PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A novel biomechanical analysis of gait changes in the MPTP mouse model of Parkinson’s disease
items: Feeding behaviour in a ‘basal’ tortoise provides insights on the transitional feeding mode at the dawn of modern land turtle evolution
items: Development and characterization of microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla
items: Selection in the dopamine receptor 2 gene: a candidate SNP study
items: Field-measured drag area is a key correlate of level cycling time trial performance
items: Prey type and foraging ecology of Sanderlings Calidris alba in different climate zones: are tropical areas more favourable than temperate sites?
items: Choosing mates based on the diet of your ancestors: replication of non-genetic assortative mating in Drosophila melanogaster
items: Cryptic species obscure introduction pathway of the blue Caribbean sponge (Haliclona (Soestella) caerulea), (order: Haplosclerida) to Palmyra Atoll, Central Pacific
items: Sight or smell? Behavioural and heart rate responses in subordinate rainbow trout exposed to cues from dominant fish
items: Non-repeatable science: assessing the frequency of voucher specimen deposition reveals that most arthropod research cannot be verified

A novel biomechanical analysis of gait changes in the MPTP mouse model of Parkinson’s disease
type: item
type: AcademicArticle
description: Parkinson’s disease (PD) is an age-associated neurodegenerative disorder hallmarked by a loss of mesencephalic dopaminergic neurons. Accurate recapitulation of the PD movement phenotype in animal models of the disease is critical for understanding disease etiology and developing novel therapeutic treatments. However, most existing behavioral assays currently applied to such animal models fail to adequately detect and subsequently quantify the subtle changes associated with the progressive stages of PD. In this study, we used a video-based analysis system to develop and validate a novel protocol for tracking locomotor performance in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of PD. We anticipated that (1) treated mice should use slower, shorter, and less frequent strides and (2) that gait deficits should monotonically increase following MPTP administration, as the effects of neurodegeneration become manifest. Video-based biomechanical analyses, utilizing behavioral measures motivated by the comparative biomechanics literature, were used to quantify gait dynamics over a seven-day period following MPTP treatment. Analyses revealed shuffling behaviors consistent with the gait symptoms of advanced PD in humans. Here we also document dramatic gender-based differences in locomotor performance during the progression of the MPTP-induced lesion, despite male and female mice showing similar losses of striatal dopaminergic cells following MPTP administration. Whereas female mice appeared to be protected against gait deficits, males showed multiple changes in gait kinematics, consistent with the loss of locomotor agility and stability. Overall, these data show that the novel video analysis protocol presented here is a robust method capable of detecting subtle changes in gait biomechanics in a mouse model of PD. Our findings indicate that this method is a useful means by which to easily and economically screen preclinical therapeutic compounds for protect…
format: application/pdf
format: text/html
creator: Werner J. Geldenhuys
creator: Tamara L. Guseman
creator: Ilse S. Pienaar
creator: Dean E. Dluzen
creator: Jesse W. Young
subject: Neuroscience
subject: Neurology
description: doi:10.7717/peerj.1175
publisher: PeerJ Inc.
rights: © 2015 Geldenhuys et al.
abstract: Parkinson’s disease (PD) is an age-associated neurodegenerative disorder hallmarked by a loss of mesencephalic dopaminergic neurons. Accurate recapitulation of the PD movement phenotype in animal models of the disease is critical for understanding disease etiology and developing novel therapeutic treatments. However, most existing behavioral assays currently applied to such animal models fail to adequately detect and subsequently quantify the subtle changes associated with the progressive stages of PD. In this study, we used a video-based analysis system to develop and validate a novel protocol for tracking locomotor performance in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of PD. We anticipated that (1) treated mice should use slower, shorter, and less frequent strides and (2) that gait deficits should monotonically increase following MPTP administration, as the effects of neurodegeneration become manifest. Video-based biomechanical analyses, utilizing behavioral measures motivated by the comparative biomechanics literature, were used to quantify gait dynamics over a seven-day period following MPTP treatment. Analyses revealed shuffling behaviors consistent with the gait symptoms of advanced PD in humans. Here we also document dramatic gender-based differences in locomotor performance during the progression of the MPTP-induced lesion, despite male and female mice showing similar losses of striatal dopaminergic cells following MPTP administration. Whereas female mice appeared to be protected against gait deficits, males showed multiple changes in gait kinematics, consistent with the loss of locomotor agility and stability. Overall, these data show that the novel video analysis protocol presented here is a robust method capable of detecting subtle changes in gait biomechanics in a mouse model of PD. Our findings indicate that this method is a useful means by which to easily and economically screen preclinical therapeutic compounds for protect…
bibliographic citation: Geldenhuys et al. (2015) A novel biomechanical analysis of gait changes in the MPTP mouse model of Parkinson’s disease. PeerJ 3:e1175 https://doi.org/10.7717/peerj.1175
date submitted: 2015-03-11
date accepted: 2015-07-21
issued: 2015-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Geldenhuys
  given name: Werner J.
author list: Agent
  family name: Guseman
  given name: Tamara L.
author list: Agent
  family name: Pienaar
  given name: Ilse S.
author list: Agent
  family name: Dluzen
  given name: Dean E.
author list: Agent
  family name: Young
  given name: Jesse W.
doi: 10.7717/peerj.1175
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-11
copyright: © 2015 Geldenhuys et al.
attribution name: Geldenhuys et al.

