PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Reproductive biology of little tunny Euthynnus alletteratus (Rafinesque, 1810) in the southwest Gulf of Mexico
items: Comparison of shallow-water seston among biogenic habitats on tidal flats
items: Prevalence of malocclusion and occlusal traits in the early mixed dentition in Shanghai, China
items: On the half-life of thiocyanate in the plasma of the marine fish Amphiprion ocellaris: implications for cyanide detection
items: Revision of the Late Jurassic deep-water teleosauroid crocodylomorph Teleosaurus megarhinus Hulke, 1871 and evidence of pelagic adaptations in Teleosauroidea
items: Behavioral responses around conspecific corpses in adult eastern gorillas (Gorilla beringei spp.)
items: Mapping-by-sequencing using NGS-based 3′-MACE-Seq reveals a new mutant allele of the essential nodulation gene Sym33 (IPD3) in pea (Pisum sativum L.)
items: Spatial variation in allometric growth of invasive lionfish has management implications
items: Epizootic ulcerative syndrome causes cutaneous dysbacteriosis in hybrid snakehead (Channa maculata♀ × Channa argus♂)
items: Mahalanobis distances and ecological niche modelling: correcting a chi-squared probability error

Reproductive biology of little tunny Euthynnus alletteratus (Rafinesque, 1810) in the southwest Gulf of Mexico
type: item
type: AcademicArticle
description: The aim of this study was to describe the reproductive dynamic of Euthynnus alletteratus in the southwest Gulf of Mexico. The annual variation of the volume fraction occupied by gametes and tissues in gonads were related with main body indexes, such as the gonadosomatic index (IG), the hepatosomatic index (IH), and the nutrition index (IN), and compared with the sea surface temperature. A total of 951 E. alletteratus individuals were sampled, where a sex ratio of 1:1 and a size interval strongly skewed towards organisms with a fork length (LF) of 36–40 cm were observed. The IG showed an increase from March to September with maximum values in April and July. Two clearly defined peaks were observed, and they were consistent with the histological analysis, where the percentage of ripe gametes predominated from April to September. The optimum thermal window for reproductive activity was from 24 to 28 °C. The size of first sex maturity was 34.35 cm of LF for males and 34.60 (LF) for females, without significant difference between sexes.
format: application/pdf
format: text/html
creator: Roberto Cruz-Castán
creator: César Meiners-Mandujano
creator: David Macías
creator: Lourdes Jiménez-Badillo
creator: Sergio Curiel-Ramírez
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.6558
publisher: PeerJ Inc.
rights: © 2019 Cruz-Castán et al.
abstract: The aim of this study was to describe the reproductive dynamic of Euthynnus alletteratus in the southwest Gulf of Mexico. The annual variation of the volume fraction occupied by gametes and tissues in gonads were related with main body indexes, such as the gonadosomatic index (IG), the hepatosomatic index (IH), and the nutrition index (IN), and compared with the sea surface temperature. A total of 951 E. alletteratus individuals were sampled, where a sex ratio of 1:1 and a size interval strongly skewed towards organisms with a fork length (LF) of 36–40 cm were observed. The IG showed an increase from March to September with maximum values in April and July. Two clearly defined peaks were observed, and they were consistent with the histological analysis, where the percentage of ripe gametes predominated from April to September. The optimum thermal window for reproductive activity was from 24 to 28 °C. The size of first sex maturity was 34.35 cm of LF for males and 34.60 (LF) for females, without significant difference between sexes.
bibliographic citation: Cruz-Castán et al. (2019) Reproductive biology of little tunny Euthynnus alletteratus (Rafinesque, 1810) in the southwest Gulf of Mexico. PeerJ 7:e6558 https://doi.org/10.7717/peerj.6558
date submitted: 2018-12-31
date accepted: 2019-02-01
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cruz-Castán
  given name: Roberto
author list: Agent
  family name: Meiners-Mandujano
  given name: César
author list: Agent
  family name: Macías
  given name: David
author list: Agent
  family name: Jiménez-Badillo
  given name: Lourdes
author list: Agent
  family name: Curiel-Ramírez
  given name: Sergio
doi: 10.7717/peerj.6558
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: © 2019 Cruz-Castán et al.
attribution name: Cruz-Castán et al.

Comparison of shallow-water seston among biogenic habitats on tidal flats
type: item
type: AcademicArticle
description: Aquatic structure-formers have the potential to establish mosaics of seston in shallow water if they modify the relative amounts of deposition (or filtration) and resuspension of particles. By sampling surface water adjacent to Lagrangian drifters traveling 0.1 to 2 m above the bottom, we tested the modification of seston in water masses flowing over two biogenic marine species (native eelgrass, Zostera marina; introduced oysters, Crassostrea gigas) in comparison to unstructured tidal flats. Water properties were examined at five intertidal sites in Washington State, USA, each with 27 drifts (three drifts at different stages of the tidal cycle in each of three patches of three habitat types; drift distance 116 m (109SD), duration 24 min (15SD)). At the initiation of each drift, habitat differences in water properties were already apparent: chlorophyll-a and total suspended solid (TSS) concentrations were greater in structured habitats than bare, and TSS was also inversely related to water depth. Water flowed more slowly across eelgrass than other habitat types. As water flowed across each habitat type, TSS generally increased, especially in shallow water, but without habitat differences; chlorophyll-a in these surface-water samples showed no consistent change during drifts. At higher TSS concentrations, quality in terms of organic content declined, and this relationship was not habitat-specific. However, quality in terms of chlorophyll-a concentration increased with TSS, as well as being greater in water over eelgrass than over other habitat types. These results support widespread mobilization of seston in shallow water ebbing or flooding across Washington State’s tidal flats, especially as water passes into patches of biogenic species.
