PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A white-box model of S-shaped and double S-shaped single-species population growth
items: Longitudinal relations among inattention, working memory, and academic achievement: testing mediation and the moderating role of gender
items: Genes affecting novel seed constituents in Limnanthes alba Benth: transcriptome analysis of developing embryos and a new genetic map of meadowfoam
items: Copepods enhance nutritional status, growth and development in Atlantic cod (Gadus morhua L.) larvae — can we identify the underlying factors?
items: Swabs to genomes: a comprehensive workflow
items: Childhood socioeconomic deprivation, but not current mood, is associated with behavioural disinhibition in adults
items: Individual consistency in the behaviors of newly-settled reef fish
items: Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest
items: Self-generated morphology in lagoon reefs
items: Impacts of sea level rise and climate change on coastal plant species in the central California coast

A white-box model of S-shaped and double S-shaped single-species population growth
type: item
type: AcademicArticle
description: Complex systems may be mechanistically modelled by white-box modeling with using logical deterministic individual-based cellular automata. Mathematical models of complex systems are of three types: black-box (phenomenological), white-box (mechanistic, based on the first principles) and grey-box (mixtures of phenomenological and mechanistic models). Most basic ecological models are of black-box type, including Malthusian, Verhulst, Lotka–Volterra models. In black-box models, the individual-based (mechanistic) mechanisms of population dynamics remain hidden. Here we mechanistically model the S-shaped and double S-shaped population growth of vegetatively propagated rhizomatous lawn grasses. Using purely logical deterministic individual-based cellular automata we create a white-box model. From a general physical standpoint, the vegetative propagation of plants is an analogue of excitation propagation in excitable media. Using the Monte Carlo method, we investigate a role of different initial positioning of an individual in the habitat. We have investigated mechanisms of the single-species population growth limited by habitat size, intraspecific competition, regeneration time and fecundity of individuals in two types of boundary conditions and at two types of fecundity. Besides that, we have compared the S-shaped and J-shaped population growth. We consider this white-box modeling approach as a method of artificial intelligence which works as automatic hyper-logical inference from the first principles of the studied subject. This approach is perspective for direct mechanistic insights into nature of any complex systems.
format: application/pdf
format: text/html
creator: Lev V. Kalmykov
creator: Vyacheslav L. Kalmykov
subject: Biophysics
subject: Computational Biology
subject: Ecology
subject: Mathematical Biology
subject: Computational Science
description: doi:10.7717/peerj.948
publisher: PeerJ Inc.
rights: © 2015 Kalmykov and Kalmykov
abstract: Complex systems may be mechanistically modelled by white-box modeling with using logical deterministic individual-based cellular automata. Mathematical models of complex systems are of three types: black-box (phenomenological), white-box (mechanistic, based on the first principles) and grey-box (mixtures of phenomenological and mechanistic models). Most basic ecological models are of black-box type, including Malthusian, Verhulst, Lotka–Volterra models. In black-box models, the individual-based (mechanistic) mechanisms of population dynamics remain hidden. Here we mechanistically model the S-shaped and double S-shaped population growth of vegetatively propagated rhizomatous lawn grasses. Using purely logical deterministic individual-based cellular automata we create a white-box model. From a general physical standpoint, the vegetative propagation of plants is an analogue of excitation propagation in excitable media. Using the Monte Carlo method, we investigate a role of different initial positioning of an individual in the habitat. We have investigated mechanisms of the single-species population growth limited by habitat size, intraspecific competition, regeneration time and fecundity of individuals in two types of boundary conditions and at two types of fecundity. Besides that, we have compared the S-shaped and J-shaped population growth. We consider this white-box modeling approach as a method of artificial intelligence which works as automatic hyper-logical inference from the first principles of the studied subject. This approach is perspective for direct mechanistic insights into nature of any complex systems.
bibliographic citation: Kalmykov et al. (2015) A white-box model of S-shaped and double S-shaped single-species population growth. PeerJ 3:e948 https://doi.org/10.7717/peerj.948
date submitted: 2014-12-31
date accepted: 2015-04-20
issued: 2015-05-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kalmykov
  given name: Lev V.
