PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Metabolic alterations in pea leaves during arbuscular mycorrhiza development
items: The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs
items: Identification of a native Bacillus thuringiensis strain from Sri Lanka active against Dipel-resistant Plutella xylostella
items: RFRP3 influences basal lamina degradation, cellular death, and progesterone secretion in cultured preantral ovarian follicles from the domestic cat
items: Gradual, temperature-induced change of secondary sexual characteristics in Trichogramma pretiosum infected with parthenogenesis-inducing Wolbachia
items: Visual search characteristics of precise map reading by orienteers
items: Revision of the Tanzanian dicynodont Dicynodon huenei (Therapsida: Anomodontia) from the Permian Usili Formation
items: Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods
items: Characterisation of bacteria isolated from the stingless bee, Heterotrigona itama, honey, bee bread and propolis
items: Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage

Metabolic alterations in pea leaves during arbuscular mycorrhiza development
type: item
type: AcademicArticle
description: Arbuscular mycorrhiza (AM) is known to be a mutually beneficial plant-fungal symbiosis; however, the effect of mycorrhization is heavily dependent on multiple biotic and abiotic factors. Therefore, for the proper employment of such plant-fungal symbiotic systems in agriculture, a detailed understanding of the molecular basis of the plant developmental response to mycorrhization is needed. The aim of this work was to uncover the physiological and metabolic alterations in pea (Pisum sativum L.) leaves associated with mycorrhization at key plant developmental stages. Plants of pea cv. Finale were grown in constant environmental conditions under phosphate deficiency. The plants were analyzed at six distinct time points, which corresponded to certain developmental stages of the pea: I: 7 days post inoculation (DPI) when the second leaf is fully unfolded with one pair of leaflets and a simple tendril; II: 21 DPI at first leaf with two pairs of leaflets and a complex tendril; III: 32 DPI when the floral bud is enclosed; IV: 42 DPI at the first open flower; V: 56 DPI when the pod is filled with green seeds; and VI: 90–110 DPI at the dry harvest stage. Inoculation with Rhizophagus irregularis had no effect on the fresh or dry shoot weight, the leaf photochemical activity, accumulation of chlorophyll a, b or carotenoids. However, at stage III (corresponding to the most active phase of mycorrhiza development), the number of internodes between cotyledons and the youngest completely developed leaf was lower in the inoculated plants than in those without inoculation. Moreover, inoculation extended the vegetation period of the host plants, and resulted in increase of the average dry weight per seed at stage VI. The leaf metabolome, as analyzed with GC-MS, included about three hundred distinct metabolites and showed a strong correlation with plant age, and, to a lesser extent, was influenced by mycorrhization. Metabolic shifts influenced the levels of sugars, amino acids and other …
format: application/pdf
format: text/html
creator: Oksana Y. Shtark
creator: Roman K. Puzanskiy
creator: Galina S. Avdeeva
creator: Andrey P. Yurkov
creator: Galina N. Smolikova
creator: Vladislav V. Yemelyanov
creator: Marina S. Kliukova
creator: Alexey L. Shavarda
creator: Anastasiia A. Kirpichnikova
creator: Aleksandr I. Zhernakov
creator: Alexey M. Afonin
creator: Igor A. Tikhonovich
creator: Vladimir A. Zhukov
creator: Maria F. Shishova
subject: Biochemistry
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.7495
publisher: PeerJ Inc.
rights: © 2019 Shtark et al.
