PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Widespread dieback of riparian trees on a dammed ephemeral river and evidence of local mitigation by tributary flows
items: Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses
items: The PARA-suite: PAR-CLIP specific sequence read simulation and processing
items: Human altruistic tendencies vary with both the costliness of selfless acts and socioeconomic status
items: Specialization on pollen or nectar in bumblebee foragers is not associated with ovary size, lipid reserves or sensory tuning
items: Evolution of genes involved in feeding preference and metabolic processes in Calliphoridae (Diptera: Calyptratae)
items: The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance
items: Who’s your mama? Riverine hybridisation of threatened freshwater Trout Cod and Murray Cod
items: Comparative internal anatomy of Staurozoa (Cnidaria), with functional and evolutionary inferences
items: Pacing during an ultramarathon running event in hilly terrain

Widespread dieback of riparian trees on a dammed ephemeral river and evidence of local mitigation by tributary flows
type: item
type: AcademicArticle
description: Ephemeral rivers act as linear oases in drylands providing key resources to people and wildlife. However, not much is known about these rivers’ sensitivities to human activities. We investigated the landscape-level determinants of riparian tree dieback along the Swakop River, a dammed ephemeral river in Namibia, focusing on the native ana tree (Faidherbia albida) and the invasive mesquite (Prosopis spp.). We surveyed over 1,900 individual trees distributed across 24 sites along a 250 km stretch of the river. General linear mixed models were used to test five hypotheses relating to three anthropogenic threats: river flow disruption from damming, human settlement and invasive species. We found widespread dieback in both tree populations: 51% mortality in ana tree, with surviving trees exhibiting 18% canopy death (median); and 26% mortality in mesquite, with surviving trees exhibiting 10% canopy death. Dieback in the ana tree was most severe where trees grew on drier stretches of the river, where tributary flow was absent and where mesquite grew more abundantly. Dieback in the mesquite, a more drought-tolerant taxon, did not show any such patterns. Our findings suggest that dieback in the ana tree is primarily driven by changes in river flow resulting from upstream dam creation and that tributary flows provide a local buffer against this loss of main channel flow. The hypothesis that the invasive mesquite may contribute to ana tree dieback was also supported. Our findings suggest that large dams along the main channels of ephemeral rivers have the ability to cause widespread mortality in downstream riparian trees. To mitigate such impacts, management might focus on the maintenance of natural tributary flows to buffer local tree populations from the disruption to main channel flow.
format: application/pdf
format: text/html
creator: Caitlin M. S. Douglas
creator: Mark Mulligan
creator: Xavier A. Harrison
creator: Joh R. Henschel
creator: Nathalie Pettorelli
creator: Guy Cowlishaw
subject: Biosphere Interactions
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Plant Science
description: doi:10.7717/peerj.2622
publisher: PeerJ Inc.
rights: © 2016 Douglas et al.
abstract: Ephemeral rivers act as linear oases in drylands providing key resources to people and wildlife. However, not much is known about these rivers’ sensitivities to human activities. We investigated the landscape-level determinants of riparian tree dieback along the Swakop River, a dammed ephemeral river in Namibia, focusing on the native ana tree (Faidherbia albida) and the invasive mesquite (Prosopis spp.). We surveyed over 1,900 individual trees distributed across 24 sites along a 250 km stretch of the river. General linear mixed models were used to test five hypotheses relating to three anthropogenic threats: river flow disruption from damming, human settlement and invasive species. We found widespread dieback in both tree populations: 51% mortality in ana tree, with surviving trees exhibiting 18% canopy death (median); and 26% mortality in mesquite, with surviving trees exhibiting 10% canopy death. Dieback in the ana tree was most severe where trees grew on drier stretches of the river, where tributary flow was absent and where mesquite grew more abundantly. Dieback in the mesquite, a more drought-tolerant taxon, did not show any such patterns. Our findings suggest that dieback in the ana tree is primarily driven by changes in river flow resulting from upstream dam creation and that tributary flows provide a local buffer against this loss of main channel flow. The hypothesis that the invasive mesquite may contribute to ana tree dieback was also supported. Our findings suggest that large dams along the main channels of ephemeral rivers have the ability to cause widespread mortality in downstream riparian trees. To mitigate such impacts, management might focus on the maintenance of natural tributary flows to buffer local tree populations from the disruption to main channel flow.
bibliographic citation: Douglas et al. (2016) Widespread dieback of riparian trees on a dammed ephemeral river and evidence of local mitigation by tributary flows. PeerJ 4:e2622 https://doi.org/10.7717/peerj.2622
date submitted: 2016-01-22
date accepted: 2016-09-27
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Douglas
  given name: Caitlin M. S.
author list: Agent
  family name: Mulligan
  given name: Mark
author list: Agent
  family name: Harrison
  given name: Xavier A.
author list: Agent
  family name: Henschel
  given name: Joh R.
author list: Agent
  family name: Pettorelli
  given name: Nathalie
author list: Agent
  family name: Cowlishaw
  given name: Guy
doi: 10.7717/peerj.2622
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: © 2016 Douglas et al.
attribution name: Douglas et al.

Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses
type: item
type: AcademicArticle
description: The proteins containing the TIFY domain belong to a plant-specific family of putative transcription factors and could be divided into four subfamilies: ZML, TIFY, PPD and JAZ. They not only function as key regulators of jasmonate hormonal response, but are also involved in responding to abiotic stress. In this study, we identified 24 TIFY genes (PeTIFYs) in Moso bamboo (Phyllostachys edulis) of Poaceae by analyzing the whole genome sequence. One PeTIFY belongs to TIFY subfamily, 18 and five belong to JAZ and ZML subfamilies, respectively. Two equivocal gene models were re-predicted and a putative retrotransposition event was found in a ZML protein. The distribution and conservation of domain or motif, and gene structure were also analyzed. Phylogenetic analysis with TIFY proteins of Arabidopsis and Oryza sativa indicated that JAZ subfamily could be further divided to four groups. Evolutionary analysis revealed intragenomic duplication and orthologous relationship between P. edulis, O. sativa, and B. distachyon. Calculation of the non-synonymous (Ka) and synonymous (Ks) substitution rates and their ratios indicated that the duplication of PeTIFY may have occurred around 16.7 million years ago (MYA), the divergence time of TIFY family among the P. edulis-O. sativa, P. edulis-B. distachyon, and O. sativa-B. distachyon was approximately 39 MYA, 39 MYA, and 45 MYA, respectively. They appear to have undergone extensive purifying selection during evolution. Transcriptome sequencing revealed that more than 50% of PeTIFY genes could be up-regulated by cold and dehydration stresses, and some PeTIFYs also share homology to know TIFYs involved in abiotic stress tolerance. Our results made insights into TIFY family of Moso bamboo, an economically important non-timber forest resource, and provided candidates for further identification of genes involved in regulating responses to abiotic stress.
format: application/pdf
format: text/html
creator: Zhuo Huang
creator: Si-Han Jin
creator: Han-Du Guo
creator: Xiao-Juan Zhong
creator: Jiao He
creator: Xi Li
creator: Ming-Yan Jiang
creator: Xiao-Fang Yu
creator: Hai Long
creator: Ming-Dong Ma
creator: Qi-Bing Chen
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.2620
publisher: PeerJ Inc.
rights: © 2016 Huang et al.
abstract: The proteins containing the TIFY domain belong to a plant-specific family of putative transcription factors and could be divided into four subfamilies: ZML, TIFY, PPD and JAZ. They not only function as key regulators of jasmonate hormonal response, but are also involved in responding to abiotic stress. In this study, we identified 24 TIFY genes (PeTIFYs) in Moso bamboo (Phyllostachys edulis) of Poaceae by analyzing the whole genome sequence. One PeTIFY belongs to TIFY subfamily, 18 and five belong to JAZ and ZML subfamilies, respectively. Two equivocal gene models were re-predicted and a putative retrotransposition event was found in a ZML protein. The distribution and conservation of domain or motif, and gene structure were also analyzed. Phylogenetic analysis with TIFY proteins of Arabidopsis and Oryza sativa indicated that JAZ subfamily could be further divided to four groups. Evolutionary analysis revealed intragenomic duplication and orthologous relationship between P. edulis, O. sativa, and B. distachyon. Calculation of the non-synonymous (Ka) and synonymous (Ks) substitution rates and their ratios indicated that the duplication of PeTIFY may have occurred around 16.7 million years ago (MYA), the divergence time of TIFY family among the P. edulis-O. sativa, P. edulis-B. distachyon, and O. sativa-B. distachyon was approximately 39 MYA, 39 MYA, and 45 MYA, respectively. They appear to have undergone extensive purifying selection during evolution. Transcriptome sequencing revealed that more than 50% of PeTIFY genes could be up-regulated by cold and dehydration stresses, and some PeTIFYs also share homology to know TIFYs involved in abiotic stress tolerance. Our results made insights into TIFY family of Moso bamboo, an economically important non-timber forest resource, and provided candidates for further identification of genes involved in regulating responses to abiotic stress.
bibliographic citation: Huang et al. (2016) Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses. PeerJ 4:e2620 https://doi.org/10.7717/peerj.2620
date submitted: 2016-06-20
date accepted: 2016-09-27
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Zhuo
author list: Agent
  family name: Jin
  given name: Si-Han
author list: Agent
  family name: Guo
  given name: Han-Du
author list: Agent
  family name: Zhong
  given name: Xiao-Juan
author list: Agent
  family name: He
  given name: Jiao
author list: Agent
  family name: Li
  given name: Xi
author list: Agent
  family name: Jiang
  given name: Ming-Yan
author list: Agent
  family name: Yu
  given name: Xiao-Fang
author list: Agent
  family name: Long
  given name: Hai
author list: Agent
  family name: Ma
  given name: Ming-Dong
author list: Agent
  family name: Chen
  given name: Qi-Bing
doi: 10.7717/peerj.2620
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Huang et al.
attribution name: Huang et al.

