PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Crystal structure and functional analysis of human C1ORF123
items: New records of the archaic dolphin Agorophius (Mammalia: Cetacea) from the upper Oligocene Chandler Bridge Formation of South Carolina, USA
items: Investigating the relationship between intergroup physical contact and attitudes towards foreigners: the mediating role of quality of intergroup contact
items: Growth and feeding of deep-sea coral Lophelia pertusa from the California margin under simulated ocean acidification conditions
items: https://peerj.com/articles/5668
items: Assessing the role of dispersed floral resources for managed bees in providing supporting ecosystem services for crop pollination
items: Analysis of relative abundances with zeros on environmental gradients: a multinomial regression model
items: Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species
items: Pre-imaginal conditioning alters adult sex pheromone response in Drosophila
items: Assessing bird avoidance of high-contrast lights using a choice test approach: implications for reducing human-induced avian mortality

Crystal structure and functional analysis of human C1ORF123
type: item
type: AcademicArticle
description: Proteins of the DUF866 superfamily are exclusively found in eukaryotic cells. A member of the DUF866 superfamily, C1ORF123, is a human protein found in the open reading frame 123 of chromosome 1. The physiological role of C1ORF123 is yet to be determined. The only available protein structure of the DUF866 family shares just 26% sequence similarity and does not contain a zinc binding motif. Here, we present the crystal structure of the recombinant human C1ORF123 protein (rC1ORF123). The structure has a 2-fold internal symmetry dividing the monomeric protein into two mirrored halves that comprise of distinct electrostatic potential. The N-terminal half of rC1ORF123 includes a zinc-binding domain interacting with a zinc ion near to a potential ligand binding cavity. Functional studies of human C1ORF123 and its homologue in the fission yeast Schizosaccharomyces pombe (SpEss1) point to a role of DUF866 protein in mitochondrial oxidative phosphorylation.
format: application/pdf
format: text/html
creator: Siti Nurulnabila A. Rahaman
creator: Jastina Mat Yusop
creator: Zeti-Azura Mohamed-Hussein
creator: Wan Mohd Aizat
creator: Kok Lian Ho
creator: Aik-Hong Teh
creator: Jitka Waterman
creator: Boon Keat Tan
creator: Hwei Ling Tan
creator: Adelicia Yongling Li
creator: Ee Sin Chen
creator: Chyan Leong Ng
subject: Biochemistry
subject: Biophysics
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.5377
publisher: PeerJ Inc.
rights: © 2018 A. Rahaman et al.
abstract: Proteins of the DUF866 superfamily are exclusively found in eukaryotic cells. A member of the DUF866 superfamily, C1ORF123, is a human protein found in the open reading frame 123 of chromosome 1. The physiological role of C1ORF123 is yet to be determined. The only available protein structure of the DUF866 family shares just 26% sequence similarity and does not contain a zinc binding motif. Here, we present the crystal structure of the recombinant human C1ORF123 protein (rC1ORF123). The structure has a 2-fold internal symmetry dividing the monomeric protein into two mirrored halves that comprise of distinct electrostatic potential. The N-terminal half of rC1ORF123 includes a zinc-binding domain interacting with a zinc ion near to a potential ligand binding cavity. Functional studies of human C1ORF123 and its homologue in the fission yeast Schizosaccharomyces pombe (SpEss1) point to a role of DUF866 protein in mitochondrial oxidative phosphorylation.
bibliographic citation: A. Rahaman et al. (2018) Crystal structure and functional analysis of human C1ORF123. PeerJ 6:e5377 https://doi.org/10.7717/peerj.5377
date submitted: 2018-05-14
date accepted: 2018-07-14
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: A. Rahaman
  given name: Siti Nurulnabila
author list: Agent
  family name: Mat Yusop
  given name: Jastina
author list: Agent
  family name: Mohamed-Hussein
  given name: Zeti-Azura
author list: Agent
  family name: Aizat
  given name: Wan Mohd
author list: Agent
  family name: Ho
  given name: Kok Lian
author list: Agent
  family name: Teh
  given name: Aik-Hong
author list: Agent
  family name: Waterman
  given name: Jitka
author list: Agent
  family name: Tan
  given name: Boon Keat
author list: Agent
  family name: Tan
  given name: Hwei Ling
author list: Agent
  family name: Li
  given name: Adelicia Yongling
author list: Agent
  family name: Chen
  given name: Ee Sin
author list: Agent
  family name: Ng
  given name: Chyan Leong
doi: 10.7717/peerj.5377
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 A. Rahaman et al.
attribution name: A. Rahaman et al.