format: application/pdf
format: text/html
creator: Jennifer L. Ruesink
creator: Cinde R. Donoghue
creator: Micah J. Horwith
creator: Alexander T. Lowe
creator: Alan C. Trimble
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Ecohydrology
description: doi:10.7717/peerj.6616
publisher: PeerJ Inc.
rights: © 2019 Ruesink et al.
abstract: Aquatic structure-formers have the potential to establish mosaics of seston in shallow water if they modify the relative amounts of deposition (or filtration) and resuspension of particles. By sampling surface water adjacent to Lagrangian drifters traveling 0.1 to 2 m above the bottom, we tested the modification of seston in water masses flowing over two biogenic marine species (native eelgrass, Zostera marina; introduced oysters, Crassostrea gigas) in comparison to unstructured tidal flats. Water properties were examined at five intertidal sites in Washington State, USA, each with 27 drifts (three drifts at different stages of the tidal cycle in each of three patches of three habitat types; drift distance 116 m (109SD), duration 24 min (15SD)). At the initiation of each drift, habitat differences in water properties were already apparent: chlorophyll-a and total suspended solid (TSS) concentrations were greater in structured habitats than bare, and TSS was also inversely related to water depth. Water flowed more slowly across eelgrass than other habitat types. As water flowed across each habitat type, TSS generally increased, especially in shallow water, but without habitat differences; chlorophyll-a in these surface-water samples showed no consistent change during drifts. At higher TSS concentrations, quality in terms of organic content declined, and this relationship was not habitat-specific. However, quality in terms of chlorophyll-a concentration increased with TSS, as well as being greater in water over eelgrass than over other habitat types. These results support widespread mobilization of seston in shallow water ebbing or flooding across Washington State’s tidal flats, especially as water passes into patches of biogenic species.
bibliographic citation: Ruesink et al. (2019) Comparison of shallow-water seston among biogenic habitats on tidal flats. PeerJ 7:e6616 https://doi.org/10.7717/peerj.6616
date submitted: 2018-09-19
date accepted: 2019-02-11
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ruesink
  given name: Jennifer L.
author list: Agent
  family name: Donoghue
  given name: Cinde R.
author list: Agent
  family name: Horwith
  given name: Micah J.
author list: Agent
  family name: Lowe
  given name: Alexander T.
author list: Agent
  family name: Trimble
  given name: Alan C.
doi: 10.7717/peerj.6616
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: ©2019 Ruesink et al.
attribution name: Ruesink et al.

Prevalence of malocclusion and occlusal traits in the early mixed dentition in Shanghai, China
type: item
type: AcademicArticle
description: Background Epidemiological data on malocclusion among Chinese children are scant. The aim of this study was to provide detailed information on the prevalence of malocclusion in early mixed dentition children in Shanghai, China. Methods A cross-sectional survey was conducted from September 2016 to April 2017, and 2,810 children aged 7- to 9- years were selected from 10 primary schools by cluster random sampling. Several occlusal parameters, including Angle molar relationship, overjet, overbite, open bite, anterior and posterior crossbite, midline displacement, scissors bite, and teeth crowding and spacing, were clinically registered by five calibrated orthodontic dentists. Results We found that 79.4% children presented one or more occlusal anomalies. Angle Class I, Class II and Class III molar relationship were recorded in 42.3%, 50.9% and 5.9% of the sample, respectively. The proportion of Class III increased from 5.0% at age 7 to 7.8% at age 9. In the sagittal plane, increased overjet >3 mm was observed in 40.8% subjects, while the prevalence of severe overjet (>8 mm), anterior edge-to-edge (zero overjet) and anterior crossbite were 5.2%, 8.1% and 10.5%, respectively. Vertically, deep overbite >2/3 overlap was found in 6.2% of the children and open bite in 4.3%. Boys exhibited a higher rate of overbite than girls. For the transversal occlusal anomalies, 36.1% of the children had a midline displacement, which was followed by posterior crossbite (2.6%) and scissors bite (1.0%). Teeth space discrepancies were also common anomalies and anterior crowding (>2 mm) affecting 28.4% of the children, while anterior spacing (>4 mm) affecting 9.5%. Girls showed a higher prevalence of anterior crowding and a lower frequency of teeth spacing than boys. Conclusions Our study demonstrated that malocclusion is prevalent among children in the early mixed dentition, and more health resources should be warranted to meet the challenge of prevention or early intervention of malocclusion.
format: application/pdf
format: text/html
creator: Xin Yu
creator: Hao Zhang
creator: Liangyan Sun
creator: Jie Pan
creator: Yuehua Liu
creator: Li Chen
subject: Dentistry
subject: Epidemiology
subject: Pediatrics
description: doi:10.7717/peerj.6630
publisher: PeerJ Inc.
rights: © 2019 Yu et al.