The PARA-suite: PAR-CLIP specific sequence read simulation and processing
type: item
type: AcademicArticle
description: Background Next-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein–RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into nascent transcripts leads to high rates of specific nucleotide conversions during reverse transcription. So far, the specific properties of PAR-CLIP-derived sequencing reads have not been assessed in depth. Methods We here compared PAR-CLIP sequencing reads to regular transcriptome sequencing reads (RNA-Seq) to identify distinctive properties that are relevant for reference-based read alignment of PAR-CLIP datasets. We developed a set of freely available tools for PAR-CLIP data analysis, called the PAR-CLIP analyzer suite (PARA-suite). The PARA-suite includes error model inference, PAR-CLIP read simulation based on PAR-CLIP specific properties, a full read alignment pipeline with a modified Burrows–Wheeler Aligner algorithm and CLIP read clustering for binding site detection. Results We show that differences in the error profiles of PAR-CLIP reads relative to regular transcriptome sequencing reads (RNA-Seq) make a distinct processing advantageous. We examine the alignment accuracy of commonly applied read aligners on 10 simulated PAR-CLIP datasets using different parameter settings and identified the most accurate setup among those read aligners. We demonstrate the performance of the PARA-suite in conjunction with different binding site detection algorithms on several real PAR-CLIP and HITS-CLIP datasets. Our processing pipeline allowed the improvement of both alignment and binding site detection accuracy. Availability The PARA-suite toolkit and the PARA-suite aligner are available at https://github.com/akloetgen/PARA-suite and https://github.com/akloetgen/PARA-suite_aligner, re…
format: application/pdf
format: text/html
creator: Andreas Kloetgen
creator: Arndt Borkhardt
creator: Jessica I. Hoell
creator: Alice C. McHardy
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.2619
publisher: PeerJ Inc.
rights: © 2016 Kloetgen et al.
abstract: Background Next-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein–RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into nascent transcripts leads to high rates of specific nucleotide conversions during reverse transcription. So far, the specific properties of PAR-CLIP-derived sequencing reads have not been assessed in depth. Methods We here compared PAR-CLIP sequencing reads to regular transcriptome sequencing reads (RNA-Seq) to identify distinctive properties that are relevant for reference-based read alignment of PAR-CLIP datasets. We developed a set of freely available tools for PAR-CLIP data analysis, called the PAR-CLIP analyzer suite (PARA-suite). The PARA-suite includes error model inference, PAR-CLIP read simulation based on PAR-CLIP specific properties, a full read alignment pipeline with a modified Burrows–Wheeler Aligner algorithm and CLIP read clustering for binding site detection. Results We show that differences in the error profiles of PAR-CLIP reads relative to regular transcriptome sequencing reads (RNA-Seq) make a distinct processing advantageous. We examine the alignment accuracy of commonly applied read aligners on 10 simulated PAR-CLIP datasets using different parameter settings and identified the most accurate setup among those read aligners. We demonstrate the performance of the PARA-suite in conjunction with different binding site detection algorithms on several real PAR-CLIP and HITS-CLIP datasets. Our processing pipeline allowed the improvement of both alignment and binding site detection accuracy. Availability The PARA-suite toolkit and the PARA-suite aligner are available at https://github.com/akloetgen/PARA-suite and https://github.com/akloetgen/PARA-suite_aligner, re…
bibliographic citation: Kloetgen et al. (2016) The PARA-suite: PAR-CLIP specific sequence read simulation and processing. PeerJ 4:e2619 https://doi.org/10.7717/peerj.2619
date submitted: 2016-05-25
date accepted: 2016-09-27
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kloetgen
  given name: Andreas
author list: Agent
  family name: Borkhardt
  given name: Arndt
author list: Agent
  family name: Hoell
  given name: Jessica I.
author list: Agent
  family name: McHardy
  given name: Alice C.
doi: 10.7717/peerj.2619
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Kloetgen et al.
attribution name: Kloetgen et al.

Human altruistic tendencies vary with both the costliness of selfless acts and socioeconomic status
type: item
type: AcademicArticle
description: Altruism toward strangers is considered a defining feature of humans. However, manifestation of this behaviour is contingent on the costliness of the selfless act. The extent of altruistic tendencies also varies cross-culturally, being more common in societies with higher levels of market integration. However, the existence of local variation in selfless behaviour within populations has received relatively little empirical attention. Using a ‘lost letter’ design, we dropped 300 letters (half of them stamped, half of them unstamped) in 15 residential suburbs of the greater Perth area that differ markedly in socioeconomic status. The number of returned letters was used as evidence of altruistic behaviour. Costliness was assessed by comparing return rates for stamped vs. unstamped letters. We predicted that there is a positive association between suburb socioeconomic status and number of letters returned and that altruistic acts decrease in frequency when costs increase, even minimally. Both predictions were solidly supported and demonstrate that socioeconomic deprivation and elevated performance costs independently impinge on the universality of altruistic behaviour in humans.