abstract: Arbuscular mycorrhiza (AM) is known to be a mutually beneficial plant-fungal symbiosis; however, the effect of mycorrhization is heavily dependent on multiple biotic and abiotic factors. Therefore, for the proper employment of such plant-fungal symbiotic systems in agriculture, a detailed understanding of the molecular basis of the plant developmental response to mycorrhization is needed. The aim of this work was to uncover the physiological and metabolic alterations in pea (Pisum sativum L.) leaves associated with mycorrhization at key plant developmental stages. Plants of pea cv. Finale were grown in constant environmental conditions under phosphate deficiency. The plants were analyzed at six distinct time points, which corresponded to certain developmental stages of the pea: I: 7 days post inoculation (DPI) when the second leaf is fully unfolded with one pair of leaflets and a simple tendril; II: 21 DPI at first leaf with two pairs of leaflets and a complex tendril; III: 32 DPI when the floral bud is enclosed; IV: 42 DPI at the first open flower; V: 56 DPI when the pod is filled with green seeds; and VI: 90–110 DPI at the dry harvest stage. Inoculation with Rhizophagus irregularis had no effect on the fresh or dry shoot weight, the leaf photochemical activity, accumulation of chlorophyll a, b or carotenoids. However, at stage III (corresponding to the most active phase of mycorrhiza development), the number of internodes between cotyledons and the youngest completely developed leaf was lower in the inoculated plants than in those without inoculation. Moreover, inoculation extended the vegetation period of the host plants, and resulted in increase of the average dry weight per seed at stage VI. The leaf metabolome, as analyzed with GC-MS, included about three hundred distinct metabolites and showed a strong correlation with plant age, and, to a lesser extent, was influenced by mycorrhization. Metabolic shifts influenced the levels of sugars, amino acids and other …
bibliographic citation: Shtark et al. (2019) Metabolic alterations in pea leaves during arbuscular mycorrhiza development. PeerJ 7:e7495 https://doi.org/10.7717/peerj.7495
date submitted: 2018-11-30
date accepted: 2019-07-16
issued: 2019-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shtark
  given name: Oksana Y.
author list: Agent
  family name: Puzanskiy
  given name: Roman K.
author list: Agent
  family name: Avdeeva
  given name: Galina S.
author list: Agent
  family name: Yurkov
  given name: Andrey P.
author list: Agent
  family name: Smolikova
  given name: Galina N.
author list: Agent
  family name: Yemelyanov
  given name: Vladislav V.
author list: Agent
  family name: Kliukova
  given name: Marina S.
author list: Agent
  family name: Shavarda
  given name: Alexey L.
author list: Agent
  family name: Kirpichnikova
  given name: Anastasiia A.
author list: Agent
  family name: Zhernakov
  given name: Aleksandr I.
author list: Agent
  family name: Afonin
  given name: Alexey M.
author list: Agent
  family name: Tikhonovich
  given name: Igor A.
author list: Agent
  family name: Zhukov
  given name: Vladimir A.
author list: Agent
  family name: Shishova
  given name: Maria F.
doi: 10.7717/peerj.7495
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-23
copyright: ©2019 Shtark et al.
attribution name: Shtark et al.

The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs
type: item
type: AcademicArticle
description: The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu (UAG), tRNALeu (UUR), tRNAThr, tRNAPro, tRNAPhe, tRNAVal, tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae).
format: application/pdf
format: text/html
creator: Yin-Yin Cai
creator: Shi-Qi Shen
creator: Li-Xu Lu
creator: Kenneth B. Storey
creator: Dan-Na Yu
creator: Jia-Yong Zhang
subject: Evolutionary Studies
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.7532
publisher: PeerJ Inc.
rights: © 2019 Cai et al.
abstract: The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu (UAG), tRNALeu (UUR), tRNAThr, tRNAPro, tRNAPhe, tRNAVal, tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae).
bibliographic citation: Cai et al. (2019) The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs. PeerJ 7:e7532 https://doi.org/10.7717/peerj.7532
date submitted: 2019-04-29
date accepted: 2019-07-22
issued: 2019-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Yin-Yin
author list: Agent
  family name: Shen
  given name: Shi-Qi
author list: Agent
  family name: Lu
  given name: Li-Xu
author list: Agent
  family name: Storey
  given name: Kenneth B.
author list: Agent
  family name: Yu
  given name: Dan-Na
author list: Agent
  family name: Zhang
  given name: Jia-Yong
doi: 10.7717/peerj.7532
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-23
copyright: © 2019 Cai et al.
attribution name: Cai et al.

