of organic minerals, enhanced bone osteogenesis by upregulating bone morphogenetic protein 2 (bmp2) gene and produced vertebrae with a larger length in relation to height. Furthermore, organic mineral forms of delivery downregulated the expression of oxidative stress related genes, such as Cu/Zn superoxide dismutase (Cu/Zn sod) and glutathione peroxidase 1 (gpx-1), suggesting thus that dietary minerals supplemented in the organic form could be reasonably considered more effective than the inorganic and encapsulated forms of supply.
bibliographic citation: Domínguez et al. (2017) Inorganic, organic, and encapsulated minerals in vegetable meal based diets for Sparus aurata (Linnaeus, 1758). PeerJ 5:e3710 https://doi.org/10.7717/peerj.3710
date submitted: 2016-12-05
date accepted: 2017-07-28
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Domínguez
  given name: David
author list: Agent
  family name: Rimoldi
  given name: Simona
author list: Agent
  family name: Robaina
  given name: Lidia E.
author list: Agent
  family name: Torrecillas
  given name: Silvia
author list: Agent
  family name: Terova
  given name: Genciana
author list: Agent
  family name: Zamorano
  given name: María J.
author list: Agent
  family name: Karalazos
  given name: Vasileios
author list: Agent
  family name: Hamre
  given name: Kristin
author list: Agent
  family name: Izquierdo
  given name: Marisol
doi: 10.7717/peerj.3710
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Domínguez et al.
attribution name: Domínguez et al.

Work-related stress, associated comorbidities and stress causes in French community pharmacies: a nationwide cross-sectional study
type: item
type: AcademicArticle
description: Background Like other health professionals, community pharmacists are exposed to stress factors (being efficient, avoiding mistakes and bearing emotional load), but they are also under the pressure of entrepreneurial responsibilities. The main objective was to assess the level of work-related stress in French community pharmacies. The other objectives of the study were to assess the associated comorbidities and causes of work-related stress. Methods This observational cross-sectional study was sent to all French community pharmacies by email. The survey was anonymous and designed to collect the following items: socio-demographic factors, professional status, characteristics of community pharmacy, work-related stress (visual analogic scale—VAS), fatigue (VAS), sleep disturbances (questions), anxiety and depression symptoms (hospital anxiety and depression scale), medical consultation for work-related stress, medication use for work related stress, psychoactive drug-use and causes of work-related stress. Participants were included in the survey if they were pharmacists (owner or assistant) or pharmacy technicians working in a community pharmacy at the time of the survey. Exclusion criteria were defined as follows: pharmacy students or other professionals involved in a community pharmacy (e.g. dietician, beautician) and lack of professional status information. There was no age limitation. Results After three months of data collection, 1,339 participants answered the survey and 1,272 participants were included in conformity with the inclusion and exclusion criteria, and to avoid missing data on the primary endpoint. Work-related stress was detected in 32.8% (417/1,272) of individuals (scores ≥70/100). Men were significantly more affected than women and there was no difference between professional statuses and no relation with the age of the participants. Work-related stress was significantly associated with anxiety, depression, fatigue, sleep disturbances, medical consu…
format: application/pdf
format: text/html
creator: David Balayssac
creator: Bruno Pereira
creator: Julie Virot
creator: Céline Lambert
creator: Aurore Collin
creator: David Alapini
creator: Jean-Marc Gagnaire
creator: Nicolas Authier
creator: Damien Cuny
creator: Brigitte Vennat
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.3973
publisher: PeerJ Inc.
rights: © 2017 Balayssac et al.