format: application/pdf
format: text/html
creator: Cyril C. Grueter
creator: Jesse A. Ingram
creator: James W. Lewisson
creator: Olivia R. Bradford
creator: Melody Taba
creator: Rebecca E. Coetzee
creator: Michelle A. Sherwood
subject: Animal Behavior
subject: Anthropology
description: doi:10.7717/peerj.2610
publisher: PeerJ Inc.
rights: © 2016 Grueter et al.
abstract: Altruism toward strangers is considered a defining feature of humans. However, manifestation of this behaviour is contingent on the costliness of the selfless act. The extent of altruistic tendencies also varies cross-culturally, being more common in societies with higher levels of market integration. However, the existence of local variation in selfless behaviour within populations has received relatively little empirical attention. Using a ‘lost letter’ design, we dropped 300 letters (half of them stamped, half of them unstamped) in 15 residential suburbs of the greater Perth area that differ markedly in socioeconomic status. The number of returned letters was used as evidence of altruistic behaviour. Costliness was assessed by comparing return rates for stamped vs. unstamped letters. We predicted that there is a positive association between suburb socioeconomic status and number of letters returned and that altruistic acts decrease in frequency when costs increase, even minimally. Both predictions were solidly supported and demonstrate that socioeconomic deprivation and elevated performance costs independently impinge on the universality of altruistic behaviour in humans.
bibliographic citation: Grueter et al. (2016) Human altruistic tendencies vary with both the costliness of selfless acts and socioeconomic status. PeerJ 4:e2610 https://doi.org/10.7717/peerj.2610
date submitted: 2016-08-02
date accepted: 2016-09-26
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grueter
  given name: Cyril C.
author list: Agent
  family name: Ingram
  given name: Jesse A.
author list: Agent
  family name: Lewisson
  given name: James W.
author list: Agent
  family name: Bradford
  given name: Olivia R.
author list: Agent
  family name: Taba
  given name: Melody
author list: Agent
  family name: Coetzee
  given name: Rebecca E.
author list: Agent
  family name: Sherwood
  given name: Michelle A.
doi: 10.7717/peerj.2610
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Grueter et al.
attribution name: Grueter et al.

Specialization on pollen or nectar in bumblebee foragers is not associated with ovary size, lipid reserves or sensory tuning
type: item
type: AcademicArticle
description: Foraging specialization allows social insects to more efficiently exploit resources in their environment. Recent research on honeybees suggests that specialization on pollen or nectar among foragers is linked to reproductive physiology and sensory tuning (the Reproductive Ground-Plan Hypothesis; RGPH). However, our understanding of the underlying physiological relationships in non-Apis bees is still limited. Here we show that the bumblebee Bombus terrestris has specialist pollen and nectar foragers, and test whether foraging specialization in B. terrestris is linked to reproductive physiology, measured as ovarian activation. We show that neither ovary size, sensory sensitivity, measured through proboscis extension response (PER), or whole-body lipid stores differed between pollen foragers, nectar foragers, or generalist foragers. Body size also did not differ between any of these three forager groups. Non-foragers had significantly larger ovaries than foragers. This suggests that potentially reproductive individuals avoid foraging.
format: application/pdf
format: text/html
creator: Adam R. Smith
creator: Peter Graystock
creator: William O.H. Hughes
subject: Animal Behavior
subject: Entomology
description: doi:10.7717/peerj.2599
publisher: PeerJ Inc.
rights: © 2016 Smith et al.
abstract: Foraging specialization allows social insects to more efficiently exploit resources in their environment. Recent research on honeybees suggests that specialization on pollen or nectar among foragers is linked to reproductive physiology and sensory tuning (the Reproductive Ground-Plan Hypothesis; RGPH). However, our understanding of the underlying physiological relationships in non-Apis bees is still limited. Here we show that the bumblebee Bombus terrestris has specialist pollen and nectar foragers, and test whether foraging specialization in B. terrestris is linked to reproductive physiology, measured as ovarian activation. We show that neither ovary size, sensory sensitivity, measured through proboscis extension response (PER), or whole-body lipid stores differed between pollen foragers, nectar foragers, or generalist foragers. Body size also did not differ between any of these three forager groups. Non-foragers had significantly larger ovaries than foragers. This suggests that potentially reproductive individuals avoid foraging.
bibliographic citation: Smith et al. (2016) Specialization on pollen or nectar in bumblebee foragers is not associated with ovary size, lipid reserves or sensory tuning. PeerJ 4:e2599 https://doi.org/10.7717/peerj.2599
date submitted: 2016-07-14
date accepted: 2016-09-23
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smith
  given name: Adam R.
author list: Agent
  family name: Graystock
  given name: Peter
author list: Agent
  family name: Hughes
  given name: William O.H.
doi: 10.7717/peerj.2599
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Smith et al.
attribution name: Smith et al.

