PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA
items: Effects of afforestation on water resource variations in the Inner Mongolian Plateau
items: Neck mobility in the Jurassic plesiosaur Cryptoclidus eurymerus: finite element analysis as a new approach to understanding the cervical skeleton in fossil vertebrates
items: Short-term vasoactive agent treatment driven by physicians’ preference in acute esophageal variceal bleeding in a tertiary center
items: Spatial genetic structure in Pinus cembroides Zucc. at population and landscape levels in central and northern Mexico
items: Enforced symmetry: the necessity of symmetric waxing and waning
items: A new alligatoroid from the Eocene of Vietnam highlights an extinct Asian clade independent from extant Alligator sinensis
items: L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus
items: Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin
items: Prey selectivity and the effect of diet on growth and development of a dragonfly, Sympetrum sanguineum

Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA
type: item
type: AcademicArticle
description: Mine tailing disasters have occurred worldwide and contemporary release of tailings of large proportions raise concerns of the chronic impacts that trace metals may have on the aquatic biodiversity. Environmental metabarcoding (eDNA) offers an as yet poorly explored opportunity for biological monitoring of impacted aquatic ecosystems from mine tailings and contaminated sediments. eDNA has been increasingly recognized to be an effective method to detect previously unrecognized small-sized Metazoan taxa, but their ecological responses to environmental pollution has not been assessed by metabarcoding. Here, we evaluated chronic effects of trace metal contamination from sediment eDNA of the Rio Doce estuary, 1.7 years after the Samarco mine tailing disaster, which released over 40 million m3 of iron tailings in the Rio Doce river basin. We identified 123 new sequence variants environmental taxonomic units (eOTUs) of benthic taxa and an assemblage composition dominated by Nematoda, Crustacea and Platyhelminthes; typical of other estuarine ecosystems. We detected environmental filtering on the meiofaunal assemblages and multivariate analysis revealed strong influence of Fe contamination, supporting chronic impacts from mine tailing deposition in the estuary. This was in contrast to environmental filtering of meiofaunal assemblages of non-polluted estuaries. Here, we suggest that the eDNA metabarcoding technique provides an opportunity to fill up biodiversity gaps in coastal marine ecology and may become a valid method for long term monitoring studies in mine tailing disasters and estuarine ecosystems with high trace metals content.
format: application/pdf
format: text/html
creator: Angelo F. Bernardino
creator: Fabiano S. Pais
creator: Louisi S. Oliveira
creator: Fabricio A. Gabriel
creator: Tiago O. Ferreira
creator: Hermano M. Queiroz
creator: Ana Carolina A. Mazzuco
subject: Environmental Impacts
subject: Biological Oceanography
description: doi:10.7717/peerj.8042
publisher: PeerJ Inc.
rights: © 2019 Bernardino et al.
abstract: Mine tailing disasters have occurred worldwide and contemporary release of tailings of large proportions raise concerns of the chronic impacts that trace metals may have on the aquatic biodiversity. Environmental metabarcoding (eDNA) offers an as yet poorly explored opportunity for biological monitoring of impacted aquatic ecosystems from mine tailings and contaminated sediments. eDNA has been increasingly recognized to be an effective method to detect previously unrecognized small-sized Metazoan taxa, but their ecological responses to environmental pollution has not been assessed by metabarcoding. Here, we evaluated chronic effects of trace metal contamination from sediment eDNA of the Rio Doce estuary, 1.7 years after the Samarco mine tailing disaster, which released over 40 million m3 of iron tailings in the Rio Doce river basin. We identified 123 new sequence variants environmental taxonomic units (eOTUs) of benthic taxa and an assemblage composition dominated by Nematoda, Crustacea and Platyhelminthes; typical of other estuarine ecosystems. We detected environmental filtering on the meiofaunal assemblages and multivariate analysis revealed strong influence of Fe contamination, supporting chronic impacts from mine tailing deposition in the estuary. This was in contrast to environmental filtering of meiofaunal assemblages of non-polluted estuaries. Here, we suggest that the eDNA metabarcoding technique provides an opportunity to fill up biodiversity gaps in coastal marine ecology and may become a valid method for long term monitoring studies in mine tailing disasters and estuarine ecosystems with high trace metals content.
bibliographic citation: Bernardino et al. (2019) Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA. PeerJ 7:e8042 https://doi.org/10.7717/peerj.8042
date submitted: 2019-08-27
date accepted: 2019-10-16
issued: 2019-11-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bernardino
  given name: Angelo F.
author list: Agent
  family name: Pais
  given name: Fabiano S.
author list: Agent
  family name: Oliveira
  given name: Louisi S.
author list: Agent
  family name: Gabriel
  given name: Fabricio A.
author list: Agent
  family name: Ferreira
  given name: Tiago O.
author list: Agent
  family name: Queiroz
  given name: Hermano M.
author list: Agent
  family name: Mazzuco
  given name: Ana Carolina A.
doi: 10.7717/peerj.8042
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-07
copyright: © 2019 Bernardino et al.
attribution name: Bernardino et al.

