PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Lionfish (Pterois spp.) invade the upper-bathyal zone in the western Atlantic
items: Energetics and evasion dynamics of large predators and prey: pumas vs. hounds
items: Diversity, abundance, and host relationships of avian malaria and related haemosporidians in New Mexico pine forests
items: https://peerj.com/articles/3689
items: Late Pleistocene songbirds of Liang Bua (Flores, Indonesia); the first fossil passerine fauna described from Wallacea
items: Mesoscale spatiotemporal variability in a complex host-parasite system influenced by intermediate host body size
items: Quercivorol as a lure for the polyphagous and Kuroshio shot hole borers, Euwallacea spp. nr. fornicatus (Coleoptera: Scolytinae), vectors of Fusarium dieback
items: Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations
items: RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis)
items: Shoreline oiling effects and recovery of salt marsh macroinvertebrates from the Deepwater Horizon Oil Spill

Lionfish (Pterois spp.) invade the upper-bathyal zone in the western Atlantic
type: item
type: AcademicArticle
description: Non-native lionfish have been recorded throughout the western Atlantic on both shallow and mesophotic reefs, where they have been linked to declines in reef health. In this study we report the first lionfish observations from the deep sea (>200 m) in Bermuda and Roatan, Honduras, with lionfish observed to a maximum depth of 304 m off the Bermuda platform, and 250 m off West End, Roatan. Placed in the context of other deeper lionfish observations and records, our results imply that lionfish may be present in the 200–300 m depth range of the upper-bathyal zone across many locations in the western Atlantic, but currently are under-sampled compared to shallow habitats. We highlight the need for considering deep-sea lionfish populations in future invasive lionfish management.
format: application/pdf
format: text/html
creator: Erika Gress
creator: Dominic A. Andradi-Brown
creator: Lucy Woodall
creator: Pamela J. Schofield
creator: Karl Stanley
creator: Alex D. Rogers
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.3683
publisher: PeerJ Inc.
rights: © 2017
abstract: Non-native lionfish have been recorded throughout the western Atlantic on both shallow and mesophotic reefs, where they have been linked to declines in reef health. In this study we report the first lionfish observations from the deep sea (>200 m) in Bermuda and Roatan, Honduras, with lionfish observed to a maximum depth of 304 m off the Bermuda platform, and 250 m off West End, Roatan. Placed in the context of other deeper lionfish observations and records, our results imply that lionfish may be present in the 200–300 m depth range of the upper-bathyal zone across many locations in the western Atlantic, but currently are under-sampled compared to shallow habitats. We highlight the need for considering deep-sea lionfish populations in future invasive lionfish management.
bibliographic citation: Gress et al. (2017) Lionfish (Pterois spp.) invade the upper-bathyal zone in the western Atlantic. PeerJ 5:e3683 https://doi.org/10.7717/peerj.3683
date submitted: 2017-05-29
date accepted: 2017-07-23
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Gress
  given name: Erika
author list: Agent
  family name: Andradi-Brown
  given name: Dominic A.
author list: Agent
  family name: Woodall
  given name: Lucy
author list: Agent
  family name: Schofield
  given name: Pamela J.
author list: Agent
  family name: Stanley
  given name: Karl
author list: Agent
  family name: Rogers
  given name: Alex D.
doi: 10.7717/peerj.3683
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17

Energetics and evasion dynamics of large predators and prey: pumas vs. hounds
type: item
type: AcademicArticle
description: Quantification of fine-scale movement, performance, and energetics of hunting by large carnivores is critical for understanding the physiological underpinnings of trophic interactions. This is particularly challenging for wide-ranging terrestrial canid and felid predators, which can each affect ecosystem structure through distinct hunting modes. To compare free-ranging pursuit and escape performance from group-hunting and solitary predators in unprecedented detail, we calibrated and deployed accelerometer-GPS collars during predator-prey chase sequences using packs of hound dogs (Canis lupus familiaris, 26 kg, n = 4–5 per chase) pursuing simultaneously instrumented solitary pumas (Puma concolor, 60 kg, n = 2). We then reconstructed chase paths, speed and turning angle profiles, and energy demands for hounds and pumas to examine performance and physiological constraints associated with cursorial and cryptic hunting modes, respectively. Interaction dynamics revealed how pumas successfully utilized terrain (e.g., fleeing up steep, wooded hillsides) as well as evasive maneuvers (e.g., jumping into trees, running in figure-8 patterns) to increase their escape distance from the overall faster hounds (avg. 2.3× faster). These adaptive strategies were essential to evasion in light of the mean 1.6× higher mass-specific energetic costs of the chase for pumas compared to hounds (mean: 0.76 vs. 1.29 kJ kg−1 min−1, respectively). On an instantaneous basis, escapes were more costly for pumas, requiring exercise at ≥90% of predicted $\dot {\mathrm{V }}{\mathrm{O}}_{2\mathrm{MAX}}$ V ̇ O 2 MAX and consuming as much energy per minute as approximately 5 min of active hunting. Our results demonstrate the marked investment of energy for evasion by a large, solitary carnivore and the advantage of dynamic maneuvers to postpone being overtaken by group-hunting canids.
format: application/pdf
format: text/html
creator: Caleb M. Bryce
creator: Christopher C. Wilmers
creator: Terrie M. Williams
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Environmental Sciences
subject: Zoology
description: doi:10.7717/peerj.3701
publisher: PeerJ Inc.
rights: © 2017 Bryce et al.
