PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Water permeability/impermeability in seeds of 15 species of Caragana (Fabaceae)
items: Heracleum sosnowskyi seed development under the effect of exogenous application of GA3
items: Intermittent reproduction, mortality patterns and lifetime breeding frequency of females in a population of the adder (Vipera berus)
items: Changes in precipitation may alter food preference in an ecosystem engineer, the black land crab, Gecarcinus ruricola
items: Circular RNAs as potential biomarkers and therapeutics for cardiovascular disease
items: Modulation of stress response and productive performance of Litopenaeus vannamei through diet
items: Comparison of microbial community structures in soils with woody organic amendments and soils with traditional local organic amendments in Ningxia of Northern China
items: Leaf functional trait variation in a humid temperate forest, and relationships with juvenile tree light requirements
items: Ecosystem effects of fishing & El Niño at the Galápagos Marine Reserve
items: Effect of isolation on coat colour polymorphism of Polynesian rats in Island Southeast Asia and the Pacific

Water permeability/impermeability in seeds of 15 species of Caragana (Fabaceae)
type: item
type: AcademicArticle
description: Majority legumes in the temperate and arctic zones have water-impermeable seeds (physical dormancy, PY). However, various authors have reported that seeds of some Caragana species are water-permeable and thus non-dormant. We (1) tested seeds of 15 species of Caragana matured in the same site in 2014, 2016 and/or 2017 for presence of PY, (2) determined if dry storage decreased or increased the percentage of seeds with PY and (3) located the site on the seed coat of 11 species where water enters the seed. Sixty-three percent and 45% of the seeds of C. roborovskyi had PY in 2016 and 2017, respectively, but only 0–14% of the seeds of the other 14 species had PY. The palisade layer in the seed coat of water impermeable seeds had no cracks in it, whereas cracks were present in the palisade layer of water-permeable seeds. Year of collection and dry storage had significant effects on imbibition of two species (C. acanthophylla and C. roborovskyi). In two (C. acanthophylla and C. roborovskyi) of the 11 species tested, the hilum was the site of water entry into seeds (control seeds, not any dormant broken treatments), but for the other nine species tested water entered through all parts of the seed coat.
format: application/pdf
format: text/html
creator: Dali Chen
creator: Rui Zhang
creator: Carol C. Baskin
creator: Xiaowen Hu
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.6870
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Majority legumes in the temperate and arctic zones have water-impermeable seeds (physical dormancy, PY). However, various authors have reported that seeds of some Caragana species are water-permeable and thus non-dormant. We (1) tested seeds of 15 species of Caragana matured in the same site in 2014, 2016 and/or 2017 for presence of PY, (2) determined if dry storage decreased or increased the percentage of seeds with PY and (3) located the site on the seed coat of 11 species where water enters the seed. Sixty-three percent and 45% of the seeds of C. roborovskyi had PY in 2016 and 2017, respectively, but only 0–14% of the seeds of the other 14 species had PY. The palisade layer in the seed coat of water impermeable seeds had no cracks in it, whereas cracks were present in the palisade layer of water-permeable seeds. Year of collection and dry storage had significant effects on imbibition of two species (C. acanthophylla and C. roborovskyi). In two (C. acanthophylla and C. roborovskyi) of the 11 species tested, the hilum was the site of water entry into seeds (control seeds, not any dormant broken treatments), but for the other nine species tested water entered through all parts of the seed coat.
bibliographic citation: Chen et al. (2019) Water permeability/impermeability in seeds of 15 species of Caragana (Fabaceae). PeerJ 7:e6870 https://doi.org/10.7717/peerj.6870
date submitted: 2018-12-20
date accepted: 2019-03-29
issued: 2019-05-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Dali
author list: Agent
  family name: Zhang
  given name: Rui
author list: Agent
  family name: Baskin
  given name: Carol C.
author list: Agent
  family name: Hu
  given name: Xiaowen
doi: 10.7717/peerj.6870
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-09
copyright: ©2019 Chen et al.
attribution name: Chen et al.

Heracleum sosnowskyi seed development under the effect of exogenous application of GA3
type: item
type: AcademicArticle
description: Numerous studies have demonstrated the impact of exogenous gibberellin on fleshy fruit formation, but the effect on dry fruits is not yet well known. To test the role of gibberellin (GA3) in dry fruit formation, we analysed the impact of exogenous GA3 on the invasive plant Sosnowsky’s hogweed (H. sosnowskyi Manden.) seed development and germination. Treatment of GA3 concentrations of 0.07 mM, 0.14 mM, 0.28 mM, 0.43 mM was applied to flowers at the early stage of development. Seeds were collected from treated satellite umbels. It was observed that GA3treatment did not have a significant effect on the size of H. sosnowskyi seeds, but caused various changes in their shape. The data on semi-thin longitudinal sections of H. sosnowskyi mericarps and SEM micrographs of embryos showed that the embryos in GA3 (0.43 mM) treated variants were at torpedo stage, while in control variants—mature embryos. The germination of seeds of each variant was estimated by burying them in the soil. Our studies indicated that GA3 application reduced the germination of H. sosnowskyi seed from 98.0% (control) to 16.5% (GA3 concentration 0.43 mM). It was assumed that exogenous application of GA3 had influence on the development of dry Sosnowsky’s hogweed seeds and could be used to inhibit the spread of this invasive plant.