Feeding behaviour in a ‘basal’ tortoise provides insights on the transitional feeding mode at the dawn of modern land turtle evolution
type: item
type: AcademicArticle
description: Almost all extant testudinids are highly associated with terrestrial habitats and the few tortoises with high affinity to aquatic environments are found within the genus Manouria. Manouria belongs to a clade which forms a sister taxon to all remaining tortoises and is suitable as a model for studying evolutionary transitions within modern turtles. We analysed the feeding behaviour of Manouria emys and due to its phylogenetic position, we hypothesise that the species might have retained some ancestral features associated with an aquatic lifestyle. We tested whether M. emys is able to feed both in aquatic and terrestrial environments. In fact, M. emys repetitively tried to reach submerged food items in water, but always failed to grasp them—no suction feeding mechanism was applied. When feeding on land, M. emys showed another peculiar behaviour; it grasped food items by its jaws—a behaviour typical for aquatic or semiaquatic turtles—and not by the tongue as generally accepted as the typical feeding mode in all tortoises studied so far. In M. emys, the hyolingual complex remained retracted during all food uptake sequences, but the food transport was entirely lingual based. The kinematical profiles significantly differed from those described for other tortoises and from those proposed from the general models on the function of the feeding systems in lower tetrapods. We conclude that the feeding behaviour of M. emys might reflect a remnant of the primordial condition expected in the aquatic ancestor of the tortoises.
format: application/pdf
format: text/html
creator: Nikolay Natchev
creator: Nikolay Tzankov
creator: Ingmar Werneburg
creator: Egon Heiss
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.1172
publisher: PeerJ Inc.
rights: © 2015 Natchev et al.
abstract: Almost all extant testudinids are highly associated with terrestrial habitats and the few tortoises with high affinity to aquatic environments are found within the genus Manouria. Manouria belongs to a clade which forms a sister taxon to all remaining tortoises and is suitable as a model for studying evolutionary transitions within modern turtles. We analysed the feeding behaviour of Manouria emys and due to its phylogenetic position, we hypothesise that the species might have retained some ancestral features associated with an aquatic lifestyle. We tested whether M. emys is able to feed both in aquatic and terrestrial environments. In fact, M. emys repetitively tried to reach submerged food items in water, but always failed to grasp them—no suction feeding mechanism was applied. When feeding on land, M. emys showed another peculiar behaviour; it grasped food items by its jaws—a behaviour typical for aquatic or semiaquatic turtles—and not by the tongue as generally accepted as the typical feeding mode in all tortoises studied so far. In M. emys, the hyolingual complex remained retracted during all food uptake sequences, but the food transport was entirely lingual based. The kinematical profiles significantly differed from those described for other tortoises and from those proposed from the general models on the function of the feeding systems in lower tetrapods. We conclude that the feeding behaviour of M. emys might reflect a remnant of the primordial condition expected in the aquatic ancestor of the tortoises.
bibliographic citation: Natchev et al. (2015) Feeding behaviour in a ‘basal’ tortoise provides insights on the transitional feeding mode at the dawn of modern land turtle evolution. PeerJ 3:e1172 https://doi.org/10.7717/peerj.1172
date submitted: 2015-03-14
date accepted: 2015-07-20
issued: 2015-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Natchev
  given name: Nikolay
author list: Agent
  family name: Tzankov
  given name: Nikolay
author list: Agent
  family name: Werneburg
  given name: Ingmar
author list: Agent
  family name: Heiss
  given name: Egon
doi: 10.7717/peerj.1172
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-11
copyright: © 2015 Natchev et al.
attribution name: Natchev et al.