abstract: Quantification of fine-scale movement, performance, and energetics of hunting by large carnivores is critical for understanding the physiological underpinnings of trophic interactions. This is particularly challenging for wide-ranging terrestrial canid and felid predators, which can each affect ecosystem structure through distinct hunting modes. To compare free-ranging pursuit and escape performance from group-hunting and solitary predators in unprecedented detail, we calibrated and deployed accelerometer-GPS collars during predator-prey chase sequences using packs of hound dogs (Canis lupus familiaris, 26 kg, n = 4–5 per chase) pursuing simultaneously instrumented solitary pumas (Puma concolor, 60 kg, n = 2). We then reconstructed chase paths, speed and turning angle profiles, and energy demands for hounds and pumas to examine performance and physiological constraints associated with cursorial and cryptic hunting modes, respectively. Interaction dynamics revealed how pumas successfully utilized terrain (e.g., fleeing up steep, wooded hillsides) as well as evasive maneuvers (e.g., jumping into trees, running in figure-8 patterns) to increase their escape distance from the overall faster hounds (avg. 2.3× faster). These adaptive strategies were essential to evasion in light of the mean 1.6× higher mass-specific energetic costs of the chase for pumas compared to hounds (mean: 0.76 vs. 1.29 kJ kg−1 min−1, respectively). On an instantaneous basis, escapes were more costly for pumas, requiring exercise at ≥90% of predicted $\dot {\mathrm{V }}{\mathrm{O}}_{2\mathrm{MAX}}$ V ̇ O 2 MAX and consuming as much energy per minute as approximately 5 min of active hunting. Our results demonstrate the marked investment of energy for evasion by a large, solitary carnivore and the advantage of dynamic maneuvers to postpone being overtaken by group-hunting canids.
bibliographic citation: Bryce et al. (2017) Energetics and evasion dynamics of large predators and prey: pumas vs. hounds. PeerJ 5:e3701 https://doi.org/10.7717/peerj.3701
date submitted: 2017-06-05
date accepted: 2017-07-26
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bryce
  given name: Caleb M.
author list: Agent
  family name: Wilmers
  given name: Christopher C.
author list: Agent
  family name: Williams
  given name: Terrie M.
doi: 10.7717/peerj.3701
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17
copyright: ©2017 Bryce et al.
attribution name: Bryce et al.

Diversity, abundance, and host relationships of avian malaria and related haemosporidians in New Mexico pine forests
type: item
type: AcademicArticle
description: Avian malaria and related haemosporidian parasites (genera Haemoproteus, Plasmodium, and Leucocytozoon) affect bird demography, species range limits, and community structure, yet they remain unsurveyed in most bird communities and populations. We conducted a community-level survey of these vector-transmitted parasites in New Mexico, USA, to describe their diversity, abundance, and host associations. We focused on the breeding-bird community in the transition zone between piñon-juniper woodland and ponderosa pine forests (elevational range: 2,150–2,460 m). We screened 186 birds representing 49 species using both standard PCR and microscopy techniques to detect infections of all three avian haemosporidian genera. We detected infections in 68 out of 186 birds (36.6%), the highest proportion of which were infected with Haemoproteus (20.9%), followed by Leucocytozoon (13.4%), then Plasmodium (8.0%). We sequenced mtDNA for 77 infections representing 43 haplotypes (25 Haemoproteus, 12 Leucocytozoon, 6 Plasmodium). When compared to all previously known haplotypes in the MalAvi and GenBank databases, 63% (27) of the haplotypes we recovered were novel. We found evidence for host specificity at the avian clade and species level, but this specificity was variable among parasite genera, in that Haemoproteus and Leucocytozoon were each restricted to three avian groups (out of six), while Plasmodium occurred in all groups except non-passerines. We found striking variation in infection rate among host species, with nearly universal infection among vireos and no infection among nuthatches. Using rarefaction and extrapolation, we estimated the total avian haemosporidian diversity to be 70 haplotypes (95% CI [43–98]); thus, we may have already sampled ∼60% of the diversity of avian haemosporidians in New Mexico pine forests. It is possible that future studies will find higher diversity in microhabitats or host species that are under-sampled or unsampled in the present study. Fortunate…
format: application/pdf
format: text/html
creator: Rosario A. Marroquin-Flores
creator: Jessie L. Williamson
creator: Andrea N. Chavez
creator: Selina M. Bauernfeind
creator: Matthew J. Baumann
creator: Chauncey R. Gadek
creator: Andrew B. Johnson
creator: Jenna M. McCullough
creator: Christopher C. Witt
creator: Lisa N. Barrow
subject: Biodiversity
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.3700
publisher: PeerJ Inc.
rights: © 2017 Marroquin-Flores et al.