format: application/pdf
format: text/html
creator: Dalia Koryznienė
creator: Sigita Jurkonienė
creator: Tautvydas Žalnierius
creator: Virgilija Gavelienė
creator: Elžbieta Jankovska-Bortkevič
creator: Nijolė Bareikienė
creator: Vincas Būda
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Histology
description: doi:10.7717/peerj.6906
publisher: PeerJ Inc.
rights: © 2019 Koryznienė et al.
abstract: Numerous studies have demonstrated the impact of exogenous gibberellin on fleshy fruit formation, but the effect on dry fruits is not yet well known. To test the role of gibberellin (GA3) in dry fruit formation, we analysed the impact of exogenous GA3 on the invasive plant Sosnowsky’s hogweed (H. sosnowskyi Manden.) seed development and germination. Treatment of GA3 concentrations of 0.07 mM, 0.14 mM, 0.28 mM, 0.43 mM was applied to flowers at the early stage of development. Seeds were collected from treated satellite umbels. It was observed that GA3treatment did not have a significant effect on the size of H. sosnowskyi seeds, but caused various changes in their shape. The data on semi-thin longitudinal sections of H. sosnowskyi mericarps and SEM micrographs of embryos showed that the embryos in GA3 (0.43 mM) treated variants were at torpedo stage, while in control variants—mature embryos. The germination of seeds of each variant was estimated by burying them in the soil. Our studies indicated that GA3 application reduced the germination of H. sosnowskyi seed from 98.0% (control) to 16.5% (GA3 concentration 0.43 mM). It was assumed that exogenous application of GA3 had influence on the development of dry Sosnowsky’s hogweed seeds and could be used to inhibit the spread of this invasive plant.
bibliographic citation: Koryznienė et al. (2019) Heracleum sosnowskyi seed development under the effect of exogenous application of GA3. PeerJ 7:e6906 https://doi.org/10.7717/peerj.6906
date submitted: 2019-01-25
date accepted: 2019-04-03
issued: 2019-05-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koryznienė
  given name: Dalia
author list: Agent
  family name: Jurkonienė
  given name: Sigita
author list: Agent
  family name: Žalnierius
  given name: Tautvydas
author list: Agent
  family name: Gavelienė
  given name: Virgilija
author list: Agent
  family name: Jankovska-Bortkevič
  given name: Elžbieta
author list: Agent
  family name: Bareikienė
  given name: Nijolė
author list: Agent
  family name: Būda
  given name: Vincas
doi: 10.7717/peerj.6906
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-09
copyright: ©2019 Koryznienė et al.
attribution name: Koryznienė et al.

Intermittent reproduction, mortality patterns and lifetime breeding frequency of females in a population of the adder (Vipera berus)
type: item
type: AcademicArticle
description: Female adders (Vipera berus) are “capital breeders” that exhibit delayed maturity and intermittent reproductive frequency. We studied the attainment of sexual maturity, the initiation of annual breeding in mature females, the energy and mortality costs associated with breeding, the length of the reproductive cycle and female lifetime reproductive frequency. We use longitudinal data obtained during an 18-year (2000–2017) mark–recapture study in a large population of adders in northern Belgium. A minority (15%) of the females gave birth to their first litter when they attained the actual age of 3 years, upon surpassing a minimum snout-vent-length of 38 cm. However, most females reproduced for the first time when they were 4 years or older. In mature females, breeding in a given year depends to a large extent on their body condition at the onset of the active season, indicating that a threshold level of energy reserves is necessary to start a reproductive cycle. During breeding years females stop growing, lose about one-third of their initial body mass and are very emaciated after parturition. The decrease in relative body mass was most notable initially in the largest and fattiest females. During the non-breeding years, females forage intensely to rebuild their fat reserves; their abilities to do so will strongly affect whether and when they engage in subsequent reproductive bouts. We used a multistate mark–recapture analytical method to simultaneously estimate the capture and survival rates of breeding and non-breeding females, a necessary procedure to obtain accurate estimates of survival probabilities. The analysis indicated much higher capture rates during the breeding years, but did not reveal a substantial effect of reproductive state on annual survival rates. Although some females were observed to breed in successive years, the reproductive cycle was most often biennial or triennial. However, most females (ca. 70%) that attained sexual maturity reproduced only …
format: application/pdf
format: text/html
creator: Dirk Bauwens
creator: Katja Claus
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.6912
publisher: PeerJ Inc.