Development and characterization of microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla
type: item
type: AcademicArticle
description: Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid–diploid primary producer.
format: application/pdf
format: text/html
creator: Nicole M. Kollars
creator: Stacy A. Krueger-Hadfield
creator: James E. Byers
creator: Thomas W. Greig
creator: Allan E. Strand
creator: Florian Weinberger
creator: Erik E. Sotka
subject: Ecology
subject: Evolutionary Studies
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.1159
publisher: PeerJ Inc.
rights: © 2015 Kollars et al.
abstract: Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid–diploid primary producer.
bibliographic citation: Kollars et al. (2015) Development and characterization of microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla. PeerJ 3:e1159 https://doi.org/10.7717/peerj.1159
date submitted: 2015-05-06
date accepted: 2015-07-16
issued: 2015-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kollars
  given name: Nicole M.
author list: Agent
  family name: Krueger-Hadfield
  given name: Stacy A.
author list: Agent
  family name: Byers
  given name: James E.
author list: Agent
  family name: Greig
  given name: Thomas W.
author list: Agent
  family name: Strand
  given name: Allan E.
author list: Agent
  family name: Weinberger
  given name: Florian
author list: Agent
  family name: Sotka
  given name: Erik E.
doi: 10.7717/peerj.1159
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-11
copyright: © 2015 Kollars et al.
attribution name: Kollars et al.

Selection in the dopamine receptor 2 gene: a candidate SNP study
type: item
type: AcademicArticle
description: Dopamine is a major neurotransmitter in the human brain and is associated with various diseases. Schizophrenia, for example, is treated by blocking the dopamine receptors type 2. Shaner, Miller & Mintz (2004) stated that schizophrenia was the low fitness variant of a highly variable mental trait. We therefore explore whether the dopamine receptor 2 gene (DRD2) underwent any selection processes. We acquired genotype data of the 1,000 Genomes project (phase I), which contains 1,093 individuals from 14 populations. We included single nucleotide polymorphisms (SNPs) with two minor allele frequencies (MAFs) in the analysis: MAF over 0.05 and over 0.01. This is equivalent to 151 SNPs (MAF > 0.05) and 246 SNPs (MAF > 0.01) for DRD2. We used two different approaches (an outlier approach and a Bayesian approach) to detect loci under selection. The combined results of both approaches yielded nine (MAF > 0.05) and two candidate SNPs (MAF > 0.01), under balancing selection. We also found weak signs for directional selection on DRD2, but in our opinion these were too weak to draw any final conclusions on directional selection in DRD2. All candidates for balancing selection are in the intronic region of the gene and only one (rs12574471) has been mentioned in the literature. Two of our candidate SNPs are located in specific regions of the gene: rs80215768 lies within a promoter flanking region and rs74751335 lies within a transcription factor binding site. We strongly encourage research on our candidate SNPs and their possible effects.
format: application/pdf
format: text/html
creator: Tobias Göllner
creator: Martin Fieder
subject: Anthropology
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.1149
publisher: PeerJ Inc.
rights: © 2015 Göllner and Fieder
abstract: Dopamine is a major neurotransmitter in the human brain and is associated with various diseases. Schizophrenia, for example, is treated by blocking the dopamine receptors type 2. Shaner, Miller & Mintz (2004) stated that schizophrenia was the low fitness variant of a highly variable mental trait. We therefore explore whether the dopamine receptor 2 gene (DRD2) underwent any selection processes. We acquired genotype data of the 1,000 Genomes project (phase I), which contains 1,093 individuals from 14 populations. We included single nucleotide polymorphisms (SNPs) with two minor allele frequencies (MAFs) in the analysis: MAF over 0.05 and over 0.01. This is equivalent to 151 SNPs (MAF > 0.05) and 246 SNPs (MAF > 0.01) for DRD2. We used two different approaches (an outlier approach and a Bayesian approach) to detect loci under selection. The combined results of both approaches yielded nine (MAF > 0.05) and two candidate SNPs (MAF > 0.01), under balancing selection. We also found weak signs for directional selection on DRD2, but in our opinion these were too weak to draw any final conclusions on directional selection in DRD2. All candidates for balancing selection are in the intronic region of the gene and only one (rs12574471) has been mentioned in the literature. Two of our candidate SNPs are located in specific regions of the gene: rs80215768 lies within a promoter flanking region and rs74751335 lies within a transcription factor binding site. We strongly encourage research on our candidate SNPs and their possible effects.