abstract: Avian malaria and related haemosporidian parasites (genera Haemoproteus, Plasmodium, and Leucocytozoon) affect bird demography, species range limits, and community structure, yet they remain unsurveyed in most bird communities and populations. We conducted a community-level survey of these vector-transmitted parasites in New Mexico, USA, to describe their diversity, abundance, and host associations. We focused on the breeding-bird community in the transition zone between piñon-juniper woodland and ponderosa pine forests (elevational range: 2,150–2,460 m). We screened 186 birds representing 49 species using both standard PCR and microscopy techniques to detect infections of all three avian haemosporidian genera. We detected infections in 68 out of 186 birds (36.6%), the highest proportion of which were infected with Haemoproteus (20.9%), followed by Leucocytozoon (13.4%), then Plasmodium (8.0%). We sequenced mtDNA for 77 infections representing 43 haplotypes (25 Haemoproteus, 12 Leucocytozoon, 6 Plasmodium). When compared to all previously known haplotypes in the MalAvi and GenBank databases, 63% (27) of the haplotypes we recovered were novel. We found evidence for host specificity at the avian clade and species level, but this specificity was variable among parasite genera, in that Haemoproteus and Leucocytozoon were each restricted to three avian groups (out of six), while Plasmodium occurred in all groups except non-passerines. We found striking variation in infection rate among host species, with nearly universal infection among vireos and no infection among nuthatches. Using rarefaction and extrapolation, we estimated the total avian haemosporidian diversity to be 70 haplotypes (95% CI [43–98]); thus, we may have already sampled ∼60% of the diversity of avian haemosporidians in New Mexico pine forests. It is possible that future studies will find higher diversity in microhabitats or host species that are under-sampled or unsampled in the present study. Fortunate…
bibliographic citation: Marroquin-Flores et al. (2017) Diversity, abundance, and host relationships of avian malaria and related haemosporidians in New Mexico pine forests. PeerJ 5:e3700 https://doi.org/10.7717/peerj.3700
date submitted: 2017-05-29
date accepted: 2017-07-26
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marroquin-Flores
  given name: Rosario A.
author list: Agent
  family name: Williamson
  given name: Jessie L.
author list: Agent
  family name: Chavez
  given name: Andrea N.
author list: Agent
  family name: Bauernfeind
  given name: Selina M.
author list: Agent
  family name: Baumann
  given name: Matthew J.
author list: Agent
  family name: Gadek
  given name: Chauncey R.
author list: Agent
  family name: Johnson
  given name: Andrew B.
author list: Agent
  family name: McCullough
  given name: Jenna M.
author list: Agent
  family name: Witt
  given name: Christopher C.
author list: Agent
  family name: Barrow
  given name: Lisa N.
doi: 10.7717/peerj.3700
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17
copyright: ©2017 Marroquin-Flores et al.
attribution name: Marroquin-Flores et al.

https://peerj.com/articles/3689
type: item
type: AcademicArticle
title: Diversity of compounds in femoral secretions of Galápagos iguanas (genera: Amblyrhynchus and Conolophus), and their potential role in sexual communication in lek-mating marine iguanas (Amblyrhynchus cristatus)
description: Background Chemical signals are widely used in the animal kingdom, enabling communication in various social contexts, including mate selection and the establishment of dominance. Femoral glands, which produce and release waxy secretions into the environment, are organs of central importance in lizard chemical communication. The Galápagos marine iguana (Amblyrhynchus cristatus) is a squamate reptile with a lek-mating system. Although the lekking behaviour of marine iguanas has been well-studied, their potential for sexual communication via chemical cues has not yet been investigated. Here we describe the diversity of the lipophilic fraction of males’ femoral gland secretions among 11 island populations of marine iguanas, and compare it with the composition of its sister species, the Galápagos land iguana (Conolophus subcristatus). We also conducted behavioural observations in marine iguana territorial males in order to explore the possible function of these substances in the context of male dominance in leks. Methods Femoral secretions were analysed by gas chromatography coupled to mass spectrometry (GC–MS), and chromatography with a flame ionisation detector (GC-FID) in order to characterise the lipophilic composition. To understand the potential role of femoral secretions in marine iguana intraspecific communication, territorial males were sampled for their femoral glands and monitored to record their head bob rate—a territorial display behaviour in males—as well as the number of females present in their leks. Results We found that the gland secretions were composed of ten saturated and unsaturated carboxylic acids ranging in chain length between C16 and C24, as well as three sterols. Cholesterol was the main compound found. Intriguingly, land iguanas have a higher diversity of lipophilic compounds, with structural group of lipids (i.e. aldehydes) entirely absent in marine iguanas; overall the chemical signals of both species were strongly differentiated. Lipid pro…
format: application/pdf
format: text/html
creator: Alejandro Ibáñez
creator: Markus Menke
creator: Galo Quezada
creator: Gustavo Jiménez-Uzcátegui
creator: Stefan Schulz
creator: Sebastian Steinfartz
subject: Animal Behavior
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.3689
publisher: PeerJ Inc.
rights: © 2017 Ibáñez et al.
abstract: Background Chemical signals are widely used in the animal kingdom, enabling communication in various social contexts, including mate selection and the establishment of dominance. Femoral glands, which produce and release waxy secretions into the environment, are organs of central importance in lizard chemical communication. The Galápagos marine iguana (Amblyrhynchus cristatus) is a squamate reptile with a lek-mating system. Although the lekking behaviour of marine iguanas has been well-studied, their potential for sexual communication via chemical cues has not yet been investigated. Here we describe the diversity of the lipophilic fraction of males’ femoral gland secretions among 11 island populations of marine iguanas, and compare it with the composition of its sister species, the Galápagos land iguana (Conolophus subcristatus). We also conducted behavioural observations in marine iguana territorial males in order to explore the possible function of these substances in the context of male dominance in leks. Methods Femoral secretions were analysed by gas chromatography coupled to mass spectrometry (GC–MS), and chromatography with a flame ionisation detector (GC-FID) in order to characterise the lipophilic composition. To understand the potential role of femoral secretions in marine iguana intraspecific communication, territorial males were sampled for their femoral glands and monitored to record their head bob rate—a territorial display behaviour in males—as well as the number of females present in their leks. Results We found that the gland secretions were composed of ten saturated and unsaturated carboxylic acids ranging in chain length between C16 and C24, as well as three sterols. Cholesterol was the main compound found. Intriguingly, land iguanas have a higher diversity of lipophilic compounds, with structural group of lipids (i.e. aldehydes) entirely absent in marine iguanas; overall the chemical signals of both species were strongly differentiated. Lipid pro…
bibliographic citation: Ibáñez et al. (2017) Diversity of compounds in femoral secretions of Galápagos iguanas (genera: Amblyrhynchus and Conolophus), and their potential role in sexual communication in lek-mating marine iguanas (Amblyrhynchus cristatus). PeerJ 5:e3689 https://doi.org/10.7717/peerj.3689
date submitted: 2017-06-12
date accepted: 2017-07-24
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ibáñez
  given name: Alejandro
author list: Agent
  family name: Menke
  given name: Markus
author list: Agent
  family name: Quezada
  given name: Galo
author list: Agent
  family name: Jiménez-Uzcátegui
  given name: Gustavo
author list: Agent
  family name: Schulz
  given name: Stefan
author list: Agent
  family name: Steinfartz
  given name: Sebastian
doi: 10.7717/peerj.3689
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17
copyright: © 2017 Ibáñez et al.