rights: © 2019 Bauwens and Claus
abstract: Female adders (Vipera berus) are “capital breeders” that exhibit delayed maturity and intermittent reproductive frequency. We studied the attainment of sexual maturity, the initiation of annual breeding in mature females, the energy and mortality costs associated with breeding, the length of the reproductive cycle and female lifetime reproductive frequency. We use longitudinal data obtained during an 18-year (2000–2017) mark–recapture study in a large population of adders in northern Belgium. A minority (15%) of the females gave birth to their first litter when they attained the actual age of 3 years, upon surpassing a minimum snout-vent-length of 38 cm. However, most females reproduced for the first time when they were 4 years or older. In mature females, breeding in a given year depends to a large extent on their body condition at the onset of the active season, indicating that a threshold level of energy reserves is necessary to start a reproductive cycle. During breeding years females stop growing, lose about one-third of their initial body mass and are very emaciated after parturition. The decrease in relative body mass was most notable initially in the largest and fattiest females. During the non-breeding years, females forage intensely to rebuild their fat reserves; their abilities to do so will strongly affect whether and when they engage in subsequent reproductive bouts. We used a multistate mark–recapture analytical method to simultaneously estimate the capture and survival rates of breeding and non-breeding females, a necessary procedure to obtain accurate estimates of survival probabilities. The analysis indicated much higher capture rates during the breeding years, but did not reveal a substantial effect of reproductive state on annual survival rates. Although some females were observed to breed in successive years, the reproductive cycle was most often biennial or triennial. However, most females (ca. 70%) that attained sexual maturity reproduced only …
bibliographic citation: Bauwens et al. (2019) Intermittent reproduction, mortality patterns and lifetime breeding frequency of females in a population of the adder (Vipera berus). PeerJ 7:e6912 https://doi.org/10.7717/peerj.6912
date submitted: 2019-01-02
date accepted: 2019-04-05
issued: 2019-05-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bauwens
  given name: Dirk
author list: Agent
  family name: Claus
  given name: Katja
doi: 10.7717/peerj.6912
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-09
copyright: ©2019 Bauwens and Claus
attribution name: Bauwens and Claus

Changes in precipitation may alter food preference in an ecosystem engineer, the black land crab, Gecarcinus ruricola
type: item
type: AcademicArticle
description: Gecarcinid land crabs are ecosystem engineers playing an important role in nutrient recycling and seedling propagation in coastal forests. Given a predicted future decline in precipitation for the Caribbean, the effects of dehydration on feeding preferences of the black land crab Gecarcinus ruricola were investigated. G. ruricola were offered novel food items of lettuce, apple, or herring to test for food choice based on water and nutritional (energetic) content in single and multiple choice experimental designs. The effect of dehydration was incorporated by depriving crabs of water for 0, 4, or 8 days, leading to an average body water loss of 0%, 9%, and 17%, respectively, (crabs survived a body water loss of 23% + 2% and 14–16 days without access to water). The results were consistent between the single and multiple choice experiments: crabs consumed relatively more apple and fish and only small amounts of lettuce. Overall, no selective preferences were observed as a function of dehydration, but crabs did consume less dry food when deprived of water and an overall lower food intake with increasing dehydration levels occurred. The decrease in feeding was likely due to loss of water from the gut resulting in the inability to produce ample digestive juices. Future climatic predictions suggest a 25–50% decline in rainfall in the Caribbean, which may lead to a lower food intake by the crabs, resulting in compromised growth. The subsequent reduction in nutrient recycling highlights possible long-term effects on coastal ecosystems and highlights the importance of future work on climate relative behavioral interactions that influence ecosystem function.
format: application/pdf
format: text/html
creator: Iain J. McGaw
creator: Travis E. Van Leeuwen
creator: Rebekah H. Trehern
creator: Amanda E. Bates
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.6818
publisher: PeerJ Inc.
rights: © 2019 McGaw et al.
abstract: Gecarcinid land crabs are ecosystem engineers playing an important role in nutrient recycling and seedling propagation in coastal forests. Given a predicted future decline in precipitation for the Caribbean, the effects of dehydration on feeding preferences of the black land crab Gecarcinus ruricola were investigated. G. ruricola were offered novel food items of lettuce, apple, or herring to test for food choice based on water and nutritional (energetic) content in single and multiple choice experimental designs. The effect of dehydration was incorporated by depriving crabs of water for 0, 4, or 8 days, leading to an average body water loss of 0%, 9%, and 17%, respectively, (crabs survived a body water loss of 23% + 2% and 14–16 days without access to water). The results were consistent between the single and multiple choice experiments: crabs consumed relatively more apple and fish and only small amounts of lettuce. Overall, no selective preferences were observed as a function of dehydration, but crabs did consume less dry food when deprived of water and an overall lower food intake with increasing dehydration levels occurred. The decrease in feeding was likely due to loss of water from the gut resulting in the inability to produce ample digestive juices. Future climatic predictions suggest a 25–50% decline in rainfall in the Caribbean, which may lead to a lower food intake by the crabs, resulting in compromised growth. The subsequent reduction in nutrient recycling highlights possible long-term effects on coastal ecosystems and highlights the importance of future work on climate relative behavioral interactions that influence ecosystem function.