Identification of a native Bacillus thuringiensis strain from Sri Lanka active against Dipel-resistant Plutella xylostella
type: item
type: AcademicArticle
description: Background Biopesticides based on strains of the bacterium Bacillus thuringiensis (Bt) are used globally for effective and environmentally friendly pest control. The most serious threat to the sustainable use of these microbial pesticides is the development of resistance on targeted pests. Populations of Plutella xylostella (diamondback moth) have evolved field resistance to Bt pesticides at diverse locations worldwide. Discovery of novel Bt strains with varied toxin profiles that overcome resistance is one of the strategies to increase sustainability of Bt pesticides against P. xylostella. In this study, we report isolation and characterization of a Bt strain named AB1 from Sri Lanka displaying toxicity towards larvae of P. xylostella resistant to the commercial Bt pesticide Dipel. Methods Strains of Bt from diverse environments in Sri Lanka were evaluated for protein crystal production through Differential Interference Contrast (DIC) microscopic examination, and for insecticidal activity against P. xylostella in bioassays. The genome of the AB1 strain was sequenced by Hiseq Illumina sequencing to identify the insecticidal genes present in the genome and nano liquid chromatography followed by tandem mass spectrometry (nanoLC/MS/MS) of purified crystal proteins of AB1 was performed to identify the expressed insecticidal proteins. Multilocus sequence typing and Gyrase B gene sequence analyses were performed to identify the phylogenetic origin of the AB1 strain. Results The AB1 strain was identified as producing high levels of bipyramidal crystals and displaying insecticidal activity against susceptible and Dipel-resistant strains of P. xylostella. Multilocus sequence typing and phylogenetic analysis of the Gyrase B gene identified that AB1 belongs to the B. thuringiensis subsp. aizawai serotype. Comparative analysis of genomic and proteomic data showed that among the insecticidal protein coding genes annotated from the AB1 genome (cry1Aa, cry1Ca, cry1Da, cry1Ia, cry2…
format: application/pdf
format: text/html
creator: Rashini Yasara Baragamaarachchi
creator: Jayanetti Koralage Ramani Radhika Samarasekera
creator: Ovitigala Vithanage Don Sisira Jagathpriya Weerasena
creator: Kurt Lamour
creator: Juan Luis Jurat-Fuentes
subject: Agricultural Science
subject: Entomology
subject: Microbiology
description: doi:10.7717/peerj.7535
publisher: PeerJ Inc.
rights: © 2019 Baragamaarachchi et al.
abstract: Background Biopesticides based on strains of the bacterium Bacillus thuringiensis (Bt) are used globally for effective and environmentally friendly pest control. The most serious threat to the sustainable use of these microbial pesticides is the development of resistance on targeted pests. Populations of Plutella xylostella (diamondback moth) have evolved field resistance to Bt pesticides at diverse locations worldwide. Discovery of novel Bt strains with varied toxin profiles that overcome resistance is one of the strategies to increase sustainability of Bt pesticides against P. xylostella. In this study, we report isolation and characterization of a Bt strain named AB1 from Sri Lanka displaying toxicity towards larvae of P. xylostella resistant to the commercial Bt pesticide Dipel. Methods Strains of Bt from diverse environments in Sri Lanka were evaluated for protein crystal production through Differential Interference Contrast (DIC) microscopic examination, and for insecticidal activity against P. xylostella in bioassays. The genome of the AB1 strain was sequenced by Hiseq Illumina sequencing to identify the insecticidal genes present in the genome and nano liquid chromatography followed by tandem mass spectrometry (nanoLC/MS/MS) of purified crystal proteins of AB1 was performed to identify the expressed insecticidal proteins. Multilocus sequence typing and Gyrase B gene sequence analyses were performed to identify the phylogenetic origin of the AB1 strain. Results The AB1 strain was identified as producing high levels of bipyramidal crystals and displaying insecticidal activity against susceptible and Dipel-resistant strains of P. xylostella. Multilocus sequence typing and phylogenetic analysis of the Gyrase B gene identified that AB1 belongs to the B. thuringiensis subsp. aizawai serotype. Comparative analysis of genomic and proteomic data showed that among the insecticidal protein coding genes annotated from the AB1 genome (cry1Aa, cry1Ca, cry1Da, cry1Ia, cry2…
bibliographic citation: Baragamaarachchi et al. (2019) Identification of a native Bacillus thuringiensis strain from Sri Lanka active against Dipel-resistant Plutella xylostella. PeerJ 7:e7535 https://doi.org/10.7717/peerj.7535
date submitted: 2019-04-07
date accepted: 2019-07-23
issued: 2019-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baragamaarachchi
  given name: Rashini Yasara
author list: Agent
  family name: Samarasekera
  given name: Jayanetti Koralage Ramani Radhika
author list: Agent
  family name: Weerasena
  given name: Ovitigala Vithanage Don Sisira Jagathpriya
author list: Agent
  family name: Lamour
  given name: Kurt
author list: Agent
  family name: Jurat-Fuentes
  given name: Juan Luis
doi: 10.7717/peerj.7535
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-23
copyright: ©2019 Baragamaarachchi et al.
attribution name: Baragamaarachchi et al.

