PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The inheritance of female colour polymorphism in Ischnura genei (Zygoptera: Coenagrionidae), with observations on melanism under laboratory conditions
items: Transcriptome analysis of colored calla lily (Zantedeschia rehmannii Engl.) by Illumina sequencing: de novo assembly, annotation and EST-SSR marker development
items: Stable isotope analysis (δ13C and δ15N) of soil nematodes from four feeding groups
items: Identification of a R2R3-MYB gene regulating anthocyanin biosynthesis and relationships between its variation and flower color difference in lotus (Nelumbo Adans.)
items: Specific carotenoid pigments in the diet and a bit of oxidative stress in the recipe for producing red carotenoid-based signals
items: Continent-wide survey reveals massive decline in African savannah elephants
items: Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification
items: Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement
items: Male foraging efficiency, but not male problem-solving performance, influences female mating preferences in zebra finches
items: Influence of droplet coverage on the electrochemical response of planar microelectrodes and potential solving strategies based on nesting concept

The inheritance of female colour polymorphism in Ischnura genei (Zygoptera: Coenagrionidae), with observations on melanism under laboratory conditions
type: item
type: AcademicArticle
description: Current research on female colour polymorphism in Ischnura damselflies suggests that a balanced fitness trade-off between morphotypes contributes to the maintenance of polymorphism inside populations. The genetic inheritance system constitutes a key factor to understand morph fluctuation and fitness. Ischnura genei, an endemic species of some Mediterranean islands, has three female colour morphs, including one androchrome (male-coloured) and two gynochromes. In this study, we reared two generations of I. genei under laboratory conditions and tested male behavioural responses to female colour morphs in the field. We recorded ontogenetic colour changes and studied morph frequency in three populations from Sardinia (Italy). Morph frequencies of laboratory crosses can be explained by a model based on an autosomal locus with three alleles and sex-restricted expression, except for one crossing of 42 families with unexpected offspring. The allelic dominance relationship was androchrome > infuscans > aurantiaca. Old individuals reared in the laboratory exhibited different levels of melanism in variable extent depending on sex and morph. Results of model presentations indicate a male preference for gynochrome females and the lack of recognition of androchromes as potential mates. Aurantiaca females were the most frequent morph in the field (63–87%). Further studies in other populations and islands are needed to understand the maintenance of this polymorphism.
format: application/pdf
format: text/html
creator: Iago Sanmartín-Villar
creator: Adolfo Cordero-Rivera
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Genetics
description: doi:10.7717/peerj.2380
publisher: PeerJ Inc.
rights: © 2016 Sanmartín-Villar and Cordero-Rivera
abstract: Current research on female colour polymorphism in Ischnura damselflies suggests that a balanced fitness trade-off between morphotypes contributes to the maintenance of polymorphism inside populations. The genetic inheritance system constitutes a key factor to understand morph fluctuation and fitness. Ischnura genei, an endemic species of some Mediterranean islands, has three female colour morphs, including one androchrome (male-coloured) and two gynochromes. In this study, we reared two generations of I. genei under laboratory conditions and tested male behavioural responses to female colour morphs in the field. We recorded ontogenetic colour changes and studied morph frequency in three populations from Sardinia (Italy). Morph frequencies of laboratory crosses can be explained by a model based on an autosomal locus with three alleles and sex-restricted expression, except for one crossing of 42 families with unexpected offspring. The allelic dominance relationship was androchrome > infuscans > aurantiaca. Old individuals reared in the laboratory exhibited different levels of melanism in variable extent depending on sex and morph. Results of model presentations indicate a male preference for gynochrome females and the lack of recognition of androchromes as potential mates. Aurantiaca females were the most frequent morph in the field (63–87%). Further studies in other populations and islands are needed to understand the maintenance of this polymorphism.
bibliographic citation: Sanmartín-Villar et al. (2016) The inheritance of female colour polymorphism in Ischnura genei (Zygoptera: Coenagrionidae), with observations on melanism under laboratory conditions . PeerJ 4:e2380 https://doi.org/10.7717/peerj.2380
date submitted: 2016-05-17
date accepted: 2016-07-29
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sanmartín-Villar
  given name: Iago
author list: Agent
  family name: Cordero-Rivera
  given name: Adolfo
doi: 10.7717/peerj.2380
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Sanmartín-Villar and Cordero-Rivera
attribution name: Sanmartín-Villar and Cordero-Rivera

Transcriptome analysis of colored calla lily (Zantedeschia rehmannii Engl.) by Illumina sequencing: de novo assembly, annotation and EST-SSR marker development
type: item
type: AcademicArticle
description: Colored calla lily is the short name for the species or hybrids in section Aestivae of genus Zantedeschia. It is currently one of the most popular flower plants in the world due to its beautiful flower spathe and long postharvest life. However, little genomic information and few molecular markers are available for its genetic improvement. Here, de novo transcriptome sequencing was performed to produce large transcript sequences for Z. rehmannii cv. ‘Rehmannii’ using an Illumina HiSeq 2000 instrument. More than 59.9 million cDNA sequence reads were obtained and assembled into 39,298 unigenes with an average length of 1,038 bp. Among these, 21,077 unigenes showed significant similarity to protein sequences in the non-redundant protein database (Nr) and in the Swiss-Prot, Gene Ontology (GO), Cluster of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, a total of 117 unique transcripts were then defined that might regulate the flower spathe development of colored calla lily. Additionally, 9,933 simple sequence repeats (SSRs) and 7,162 single nucleotide polymorphisms (SNPs) were identified as putative molecular markers. High-quality primers for 200 SSR loci were designed and selected, of which 58 amplified reproducible amplicons were polymorphic among 21 accessions of colored calla lily. The sequence information and molecular markers in the present study will provide valuable resources for genetic diversity analysis, germplasm characterization and marker-assisted selection in the genus Zantedeschia.