New records of the archaic dolphin Agorophius (Mammalia: Cetacea) from the upper Oligocene Chandler Bridge Formation of South Carolina, USA
type: item
type: AcademicArticle
description: The stem odontocete Agorophius pygmaeus (Ashley Formation, lower Oligocene, South Carolina; 29.0–26.57 Ma) has been a critical point of comparison for studies of early neocete evolution owing to its early discovery as well as its transitional anatomy relative to archaeocete whales and modern odontocetes. Some time during the late nineteenth century the holotype skull went missing and has never been relocated; supplementary reference specimens have since been recently referred to the species from the Ashley Formation and the overlying Chandler Bridge Formation (upper Oligocene; 24.7–23.5). New crania referable to Agorophius sp. are identifiable to the genus based on several features of the intertemporal region. Furthermore, all published specimens from the Chandler Bridge Formation consistently share larger absolute size and a proportionally shorter exposure of the parietal in the skull roof than specimens from the Ashley Formation (including the holotype). Furthermore, these specimens include well-preserved ethmoid labyrinths and cribriform plates, indicating that Agorophius primitively retained a strong olfactory sense. These new crania suggest that at least two species of Agorophius are present in the Oligocene of South Carolina, revealing a somewhat more complicated taxonomic perspective.
format: application/pdf
format: text/html
creator: Robert W. Boessenecker
creator: Jonathan H. Geisler
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.5290
publisher: PeerJ Inc.
rights: © 2018 Boessenecker and Geisler
abstract: The stem odontocete Agorophius pygmaeus (Ashley Formation, lower Oligocene, South Carolina; 29.0–26.57 Ma) has been a critical point of comparison for studies of early neocete evolution owing to its early discovery as well as its transitional anatomy relative to archaeocete whales and modern odontocetes. Some time during the late nineteenth century the holotype skull went missing and has never been relocated; supplementary reference specimens have since been recently referred to the species from the Ashley Formation and the overlying Chandler Bridge Formation (upper Oligocene; 24.7–23.5). New crania referable to Agorophius sp. are identifiable to the genus based on several features of the intertemporal region. Furthermore, all published specimens from the Chandler Bridge Formation consistently share larger absolute size and a proportionally shorter exposure of the parietal in the skull roof than specimens from the Ashley Formation (including the holotype). Furthermore, these specimens include well-preserved ethmoid labyrinths and cribriform plates, indicating that Agorophius primitively retained a strong olfactory sense. These new crania suggest that at least two species of Agorophius are present in the Oligocene of South Carolina, revealing a somewhat more complicated taxonomic perspective.
bibliographic citation: Boessenecker et al. (2018) New records of the archaic dolphin Agorophius (Mammalia: Cetacea) from the upper Oligocene Chandler Bridge Formation of South Carolina, USA. PeerJ 6:e5290 https://doi.org/10.7717/peerj.5290
date submitted: 2018-03-20
date accepted: 2018-07-02
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boessenecker
  given name: Robert W.
author list: Agent
  family name: Geisler
  given name: Jonathan H.
doi: 10.7717/peerj.5290
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Boessenecker and Geisler
attribution name: Boessenecker and Geisler

Investigating the relationship between intergroup physical contact and attitudes towards foreigners: the mediating role of quality of intergroup contact
type: item
type: AcademicArticle
description: Recent research has shown that a brief, casual touch administered by an outgroup member reduces prejudice towards the group to which the toucher belongs. In this study, we take the research on physical contact and prejudice a step further by addressing the relation between individuals’ amount of Experienced Intergroup Physical Contact (EIPC), across distinct contexts and involving different body parts, and attitudes towards foreign people. Specifically, we hypothesized that the amount of EIPC would be positively associated with both quantity and quality of intergroup contact, but that only quality would mediate the relationship between the amount of EIPC and outgroup attitudes, quality being more directly linked to the evaluative component of outgroup attitudes. To attain this aim, we asked participants to self-report the amount of EIPC, the quantity and quality of their intergroup contact and their attitudes towards foreign people. Consistent with our hypothesis: (1) as EIPC increased, positive attitudes towards foreign people increased; (2) higher levels of EIPC were associated with better quality and higher quantity of intergroup contact; (3) only quality of intergroup contact mediated the relationship between the amount of EIPC and attitudes towards foreign people. Results were discussed in relation to research on intergroup contact and physical contact.
format: application/pdf
format: text/html
creator: Soraya E. Shamloo
creator: Andrea Carnaghi
creator: Carlo Fantoni
subject: Anthropology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.5680
publisher: PeerJ Inc.
rights: © 2018 Shamloo et al.