author list: Agent
  family name: Kalmykov
  given name: Vyacheslav L.
doi: 10.7717/peerj.948
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-19
copyright: © 2015 Kalmykov and Kalmykov
attribution name: Kalmykov and Kalmykov

Longitudinal relations among inattention, working memory, and academic achievement: testing mediation and the moderating role of gender
type: item
type: AcademicArticle
description: Introduction. Behavioral inattention, working memory (WM), and academic achievement share significant variance, but the direction of relationships across development is unknown. The aim of the present study was to determine whether WM mediates the pathway between inattentive behaviour and subsequent academic outcomes. Methods. 204 students from grades 1–4 (49.5% female) were recruited from elementary schools. Participants received assessments of WM and achievement at baseline and one year later. WM measures included a visual-spatial storage task and auditory-verbal storage and manipulation tasks. Teachers completed the SWAN behaviour rating scale both years. Mediation analysis with PROCESS (Hayes, 2013) was used to determine mediation pathways. Results. Teacher-rated inattention indirectly influenced math addition fluency, subtraction fluency and calculation scores through its effect on visual-spatial WM, only for boys. There was a direct relationship between inattention and math outcomes one year later for girls and boys. Children who displayed better attention had higher WM scores, and children with higher WM scores had stronger scores on math outcomes. Bias-corrected bootstrap confidence intervals for the indirect effects were entirely below zero for boys, for the three math outcomes. WM did not mediate the direct relationship between inattention and reading scores. Discussion. Findings identify inattention and WM as longitudinal predictors for math addition and subtraction fluency and math calculation outcomes one year later, with visual-spatial WM as a significant mediator for boys. Results highlight the close relationship between inattention and WM and their importance in the development of math skills.
format: application/pdf
format: text/html
creator: Sarah A. Gray
creator: Maria Rogers
creator: Rhonda Martinussen
creator: Rosemary Tannock
subject: Psychiatry and Psychology
subject: Science and Medical Education
description: doi:10.7717/peerj.939
publisher: PeerJ Inc.
rights: © 2015 Gray et al.
abstract: Introduction. Behavioral inattention, working memory (WM), and academic achievement share significant variance, but the direction of relationships across development is unknown. The aim of the present study was to determine whether WM mediates the pathway between inattentive behaviour and subsequent academic outcomes. Methods. 204 students from grades 1–4 (49.5% female) were recruited from elementary schools. Participants received assessments of WM and achievement at baseline and one year later. WM measures included a visual-spatial storage task and auditory-verbal storage and manipulation tasks. Teachers completed the SWAN behaviour rating scale both years. Mediation analysis with PROCESS (Hayes, 2013) was used to determine mediation pathways. Results. Teacher-rated inattention indirectly influenced math addition fluency, subtraction fluency and calculation scores through its effect on visual-spatial WM, only for boys. There was a direct relationship between inattention and math outcomes one year later for girls and boys. Children who displayed better attention had higher WM scores, and children with higher WM scores had stronger scores on math outcomes. Bias-corrected bootstrap confidence intervals for the indirect effects were entirely below zero for boys, for the three math outcomes. WM did not mediate the direct relationship between inattention and reading scores. Discussion. Findings identify inattention and WM as longitudinal predictors for math addition and subtraction fluency and math calculation outcomes one year later, with visual-spatial WM as a significant mediator for boys. Results highlight the close relationship between inattention and WM and their importance in the development of math skills.
bibliographic citation: Gray et al. (2015) Longitudinal relations among inattention, working memory, and academic achievement: testing mediation and the moderating role of gender. PeerJ 3:e939 https://doi.org/10.7717/peerj.939
date submitted: 2014-12-20
date accepted: 2015-04-16
issued: 2015-05-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gray
  given name: Sarah A.
author list: Agent
  family name: Rogers
  given name: Maria
author list: Agent
  family name: Martinussen
  given name: Rhonda
author list: Agent
  family name: Tannock
  given name: Rosemary
doi: 10.7717/peerj.939
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-19
copyright: © 2015 Gray et al.
attribution name: Gray et al.