Evolution of genes involved in feeding preference and metabolic processes in Calliphoridae (Diptera: Calyptratae)
type: item
type: AcademicArticle
description: Background The genotype-phenotype interactions among traits governing feeding preference are of fundamental importance to behavioral genetics and evolutionary biology. The genetic basis of behavioral traits has been explored in different taxa using different approaches. However, the complex nature of the genetic mechanisms undergirding behavior is poorly understood. Here, we present an evolutionary study of candidate genes related to parasitism in Calliphoridae (Diptera: Calyptratae). Closely related species in this family exhibit distinct larval feeding habits, most notably necro-saprophagy and obligate parasitism. Methods To understand the genetic and molecular bases underlying these habits, expression levels of eight candidate genes for feeding behavior—Cyp6g2, foraging, glutamate dehydrogenase, Jonah65aiv, Malvolio, PGRP-SC2, RPS6-p70-protein kinase, and smooth—were measured in four species using qPCR. Moreover we used expression values and sequence information to reconstruct the relationship among species and the dN/dS rate to infer possible sites under selection. Results For most candidate genes, no statistically significant differences were observed, indicating a high degree of conservation in expression. However, Malvolio was differentially expressed between habits. Evolutionary analyses based on transcript levels and nucleotide sequences of Malvolio coding region suggest that transcript levels were correlated to feeding habit preferences among species, although deviations under a strictly neutral model were also observed in statistical tests. Discussion Malvolio was the only gene demonstrating a possible connection to feeding habit. Differences in gene expression may be involved in (or be a result of) the genetic regulation of Calliphoridae feeding habit. Our results are the first steps towards understanding the genetic basis and evolution of feeding behavior in Calliphoridae using a functional approach.
format: application/pdf
format: text/html
creator: Gisele Antoniazzi Cardoso
creator: Marco Antonio Tonus Marinho
creator: Raquel Dietsche Monfardini
creator: Ana Maria Lima de Azeredo Espin
creator: Tatiana Teixeira Torres
subject: Entomology
subject: Molecular Biology
subject: Parasitology
description: doi:10.7717/peerj.2598
publisher: PeerJ Inc.
rights: © 2016 Cardoso et al.
abstract: Background The genotype-phenotype interactions among traits governing feeding preference are of fundamental importance to behavioral genetics and evolutionary biology. The genetic basis of behavioral traits has been explored in different taxa using different approaches. However, the complex nature of the genetic mechanisms undergirding behavior is poorly understood. Here, we present an evolutionary study of candidate genes related to parasitism in Calliphoridae (Diptera: Calyptratae). Closely related species in this family exhibit distinct larval feeding habits, most notably necro-saprophagy and obligate parasitism. Methods To understand the genetic and molecular bases underlying these habits, expression levels of eight candidate genes for feeding behavior—Cyp6g2, foraging, glutamate dehydrogenase, Jonah65aiv, Malvolio, PGRP-SC2, RPS6-p70-protein kinase, and smooth—were measured in four species using qPCR. Moreover we used expression values and sequence information to reconstruct the relationship among species and the dN/dS rate to infer possible sites under selection. Results For most candidate genes, no statistically significant differences were observed, indicating a high degree of conservation in expression. However, Malvolio was differentially expressed between habits. Evolutionary analyses based on transcript levels and nucleotide sequences of Malvolio coding region suggest that transcript levels were correlated to feeding habit preferences among species, although deviations under a strictly neutral model were also observed in statistical tests. Discussion Malvolio was the only gene demonstrating a possible connection to feeding habit. Differences in gene expression may be involved in (or be a result of) the genetic regulation of Calliphoridae feeding habit. Our results are the first steps towards understanding the genetic basis and evolution of feeding behavior in Calliphoridae using a functional approach.
bibliographic citation: Cardoso et al. (2016) Evolution of genes involved in feeding preference and metabolic processes in Calliphoridae (Diptera: Calyptratae). PeerJ 4:e2598 https://doi.org/10.7717/peerj.2598
date submitted: 2016-06-20
date accepted: 2016-09-23
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cardoso
  given name: Gisele Antoniazzi
author list: Agent
  family name: Marinho
  given name: Marco Antonio Tonus
author list: Agent
  family name: Monfardini
  given name: Raquel Dietsche
author list: Agent
  family name: Espin
  given name: Ana Maria Lima de Azeredo
author list: Agent
  family name: Torres
  given name: Tatiana Teixeira
doi: 10.7717/peerj.2598
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Cardoso et al.
attribution name: Cardoso et al.