abstract: Recent research has shown that a brief, casual touch administered by an outgroup member reduces prejudice towards the group to which the toucher belongs. In this study, we take the research on physical contact and prejudice a step further by addressing the relation between individuals’ amount of Experienced Intergroup Physical Contact (EIPC), across distinct contexts and involving different body parts, and attitudes towards foreign people. Specifically, we hypothesized that the amount of EIPC would be positively associated with both quantity and quality of intergroup contact, but that only quality would mediate the relationship between the amount of EIPC and outgroup attitudes, quality being more directly linked to the evaluative component of outgroup attitudes. To attain this aim, we asked participants to self-report the amount of EIPC, the quantity and quality of their intergroup contact and their attitudes towards foreign people. Consistent with our hypothesis: (1) as EIPC increased, positive attitudes towards foreign people increased; (2) higher levels of EIPC were associated with better quality and higher quantity of intergroup contact; (3) only quality of intergroup contact mediated the relationship between the amount of EIPC and attitudes towards foreign people. Results were discussed in relation to research on intergroup contact and physical contact.
bibliographic citation: Shamloo et al. (2018) Investigating the relationship between intergroup physical contact and attitudes towards foreigners: the mediating role of quality of intergroup contact. PeerJ 6:e5680 https://doi.org/10.7717/peerj.5680
date submitted: 2018-03-06
date accepted: 2018-08-31
issued: 2018-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shamloo
  given name: Soraya E.
author list: Agent
  family name: Carnaghi
  given name: Andrea
author list: Agent
  family name: Fantoni
  given name: Carlo
doi: 10.7717/peerj.5680
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-27
copyright: ©2018 Shamloo et al.
attribution name: Shamloo et al.

Growth and feeding of deep-sea coral Lophelia pertusa from the California margin under simulated ocean acidification conditions
type: item
type: AcademicArticle
description: The global decrease in seawater pH known as ocean acidification has important ecological consequences and is an imminent threat for numerous marine organisms. Even though the deep sea is generally considered to be a stable environment, it can be dynamic and vulnerable to anthropogenic disturbances including increasing temperature, deoxygenation, ocean acidification and pollution. Lophelia pertusa is among the better-studied cold-water corals but was only recently documented along the US West Coast, growing in acidified conditions. In the present study, coral fragments were collected at ∼300 m depth along the southern California margin and kept in recirculating tanks simulating conditions normally found in the natural environment for this species. At the collection site, waters exhibited persistently low pH and aragonite saturation states (Ωarag) with average values for pH of 7.66 ± 0.01 and Ωarag of 0.81 ± 0.07. In the laboratory, fragments were grown for three weeks in “favorable” pH/Ωarag of 7.9/1.47 (aragonite saturated) and “unfavorable” pH/Ωarag of 7.6/0.84 (aragonite undersaturated) conditions. There was a highly significant treatment effect (P < 0.001) with an average% net calcification for favorable conditions of 0.023 ± 0.009% d−1 and net dissolution of −0.010 ± 0.014% d-1 for unfavorable conditions. We did not find any treatment effect on feeding rates, which suggests that corals did not depress feeding in low pH/ Ωarag in an attempt to conserve energy. However, these results suggest that the suboptimal conditions for L. pertusa from the California margin could potentially threaten the persistence of this cold-water coral with negative consequences for the future stability of this already fragile ecosystem.
format: application/pdf
format: text/html
creator: Carlos E. Gómez
creator: Leslie Wickes
creator: Dan Deegan
creator: Peter J. Etnoyer
creator: Erik E. Cordes
subject: Marine Biology
subject: Climate Change Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.5671
publisher: PeerJ Inc.
rights: © 2018 Gómez et al.
abstract: The global decrease in seawater pH known as ocean acidification has important ecological consequences and is an imminent threat for numerous marine organisms. Even though the deep sea is generally considered to be a stable environment, it can be dynamic and vulnerable to anthropogenic disturbances including increasing temperature, deoxygenation, ocean acidification and pollution. Lophelia pertusa is among the better-studied cold-water corals but was only recently documented along the US West Coast, growing in acidified conditions. In the present study, coral fragments were collected at ∼300 m depth along the southern California margin and kept in recirculating tanks simulating conditions normally found in the natural environment for this species. At the collection site, waters exhibited persistently low pH and aragonite saturation states (Ωarag) with average values for pH of 7.66 ± 0.01 and Ωarag of 0.81 ± 0.07. In the laboratory, fragments were grown for three weeks in “favorable” pH/Ωarag of 7.9/1.47 (aragonite saturated) and “unfavorable” pH/Ωarag of 7.6/0.84 (aragonite undersaturated) conditions. There was a highly significant treatment effect (P < 0.001) with an average% net calcification for favorable conditions of 0.023 ± 0.009% d−1 and net dissolution of −0.010 ± 0.014% d-1 for unfavorable conditions. We did not find any treatment effect on feeding rates, which suggests that corals did not depress feeding in low pH/ Ωarag in an attempt to conserve energy. However, these results suggest that the suboptimal conditions for L. pertusa from the California margin could potentially threaten the persistence of this cold-water coral with negative consequences for the future stability of this already fragile ecosystem.