Genes affecting novel seed constituents in Limnanthes alba Benth: transcriptome analysis of developing embryos and a new genetic map of meadowfoam
type: item
type: AcademicArticle
description: The seed oil of meadowfoam, a new crop in the Limnanthaceae family, is highly enriched in very long chain fatty acids that are desaturated at the Δ5 position. The unusual oil is desirable for cosmetics and innovative industrial applications and the seed meal remaining after oil extraction contains glucolimnanthin, a methoxylated benzylglucosinolate whose degradation products are herbicidal and anti-microbial. Here we describe EST analysis of the developing seed transcriptome that identified major genes involved in biosynthesis and assembly of the seed oil and in glucosinolate metabolic pathways. mRNAs encoding acyl-CoA Δ5 desaturase were notably abundant. The library was searched for simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). Fifty-four new SSR markers and eight candidate gene markers were developed and combined with previously developed SSRs to construct a new genetic map for Limnanthes alba. Mapped genes in the lipid biosynthetic pathway encode 3-ketoacyl-CoA synthase (KCS), Δ5 desaturase (Δ5DS), lysophosphatidylacyl-acyl transferase (LPAT), and acyl-CoA diacylglycerol acyl transferase (DGAT). Mapped genes in glucosinolate biosynthetic and degradation pathways encode CYP79A, myrosinase (TGG), and epithiospecifier modifier protein (ESM). The resources developed in this study will further the domestication and improvement of meadowfoam as an oilseed crop.
format: application/pdf
format: text/html
creator: Mary B. Slabaugh
creator: Laurel D. Cooper
creator: Venkata K. Kishore
creator: Steven J. Knapp
creator: Jennifer G. Kling
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.915
publisher: PeerJ Inc.
rights: © 2015 Slabaugh et al.
abstract: The seed oil of meadowfoam, a new crop in the Limnanthaceae family, is highly enriched in very long chain fatty acids that are desaturated at the Δ5 position. The unusual oil is desirable for cosmetics and innovative industrial applications and the seed meal remaining after oil extraction contains glucolimnanthin, a methoxylated benzylglucosinolate whose degradation products are herbicidal and anti-microbial. Here we describe EST analysis of the developing seed transcriptome that identified major genes involved in biosynthesis and assembly of the seed oil and in glucosinolate metabolic pathways. mRNAs encoding acyl-CoA Δ5 desaturase were notably abundant. The library was searched for simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). Fifty-four new SSR markers and eight candidate gene markers were developed and combined with previously developed SSRs to construct a new genetic map for Limnanthes alba. Mapped genes in the lipid biosynthetic pathway encode 3-ketoacyl-CoA synthase (KCS), Δ5 desaturase (Δ5DS), lysophosphatidylacyl-acyl transferase (LPAT), and acyl-CoA diacylglycerol acyl transferase (DGAT). Mapped genes in glucosinolate biosynthetic and degradation pathways encode CYP79A, myrosinase (TGG), and epithiospecifier modifier protein (ESM). The resources developed in this study will further the domestication and improvement of meadowfoam as an oilseed crop.
bibliographic citation: Slabaugh et al. (2015) Genes affecting novel seed constituents in Limnanthes alba Benth: transcriptome analysis of developing embryos and a new genetic map of meadowfoam. PeerJ 3:e915 https://doi.org/10.7717/peerj.915
date submitted: 2015-02-21
date accepted: 2015-04-06
issued: 2015-05-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Slabaugh
  given name: Mary B.
author list: Agent
  family name: Cooper
  given name: Laurel D.
author list: Agent
  family name: Kishore
  given name: Venkata K.
author list: Agent
  family name: Knapp
  given name: Steven J.
author list: Agent
  family name: Kling
  given name: Jennifer G.
doi: 10.7717/peerj.915
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-19
copyright: © 2015 Slabaugh et al.
attribution name: Slabaugh et al.