bibliographic citation: McGaw et al. (2019) Changes in precipitation may alter food preference in an ecosystem engineer, the black land crab, Gecarcinus ruricola. PeerJ 7:e6818 https://doi.org/10.7717/peerj.6818
date submitted: 2018-09-18
date accepted: 2019-03-14
issued: 2019-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McGaw
  given name: Iain J.
author list: Agent
  family name: Van Leeuwen
  given name: Travis E.
author list: Agent
  family name: Trehern
  given name: Rebekah H.
author list: Agent
  family name: Bates
  given name: Amanda E.
doi: 10.7717/peerj.6818
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-08
copyright: © 2019 McGaw et al.
attribution name: McGaw et al.

Circular RNAs as potential biomarkers and therapeutics for cardiovascular disease
type: item
type: AcademicArticle
description: Circular RNAs (circRNAs) are genetic regulators that were earlier considered as “junk”. In contrast to linear RNAs, they have covalently linked ends with no polyadenylated tails. CircRNAs can act as RNA-binding proteins, sequestering agents, transcriptional regulators, as well as microRNA sponges. In addition, it is reported that some selected circRNAs are transformed into functional proteins. These RNA molecules always circularize through covalent bonds, and their presence has been demonstrated across species. They are usually abundant and stable as well as evolutionarily conserved in tissues (liver, lung, stomach), saliva, exosomes, and blood. Therefore, they have been proposed as the “next big thing” in molecular biomarkers for several diseases, particularly in cancer. Recently, circRNAs have been investigated in cardiovascular diseases (CVD) and reported to play important roles in heart failure, coronary artery disease, and myocardial infarction. Here, we review the recent literature and discuss the impact and the diagnostic and prognostic values of circRNAs in CVD.
format: application/pdf
format: text/html
creator: Weitie Wang
creator: Yong Wang
creator: Hulin Piao
creator: Bo Li
creator: Maoxun Huang
creator: Zhicheng Zhu
creator: Dan Li
creator: Tiance Wang
creator: Rihao Xu
creator: Kexiang Liu
subject: Bioinformatics
description: doi:10.7717/peerj.6831
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Circular RNAs (circRNAs) are genetic regulators that were earlier considered as “junk”. In contrast to linear RNAs, they have covalently linked ends with no polyadenylated tails. CircRNAs can act as RNA-binding proteins, sequestering agents, transcriptional regulators, as well as microRNA sponges. In addition, it is reported that some selected circRNAs are transformed into functional proteins. These RNA molecules always circularize through covalent bonds, and their presence has been demonstrated across species. They are usually abundant and stable as well as evolutionarily conserved in tissues (liver, lung, stomach), saliva, exosomes, and blood. Therefore, they have been proposed as the “next big thing” in molecular biomarkers for several diseases, particularly in cancer. Recently, circRNAs have been investigated in cardiovascular diseases (CVD) and reported to play important roles in heart failure, coronary artery disease, and myocardial infarction. Here, we review the recent literature and discuss the impact and the diagnostic and prognostic values of circRNAs in CVD.
bibliographic citation: Wang et al. (2019) Circular RNAs as potential biomarkers and therapeutics for cardiovascular disease. PeerJ 7:e6831 https://doi.org/10.7717/peerj.6831
date submitted: 2019-01-10
date accepted: 2019-03-21
issued: 2019-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Weitie
author list: Agent
  family name: Wang
  given name: Yong
author list: Agent
  family name: Piao
  given name: Hulin
author list: Agent
  family name: Li
  given name: Bo
author list: Agent
  family name: Huang
  given name: Maoxun
author list: Agent
  family name: Zhu
  given name: Zhicheng
author list: Agent
  family name: Li
  given name: Dan
author list: Agent
  family name: Wang
  given name: Tiance
author list: Agent
  family name: Xu
  given name: Rihao
author list: Agent
  family name: Liu
  given name: Kexiang
doi: 10.7717/peerj.6831
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-08
copyright: © 2019 Wang et al.
attribution name: Wang et al.