bibliographic citation: Göllner et al. (2015) Selection in the dopamine receptor 2 gene: a candidate SNP study. PeerJ 3:e1149 https://doi.org/10.7717/peerj.1149
date submitted: 2015-05-15
date accepted: 2015-07-12
issued: 2015-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Göllner
  given name: Tobias
author list: Agent
  family name: Fieder
  given name: Martin
doi: 10.7717/peerj.1149
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-11
copyright: © 2015 Göllner and Fieder
attribution name: Göllner and Fieder

Field-measured drag area is a key correlate of level cycling time trial performance
type: item
type: AcademicArticle
description: Drag area (Ad) is a primary factor determining aerodynamic resistance during level cycling and is therefore a key determinant of level time trial performance. However, Ad has traditionally been difficult to measure. Our purpose was to determine the value of adding field-measured Ad as a correlate of level cycling time trial performance. In the field, 19 male cyclists performed a level (22.1 km) time trial. Separately, field-determined Ad and rolling resistance were calculated for subjects along with projected frontal area assessed directly (AP) and indirectly (Est AP). Also, a graded exercise test was performed to determine $\dot {V}{O}_{2}$V̇O2 peak, lactate threshold (LT), and economy. $\dot {V}{O}_{2}$V̇O2 peak ($\mathrm{l}~\min ^{-1}$lmin−1) and power at LT were significantly correlated to power measured during the time trial (r = 0.83 and 0.69, respectively) but were not significantly correlated to performance time (r = − 0.42 and −0.45). The correlation with performance time improved significantly (p < 0.05) when these variables were normalized to Ad. Of note, Ad alone was better correlated to performance time (r = 0.85, p < 0.001) than any combination of non-normalized physiological measure. The best correlate with performance time was field-measured power output during the time trial normalized to Ad (r = − 0.92). AP only accounted for 54% of the variability in Ad. Accordingly, the correlation to performance time was significantly lower using power normalized to AP (r = − 0.75) or Est AP (r = − 0.71). In conclusion, unless normalized to Ad, level time trial performance in the field was not highly correlated to common laboratory measures. Furthermore, our field-measured Ad is easy to determine and was the single best predictor of level time trial performance.
format: application/pdf
format: text/html
creator: James E. Peterman
creator: Allen C. Lim
creator: Ryan I. Ignatz
creator: Andrew G. Edwards
creator: William C. Byrnes
subject: Biophysics
subject: Anatomy and Physiology
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.1144
publisher: PeerJ Inc.
rights: © 2015 Peterman et al.
abstract: Drag area (Ad) is a primary factor determining aerodynamic resistance during level cycling and is therefore a key determinant of level time trial performance. However, Ad has traditionally been difficult to measure. Our purpose was to determine the value of adding field-measured Ad as a correlate of level cycling time trial performance. In the field, 19 male cyclists performed a level (22.1 km) time trial. Separately, field-determined Ad and rolling resistance were calculated for subjects along with projected frontal area assessed directly (AP) and indirectly (Est AP). Also, a graded exercise test was performed to determine $\dot {V}{O}_{2}$V̇O2 peak, lactate threshold (LT), and economy. $\dot {V}{O}_{2}$V̇O2 peak ($\mathrm{l}~\min ^{-1}$lmin−1) and power at LT were significantly correlated to power measured during the time trial (r = 0.83 and 0.69, respectively) but were not significantly correlated to performance time (r = − 0.42 and −0.45). The correlation with performance time improved significantly (p < 0.05) when these variables were normalized to Ad. Of note, Ad alone was better correlated to performance time (r = 0.85, p < 0.001) than any combination of non-normalized physiological measure. The best correlate with performance time was field-measured power output during the time trial normalized to Ad (r = − 0.92). AP only accounted for 54% of the variability in Ad. Accordingly, the correlation to performance time was significantly lower using power normalized to AP (r = − 0.75) or Est AP (r = − 0.71). In conclusion, unless normalized to Ad, level time trial performance in the field was not highly correlated to common laboratory measures. Furthermore, our field-measured Ad is easy to determine and was the single best predictor of level time trial performance.
bibliographic citation: Peterman et al. (2015) Field-measured drag area is a key correlate of level cycling time trial performance. PeerJ 3:e1144 https://doi.org/10.7717/peerj.1144
date submitted: 2015-05-11
date accepted: 2015-07-10
issued: 2015-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peterman
  given name: James E.
author list: Agent
  family name: Lim
  given name: Allen C.
author list: Agent
  family name: Ignatz
  given name: Ryan I.
author list: Agent
  family name: Edwards
  given name: Andrew G.
author list: Agent
  family name: Byrnes
  given name: William C.
doi: 10.7717/peerj.1144
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-11
copyright: © 2015 Peterman et al.
attribution name: Peterman et al.