Effects of afforestation on water resource variations in the Inner Mongolian Plateau
type: item
type: AcademicArticle
description: Afforestation is a key approach used to effectively prevent ecosystem degradation, which in itself is a key reason for the obstruction of sustainable societal development. In order to suppress sand and dust storms as a result of ecological environmental degradation in North China, the Government of China has sanctioned the planting of a large number of trees in Inner Mongolia. However, water resources in the Inner Mongolian Plateau are insufficient to sustain this effort because such a large number of trees consume a large amount of water, which also significantly increases evapotranspiration. This study uses spatiotemporal trend analyses and abrupt change analyses to determine the effects of afforestation on water resource variations in the Inner Mongolian Plateau. Results show that even though water resources in Inner Mongolia fluctuate, this resource has generally exhibited a declining trend from 1980 to 2015, corresponding to the NDVI trend. On spatial-temporal scales, water resources decreased significantly in the eastern section of the plateau, especially in the Horqin District and the Hulunbuir Plateau. By contrast, water resources increased as a whole in the western section of the plateau (Alxa Plateau). Driving analysis results show that water resource variation is mainly due to the contribution of change in precipitation (positive effect), which accounted for 39.35% of total changes in water resources, followed by the evapotranspiration (negative effect). In other words, afforestation with the primary aim of improving ecosystem has effectually upset the water resource balance of Inner Mongolia Plateau.
format: application/pdf
format: text/html
creator: Qiang Xiao
creator: Yang Xiao
creator: Ying Luo
creator: Changsu Song
creator: Jiacheng Bi
subject: Biodiversity
subject: Bioengineering
subject: Biogeography
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.7525
publisher: PeerJ Inc.
rights: © 2019 Xiao et al.
abstract: Afforestation is a key approach used to effectively prevent ecosystem degradation, which in itself is a key reason for the obstruction of sustainable societal development. In order to suppress sand and dust storms as a result of ecological environmental degradation in North China, the Government of China has sanctioned the planting of a large number of trees in Inner Mongolia. However, water resources in the Inner Mongolian Plateau are insufficient to sustain this effort because such a large number of trees consume a large amount of water, which also significantly increases evapotranspiration. This study uses spatiotemporal trend analyses and abrupt change analyses to determine the effects of afforestation on water resource variations in the Inner Mongolian Plateau. Results show that even though water resources in Inner Mongolia fluctuate, this resource has generally exhibited a declining trend from 1980 to 2015, corresponding to the NDVI trend. On spatial-temporal scales, water resources decreased significantly in the eastern section of the plateau, especially in the Horqin District and the Hulunbuir Plateau. By contrast, water resources increased as a whole in the western section of the plateau (Alxa Plateau). Driving analysis results show that water resource variation is mainly due to the contribution of change in precipitation (positive effect), which accounted for 39.35% of total changes in water resources, followed by the evapotranspiration (negative effect). In other words, afforestation with the primary aim of improving ecosystem has effectually upset the water resource balance of Inner Mongolia Plateau.
bibliographic citation: Xiao et al. (2019) Effects of afforestation on water resource variations in the Inner Mongolian Plateau. PeerJ 7:e7525 https://doi.org/10.7717/peerj.7525
date submitted: 2018-09-10
date accepted: 2019-07-21
issued: 2019-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Qiang
author list: Agent
  family name: Xiao
  given name: Yang
author list: Agent
  family name: Luo
  given name: Ying
author list: Agent
  family name: Song
  given name: Changsu
author list: Agent
  family name: Bi
  given name: Jiacheng
doi: 10.7717/peerj.7525
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-06
copyright: ©2019 Xiao et al.
attribution name: Xiao et al.

