PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: 13C values of glycolytic amino acids as indicators of carbohydrate utilization in carnivorous fish
items: Dynamics of carbon and nitrogen storage in two typical plantation ecosystems of different stand ages on the Loess Plateau of China
items: Mismatches between the genetic and phenotypic sex in the wild Kou population of Nile tilapia Oreochromis niloticus
items: Chemical characterisation of potential pheromones from the shoulder gland of the Northern yellow-shouldered-bat, Sturnira parvidens (Phyllostomidae: Stenodermatinae)
items: The effect of elevational gradient on alpine gingers (Roscoea alpina and R. purpurea) in the Himalayas
items: A novel methodology for optimal land allocation for agricultural crops using Social Spider Algorithm
items: Estimation of maize above-ground biomass based on stem-leaf separation strategy integrated with LiDAR and optical remote sensing data
items: Undesirable immigrants: hobbyist vivaria as a potential source of alien invertebrate species
items: From habitat use to social behavior: natural history of a voiceless poison frog, Dendrobates tinctorius
items: Collisional mechanics of the diagonal gaits of horses over a range of speeds

13C values of glycolytic amino acids as indicators of carbohydrate utilization in carnivorous fish
type: item
type: AcademicArticle
description: Background Stable isotope analysis of single amino acids (AA) is usually applied in food web studies for tracing biosynthetic origins of AA carbon backbones and establishing trophic positions of consumers, but the method is also showing promise for characterizing quantity and quality of dietary lipids and carbohydrates. Methods To investigate whether changes in high- and low-digestible carbohydrates affect δ13C values of glycolytic AA, i.e., AA carbon backbones sourced from the glycolytic pathway, we compared Atlantic salmon (Salmo salar) from a feeding experiment with and without dietary inclusion of the red macroalga Palmaria palmata. The Control and experimental diets had similar relative proportions of macronutrients, but their ingredients differed; in the experimental treatment, 15% Palmaria inclusion substituted proteins from fishmeal and carbohydrates from corn starch. Results We found that 13C values of the glycolytic AA were highly sensitive to substitution of corn starch with Palmaria. The δ13C offsets of glycolytic AA between salmon and their diets were significantly greater in the Palmaria inclusion than Control treatment. This greater offset can be attributed to the different utilization of high- vs. low-digestible carbohydrate sources, i.e., corn starch vs. Palmaria, in the two treatments, and metabolic routing of dietary lipids. In addition, similar δ13C values of essential AA between treatments indicate similar nutrient assimilation efficiency for all terrestrial (pea protein concentrate and wheat gluten meal) and marine (fishmeal and red alga) derived protein sources. These results show that δ13CAA analysis is a promising tool for improving our understanding of how carnivorous fish utilize macronutrient and route metabolic intermediates to tissue.
format: application/pdf
format: text/html
creator: Yiming V. Wang
creator: Alex H.L. Wan
creator: Åshild Krogdahl
creator: Mark Johnson
creator: Thomas Larsen
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Ecology
description: doi:10.7717/peerj.7701
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Stable isotope analysis of single amino acids (AA) is usually applied in food web studies for tracing biosynthetic origins of AA carbon backbones and establishing trophic positions of consumers, but the method is also showing promise for characterizing quantity and quality of dietary lipids and carbohydrates. Methods To investigate whether changes in high- and low-digestible carbohydrates affect δ13C values of glycolytic AA, i.e., AA carbon backbones sourced from the glycolytic pathway, we compared Atlantic salmon (Salmo salar) from a feeding experiment with and without dietary inclusion of the red macroalga Palmaria palmata. The Control and experimental diets had similar relative proportions of macronutrients, but their ingredients differed; in the experimental treatment, 15% Palmaria inclusion substituted proteins from fishmeal and carbohydrates from corn starch. Results We found that 13C values of the glycolytic AA were highly sensitive to substitution of corn starch with Palmaria. The δ13C offsets of glycolytic AA between salmon and their diets were significantly greater in the Palmaria inclusion than Control treatment. This greater offset can be attributed to the different utilization of high- vs. low-digestible carbohydrate sources, i.e., corn starch vs. Palmaria, in the two treatments, and metabolic routing of dietary lipids. In addition, similar δ13C values of essential AA between treatments indicate similar nutrient assimilation efficiency for all terrestrial (pea protein concentrate and wheat gluten meal) and marine (fishmeal and red alga) derived protein sources. These results show that δ13CAA analysis is a promising tool for improving our understanding of how carnivorous fish utilize macronutrient and route metabolic intermediates to tissue.
bibliographic citation: Wang et al. (2019) 13C values of glycolytic amino acids as indicators of carbohydrate utilization in carnivorous fish. PeerJ 7:e7701 https://doi.org/10.7717/peerj.7701
date submitted: 2019-06-15
date accepted: 2019-08-19
issued: 2019-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yiming V.
author list: Agent
  family name: Wan
  given name: Alex H.L.