abstract: Background Like other health professionals, community pharmacists are exposed to stress factors (being efficient, avoiding mistakes and bearing emotional load), but they are also under the pressure of entrepreneurial responsibilities. The main objective was to assess the level of work-related stress in French community pharmacies. The other objectives of the study were to assess the associated comorbidities and causes of work-related stress. Methods This observational cross-sectional study was sent to all French community pharmacies by email. The survey was anonymous and designed to collect the following items: socio-demographic factors, professional status, characteristics of community pharmacy, work-related stress (visual analogic scale—VAS), fatigue (VAS), sleep disturbances (questions), anxiety and depression symptoms (hospital anxiety and depression scale), medical consultation for work-related stress, medication use for work related stress, psychoactive drug-use and causes of work-related stress. Participants were included in the survey if they were pharmacists (owner or assistant) or pharmacy technicians working in a community pharmacy at the time of the survey. Exclusion criteria were defined as follows: pharmacy students or other professionals involved in a community pharmacy (e.g. dietician, beautician) and lack of professional status information. There was no age limitation. Results After three months of data collection, 1,339 participants answered the survey and 1,272 participants were included in conformity with the inclusion and exclusion criteria, and to avoid missing data on the primary endpoint. Work-related stress was detected in 32.8% (417/1,272) of individuals (scores ≥70/100). Men were significantly more affected than women and there was no difference between professional statuses and no relation with the age of the participants. Work-related stress was significantly associated with anxiety, depression, fatigue, sleep disturbances, medical consu…
bibliographic citation: Balayssac et al. (2017) Work-related stress, associated comorbidities and stress causes in French community pharmacies: a nationwide cross-sectional study. PeerJ 5:e3973 https://doi.org/10.7717/peerj.3973
date submitted: 2017-06-12
date accepted: 2017-10-08
issued: 2017-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Balayssac
  given name: David
author list: Agent
  family name: Pereira
  given name: Bruno
author list: Agent
  family name: Virot
  given name: Julie
author list: Agent
  family name: Lambert
  given name: Céline
author list: Agent
  family name: Collin
  given name: Aurore
author list: Agent
  family name: Alapini
  given name: David
author list: Agent
  family name: Gagnaire
  given name: Jean-Marc
author list: Agent
  family name: Authier
  given name: Nicolas
author list: Agent
  family name: Cuny
  given name: Damien
author list: Agent
  family name: Vennat
  given name: Brigitte
doi: 10.7717/peerj.3973
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-26
copyright: ©2017 Balayssac et al.
attribution name: Balayssac et al.

Constructing stage-structured matrix population models from life tables: comparison of methods
type: item
type: AcademicArticle
description: A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates) of a population and can be used for calculating an asymptotic finite population growth rate (λ) and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism’s life history type and the true values of λ. In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ. Here, the weights are given by survivorship curve after discounting with λ. To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used for discounting the rate, was…
format: application/pdf
format: text/html
creator: Masami Fujiwara
creator: Jasmin Diaz-Lopez
subject: Conservation Biology
subject: Ecology
subject: Statistics
subject: Natural Resource Management
description: doi:10.7717/peerj.3971
publisher: PeerJ Inc.
rights: © 2017 Fujiwara and Diaz-Lopez
abstract: A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates) of a population and can be used for calculating an asymptotic finite population growth rate (λ) and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism’s life history type and the true values of λ. In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ. Here, the weights are given by survivorship curve after discounting with λ. To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used for discounting the rate, was…
bibliographic citation: Fujiwara et al. (2017) Constructing stage-structured matrix population models from life tables: comparison of methods. PeerJ 5:e3971 https://doi.org/10.7717/peerj.3971
date submitted: 2017-06-15
date accepted: 2017-10-09
issued: 2017-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fujiwara
  given name: Masami
author list: Agent
  family name: Diaz-Lopez
  given name: Jasmin
doi: 10.7717/peerj.3971
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-26
copyright: ©2017 Fujiwara and Diaz-Lopez
attribution name: Fujiwara and Diaz-Lopez

Species–specific crab predation on the hydrozoan clinging jellyfish Gonionemus sp. (Cnidaria, Hydrozoa), subsequent crab mortality, and possible ecological consequences
type: item
type: AcademicArticle
description: Here we report a unique trophic interaction between the cryptogenic and sometimes highly toxic hydrozoan clinging jellyfish Gonionemus sp. and the spider crab Libinia dubia. We assessed species–specific predation on the Gonionemus medusae by crabs found in eelgrass meadows in Massachusetts, USA. The native spider crab species L. dubia consumed Gonionemus medusae, often enthusiastically, but the invasive green crab Carcinus maenus avoided consumption in all trials. One out of two blue crabs (Callinectes sapidus) also consumed Gonionemus, but this species was too rare in our study system to evaluate further. Libinia crabs could consume up to 30 jellyfish, which was the maximum jellyfish density treatment in our experiments, over a 24-hour period. Gonionemus consumption was associated with Libinia mortality. Spider crab mortality increased with Gonionemus consumption, and 100% of spider crabs tested died within 24 h of consuming jellyfish in our maximum jellyfish density containers. As the numbers of Gonionemus medusae used in our experiments likely underestimate the number of medusae that could be encountered by spider crabs over a 24-hour period in the field, we expect that Gonionemus may be having a negative effect on natural Libinia populations. Furthermore, given that Libinia overlaps in habitat and resource use with Carcinus, which avoids Gonionemus consumption, Carcinus populations could be indirectly benefiting from this unusual crab–jellyfish trophic relationship.