Prey type and foraging ecology of Sanderlings Calidris alba in different climate zones: are tropical areas more favourable than temperate sites?
type: item
type: AcademicArticle
description: Sanderlings (Calidris alba) are long-distance migratory shorebirds with a non-breeding range that spans temperate and tropical coastal habitats. Breeding in the High Arctic combined with non-breeding seasons in the tropics necessitate long migrations, which are energetically demanding. On an annual basis, the higher energy expenditures during migration might pay off if food availability in the tropics is higher than at temperate latitudes. We compared foraging behaviour of birds at a north temperate and a tropical non-breeding site in the Netherlands and Ghana, respectively. In both cases the birds used similar habitats (open beaches), and experienced similar periods of daylight, which enabled us to compare food abundance and availability, and behavioural time budgets and food intake. During the non-breeding season, Sanderlings in the Netherlands spent 79% of their day foraging; in Ghana birds spent only 38% of the daytime period foraging and the largest proportion of their time resting (58%). The main prey item in the Netherlands was the soft-bodied polychaete Scolelepis squamata, while Sanderlings in Ghana fed almost exclusively on the bivalve Donax pulchellus, which they swallowed whole and crushed internally. Average availability of polychaete worms in the Netherlands was 7.4 g ash free dry mass (AFDM) m−2, which was one tenth of the 77.1 g AFDM m−2 estimated for the beach in Ghana. In the tropical environment of Ghana the Sanderlings combined relatively low energy requirements with high prey intake rates (1.64 mg opposed to 0.13 mg AFDM s−1 for Ghana and the Netherlands respectively). Although this may suggest that the Ghana beaches are the most favourable environment, processing the hard-shelled bivalve (D. pulchellus) which is the staple food could be costly. The large amount of daytime spent resting in Ghana may be indicative of the time needed to process the shell fragments, rather than indicate rest.
format: application/pdf
format: text/html
creator: Kirsten Grond
creator: Yaa Ntiamoa-Baidu
creator: Theunis Piersma
creator: Jeroen Reneerkens
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.1125
publisher: PeerJ Inc.
rights: © 2015 Grond et al.
abstract: Sanderlings (Calidris alba) are long-distance migratory shorebirds with a non-breeding range that spans temperate and tropical coastal habitats. Breeding in the High Arctic combined with non-breeding seasons in the tropics necessitate long migrations, which are energetically demanding. On an annual basis, the higher energy expenditures during migration might pay off if food availability in the tropics is higher than at temperate latitudes. We compared foraging behaviour of birds at a north temperate and a tropical non-breeding site in the Netherlands and Ghana, respectively. In both cases the birds used similar habitats (open beaches), and experienced similar periods of daylight, which enabled us to compare food abundance and availability, and behavioural time budgets and food intake. During the non-breeding season, Sanderlings in the Netherlands spent 79% of their day foraging; in Ghana birds spent only 38% of the daytime period foraging and the largest proportion of their time resting (58%). The main prey item in the Netherlands was the soft-bodied polychaete Scolelepis squamata, while Sanderlings in Ghana fed almost exclusively on the bivalve Donax pulchellus, which they swallowed whole and crushed internally. Average availability of polychaete worms in the Netherlands was 7.4 g ash free dry mass (AFDM) m−2, which was one tenth of the 77.1 g AFDM m−2 estimated for the beach in Ghana. In the tropical environment of Ghana the Sanderlings combined relatively low energy requirements with high prey intake rates (1.64 mg opposed to 0.13 mg AFDM s−1 for Ghana and the Netherlands respectively). Although this may suggest that the Ghana beaches are the most favourable environment, processing the hard-shelled bivalve (D. pulchellus) which is the staple food could be costly. The large amount of daytime spent resting in Ghana may be indicative of the time needed to process the shell fragments, rather than indicate rest.
bibliographic citation: Grond et al. (2015) Prey type and foraging ecology of Sanderlings Calidris alba in different climate zones: are tropical areas more favourable than temperate sites?. PeerJ 3:e1125 https://doi.org/10.7717/peerj.1125
date submitted: 2015-05-02
date accepted: 2015-07-04
issued: 2015-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grond
  given name: Kirsten
author list: Agent
  family name: Ntiamoa-Baidu
  given name: Yaa
author list: Agent
  family name: Piersma
  given name: Theunis
author list: Agent
  family name: Reneerkens
  given name: Jeroen
doi: 10.7717/peerj.1125
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-11
copyright: © 2015 Grond et al.
attribution name: Grond et al.

Choosing mates based on the diet of your ancestors: replication of non-genetic assortative mating in Drosophila melanogaster
type: item
type: AcademicArticle
description: Assortative mating has been a focus of considerable research because of its potential to influence biodiversity at many scales. Sharon et al. (2010) discovered that an inbred strain of Drosophila melanogaster mated assortatively based on the diet of previous generations, leading to initial reproductive isolation without genetic evolution. This behavior was reproduced by manipulating the microbiome independently of the diet, pointing to extracellular bacterial symbionts as the assortative mating cue. To further investigate the biological significance of this result, we attempted to reproduce this phenomenon in an independent laboratory using different genotypes and additional mating assays. Supporting the previous result, we found that a different inbred strain also mated assortatively based on the diets of previous generations. However, we were unable to generate assortative mating in an outbred strain from North Carolina. Our results support the potential for non-genetic mechanisms to influence reproductive isolation, but additional work is needed to investigate the importance of this mechanism in natural populations of Drosophila.