bibliographic citation: Gómez et al. (2018) Growth and feeding of deep-sea coral Lophelia pertusa from the California margin under simulated ocean acidification conditions. PeerJ 6:e5671 https://doi.org/10.7717/peerj.5671
date submitted: 2018-05-02
date accepted: 2018-08-30
issued: 2018-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gómez
  given name: Carlos E.
author list: Agent
  family name: Wickes
  given name: Leslie
author list: Agent
  family name: Deegan
  given name: Dan
author list: Agent
  family name: Etnoyer
  given name: Peter J.
author list: Agent
  family name: Cordes
  given name: Erik E.
doi: 10.7717/peerj.5671
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-27
copyright: ©2018 Gómez et al.
attribution name: Gómez et al.

https://peerj.com/articles/5668
type: item
type: AcademicArticle
title: Distribution, habitat associations, and conservation status updates for the pilose crayfish Pacifastacus gambelii (Girard, 1852) and Snake River pilose crayfish Pacifastacus connectens (Faxon, 1914) of the western United States
description: Our study evaluates the distribution, habitat associations, and current conservation status of the Snake River pilose crayfish Pacifastacus connectens (Faxon, 1914) and pilose crayfish Pacifastacus gambelii (Girard, 1852), two little-studied and data-deficient species endemic to the western United States. We first developed a species distribution model (SDM) for the pilose crayfishes based on their historical occurrence records using boosted regression trees and freshwater GIS data layers. We then sampled 163 sites in the summers of 2016 and 2017 within the distribution of these crayfishes, including 50 where these species were observed historically. We next compared our field results to modeled predictions of suitable habitat from the SDM. Our SDM predicted 73 sites (45%) we sampled as suitable for the pilose crayfishes, with a moderate AUC value of 0.824. The pilose crayfishes were generally predicted to occur in larger streams and rivers with less extreme upstream temperature and precipitation seasonality. We found the pilose crayfishes at only 20 (12%) of the 163 total sites we sampled, 14 (20%) of the 73 sites predicted as suitable for them by our SDM, and 12 (24%) of 50 historical sites that we sampled. We found the invasive virile crayfish Faxonius virilis (Hagen, 1870) at 22 sites total and 12 (24%) historical sites for the pilose crayfishes, and we found the “native invader” signal crayfish Pacifastacus leniusculus (Dana, 1852) at 29 sites total and 6 (12%) historical sites for the pilose crayfishes. We subsequently used a single classification tree to identify factors associated with our high rate of false positives for contemporary pilose crayfish distributions relative to our SDM. This classification tree identified the presence of invasive crayfishes, impairment of the benthic community, and sampling method as some of the factors differentiating false positives relative to true positives for the pilose crayfishes. Our study identified the historical dis…
format: application/pdf
format: text/html
creator: Rachel M. Egly
creator: Eric R. Larson
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.5668
publisher: PeerJ Inc.
rights: © 2018 Egly and Larson
abstract: Our study evaluates the distribution, habitat associations, and current conservation status of the Snake River pilose crayfish Pacifastacus connectens (Faxon, 1914) and pilose crayfish Pacifastacus gambelii (Girard, 1852), two little-studied and data-deficient species endemic to the western United States. We first developed a species distribution model (SDM) for the pilose crayfishes based on their historical occurrence records using boosted regression trees and freshwater GIS data layers. We then sampled 163 sites in the summers of 2016 and 2017 within the distribution of these crayfishes, including 50 where these species were observed historically. We next compared our field results to modeled predictions of suitable habitat from the SDM. Our SDM predicted 73 sites (45%) we sampled as suitable for the pilose crayfishes, with a moderate AUC value of 0.824. The pilose crayfishes were generally predicted to occur in larger streams and rivers with less extreme upstream temperature and precipitation seasonality. We found the pilose crayfishes at only 20 (12%) of the 163 total sites we sampled, 14 (20%) of the 73 sites predicted as suitable for them by our SDM, and 12 (24%) of 50 historical sites that we sampled. We found the invasive virile crayfish Faxonius virilis (Hagen, 1870) at 22 sites total and 12 (24%) historical sites for the pilose crayfishes, and we found the “native invader” signal crayfish Pacifastacus leniusculus (Dana, 1852) at 29 sites total and 6 (12%) historical sites for the pilose crayfishes. We subsequently used a single classification tree to identify factors associated with our high rate of false positives for contemporary pilose crayfish distributions relative to our SDM. This classification tree identified the presence of invasive crayfishes, impairment of the benthic community, and sampling method as some of the factors differentiating false positives relative to true positives for the pilose crayfishes. Our study identified the historical dis…
bibliographic citation: Egly et al. (2018) Distribution, habitat associations, and conservation status updates for the pilose crayfish Pacifastacus gambelii (Girard, 1852) and Snake River pilose crayfish Pacifastacus connectens (Faxon, 1914) of the western United States. PeerJ 6:e5668 https://doi.org/10.7717/peerj.5668
date submitted: 2018-06-12
date accepted: 2018-08-29
issued: 2018-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Egly
  given name: Rachel M.