RFRP3 influences basal lamina degradation, cellular death, and progesterone secretion in cultured preantral ovarian follicles from the domestic cat
type: item
type: AcademicArticle
description: The hypothalamic neuropeptide RFRP3 can suppress hypothalamic GnRH neuron activation and inhibit gonadotropin release from the anterior pituitary. RFRP3 is also produced locally in the ovary and can inhibit steroidogenesis and follicle development in many vertebrates. However, almost nothing is known about the presence and regulatory action of RFRP3 in gonads of any carnivore species. Such knowledge is important for developing captive breeding programs for endangered carnivores and for inhibiting reproduction in feral species. Using the domestic cat as a model, our objectives were to (1) demonstrate the expression of feline RFRP3 (fRFRP3) and its receptor in the cat ovary and (2) assess the influence of fRFRP3 on ovarian follicle integrity, survival, and steroidogenesis in vitro. We first confirmed that fRFRP3 and its receptors (NPFFR1 and NPFFR2) were expressed in cat ovaries by sequencing PCR products from ovarian RNA. We then isolated and cultured preantral ovarian follicles in the presence of 10 or 1 µM fRFRP3 + FSH (1 µg/mL). We recorded the percentage of morphologically viable follicles (basal lamina integrity) over 8 days and calculated percentage survival of follicles on Day 8 (using fluorescent markers for cell survival and death). Last, we quantified progesterone accumulation in media. 10 µM fRFRP3 had no observable effect on viability, survival, or steroid production compared to follicles exposed to only FSH. However, 1 µM fRFRP3 decreased the percentage of morphologically viable follicles and the percentage of surviving follicles on Day 8. At the same time, 1 µM fRFRP3 increased the accumulation of progesterone in media. Our study shows, for the first time, direct action of RFRP3 on the follicle as a functional unit, and it is the first in a carnivore species. More broadly, our results support a conserved, inhibitory action of RFRP3 on ovarian follicle development and underscore the importance of comparative functional studies.
format: application/pdf
format: text/html
creator: Kathryn Wilsterman
creator: George E. Bentley
creator: Pierre Comizzoli
subject: Molecular Biology
subject: Veterinary Medicine
subject: Gynecology and Obstetrics
description: doi:10.7717/peerj.7540
publisher: PeerJ Inc.
rights: © 2019 Wilsterman et al.
abstract: The hypothalamic neuropeptide RFRP3 can suppress hypothalamic GnRH neuron activation and inhibit gonadotropin release from the anterior pituitary. RFRP3 is also produced locally in the ovary and can inhibit steroidogenesis and follicle development in many vertebrates. However, almost nothing is known about the presence and regulatory action of RFRP3 in gonads of any carnivore species. Such knowledge is important for developing captive breeding programs for endangered carnivores and for inhibiting reproduction in feral species. Using the domestic cat as a model, our objectives were to (1) demonstrate the expression of feline RFRP3 (fRFRP3) and its receptor in the cat ovary and (2) assess the influence of fRFRP3 on ovarian follicle integrity, survival, and steroidogenesis in vitro. We first confirmed that fRFRP3 and its receptors (NPFFR1 and NPFFR2) were expressed in cat ovaries by sequencing PCR products from ovarian RNA. We then isolated and cultured preantral ovarian follicles in the presence of 10 or 1 µM fRFRP3 + FSH (1 µg/mL). We recorded the percentage of morphologically viable follicles (basal lamina integrity) over 8 days and calculated percentage survival of follicles on Day 8 (using fluorescent markers for cell survival and death). Last, we quantified progesterone accumulation in media. 10 µM fRFRP3 had no observable effect on viability, survival, or steroid production compared to follicles exposed to only FSH. However, 1 µM fRFRP3 decreased the percentage of morphologically viable follicles and the percentage of surviving follicles on Day 8. At the same time, 1 µM fRFRP3 increased the accumulation of progesterone in media. Our study shows, for the first time, direct action of RFRP3 on the follicle as a functional unit, and it is the first in a carnivore species. More broadly, our results support a conserved, inhibitory action of RFRP3 on ovarian follicle development and underscore the importance of comparative functional studies.
bibliographic citation: Wilsterman et al. (2019) RFRP3 influences basal lamina degradation, cellular death, and progesterone secretion in cultured preantral ovarian follicles from the domestic cat. PeerJ 7:e7540 https://doi.org/10.7717/peerj.7540
date submitted: 2019-05-18
date accepted: 2019-07-23
issued: 2019-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilsterman
  given name: Kathryn
author list: Agent
  family name: Bentley
  given name: George E.
author list: Agent
  family name: Comizzoli
  given name: Pierre
doi: 10.7717/peerj.7540
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-23
copyright: ©2019 Wilsterman et al.
attribution name: Wilsterman et al.