format: application/pdf
format: text/html
creator: Michael A. Najarro
creator: Matt Sumethasorn
creator: Alexandra Lamoureux
creator: Thomas L. Turner
subject: Animal Behavior
subject: Biodiversity
subject: Evolutionary Studies
description: doi:10.7717/peerj.1173
publisher: PeerJ Inc.
rights: © 2015 Najarro et al.
abstract: Assortative mating has been a focus of considerable research because of its potential to influence biodiversity at many scales. Sharon et al. (2010) discovered that an inbred strain of Drosophila melanogaster mated assortatively based on the diet of previous generations, leading to initial reproductive isolation without genetic evolution. This behavior was reproduced by manipulating the microbiome independently of the diet, pointing to extracellular bacterial symbionts as the assortative mating cue. To further investigate the biological significance of this result, we attempted to reproduce this phenomenon in an independent laboratory using different genotypes and additional mating assays. Supporting the previous result, we found that a different inbred strain also mated assortatively based on the diets of previous generations. However, we were unable to generate assortative mating in an outbred strain from North Carolina. Our results support the potential for non-genetic mechanisms to influence reproductive isolation, but additional work is needed to investigate the importance of this mechanism in natural populations of Drosophila.
bibliographic citation: Najarro et al. (2015) Choosing mates based on the diet of your ancestors: replication of non-genetic assortative mating in Drosophila melanogaster. PeerJ 3:e1173 https://doi.org/10.7717/peerj.1173
date submitted: 2015-05-26
date accepted: 2015-07-20
issued: 2015-08-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Najarro
  given name: Michael A.
author list: Agent
  family name: Sumethasorn
  given name: Matt
author list: Agent
  family name: Lamoureux
  given name: Alexandra
author list: Agent
  family name: Turner
  given name: Thomas L.
doi: 10.7717/peerj.1173
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-06
copyright: © 2015 Najarro et al.
attribution name: Najarro et al.

Cryptic species obscure introduction pathway of the blue Caribbean sponge (Haliclona (Soestella) caerulea), (order: Haplosclerida) to Palmyra Atoll, Central Pacific
type: item
type: AcademicArticle
description: Cryptic species are widespread across the phylum Porifera making the identification of non-indigenous species difficult, an issue not easily resolved by the use of morphological characteristics. The widespread order Haplosclerida is a prime example due to limited and plastic morphological features. Here, we study the reported introduction of Haliclona (Soestella) caerulea from the Caribbean to Palmyra Atoll via Hawaiʻi using morphological characteristics and genetic analyses based on one nuclear (18s rDNA) and three mitochondrial (COI, the barcoding COI extension (COI ext.) and rnl rDNA) markers. Despite no clear division in lengths of the oxea spicules between the samples, both mtDNA and nDNA phylogenetic trees supported similar topologies resolving two distinct clades. Across the two clades, the concatenated mtDNA tree resolved twelve subclades, with the COI ext. yielding most of the variability between the samples. Low sequence divergence values (0.68%) between two of the subclades indicate that the same species is likely to occur at Palmyra, Hawaiʻi and the Caribbean, supporting the hypothesis that H. caerulea was introduced to Palmyra from the Caribbean, although whether species came directly from the Caribbean to Palmyra or from Hawaiʻi remains unresolved. Conversely, the pattern of highly divergent cryptic species supports the notion that traditionally used spicule measurements are taxonomically unreliable in this group. This study illustrates how understanding the scale of within- as opposed to between-species level genetic variation is critical for interpreting biogeographic patterns and inferring the origins of introduced organisms.
format: application/pdf
format: text/html
creator: Ingrid S. Knapp
creator: Zac H. Forsman
creator: Gareth J. Williams
creator: Robert J. Toonen
creator: James J. Bell
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.1170
publisher: PeerJ Inc.
rights: © 2015 Knapp et al.
abstract: Cryptic species are widespread across the phylum Porifera making the identification of non-indigenous species difficult, an issue not easily resolved by the use of morphological characteristics. The widespread order Haplosclerida is a prime example due to limited and plastic morphological features. Here, we study the reported introduction of Haliclona (Soestella) caerulea from the Caribbean to Palmyra Atoll via Hawaiʻi using morphological characteristics and genetic analyses based on one nuclear (18s rDNA) and three mitochondrial (COI, the barcoding COI extension (COI ext.) and rnl rDNA) markers. Despite no clear division in lengths of the oxea spicules between the samples, both mtDNA and nDNA phylogenetic trees supported similar topologies resolving two distinct clades. Across the two clades, the concatenated mtDNA tree resolved twelve subclades, with the COI ext. yielding most of the variability between the samples. Low sequence divergence values (0.68%) between two of the subclades indicate that the same species is likely to occur at Palmyra, Hawaiʻi and the Caribbean, supporting the hypothesis that H. caerulea was introduced to Palmyra from the Caribbean, although whether species came directly from the Caribbean to Palmyra or from Hawaiʻi remains unresolved. Conversely, the pattern of highly divergent cryptic species supports the notion that traditionally used spicule measurements are taxonomically unreliable in this group. This study illustrates how understanding the scale of within- as opposed to between-species level genetic variation is critical for interpreting biogeographic patterns and inferring the origins of introduced organisms.