Modulation of stress response and productive performance of Litopenaeus vannamei through diet
type: item
type: AcademicArticle
description: The high tolerance of Litopenaeus vannamei to a wide range of salinity (1–50 psu) makes this species an excellent candidate for culture under low salinity, decreasing shrimp epidemics and water pollution in some coastal areas. However, salinity levels outside the optimal range could impose several physiological constraints that would in turn affect growth and survival, particularly in the presence of additional stressors (e.g. high densities, handling practices, and hypoxia). Despite shrimp susceptibility to individual stressors has been widely addressed, information regarding response to chronic and acute stressors combined and its relation to diet is scarce. Thus, the aim of our study was to determine the effect of diet on the susceptibility to chronic (low salinity) and acute (hypoxia and escape response) stressors in terms of culture performance and physiological indicators. We evaluated overall performance during culture of L. vannamei at low salinity (6 psu), fed with an experimental diet with low protein and high carbohydrate content (26% protein and 6% fish meal plus probiotic mixture) and compared to a commercial formula with high protein and low carbohydrate content (40% crude protein and 20% fish meal without probiotic mixture). At the end of the rearing experiment, shrimp were exposed to two types of acute stress, hypoxia and escape. Biochemical (hemocyanin, total proteins, glucose, and lactate) and bioenergetic (adenylic energy charge and arginine phosphate levels) variables were measured to assess chronic stress response (salinity) and acute stress response (hypoxia or escape). The experimental diet resulted in higher muscle energy status that was not affected by low salinity, although lipid levels were lower under this condition. This diet partially counteracted the low performance at low salinity and promoted greater protein efficiency. Hypoxia induced strong hyperglycemic and lactate increase as response, whereas escape response was characterized by…
format: application/pdf
format: text/html
creator: Eliza M. Martínez-Antonio
creator: Ilie S. Racotta
creator: Juan C. Ruvalcaba-Márquez
creator: Francisco Magallón-Barajas
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.6850
publisher: PeerJ Inc.
rights: © 2019 Martínez-Antonio et al.
abstract: The high tolerance of Litopenaeus vannamei to a wide range of salinity (1–50 psu) makes this species an excellent candidate for culture under low salinity, decreasing shrimp epidemics and water pollution in some coastal areas. However, salinity levels outside the optimal range could impose several physiological constraints that would in turn affect growth and survival, particularly in the presence of additional stressors (e.g. high densities, handling practices, and hypoxia). Despite shrimp susceptibility to individual stressors has been widely addressed, information regarding response to chronic and acute stressors combined and its relation to diet is scarce. Thus, the aim of our study was to determine the effect of diet on the susceptibility to chronic (low salinity) and acute (hypoxia and escape response) stressors in terms of culture performance and physiological indicators. We evaluated overall performance during culture of L. vannamei at low salinity (6 psu), fed with an experimental diet with low protein and high carbohydrate content (26% protein and 6% fish meal plus probiotic mixture) and compared to a commercial formula with high protein and low carbohydrate content (40% crude protein and 20% fish meal without probiotic mixture). At the end of the rearing experiment, shrimp were exposed to two types of acute stress, hypoxia and escape. Biochemical (hemocyanin, total proteins, glucose, and lactate) and bioenergetic (adenylic energy charge and arginine phosphate levels) variables were measured to assess chronic stress response (salinity) and acute stress response (hypoxia or escape). The experimental diet resulted in higher muscle energy status that was not affected by low salinity, although lipid levels were lower under this condition. This diet partially counteracted the low performance at low salinity and promoted greater protein efficiency. Hypoxia induced strong hyperglycemic and lactate increase as response, whereas escape response was characterized by…
bibliographic citation: Martínez-Antonio et al. (2019) Modulation of stress response and productive performance of Litopenaeus vannamei through diet. PeerJ 7:e6850 https://doi.org/10.7717/peerj.6850
date submitted: 2018-12-26
date accepted: 2019-03-26
issued: 2019-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez-Antonio
  given name: Eliza M.
author list: Agent
  family name: Racotta
  given name: Ilie S.
author list: Agent
  family name: Ruvalcaba-Márquez
  given name: Juan C.
author list: Agent
  family name: Magallón-Barajas
  given name: Francisco
doi: 10.7717/peerj.6850
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-08
copyright: ©2019 Martínez-Antonio et al.
attribution name: Martínez-Antonio et al.