Copepods enhance nutritional status, growth and development in Atlantic cod (Gadus morhua L.) larvae — can we identify the underlying factors?
type: item
type: AcademicArticle
description: The current commercial production protocols for Atlantic cod depend on enriched rotifers and Artemia during first-feeding, but development and growth remain inferior to fish fed natural zooplankton. Two experiments were conducted in order to identify the underlying factors for this phenomenon. In the first experiment (Exp-1), groups of cod larvae were fed either (a) natural zooplankton, mainly copepods, increasing the size of prey as the larvae grew or (b) enriched rotifers followed by Artemia (the intensive group). In the second experiment (Exp-2), two groups of larvae were fed as in Exp-1, while a third group was fed copepod nauplii (approximately the size of rotifers) throughout the larval stage. In both experiments, growth was not significantly different between the groups during the first three weeks after hatching, but from the last part of the rotifer feeding period and onwards, the growth of the larvae fed copepods was higher than that of the intensive group. In Exp-2, the growth was similar between the two copepod groups during the expeimental period, indicating that nutrient composition, not prey size caused the better growth on copepods. Analyses of the prey showed that total fatty acid composition and the ratio of phospholipids to total lipids was slightly different in the prey organisms, and that protein, taurine, astaxanthin and zinc were lower on a dry weight basis in rotifers than in copepods. Other measured nutrients as DHA, all analysed vitamins, manganese, copper and selenium were similar or higher in the rotifers. When compared to the present knowledge on nutrient requirements, protein and taurine appeared to be the most likely limiting nutrients for growth in cod larvae fed rotifers and Artemia. Larvae fed rotifers/Artemia had a higher whole body lipid content than larvae fed copepods at the end of the experiment (stage 5) after the fish had been fed the same formulated diet for approximately 2 weeks.
format: application/pdf
format: text/html
creator: Ørjan Karlsen
creator: Terje van der Meeren
creator: Ivar Rønnestad
creator: Anders Mangor-Jensen
creator: Trina F. Galloway
creator: Elin Kjørsvik
creator: Kristin Hamre
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
description: doi:10.7717/peerj.902
publisher: PeerJ Inc.
rights: © 2015 Karlsen et al.
abstract: The current commercial production protocols for Atlantic cod depend on enriched rotifers and Artemia during first-feeding, but development and growth remain inferior to fish fed natural zooplankton. Two experiments were conducted in order to identify the underlying factors for this phenomenon. In the first experiment (Exp-1), groups of cod larvae were fed either (a) natural zooplankton, mainly copepods, increasing the size of prey as the larvae grew or (b) enriched rotifers followed by Artemia (the intensive group). In the second experiment (Exp-2), two groups of larvae were fed as in Exp-1, while a third group was fed copepod nauplii (approximately the size of rotifers) throughout the larval stage. In both experiments, growth was not significantly different between the groups during the first three weeks after hatching, but from the last part of the rotifer feeding period and onwards, the growth of the larvae fed copepods was higher than that of the intensive group. In Exp-2, the growth was similar between the two copepod groups during the expeimental period, indicating that nutrient composition, not prey size caused the better growth on copepods. Analyses of the prey showed that total fatty acid composition and the ratio of phospholipids to total lipids was slightly different in the prey organisms, and that protein, taurine, astaxanthin and zinc were lower on a dry weight basis in rotifers than in copepods. Other measured nutrients as DHA, all analysed vitamins, manganese, copper and selenium were similar or higher in the rotifers. When compared to the present knowledge on nutrient requirements, protein and taurine appeared to be the most likely limiting nutrients for growth in cod larvae fed rotifers and Artemia. Larvae fed rotifers/Artemia had a higher whole body lipid content than larvae fed copepods at the end of the experiment (stage 5) after the fish had been fed the same formulated diet for approximately 2 weeks.
bibliographic citation: Karlsen et al. (2015) Copepods enhance nutritional status, growth and development in Atlantic cod (Gadus morhua L.) larvae — can we identify the underlying factors?. PeerJ 3:e902 https://doi.org/10.7717/peerj.902
date submitted: 2014-12-28
date accepted: 2015-03-31
issued: 2015-05-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karlsen
  given name: Ørjan
author list: Agent
  family name: van der Meeren
  given name: Terje
author list: Agent
  family name: Rønnestad
  given name: Ivar
author list: Agent
  family name: Mangor-Jensen
  given name: Anders
author list: Agent
  family name: Galloway
  given name: Trina F.
author list: Agent
  family name: Kjørsvik
  given name: Elin
author list: Agent
  family name: Hamre
  given name: Kristin
doi: 10.7717/peerj.902
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-19
copyright: © 2015 Karlsen et al.
attribution name: Karlsen et al.