abstract: Background Epidemiological data on malocclusion among Chinese children are scant. The aim of this study was to provide detailed information on the prevalence of malocclusion in early mixed dentition children in Shanghai, China. Methods A cross-sectional survey was conducted from September 2016 to April 2017, and 2,810 children aged 7- to 9- years were selected from 10 primary schools by cluster random sampling. Several occlusal parameters, including Angle molar relationship, overjet, overbite, open bite, anterior and posterior crossbite, midline displacement, scissors bite, and teeth crowding and spacing, were clinically registered by five calibrated orthodontic dentists. Results We found that 79.4% children presented one or more occlusal anomalies. Angle Class I, Class II and Class III molar relationship were recorded in 42.3%, 50.9% and 5.9% of the sample, respectively. The proportion of Class III increased from 5.0% at age 7 to 7.8% at age 9. In the sagittal plane, increased overjet >3 mm was observed in 40.8% subjects, while the prevalence of severe overjet (>8 mm), anterior edge-to-edge (zero overjet) and anterior crossbite were 5.2%, 8.1% and 10.5%, respectively. Vertically, deep overbite >2/3 overlap was found in 6.2% of the children and open bite in 4.3%. Boys exhibited a higher rate of overbite than girls. For the transversal occlusal anomalies, 36.1% of the children had a midline displacement, which was followed by posterior crossbite (2.6%) and scissors bite (1.0%). Teeth space discrepancies were also common anomalies and anterior crowding (>2 mm) affecting 28.4% of the children, while anterior spacing (>4 mm) affecting 9.5%. Girls showed a higher prevalence of anterior crowding and a lower frequency of teeth spacing than boys. Conclusions Our study demonstrated that malocclusion is prevalent among children in the early mixed dentition, and more health resources should be warranted to meet the challenge of prevention or early intervention of malocclusion.
bibliographic citation: Yu et al. (2019) Prevalence of malocclusion and occlusal traits in the early mixed dentition in Shanghai, China. PeerJ 7:e6630 https://doi.org/10.7717/peerj.6630
date submitted: 2018-07-31
date accepted: 2019-02-15
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Xin
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: Sun
  given name: Liangyan
author list: Agent
  family name: Pan
  given name: Jie
author list: Agent
  family name: Liu
  given name: Yuehua
author list: Agent
  family name: Chen
  given name: Li
doi: 10.7717/peerj.6630
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: ©2019 Yu et al.
attribution name: Yu et al.

On the half-life of thiocyanate in the plasma of the marine fish Amphiprion ocellaris: implications for cyanide detection
type: item
type: AcademicArticle
description: The illegal practice of using cyanide (CN) as a stunning agent to collect fish for both the marine aquarium and live fish food trades has been used throughout the Indo-Pacific for over 50 years. CN fishing is destructive to all life forms within the coral reef ecosystems where it is used and is certainly one of many anthropogenic activities that have led to 95% of the reefs in the Indo-Pacific being labeled at risk for degradation and loss. A field-deployable test for detecting fish caught using CN would assist in combating the use of this destructive practice, however, no reliable and robust test exists. Further, there is little toxicokinetic data available on marine fish to support the development of such a test, yet such data is critical to establishing the concentration range and time scale over which such a test would be viable. This study presents the first direct measurement of the half-life of the metabolite thiocyanate (SCN) after pulsed exposure to CN in a marine fish. SCN was measured in the plasma of Amphiprion ocellaris after exposure to 50 ppm CN for three exposure times (20, 45, and 60 s) using HPLC-UV and a C30 column pre-treated with polyethylene glycol. Plasma SCN levels observed are dose-dependent, reflecting a longer time for conversion of CN to SCN as the dose of CN increases. SCN plasma levels reached a maximum concentration (1.2–2.3 ppm) 12–20 h after exposure to CN. The half-life for the elimination of SCN was 1.01 ± 0.26 days for 45 s exposure and 0.44 ± 0.15 days for 20 s exposure. Fish were also directly exposed to SCN (100 ppm for 11 days) and the observed half-life for SCN elimination was 0.35 ± 0.07 days. Plasma SCN levels did not return to control levels, even after 41 days when exposed to CN but did return to control levels after 48 days when exposed to SCN. The similar half-lives observed for CN and SCN exposure suggests that SCN exposure can be used as a proxy for measuring the rate of SCN elimination following CN exposure. In order…
format: application/pdf
format: text/html
creator: Nancy E. Breen
creator: J. Alexander Bonanno
creator: Sara Hunt
creator: Julia Grossman
creator: Jordan Brown
creator: Hannah Nolte
creator: Andrew L. Rhyne
subject: Conservation Biology
subject: Marine Biology
subject: Toxicology
subject: Ecotoxicology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.6644
publisher: PeerJ Inc.
rights: © 2019 Breen et al.