attribution name: Ibáñez et al.

Late Pleistocene songbirds of Liang Bua (Flores, Indonesia); the first fossil passerine fauna described from Wallacea
type: item
type: AcademicArticle
description: Background Passerines (Aves: Passeriformes) dominate modern terrestrial bird communities yet their fossil record is limited. Liang Bua is a large cave on the Indonesian island of Flores that preserves Late Pleistocene–Holocene deposits (∼190 ka to present day). Birds are the most diverse faunal group at Liang Bua and are present throughout the stratigraphic sequence. Methods We examined avian remains from the Late Pleistocene deposits of Sector XII, a 2 × 2 m area excavated to about 8.5 m depth. Although postcranial passerine remains are typically challenging to identify, we found several humeral characters particularly useful in discriminating between groups, and identified 89 skeletal elements of passerines. Results At least eight species from eight families are represented, including the Large-billed Crow (Corvus cf. macrorhynchos), the Australasian Bushlark (Mirafra javanica), a friarbird (Philemon sp.), and the Pechora Pipit (Anthus cf. gustavi). Discussion These remains constitute the first sample of fossil passerines described in Wallacea. Two of the taxa no longer occur on Flores today; a large sturnid (cf. Acridotheres) and a grassbird (Megalurus sp.). Palaeoecologically, the songbird assemblage suggests open grassland and tall forests, which is consistent with conditions inferred from the non-passerine fauna at the site. Corvus cf. macrorhynchos, found in the Homo floresiensis-bearing layers, was likely part of a scavenging guild that fed on carcasses of Stegodon florensis insularis alongside vultures (Trigonoceps sp.), giant storks (Leptoptilos robustus), komodo dragons (Varanus komodoensis), and probably H. floresiensis as well.
format: application/pdf
format: text/html
creator: Hanneke J.M. Meijer
creator: Rokus Awe Due
creator: Thomas Sutikna
creator: Wahyu Saptomo
creator: Jatmiko
creator: Sri Wasisto
creator: Matthew W. Tocheri
creator: Gerald Mayr
subject: Biogeography
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.3676
publisher: PeerJ Inc.
rights: © 2017 Meijer et al.
abstract: Background Passerines (Aves: Passeriformes) dominate modern terrestrial bird communities yet their fossil record is limited. Liang Bua is a large cave on the Indonesian island of Flores that preserves Late Pleistocene–Holocene deposits (∼190 ka to present day). Birds are the most diverse faunal group at Liang Bua and are present throughout the stratigraphic sequence. Methods We examined avian remains from the Late Pleistocene deposits of Sector XII, a 2 × 2 m area excavated to about 8.5 m depth. Although postcranial passerine remains are typically challenging to identify, we found several humeral characters particularly useful in discriminating between groups, and identified 89 skeletal elements of passerines. Results At least eight species from eight families are represented, including the Large-billed Crow (Corvus cf. macrorhynchos), the Australasian Bushlark (Mirafra javanica), a friarbird (Philemon sp.), and the Pechora Pipit (Anthus cf. gustavi). Discussion These remains constitute the first sample of fossil passerines described in Wallacea. Two of the taxa no longer occur on Flores today; a large sturnid (cf. Acridotheres) and a grassbird (Megalurus sp.). Palaeoecologically, the songbird assemblage suggests open grassland and tall forests, which is consistent with conditions inferred from the non-passerine fauna at the site. Corvus cf. macrorhynchos, found in the Homo floresiensis-bearing layers, was likely part of a scavenging guild that fed on carcasses of Stegodon florensis insularis alongside vultures (Trigonoceps sp.), giant storks (Leptoptilos robustus), komodo dragons (Varanus komodoensis), and probably H. floresiensis as well.
bibliographic citation: Meijer et al. (2017) Late Pleistocene songbirds of Liang Bua (Flores, Indonesia); the first fossil passerine fauna described from Wallacea. PeerJ 5:e3676 https://doi.org/10.7717/peerj.3676
date submitted: 2017-04-18
date accepted: 2017-07-20
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meijer
  given name: Hanneke J.M.
author list: Agent
  family name: Awe Due
  given name: Rokus
author list: Agent
  family name: Sutikna
  given name: Thomas
author list: Agent
  family name: Saptomo
  given name: Wahyu
author list: Agent
  family name: Jatmiko
author list: Agent
  family name: Wasisto
  given name: Sri
author list: Agent
  family name: Tocheri
  given name: Matthew W.
author list: Agent
  family name: Mayr
  given name: Gerald
doi: 10.7717/peerj.3676
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17
copyright: ©2017 Meijer et al.
attribution name: Meijer et al.