format: application/pdf
format: text/html
creator: Mary R. Carman
creator: David W. Grunden
creator: Annette F. Govindarajan
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.3966
publisher: PeerJ Inc.
rights: © 2017 Carman et al.
abstract: Here we report a unique trophic interaction between the cryptogenic and sometimes highly toxic hydrozoan clinging jellyfish Gonionemus sp. and the spider crab Libinia dubia. We assessed species–specific predation on the Gonionemus medusae by crabs found in eelgrass meadows in Massachusetts, USA. The native spider crab species L. dubia consumed Gonionemus medusae, often enthusiastically, but the invasive green crab Carcinus maenus avoided consumption in all trials. One out of two blue crabs (Callinectes sapidus) also consumed Gonionemus, but this species was too rare in our study system to evaluate further. Libinia crabs could consume up to 30 jellyfish, which was the maximum jellyfish density treatment in our experiments, over a 24-hour period. Gonionemus consumption was associated with Libinia mortality. Spider crab mortality increased with Gonionemus consumption, and 100% of spider crabs tested died within 24 h of consuming jellyfish in our maximum jellyfish density containers. As the numbers of Gonionemus medusae used in our experiments likely underestimate the number of medusae that could be encountered by spider crabs over a 24-hour period in the field, we expect that Gonionemus may be having a negative effect on natural Libinia populations. Furthermore, given that Libinia overlaps in habitat and resource use with Carcinus, which avoids Gonionemus consumption, Carcinus populations could be indirectly benefiting from this unusual crab–jellyfish trophic relationship.
bibliographic citation: Carman et al. (2017) Species–specific crab predation on the hydrozoan clinging jellyfish Gonionemus sp. (Cnidaria, Hydrozoa), subsequent crab mortality, and possible ecological consequences. PeerJ 5:e3966 https://doi.org/10.7717/peerj.3966
date submitted: 2017-08-16
date accepted: 2017-10-06
issued: 2017-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carman
  given name: Mary R.
author list: Agent
  family name: Grunden
  given name: David W.
author list: Agent
  family name: Govindarajan
  given name: Annette F.
doi: 10.7717/peerj.3966
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-26
copyright: ©2017 Carman et al.
attribution name: Carman et al.

Indigenous Australian household structure: a simple data collection tool and implications for close contact transmission of communicable diseases
type: item
type: AcademicArticle
description: Households are an important location for the transmission of communicable diseases. Social contact between household members is typically more frequent, of greater intensity, and is more likely to involve people of different age groups than contact occurring in the general community. Understanding household structure in different populations is therefore fundamental to explaining patterns of disease transmission in these populations. Indigenous populations in Australia tend to live in larger households than non-Indigenous populations, but limited data are available on the structure of these households, and how they differ between remote and urban communities. We have developed a novel approach to the collection of household structure data, suitable for use in a variety of contexts, which provides a detailed view of age, gender, and room occupancy patterns in remote and urban Australian Indigenous households. Here we report analysis of data collected using this tool, which quantifies the extent of crowding in Indigenous households, particularly in remote areas. We use these data to generate matrices of age-specific contact rates, as used by mathematical models of infectious disease transmission. To demonstrate the impact of household structure, we use a mathematical model to simulate an influenza-like illness in different populations. Our simulations suggest that outbreaks in remote populations are likely to spread more rapidly and to a greater extent than outbreaks in non-Indigenous populations.