Gradual, temperature-induced change of secondary sexual characteristics in Trichogramma pretiosum infected with parthenogenesis-inducing Wolbachia
type: item
type: AcademicArticle
description: Intersex is an intermediate stage of sexual differentiation in insects. Determining intersex morphology and the cause of its production will aid in the understanding of the mechanism of sexual differentiation in insects. In this paper, Wolbachia-infected Trichogramma pretiosum (T. preW+) that shows thelytokous parthenogenesis were used as subjects. In order to determine the causes of the T. preW+ intersex and the influence of parental generation temperature on gradual changes in secondary masculinization in intersex offspring, we examined the occurrence of intersex offspring (F1 and F2 generation) after the parental generations were treated with high temperature (27, 29, 31, and 33 °C) and described the external morphology of the intersexes. The results showed that the T. preW+ parental generation temperature is positively correlated with the probability of intersex offspring. The probability of F1 intersex is significantly higher than that of F2 intersex in different high temperature. The degree of secondary masculinization in T. preW+ intersexes increases as parental generation temperature increases. In addition, our study first identified 11 intersex types in T. preW+ and found that the primary and secondary sexual characteristics showed a regular distribution. We also found that the D type and H type of intersex have the highest frequency of appearance. The external genitalia of most intersexes were female, and only three intersex types have male external genitalia. Conclusions were ultimately obtained: Wolbachia is a direct factor that causes the occurrence of intersexes, while high temperature is an indirect factor that determines the external morphology of intersexes. The effects of high temperature on T. preW+ intersexes is passed through the parental generation to offspring, and this maternal effect weakens as the number of generations increases. In T. preW+ intersex individuals, most exhibit female primary sexual characteristics, and secondary sexual chara…
format: application/pdf
format: text/html
creator: Su-fang Ning
creator: Jin-cheng Zhou
creator: Quan-quan Liu
creator: Qian Zhao
creator: Hui Dong
subject: Agricultural Science
subject: Biodiversity
subject: Entomology
subject: Evolutionary Studies
subject: Parasitology
description: doi:10.7717/peerj.7567
publisher: PeerJ Inc.
rights: © 2019 Ning et al.
abstract: Intersex is an intermediate stage of sexual differentiation in insects. Determining intersex morphology and the cause of its production will aid in the understanding of the mechanism of sexual differentiation in insects. In this paper, Wolbachia-infected Trichogramma pretiosum (T. preW+) that shows thelytokous parthenogenesis were used as subjects. In order to determine the causes of the T. preW+ intersex and the influence of parental generation temperature on gradual changes in secondary masculinization in intersex offspring, we examined the occurrence of intersex offspring (F1 and F2 generation) after the parental generations were treated with high temperature (27, 29, 31, and 33 °C) and described the external morphology of the intersexes. The results showed that the T. preW+ parental generation temperature is positively correlated with the probability of intersex offspring. The probability of F1 intersex is significantly higher than that of F2 intersex in different high temperature. The degree of secondary masculinization in T. preW+ intersexes increases as parental generation temperature increases. In addition, our study first identified 11 intersex types in T. preW+ and found that the primary and secondary sexual characteristics showed a regular distribution. We also found that the D type and H type of intersex have the highest frequency of appearance. The external genitalia of most intersexes were female, and only three intersex types have male external genitalia. Conclusions were ultimately obtained: Wolbachia is a direct factor that causes the occurrence of intersexes, while high temperature is an indirect factor that determines the external morphology of intersexes. The effects of high temperature on T. preW+ intersexes is passed through the parental generation to offspring, and this maternal effect weakens as the number of generations increases. In T. preW+ intersex individuals, most exhibit female primary sexual characteristics, and secondary sexual chara…
bibliographic citation: Ning et al. (2019) Gradual, temperature-induced change of secondary sexual characteristics in Trichogramma pretiosum infected with parthenogenesis-inducing Wolbachia. PeerJ 7:e7567 https://doi.org/10.7717/peerj.7567
date submitted: 2019-03-28
date accepted: 2019-07-29
issued: 2019-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ning
  given name: Su-fang
author list: Agent
  family name: Zhou
  given name: Jin-cheng
author list: Agent
  family name: Liu
  given name: Quan-quan
author list: Agent
  family name: Zhao
  given name: Qian
author list: Agent
  family name: Dong
  given name: Hui
doi: 10.7717/peerj.7567
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-23
copyright: © 2019 Ning et al.
attribution name: Ning et al.