author list: Agent
  family name: Krogdahl
  given name: Åshild
author list: Agent
  family name: Johnson
  given name: Mark
author list: Agent
  family name: Larsen
  given name: Thomas
doi: 10.7717/peerj.7701
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-18
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Dynamics of carbon and nitrogen storage in two typical plantation ecosystems of different stand ages on the Loess Plateau of China
type: item
type: AcademicArticle
description: In China’s Loess Plateau, afforestation and reforestation are considered the foremost practices for sequestering carbon and conserving soil and water. In order to evaluate the carbon storage changes of tree, soil, and litter, and the soil total nitrogen (STN) in two typical artificial forests in the region, we conducted plot surveys for different ages of both artificial forest types. Soil samples were collected at different depths from 0–100 cm. The results indicated that forest ecosystem carbon storage increased with tree development. The rates of mean annual carbon sequestration of Pinus tabulaeformis and Robinia pseudoacacia plantation ecosystems were 3.31 and 3.53 Mg ha−1 year−1, respectively. The rate of mean annual carbon sequestration of R. pseudoacacia plantation ecosystems was higher by 6.65% than that of P. tabulaeformis plantation ecosystems. The soil organic carbon (SOC) and STN decreased at deeper soil depths in both plantations at different stand ages, significantly decreasing in the 0–60 cm of soil (P < 0.05), and the highest SOC content and storage were in the top 0–20 cm of soil. The temporal patterns for SOC and STN changes at different soil sampling depths from 0 to 100 cm all showed an initial decrease during the early stage of restoration, and then an increase that coincided with the development of the two plantation forests. At 0–100 cm depth, the SOC storage was in the range of 40.95–106.79 and 45.13–113.61 Mg ha−1 for the P. tabulaeformis forest and R. pseudoacacia forest, respectively. The STN storage in the 0–100 cm soil layer with the stand age development ranged from 4.16 to 8.34 Mg ha−1 in the R. pseudoacacia plantation and 4.19–7.55 Mg ha−1 in the P. tabulaeformis forest. The results showed a significant positive correlation between SOC and STN. This study suggests that we should pay more attention to changes in soil carbon and nitrogen sequestration during long-term vegetation restoration.
format: application/pdf
format: text/html
creator: Yanfang Wang
creator: Ling Liu
creator: Feixue Yue
creator: Dong Li
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.7708
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: In China’s Loess Plateau, afforestation and reforestation are considered the foremost practices for sequestering carbon and conserving soil and water. In order to evaluate the carbon storage changes of tree, soil, and litter, and the soil total nitrogen (STN) in two typical artificial forests in the region, we conducted plot surveys for different ages of both artificial forest types. Soil samples were collected at different depths from 0–100 cm. The results indicated that forest ecosystem carbon storage increased with tree development. The rates of mean annual carbon sequestration of Pinus tabulaeformis and Robinia pseudoacacia plantation ecosystems were 3.31 and 3.53 Mg ha−1 year−1, respectively. The rate of mean annual carbon sequestration of R. pseudoacacia plantation ecosystems was higher by 6.65% than that of P. tabulaeformis plantation ecosystems. The soil organic carbon (SOC) and STN decreased at deeper soil depths in both plantations at different stand ages, significantly decreasing in the 0–60 cm of soil (P < 0.05), and the highest SOC content and storage were in the top 0–20 cm of soil. The temporal patterns for SOC and STN changes at different soil sampling depths from 0 to 100 cm all showed an initial decrease during the early stage of restoration, and then an increase that coincided with the development of the two plantation forests. At 0–100 cm depth, the SOC storage was in the range of 40.95–106.79 and 45.13–113.61 Mg ha−1 for the P. tabulaeformis forest and R. pseudoacacia forest, respectively. The STN storage in the 0–100 cm soil layer with the stand age development ranged from 4.16 to 8.34 Mg ha−1 in the R. pseudoacacia plantation and 4.19–7.55 Mg ha−1 in the P. tabulaeformis forest. The results showed a significant positive correlation between SOC and STN. This study suggests that we should pay more attention to changes in soil carbon and nitrogen sequestration during long-term vegetation restoration.
bibliographic citation: Wang et al. (2019) Dynamics of carbon and nitrogen storage in two typical plantation ecosystems of different stand ages on the Loess Plateau of China. PeerJ 7:e7708 https://doi.org/10.7717/peerj.7708
date submitted: 2019-03-20
date accepted: 2019-08-20
issued: 2019-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yanfang
author list: Agent
  family name: Liu
  given name: Ling
author list: Agent
  family name: Yue
  given name: Feixue
author list: Agent
  family name: Li
  given name: Dong
doi: 10.7717/peerj.7708
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-18
copyright: © 2019 Wang et al.
attribution name: Wang et al.