format: application/pdf
format: text/html
creator: Thiripura Vino
creator: Gurmeet R. Singh
creator: Belinda Davison
creator: Patricia T. Campbell
creator: Michael J. Lydeamore
creator: Andrew Robinson
creator: Jodie McVernon
creator: Steven Y.C. Tong
creator: Nicholas Geard
subject: Anthropology
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.3958
publisher: PeerJ Inc.
rights: © 2017 Vino et al.
abstract: Households are an important location for the transmission of communicable diseases. Social contact between household members is typically more frequent, of greater intensity, and is more likely to involve people of different age groups than contact occurring in the general community. Understanding household structure in different populations is therefore fundamental to explaining patterns of disease transmission in these populations. Indigenous populations in Australia tend to live in larger households than non-Indigenous populations, but limited data are available on the structure of these households, and how they differ between remote and urban communities. We have developed a novel approach to the collection of household structure data, suitable for use in a variety of contexts, which provides a detailed view of age, gender, and room occupancy patterns in remote and urban Australian Indigenous households. Here we report analysis of data collected using this tool, which quantifies the extent of crowding in Indigenous households, particularly in remote areas. We use these data to generate matrices of age-specific contact rates, as used by mathematical models of infectious disease transmission. To demonstrate the impact of household structure, we use a mathematical model to simulate an influenza-like illness in different populations. Our simulations suggest that outbreaks in remote populations are likely to spread more rapidly and to a greater extent than outbreaks in non-Indigenous populations.
bibliographic citation: Vino et al. (2017) Indigenous Australian household structure: a simple data collection tool and implications for close contact transmission of communicable diseases. PeerJ 5:e3958 https://doi.org/10.7717/peerj.3958
date submitted: 2017-06-08
date accepted: 2017-10-04
issued: 2017-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vino
  given name: Thiripura
author list: Agent
  family name: Singh
  given name: Gurmeet R.
author list: Agent
  family name: Davison
  given name: Belinda
author list: Agent
  family name: Campbell
  given name: Patricia T.
author list: Agent
  family name: Lydeamore
  given name: Michael J.
author list: Agent
  family name: Robinson
  given name: Andrew
author list: Agent
  family name: McVernon
  given name: Jodie
author list: Agent
  family name: Tong
  given name: Steven Y.C.
author list: Agent
  family name: Geard
  given name: Nicholas
doi: 10.7717/peerj.3958
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-26
copyright: ©2017 Vino et al.
attribution name: Vino et al.

Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data
type: item
type: AcademicArticle
description: The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships a…
format: application/pdf
format: text/html
creator: Alejandra Panzera
creator: Adam D. Leaché
creator: Guillermo D’Elía
creator: Pedro F. Victoriano
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.3941
publisher: PeerJ Inc.
rights: © 2017 Panzera et al.
abstract: The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships a…
bibliographic citation: Panzera et al. (2017) Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data. PeerJ 5:e3941 https://doi.org/10.7717/peerj.3941
date submitted: 2017-05-05
date accepted: 2017-09-27
issued: 2017-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Panzera
  given name: Alejandra
author list: Agent
  family name: Leaché
  given name: Adam D.
author list: Agent
  family name: D’Elía
  given name: Guillermo
author list: Agent
  family name: Victoriano
  given name: Pedro F.
doi: 10.7717/peerj.3941
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-26
copyright: ©2017 Panzera et al.
attribution name: Panzera et al.