Mesoscale spatiotemporal variability in a complex host-parasite system influenced by intermediate host body size
type: item
type: AcademicArticle
description: Background Parasites are essential components of natural communities, but the factors that generate skewed distributions of parasite occurrences and abundances across host populations are not well understood. Methods Here, we analyse at a seascape scale the spatiotemporal relationships of parasite exposure and host body-size with the proportion of infected hosts (i.e., prevalence) and aggregation of parasite burden across ca. 150 km of the coast and over 22 months. We predicted that the effects of parasite exposure on prevalence and aggregation are dependent on host body-sizes. We used an indirect host-parasite interaction in which migratory seagulls, sandy-shore molecrabs, and an acanthocephalan worm constitute the definitive hosts, intermediate hosts, and endoparasite, respectively. In such complex systems, increments in the abundance of definitive hosts imply increments in intermediate hosts’ exposure to the parasite’s dispersive stages. Results Linear mixed-effects models showed a significant, albeit highly variable, positive relationship between seagull density and prevalence. This relationship was stronger for small (cephalothorax length >15 mm) than large molecrabs (<15 mm). Independently of seagull density, large molecrabs carried significantly more parasites than small molecrabs. The analysis of the variance-to-mean ratio of per capita parasite burden showed no relationship between seagull density and mean parasite aggregation across host populations. However, the amount of unexplained variability in aggregation was strikingly higher in larger than smaller intermediate hosts. This unexplained variability was driven by a decrease in the mean-variance scaling in heavily infected large molecrabs. Conclusions These results show complex interdependencies between extrinsic and intrinsic population attributes on the structure of host-parasite interactions. We suggest that parasite accumulation—a characteristic of indirect host-parasite interactions—and subsequent …
format: application/pdf
format: text/html
creator: Sara M. Rodríguez
creator: Nelson Valdivia
subject: Animal Behavior
subject: Biodiversity
subject: Parasitology
description: doi:10.7717/peerj.3675
publisher: PeerJ Inc.
rights: © 2017 Rodríguez and Valdivia
abstract: Background Parasites are essential components of natural communities, but the factors that generate skewed distributions of parasite occurrences and abundances across host populations are not well understood. Methods Here, we analyse at a seascape scale the spatiotemporal relationships of parasite exposure and host body-size with the proportion of infected hosts (i.e., prevalence) and aggregation of parasite burden across ca. 150 km of the coast and over 22 months. We predicted that the effects of parasite exposure on prevalence and aggregation are dependent on host body-sizes. We used an indirect host-parasite interaction in which migratory seagulls, sandy-shore molecrabs, and an acanthocephalan worm constitute the definitive hosts, intermediate hosts, and endoparasite, respectively. In such complex systems, increments in the abundance of definitive hosts imply increments in intermediate hosts’ exposure to the parasite’s dispersive stages. Results Linear mixed-effects models showed a significant, albeit highly variable, positive relationship between seagull density and prevalence. This relationship was stronger for small (cephalothorax length >15 mm) than large molecrabs (<15 mm). Independently of seagull density, large molecrabs carried significantly more parasites than small molecrabs. The analysis of the variance-to-mean ratio of per capita parasite burden showed no relationship between seagull density and mean parasite aggregation across host populations. However, the amount of unexplained variability in aggregation was strikingly higher in larger than smaller intermediate hosts. This unexplained variability was driven by a decrease in the mean-variance scaling in heavily infected large molecrabs. Conclusions These results show complex interdependencies between extrinsic and intrinsic population attributes on the structure of host-parasite interactions. We suggest that parasite accumulation—a characteristic of indirect host-parasite interactions—and subsequent …
bibliographic citation: Rodríguez et al. (2017) Mesoscale spatiotemporal variability in a complex host-parasite system influenced by intermediate host body size. PeerJ 5:e3675 https://doi.org/10.7717/peerj.3675
date submitted: 2017-05-18
date accepted: 2017-07-21
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodríguez
  given name: Sara M.
author list: Agent
  family name: Valdivia
  given name: Nelson
doi: 10.7717/peerj.3675
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17
copyright: ©2017 Rodríguez and Valdivia
attribution name: Rodríguez and Valdivia

Quercivorol as a lure for the polyphagous and Kuroshio shot hole borers, Euwallacea spp. nr. fornicatus (Coleoptera: Scolytinae), vectors of Fusarium dieback
type: item
type: AcademicArticle
description: The polyphagous shot hole borer and Kuroshio shot hole borer, two members of the Euwallacea fornicatus species complex (Coleoptera: Curculionidae: Scolytinae), are invasive ambrosia beetles that harbor distinct species of Fusarium fungal symbionts. Together with the damage caused by gallery construction, these two phytopathogenic Fusarium species are responsible for the emerging tree disease Fusarium dieback, which affects over 50 common tree species in Southern California. Host trees suffer branch dieback as the xylem is blocked by invading beetles and fungi, forcing the costly removal of dead and dying trees in urban areas. The beetles are also threatening natural riparian habitats, and avocado is susceptible to Fusarium dieback as well, resulting in damage to the avocado industries in California and Israel. Currently there are no adequate control mechanisms for shot hole borers. This paper summarizes efforts to find a suitable lure to monitor shot hole borer invasions and dispersal. Field trials were conducted in two counties in Southern California over a span of two years. We find that the chemical quercivorol is highly attractive to these beetles, and perform subsequent field experiments attempting to optimize this lure. We also explore other methods of increasing trap catch and effects of other potential attractants, as well as the deterrents verbenone and piperitone.