Visual search characteristics of precise map reading by orienteers
type: item
type: AcademicArticle
description: This article compares the differences in eye movements between orienteers of different skill levels on map information searches and explores the visual search patterns of orienteers during precise map reading so as to explore the cognitive characteristics of orienteers’ visual search. We recruited 44 orienteers at different skill levels (experts, advanced beginners, and novices), and recorded their behavioral responses and eye movement data when reading maps of different complexities. We found that the complexity of map (complex vs. simple) affects the quality of orienteers’ route planning during precise map reading. Specifically, when observing complex maps, orienteers of higher competency tend to have a better quality of route planning (i.e., a shorter route planning time, a longer gaze time, and a more concentrate distribution of gazes). Expert orienteers demonstrated obvious cognitive advantages in the ability to find key information. We also found that in the stage of route planning, expert orienteers and advanced beginners first pay attention to the checkpoint description table. The expert group extracted information faster, and their attention was more concentrated, whereas the novice group paid less attention to the checkpoint description table, and their gaze was scattered. We found that experts regarded the information in the checkpoint description table as the key to the problem and they give priority to this area in route decision making. These results advance our understanding of professional knowledge and problem solving in orienteering.
format: application/pdf
format: text/html
creator: Yang Liu
subject: Neuroscience
subject: Psychiatry and Psychology
subject: Statistics
description: doi:10.7717/peerj.7592
publisher: PeerJ Inc.
rights: © 2019 Liu
abstract: This article compares the differences in eye movements between orienteers of different skill levels on map information searches and explores the visual search patterns of orienteers during precise map reading so as to explore the cognitive characteristics of orienteers’ visual search. We recruited 44 orienteers at different skill levels (experts, advanced beginners, and novices), and recorded their behavioral responses and eye movement data when reading maps of different complexities. We found that the complexity of map (complex vs. simple) affects the quality of orienteers’ route planning during precise map reading. Specifically, when observing complex maps, orienteers of higher competency tend to have a better quality of route planning (i.e., a shorter route planning time, a longer gaze time, and a more concentrate distribution of gazes). Expert orienteers demonstrated obvious cognitive advantages in the ability to find key information. We also found that in the stage of route planning, expert orienteers and advanced beginners first pay attention to the checkpoint description table. The expert group extracted information faster, and their attention was more concentrated, whereas the novice group paid less attention to the checkpoint description table, and their gaze was scattered. We found that experts regarded the information in the checkpoint description table as the key to the problem and they give priority to this area in route decision making. These results advance our understanding of professional knowledge and problem solving in orienteering.
bibliographic citation: Liu (2019) Visual search characteristics of precise map reading by orienteers. PeerJ 7:e7592 https://doi.org/10.7717/peerj.7592
date submitted: 2019-02-27
date accepted: 2019-07-30
issued: 2019-08-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yang
doi: 10.7717/peerj.7592
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-23
copyright: © 2019 Liu
attribution name: Liu

Revision of the Tanzanian dicynodont Dicynodon huenei (Therapsida: Anomodontia) from the Permian Usili Formation
type: item
type: AcademicArticle
description: A single species of the dicynodontoid dicynodont Dicynodon is currently recognized from the late Permian Usili Formation of Tanzania: Dicynodon huenei Haughton, 1932. Restudy of the known Tanzanian materials of D. huenei demonstrates that they represent two distinct morphotypes, here considered separate taxa. The holotype of D. huenei is not referable to Dicynodon and instead is transferred to the genus Daptocephalus (but retained as a valid species, Daptocephalus huenei comb. nov.). A number of published dicynodontoid specimens from the Usili Formation, however, are referable to Dicynodon, and are here recognized as a new species (Dicynodon angielczyki sp. nov.) Dicynodon angielczyki can be distinguished from its South African congener Dicynodon lacerticeps by the presence of an expansion of the squamosal and jugal beneath the postorbital bar and a curved, posterolateral expansion of the squamosal behind the temporal fenestra. Inclusion of Dicynodon angielczyki and D. huenei in a phylogenetic analysis supports their referral to Dicynodon and Daptocephalus (respectively). These results indicate higher basinal endemism in large late Permian dicynodonts than previously thought, a sharp contrast to the cosmopolitanism in the group in the earliest Triassic.