Mismatches between the genetic and phenotypic sex in the wild Kou population of Nile tilapia Oreochromis niloticus
type: item
type: AcademicArticle
description: Sex determination and sex chromosomes can be very diverse between teleost species. The group of tilapias shows a polymorphism in sex determination not only between closely related species but also between domestic strains within a species. In the Nile tilapia, the major effect genes and therefore the Y chromosome have been located on either linkage group 1 (LG1) or LG23 depending on the strains. In a Japanese strain, the sex determinant of LG23 (the amhY gene) has been identified as a duplicated amh (anti-Müllerian hormone) gene, with its gametolog found on the X chromosome (amhX). AmhY is located in tandem with the amhΔY gene (a truncated form) on the Y chromosome. X and Y chromosome markers based on the amh genes have been validated only on a few domestic strains but not in wild populations. Here, we used four of these markers in order to examine (1) the possible variation in sex determination of a wild population of Nile tilapia living in Lake Kou (Burkina Faso), (2) putative polymorphisms for these amh copies and (3) the existence of sex reversed individuals in the wild. Our genotyping of 91 wild Kou individuals with the amh sex-diagnostic markers of LG23 showed that while phenotypic females were all XX, phenotypic males were either XY or XX. Progeny testing of eight of these XX males revealed that one of these males consistently sired all-female progenies, suggesting that it is a wild sex reversed male (which could result from high temperature effects). The other XX males gave balanced sex ratios, suggesting that sex is controlled by another locus (possibly on another LG) which may be epistatically dominant over the LG23 locus. Finally, identification of unexpected amh genotypes was found for two individuals. They produced either balanced or female-biased sex ratios, depending on the breeder with whom they were crossed, suggesting possible recombination between the X and the Y chromosomes.
format: application/pdf
format: text/html
creator: Rokyatou Sissao
creator: Helena D’Cotta
creator: Jean-François Baroiller
creator: Aboubacar Toguyeni
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Ecology
subject: Genetics
description: doi:10.7717/peerj.7709
publisher: PeerJ Inc.
rights: © 2019 Sissao et al.
abstract: Sex determination and sex chromosomes can be very diverse between teleost species. The group of tilapias shows a polymorphism in sex determination not only between closely related species but also between domestic strains within a species. In the Nile tilapia, the major effect genes and therefore the Y chromosome have been located on either linkage group 1 (LG1) or LG23 depending on the strains. In a Japanese strain, the sex determinant of LG23 (the amhY gene) has been identified as a duplicated amh (anti-Müllerian hormone) gene, with its gametolog found on the X chromosome (amhX). AmhY is located in tandem with the amhΔY gene (a truncated form) on the Y chromosome. X and Y chromosome markers based on the amh genes have been validated only on a few domestic strains but not in wild populations. Here, we used four of these markers in order to examine (1) the possible variation in sex determination of a wild population of Nile tilapia living in Lake Kou (Burkina Faso), (2) putative polymorphisms for these amh copies and (3) the existence of sex reversed individuals in the wild. Our genotyping of 91 wild Kou individuals with the amh sex-diagnostic markers of LG23 showed that while phenotypic females were all XX, phenotypic males were either XY or XX. Progeny testing of eight of these XX males revealed that one of these males consistently sired all-female progenies, suggesting that it is a wild sex reversed male (which could result from high temperature effects). The other XX males gave balanced sex ratios, suggesting that sex is controlled by another locus (possibly on another LG) which may be epistatically dominant over the LG23 locus. Finally, identification of unexpected amh genotypes was found for two individuals. They produced either balanced or female-biased sex ratios, depending on the breeder with whom they were crossed, suggesting possible recombination between the X and the Y chromosomes.
bibliographic citation: Sissao et al. (2019) Mismatches between the genetic and phenotypic sex in the wild Kou population of Nile tilapia Oreochromis niloticus. PeerJ 7:e7709 https://doi.org/10.7717/peerj.7709
date submitted: 2019-03-20
date accepted: 2019-08-20
issued: 2019-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sissao
  given name: Rokyatou
author list: Agent
  family name: D’Cotta
  given name: Helena
author list: Agent
  family name: Baroiller
  given name: Jean-François
author list: Agent
  family name: Toguyeni
  given name: Aboubacar
doi: 10.7717/peerj.7709
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-18
copyright: ©2019 Sissao et al.
attribution name: Sissao et al.

Chemical characterisation of potential pheromones from the shoulder gland of the Northern yellow-shouldered-bat, Sturnira parvidens (Phyllostomidae: Stenodermatinae)
type: item
type: AcademicArticle
description: Bats of the genus Sturnira (Family Phyllostomidae) are characterised by shoulder glands that are more developed in reproductively mature adult males. The glands produce a waxy secretion that accumulates on the fur around the gland, dyeing the fur a dark colour and giving off a pungent odour. These shoulder glands are thought to play a role in their reproductive behaviour. Using gas chromatography–mass spectrometry, we analysed solvent extracts of fur surrounding the shoulder gland in the northern-shouldered bat, Sturnira parvidens to (i) characterise the chemical composition of shoulder gland secretions for the first time, and (ii) look for differences in chemical composition among and between adult males, sub-adult/juvenile males and adult females. Fur solvent extracts were analysed as liquids and also further extracted using headspace solid-phase microextraction to identify volatile components in the odour itself. Odour fingerprint analysis using non-metric multidimensional scaling plots and multivariate analysis revealed clear and significant differences (P < 0.001) between adult males vs both juvenile males and adult females. The chemical components of the shoulder gland secretion included terpenes and phenolics, together with alcohols and esters, most likely derived from the frugivorous diet of the bat. Many of the compounds identified were found exclusively or in elevated quantities among adult (reproductive) males compared with adult females and non-reproductive (juvenile) males. This strongly suggests a specific role in male–female attraction although a function in male–male competition and/or species recognition is also possible.