format: application/pdf
format: text/html
creator: Christine Dodge
creator: Jessica Coolidge
creator: Miriam Cooperband
creator: Allard Cossé
creator: Daniel Carrillo
creator: Richard Stouthamer
subject: Agricultural Science
subject: Animal Behavior
subject: Entomology
description: doi:10.7717/peerj.3656
publisher: PeerJ Inc.
rights: © 2017 Dodge et al.
abstract: The polyphagous shot hole borer and Kuroshio shot hole borer, two members of the Euwallacea fornicatus species complex (Coleoptera: Curculionidae: Scolytinae), are invasive ambrosia beetles that harbor distinct species of Fusarium fungal symbionts. Together with the damage caused by gallery construction, these two phytopathogenic Fusarium species are responsible for the emerging tree disease Fusarium dieback, which affects over 50 common tree species in Southern California. Host trees suffer branch dieback as the xylem is blocked by invading beetles and fungi, forcing the costly removal of dead and dying trees in urban areas. The beetles are also threatening natural riparian habitats, and avocado is susceptible to Fusarium dieback as well, resulting in damage to the avocado industries in California and Israel. Currently there are no adequate control mechanisms for shot hole borers. This paper summarizes efforts to find a suitable lure to monitor shot hole borer invasions and dispersal. Field trials were conducted in two counties in Southern California over a span of two years. We find that the chemical quercivorol is highly attractive to these beetles, and perform subsequent field experiments attempting to optimize this lure. We also explore other methods of increasing trap catch and effects of other potential attractants, as well as the deterrents verbenone and piperitone.
bibliographic citation: Dodge et al. (2017) Quercivorol as a lure for the polyphagous and Kuroshio shot hole borers, Euwallacea spp. nr. fornicatus (Coleoptera: Scolytinae), vectors of Fusarium dieback. PeerJ 5:e3656 https://doi.org/10.7717/peerj.3656
date submitted: 2017-06-19
date accepted: 2017-07-14
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dodge
  given name: Christine
author list: Agent
  family name: Coolidge
  given name: Jessica
author list: Agent
  family name: Cooperband
  given name: Miriam
author list: Agent
  family name: Cossé
  given name: Allard
author list: Agent
  family name: Carrillo
  given name: Daniel
author list: Agent
  family name: Stouthamer
  given name: Richard
doi: 10.7717/peerj.3656
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17
copyright: © 2017 Dodge et al.
attribution name: Dodge et al.

Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations
type: item
type: AcademicArticle
description: The prevalence of Type II Diabetes (T2D) has been increasing and has become a disease of significant public health burden in Jordan. None of the previous genome-wide association studies (GWAS) have specifically investigated the Middle East populations. The Circassian and Chechen communities in Jordan represent unique populations that are genetically distinct from the Arab population and other populations in the Caucasus. Prevalence of T2D is very high in both the Circassian and Chechen communities in Jordan despite low obesity prevalence. We conducted GWAS on T2D in these two populations and further performed meta-analysis of the results. We identified a novel T2D locus at chr20p12.2 at genome-wide significance (rs6134031, P = 1.12 × 10−8) and we replicated the results in the Wellcome Trust Case Control Consortium (WTCCC) dataset. Another locus at chr12q24.31 is associated with T2D at suggestive significance level (top SNP rs4758690, P = 4.20 × 10−5) and it is a robust eQTL for the gene, MLXIP (P = 1.10 × 10−14), and is significantly associated with methylation level in MLXIP, the functions of which involves cellular glucose response. Therefore, in this first GWAS of T2D in Jordan subpopulations, we identified novel and unique susceptibility loci which may help inform the genetic underpinnings of T2D in other populations.
format: application/pdf
format: text/html
creator: Rana Dajani
creator: Jin Li
creator: Zhi Wei
creator: Michael E. March
creator: Qianghua Xia
creator: Yousef Khader
creator: Nancy Hakooz
creator: Raja Fatahallah
creator: Mohammed El-Khateeb
creator: Ala Arafat
creator: Tareq Saleh
creator: Abdel Rahman Dajani
creator: Zaid Al-Abbadi
creator: Mohamed Abdul Qader
creator: Abdel Halim Shiyab
creator: Anwar Bateiha
creator: Kamel Ajlouni
creator: Hakon Hakonarson
subject: Genetics
subject: Genomics
subject: Diabetes and Endocrinology
subject: Medical Genetics
description: doi:10.7717/peerj.3618
publisher: PeerJ Inc.
rights: © 2017 Dajani et al.
abstract: The prevalence of Type II Diabetes (T2D) has been increasing and has become a disease of significant public health burden in Jordan. None of the previous genome-wide association studies (GWAS) have specifically investigated the Middle East populations. The Circassian and Chechen communities in Jordan represent unique populations that are genetically distinct from the Arab population and other populations in the Caucasus. Prevalence of T2D is very high in both the Circassian and Chechen communities in Jordan despite low obesity prevalence. We conducted GWAS on T2D in these two populations and further performed meta-analysis of the results. We identified a novel T2D locus at chr20p12.2 at genome-wide significance (rs6134031, P = 1.12 × 10−8) and we replicated the results in the Wellcome Trust Case Control Consortium (WTCCC) dataset. Another locus at chr12q24.31 is associated with T2D at suggestive significance level (top SNP rs4758690, P = 4.20 × 10−5) and it is a robust eQTL for the gene, MLXIP (P = 1.10 × 10−14), and is significantly associated with methylation level in MLXIP, the functions of which involves cellular glucose response. Therefore, in this first GWAS of T2D in Jordan subpopulations, we identified novel and unique susceptibility loci which may help inform the genetic underpinnings of T2D in other populations.