Neck mobility in the Jurassic plesiosaur Cryptoclidus eurymerus: finite element analysis as a new approach to understanding the cervical skeleton in fossil vertebrates
type: item
type: AcademicArticle
description: The sauropterygian clade Plesiosauria arose in the Late Triassic and survived to the very end of the Cretaceous. Plesiosauria evolved the greatest species diversity of any marine reptile clade, attaining a global distribution. Plesiosauria consist of two clades, Rhomaleosauridae and Neoplesiosauria. Basal Neoplesiosauria have long necks with at least 30 cervicals, but show qualitative osteological evidence for a stiff neck. Here we quantify neck mobility in lateral, ventral, and dorsal directions based on finite element modeling of neck vertebrae from the Middle Jurassic plesiosaur Cryptoclidus eurymerus. We model the mobility in a single motion segment, consisting of two adjacent cervical vertebrae and the joints connecting them. Based on the model with a maximum intervertebral spacing of 3 mm, we find that in Cryptoclidus, the maximum angle of lateral deflection in the motion segment was 2°. The maximum angle of ventral deflection was 5° and of dorsal deflection was 5°. When these values are multiplied by the number of cervical vertebrae, it becomes apparent that neck mobility was limited in all directions. The maximum angle of total lateral deflection in the neck was 67°. The maximum angle of total ventral deflection was 148° and of total dorsal deflection was 157°. This raises the question of the function of such a long, multi-segment but immobile neck. We posit that the long neck served in hydrodynamic and visual camouflage, hiding the bulk of the body from the small but abundant prey, such as schooling fish and squid. Neck immobility may have been advantageous in withstanding strong hydrodynamic forces acting on the neck during predatory strikes.
format: application/pdf
format: text/html
creator: Tanja Wintrich
creator: René Jonas
creator: Hans-Joachim Wilke
creator: Lars Schmitz
creator: P. Martin Sander
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.7658
publisher: PeerJ Inc.
rights: © 2019 Wintrich et al.
abstract: The sauropterygian clade Plesiosauria arose in the Late Triassic and survived to the very end of the Cretaceous. Plesiosauria evolved the greatest species diversity of any marine reptile clade, attaining a global distribution. Plesiosauria consist of two clades, Rhomaleosauridae and Neoplesiosauria. Basal Neoplesiosauria have long necks with at least 30 cervicals, but show qualitative osteological evidence for a stiff neck. Here we quantify neck mobility in lateral, ventral, and dorsal directions based on finite element modeling of neck vertebrae from the Middle Jurassic plesiosaur Cryptoclidus eurymerus. We model the mobility in a single motion segment, consisting of two adjacent cervical vertebrae and the joints connecting them. Based on the model with a maximum intervertebral spacing of 3 mm, we find that in Cryptoclidus, the maximum angle of lateral deflection in the motion segment was 2°. The maximum angle of ventral deflection was 5° and of dorsal deflection was 5°. When these values are multiplied by the number of cervical vertebrae, it becomes apparent that neck mobility was limited in all directions. The maximum angle of total lateral deflection in the neck was 67°. The maximum angle of total ventral deflection was 148° and of total dorsal deflection was 157°. This raises the question of the function of such a long, multi-segment but immobile neck. We posit that the long neck served in hydrodynamic and visual camouflage, hiding the bulk of the body from the small but abundant prey, such as schooling fish and squid. Neck immobility may have been advantageous in withstanding strong hydrodynamic forces acting on the neck during predatory strikes.
bibliographic citation: Wintrich et al. (2019) Neck mobility in the Jurassic plesiosaur Cryptoclidus eurymerus: finite element analysis as a new approach to understanding the cervical skeleton in fossil vertebrates. PeerJ 7:e7658 https://doi.org/10.7717/peerj.7658
date submitted: 2018-10-24
date accepted: 2019-08-11
issued: 2019-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wintrich
  given name: Tanja
author list: Agent
  family name: Jonas
  given name: René
author list: Agent
  family name: Wilke
  given name: Hans-Joachim
author list: Agent
  family name: Schmitz
  given name: Lars
author list: Agent
  family name: Sander
  given name: P. Martin
doi: 10.7717/peerj.7658
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-06
copyright: ©2019 Wintrich et al.
attribution name: Wintrich et al.

Short-term vasoactive agent treatment driven by physicians’ preference in acute esophageal variceal bleeding in a tertiary center
type: item
type: AcademicArticle
description: Background Vasoactive drugs are frequently used in combination with endoscopic variceal ligation (EVL) in treatment of acute esophageal variceal bleeding (EVB). The aim of study was to assess physicians’ preference of vasoactive agents in acute EVB, their reasons of preference and efficacy and safety of these short course regimens. Methods Cirrhotic patients with suspected EVB were screened (n = 352). Eligible patients were assigned based on the physician’s preference to either somatostatin (group S) or terlipressin (group T) followed by EVL. In group S, intravenous bolus (250 µg) of somatostatin followed by 250 µg/hour was continued for three days. In group T, 2 mg bolus injection of terlipressin was followed by 1 mg infusion every 6 h for three days. Results A total of 150 patients were enrolled; 41 in group S and 109 in group T. Reasons for physician preference was convenience in administration (77.1%) for group T and good safety profile (73.2%) for group S. Very early rebleeding within 49–120 h occurred in one patient in groups S and T (p = 0.469). Four patients in group S and 14 patients in group T have variceal rebleeding episodes within 6–42 d (p = 0.781). Overall treatment-related adverse effects were compatible in groups S and T (p = 0.878), but the total cost of terlipressin and somatostatin differed i.e., USD 621.32 and USD 496.43 respectively. Conclusions Terlipressin is the preferred vasoactive agent by physicians in our institution for acute EVB. Convenience in administration and safety profile are main considerations of physicians. Safety and hemostatic effects did not differ significantly between short-course somatostatin or terlipressin, although terlipressin is more expensive.