abstract: The illegal practice of using cyanide (CN) as a stunning agent to collect fish for both the marine aquarium and live fish food trades has been used throughout the Indo-Pacific for over 50 years. CN fishing is destructive to all life forms within the coral reef ecosystems where it is used and is certainly one of many anthropogenic activities that have led to 95% of the reefs in the Indo-Pacific being labeled at risk for degradation and loss. A field-deployable test for detecting fish caught using CN would assist in combating the use of this destructive practice, however, no reliable and robust test exists. Further, there is little toxicokinetic data available on marine fish to support the development of such a test, yet such data is critical to establishing the concentration range and time scale over which such a test would be viable. This study presents the first direct measurement of the half-life of the metabolite thiocyanate (SCN) after pulsed exposure to CN in a marine fish. SCN was measured in the plasma of Amphiprion ocellaris after exposure to 50 ppm CN for three exposure times (20, 45, and 60 s) using HPLC-UV and a C30 column pre-treated with polyethylene glycol. Plasma SCN levels observed are dose-dependent, reflecting a longer time for conversion of CN to SCN as the dose of CN increases. SCN plasma levels reached a maximum concentration (1.2–2.3 ppm) 12–20 h after exposure to CN. The half-life for the elimination of SCN was 1.01 ± 0.26 days for 45 s exposure and 0.44 ± 0.15 days for 20 s exposure. Fish were also directly exposed to SCN (100 ppm for 11 days) and the observed half-life for SCN elimination was 0.35 ± 0.07 days. Plasma SCN levels did not return to control levels, even after 41 days when exposed to CN but did return to control levels after 48 days when exposed to SCN. The similar half-lives observed for CN and SCN exposure suggests that SCN exposure can be used as a proxy for measuring the rate of SCN elimination following CN exposure. In order…
bibliographic citation: Breen et al. (2019) On the half-life of thiocyanate in the plasma of the marine fish Amphiprion ocellaris: implications for cyanide detection. PeerJ 7:e6644 https://doi.org/10.7717/peerj.6644
date submitted: 2018-10-18
date accepted: 2019-02-19
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Breen
  given name: Nancy E.
author list: Agent
  family name: Bonanno
  given name: J. Alexander
author list: Agent
  family name: Hunt
  given name: Sara
author list: Agent
  family name: Grossman
  given name: Julia
author list: Agent
  family name: Brown
  given name: Jordan
author list: Agent
  family name: Nolte
  given name: Hannah
author list: Agent
  family name: Rhyne
  given name: Andrew L.
doi: 10.7717/peerj.6644
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: © 2019 Breen et al.
attribution name: Breen et al.

Revision of the Late Jurassic deep-water teleosauroid crocodylomorph Teleosaurus megarhinus Hulke, 1871 and evidence of pelagic adaptations in Teleosauroidea
type: item
type: AcademicArticle
description: Teleosauroids were a successful group of semi-aquatic crocodylomorphs that were an integral part of coastal marine/lagoonal faunas during the Jurassic. Their fossil record suggests that the group declined in diversity and abundance in deep water deposits during the Late Jurassic. One of the few known teleosauroid species from the deeper water horizons of the well-known Kimmeridge Clay Formation is ‘Teleosaurus’ megarhinus Hulke, 1871, a poorly studied, gracile longirostrine form. The holotype is an incomplete snout from the Aulacostephanus autissiodorensis Sub-Boreal ammonite Zone of Kimmeridge, England. The only other referred specimen is an almost complete skull from the slightly older A. eudoxus Sub-Boreal ammonite Zone of Quercy, France. Recently, the validity of this species has been called into question. Here we re-describe the holotype as well as the referred French specimen and another incomplete teleosauroid, DORCM G.05067i-v (an anterior rostrum with three osteoderms and an isolated tooth crown), from the same horizon and locality as the holotype. We demonstrate that all specimens are referable to ‘Teleosaurus’ megarhinus and that the species is indeed a valid taxon, which we assign to a new monotypic genus, Bathysuchus. In our phylogenetic analysis, the latest iteration of the ongoing Crocodylomorph SuperMatrix Project, Bathysuchus megarhinus is found as sister taxon to Aeolodon priscus within a subclade containing Mycterosuchus nasutus and Teleosaurus cadomensis. Notably Bathysuchus has an extreme reduction in dermatocranial ornamentation and osteoderm size, thickness and ornamentation. These features are mirrored in Aeolodon priscus, a species with a well-preserved post-cranial skeleton and a similar shallow and inconspicuous dermal ornamentation. Based on these morphological features, and sedimentological evidence, we hypothesise that the Bathysuchus + Aeolodon clade is the first known teleosauroid lineage that evolved a more pelagic lifestyle.
format: application/pdf
format: text/html
creator: Davide Foffa
creator: Michela M. Johnson
creator: Mark T. Young
creator: Lorna Steel
creator: Stephen L. Brusatte
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6646
publisher: PeerJ Inc.
rights: © 2019 Foffa et al.
abstract: Teleosauroids were a successful group of semi-aquatic crocodylomorphs that were an integral part of coastal marine/lagoonal faunas during the Jurassic. Their fossil record suggests that the group declined in diversity and abundance in deep water deposits during the Late Jurassic. One of the few known teleosauroid species from the deeper water horizons of the well-known Kimmeridge Clay Formation is ‘Teleosaurus’ megarhinus Hulke, 1871, a poorly studied, gracile longirostrine form. The holotype is an incomplete snout from the Aulacostephanus autissiodorensis Sub-Boreal ammonite Zone of Kimmeridge, England. The only other referred specimen is an almost complete skull from the slightly older A. eudoxus Sub-Boreal ammonite Zone of Quercy, France. Recently, the validity of this species has been called into question. Here we re-describe the holotype as well as the referred French specimen and another incomplete teleosauroid, DORCM G.05067i-v (an anterior rostrum with three osteoderms and an isolated tooth crown), from the same horizon and locality as the holotype. We demonstrate that all specimens are referable to ‘Teleosaurus’ megarhinus and that the species is indeed a valid taxon, which we assign to a new monotypic genus, Bathysuchus. In our phylogenetic analysis, the latest iteration of the ongoing Crocodylomorph SuperMatrix Project, Bathysuchus megarhinus is found as sister taxon to Aeolodon priscus within a subclade containing Mycterosuchus nasutus and Teleosaurus cadomensis. Notably Bathysuchus has an extreme reduction in dermatocranial ornamentation and osteoderm size, thickness and ornamentation. These features are mirrored in Aeolodon priscus, a species with a well-preserved post-cranial skeleton and a similar shallow and inconspicuous dermal ornamentation. Based on these morphological features, and sedimentological evidence, we hypothesise that the Bathysuchus + Aeolodon clade is the first known teleosauroid lineage that evolved a more pelagic lifestyle.