Erwinia amylovora psychrotrophic adaptations: evidence of pathogenic potential and survival at temperate and low environmental temperatures
type: item
type: AcademicArticle
description: The fire blight pathogen Erwinia amylovora can be considered a psychrotrophic bacterial species since it can grow at temperatures ranging from 4 °C to 37 °C, with an optimum of 28 °C. In many plant pathogens the expression of virulence determinants is restricted to a certain range of temperatures. In the case of E. amylovora, temperatures above 18 °C are required for blossom blight epidemics under field conditions. Moreover, this bacterium is able to infect a variety of host tissues/organs apart from flowers, but it is still unknown how environmental temperatures, especially those below 18 °C, affect the pathogen ability to cause fire blight disease symptoms in such tissues/organs. There is also scarce information on how temperatures below 18 °C affect the E. amylovora starvation-survival responses, which might determine its persistence in the environment and probably contribute to the seasonal development of fire blight disease, as occurs in other pathogens. To characterize the virulence and survival of E. amylovora at temperate and low temperatures, we evaluated the effect of three temperatures (4 °C, 14 °C, 28 °C) on symptom development, and on different parameters linked to starvation and virulence. E. amylovora was pathogenic at the three assayed temperatures, with a slow-down of symptom development correlating with colder temperatures and slower growth rates. Siderophore secretion and motility also decreased in parallel to incubation temperatures. However, production of the exopolysaccharides amylovoran and levan was enhanced at 4 °C and 14 °C, respectively. Similarly, biofilm formation, and oxidative stress resistance were improved at 14 °C, with this temperature also favoring the maintenance of culturability, together with a reduction in cell size and the acquisition of rounded shapes in E. amylovora cells subjected to long-term starvation. However, starvation at 28 °C and 4 °C induced an enhanced viable but nonculturable (VBNC) response (to a lesser extent …
format: application/pdf
format: text/html
creator: Ricardo D. Santander
creator: Elena G. Biosca
subject: Agricultural Science
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.3931
publisher: PeerJ Inc.
rights: © 2017 Santander and Biosca
abstract: The fire blight pathogen Erwinia amylovora can be considered a psychrotrophic bacterial species since it can grow at temperatures ranging from 4 °C to 37 °C, with an optimum of 28 °C. In many plant pathogens the expression of virulence determinants is restricted to a certain range of temperatures. In the case of E. amylovora, temperatures above 18 °C are required for blossom blight epidemics under field conditions. Moreover, this bacterium is able to infect a variety of host tissues/organs apart from flowers, but it is still unknown how environmental temperatures, especially those below 18 °C, affect the pathogen ability to cause fire blight disease symptoms in such tissues/organs. There is also scarce information on how temperatures below 18 °C affect the E. amylovora starvation-survival responses, which might determine its persistence in the environment and probably contribute to the seasonal development of fire blight disease, as occurs in other pathogens. To characterize the virulence and survival of E. amylovora at temperate and low temperatures, we evaluated the effect of three temperatures (4 °C, 14 °C, 28 °C) on symptom development, and on different parameters linked to starvation and virulence. E. amylovora was pathogenic at the three assayed temperatures, with a slow-down of symptom development correlating with colder temperatures and slower growth rates. Siderophore secretion and motility also decreased in parallel to incubation temperatures. However, production of the exopolysaccharides amylovoran and levan was enhanced at 4 °C and 14 °C, respectively. Similarly, biofilm formation, and oxidative stress resistance were improved at 14 °C, with this temperature also favoring the maintenance of culturability, together with a reduction in cell size and the acquisition of rounded shapes in E. amylovora cells subjected to long-term starvation. However, starvation at 28 °C and 4 °C induced an enhanced viable but nonculturable (VBNC) response (to a lesser extent …
bibliographic citation: Santander et al. (2017) Erwinia amylovora psychrotrophic adaptations: evidence of pathogenic potential and survival at temperate and low environmental temperatures. PeerJ 5:e3931 https://doi.org/10.7717/peerj.3931
date submitted: 2017-03-26
date accepted: 2017-09-26
issued: 2017-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santander
  given name: Ricardo D.
author list: Agent
  family name: Biosca
  given name: Elena G.