author list: Agent
  family name: Larson
  given name: Eric R.
doi: 10.7717/peerj.5668
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-27
copyright: ©2018 Egly and Larson
attribution name: Egly and Larson

Assessing the role of dispersed floral resources for managed bees in providing supporting ecosystem services for crop pollination
type: item
type: AcademicArticle
description: Most pollination ecosystem services studies have focussed on wild pollinators and their dependence on natural floral resources adjacent to crop fields. However, managed pollinators depend on a mixture of floral resources that are spatially separated from the crop field. Here, we consider the supporting role these resources play as an ecosystem services provider to quantify the use and availability of floral resources, and to estimate their relative contribution to support pollination services of managed honeybees. Beekeepers supplying pollination services to the Western Cape deciduous fruit industry were interviewed to obtain information on their use of floral resources. For 120 apiary sites, we also analysed floral resources within a two km radius of each site based on geographic data. The relative availability of floral resources at sites was compared to regional availability. The relative contribution of floral resources-types to sustain managed honeybees was estimated. Beekeepers showed a strong preference for eucalypts and canola. Beekeepers selectively placed more hives at sites with eucalypt and canola and less with natural vegetation. However, at the landscape-scale, eucalypt was the least available resource, whereas natural vegetation was most common. Based on analysis of apiary sites, we estimated that 700,818 ha of natural vegetation, 73,910 ha of canola fields, and 10,485 ha of eucalypt are used to support the managed honeybee industry in the Western Cape. Whereas the Cape managed honeybee system uses a bee native to the region, alien plant species appear disproportionately important among the floral resources being exploited. We suggest that an integrated approach, including evidence from interview and landscape data, and fine-scale biological data is needed to study floral resources supporting managed honeybees.
format: application/pdf
format: text/html
creator: Annalie Melin
creator: Mathieu Rouget
creator: Jonathan F. Colville
creator: Jeremy J. Midgley
creator: John S. Donaldson
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Entomology
description: doi:10.7717/peerj.5654
publisher: PeerJ Inc.
rights: © 2018 Melin et al.
abstract: Most pollination ecosystem services studies have focussed on wild pollinators and their dependence on natural floral resources adjacent to crop fields. However, managed pollinators depend on a mixture of floral resources that are spatially separated from the crop field. Here, we consider the supporting role these resources play as an ecosystem services provider to quantify the use and availability of floral resources, and to estimate their relative contribution to support pollination services of managed honeybees. Beekeepers supplying pollination services to the Western Cape deciduous fruit industry were interviewed to obtain information on their use of floral resources. For 120 apiary sites, we also analysed floral resources within a two km radius of each site based on geographic data. The relative availability of floral resources at sites was compared to regional availability. The relative contribution of floral resources-types to sustain managed honeybees was estimated. Beekeepers showed a strong preference for eucalypts and canola. Beekeepers selectively placed more hives at sites with eucalypt and canola and less with natural vegetation. However, at the landscape-scale, eucalypt was the least available resource, whereas natural vegetation was most common. Based on analysis of apiary sites, we estimated that 700,818 ha of natural vegetation, 73,910 ha of canola fields, and 10,485 ha of eucalypt are used to support the managed honeybee industry in the Western Cape. Whereas the Cape managed honeybee system uses a bee native to the region, alien plant species appear disproportionately important among the floral resources being exploited. We suggest that an integrated approach, including evidence from interview and landscape data, and fine-scale biological data is needed to study floral resources supporting managed honeybees.
bibliographic citation: Melin et al. (2018) Assessing the role of dispersed floral resources for managed bees in providing supporting ecosystem services for crop pollination. PeerJ 6:e5654 https://doi.org/10.7717/peerj.5654
date submitted: 2018-03-07
date accepted: 2018-08-28
issued: 2018-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Melin
  given name: Annalie
author list: Agent
  family name: Rouget
  given name: Mathieu
author list: Agent
  family name: Colville
  given name: Jonathan F.
author list: Agent
  family name: Midgley
  given name: Jeremy J.
author list: Agent
  family name: Donaldson
  given name: John S.
doi: 10.7717/peerj.5654
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-27
copyright: ©2018 Melin et al.
attribution name: Melin et al.