bibliographic citation: Foffa et al. (2019) Revision of the Late Jurassic deep-water teleosauroid crocodylomorph Teleosaurus megarhinus Hulke, 1871 and evidence of pelagic adaptations in Teleosauroidea. PeerJ 7:e6646 https://doi.org/10.7717/peerj.6646
date submitted: 2018-03-12
date accepted: 2019-02-19
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Foffa
  given name: Davide
author list: Agent
  family name: Johnson
  given name: Michela M.
author list: Agent
  family name: Young
  given name: Mark T.
author list: Agent
  family name: Steel
  given name: Lorna
author list: Agent
  family name: Brusatte
  given name: Stephen L.
doi: 10.7717/peerj.6646
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: ©2019 Foffa et al.
attribution name: Foffa et al.

Behavioral responses around conspecific corpses in adult eastern gorillas (Gorilla beringei spp.)
type: item
type: AcademicArticle
description: Humans were once considered unique in having a concept of death but a growing number of observations of animal responses to dying and dead conspecifics suggests otherwise. Complex arrays of behaviors have been described ranging from corpse removal and burial among social insects to quiet attendance and caregiving among elephants and primates. Less frequently described, however, are behavioral responses of individuals from different age/sex classes or social position toward the death of conspecifics. We describe behavioral responses of mountain gorillas (Gorilla beringei beringei) to the deaths of a dominant silverback and a dominant adult female from the same social group in Volcanoes National Park in Rwanda and the responses of Grauer’s gorillas (Gorilla b. graueri) to the corpse of an extra-group silverback in Kahuzi-Biega National Park, Democratic Republic of Congo. In gorillas, interactions between groups or with a lone silverback often result in avoidance or aggression. We predicted that: (i) more individuals should interact with the corpses of same-group members than with the corpse of the extra-group silverback; (ii) adult females with infants should avoid the corpse of the extra-group silverback; and (iii) in the mountain gorilla cases, individuals that shared close social relationships with the dead individual should spend more time with the corpse than other individuals in the group. We used a combination of detailed qualitative reports, photos, and videos to describe all occurrences of affiliative/investigative and agonistic behaviors observed at the corpses. We observed similar responses toward the corpses of group and extra-group individuals. Animals in all three cases showed a variety of affiliative/investigative and agonistic behaviors directed to the corpses. Animals of all age/sex classes interacted with the corpses in affiliative/investigative ways but there was a notable absence of all adult females at the corpse of the extra-group silverback. In …
format: application/pdf
format: text/html
creator: Amy Porter
creator: Winnie Eckardt
creator: Veronica Vecellio
creator: Katerina Guschanski
creator: Peter Philip Niehoff
creator: Urbain Ngobobo-As-Ibungu
creator: Radar Nishuli Pekeyake
creator: Tara Stoinski
creator: Damien Caillaud
subject: Animal Behavior
subject: Anthropology
subject: Zoology
description: doi:10.7717/peerj.6655
publisher: PeerJ Inc.
rights: © 2019 Porter et al.
abstract: Humans were once considered unique in having a concept of death but a growing number of observations of animal responses to dying and dead conspecifics suggests otherwise. Complex arrays of behaviors have been described ranging from corpse removal and burial among social insects to quiet attendance and caregiving among elephants and primates. Less frequently described, however, are behavioral responses of individuals from different age/sex classes or social position toward the death of conspecifics. We describe behavioral responses of mountain gorillas (Gorilla beringei beringei) to the deaths of a dominant silverback and a dominant adult female from the same social group in Volcanoes National Park in Rwanda and the responses of Grauer’s gorillas (Gorilla b. graueri) to the corpse of an extra-group silverback in Kahuzi-Biega National Park, Democratic Republic of Congo. In gorillas, interactions between groups or with a lone silverback often result in avoidance or aggression. We predicted that: (i) more individuals should interact with the corpses of same-group members than with the corpse of the extra-group silverback; (ii) adult females with infants should avoid the corpse of the extra-group silverback; and (iii) in the mountain gorilla cases, individuals that shared close social relationships with the dead individual should spend more time with the corpse than other individuals in the group. We used a combination of detailed qualitative reports, photos, and videos to describe all occurrences of affiliative/investigative and agonistic behaviors observed at the corpses. We observed similar responses toward the corpses of group and extra-group individuals. Animals in all three cases showed a variety of affiliative/investigative and agonistic behaviors directed to the corpses. Animals of all age/sex classes interacted with the corpses in affiliative/investigative ways but there was a notable absence of all adult females at the corpse of the extra-group silverback. In …
bibliographic citation: Porter et al. (2019) Behavioral responses around conspecific corpses in adult eastern gorillas (Gorilla beringei spp.). PeerJ 7:e6655 https://doi.org/10.7717/peerj.6655
date submitted: 2018-06-06
date accepted: 2019-02-20
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Porter
  given name: Amy
author list: Agent
  family name: Eckardt
  given name: Winnie
author list: Agent
  family name: Vecellio
  given name: Veronica
author list: Agent
  family name: Guschanski
  given name: Katerina
author list: Agent
  family name: Niehoff
  given name: Peter Philip
author list: Agent
  family name: Ngobobo-As-Ibungu
  given name: Urbain
author list: Agent
  family name: Nishuli Pekeyake
  given name: Radar
author list: Agent
  family name: Stoinski
  given name: Tara
author list: Agent
  family name: Caillaud
  given name: Damien
doi: 10.7717/peerj.6655
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: ©2019 Porter et al.
attribution name: Porter et al.