format: application/pdf
format: text/html
creator: Christian F. Kammerer
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7420
publisher: PeerJ Inc.
rights: © 2019 Kammerer
abstract: A single species of the dicynodontoid dicynodont Dicynodon is currently recognized from the late Permian Usili Formation of Tanzania: Dicynodon huenei Haughton, 1932. Restudy of the known Tanzanian materials of D. huenei demonstrates that they represent two distinct morphotypes, here considered separate taxa. The holotype of D. huenei is not referable to Dicynodon and instead is transferred to the genus Daptocephalus (but retained as a valid species, Daptocephalus huenei comb. nov.). A number of published dicynodontoid specimens from the Usili Formation, however, are referable to Dicynodon, and are here recognized as a new species (Dicynodon angielczyki sp. nov.) Dicynodon angielczyki can be distinguished from its South African congener Dicynodon lacerticeps by the presence of an expansion of the squamosal and jugal beneath the postorbital bar and a curved, posterolateral expansion of the squamosal behind the temporal fenestra. Inclusion of Dicynodon angielczyki and D. huenei in a phylogenetic analysis supports their referral to Dicynodon and Daptocephalus (respectively). These results indicate higher basinal endemism in large late Permian dicynodonts than previously thought, a sharp contrast to the cosmopolitanism in the group in the earliest Triassic.
bibliographic citation: Kammerer (2019) Revision of the Tanzanian dicynodont Dicynodon huenei (Therapsida: Anomodontia) from the Permian Usili Formation. PeerJ 7:e7420 https://doi.org/10.7717/peerj.7420
date submitted: 2019-05-07
date accepted: 2019-07-05
issued: 2019-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kammerer
  given name: Christian F.
doi: 10.7717/peerj.7420
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-22
copyright: © 2019 Kammerer
attribution name: Kammerer

Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods
type: item
type: AcademicArticle
description: Background In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods. Methods We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure. Results Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance …
format: application/pdf
format: text/html
creator: Eduardo Ascarrunz
creator: Julien Claude
creator: Walter G. Joyce
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7476
publisher: PeerJ Inc.
rights: © 2019 Ascarrunz et al.
abstract: Background In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods. Methods We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure. Results Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance …
bibliographic citation: Ascarrunz et al. (2019) Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods. PeerJ 7:e7476 https://doi.org/10.7717/peerj.7476
date submitted: 2019-04-18
date accepted: 2019-07-15
issued: 2019-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ascarrunz
  given name: Eduardo
author list: Agent
  family name: Claude
  given name: Julien
author list: Agent
  family name: Joyce
  given name: Walter G.
doi: 10.7717/peerj.7476
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-22
copyright: © 2019 Ascarrunz et al.
attribution name: Ascarrunz et al.

Characterisation of bacteria isolated from the stingless bee, Heterotrigona itama, honey, bee bread and propolis
type: item
type: AcademicArticle
description: Bacteria are present in stingless bee nest products. However, detailed information on their characteristics is scarce. Thus, this study aims to investigate the characteristics of bacterial species isolated from Malaysian stingless bee, Heterotrigona itama, nest products. Honey, bee bread and propolis were collected aseptically from four geographical localities of Malaysia. Total plate count (TPC), bacterial identification, phenotypic profile and enzymatic and antibacterial activities were studied. The results indicated that the number of TPC varies from one location to another. A total of 41 different bacterial isolates from the phyla Firmicutes, Proteobacteria and Actinobacteria were identified. Bacillus species were the major bacteria found. Therein, Bacillus cereus was the most frequently isolated species followed by Bacillus aryabhattai, Bacillus oleronius, Bacillus stratosphericus, Bacillus altitudinis, Bacillus amyloliquefaciens, Bacillus nealsonii, Bacillus toyonensis, Bacillus subtilis, Bacillus safensis, Bacillus pseudomycoides, Enterobacter asburiae, Enterobacter cloacae, Pantoea dispersa and Streptomyces kunmingensis. Phenotypic profile of 15 bacterial isolates using GEN III MicroPlate™ system revealed most of the isolates as capable to utilise carbohydrates as well as amino acids and carboxylic acids and derivatives. Proteolytic, lipolytic and cellulolytic activities as determined by enzymatic assays were detected in Bacillus stratosphericus PD6, Bacillus amyloliquefaciens PD9, Bacillus subtilis BD3 and Bacillus safensis BD9. Bacillus amyloliquefaciens PD9 showed broad-spectrum of antimicrobial activity against Gram-positive and Gram-negative bacteria in vitro. The multienzymes and antimicrobial activities exhibited by the bacterial isolates from H. itama nest products could provide potential sources of enzymes and antimicrobial compounds for biotechnological applications.