Comparison of microbial community structures in soils with woody organic amendments and soils with traditional local organic amendments in Ningxia of Northern China
type: item
type: AcademicArticle
description: Background Addition of organic amendments has been commonly adopted as a means to restore degraded soils globally. More recently, the use of woody organic amendments has been recognized as a viable method of capturing and retaining water and restoring degraded and desertified soil, especially in semi-arid regions. However, the impacts of woody amendments on soil microbial community structure, versus other traditional organic supplements is less understood. Methods Three locally available natural organic materials of different qualities, i.e., cow manure (CM), corn straw (CS), and chipped poplar branches (PB) were selected as treatments in Ningxia, Northern China and compared with control soils. Four microcosms served as replicates for each treatment. All treatments contained desertified soil; treatments with amendments were mixed with 3% (w/w) of one of the above organic materials. After 7 and 15 months from the start of the experiment, soil samples were analyzed for chemical and physical properties, along with biological properties, which included microbial α-diversity, community structure, and relative abundance of microbial phyla. Results Both bacterial and fungal α-diversity indices were weakly affected by amendments throughout the experimental period. All amendments yielded different microbial community compositions than the Control soils. The microbial community composition in the CS and PB treatments also were different from the CM treatment. After 15 months of the experiment, CS and PB exhibited similar microbial community composition, which was consistent with their similar soil physical and chemical properties. Moreover, CS and PB also appeared to exert similar effects on the abundance of some microbial taxa, and both of these treatments yield different abundances of microbial taxa than the CM treatment. Conclusion New local organic amendment with PB tended to affect the microbial community in a similar way to the traditional local organic amendment with C…
format: application/pdf
format: text/html
creator: Zhigang Li
creator: Kaiyang Qiu
creator: Rebecca L. Schneider
creator: Stephen J. Morreale
creator: Yingzhong Xie
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.6854
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background Addition of organic amendments has been commonly adopted as a means to restore degraded soils globally. More recently, the use of woody organic amendments has been recognized as a viable method of capturing and retaining water and restoring degraded and desertified soil, especially in semi-arid regions. However, the impacts of woody amendments on soil microbial community structure, versus other traditional organic supplements is less understood. Methods Three locally available natural organic materials of different qualities, i.e., cow manure (CM), corn straw (CS), and chipped poplar branches (PB) were selected as treatments in Ningxia, Northern China and compared with control soils. Four microcosms served as replicates for each treatment. All treatments contained desertified soil; treatments with amendments were mixed with 3% (w/w) of one of the above organic materials. After 7 and 15 months from the start of the experiment, soil samples were analyzed for chemical and physical properties, along with biological properties, which included microbial α-diversity, community structure, and relative abundance of microbial phyla. Results Both bacterial and fungal α-diversity indices were weakly affected by amendments throughout the experimental period. All amendments yielded different microbial community compositions than the Control soils. The microbial community composition in the CS and PB treatments also were different from the CM treatment. After 15 months of the experiment, CS and PB exhibited similar microbial community composition, which was consistent with their similar soil physical and chemical properties. Moreover, CS and PB also appeared to exert similar effects on the abundance of some microbial taxa, and both of these treatments yield different abundances of microbial taxa than the CM treatment. Conclusion New local organic amendment with PB tended to affect the microbial community in a similar way to the traditional local organic amendment with C…
bibliographic citation: Li et al. (2019) Comparison of microbial community structures in soils with woody organic amendments and soils with traditional local organic amendments in Ningxia of Northern China. PeerJ 7:e6854 https://doi.org/10.7717/peerj.6854
date submitted: 2019-01-08
date accepted: 2019-03-19
issued: 2019-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhigang
author list: Agent
  family name: Qiu
  given name: Kaiyang
author list: Agent
  family name: Schneider
  given name: Rebecca L.
author list: Agent
  family name: Morreale
  given name: Stephen J.
author list: Agent
  family name: Xie
  given name: Yingzhong
doi: 10.7717/peerj.6854
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-08
copyright: ©2019 Li et al.
attribution name: Li et al.

Leaf functional trait variation in a humid temperate forest, and relationships with juvenile tree light requirements
type: item
type: AcademicArticle
description: The species-rich arborescent assemblages of humid tropical forests encompass much of the known range of the leaf economics spectrum, often including >20-fold variation in leaf lifespan. This suite of traits underpins a life-history continuum from fast-growing pioneers to slow-growing shade-tolerant species. Less is known about the range of leaf traits in humid temperate forests, and there are conflicting reports about relationships of these traits with the light requirements of temperate evergreen angiosperms. Here I quantify the range of leaf functional traits in a New Zealand temperate evergreen forest, and relationships of these traits with light requirements of juvenile trees and shrubs. Foliage turnover of saplings of 19 evergreen angiosperms growing beneath gaps (12–29% canopy openness) and in understories (1.2–2.9%) was measured over 12 months. Dry mass per area (LMA), dry matter content, thickness, density and nitrogen content (N) of leaves were also measured. Species minimum light requirements were indexed as the 10th percentile of the distribution of saplings in relation to canopy openness. Interspecific variation of leaf lifespan was ∼6-fold in gaps (0.6 to 3.8 yrs), and ∼11-fold in the understorey (0.7 to 7.7 yrs). Six small tree and shrub species are effectively leaf-exchangers, with leaf lifespans of c.1 year in gaps—albeit usually longer in the shade. Interspecific variation in other leaf traits was 2.5 to 4-fold. Lifespans and LMA of both sun and shade leaves were negatively correlated with species light requirements i.e., positively correlated with shade tolerance. However, light environment (gap vs shade) explained about the same amount of variation in LMA as species’ identity did. Species light requirements were not significantly correlated with leaf N, dry matter content, density or thickness—except for a marginally significant correlation with dry matter content of shade leaves. Species light requirements were thus less consistently related to l…
format: application/pdf
format: text/html
creator: Christopher H. Lusk
subject: Biodiversity
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.6855
publisher: PeerJ Inc.