Swabs to genomes: a comprehensive workflow
type: item
type: AcademicArticle
description: The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
format: application/pdf
format: text/html
creator: Madison I. Dunitz
creator: Jenna M. Lang
creator: Guillaume Jospin
creator: Aaron E. Darling
creator: Jonathan A. Eisen
creator: David A. Coil
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.960
publisher: PeerJ Inc.
rights: © 2015 Dunitz et al.
abstract: The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
bibliographic citation: Dunitz et al. (2015) Swabs to genomes: a comprehensive workflow. PeerJ 3:e960 https://doi.org/10.7717/peerj.960
date submitted: 2015-01-30
date accepted: 2015-04-24
issued: 2015-05-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dunitz
  given name: Madison I.
author list: Agent
  family name: Lang
  given name: Jenna M.
author list: Agent
  family name: Jospin
  given name: Guillaume
author list: Agent
  family name: Darling
  given name: Aaron E.
author list: Agent
  family name: Eisen
  given name: Jonathan A.
author list: Agent
  family name: Coil
  given name: David A.
doi: 10.7717/peerj.960
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-14
copyright: © 2015 Dunitz et al.
attribution name: Dunitz et al.

Childhood socioeconomic deprivation, but not current mood, is associated with behavioural disinhibition in adults
type: item
type: AcademicArticle
description: There is evidence to suggest that impulsivity is predicted by socioeconomic background, with people from more deprived backgrounds tending to be more impulsive, and by current mood, with poorer mood associated with greater impulsivity. However, impulsivity is not a unitary construct, and previous research in this area has focused on measures of ‘waiting’ impulsivity rather than behavioural disinhibition. We administered a standard measure of behavioural disinhibition, the stop-signal task, to 58 adult participants from a community sample. We had measured socioeconomic background using participant postcode at age 16, and assigned participants to receive either a neutral or a negative mood induction. We found no effects of mood on behavioural disinhibition, but we found a significant effect of socioeconomic background. Participants who had lived in more deprived postcodes at age 16 showed longer stop-signal reaction times, and hence greater behavioural disinhibition. The pattern was independent of participant age and overall reaction time. Though caution is required inferring causality from correlation, it is possible that that experiencing socioeconomic deprivation in childhood and adolescence may lead to greater behavioural disinhibition in adulthood.
format: application/pdf
format: text/html
creator: Tünde Paál
creator: Thomas Carpenter
creator: Daniel Nettle
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.964
publisher: PeerJ Inc.
rights: © 2015 Paál et al.
abstract: There is evidence to suggest that impulsivity is predicted by socioeconomic background, with people from more deprived backgrounds tending to be more impulsive, and by current mood, with poorer mood associated with greater impulsivity. However, impulsivity is not a unitary construct, and previous research in this area has focused on measures of ‘waiting’ impulsivity rather than behavioural disinhibition. We administered a standard measure of behavioural disinhibition, the stop-signal task, to 58 adult participants from a community sample. We had measured socioeconomic background using participant postcode at age 16, and assigned participants to receive either a neutral or a negative mood induction. We found no effects of mood on behavioural disinhibition, but we found a significant effect of socioeconomic background. Participants who had lived in more deprived postcodes at age 16 showed longer stop-signal reaction times, and hence greater behavioural disinhibition. The pattern was independent of participant age and overall reaction time. Though caution is required inferring causality from correlation, it is possible that that experiencing socioeconomic deprivation in childhood and adolescence may lead to greater behavioural disinhibition in adulthood.
bibliographic citation: Paál et al. (2015) Childhood socioeconomic deprivation, but not current mood, is associated with behavioural disinhibition in adults. PeerJ 3:e964 https://doi.org/10.7717/peerj.964
date submitted: 2015-03-05
date accepted: 2015-04-27
issued: 2015-05-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paál
  given name: Tünde
author list: Agent
  family name: Carpenter
  given name: Thomas
author list: Agent
  family name: Nettle
  given name: Daniel
doi: 10.7717/peerj.964
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-14
copyright: © 2015 Paál et al.
attribution name: Paál et al.