format: application/pdf
format: text/html
creator: Chris G. Faulkes
creator: J. Stephen Elmore
creator: David A. Baines
creator: Brock Fenton
creator: Nancy B. Simmons
creator: Elizabeth L. Clare
subject: Animal Behavior
subject: Biochemistry
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.7734
publisher: PeerJ Inc.
rights: © 2019 Faulkes et al.
abstract: Bats of the genus Sturnira (Family Phyllostomidae) are characterised by shoulder glands that are more developed in reproductively mature adult males. The glands produce a waxy secretion that accumulates on the fur around the gland, dyeing the fur a dark colour and giving off a pungent odour. These shoulder glands are thought to play a role in their reproductive behaviour. Using gas chromatography–mass spectrometry, we analysed solvent extracts of fur surrounding the shoulder gland in the northern-shouldered bat, Sturnira parvidens to (i) characterise the chemical composition of shoulder gland secretions for the first time, and (ii) look for differences in chemical composition among and between adult males, sub-adult/juvenile males and adult females. Fur solvent extracts were analysed as liquids and also further extracted using headspace solid-phase microextraction to identify volatile components in the odour itself. Odour fingerprint analysis using non-metric multidimensional scaling plots and multivariate analysis revealed clear and significant differences (P < 0.001) between adult males vs both juvenile males and adult females. The chemical components of the shoulder gland secretion included terpenes and phenolics, together with alcohols and esters, most likely derived from the frugivorous diet of the bat. Many of the compounds identified were found exclusively or in elevated quantities among adult (reproductive) males compared with adult females and non-reproductive (juvenile) males. This strongly suggests a specific role in male–female attraction although a function in male–male competition and/or species recognition is also possible.
bibliographic citation: Faulkes et al. (2019) Chemical characterisation of potential pheromones from the shoulder gland of the Northern yellow-shouldered-bat, Sturnira parvidens (Phyllostomidae: Stenodermatinae). PeerJ 7:e7734 https://doi.org/10.7717/peerj.7734
date submitted: 2019-04-25
date accepted: 2019-08-23
issued: 2019-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Faulkes
  given name: Chris G.
author list: Agent
  family name: Elmore
  given name: J. Stephen
author list: Agent
  family name: Baines
  given name: David A.
author list: Agent
  family name: Fenton
  given name: Brock
author list: Agent
  family name: Simmons
  given name: Nancy B.
author list: Agent
  family name: Clare
  given name: Elizabeth L.
doi: 10.7717/peerj.7734
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-18
copyright: © 2019 Faulkes et al.
attribution name: Faulkes et al.

The effect of elevational gradient on alpine gingers (Roscoea alpina and R. purpurea) in the Himalayas
type: item
type: AcademicArticle
description: There is currently enormous interest in how morphological and physiological responses of herbaceous plants may be affected by changing elevational gradient. Mountain regions provide an excellent opportunity to understand how closely related species may adapt to the conditions that rapidly change with elevation. We investigated the morphological and physiological responses of two Himalayan alpine gingers (Roscoea alpina and R. purpurea) along two different vertical transects of 400 m, R. purpurea between 2,174–2,574 m a.s.l and R. alpina between 2,675–3,079 m a.s.l. We measured the variables of plant height, leaf length, leaf area, specific leaf area, and stomata density at five plots, along the vertical transect at an elevational gap of ca. 100 m. Results revealed that with increased elevation plant height, and leaf area decreased while stomata density increased, whereas changes in specific leaf area, were not correlated with the elevation. Our results reveal that these alpine gingers undergo local adaptation by modifying their plant height, leaf area and stomata density in response to the varying selection pressure associated with the elevational gradient. Thus, the findings of this research provide valuable information on how a narrow range of elevational gradient affects the herbaceous plants at the alpine habitat of the Himalayas.
format: application/pdf
format: text/html
creator: Babu Ram Paudel
creator: Adrian G. Dyer
creator: Jair E. Garcia
creator: Mani Shrestha
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.7503
publisher: PeerJ Inc.
rights: © 2019 Paudel et al.
abstract: There is currently enormous interest in how morphological and physiological responses of herbaceous plants may be affected by changing elevational gradient. Mountain regions provide an excellent opportunity to understand how closely related species may adapt to the conditions that rapidly change with elevation. We investigated the morphological and physiological responses of two Himalayan alpine gingers (Roscoea alpina and R. purpurea) along two different vertical transects of 400 m, R. purpurea between 2,174–2,574 m a.s.l and R. alpina between 2,675–3,079 m a.s.l. We measured the variables of plant height, leaf length, leaf area, specific leaf area, and stomata density at five plots, along the vertical transect at an elevational gap of ca. 100 m. Results revealed that with increased elevation plant height, and leaf area decreased while stomata density increased, whereas changes in specific leaf area, were not correlated with the elevation. Our results reveal that these alpine gingers undergo local adaptation by modifying their plant height, leaf area and stomata density in response to the varying selection pressure associated with the elevational gradient. Thus, the findings of this research provide valuable information on how a narrow range of elevational gradient affects the herbaceous plants at the alpine habitat of the Himalayas.