Mapping-by-sequencing using NGS-based 3′-MACE-Seq reveals a new mutant allele of the essential nodulation gene Sym33 (IPD3) in pea (Pisum sativum L.)
type: item
type: AcademicArticle
description: Large collections of pea symbiotic mutants were accumulated in the 1990s, but the causal genes for a large portion of the mutations are still not identified due to the complexity of the task. We applied a Mapping-by-Sequencing approach including Bulk Segregant Analysis and Massive Analysis of cDNA Ends (MACE-Seq) sequencing technology for genetic mapping the Sym11 gene of pea which controls the formation of symbioses with both nodule bacteria and arbuscular-mycorrhizal fungi. For mapping we developed an F2-population from the cross between pea line N24 carrying the mutant allele of sym11 and the wild type NGB1238 (=JI0073) line. Sequencing libraries were prepared from bulks of 20 plants with mutant and 12 with wild-type phenotype. MACE-Seq differential gene expression analysis between mutant-phenotype and wild-type-phenotype bulks revealed 2,235 genes, of which 514 (23%) were up-regulated and 1,721 (77%) were down-regulated in plant roots inoculated with rhizobia as a consequence of sym11 mutation. MACE-Seq also detected single nucleotide variants between bulks in 217 pea genes. Using a novel mathematical model we calculated the recombination frequency (RF) between the Sym11 gene and these 217 polymorphic genes. Six genes with the lowest RF were converted into CAPS or dCAPS markers and genetically mapped on the complete mapping population of 108 F2-plants which confirmed their tight linkage to Sym11 and to each other. The Medicago truncatula Gaertn. (Mt) homologs of these genes are located in a distinct region of Mt chromosome 5, which corresponds to linkage group I of pea. Among 94 candidate genes from this region only one was down-regulated—the pea Sym33 homolog of the Mt IPD3 gene which is essential for nodulation. Sequencing of the Sym33 allele of the N24 (sym11) mutant revealed a single nucleotide deletion (c.C319del) in its third exon resulting in a codon shift in the open reading frame and premature translation termination. Thus, we identified a novel mutant …
format: application/pdf
format: text/html
creator: Aleksandr I. Zhernakov
creator: Oksana Y. Shtark
creator: Olga A. Kulaeva
creator: Jaroslava V. Fedorina
creator: Alexey M. Afonin
creator: Anna B. Kitaeva
creator: Viktor E. Tsyganov
creator: Fabian Afonso-Grunz
creator: Klaus Hoffmeier
creator: Björn Rotter
creator: Peter Winter
creator: Igor A. Tikhonovich
creator: Vladimir A. Zhukov
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6662
publisher: PeerJ Inc.
rights: © 2019 Zhernakov et al.
abstract: Large collections of pea symbiotic mutants were accumulated in the 1990s, but the causal genes for a large portion of the mutations are still not identified due to the complexity of the task. We applied a Mapping-by-Sequencing approach including Bulk Segregant Analysis and Massive Analysis of cDNA Ends (MACE-Seq) sequencing technology for genetic mapping the Sym11 gene of pea which controls the formation of symbioses with both nodule bacteria and arbuscular-mycorrhizal fungi. For mapping we developed an F2-population from the cross between pea line N24 carrying the mutant allele of sym11 and the wild type NGB1238 (=JI0073) line. Sequencing libraries were prepared from bulks of 20 plants with mutant and 12 with wild-type phenotype. MACE-Seq differential gene expression analysis between mutant-phenotype and wild-type-phenotype bulks revealed 2,235 genes, of which 514 (23%) were up-regulated and 1,721 (77%) were down-regulated in plant roots inoculated with rhizobia as a consequence of sym11 mutation. MACE-Seq also detected single nucleotide variants between bulks in 217 pea genes. Using a novel mathematical model we calculated the recombination frequency (RF) between the Sym11 gene and these 217 polymorphic genes. Six genes with the lowest RF were converted into CAPS or dCAPS markers and genetically mapped on the complete mapping population of 108 F2-plants which confirmed their tight linkage to Sym11 and to each other. The Medicago truncatula Gaertn. (Mt) homologs of these genes are located in a distinct region of Mt chromosome 5, which corresponds to linkage group I of pea. Among 94 candidate genes from this region only one was down-regulated—the pea Sym33 homolog of the Mt IPD3 gene which is essential for nodulation. Sequencing of the Sym33 allele of the N24 (sym11) mutant revealed a single nucleotide deletion (c.C319del) in its third exon resulting in a codon shift in the open reading frame and premature translation termination. Thus, we identified a novel mutant …
bibliographic citation: Zhernakov et al. (2019) Mapping-by-sequencing using NGS-based 3′-MACE-Seq reveals a new mutant allele of the essential nodulation gene Sym33 (IPD3) in pea (Pisum sativum L.). PeerJ 7:e6662 https://doi.org/10.7717/peerj.6662
date submitted: 2018-12-02
date accepted: 2019-02-20
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhernakov
  given name: Aleksandr I.