rights: © 2019 Lusk
abstract: The species-rich arborescent assemblages of humid tropical forests encompass much of the known range of the leaf economics spectrum, often including >20-fold variation in leaf lifespan. This suite of traits underpins a life-history continuum from fast-growing pioneers to slow-growing shade-tolerant species. Less is known about the range of leaf traits in humid temperate forests, and there are conflicting reports about relationships of these traits with the light requirements of temperate evergreen angiosperms. Here I quantify the range of leaf functional traits in a New Zealand temperate evergreen forest, and relationships of these traits with light requirements of juvenile trees and shrubs. Foliage turnover of saplings of 19 evergreen angiosperms growing beneath gaps (12–29% canopy openness) and in understories (1.2–2.9%) was measured over 12 months. Dry mass per area (LMA), dry matter content, thickness, density and nitrogen content (N) of leaves were also measured. Species minimum light requirements were indexed as the 10th percentile of the distribution of saplings in relation to canopy openness. Interspecific variation of leaf lifespan was ∼6-fold in gaps (0.6 to 3.8 yrs), and ∼11-fold in the understorey (0.7 to 7.7 yrs). Six small tree and shrub species are effectively leaf-exchangers, with leaf lifespans of c.1 year in gaps—albeit usually longer in the shade. Interspecific variation in other leaf traits was 2.5 to 4-fold. Lifespans and LMA of both sun and shade leaves were negatively correlated with species light requirements i.e., positively correlated with shade tolerance. However, light environment (gap vs shade) explained about the same amount of variation in LMA as species’ identity did. Species light requirements were not significantly correlated with leaf N, dry matter content, density or thickness—except for a marginally significant correlation with dry matter content of shade leaves. Species light requirements were thus less consistently related to l…
bibliographic citation: Lusk (2019) Leaf functional trait variation in a humid temperate forest, and relationships with juvenile tree light requirements. PeerJ 7:e6855 https://doi.org/10.7717/peerj.6855
date submitted: 2018-09-19
date accepted: 2019-03-27
issued: 2019-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lusk
  given name: Christopher H.
doi: 10.7717/peerj.6855
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-08
copyright: ©2019 Lusk
attribution name: Lusk

Ecosystem effects of fishing & El Niño at the Galápagos Marine Reserve
type: item
type: AcademicArticle
description: The Galápagos Archipelago is home to a diverse range of marine bioregions due to the confluence of several cold and warm water currents, resulting in some of the most productive tropical marine ecosystems in the world. These ecosystems are strongly influenced by El Niño events which can reduce primary production by an order of magnitude, dramatically reducing energy available throughout the food web. Fisheries are an important component of the local economy, although artisanal and illegal overfishing have dramatically reduced the productivity of invertebrate and finfish resources in recent decades, resulting in reductions in catches for local fishers. The regionally-endemic sailfin grouper (Myctereoperca olfax), locally known as bacalao, was once the most important fished species in the Galápagos, but is now listed as vulnerable by the IUCN due to its limited range and dramatic declines in catch over time. It is unknown how reduction of this predatory species has affected ecosystem structure and function. In the absence of stock assessments, we used an estimate of unfished bacalao biomass from fishers’ ecological knowledge along with unfished biomass estimates of other heavily exploited stocks—lobster (Panulirus penicillatus and P. gracilis) and sea cucumber (Isostichopus fuscus)—to create historical, unfished versions of existing modern day ecosystem models. We used the unfished and modern versions of the ecosystem models to test the ecosystem effects of bacalao exploitation at the Bolivar Channel, located in the cold, west upwelling bioregion of the archipelago during both El Niño and non El Niño years, and at Floreana Island, in the warmer, central bioregion. Fishers’ ecological knowledge indicates that at present, the biomass of bacalao is at least seven times lower than when unfished. This reduced bacalao biomass is linked with a greatly reduced ecosystem role compared to when unfished, and ecosystem role is further reduced in El Niño years. Allowing bacalao po…
format: application/pdf
format: text/html
creator: Tyler D. Eddy
creator: Alan M. Friedlander
creator: Pelayo Salinas de León
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Coupled Natural and Human Systems
subject: Climate Change Biology
description: doi:10.7717/peerj.6878
publisher: PeerJ Inc.
rights: © 2019 Eddy et al.