bibliographic citation: Paudel et al. (2019) The effect of elevational gradient on alpine gingers (Roscoea alpina and R. purpurea) in the Himalayas. PeerJ 7:e7503 https://doi.org/10.7717/peerj.7503
date submitted: 2019-03-21
date accepted: 2019-07-17
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paudel
  given name: Babu Ram
author list: Agent
  family name: Dyer
  given name: Adrian G.
author list: Agent
  family name: Garcia
  given name: Jair E.
author list: Agent
  family name: Shrestha
  given name: Mani
doi: 10.7717/peerj.7503
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: ©2019 Paudel et al.
attribution name: Paudel et al.

A novel methodology for optimal land allocation for agricultural crops using Social Spider Algorithm
type: item
type: AcademicArticle
description: In the current agricultural scenario, availability of suitable land for cultivation is less and profitable allocation of the land for cultivating crops seems to be a cumbersome task. Crop planning optimization is a major research field in agriculture, in which land optimization is a significant challenge, which falls under the category of combinatorial optimization problems. The main objective of the present research is to maximize the net income from agriculture through optimal land allocation. Bio-inspired algorithms are quite popular in solving combinatorial optimization problems. Social Spider Algorithm (SSA), a new bio-inspired algorithm, is used to solve land optimization problem in this research based on the simulation of cooperative behaviour of social spiders. The agricultural area chosen for case study is the Coimbatore region, located in Tamilnadu state, India and the relevant data for the crops are collected from Tamilnadu Agricultural University Coimbatore, India. The optimal planting area, crop productivity for various land holdings and the water requirements are computed by SSA and the results have shown better directions for agricultural planning to improve the profit with constrained land area and water limitations.
format: application/pdf
format: text/html
creator: N Thilagavathi
creator: T Amudha
subject: Agricultural Science
subject: Computational Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.7559
publisher: PeerJ Inc.
rights: © 2019 Thilagavathi and Amudha
abstract: In the current agricultural scenario, availability of suitable land for cultivation is less and profitable allocation of the land for cultivating crops seems to be a cumbersome task. Crop planning optimization is a major research field in agriculture, in which land optimization is a significant challenge, which falls under the category of combinatorial optimization problems. The main objective of the present research is to maximize the net income from agriculture through optimal land allocation. Bio-inspired algorithms are quite popular in solving combinatorial optimization problems. Social Spider Algorithm (SSA), a new bio-inspired algorithm, is used to solve land optimization problem in this research based on the simulation of cooperative behaviour of social spiders. The agricultural area chosen for case study is the Coimbatore region, located in Tamilnadu state, India and the relevant data for the crops are collected from Tamilnadu Agricultural University Coimbatore, India. The optimal planting area, crop productivity for various land holdings and the water requirements are computed by SSA and the results have shown better directions for agricultural planning to improve the profit with constrained land area and water limitations.
bibliographic citation: Thilagavathi et al. (2019) A novel methodology for optimal land allocation for agricultural crops using Social Spider Algorithm. PeerJ 7:e7559 https://doi.org/10.7717/peerj.7559
date submitted: 2019-04-08
date accepted: 2019-07-26
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thilagavathi
  given name: N
author list: Agent
  family name: Amudha
  given name: T
doi: 10.7717/peerj.7559
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: ©2019 Thilagavathi and Amudha
attribution name: Thilagavathi and Amudha

Estimation of maize above-ground biomass based on stem-leaf separation strategy integrated with LiDAR and optical remote sensing data
type: item
type: AcademicArticle
description: Above-ground biomass (AGB) is an important indicator for effectively assessing crop growth and yield and, in addition, is an important ecological indicator for assessing the efficiency with which crops use light and store carbon in ecosystems. However, most existing methods using optical remote sensing to estimate AGB cannot observe structures below the maize canopy, which may lead to poor estimation accuracy. This paper proposes to use the stem-leaf separation strategy integrated with unmanned aerial vehicle LiDAR and multispectral image data to estimate the AGB in maize. First, the correlation matrix was used to screen optimal the LiDAR structural parameters (LSPs) and the spectral vegetation indices (SVIs). According to the screened indicators, the SVIs and the LSPs were subjected to multivariable linear regression (MLR) with the above-ground leaf biomass (AGLB) and above-ground stem biomass (AGSB), respectively. At the same time, all SVIs derived from multispectral data and all LSPs derived from LiDAR data were subjected to partial least squares regression (PLSR) with the AGLB and AGSB, respectively. Finally, the AGB was computed by adding the AGLB and the AGSB, and each was estimated by using the MLR and the PLSR methods, respectively. The results indicate a strong correlation between the estimated and field-observed AGB using the MLR method (R2 = 0.82, RMSE = 79.80 g/m2, NRMSE = 11.12%) and the PLSR method (R2 = 0.86, RMSE = 72.28 g/m2, NRMSE = 10.07%). The results indicate that PLSR more accurately estimates AGB than MLR, with R2 increasing by 0.04, root mean square error (RMSE) decreasing by 7.52 g/m2, and normalized root mean square error (NRMSE) decreasing by 1.05%. In addition, the AGB is more accurately estimated by combining LiDAR with multispectral data than LiDAR and multispectral data alone, with R2 increasing by 0.13 and 0.30, respectively, RMSE decreasing by 22.89 and 54.92 g/m2, respectively, and NRMSE decreasing by 4.46% and 7.65%, respectively. …
format: application/pdf
format: text/html
creator: Yaohui Zhu
creator: Chunjiang Zhao
creator: Hao Yang
creator: Guijun Yang
creator: Liang Han
creator: Zhenhai Li
creator: Haikuan Feng
creator: Bo Xu
creator: Jintao Wu
creator: Lei Lei
subject: Agricultural Science
subject: Statistics
description: doi:10.7717/peerj.7593
publisher: PeerJ Inc.