The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance
type: item
type: AcademicArticle
description: Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible existence of alternative forms of pAsa4, a large plasmid found in A. salmonicida subsp. salmonicida and bearing multiple antibiotic resistance genes. The present study reveals the existence of two newly detected pAsa4 variants, pAsa4b and pAsa4c. We present the extensive characterization of the genomic architecture, the mobile genetic elements and the antimicrobial resistance genes of these plasmids in addition to the reference pAsa4 from the strain A449. The analysis showed differences between the three architectures with consequences on the content of resistance genes. The genomic plasticity of the three pAsa4 variants could be partially explained by the action of mobile genetic elements like insertion sequences. Eight additional isolates from Canada and Europe that bore similar antibiotic resistance patterns as pAsa4-bearing strains were genotyped and specific pAsa4 variants could be attributed to phenotypic profiles. pAsa4 and pAsa4c were found in Europe, while pAsa4b was found in Canada. In accordance with their content in conjugative transfer genes, only pAsa4b and pAsa4c can be transferred by conjugation in Escherichia coli. The plasticity of pAsa4 variants related to the acquisition of antibiotic resistance indicates that these plasmids may pose a threat in terms of the dissemination of antimicrobial-resistant A. salmonicida subsp. salmonicida bacteria.
format: application/pdf
format: text/html
creator: Katherine H. Tanaka
creator: Antony T. Vincent
creator: Mélanie V. Trudel
creator: Valérie E. Paquet
creator: Michel Frenette
creator: Steve J. Charette
subject: Aquaculture, Fisheries and Fish Science
subject: Genomics
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.2595
publisher: PeerJ Inc.
rights: © 2016 Tanaka et al.
abstract: Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible existence of alternative forms of pAsa4, a large plasmid found in A. salmonicida subsp. salmonicida and bearing multiple antibiotic resistance genes. The present study reveals the existence of two newly detected pAsa4 variants, pAsa4b and pAsa4c. We present the extensive characterization of the genomic architecture, the mobile genetic elements and the antimicrobial resistance genes of these plasmids in addition to the reference pAsa4 from the strain A449. The analysis showed differences between the three architectures with consequences on the content of resistance genes. The genomic plasticity of the three pAsa4 variants could be partially explained by the action of mobile genetic elements like insertion sequences. Eight additional isolates from Canada and Europe that bore similar antibiotic resistance patterns as pAsa4-bearing strains were genotyped and specific pAsa4 variants could be attributed to phenotypic profiles. pAsa4 and pAsa4c were found in Europe, while pAsa4b was found in Canada. In accordance with their content in conjugative transfer genes, only pAsa4b and pAsa4c can be transferred by conjugation in Escherichia coli. The plasticity of pAsa4 variants related to the acquisition of antibiotic resistance indicates that these plasmids may pose a threat in terms of the dissemination of antimicrobial-resistant A. salmonicida subsp. salmonicida bacteria.
bibliographic citation: Tanaka et al. (2016) The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance. PeerJ 4:e2595 https://doi.org/10.7717/peerj.2595
date submitted: 2016-05-21
date accepted: 2016-09-21
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tanaka
  given name: Katherine H.
author list: Agent
  family name: Vincent
  given name: Antony T.
author list: Agent
  family name: Trudel
  given name: Mélanie V.
author list: Agent
  family name: Paquet
  given name: Valérie E.
author list: Agent
  family name: Frenette
  given name: Michel
author list: Agent
  family name: Charette
  given name: Steve J.
doi: 10.7717/peerj.2595
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: © 2016 Tanaka et al.
attribution name: Tanaka et al.

Who’s your mama? Riverine hybridisation of threatened freshwater Trout Cod and Murray Cod
type: item
type: AcademicArticle
description: Rates of hybridization and introgression are increasing dramatically worldwide because of translocations, restocking of organisms and habitat modifications; thus, determining whether hybridization is occuring after reintroducing extirpated congeneric species is commensurately important for conservation. Restocking programs are sometimes criticized because of the genetic consequences of hatchery-bred fish breeding with wild populations. These concerns are important to conservation restocking programs, including those from the Australian freshwater fish family, Percichthyidae. Two of the better known Australian Percichthyidae are the Murray Cod, Maccullochella peelii and Trout Cod, Maccullochella macquariensis which were formerly widespread over the Murray Darling Basin. In much of the Murrumbidgee River, Trout Cod and Murray Cod were sympatric until the late 1970s when Trout Cod were extirpated. Here we use genetic single nucleotide polymorphism (SNP) data together with mitochondrial sequences to examine hybridization and introgression between Murray Cod and Trout Cod in the upper Murrumbidgee River and consider implications for restocking programs. We have confirmed restocked riverine Trout Cod reproducing, but only as inter-specific matings, in the wild. We detected hybrid Trout Cod–Murray Cod in the Upper Murrumbidgee, recording the first hybrid larvae in the wild. Although hybrid larvae, juveniles and adults have been recorded in hatcheries and impoundments, and hybrid adults have been recorded in rivers previously, this is the first time fertile F1 have been recorded in a wild riverine population. The F1 backcrosses with Murray cod have also been found to be fertile. All backcrosses noted were with pure Murray Cod. Such introgression has not been recorded previously in these two species, and the imbalance in hybridization direction may have important implications for restocking programs.
format: application/pdf
format: text/html
creator: Alan J. Couch
creator: Peter J. Unmack
creator: Fiona J. Dyer
creator: Mark Lintermans
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.2593
publisher: PeerJ Inc.
rights: © 2016 Couch et al.