author list: Agent
  family name: Shtark
  given name: Oksana Y.
author list: Agent
  family name: Kulaeva
  given name: Olga A.
author list: Agent
  family name: Fedorina
  given name: Jaroslava V.
author list: Agent
  family name: Afonin
  given name: Alexey M.
author list: Agent
  family name: Kitaeva
  given name: Anna B.
author list: Agent
  family name: Tsyganov
  given name: Viktor E.
author list: Agent
  family name: Afonso-Grunz
  given name: Fabian
author list: Agent
  family name: Hoffmeier
  given name: Klaus
author list: Agent
  family name: Rotter
  given name: Björn
author list: Agent
  family name: Winter
  given name: Peter
author list: Agent
  family name: Tikhonovich
  given name: Igor A.
author list: Agent
  family name: Zhukov
  given name: Vladimir A.
doi: 10.7717/peerj.6662
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: © 2019 Zhernakov et al.
attribution name: Zhernakov et al.

Spatial variation in allometric growth of invasive lionfish has management implications
type: item
type: AcademicArticle
description: Lionfish (Pterois volitans/miles) are an invasive species in the Western Atlantic and the Caribbean. Improving management of invasive lionfish populations requires accurate total biomass estimates, which depend on accurate estimates of allometric growth; sedentary species like lionfish often exhibit high levels of spatial variation in life history characteristics. We reviewed 17 published length-weight relationships for lionfish taken throughout their invasive range and found regional differences that led to significant misestimates when calculating weight from length observations. The spatial pattern we observed is consistent with findings from other studies focused on genetics or length-at-age. Here, the use of ex situ parameter values resulted in total biomass estimates between 76.2% and 140% of true observed biomass, and up to a threefold under- or overestimation of total weight for an individual organism. These findings can have implications for management in terms of predicting effects on local ecosystems, evaluating the effectiveness of removal programs, or estimating biomass available for harvest.
format: application/pdf
format: text/html
creator: Juan Carlos Villaseñor-Derbez
creator: Sean Fitzgerald
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
subject: Population Biology
description: doi:10.7717/peerj.6667
publisher: PeerJ Inc.
rights: © 2019 Villaseñor-Derbez and Fitzgerald
abstract: Lionfish (Pterois volitans/miles) are an invasive species in the Western Atlantic and the Caribbean. Improving management of invasive lionfish populations requires accurate total biomass estimates, which depend on accurate estimates of allometric growth; sedentary species like lionfish often exhibit high levels of spatial variation in life history characteristics. We reviewed 17 published length-weight relationships for lionfish taken throughout their invasive range and found regional differences that led to significant misestimates when calculating weight from length observations. The spatial pattern we observed is consistent with findings from other studies focused on genetics or length-at-age. Here, the use of ex situ parameter values resulted in total biomass estimates between 76.2% and 140% of true observed biomass, and up to a threefold under- or overestimation of total weight for an individual organism. These findings can have implications for management in terms of predicting effects on local ecosystems, evaluating the effectiveness of removal programs, or estimating biomass available for harvest.
bibliographic citation: Villaseñor-Derbez et al. (2019) Spatial variation in allometric growth of invasive lionfish has management implications. PeerJ 7:e6667 https://doi.org/10.7717/peerj.6667
date submitted: 2018-11-09
date accepted: 2019-02-21
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Villaseñor-Derbez
  given name: Juan Carlos
author list: Agent
  family name: Fitzgerald
  given name: Sean
doi: 10.7717/peerj.6667
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: ©2019 Villaseñor-Derbez and Fitzgerald
attribution name: Villaseñor-Derbez and Fitzgerald

Epizootic ulcerative syndrome causes cutaneous dysbacteriosis in hybrid snakehead (Channa maculata♀ × Channa argus♂)
type: item
type: AcademicArticle
description: Cutaneous microbiota play an important role in protecting fish against pathogens. Aphanomyces infection causes epizootic ulcerative syndrome (EUS) in fish, and by perturbing the integrity of the cutaneous microbiota, increases the potential for infection by pathogenic bacteria. However, whether the composition of the cutaneous microbiota is altered in fish with EUS, and if so, which species are changed and how this might influence infected fish, is still largely unclear. Considering the importance of cutaneous microbiota in maintaining host health, we hypothesized that Aphanomyces infection significantly enhances the presence of certain bacterial pathogens in the cutaneous microbiota and causes cutaneous dysbacteriosis. To test this hypothesis, we compared the cutaneous microbiota compositions of hybrid snakehead (Channa maculata♀ × Channa argus♂) with and without Aphanomyces infection using Illumina Miseq sequencing of the 16S rRNA gene. Our results showed that the cutaneous microbiota of hybrid snakehead were significantly altered subsequent to EUS infection and that the numbers of potentially pathogenic bacteria classified into the genera Anaerosinus, Anaerovorax, Dorea, and Clostridium were significantly enhanced in the cutaneous microbiota of hybrid snakehead with EUS, whereas bacteria classified into the genera Arthrobacter, Dysgonomonas, Anoxybacillus, Bacillus, Solibacillus, Carnobacterium, Lactococcus, Streptococcus, Achromobacter, Polynucleobacter, Vogesella, and Pseudomonas were significantly reduced. These results imply that treatment for EUS should not only take into consideration the control of Aphanomyces reproduction but should also focus on regulating the cutaneous microbiota of infected fish.