format: application/pdf
format: text/html
creator: Yoen Young Chuah
creator: Ping-I Hsu
creator: Wei-Lun Tsai
creator: Hsien-Chung Yu
creator: Feng-Woei Tsay
creator: Wen-Chi Chen
creator: Kung Hung Lin
creator: Yeong Yeh Lee
creator: Huay-Min Wang
subject: Emergency and Critical Care
subject: Gastroenterology and Hepatology
subject: Internal Medicine
description: doi:10.7717/peerj.7913
publisher: PeerJ Inc.
rights: © 2019 Chuah et al.
abstract: Background Vasoactive drugs are frequently used in combination with endoscopic variceal ligation (EVL) in treatment of acute esophageal variceal bleeding (EVB). The aim of study was to assess physicians’ preference of vasoactive agents in acute EVB, their reasons of preference and efficacy and safety of these short course regimens. Methods Cirrhotic patients with suspected EVB were screened (n = 352). Eligible patients were assigned based on the physician’s preference to either somatostatin (group S) or terlipressin (group T) followed by EVL. In group S, intravenous bolus (250 µg) of somatostatin followed by 250 µg/hour was continued for three days. In group T, 2 mg bolus injection of terlipressin was followed by 1 mg infusion every 6 h for three days. Results A total of 150 patients were enrolled; 41 in group S and 109 in group T. Reasons for physician preference was convenience in administration (77.1%) for group T and good safety profile (73.2%) for group S. Very early rebleeding within 49–120 h occurred in one patient in groups S and T (p = 0.469). Four patients in group S and 14 patients in group T have variceal rebleeding episodes within 6–42 d (p = 0.781). Overall treatment-related adverse effects were compatible in groups S and T (p = 0.878), but the total cost of terlipressin and somatostatin differed i.e., USD 621.32 and USD 496.43 respectively. Conclusions Terlipressin is the preferred vasoactive agent by physicians in our institution for acute EVB. Convenience in administration and safety profile are main considerations of physicians. Safety and hemostatic effects did not differ significantly between short-course somatostatin or terlipressin, although terlipressin is more expensive.
bibliographic citation: Chuah et al. (2019) Short-term vasoactive agent treatment driven by physicians’ preference in acute esophageal variceal bleeding in a tertiary center. PeerJ 7:e7913 https://doi.org/10.7717/peerj.7913
date submitted: 2019-05-11
date accepted: 2019-09-17
issued: 2019-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chuah
  given name: Yoen Young
author list: Agent
  family name: Hsu
  given name: Ping-I
author list: Agent
  family name: Tsai
  given name: Wei-Lun
author list: Agent
  family name: Yu
  given name: Hsien-Chung
author list: Agent
  family name: Tsay
  given name: Feng-Woei
author list: Agent
  family name: Chen
  given name: Wen-Chi
author list: Agent
  family name: Lin
  given name: Kung Hung
author list: Agent
  family name: Lee
  given name: Yeong Yeh
author list: Agent
  family name: Wang
  given name: Huay-Min
doi: 10.7717/peerj.7913
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-06
copyright: ©2019 Chuah et al.
attribution name: Chuah et al.

Spatial genetic structure in Pinus cembroides Zucc. at population and landscape levels in central and northern Mexico
type: item
type: AcademicArticle
description: Background Spatial genetic structure (SGS) analysis is a powerful approach to quantifying gene flow between trees, thus clarifying the functional connectivity of trees at population and landscape scales. The findings of SGS analysis may be useful for conservation and management of natural populations and plantations. Pinus cembroides is a widely distributed tree species, covering an area of about 2.5 million hectares in Mexico. The aim of this study was to examine five natural seed stands of P. cembroides in the Sierra Madre Occidental to determine the SGS at population (within the seed stand) and landscape (among seed stands) levels in order to establish guidelines for the conservation and management of the species. We hypothesized that P. cembroides, in which the seeds are dispersed by birds and mammals, creates weaker SGS than species with wind-dispersed seeds. Methods DNA fingerprinting was performed using the amplified fragment length polymorphism (AFLP) technique. In order to estimate the SGS at population and landscape levels, we measured the geographical (spatial) distance as the Euclidean distance. We also estimated the genetic distances between individuals using the pairwise kinship coefficient. Results The results showed non-significant autocorrelation in four out of five seed stands studied (i.e., a mainly random distribution in the space of the genetic variants of P. cembroides at population level). Discussion SGS was detected at the landscape scale, supporting the theory of isolation by distance as a consequence of restricted pollen and seed dispersal. However, the SGS may also have been generated by our sampling strategy. We recommended establishing a close network of seed stands of P. cembroides to prevent greater loss of local genetic variants and alteration of SGS. We recommend seed stands of P. cembroides of a minimum width of 225 m.