bibliographic citation: Knapp et al. (2015) Cryptic species obscure introduction pathway of the blue Caribbean sponge (Haliclona (Soestella) caerulea), (order: Haplosclerida) to Palmyra Atoll, Central Pacific. PeerJ 3:e1170 https://doi.org/10.7717/peerj.1170
date submitted: 2015-03-12
date accepted: 2015-07-20
issued: 2015-08-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Knapp
  given name: Ingrid S.
author list: Agent
  family name: Forsman
  given name: Zac H.
author list: Agent
  family name: Williams
  given name: Gareth J.
author list: Agent
  family name: Toonen
  given name: Robert J.
author list: Agent
  family name: Bell
  given name: James J.
doi: 10.7717/peerj.1170
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-06
copyright: © 2015 Knapp et al.
attribution name: Knapp et al.

Sight or smell? Behavioural and heart rate responses in subordinate rainbow trout exposed to cues from dominant fish
type: item
type: AcademicArticle
description: Many animals, including fish, can utilize both vision and the chemical senses in intra-specific communication. However, the relative influence of these sensory modalities on behavioral and physiological responses in social interactions is not well understood. The aim of this study was therefore to investigate the relative effects of visual and chemical stimuli from dominant individuals on the behavioral and physiological responses of subordinate rainbow trout (Oncorhynchus mykiss). External electrodes were used to detect ECG signals from free-swimming fish. This method allowed the simultaneous recording of behavioral and physiological responses, and possible sex differences in these responses were also investigated. The results suggest that, in this context, visual cues are more important than chemical cues in settling the social hierarchy in rainbow trout because a combination of chemical and visual exposure generally yielded a response in focal fish that was similar to the response elicited by visual exposure alone. Both activity and physiological responses were most pronounced during the first ten seconds after exposure, with subordinate fish moving closer to the dominant, accompanied by a strong bradycardic response. Furthermore, females acted more boldly and moved closer to the dominant fish than males, but here the effect of the modes was additive, with a stronger effect of the combined visual and chemical exposure. Overall, the extra information furnished to the fish in the form of chemical cues did not change either the behavioral or the physiological response. This result suggests that visual cues are more important than chemically mediated ones for social communication and individual recognition in rainbow trout.
format: application/pdf
format: text/html
creator: Johan Höjesjö
creator: Michael Axelsson
creator: Ronja Dahy
creator: Lena Gustavsson
creator: Jörgen I. Johnsson
subject: Animal Behavior
subject: Biophysics
subject: Ecology
description: doi:10.7717/peerj.1169
publisher: PeerJ Inc.
rights: © 2015 Höjesjö et al.
abstract: Many animals, including fish, can utilize both vision and the chemical senses in intra-specific communication. However, the relative influence of these sensory modalities on behavioral and physiological responses in social interactions is not well understood. The aim of this study was therefore to investigate the relative effects of visual and chemical stimuli from dominant individuals on the behavioral and physiological responses of subordinate rainbow trout (Oncorhynchus mykiss). External electrodes were used to detect ECG signals from free-swimming fish. This method allowed the simultaneous recording of behavioral and physiological responses, and possible sex differences in these responses were also investigated. The results suggest that, in this context, visual cues are more important than chemical cues in settling the social hierarchy in rainbow trout because a combination of chemical and visual exposure generally yielded a response in focal fish that was similar to the response elicited by visual exposure alone. Both activity and physiological responses were most pronounced during the first ten seconds after exposure, with subordinate fish moving closer to the dominant, accompanied by a strong bradycardic response. Furthermore, females acted more boldly and moved closer to the dominant fish than males, but here the effect of the modes was additive, with a stronger effect of the combined visual and chemical exposure. Overall, the extra information furnished to the fish in the form of chemical cues did not change either the behavioral or the physiological response. This result suggests that visual cues are more important than chemically mediated ones for social communication and individual recognition in rainbow trout.
bibliographic citation: Höjesjö et al. (2015) Sight or smell? Behavioural and heart rate responses in subordinate rainbow trout exposed to cues from dominant fish. PeerJ 3:e1169 https://doi.org/10.7717/peerj.1169
date submitted: 2014-12-30
date accepted: 2015-07-20
issued: 2015-08-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Höjesjö
  given name: Johan
author list: Agent
  family name: Axelsson
  given name: Michael
author list: Agent
  family name: Dahy
  given name: Ronja
author list: Agent
  family name: Gustavsson
  given name: Lena
author list: Agent
  family name: Johnsson
  given name: Jörgen I.
doi: 10.7717/peerj.1169
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-06
copyright: © 2015 Höjesjö et al.
attribution name: Höjesjö et al.