format: application/pdf
format: text/html
creator: Zunzheng Wei
creator: Zhenzhen Sun
creator: Binbin Cui
creator: Qixiang Zhang
creator: Min Xiong
creator: Xian Wang
creator: Di Zhou
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.2378
publisher: PeerJ Inc.
rights: © 2016 Wei et al.
abstract: Colored calla lily is the short name for the species or hybrids in section Aestivae of genus Zantedeschia. It is currently one of the most popular flower plants in the world due to its beautiful flower spathe and long postharvest life. However, little genomic information and few molecular markers are available for its genetic improvement. Here, de novo transcriptome sequencing was performed to produce large transcript sequences for Z. rehmannii cv. ‘Rehmannii’ using an Illumina HiSeq 2000 instrument. More than 59.9 million cDNA sequence reads were obtained and assembled into 39,298 unigenes with an average length of 1,038 bp. Among these, 21,077 unigenes showed significant similarity to protein sequences in the non-redundant protein database (Nr) and in the Swiss-Prot, Gene Ontology (GO), Cluster of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, a total of 117 unique transcripts were then defined that might regulate the flower spathe development of colored calla lily. Additionally, 9,933 simple sequence repeats (SSRs) and 7,162 single nucleotide polymorphisms (SNPs) were identified as putative molecular markers. High-quality primers for 200 SSR loci were designed and selected, of which 58 amplified reproducible amplicons were polymorphic among 21 accessions of colored calla lily. The sequence information and molecular markers in the present study will provide valuable resources for genetic diversity analysis, germplasm characterization and marker-assisted selection in the genus Zantedeschia.
bibliographic citation: Wei et al. (2016) Transcriptome analysis of colored calla lily (Zantedeschia rehmannii Engl.) by Illumina sequencing: de novo assembly, annotation and EST-SSR marker development. PeerJ 4:e2378 https://doi.org/10.7717/peerj.2378
date submitted: 2016-04-23
date accepted: 2016-07-29
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Zunzheng
author list: Agent
  family name: Sun
  given name: Zhenzhen
author list: Agent
  family name: Cui
  given name: Binbin
author list: Agent
  family name: Zhang
  given name: Qixiang
author list: Agent
  family name: Xiong
  given name: Min
author list: Agent
  family name: Wang
  given name: Xian
author list: Agent
  family name: Zhou
  given name: Di
doi: 10.7717/peerj.2378
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Wei et al.
attribution name: Wei et al.

Stable isotope analysis (δ13C and δ15N) of soil nematodes from four feeding groups
type: item
type: AcademicArticle
description: Soil nematode feeding groups are a long-established trophic categorisation largely based on morphology and are used in ecological indices to monitor and analyse the biological state of soils. Stable isotope ratio analysis (13C/12C and 15N/14N, expressed as δ13C and δ15N) has provided verification of, and novel insights into, the feeding ecology of soil animals such as earthworms and mites. However, isotopic studies of soil nematodes have been limited to date as conventional stable isotope ratio analysis needs impractically large numbers of nematodes (up to 1,000) to achieve required minimum sample weights (typically >100 µg C and N). Here, micro-sample near-conventional elemental analysis–isotopic ratio mass spectrometry (μEA–IRMS) of C and N using microgram samples (typically 20 µg dry weight), was employed to compare the trophic position of selected soil nematode taxa from four feeding groups: predators (Anatonchus and Mononchus), bacterial feeders (Plectus and Rhabditis), omnivores (Aporcelaimidae and Qudsianematidae) and plant feeder (Rotylenchus). Free-living nematodes were collected from conventionally and organically managed arable soils. As few as 15 nematodes, for omnivores and predators, were sufficient to reach the 20 µg dry weight target. There was no significant difference in δ15N (p = 0.290) or δ13C (p = 0.706) between conventional and organic agronomic treatments but, within treatments, there was a significant difference in N and C stable isotope ratios between the plant feeder, Rotylenchus (δ15N = 1.08 to 3.22 mUr‰, δ13C = –29.58 to –27.87 mUr) and all other groups. There was an average difference of 9.62 mUr in δ15N between the plant feeder and the predator group (δ15N = 9.89 to 12.79 mUr, δ13C = –27.04 to –25.51 mUr). Isotopic niche widths were calculated as Bayesian derived standard ellipse areas and were smallest for the plant feeder (1.37 mUr2) and the predators (1.73 mUr2), but largest for omnivores (3.83 mUr2). These data may reflect more pref…
format: application/pdf
format: text/html
creator: Carol Melody
creator: Bryan Griffiths
creator: Jens Dyckmans
creator: Olaf Schmidt
subject: Agricultural Science
subject: Ecology
subject: Environmental Sciences
subject: Soil Science
subject: Zoology
description: doi:10.7717/peerj.2372
publisher: PeerJ Inc.