format: application/pdf
format: text/html
creator: Luis C. García-Zubia
creator: Javier Hernández-Velasco
creator: José C. Hernández-Díaz
creator: Sergio L. Simental-Rodríguez
creator: Carlos A. López-Sánchez
creator: Carmen Z. Quiñones-Pérez
creator: Artemio Carrillo-Parra
creator: Christian Wehenkel
subject: Agricultural Science
subject: Genetics
description: doi:10.7717/peerj.8002
publisher: PeerJ Inc.
rights: © 2019 García-Zubia et al.
abstract: Background Spatial genetic structure (SGS) analysis is a powerful approach to quantifying gene flow between trees, thus clarifying the functional connectivity of trees at population and landscape scales. The findings of SGS analysis may be useful for conservation and management of natural populations and plantations. Pinus cembroides is a widely distributed tree species, covering an area of about 2.5 million hectares in Mexico. The aim of this study was to examine five natural seed stands of P. cembroides in the Sierra Madre Occidental to determine the SGS at population (within the seed stand) and landscape (among seed stands) levels in order to establish guidelines for the conservation and management of the species. We hypothesized that P. cembroides, in which the seeds are dispersed by birds and mammals, creates weaker SGS than species with wind-dispersed seeds. Methods DNA fingerprinting was performed using the amplified fragment length polymorphism (AFLP) technique. In order to estimate the SGS at population and landscape levels, we measured the geographical (spatial) distance as the Euclidean distance. We also estimated the genetic distances between individuals using the pairwise kinship coefficient. Results The results showed non-significant autocorrelation in four out of five seed stands studied (i.e., a mainly random distribution in the space of the genetic variants of P. cembroides at population level). Discussion SGS was detected at the landscape scale, supporting the theory of isolation by distance as a consequence of restricted pollen and seed dispersal. However, the SGS may also have been generated by our sampling strategy. We recommended establishing a close network of seed stands of P. cembroides to prevent greater loss of local genetic variants and alteration of SGS. We recommend seed stands of P. cembroides of a minimum width of 225 m.
bibliographic citation: García-Zubia et al. (2019) Spatial genetic structure in Pinus cembroides Zucc. at population and landscape levels in central and northern Mexico. PeerJ 7:e8002 https://doi.org/10.7717/peerj.8002
date submitted: 2019-07-17
date accepted: 2019-10-07
issued: 2019-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Zubia
  given name: Luis C.
author list: Agent
  family name: Hernández-Velasco
  given name: Javier
author list: Agent
  family name: Hernández-Díaz
  given name: José C.
author list: Agent
  family name: Simental-Rodríguez
  given name: Sergio L.
author list: Agent
  family name: López-Sánchez
  given name: Carlos A.
author list: Agent
  family name: Quiñones-Pérez
  given name: Carmen Z.
author list: Agent
  family name: Carrillo-Parra
  given name: Artemio
author list: Agent
  family name: Wehenkel
  given name: Christian
doi: 10.7717/peerj.8002
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-06
copyright: ©2019 García-Zubia et al.
attribution name: García-Zubia et al.

Enforced symmetry: the necessity of symmetric waxing and waning
type: item
type: AcademicArticle
description: A fundamental question in ecology is how the success of a taxon changes through time and what drives this change. This question is commonly approached using trajectories averaged over a group of taxa. Using results from probability theory, we show analytically and using examples that averaged trajectories will be more symmetric as the number of averaged trajectories increases, even if none of the original trajectories they were derived from is symmetric. This effect is not only based on averaging, but also on the introduction of noise and the incorporation of a priori known origination and extinction times. This implies that averaged trajectories are not suitable for deriving information about the processes driving the success of taxa. In particular, symmetric waxing and waning, which is commonly observed and interpreted to be linked to a number of different paleobiological processes, does not allow drawing any conclusions about the nature of the underlying process.