format: application/pdf
format: text/html
creator: Zhifei Li
creator: Guangjun Wang
creator: Kai Zhang
creator: Wangbao Gong
creator: Ermeng Yu
creator: Jingjing Tian
creator: Jun Xie
creator: Deguang Yu
subject: Aquaculture, Fisheries and Fish Science
subject: Microbiology
description: doi:10.7717/peerj.6674
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Cutaneous microbiota play an important role in protecting fish against pathogens. Aphanomyces infection causes epizootic ulcerative syndrome (EUS) in fish, and by perturbing the integrity of the cutaneous microbiota, increases the potential for infection by pathogenic bacteria. However, whether the composition of the cutaneous microbiota is altered in fish with EUS, and if so, which species are changed and how this might influence infected fish, is still largely unclear. Considering the importance of cutaneous microbiota in maintaining host health, we hypothesized that Aphanomyces infection significantly enhances the presence of certain bacterial pathogens in the cutaneous microbiota and causes cutaneous dysbacteriosis. To test this hypothesis, we compared the cutaneous microbiota compositions of hybrid snakehead (Channa maculata♀ × Channa argus♂) with and without Aphanomyces infection using Illumina Miseq sequencing of the 16S rRNA gene. Our results showed that the cutaneous microbiota of hybrid snakehead were significantly altered subsequent to EUS infection and that the numbers of potentially pathogenic bacteria classified into the genera Anaerosinus, Anaerovorax, Dorea, and Clostridium were significantly enhanced in the cutaneous microbiota of hybrid snakehead with EUS, whereas bacteria classified into the genera Arthrobacter, Dysgonomonas, Anoxybacillus, Bacillus, Solibacillus, Carnobacterium, Lactococcus, Streptococcus, Achromobacter, Polynucleobacter, Vogesella, and Pseudomonas were significantly reduced. These results imply that treatment for EUS should not only take into consideration the control of Aphanomyces reproduction but should also focus on regulating the cutaneous microbiota of infected fish.
bibliographic citation: Li et al. (2019) Epizootic ulcerative syndrome causes cutaneous dysbacteriosis in hybrid snakehead (Channa maculata♀ × Channa argus♂). PeerJ 7:e6674 https://doi.org/10.7717/peerj.6674
date submitted: 2018-11-05
date accepted: 2019-02-23
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhifei
author list: Agent
  family name: Wang
  given name: Guangjun
author list: Agent
  family name: Zhang
  given name: Kai
author list: Agent
  family name: Gong
  given name: Wangbao
author list: Agent
  family name: Yu
  given name: Ermeng
author list: Agent
  family name: Tian
  given name: Jingjing
author list: Agent
  family name: Xie
  given name: Jun
author list: Agent
  family name: Yu
  given name: Deguang
doi: 10.7717/peerj.6674
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: © 2019 Li et al.
attribution name: Li et al.

Mahalanobis distances and ecological niche modelling: correcting a chi-squared probability error
type: item
type: AcademicArticle
description: The Mahalanobis distance is a statistical technique that can be used to measure how distant a point is from the centre of a multivariate normal distribution. By measuring Mahalanobis distances in environmental space ecologists have also used the technique to model: ecological niches, habitat suitability, species distributions, and resource selection functions. Unfortunately, the original description of the Mahalanobis distance technique for ecological modelling contained an error describing how Mahalanobis distances could be converted into probabilities using a chi-squared distribution. This error has been repeated in the literature, and is present in popular modelling software. In the hope of correcting this error to maximise the potential application of the Mahalanobis distance technique within the ecological modelling community, I explain how Mahalanobis distances are calculated, and through a virtual ecology experiment demonstrate how to correctly produce probabilities and discuss the implications of the error for previous Mahalanobis distance studies.
format: application/pdf
format: text/html
creator: Thomas R. Etherington
subject: Biogeography
subject: Ecology
subject: Statistics
description: doi:10.7717/peerj.6678
publisher: PeerJ Inc.
rights: © 2019 Etherington
abstract: The Mahalanobis distance is a statistical technique that can be used to measure how distant a point is from the centre of a multivariate normal distribution. By measuring Mahalanobis distances in environmental space ecologists have also used the technique to model: ecological niches, habitat suitability, species distributions, and resource selection functions. Unfortunately, the original description of the Mahalanobis distance technique for ecological modelling contained an error describing how Mahalanobis distances could be converted into probabilities using a chi-squared distribution. This error has been repeated in the literature, and is present in popular modelling software. In the hope of correcting this error to maximise the potential application of the Mahalanobis distance technique within the ecological modelling community, I explain how Mahalanobis distances are calculated, and through a virtual ecology experiment demonstrate how to correctly produce probabilities and discuss the implications of the error for previous Mahalanobis distance studies.
bibliographic citation: Etherington (2019) Mahalanobis distances and ecological niche modelling: correcting a chi-squared probability error. PeerJ 7:e6678 https://doi.org/10.7717/peerj.6678
date submitted: 2019-01-09
date accepted: 2019-02-25
issued: 2019-04-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Etherington
  given name: Thomas R.
doi: 10.7717/peerj.6678
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-02
copyright: ©2019 Etherington
attribution name: Etherington

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