Individual consistency in the behaviors of newly-settled reef fish
type: item
type: AcademicArticle
description: Flexibility in behavior is advantageous for organisms that transition between stages of a complex life history. However, various constraints can set limits on plasticity, giving rise to the existence of personalities that have associated costs and benefits. Here, we document a field and laboratory experiment that examines the consistency of measures of boldness, activity, and aggressive behavior in the young of a tropical reef fish, Pomacentrus amboinensis (Pomacentridae) immediately following their transition between pelagic larval and benthic juvenile habitats. Newly-settled fish were observed in aquaria and in the field on replicated patches of natural habitat cleared of resident fishes. Seven behavioral traits representing aspects of boldness, activity and aggression were monitored directly and via video camera over short (minutes), medium (hours), and long (3 days) time scales. With the exception of aggression, these behaviors were found to be moderately or highly consistent over all time scales in both laboratory and field settings, implying that these fish show stable personalities within various settings. Our study is the first to examine the temporal constancy of behaviors in both field and laboratory settings in over various time scales at a critically important phase during the life cycle of a reef fish.
format: application/pdf
format: text/html
creator: James R. White
creator: Mark G. Meekan
creator: Mark I. McCormick
subject: Animal Behavior
subject: Marine Biology
description: doi:10.7717/peerj.961
publisher: PeerJ Inc.
rights: © 2015 White et al.
abstract: Flexibility in behavior is advantageous for organisms that transition between stages of a complex life history. However, various constraints can set limits on plasticity, giving rise to the existence of personalities that have associated costs and benefits. Here, we document a field and laboratory experiment that examines the consistency of measures of boldness, activity, and aggressive behavior in the young of a tropical reef fish, Pomacentrus amboinensis (Pomacentridae) immediately following their transition between pelagic larval and benthic juvenile habitats. Newly-settled fish were observed in aquaria and in the field on replicated patches of natural habitat cleared of resident fishes. Seven behavioral traits representing aspects of boldness, activity and aggression were monitored directly and via video camera over short (minutes), medium (hours), and long (3 days) time scales. With the exception of aggression, these behaviors were found to be moderately or highly consistent over all time scales in both laboratory and field settings, implying that these fish show stable personalities within various settings. Our study is the first to examine the temporal constancy of behaviors in both field and laboratory settings in over various time scales at a critically important phase during the life cycle of a reef fish.
bibliographic citation: White et al. (2015) Individual consistency in the behaviors of newly-settled reef fish. PeerJ 3:e961 https://doi.org/10.7717/peerj.961
date submitted: 2015-03-28
date accepted: 2015-04-25
issued: 2015-05-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: White
  given name: James R.
author list: Agent
  family name: Meekan
  given name: Mark G.
author list: Agent
  family name: McCormick
  given name: Mark I.
doi: 10.7717/peerj.961
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-14
copyright: © 2015 White et al.
attribution name: White et al.

Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest
type: item
type: AcademicArticle
description: Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m2 and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that could b…
format: application/pdf
format: text/html
creator: Ahmed A. Siddig
creator: Aaron M. Ellison
creator: Scott Jackson
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
description: doi:10.7717/peerj.952
publisher: PeerJ Inc.
rights: © 2015 Siddig et al.
abstract: Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m2 and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that could b…
bibliographic citation: Siddig et al. (2015) Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest. PeerJ 3:e952 https://doi.org/10.7717/peerj.952
date submitted: 2015-02-12
date accepted: 2015-04-21
issued: 2015-05-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Siddig
  given name: Ahmed A.
author list: Agent
  family name: Ellison
  given name: Aaron M.
author list: Agent
  family name: Jackson
  given name: Scott
doi: 10.7717/peerj.952
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-14
copyright: © 2015 Siddig et al.
attribution name: Siddig et al.