rights: © 2019 Zhu et al.
abstract: Above-ground biomass (AGB) is an important indicator for effectively assessing crop growth and yield and, in addition, is an important ecological indicator for assessing the efficiency with which crops use light and store carbon in ecosystems. However, most existing methods using optical remote sensing to estimate AGB cannot observe structures below the maize canopy, which may lead to poor estimation accuracy. This paper proposes to use the stem-leaf separation strategy integrated with unmanned aerial vehicle LiDAR and multispectral image data to estimate the AGB in maize. First, the correlation matrix was used to screen optimal the LiDAR structural parameters (LSPs) and the spectral vegetation indices (SVIs). According to the screened indicators, the SVIs and the LSPs were subjected to multivariable linear regression (MLR) with the above-ground leaf biomass (AGLB) and above-ground stem biomass (AGSB), respectively. At the same time, all SVIs derived from multispectral data and all LSPs derived from LiDAR data were subjected to partial least squares regression (PLSR) with the AGLB and AGSB, respectively. Finally, the AGB was computed by adding the AGLB and the AGSB, and each was estimated by using the MLR and the PLSR methods, respectively. The results indicate a strong correlation between the estimated and field-observed AGB using the MLR method (R2 = 0.82, RMSE = 79.80 g/m2, NRMSE = 11.12%) and the PLSR method (R2 = 0.86, RMSE = 72.28 g/m2, NRMSE = 10.07%). The results indicate that PLSR more accurately estimates AGB than MLR, with R2 increasing by 0.04, root mean square error (RMSE) decreasing by 7.52 g/m2, and normalized root mean square error (NRMSE) decreasing by 1.05%. In addition, the AGB is more accurately estimated by combining LiDAR with multispectral data than LiDAR and multispectral data alone, with R2 increasing by 0.13 and 0.30, respectively, RMSE decreasing by 22.89 and 54.92 g/m2, respectively, and NRMSE decreasing by 4.46% and 7.65%, respectively. …
bibliographic citation: Zhu et al. (2019) Estimation of maize above-ground biomass based on stem-leaf separation strategy integrated with LiDAR and optical remote sensing data. PeerJ 7:e7593 https://doi.org/10.7717/peerj.7593
date submitted: 2019-04-19
date accepted: 2019-07-31
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Yaohui
author list: Agent
  family name: Zhao
  given name: Chunjiang
author list: Agent
  family name: Yang
  given name: Hao
author list: Agent
  family name: Yang
  given name: Guijun
author list: Agent
  family name: Han
  given name: Liang
author list: Agent
  family name: Li
  given name: Zhenhai
author list: Agent
  family name: Feng
  given name: Haikuan
author list: Agent
  family name: Xu
  given name: Bo
author list: Agent
  family name: Wu
  given name: Jintao
author list: Agent
  family name: Lei
  given name: Lei
doi: 10.7717/peerj.7593
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: © 2019 Zhu et al.
attribution name: Zhu et al.

Undesirable immigrants: hobbyist vivaria as a potential source of alien invertebrate species
type: item
type: AcademicArticle
description: Background Small size and large diversity of adaptations make invertebrates a group of animals which can be easily transported by different human activities. Many species can travel as “hitchhikers” with plant material (both on plant surfaces and in the soil), including plants used for decoration in vivaria. Vivaria are often tropical in nature environments, with high temperatures and humidity, suitable for invertebrates from tropical regions. Although many of such invertebrates cannot survive in temperate regions where harsh weather conditions are present, it is also known that some can successfully acclimatise. As a result, their negative impact on local flora and fauna cannot be excluded. Material and methods Terrestrial invertebrates were collected in several cities of Poland from tropical vivaria where poison dart frogs (Dendrobatidae) and/or orchids (Orchidaceae) were kept by hobbyists. Collecting of the material was preceded by a simple questionnaire placed on the biggest Polish forum devoted to poison dart frogs. Moreover, we contacted some Polish wholesalers offering tropical invertebrates (Isopoda and Collembola), used as the food source for frogs, hoping to receive information about locations where those invertebrates were delivered, over the period of one year. We obtained mtDNA barcodes using the COI marker (cytochrome c oxidase subunit I gene) for seven potential morphospecies. Results In total, 12 taxa classified as Turbellaria, Annelida, Gastropoda, Isopoda, Diplopoda, Chilopoda and Collembola were collected and preserved in pure ethanol. We collected material and/or information from 65 locations, including 56 cities to which exotic isopods and springtails were sold by wholesalers over the period of nine months (average number per month = 18 cities). We obtained 18 COI sequences which were assigned to seven BINs and thus confirmed identification of seven species. The results indicate that the number of species transported with exotic plants is not sm…
format: application/pdf
format: text/html
creator: Radomir Jaskuła
creator: Anna Sulikowska-Drozd
creator: Aleksandra Jabłońska
creator: Krzysztof Banaś
creator: Tomasz Rewicz
subject: Biodiversity
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.7617
publisher: PeerJ Inc.