format: application/pdf
format: text/html
creator: Niklas Hohmann
creator: Emilia Jarochowska
subject: Biodiversity
subject: Ecology
subject: Mathematical Biology
subject: Paleontology
subject: Statistics
description: doi:10.7717/peerj.8011
publisher: PeerJ Inc.
rights: © 2019 Hohmann and Jarochowska
abstract: A fundamental question in ecology is how the success of a taxon changes through time and what drives this change. This question is commonly approached using trajectories averaged over a group of taxa. Using results from probability theory, we show analytically and using examples that averaged trajectories will be more symmetric as the number of averaged trajectories increases, even if none of the original trajectories they were derived from is symmetric. This effect is not only based on averaging, but also on the introduction of noise and the incorporation of a priori known origination and extinction times. This implies that averaged trajectories are not suitable for deriving information about the processes driving the success of taxa. In particular, symmetric waxing and waning, which is commonly observed and interpreted to be linked to a number of different paleobiological processes, does not allow drawing any conclusions about the nature of the underlying process.
bibliographic citation: Hohmann et al. (2019) Enforced symmetry: the necessity of symmetric waxing and waning. PeerJ 7:e8011 https://doi.org/10.7717/peerj.8011
date submitted: 2019-05-03
date accepted: 2019-10-08
issued: 2019-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hohmann
  given name: Niklas
author list: Agent
  family name: Jarochowska
  given name: Emilia
doi: 10.7717/peerj.8011
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-06
copyright: ©2019 Hohmann and Jarochowska
attribution name: Hohmann and Jarochowska

A new alligatoroid from the Eocene of Vietnam highlights an extinct Asian clade independent from extant Alligator sinensis
type: item
type: AcademicArticle
description: During systematic paleontological surveys in the Na Duong Basin in North Vietnam between 2009 and 2012, well-preserved fossilized cranial and postcranial remains belonging to at least 29 individuals of a middle to late Eocene (late Bartonian to Priabonian age (39–35 Ma)) alligatoroid were collected. Comparative anatomical study of the material warrants the diagnosis of a new taxon, Orientalosuchus naduongensis gen. et sp. nov. The combined presence of an enlarged fifth maxillary tooth, prominent preorbital ridges, a large supraoccipital exposure on the skull table, a palatine-pterygoid suture anterior to the posterior end of the suborbital fenestra, and a pterygoid forming a neck surrounding the choana is unique to this species. Unlike previous phylogenies, our parsimony analysis recovers a monophyletic Late Cretaceous to Paleogene East to Southeastern Asian alligatoroid group, here named Orientalosuchina. The group includes Orientalosuchus naduongensis, Krabisuchus siamogallicus, Eoalligator chunyii, Jiangxisuchus nankangensis and Protoalligator huiningensis, all of them sharing a medial shifted quadrate foramen aerum. The recognition of this clade indicates at least two separate dispersal events from North America to Asia: one during the Late Cretaceous by Orientalosuchina and one by the ancestor of Alligator sinensis during the Paleogene or Neogene, the timing of which is poorly constrained.
format: application/pdf
format: text/html
creator: Tobias Massonne
creator: Davit Vasilyan
creator: Márton Rabi
creator: Madelaine Böhme
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7562
publisher: PeerJ Inc.
rights: © 2019 Massonne et al.
abstract: During systematic paleontological surveys in the Na Duong Basin in North Vietnam between 2009 and 2012, well-preserved fossilized cranial and postcranial remains belonging to at least 29 individuals of a middle to late Eocene (late Bartonian to Priabonian age (39–35 Ma)) alligatoroid were collected. Comparative anatomical study of the material warrants the diagnosis of a new taxon, Orientalosuchus naduongensis gen. et sp. nov. The combined presence of an enlarged fifth maxillary tooth, prominent preorbital ridges, a large supraoccipital exposure on the skull table, a palatine-pterygoid suture anterior to the posterior end of the suborbital fenestra, and a pterygoid forming a neck surrounding the choana is unique to this species. Unlike previous phylogenies, our parsimony analysis recovers a monophyletic Late Cretaceous to Paleogene East to Southeastern Asian alligatoroid group, here named Orientalosuchina. The group includes Orientalosuchus naduongensis, Krabisuchus siamogallicus, Eoalligator chunyii, Jiangxisuchus nankangensis and Protoalligator huiningensis, all of them sharing a medial shifted quadrate foramen aerum. The recognition of this clade indicates at least two separate dispersal events from North America to Asia: one during the Late Cretaceous by Orientalosuchina and one by the ancestor of Alligator sinensis during the Paleogene or Neogene, the timing of which is poorly constrained.
bibliographic citation: Massonne et al. (2019) A new alligatoroid from the Eocene of Vietnam highlights an extinct Asian clade independent from extant Alligator sinensis. PeerJ 7:e7562 https://doi.org/10.7717/peerj.7562
date submitted: 2019-02-07
date accepted: 2019-07-27
issued: 2019-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Massonne
  given name: Tobias
author list: Agent
  family name: Vasilyan
  given name: Davit
author list: Agent
  family name: Rabi
  given name: Márton
author list: Agent
  family name: Böhme
  given name: Madelaine
doi: 10.7717/peerj.7562
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-05
copyright: © 2019 Massonne et al.
attribution name: Massonne et al.