Self-generated morphology in lagoon reefs
type: item
type: AcademicArticle
description: The three-dimensional form of a coral reef develops through interactions and feedbacks between its constituent organisms and their environment. Reef morphology therefore contains a potential wealth of ecological information, accessible if the relationships between morphology and ecology can be decoded. Traditionally, reef morphology has been attributed to external controls such as substrate topography or hydrodynamic influences. Little is known about inherent reef morphology in the absence of external control. Here we use reef growth simulations, based on observations in the cellular reefs of Western Australia’s Houtman Abrolhos Islands, to show that reef morphology is fundamentally determined by the mechanical behaviour of the reef-building organisms themselves—specifically their tendency to either remain in place or to collapse. Reef-building organisms that tend to remain in place, such as massive and encrusting corals or coralline algae, produce nodular reefs, whereas those that tend to collapse, such as branching Acropora, produce cellular reefs. The purest reef growth forms arise in sheltered lagoons dominated by a single type of reef builder, as in the branching Acropora-dominated lagoons of the Abrolhos. In these situations reef morphology can be considered a phenotype of the predominant reef building organism. The capacity to infer coral type from reef morphology can potentially be used to identify and map specific coral habitat in remotely sensed images. More generally, identifying ecological mechanisms underlying other examples of self-generated reef morphology can potentially improve our understanding of present-day reef ecology, because any ecological process capable of shaping a reef will almost invariably be an important process in real time on the living reef.
format: application/pdf
format: text/html
creator: David Blakeway
creator: Michael G. Hamblin
subject: Computational Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.935
publisher: PeerJ Inc.
rights: © 2015 Blakeway and Hamblin
abstract: The three-dimensional form of a coral reef develops through interactions and feedbacks between its constituent organisms and their environment. Reef morphology therefore contains a potential wealth of ecological information, accessible if the relationships between morphology and ecology can be decoded. Traditionally, reef morphology has been attributed to external controls such as substrate topography or hydrodynamic influences. Little is known about inherent reef morphology in the absence of external control. Here we use reef growth simulations, based on observations in the cellular reefs of Western Australia’s Houtman Abrolhos Islands, to show that reef morphology is fundamentally determined by the mechanical behaviour of the reef-building organisms themselves—specifically their tendency to either remain in place or to collapse. Reef-building organisms that tend to remain in place, such as massive and encrusting corals or coralline algae, produce nodular reefs, whereas those that tend to collapse, such as branching Acropora, produce cellular reefs. The purest reef growth forms arise in sheltered lagoons dominated by a single type of reef builder, as in the branching Acropora-dominated lagoons of the Abrolhos. In these situations reef morphology can be considered a phenotype of the predominant reef building organism. The capacity to infer coral type from reef morphology can potentially be used to identify and map specific coral habitat in remotely sensed images. More generally, identifying ecological mechanisms underlying other examples of self-generated reef morphology can potentially improve our understanding of present-day reef ecology, because any ecological process capable of shaping a reef will almost invariably be an important process in real time on the living reef.
bibliographic citation: Blakeway et al. (2015) Self-generated morphology in lagoon reefs. PeerJ 3:e935 https://doi.org/10.7717/peerj.935
date submitted: 2014-11-01
date accepted: 2015-04-15
issued: 2015-05-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Blakeway
  given name: David
author list: Agent
  family name: Hamblin
  given name: Michael G.