Analysis of relative abundances with zeros on environmental gradients: a multinomial regression model
type: item
type: AcademicArticle
description: Ecologists often analyze relative abundances, which are an example of compositional data. However, they have made surprisingly little use of recent advances in the field of compositional data analysis. Compositions form a vector space in which addition and scalar multiplication are replaced by operations known as perturbation and powering. This algebraic structure makes it easy to understand how relative abundances change along environmental gradients. We illustrate this with an analysis of changes in hard-substrate marine communities along a depth gradient. We fit a quadratic multivariate regression model with multinomial observations to point count data obtained from video transects. As well as being an appropriate observation model in this case, the multinomial deals with the problem of zeros, which often makes compositional data analysis difficult. We show how the algebra of compositions can be used to understand patterns in dissimilarity. We use the calculus of simplex-valued functions to estimate rates of change, and to summarize the structure of the community over a vertical slice. We discuss the benefits of the compositional approach in the interpretation and visualization of relative abundance data.
format: application/pdf
format: text/html
creator: Fiona Chong
creator: Matthew Spencer
subject: Ecology
subject: Marine Biology
subject: Mathematical Biology
description: doi:10.7717/peerj.5643
publisher: PeerJ Inc.
rights: © 2018 Chong and Spencer
abstract: Ecologists often analyze relative abundances, which are an example of compositional data. However, they have made surprisingly little use of recent advances in the field of compositional data analysis. Compositions form a vector space in which addition and scalar multiplication are replaced by operations known as perturbation and powering. This algebraic structure makes it easy to understand how relative abundances change along environmental gradients. We illustrate this with an analysis of changes in hard-substrate marine communities along a depth gradient. We fit a quadratic multivariate regression model with multinomial observations to point count data obtained from video transects. As well as being an appropriate observation model in this case, the multinomial deals with the problem of zeros, which often makes compositional data analysis difficult. We show how the algebra of compositions can be used to understand patterns in dissimilarity. We use the calculus of simplex-valued functions to estimate rates of change, and to summarize the structure of the community over a vertical slice. We discuss the benefits of the compositional approach in the interpretation and visualization of relative abundance data.
bibliographic citation: Chong et al. (2018) Analysis of relative abundances with zeros on environmental gradients: a multinomial regression model. PeerJ 6:e5643 https://doi.org/10.7717/peerj.5643
date submitted: 2018-04-26
date accepted: 2018-08-27
issued: 2018-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chong
  given name: Fiona
author list: Agent
  family name: Spencer
  given name: Matthew
doi: 10.7717/peerj.5643
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-27
copyright: ©2018 Chong and Spencer
attribution name: Chong and Spencer

Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species
type: item
type: AcademicArticle
description: The Gila robusta species complex in the Lower Colorado River Basin has a complicated taxonomic history. Recent authors have separated this group into three nominal taxa, G. robusta, G. intermedia, and G. nigra, however aside from location, no reliable method of distinguishing individuals of these species currently exists. To assess relationships within this group, we examined morphology of type specimens and fresh material, and used RADseq methods to assess phylogenetic relationship among these nominal species. Maximum likelihood and Bayesian inference tree building methods reveal high concordance between tree topologies based on the mitochondrial and nuclear datasets. Coalescent SNAPP analysis resolved a similar tree topology. Neither morphological nor molecular data reveal diagnostic differences between these species as currently defined. As such, G. intermedia and G. nigra should be considered synonyms of the senior G. robusta. We hypothesize that climate driven wet and dry cycles have led to periodic isolation of population subunits and subsequent local divergence followed by reestablished connectivity and mixing. Management plans should therefore focus on retaining genetic variability and viability of geographic populations to preserve adaptability to changing climate conditions.
format: application/pdf
format: text/html
creator: Joshua M. Copus
creator: W. L. Montgomery
creator: Zac H. Forsman
creator: Brian W. Bowen
creator: Robert J. Toonen
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Genomics
subject: Taxonomy
description: doi:10.7717/peerj.5605
publisher: PeerJ Inc.