bibliographic citation: Dajani et al. (2017) Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations. PeerJ 5:e3618 https://doi.org/10.7717/peerj.3618
date submitted: 2017-04-03
date accepted: 2017-07-06
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dajani
  given name: Rana
author list: Agent
  family name: Li
  given name: Jin
author list: Agent
  family name: Wei
  given name: Zhi
author list: Agent
  family name: March
  given name: Michael E.
author list: Agent
  family name: Xia
  given name: Qianghua
author list: Agent
  family name: Khader
  given name: Yousef
author list: Agent
  family name: Hakooz
  given name: Nancy
author list: Agent
  family name: Fatahallah
  given name: Raja
author list: Agent
  family name: El-Khateeb
  given name: Mohammed
author list: Agent
  family name: Arafat
  given name: Ala
author list: Agent
  family name: Saleh
  given name: Tareq
author list: Agent
  family name: Dajani
  given name: Abdel Rahman
author list: Agent
  family name: Al-Abbadi
  given name: Zaid
author list: Agent
  family name: Abdul Qader
  given name: Mohamed
author list: Agent
  family name: Shiyab
  given name: Abdel Halim
author list: Agent
  family name: Bateiha
  given name: Anwar
author list: Agent
  family name: Ajlouni
  given name: Kamel
author list: Agent
  family name: Hakonarson
  given name: Hakon
doi: 10.7717/peerj.3618
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17
copyright: ©2017 Dajani et al.
attribution name: Dajani et al.

RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis)
type: item
type: AcademicArticle
description: The cynomolgus macaque (Macaca fascicularis) is an extensively utilised nonhuman primate model for biomedical research due to its biological, behavioural, and genetic similarities to humans. Genomic information of cynomolgus macaque is vital for research in various fields; however, there is presently a shortage of genomic information on the Malaysian cynomolgus macaque. This study aimed to sequence, assemble, annotate, and profile the Peninsular Malaysian cynomolgus macaque transcriptome derived from three tissues (lymph node, spleen, and thymus) using RNA sequencing (RNA-Seq) technology. A total of 174,208,078 paired end 70 base pair sequencing reads were obtained from the Illumina Hi-Seq 2500 sequencer. The overall mapping percentage of the sequencing reads to the M. fascicularis reference genome ranged from 53–63%. Categorisation of expressed genes to Gene Ontology (GO) and KEGG pathway categories revealed that GO terms with the highest number of associated expressed genes include Cellular process, Catalytic activity, and Cell part, while for pathway categorisation, the majority of expressed genes in lymph node, spleen, and thymus fall under the Global overview and maps pathway category, while 266, 221, and 138 genes from lymph node, spleen, and thymus were respectively enriched in the Immune system category. Enriched Immune system pathways include Platelet activation pathway, Antigen processing and presentation, B cell receptor signalling pathway, and Intestinal immune network for IgA production. Differential gene expression analysis among the three tissues revealed 574 differentially expressed genes (DEG) between lymph and spleen, 5402 DEGs between lymph and thymus, and 7008 DEGs between spleen and thymus. Venn diagram analysis of expressed genes revealed a total of 2,630, 253, and 279 tissue-specific genes respectively for lymph node, spleen, and thymus tissues. This is the first time the lymph node, spleen, and thymus transcriptome of the Peninsular Malaysian…
format: application/pdf
format: text/html
creator: Joey Ee Uli
creator: Christina Seok Yien Yong
creator: Swee Keong Yeap
creator: Jeffrine J. Rovie-Ryan
creator: Nurulfiza Mat Isa
creator: Soon Guan Tan
creator: Noorjahan Banu Alitheen
subject: Bioinformatics
subject: Genomics
subject: Zoology
subject: Immunology
description: doi:10.7717/peerj.3566
publisher: PeerJ Inc.
rights: © 2017 Ee Uli et al.
abstract: The cynomolgus macaque (Macaca fascicularis) is an extensively utilised nonhuman primate model for biomedical research due to its biological, behavioural, and genetic similarities to humans. Genomic information of cynomolgus macaque is vital for research in various fields; however, there is presently a shortage of genomic information on the Malaysian cynomolgus macaque. This study aimed to sequence, assemble, annotate, and profile the Peninsular Malaysian cynomolgus macaque transcriptome derived from three tissues (lymph node, spleen, and thymus) using RNA sequencing (RNA-Seq) technology. A total of 174,208,078 paired end 70 base pair sequencing reads were obtained from the Illumina Hi-Seq 2500 sequencer. The overall mapping percentage of the sequencing reads to the M. fascicularis reference genome ranged from 53–63%. Categorisation of expressed genes to Gene Ontology (GO) and KEGG pathway categories revealed that GO terms with the highest number of associated expressed genes include Cellular process, Catalytic activity, and Cell part, while for pathway categorisation, the majority of expressed genes in lymph node, spleen, and thymus fall under the Global overview and maps pathway category, while 266, 221, and 138 genes from lymph node, spleen, and thymus were respectively enriched in the Immune system category. Enriched Immune system pathways include Platelet activation pathway, Antigen processing and presentation, B cell receptor signalling pathway, and Intestinal immune network for IgA production. Differential gene expression analysis among the three tissues revealed 574 differentially expressed genes (DEG) between lymph and spleen, 5402 DEGs between lymph and thymus, and 7008 DEGs between spleen and thymus. Venn diagram analysis of expressed genes revealed a total of 2,630, 253, and 279 tissue-specific genes respectively for lymph node, spleen, and thymus tissues. This is the first time the lymph node, spleen, and thymus transcriptome of the Peninsular Malaysian…
bibliographic citation: Ee Uli et al. (2017) RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis). PeerJ 5:e3566 https://doi.org/10.7717/peerj.3566
date submitted: 2017-03-02
date accepted: 2017-06-21
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ee Uli
  given name: Joey
author list: Agent
  family name: Yong
  given name: Christina Seok Yien
author list: Agent
  family name: Yeap
  given name: Swee Keong
author list: Agent
  family name: Rovie-Ryan
  given name: Jeffrine J.