L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus
type: item
type: AcademicArticle
description: Phenotypic differences between Campylobacter fetus fetus and C. fetus venerealis subspecies allow the differential diagnosis of bovine genital campylobacteriosis. The hydrogen sulfide production, for example, is a trait exclusive to C. fetus fetus and C. fetus venerealis biovar intermedius. This gas that can be biochemically tested can be produced from L-cysteine (L-Cys). Herein, we report a novel multiplex-PCR to differentiate C. fetus based on the evaluation of a deletion of an ATP-binding cassette-type L-Cys transporter that could be involved in hydrogen sulfide production, as previously described. A wet lab approach combined with an in silico whole genome data analysis showed complete agreement between this L-Cys transporter-PCR and the hydrogen sulfide production biochemical test. This multiplex-PCR may complement the tests currently employed for the differential diagnosis of C. fetus.
format: application/pdf
format: text/html
creator: Pablo D. Farace
creator: Claudia G. Morsella
creator: Silvio L. Cravero
creator: Bernardo A. Sioya
creator: Ariel F. Amadio
creator: Fernando A. Paolicchi
creator: Andrea K. Gioffré
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
description: doi:10.7717/peerj.7820
publisher: PeerJ Inc.
rights: © 2019 Farace et al.
abstract: Phenotypic differences between Campylobacter fetus fetus and C. fetus venerealis subspecies allow the differential diagnosis of bovine genital campylobacteriosis. The hydrogen sulfide production, for example, is a trait exclusive to C. fetus fetus and C. fetus venerealis biovar intermedius. This gas that can be biochemically tested can be produced from L-cysteine (L-Cys). Herein, we report a novel multiplex-PCR to differentiate C. fetus based on the evaluation of a deletion of an ATP-binding cassette-type L-Cys transporter that could be involved in hydrogen sulfide production, as previously described. A wet lab approach combined with an in silico whole genome data analysis showed complete agreement between this L-Cys transporter-PCR and the hydrogen sulfide production biochemical test. This multiplex-PCR may complement the tests currently employed for the differential diagnosis of C. fetus.
bibliographic citation: Farace et al. (2019) L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus. PeerJ 7:e7820 https://doi.org/10.7717/peerj.7820
date submitted: 2019-04-26
date accepted: 2019-09-03
issued: 2019-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Farace
  given name: Pablo D.
author list: Agent
  family name: Morsella
  given name: Claudia G.
author list: Agent
  family name: Cravero
  given name: Silvio L.
author list: Agent
  family name: Sioya
  given name: Bernardo A.
author list: Agent
  family name: Amadio
  given name: Ariel F.
author list: Agent
  family name: Paolicchi
  given name: Fernando A.
author list: Agent
  family name: Gioffré
  given name: Andrea K.
doi: 10.7717/peerj.7820
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-05
copyright: © 2019 Farace et al.
attribution name: Farace et al.

Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin
type: item
type: AcademicArticle
description: Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as “blue crab” and “Product of the USA” may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as “Product of the USA” and “Product of Venezuela.” In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise Fst values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide diversity values. Lineages 1 and 2 were separated by a mean pairwise distance (p-distance) of 3.15%, whereas Lineage 3 had a mean p-distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p-distances …
format: application/pdf
format: text/html
creator: Amanda M. Windsor
creator: M. Katherine Moore
creator: Kimberly A. Warner
creator: Sarah R. Stadig
creator: Jonathan R. Deeds
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Food Science and Technology
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.7827
publisher: PeerJ Inc.
rights: © 2019
abstract: Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as “blue crab” and “Product of the USA” may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as “Product of the USA” and “Product of Venezuela.” In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise Fst values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide diversity values. Lineages 1 and 2 were separated by a mean pairwise distance (p-distance) of 3.15%, whereas Lineage 3 had a mean p-distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p-distances …
bibliographic citation: Windsor et al. (2019) Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin. PeerJ 7:e7827 https://doi.org/10.7717/peerj.7827
date submitted: 2019-05-16
date accepted: 2019-09-03
issued: 2019-11-05
is part of: PeerJ
license: open-government-licence
author list: Agent
  family name: Windsor
  given name: Amanda M.