rights: © 2019 Jaskuła et al.
abstract: Background Small size and large diversity of adaptations make invertebrates a group of animals which can be easily transported by different human activities. Many species can travel as “hitchhikers” with plant material (both on plant surfaces and in the soil), including plants used for decoration in vivaria. Vivaria are often tropical in nature environments, with high temperatures and humidity, suitable for invertebrates from tropical regions. Although many of such invertebrates cannot survive in temperate regions where harsh weather conditions are present, it is also known that some can successfully acclimatise. As a result, their negative impact on local flora and fauna cannot be excluded. Material and methods Terrestrial invertebrates were collected in several cities of Poland from tropical vivaria where poison dart frogs (Dendrobatidae) and/or orchids (Orchidaceae) were kept by hobbyists. Collecting of the material was preceded by a simple questionnaire placed on the biggest Polish forum devoted to poison dart frogs. Moreover, we contacted some Polish wholesalers offering tropical invertebrates (Isopoda and Collembola), used as the food source for frogs, hoping to receive information about locations where those invertebrates were delivered, over the period of one year. We obtained mtDNA barcodes using the COI marker (cytochrome c oxidase subunit I gene) for seven potential morphospecies. Results In total, 12 taxa classified as Turbellaria, Annelida, Gastropoda, Isopoda, Diplopoda, Chilopoda and Collembola were collected and preserved in pure ethanol. We collected material and/or information from 65 locations, including 56 cities to which exotic isopods and springtails were sold by wholesalers over the period of nine months (average number per month = 18 cities). We obtained 18 COI sequences which were assigned to seven BINs and thus confirmed identification of seven species. The results indicate that the number of species transported with exotic plants is not sm…
bibliographic citation: Jaskuła et al. (2019) Undesirable immigrants: hobbyist vivaria as a potential source of alien invertebrate species. PeerJ 7:e7617 https://doi.org/10.7717/peerj.7617
date submitted: 2018-03-31
date accepted: 2019-08-05
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jaskuła
  given name: Radomir
author list: Agent
  family name: Sulikowska-Drozd
  given name: Anna
author list: Agent
  family name: Jabłońska
  given name: Aleksandra
author list: Agent
  family name: Banaś
  given name: Krzysztof
author list: Agent
  family name: Rewicz
  given name: Tomasz
doi: 10.7717/peerj.7617
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: ©2019 Jaskuła et al.
attribution name: Jaskuła et al.

From habitat use to social behavior: natural history of a voiceless poison frog, Dendrobates tinctorius
type: item
type: AcademicArticle
description: Descriptive studies of natural history have always been a source of knowledge on which experimental work and scientific progress rely. Poison frogs are a well-studied group of small Neotropical frogs with diverse parental behaviors, distinct calls, and bright colors that warn predators about their toxicity; and a showcase of advances in fundamental biology through natural history observations. The dyeing poison frog, Dendrobates tinctorius, is emblematic of the Guianas region, widespread in the pet trade, and increasingly popular in research. This species shows several unusual behaviors, such as the lack of advertisement calls and the aggregation around tree-fall gaps, which remain poorly described and understood. Here, we summarize our observations from a natural population of D. tinctorius in French Guiana collected over various field trips between 2009 and 2017; our aim is to provide groundwork for future fundamental and applied research spanning parental care, animal dispersal, disease spread, habitat use in relation to color patterns, and intra-specific communication, to name a few. We report sex differences in habitat use and the striking invasion of tree-fall gaps; describe their courtship and aggressive behaviors; document egg development and tadpole transport; and discuss how the knowledge generated by this study could set the grounds for further research on the behavior, ecology, and conservation of this species.
format: application/pdf
format: text/html
creator: Bibiana Rojas
creator: Andrius Pašukonis
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.7648
publisher: PeerJ Inc.
rights: © 2019 Rojas and Pašukonis
abstract: Descriptive studies of natural history have always been a source of knowledge on which experimental work and scientific progress rely. Poison frogs are a well-studied group of small Neotropical frogs with diverse parental behaviors, distinct calls, and bright colors that warn predators about their toxicity; and a showcase of advances in fundamental biology through natural history observations. The dyeing poison frog, Dendrobates tinctorius, is emblematic of the Guianas region, widespread in the pet trade, and increasingly popular in research. This species shows several unusual behaviors, such as the lack of advertisement calls and the aggregation around tree-fall gaps, which remain poorly described and understood. Here, we summarize our observations from a natural population of D. tinctorius in French Guiana collected over various field trips between 2009 and 2017; our aim is to provide groundwork for future fundamental and applied research spanning parental care, animal dispersal, disease spread, habitat use in relation to color patterns, and intra-specific communication, to name a few. We report sex differences in habitat use and the striking invasion of tree-fall gaps; describe their courtship and aggressive behaviors; document egg development and tadpole transport; and discuss how the knowledge generated by this study could set the grounds for further research on the behavior, ecology, and conservation of this species.