abstract: Rates of hybridization and introgression are increasing dramatically worldwide because of translocations, restocking of organisms and habitat modifications; thus, determining whether hybridization is occuring after reintroducing extirpated congeneric species is commensurately important for conservation. Restocking programs are sometimes criticized because of the genetic consequences of hatchery-bred fish breeding with wild populations. These concerns are important to conservation restocking programs, including those from the Australian freshwater fish family, Percichthyidae. Two of the better known Australian Percichthyidae are the Murray Cod, Maccullochella peelii and Trout Cod, Maccullochella macquariensis which were formerly widespread over the Murray Darling Basin. In much of the Murrumbidgee River, Trout Cod and Murray Cod were sympatric until the late 1970s when Trout Cod were extirpated. Here we use genetic single nucleotide polymorphism (SNP) data together with mitochondrial sequences to examine hybridization and introgression between Murray Cod and Trout Cod in the upper Murrumbidgee River and consider implications for restocking programs. We have confirmed restocked riverine Trout Cod reproducing, but only as inter-specific matings, in the wild. We detected hybrid Trout Cod–Murray Cod in the Upper Murrumbidgee, recording the first hybrid larvae in the wild. Although hybrid larvae, juveniles and adults have been recorded in hatcheries and impoundments, and hybrid adults have been recorded in rivers previously, this is the first time fertile F1 have been recorded in a wild riverine population. The F1 backcrosses with Murray cod have also been found to be fertile. All backcrosses noted were with pure Murray Cod. Such introgression has not been recorded previously in these two species, and the imbalance in hybridization direction may have important implications for restocking programs.
bibliographic citation: Couch et al. (2016) Who’s your mama? Riverine hybridisation of threatened freshwater Trout Cod and Murray Cod. PeerJ 4:e2593 https://doi.org/10.7717/peerj.2593
date submitted: 2016-06-14
date accepted: 2016-09-20
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Couch
  given name: Alan J.
author list: Agent
  family name: Unmack
  given name: Peter J.
author list: Agent
  family name: Dyer
  given name: Fiona J.
author list: Agent
  family name: Lintermans
  given name: Mark
doi: 10.7717/peerj.2593
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Couch et al.
attribution name: Couch et al.

Comparative internal anatomy of Staurozoa (Cnidaria), with functional and evolutionary inferences
type: item
type: AcademicArticle
description: Comparative efforts to understand the body plan evolution of stalked jellyfishes are scarce. Most characters, and particularly internal anatomy, have neither been explored for the class Staurozoa, nor broadly applied in its taxonomy and classification. Recently, a molecular phylogenetic hypothesis was derived for Staurozoa, allowing for the first broad histological comparative study of staurozoan taxa. This study uses comparative histology to describe the body plans of nine staurozoan species, inferring functional and evolutionary aspects of internal morphology based on the current phylogeny of Staurozoa. We document rarely-studied structures, such as ostia between radial pockets, intertentacular lobules, gametoducts, pad-like adhesive structures, and white spots of nematocysts (the last four newly proposed putative synapomorphies for Staurozoa). Two different regions of nematogenesis are documented. This work falsifies the view that the peduncle region of stauromedusae only retains polypoid characters; metamorphosis from stauropolyp to stauromedusa occurs both at the apical region (calyx) and basal region (peduncle). Intertentacular lobules, observed previously in only a small number of species, are shown to be widespread. Similarly, gametoducts were documented in all analyzed genera, both in males and females, thereby elucidating gamete release. Finally, ostia connecting adjacent gastric radial pockets appear to be universal for Staurozoa. Detailed histological studies of medusozoan polyps and medusae are necessary to further understand the relationships between staurozoan features and those of other medusozoan cnidarians.
format: application/pdf
format: text/html
creator: Lucília S. Miranda
creator: Allen G. Collins
creator: Yayoi M. Hirano
creator: Claudia E. Mills
creator: Antonio C. Marques
subject: Biodiversity
subject: Evolutionary Studies
subject: Marine Biology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.2594
publisher: PeerJ Inc.
rights: © 2016 Miranda et al.
abstract: Comparative efforts to understand the body plan evolution of stalked jellyfishes are scarce. Most characters, and particularly internal anatomy, have neither been explored for the class Staurozoa, nor broadly applied in its taxonomy and classification. Recently, a molecular phylogenetic hypothesis was derived for Staurozoa, allowing for the first broad histological comparative study of staurozoan taxa. This study uses comparative histology to describe the body plans of nine staurozoan species, inferring functional and evolutionary aspects of internal morphology based on the current phylogeny of Staurozoa. We document rarely-studied structures, such as ostia between radial pockets, intertentacular lobules, gametoducts, pad-like adhesive structures, and white spots of nematocysts (the last four newly proposed putative synapomorphies for Staurozoa). Two different regions of nematogenesis are documented. This work falsifies the view that the peduncle region of stauromedusae only retains polypoid characters; metamorphosis from stauropolyp to stauromedusa occurs both at the apical region (calyx) and basal region (peduncle). Intertentacular lobules, observed previously in only a small number of species, are shown to be widespread. Similarly, gametoducts were documented in all analyzed genera, both in males and females, thereby elucidating gamete release. Finally, ostia connecting adjacent gastric radial pockets appear to be universal for Staurozoa. Detailed histological studies of medusozoan polyps and medusae are necessary to further understand the relationships between staurozoan features and those of other medusozoan cnidarians.