rights: © 2018 Copus et al.
abstract: The Gila robusta species complex in the Lower Colorado River Basin has a complicated taxonomic history. Recent authors have separated this group into three nominal taxa, G. robusta, G. intermedia, and G. nigra, however aside from location, no reliable method of distinguishing individuals of these species currently exists. To assess relationships within this group, we examined morphology of type specimens and fresh material, and used RADseq methods to assess phylogenetic relationship among these nominal species. Maximum likelihood and Bayesian inference tree building methods reveal high concordance between tree topologies based on the mitochondrial and nuclear datasets. Coalescent SNAPP analysis resolved a similar tree topology. Neither morphological nor molecular data reveal diagnostic differences between these species as currently defined. As such, G. intermedia and G. nigra should be considered synonyms of the senior G. robusta. We hypothesize that climate driven wet and dry cycles have led to periodic isolation of population subunits and subsequent local divergence followed by reestablished connectivity and mixing. Management plans should therefore focus on retaining genetic variability and viability of geographic populations to preserve adaptability to changing climate conditions.
bibliographic citation: Copus et al. (2018) Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species. PeerJ 6:e5605 https://doi.org/10.7717/peerj.5605
date submitted: 2017-09-15
date accepted: 2018-08-17
issued: 2018-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Copus
  given name: Joshua M.
author list: Agent
  family name: Montgomery
  given name: W. L.
author list: Agent
  family name: Forsman
  given name: Zac H.
author list: Agent
  family name: Bowen
  given name: Brian W.
author list: Agent
  family name: Toonen
  given name: Robert J.
doi: 10.7717/peerj.5605
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-27
copyright: © 2018 Copus et al.
attribution name: Copus et al.

Pre-imaginal conditioning alters adult sex pheromone response in Drosophila
type: item
type: AcademicArticle
description: Pheromones are chemical signals that induce innate responses in individuals of the same species that may vary with physiological and developmental state. In Drosophila melanogaster, the most intensively studied pheromone is 11-cis-vaccenyl acetate (cVA), which is synthezised in the male ejaculatory bulb and is transferred to the female during copulation. Among other effects, cVA inhibits male courtship of mated females. We found that male courtship inhibition depends on the amount of cVA and this effect is reduced in male flies derived from eggs covered with low to zero levels of cVA. This effect is not observed if the eggs are washed, or if the eggs are laid several days after copulation. This suggests that courtship suppression involves a form of pre-imaginal conditioning, which we show occurs during the early larval stage. The conditioning effect could not be rescued by synthetic cVA, indicating that it largely depends on conditioning by cVA and other maternally-transmitted factor(s). These experiments suggest that one of the primary behavioral effects of cVA is more plastic and less stereotypical than had hitherto been realised.
format: application/pdf
format: text/html
creator: Claude Everaerts
creator: Laurie Cazalé-Debat
creator: Alexis Louis
creator: Emilie Pereira
creator: Jean-Pierre Farine
creator: Matthew Cobb
creator: Jean-François Ferveur
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.5585
publisher: PeerJ Inc.
rights: © 2018 Everaerts et al.
abstract: Pheromones are chemical signals that induce innate responses in individuals of the same species that may vary with physiological and developmental state. In Drosophila melanogaster, the most intensively studied pheromone is 11-cis-vaccenyl acetate (cVA), which is synthezised in the male ejaculatory bulb and is transferred to the female during copulation. Among other effects, cVA inhibits male courtship of mated females. We found that male courtship inhibition depends on the amount of cVA and this effect is reduced in male flies derived from eggs covered with low to zero levels of cVA. This effect is not observed if the eggs are washed, or if the eggs are laid several days after copulation. This suggests that courtship suppression involves a form of pre-imaginal conditioning, which we show occurs during the early larval stage. The conditioning effect could not be rescued by synthetic cVA, indicating that it largely depends on conditioning by cVA and other maternally-transmitted factor(s). These experiments suggest that one of the primary behavioral effects of cVA is more plastic and less stereotypical than had hitherto been realised.
bibliographic citation: Everaerts et al. (2018) Pre-imaginal conditioning alters adult sex pheromone response in Drosophila. PeerJ 6:e5585 https://doi.org/10.7717/peerj.5585
date submitted: 2018-04-30
date accepted: 2018-08-15
issued: 2018-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Everaerts
  given name: Claude
author list: Agent
  family name: Cazalé-Debat
  given name: Laurie
author list: Agent
  family name: Louis
  given name: Alexis
author list: Agent
  family name: Pereira
  given name: Emilie
author list: Agent
  family name: Farine
  given name: Jean-Pierre
author list: Agent
  family name: Cobb
  given name: Matthew
author list: Agent
  family name: Ferveur
  given name: Jean-François
doi: 10.7717/peerj.5585
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-27
copyright: ©2018 Everaerts et al.
attribution name: Everaerts et al.