bibliographic citation: Rojas et al. (2019) From habitat use to social behavior: natural history of a voiceless poison frog, Dendrobates tinctorius. PeerJ 7:e7648 https://doi.org/10.7717/peerj.7648
date submitted: 2019-01-21
date accepted: 2019-08-09
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rojas
  given name: Bibiana
author list: Agent
  family name: Pašukonis
  given name: Andrius
doi: 10.7717/peerj.7648
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: © 2019 Rojas and Pašukonis
attribution name: Rojas and Pašukonis

Collisional mechanics of the diagonal gaits of horses over a range of speeds
type: item
type: AcademicArticle
description: One of the goals of the neuromotor control system is to minimize the cost of locomotion by reducing mechanical energy losses. Collisional mechanics, which studies the redirection of the downwards motion of the center of mass (COM) by ground reaction forces (GRF) generated by the limbs, represents an important source of energy loss. The primary objective of this study was to compare collisional mechanics and the associated mechanical energy losses in horses performing diagonally-synchronized gaits over a range of speeds. It is to be expected that collisional energy losses will be high when the COM velocity vector is closely aligned with the GRF vector. This condition is achieved in piaffe, an artificial gait performed in dressage competitions that has a diagonal limb coordination pattern similar to trot but performed with little or no forward velocity. Therefore, we hypothesized that collisional energy losses would be higher in piaffe than in trot. Synchronized kinematic and GRF data were collected from three highly-trained horses performing piaffe, passage and trot at a range of speeds. Derived variables were vertical excursion and velocity of the trunk COM, fore and hind limb compression expressed as percentage reduction of standing limb lengths, range of limb pro-retraction, GRF vector magnitude and vector angle, collision angle (Φ), and mechanical cost of motion (CoMotmech). Linear regression was used to investigate the relationship between CoMotmech and speed for each gait. Partial correlation was used to seek relationships between COM excursion and limb mechanics for each gait. Piaffe, passage and trot were clearly separated on the basis of speed. In all gaits the trunk was high at contact and lift off and descended to its lowest point in midstance following the pattern typical of spring mass mechanics. Mechanical cost was significantly (p < .05) and inversely related to speed in trot and piaffe with the value increasing steeply as speed approached zero due to …
format: application/pdf
format: text/html
creator: Sarah Jane Hobbs
creator: Hilary M. Clayton
subject: Bioengineering
subject: Zoology
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.7689
publisher: PeerJ Inc.
rights: © 2019 Hobbs and Clayton
abstract: One of the goals of the neuromotor control system is to minimize the cost of locomotion by reducing mechanical energy losses. Collisional mechanics, which studies the redirection of the downwards motion of the center of mass (COM) by ground reaction forces (GRF) generated by the limbs, represents an important source of energy loss. The primary objective of this study was to compare collisional mechanics and the associated mechanical energy losses in horses performing diagonally-synchronized gaits over a range of speeds. It is to be expected that collisional energy losses will be high when the COM velocity vector is closely aligned with the GRF vector. This condition is achieved in piaffe, an artificial gait performed in dressage competitions that has a diagonal limb coordination pattern similar to trot but performed with little or no forward velocity. Therefore, we hypothesized that collisional energy losses would be higher in piaffe than in trot. Synchronized kinematic and GRF data were collected from three highly-trained horses performing piaffe, passage and trot at a range of speeds. Derived variables were vertical excursion and velocity of the trunk COM, fore and hind limb compression expressed as percentage reduction of standing limb lengths, range of limb pro-retraction, GRF vector magnitude and vector angle, collision angle (Φ), and mechanical cost of motion (CoMotmech). Linear regression was used to investigate the relationship between CoMotmech and speed for each gait. Partial correlation was used to seek relationships between COM excursion and limb mechanics for each gait. Piaffe, passage and trot were clearly separated on the basis of speed. In all gaits the trunk was high at contact and lift off and descended to its lowest point in midstance following the pattern typical of spring mass mechanics. Mechanical cost was significantly (p < .05) and inversely related to speed in trot and piaffe with the value increasing steeply as speed approached zero due to …
bibliographic citation: Hobbs et al. (2019) Collisional mechanics of the diagonal gaits of horses over a range of speeds. PeerJ 7:e7689 https://doi.org/10.7717/peerj.7689
date submitted: 2019-06-13
date accepted: 2019-08-19
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hobbs
  given name: Sarah Jane
author list: Agent
  family name: Clayton
  given name: Hilary M.
doi: 10.7717/peerj.7689
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: ©2019 Hobbs and Clayton
attribution name: Hobbs and Clayton

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