abstract: The Galápagos Archipelago is home to a diverse range of marine bioregions due to the confluence of several cold and warm water currents, resulting in some of the most productive tropical marine ecosystems in the world. These ecosystems are strongly influenced by El Niño events which can reduce primary production by an order of magnitude, dramatically reducing energy available throughout the food web. Fisheries are an important component of the local economy, although artisanal and illegal overfishing have dramatically reduced the productivity of invertebrate and finfish resources in recent decades, resulting in reductions in catches for local fishers. The regionally-endemic sailfin grouper (Myctereoperca olfax), locally known as bacalao, was once the most important fished species in the Galápagos, but is now listed as vulnerable by the IUCN due to its limited range and dramatic declines in catch over time. It is unknown how reduction of this predatory species has affected ecosystem structure and function. In the absence of stock assessments, we used an estimate of unfished bacalao biomass from fishers’ ecological knowledge along with unfished biomass estimates of other heavily exploited stocks—lobster (Panulirus penicillatus and P. gracilis) and sea cucumber (Isostichopus fuscus)—to create historical, unfished versions of existing modern day ecosystem models. We used the unfished and modern versions of the ecosystem models to test the ecosystem effects of bacalao exploitation at the Bolivar Channel, located in the cold, west upwelling bioregion of the archipelago during both El Niño and non El Niño years, and at Floreana Island, in the warmer, central bioregion. Fishers’ ecological knowledge indicates that at present, the biomass of bacalao is at least seven times lower than when unfished. This reduced bacalao biomass is linked with a greatly reduced ecosystem role compared to when unfished, and ecosystem role is further reduced in El Niño years. Allowing bacalao po…
bibliographic citation: Eddy et al. (2019) Ecosystem effects of fishing & El Niño at the Galápagos Marine Reserve. PeerJ 7:e6878 https://doi.org/10.7717/peerj.6878
date submitted: 2018-11-08
date accepted: 2019-03-31
issued: 2019-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eddy
  given name: Tyler D.
author list: Agent
  family name: Friedlander
  given name: Alan M.
author list: Agent
  family name: Salinas de León
  given name: Pelayo
doi: 10.7717/peerj.6878
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-08
copyright: © 2019 Eddy et al.
attribution name: Eddy et al.

Effect of isolation on coat colour polymorphism of Polynesian rats in Island Southeast Asia and the Pacific
type: item
type: AcademicArticle
description: Populations of vertebrate species introduced onto islands regularly develop similar phenotypic changes, e.g., larger or smaller body size, shortened limbs, duller coats, as well as behavioural changes such as increased tameness and reduced flight-initiation distance. These changes overlap in part with those associated with the ‘domestication syndrome’, especially tameness and changes in coat patterns, and might indicate a similar neural crest involvement in the concurrent development of multiple phenotypic traits. Here I examine long-term data on free-living populations of wild Polynesian rats from seven mainland countries and 117 islands (n = 3,034), covering the species’ native and introduced range. Mainland populations showed no aberrant coat patterns, with the exception of one albino, whereas aberrant coat patterns were found in 12 island populations. Observed coat colour polymorphisms consisted of leucistic (including singular white patches), melanistic (darkly pigmented) and piebald (mixed) coat patterns. After isolation for at least seven centuries, wild Polynesian rat populations on islands seem to exhibit a trend towards a higher incidence of aberrant coat patterns. These phenotypic changes are here explained as a neutral, non-adaptive process, likely part of the ‘domestication syndrome’ (via the commensal pathway of domestication), in combination with genetic drift, little or no gene flow between the islands and/or the mainland and a relaxed selection (as a result of the weakening or removal of competitor/predator pressure) under commensality.
format: application/pdf
format: text/html
creator: Alexandra A.E. van der Geer
subject: Biogeography
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6894
publisher: PeerJ Inc.
rights: © 2019 van der Geer
abstract: Populations of vertebrate species introduced onto islands regularly develop similar phenotypic changes, e.g., larger or smaller body size, shortened limbs, duller coats, as well as behavioural changes such as increased tameness and reduced flight-initiation distance. These changes overlap in part with those associated with the ‘domestication syndrome’, especially tameness and changes in coat patterns, and might indicate a similar neural crest involvement in the concurrent development of multiple phenotypic traits. Here I examine long-term data on free-living populations of wild Polynesian rats from seven mainland countries and 117 islands (n = 3,034), covering the species’ native and introduced range. Mainland populations showed no aberrant coat patterns, with the exception of one albino, whereas aberrant coat patterns were found in 12 island populations. Observed coat colour polymorphisms consisted of leucistic (including singular white patches), melanistic (darkly pigmented) and piebald (mixed) coat patterns. After isolation for at least seven centuries, wild Polynesian rat populations on islands seem to exhibit a trend towards a higher incidence of aberrant coat patterns. These phenotypic changes are here explained as a neutral, non-adaptive process, likely part of the ‘domestication syndrome’ (via the commensal pathway of domestication), in combination with genetic drift, little or no gene flow between the islands and/or the mainland and a relaxed selection (as a result of the weakening or removal of competitor/predator pressure) under commensality.
bibliographic citation: van der Geer (2019) Effect of isolation on coat colour polymorphism of Polynesian rats in Island Southeast Asia and the Pacific. PeerJ 7:e6894 https://doi.org/10.7717/peerj.6894
date submitted: 2018-11-19
date accepted: 2019-04-02
issued: 2019-05-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van der Geer
  given name: Alexandra A.E.
doi: 10.7717/peerj.6894
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-08
copyright: ©2019 van der Geer
attribution name: van der Geer

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