Assessing bird avoidance of high-contrast lights using a choice test approach: implications for reducing human-induced avian mortality
type: item
type: AcademicArticle
description: Background Avian collisions with man-made objects and vehicles (e.g., buildings, cars, airplanes, power lines) have increased recently. Lights have been proposed to alert birds and minimize the chances of collisions, but it is challenging to choose lights that are tuned to the avian eye and can also lead to avoidance given the differences between human and avian vision. We propose a choice test to address this problem by first identifying wavelengths of light that would over-stimulate the retina using species-specific perceptual models and by then assessing the avoidance/attraction responses of brown-headed cowbirds to these lights during daytime using a behavioral assay. Methods We used perceptual models to estimate wavelength-specific light emitting diode (LED) lights with high chromatic contrast. The behavioral assay consisted of an arena where the bird moved in a single direction and was forced to make a choice (right/left) using a single-choice design (one side with the light on, the other with the light off) under diurnal light conditions. Results First, we identified lights with high saliency from the cowbird visual perspective: LED lights with peaks at 380 nm (ultraviolet), 470 nm (blue), 525 nm (green), 630 nm (red), and broad-spectrum (white) LED lights. Second, we found that cowbirds significantly avoided LED lights with peaks at 470 and 630 nm, but did not avoid or prefer LED lights with peaks at 380 and 525 nm or white lights. Discussion The two lights avoided had the highest chromatic contrast but relatively lower levels of achromatic contrast. Our approach can optimize limited resources to narrow down wavelengths of light with high visual saliency for a target species leading to avoidance. These lights can be used as candidates for visual deterrents to reduce collisions with man-made objects and vehicles.
format: application/pdf
format: text/html
creator: Benjamin Goller
creator: Bradley F. Blackwell
creator: Travis L. DeVault
creator: Patrice E. Baumhardt
creator: Esteban Fernández-Juricic
subject: Animal Behavior
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.5404
publisher: PeerJ Inc.
rights: © 2018 Goller et al.
abstract: Background Avian collisions with man-made objects and vehicles (e.g., buildings, cars, airplanes, power lines) have increased recently. Lights have been proposed to alert birds and minimize the chances of collisions, but it is challenging to choose lights that are tuned to the avian eye and can also lead to avoidance given the differences between human and avian vision. We propose a choice test to address this problem by first identifying wavelengths of light that would over-stimulate the retina using species-specific perceptual models and by then assessing the avoidance/attraction responses of brown-headed cowbirds to these lights during daytime using a behavioral assay. Methods We used perceptual models to estimate wavelength-specific light emitting diode (LED) lights with high chromatic contrast. The behavioral assay consisted of an arena where the bird moved in a single direction and was forced to make a choice (right/left) using a single-choice design (one side with the light on, the other with the light off) under diurnal light conditions. Results First, we identified lights with high saliency from the cowbird visual perspective: LED lights with peaks at 380 nm (ultraviolet), 470 nm (blue), 525 nm (green), 630 nm (red), and broad-spectrum (white) LED lights. Second, we found that cowbirds significantly avoided LED lights with peaks at 470 and 630 nm, but did not avoid or prefer LED lights with peaks at 380 and 525 nm or white lights. Discussion The two lights avoided had the highest chromatic contrast but relatively lower levels of achromatic contrast. Our approach can optimize limited resources to narrow down wavelengths of light with high visual saliency for a target species leading to avoidance. These lights can be used as candidates for visual deterrents to reduce collisions with man-made objects and vehicles.
bibliographic citation: Goller et al. (2018) Assessing bird avoidance of high-contrast lights using a choice test approach: implications for reducing human-induced avian mortality. PeerJ 6:e5404 https://doi.org/10.7717/peerj.5404
date submitted: 2018-03-05
date accepted: 2018-07-18
issued: 2018-09-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Goller
  given name: Benjamin
author list: Agent
  family name: Blackwell
  given name: Bradley F.
author list: Agent
  family name: DeVault
  given name: Travis L.
author list: Agent
  family name: Baumhardt
  given name: Patrice E.
author list: Agent
  family name: Fernández-Juricic
  given name: Esteban
doi: 10.7717/peerj.5404
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-26
copyright: © 2018 Goller et al.
attribution name: Goller et al.

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