format: application/pdf
format: text/html
creator: Mohamad Syazwan Ngalimat
creator: Raja Noor Zaliha Raja Abd. Rahman
creator: Mohd Termizi Yusof
creator: Amir Syahir
creator: Suriana Sabri
subject: Biotechnology
subject: Entomology
subject: Microbiology
description: doi:10.7717/peerj.7478
publisher: PeerJ Inc.
rights: © 2019 Ngalimat et al.
abstract: Bacteria are present in stingless bee nest products. However, detailed information on their characteristics is scarce. Thus, this study aims to investigate the characteristics of bacterial species isolated from Malaysian stingless bee, Heterotrigona itama, nest products. Honey, bee bread and propolis were collected aseptically from four geographical localities of Malaysia. Total plate count (TPC), bacterial identification, phenotypic profile and enzymatic and antibacterial activities were studied. The results indicated that the number of TPC varies from one location to another. A total of 41 different bacterial isolates from the phyla Firmicutes, Proteobacteria and Actinobacteria were identified. Bacillus species were the major bacteria found. Therein, Bacillus cereus was the most frequently isolated species followed by Bacillus aryabhattai, Bacillus oleronius, Bacillus stratosphericus, Bacillus altitudinis, Bacillus amyloliquefaciens, Bacillus nealsonii, Bacillus toyonensis, Bacillus subtilis, Bacillus safensis, Bacillus pseudomycoides, Enterobacter asburiae, Enterobacter cloacae, Pantoea dispersa and Streptomyces kunmingensis. Phenotypic profile of 15 bacterial isolates using GEN III MicroPlate™ system revealed most of the isolates as capable to utilise carbohydrates as well as amino acids and carboxylic acids and derivatives. Proteolytic, lipolytic and cellulolytic activities as determined by enzymatic assays were detected in Bacillus stratosphericus PD6, Bacillus amyloliquefaciens PD9, Bacillus subtilis BD3 and Bacillus safensis BD9. Bacillus amyloliquefaciens PD9 showed broad-spectrum of antimicrobial activity against Gram-positive and Gram-negative bacteria in vitro. The multienzymes and antimicrobial activities exhibited by the bacterial isolates from H. itama nest products could provide potential sources of enzymes and antimicrobial compounds for biotechnological applications.
bibliographic citation: Ngalimat et al. (2019) Characterisation of bacteria isolated from the stingless bee, Heterotrigona itama, honey, bee bread and propolis. PeerJ 7:e7478 https://doi.org/10.7717/peerj.7478
date submitted: 2018-11-23
date accepted: 2019-07-15
issued: 2019-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ngalimat
  given name: Mohamad Syazwan
author list: Agent
  family name: Raja Abd. Rahman
  given name: Raja Noor Zaliha
author list: Agent
  family name: Yusof
  given name: Mohd Termizi
author list: Agent
  family name: Syahir
  given name: Amir
author list: Agent
  family name: Sabri
  given name: Suriana
doi: 10.7717/peerj.7478
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-22
copyright: © 2019 Ngalimat et al.
attribution name: Ngalimat et al.

Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage
type: item
type: AcademicArticle
description: The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699–30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, Corbicula sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401–2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27 to 0.44 my. We recovered very little evidence of nuclear genomic admixture among the four invasive lineag…
format: application/pdf
format: text/html
creator: Amanda E. Haponski
creator: Diarmaid Ó Foighil
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.7484
publisher: PeerJ Inc.
rights: © 2019 Haponski and Ó Foighil
abstract: The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699–30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, Corbicula sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401–2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27 to 0.44 my. We recovered very little evidence of nuclear genomic admixture among the four invasive lineag…
bibliographic citation: Haponski et al. (2019) Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage. PeerJ 7:e7484 https://doi.org/10.7717/peerj.7484
date submitted: 2019-03-25
date accepted: 2019-07-15
issued: 2019-08-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Haponski
  given name: Amanda E.
author list: Agent
  family name: Ó Foighil
  given name: Diarmaid
doi: 10.7717/peerj.7484
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-22
copyright: © 2019 Haponski and Ó Foighil
attribution name: Haponski and Ó Foighil

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