doi: 10.7717/peerj.3931
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-26
copyright: ©2017 Santander and Biosca
attribution name: Santander and Biosca

Evaluation of genetic variability among “Early Mature” Juglans regia using microsatellite markers and morphological traits
type: item
type: AcademicArticle
description: Limiting the juvenile phase and reducing tree size are the two main challenges for breeders to improve most fruit crops. Early maturation and dwarf cultivars have been reported for many fruit species. “Early mature” and low vigor walnut genotypes were found among seedlings of Persian walnut. Nine microsatellite markers were used to evaluate genetic diversity among “Early Mature” Persian walnut accessions and provide a comparison with “normal growth” accessions. Six maturation related characteristics were also measured in “Early Mature” samples. Phenotypic traits and diversity indices showed relatively high levels of genetic diversity in “Early Mature” seedlings and indicated high differentiation between individuals. Seedling height, the most diverse phenotypic trait, has an important role in the clustering of “Early Mature” accessions. The “Early Mature” type had higher number of alleles, number of effective allele, and Shannon index compared to the “Normal Growth” group. The two types of studied walnuts had different alleles, with more than half of produced alleles specific to a specific group. “Early Mature” and “Normal Growth” walnuts had 27 and 17 private alleles, respectively. Grouping with different methods separated “Early Mature” and “Normal Growth” samples entirely. The presence of moderate to high genetic diversity in “Early Mature” walnuts and high genetic differentiation with “Normal Growth” walnuts, indicated that “Early Mature” walnuts were more diverse and distinct from “Normal Growth” samples. Moreover, our results showed SSR markers were useful for differentiating between “Early Mature” and “Normal Growth” walnuts. A number of identified loci have potential in breeding programs for identification of “Early Mature” walnuts at the germination phase.
format: application/pdf
format: text/html
creator: Aziz Ebrahimi
creator: Abdolkarim Zarei
creator: Mojtaba Zamani Fardadonbeh
creator: Shaneka Lawson
subject: Agricultural Science
subject: Biodiversity
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.3834
publisher: PeerJ Inc.
rights: © 2017 Ebrahimi et al.
abstract: Limiting the juvenile phase and reducing tree size are the two main challenges for breeders to improve most fruit crops. Early maturation and dwarf cultivars have been reported for many fruit species. “Early mature” and low vigor walnut genotypes were found among seedlings of Persian walnut. Nine microsatellite markers were used to evaluate genetic diversity among “Early Mature” Persian walnut accessions and provide a comparison with “normal growth” accessions. Six maturation related characteristics were also measured in “Early Mature” samples. Phenotypic traits and diversity indices showed relatively high levels of genetic diversity in “Early Mature” seedlings and indicated high differentiation between individuals. Seedling height, the most diverse phenotypic trait, has an important role in the clustering of “Early Mature” accessions. The “Early Mature” type had higher number of alleles, number of effective allele, and Shannon index compared to the “Normal Growth” group. The two types of studied walnuts had different alleles, with more than half of produced alleles specific to a specific group. “Early Mature” and “Normal Growth” walnuts had 27 and 17 private alleles, respectively. Grouping with different methods separated “Early Mature” and “Normal Growth” samples entirely. The presence of moderate to high genetic diversity in “Early Mature” walnuts and high genetic differentiation with “Normal Growth” walnuts, indicated that “Early Mature” walnuts were more diverse and distinct from “Normal Growth” samples. Moreover, our results showed SSR markers were useful for differentiating between “Early Mature” and “Normal Growth” walnuts. A number of identified loci have potential in breeding programs for identification of “Early Mature” walnuts at the germination phase.
bibliographic citation: Ebrahimi et al. (2017) Evaluation of genetic variability among “Early Mature” Juglans regia using microsatellite markers and morphological traits. PeerJ 5:e3834 https://doi.org/10.7717/peerj.3834
date submitted: 2017-07-14
date accepted: 2017-08-30
issued: 2017-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ebrahimi
  given name: Aziz
author list: Agent
  family name: Zarei
  given name: Abdolkarim
author list: Agent
  family name: Zamani Fardadonbeh
  given name: Mojtaba
author list: Agent
  family name: Lawson
  given name: Shaneka
doi: 10.7717/peerj.3834
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-26
copyright: ©2017 Ebrahimi et al.
attribution name: Ebrahimi et al.

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