bibliographic citation: Miranda et al. (2016) Comparative internal anatomy of Staurozoa (Cnidaria), with functional and evolutionary inferences. PeerJ 4:e2594 https://doi.org/10.7717/peerj.2594
date submitted: 2016-06-18
date accepted: 2016-09-20
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miranda
  given name: Lucília S.
author list: Agent
  family name: Collins
  given name: Allen G.
author list: Agent
  family name: Hirano
  given name: Yayoi M.
author list: Agent
  family name: Mills
  given name: Claudia E.
author list: Agent
  family name: Marques
  given name: Antonio C.
doi: 10.7717/peerj.2594
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: © 2016 Miranda et al.
attribution name: Miranda et al.

Pacing during an ultramarathon running event in hilly terrain
type: item
type: AcademicArticle
description: Purpose The dynamics of speed selection as a function of distance, or pacing, are used in recreational, competitive, and scientific research situations as an indirect measure of the psycho-physiological status of an individual. The purpose of this study was to determine pacing on level, uphill and downhill sections of participants in a long (>80 km) ultramarathon performed on trails in hilly terrain. Methods Fifteen ultramarathon runners competed in a 173 km event (five finished at 103 km) carrying a Global-Positioning System (GPS) device. Using the GPS data, we determined the speed, relative to average total speed, in level (LEV), uphill (UH) and downhill (DH) gradient categories as a function of total distance, as well as the correlation between overall performance and speed variability, speed loss, and total time stopped. Results There were no significant differences in normality, variances or means in the relative speed in 173-km and 103-km participants. Relative speed decreased in LEV, UH and DH. The main component of speed loss occurred between 5% and 50% of the event distance in LEV, and between 5% and 95% in UH and DH. There were no significant correlations between overall performance and speed loss, the variability of speed, or total time stopped. Conclusions Positive pacing was observed at all gradients, with the main component of speed loss occurring earlier (mixed pacing) in LEV compared to UH and DH. A speed reserve (increased speed in the last section) was observed in LEV and UH. The decrease in speed and variability of speed were more important in LEV and DH than in UH. The absence of a significant correlation between overall performance and descriptors of pacing is novel and indicates that pacing in ultramarathons in trails and hilly terrain differs to other types of running events.
format: application/pdf
format: text/html
creator: Hugo A. Kerhervé
creator: Tom Cole-Hunter
creator: Aaron N. Wiegand
creator: Colin Solomon
subject: Kinesiology
description: doi:10.7717/peerj.2591
publisher: PeerJ Inc.
rights: © 2016 Kerhervé et al.
abstract: Purpose The dynamics of speed selection as a function of distance, or pacing, are used in recreational, competitive, and scientific research situations as an indirect measure of the psycho-physiological status of an individual. The purpose of this study was to determine pacing on level, uphill and downhill sections of participants in a long (>80 km) ultramarathon performed on trails in hilly terrain. Methods Fifteen ultramarathon runners competed in a 173 km event (five finished at 103 km) carrying a Global-Positioning System (GPS) device. Using the GPS data, we determined the speed, relative to average total speed, in level (LEV), uphill (UH) and downhill (DH) gradient categories as a function of total distance, as well as the correlation between overall performance and speed variability, speed loss, and total time stopped. Results There were no significant differences in normality, variances or means in the relative speed in 173-km and 103-km participants. Relative speed decreased in LEV, UH and DH. The main component of speed loss occurred between 5% and 50% of the event distance in LEV, and between 5% and 95% in UH and DH. There were no significant correlations between overall performance and speed loss, the variability of speed, or total time stopped. Conclusions Positive pacing was observed at all gradients, with the main component of speed loss occurring earlier (mixed pacing) in LEV compared to UH and DH. A speed reserve (increased speed in the last section) was observed in LEV and UH. The decrease in speed and variability of speed were more important in LEV and DH than in UH. The absence of a significant correlation between overall performance and descriptors of pacing is novel and indicates that pacing in ultramarathons in trails and hilly terrain differs to other types of running events.
bibliographic citation: Kerhervé et al. (2016) Pacing during an ultramarathon running event in hilly terrain. PeerJ 4:e2591 https://doi.org/10.7717/peerj.2591
date submitted: 2016-05-13
date accepted: 2016-09-21
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kerhervé
  given name: Hugo A.
author list: Agent
  family name: Cole-Hunter
  given name: Tom
author list: Agent
  family name: Wiegand
  given name: Aaron N.
author list: Agent
  family name: Solomon
  given name: Colin
doi: 10.7717/peerj.2591
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Kerhervé et al.
attribution name: Kerhervé et al.

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