Non-repeatable science: assessing the frequency of voucher specimen deposition reveals that most arthropod research cannot be verified
type: item
type: AcademicArticle
description: Scientific findings need to be verifiable and grounded in repeatability. With specimen-level research this is in part achieved with the deposition of voucher specimens. These are labeled, curated, data-based specimens that have been deposited in a collection or museum, available for verification of the work and to ensure researchers are calling the same taxa by the same names. Voucher specimens themselves are the subject of research, from the discovery of new species by taxonomists to ecologists documenting historical records of invasive species. Our objective was to quantify the frequency of voucher specimen deposition in biodiversity and community ecology research through a survey of the peer-reviewed literature about arthropods, from 1989 until 2014. Overall rates of voucher deposition were alarmingly low, at under 25%. This rate increased significantly over time, with 35% of papers reporting on vouchers in 2014. Relative to the global mean, entomological research had a significantly higher rate of voucher deposition (46%), whereas researchers studying crustaceans deposited vouchers less than 6% of the time, significantly less than the mean. Researchers working in museums had a significantly higher frequency of voucher deposition. Our results suggest a significant culture shift about the process of vouchering specimens is required. There must be more education and mentoring about voucher specimens within laboratories and across different fields of study. Principal investigators and granting agencies need a proactive approach to ensuring specimen-level data are properly, long-term curated. Editorial boards and journals can also adopt policies to ensure papers are published only if explicit statements about the deposition of voucher specimens is provided. Although the gap is significant, achieving a higher rate of voucher specimen deposition is a worthy goal to ensure all research efforts are preserved for future generations.
format: application/pdf
format: text/html
creator: Shaun Turney
creator: Elyssa R. Cameron
creator: Christopher A. Cloutier
creator: Christopher M. Buddle
subject: Biodiversity
subject: Entomology
subject: Taxonomy
subject: Science Policy
description: doi:10.7717/peerj.1168
publisher: PeerJ Inc.
rights: © 2015 Turney et al.
abstract: Scientific findings need to be verifiable and grounded in repeatability. With specimen-level research this is in part achieved with the deposition of voucher specimens. These are labeled, curated, data-based specimens that have been deposited in a collection or museum, available for verification of the work and to ensure researchers are calling the same taxa by the same names. Voucher specimens themselves are the subject of research, from the discovery of new species by taxonomists to ecologists documenting historical records of invasive species. Our objective was to quantify the frequency of voucher specimen deposition in biodiversity and community ecology research through a survey of the peer-reviewed literature about arthropods, from 1989 until 2014. Overall rates of voucher deposition were alarmingly low, at under 25%. This rate increased significantly over time, with 35% of papers reporting on vouchers in 2014. Relative to the global mean, entomological research had a significantly higher rate of voucher deposition (46%), whereas researchers studying crustaceans deposited vouchers less than 6% of the time, significantly less than the mean. Researchers working in museums had a significantly higher frequency of voucher deposition. Our results suggest a significant culture shift about the process of vouchering specimens is required. There must be more education and mentoring about voucher specimens within laboratories and across different fields of study. Principal investigators and granting agencies need a proactive approach to ensuring specimen-level data are properly, long-term curated. Editorial boards and journals can also adopt policies to ensure papers are published only if explicit statements about the deposition of voucher specimens is provided. Although the gap is significant, achieving a higher rate of voucher specimen deposition is a worthy goal to ensure all research efforts are preserved for future generations.
bibliographic citation: Turney et al. (2015) Non-repeatable science: assessing the frequency of voucher specimen deposition reveals that most arthropod research cannot be verified. PeerJ 3:e1168 https://doi.org/10.7717/peerj.1168
date submitted: 2015-05-08
date accepted: 2015-07-18
issued: 2015-08-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Turney
  given name: Shaun
author list: Agent
  family name: Cameron
  given name: Elyssa R.
author list: Agent
  family name: Cloutier
  given name: Christopher A.
author list: Agent
  family name: Buddle
  given name: Christopher M.
doi: 10.7717/peerj.1168
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-06
copyright: © 2015 Turney et al.
attribution name: Turney et al.

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