doi: 10.7717/peerj.935
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-12
copyright: © 2015 Blakeway and Hamblin
attribution name: Blakeway and Hamblin

Impacts of sea level rise and climate change on coastal plant species in the central California coast
type: item
type: AcademicArticle
description: Local increases in sea level caused by global climate change pose a significant threat to the persistence of many coastal plant species through exacerbating inundation, flooding, and erosion. In addition to sea level rise (SLR), climate changes in the form of air temperature and precipitation regimes will also alter habitats of coastal plant species. Although numerous studies have analyzed the effect of climate change on future habitats through species distribution models (SDMs), none have incorporated the threat of exposure to SLR. We developed a model that quantified the effect of both SLR and climate change on habitat for 88 rare coastal plant species in San Luis Obispo, Santa Barbara, and Ventura Counties, California, USA (an area of 23,948 km2). Our SLR model projects that by the year 2100, 60 of the 88 species will be threatened by SLR. We found that the probability of being threatened by SLR strongly correlates with a species’ area, elevation, and distance from the coast, and that 10 species could lose their entire current habitat in the study region. We modeled the habitat suitability of these 10 species under future climate using a species distribution model (SDM). Our SDM projects that 4 of the 10 species will lose all suitable current habitats in the region as a result of climate change. While SLR accounts for up to 9.2 km2 loss in habitat, climate change accounts for habitat suitability changes ranging from a loss of 1,439 km2 for one species to a gain of 9,795 km2 for another species. For three species, SLR is projected to reduce future suitable area by as much as 28% of total area. This suggests that while SLR poses a higher risk, climate changes in precipitation and air temperature represents a lesser known but potentially larger risk and a small cumulative effect from both.
format: application/pdf
format: text/html
creator: Kendra L. Garner
creator: Michelle Y. Chang
creator: Matthew T. Fulda
creator: Jonathan A. Berlin
creator: Rachel E. Freed
creator: Melissa M. Soo-Hoo
creator: Dave L. Revell
creator: Makihiko Ikegami
creator: Lorraine E. Flint
creator: Alan L. Flint
creator: Bruce E. Kendall
subject: Biodiversity
subject: Conservation Biology
description: doi:10.7717/peerj.958
publisher: PeerJ Inc.
rights: © 2015 Garner et al.
abstract: Local increases in sea level caused by global climate change pose a significant threat to the persistence of many coastal plant species through exacerbating inundation, flooding, and erosion. In addition to sea level rise (SLR), climate changes in the form of air temperature and precipitation regimes will also alter habitats of coastal plant species. Although numerous studies have analyzed the effect of climate change on future habitats through species distribution models (SDMs), none have incorporated the threat of exposure to SLR. We developed a model that quantified the effect of both SLR and climate change on habitat for 88 rare coastal plant species in San Luis Obispo, Santa Barbara, and Ventura Counties, California, USA (an area of 23,948 km2). Our SLR model projects that by the year 2100, 60 of the 88 species will be threatened by SLR. We found that the probability of being threatened by SLR strongly correlates with a species’ area, elevation, and distance from the coast, and that 10 species could lose their entire current habitat in the study region. We modeled the habitat suitability of these 10 species under future climate using a species distribution model (SDM). Our SDM projects that 4 of the 10 species will lose all suitable current habitats in the region as a result of climate change. While SLR accounts for up to 9.2 km2 loss in habitat, climate change accounts for habitat suitability changes ranging from a loss of 1,439 km2 for one species to a gain of 9,795 km2 for another species. For three species, SLR is projected to reduce future suitable area by as much as 28% of total area. This suggests that while SLR poses a higher risk, climate changes in precipitation and air temperature represents a lesser known but potentially larger risk and a small cumulative effect from both.
bibliographic citation: Garner et al. (2015) Impacts of sea level rise and climate change on coastal plant species in the central California coast. PeerJ 3:e958 https://doi.org/10.7717/peerj.958
date submitted: 2014-12-19
date accepted: 2015-04-24
issued: 2015-05-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garner
  given name: Kendra L.
author list: Agent
  family name: Chang
  given name: Michelle Y.
author list: Agent
  family name: Fulda
  given name: Matthew T.
author list: Agent
  family name: Berlin
  given name: Jonathan A.
author list: Agent
  family name: Freed
  given name: Rachel E.
author list: Agent
  family name: Soo-Hoo
  given name: Melissa M.
author list: Agent
  family name: Revell
  given name: Dave L.
author list: Agent
  family name: Ikegami
  given name: Makihiko
author list: Agent
  family name: Flint
  given name: Lorraine E.
author list: Agent
  family name: Flint
  given name: Alan L.
author list: Agent
  family name: Kendall
  given name: Bruce E.
doi: 10.7717/peerj.958
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-12
copyright: © 2015 Garner et al.
attribution name: Garner et al.

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