author list: Agent
  family name: Mat Isa
  given name: Nurulfiza
author list: Agent
  family name: Tan
  given name: Soon Guan
author list: Agent
  family name: Alitheen
  given name: Noorjahan Banu
doi: 10.7717/peerj.3566
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17
copyright: ©2017 Ee Uli et al.
attribution name: Ee Uli et al.

Shoreline oiling effects and recovery of salt marsh macroinvertebrates from the Deepwater Horizon Oil Spill
type: item
type: AcademicArticle
description: Salt marshes in northern Barataria Bay, Louisiana, USA were oiled, sometimes heavily, in the aftermath of the Deepwater Horizon oil spill. Previous studies indicate that fiddler crabs (in the genus Uca) and the salt marsh periwinkle (Littoraria irrorata) were negatively impacted in the short term by the spill. Here, we detail longer-term effects and recovery from moderate and heavy oiling over a 3-year span, beginning 30 months after the spill. Although neither fiddler crab burrow density nor diameter differed between oiled and reference sites when combined across all sampling events, these traits differed among some individual sampling periods consistent with a pattern of lingering oiling impacts. Periwinkle density, however, increased in all oiling categories and shell-length groups during our sampling period, and periwinkle densities were consistently highest at moderately oiled sites where Spartina alterniflora aboveground biomass was highest. Periwinkle shell length linearly increased from a mean of 16.5 to 19.2 mm over the study period at reference sites. In contrast, shell lengths at moderately oiled and heavily oiled sites increased through month 48 after the spill, but then decreased. This decrease was associated with a decline in the relative abundance of large adults (shell length 21–26 mm) at oiled sites which was likely caused by chronic hydrocarbon toxicity or oil-induced effects on habitat quality or food resources. Overall, the recovery of S. alterniflora facilitated the recovery of fiddler crabs and periwinkles. However, our long-term record not only indicates that variation in periwinkle mean shell length and length-frequency distributions are sensitive indicators of the health and recovery of the marsh, but agrees with synoptic studies of vegetation and infaunal communities that full recovery of heavily oiled sites will take longer than 66 months.
format: application/pdf
format: text/html
creator: Donald R. Deis
creator: John W. Fleeger
creator: Stefan M. Bourgoin
creator: Irving A. Mendelssohn
creator: Qianxin Lin
creator: Aixin Hou
subject: Ecology
subject: Environmental Sciences
subject: Zoology
subject: Biosphere Interactions
subject: Ecotoxicology
description: doi:10.7717/peerj.3680
publisher: PeerJ Inc.
rights: © 2017 Deis et al.
abstract: Salt marshes in northern Barataria Bay, Louisiana, USA were oiled, sometimes heavily, in the aftermath of the Deepwater Horizon oil spill. Previous studies indicate that fiddler crabs (in the genus Uca) and the salt marsh periwinkle (Littoraria irrorata) were negatively impacted in the short term by the spill. Here, we detail longer-term effects and recovery from moderate and heavy oiling over a 3-year span, beginning 30 months after the spill. Although neither fiddler crab burrow density nor diameter differed between oiled and reference sites when combined across all sampling events, these traits differed among some individual sampling periods consistent with a pattern of lingering oiling impacts. Periwinkle density, however, increased in all oiling categories and shell-length groups during our sampling period, and periwinkle densities were consistently highest at moderately oiled sites where Spartina alterniflora aboveground biomass was highest. Periwinkle shell length linearly increased from a mean of 16.5 to 19.2 mm over the study period at reference sites. In contrast, shell lengths at moderately oiled and heavily oiled sites increased through month 48 after the spill, but then decreased. This decrease was associated with a decline in the relative abundance of large adults (shell length 21–26 mm) at oiled sites which was likely caused by chronic hydrocarbon toxicity or oil-induced effects on habitat quality or food resources. Overall, the recovery of S. alterniflora facilitated the recovery of fiddler crabs and periwinkles. However, our long-term record not only indicates that variation in periwinkle mean shell length and length-frequency distributions are sensitive indicators of the health and recovery of the marsh, but agrees with synoptic studies of vegetation and infaunal communities that full recovery of heavily oiled sites will take longer than 66 months.
bibliographic citation: Deis et al. (2017) Shoreline oiling effects and recovery of salt marsh macroinvertebrates from the Deepwater Horizon Oil Spill. PeerJ 5:e3680 https://doi.org/10.7717/peerj.3680
date submitted: 2015-11-01
date accepted: 2017-07-22
issued: 2017-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deis
  given name: Donald R.
author list: Agent
  family name: Fleeger
  given name: John W.
author list: Agent
  family name: Bourgoin
  given name: Stefan M.
author list: Agent
  family name: Mendelssohn
  given name: Irving A.
author list: Agent
  family name: Lin
  given name: Qianxin
author list: Agent
  family name: Hou
  given name: Aixin
doi: 10.7717/peerj.3680
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-16
copyright: ©2017 Deis et al.
attribution name: Deis et al.

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