author list: Agent
  family name: Moore
  given name: M. Katherine
author list: Agent
  family name: Warner
  given name: Kimberly A.
author list: Agent
  family name: Stadig
  given name: Sarah R.
author list: Agent
  family name: Deeds
  given name: Jonathan R.
doi: 10.7717/peerj.7827
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-05

Prey selectivity and the effect of diet on growth and development of a dragonfly, Sympetrum sanguineum
type: item
type: AcademicArticle
description: Despite a long tradition of research, our understanding of mechanisms driving prey selectivity in predatory insects is limited. According to optimal foraging theory, predators should prefer prey which provides the highest amount of energy per unit time. However, prey selectivity may also depend on previous diet and specific nutritional demands of the predator. From the long-term perspective, diet composition affects predator fitness. An open question is whether short-term selectivity of predators provides a diet which is optimal in the long-term. To shed more light on these issues, we conducted laboratory experiments on prey selectivity and its long-term consequences in larvae of the dragonfly Sympetrum sanguineum. We conditioned the larvae to one of two prey types, the cladoceran Daphnia magna and larvae of a non-biting midge Chironomus sp., and then exposed them to various combinations of the two prey types. We found that dragonfly larvae conditioned to Chironomus larvae consumed the same amount of D. magna, but significantly less Chironomus larvae compared to dragonfly larvae conditioned to D. magna. However, there was no effect of previous diet on their success of capture and handling time, suggesting a limited role of learning in their ability to process prey. We then tested the long-term effects of diets with different proportions of both prey for survival and growth of the dragonfly larvae. Individuals fed Chironomus-only diet had higher mortality and slower growth than dragonflies fed D. magna, while larvae fed a mixed diet had the highest survival and growth rate. In conclusion, we show that dragonfly larvae fed by Chironomus larvae performed poorly and compensated by preferring D. magna when both prey types were available. The superiority of the mixed diet suggests that a diverse diet may be needed to satisfy nutritional demands in S. sanguineum larvae. We demonstrate that merging short-term predation experiments with relevant data on predator fitness may …
format: application/pdf
format: text/html
creator: Pavla Dudová
creator: David S. Boukal
creator: Jan Klecka
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.7881
publisher: PeerJ Inc.
rights: © 2019 Dudová et al.
abstract: Despite a long tradition of research, our understanding of mechanisms driving prey selectivity in predatory insects is limited. According to optimal foraging theory, predators should prefer prey which provides the highest amount of energy per unit time. However, prey selectivity may also depend on previous diet and specific nutritional demands of the predator. From the long-term perspective, diet composition affects predator fitness. An open question is whether short-term selectivity of predators provides a diet which is optimal in the long-term. To shed more light on these issues, we conducted laboratory experiments on prey selectivity and its long-term consequences in larvae of the dragonfly Sympetrum sanguineum. We conditioned the larvae to one of two prey types, the cladoceran Daphnia magna and larvae of a non-biting midge Chironomus sp., and then exposed them to various combinations of the two prey types. We found that dragonfly larvae conditioned to Chironomus larvae consumed the same amount of D. magna, but significantly less Chironomus larvae compared to dragonfly larvae conditioned to D. magna. However, there was no effect of previous diet on their success of capture and handling time, suggesting a limited role of learning in their ability to process prey. We then tested the long-term effects of diets with different proportions of both prey for survival and growth of the dragonfly larvae. Individuals fed Chironomus-only diet had higher mortality and slower growth than dragonflies fed D. magna, while larvae fed a mixed diet had the highest survival and growth rate. In conclusion, we show that dragonfly larvae fed by Chironomus larvae performed poorly and compensated by preferring D. magna when both prey types were available. The superiority of the mixed diet suggests that a diverse diet may be needed to satisfy nutritional demands in S. sanguineum larvae. We demonstrate that merging short-term predation experiments with relevant data on predator fitness may …
bibliographic citation: Dudová et al. (2019) Prey selectivity and the effect of diet on growth and development of a dragonfly, Sympetrum sanguineum. PeerJ 7:e7881 https://doi.org/10.7717/peerj.7881
date submitted: 2019-05-07
date accepted: 2019-09-12
issued: 2019-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dudová
  given name: Pavla
author list: Agent
  family name: Boukal
  given name: David S.
author list: Agent
  family name: Klecka
  given name: Jan
doi: 10.7717/peerj.7881
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-05
copyright: © 2019 Dudová et al.
attribution name: Dudová et al.

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