rights: © 2016 Melody et al.
abstract: Soil nematode feeding groups are a long-established trophic categorisation largely based on morphology and are used in ecological indices to monitor and analyse the biological state of soils. Stable isotope ratio analysis (13C/12C and 15N/14N, expressed as δ13C and δ15N) has provided verification of, and novel insights into, the feeding ecology of soil animals such as earthworms and mites. However, isotopic studies of soil nematodes have been limited to date as conventional stable isotope ratio analysis needs impractically large numbers of nematodes (up to 1,000) to achieve required minimum sample weights (typically >100 µg C and N). Here, micro-sample near-conventional elemental analysis–isotopic ratio mass spectrometry (μEA–IRMS) of C and N using microgram samples (typically 20 µg dry weight), was employed to compare the trophic position of selected soil nematode taxa from four feeding groups: predators (Anatonchus and Mononchus), bacterial feeders (Plectus and Rhabditis), omnivores (Aporcelaimidae and Qudsianematidae) and plant feeder (Rotylenchus). Free-living nematodes were collected from conventionally and organically managed arable soils. As few as 15 nematodes, for omnivores and predators, were sufficient to reach the 20 µg dry weight target. There was no significant difference in δ15N (p = 0.290) or δ13C (p = 0.706) between conventional and organic agronomic treatments but, within treatments, there was a significant difference in N and C stable isotope ratios between the plant feeder, Rotylenchus (δ15N = 1.08 to 3.22 mUr‰, δ13C = –29.58 to –27.87 mUr) and all other groups. There was an average difference of 9.62 mUr in δ15N between the plant feeder and the predator group (δ15N = 9.89 to 12.79 mUr, δ13C = –27.04 to –25.51 mUr). Isotopic niche widths were calculated as Bayesian derived standard ellipse areas and were smallest for the plant feeder (1.37 mUr2) and the predators (1.73 mUr2), but largest for omnivores (3.83 mUr2). These data may reflect more pref…
bibliographic citation: Melody et al. (2016) Stable isotope analysis (δ13C and δ15N) of soil nematodes from four feeding groups. PeerJ 4:e2372 https://doi.org/10.7717/peerj.2372
date submitted: 2015-12-28
date accepted: 2016-07-26
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Melody
  given name: Carol
author list: Agent
  family name: Griffiths
  given name: Bryan
author list: Agent
  family name: Dyckmans
  given name: Jens
author list: Agent
  family name: Schmidt
  given name: Olaf
doi: 10.7717/peerj.2372
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: ©2016 Melody et al.
attribution name: Melody et al.

Identification of a R2R3-MYB gene regulating anthocyanin biosynthesis and relationships between its variation and flower color difference in lotus (Nelumbo Adans.)
type: item
type: AcademicArticle
description: The lotus (Nelumbonaceae: Nelumbo Adans.) is a highly desired ornamental plant, comprising only two extant species, the sacred lotus (N. nucifera Gaerten.) with red flowers and the American lotus (N. lutea Willd.) with yellow flowers. Flower color is the most obvious difference of two species. To better understand the mechanism of flower color differentiation, the content of anthocyanins and the expression levels of four key structural genes (e.g., DFR, ANS, UFGT and GST) were analyzed in two species. Our results revealed that anthocyanins were detected in red flowers, not yellow flowers. Expression analysis showed that no transcripts of GST gene and low expression level of three UFGT genes were detected in yellow flowers. In addition, three regulatory genes (NnMYB5, NnbHLH1 and NnTTG1) were isolated from red flowers and showed a high similarity to corresponding regulatory genes of other species. Sequence analysis of MYB5, bHLH1 and TTG1 in two species revealed striking differences in coding region and promoter region of MYB5 gene. Population analysis identified three MYB5 variants in Nelumbo: a functional allele existed in red flowers and two inactive forms existed in yellow flowers. This result revealed that there was an association between allelic variation in MYB5 gene and flower color difference. Yeast two-hybrid experiments showed that NnMYB5 interacts with NnbHLH1, NlbHLH1 and NnTTG1, and NnTTG1 also interacts with NnbHLH1 and NlbHLH1. The over-expression of NnMYB5 led to anthocyanin accumulation in immature seeds and flower stalks and up-regulation of expression of TT19 in Arabidopsis. Therefore, NnMYB5 is a transcription activator of anthocyanin synthesis. This study helps to elucidate the function of NnMYB5 and will contribute to clarify the mechanism of flower coloration and genetic engineering of flower color in lotus.
format: application/pdf
format: text/html
creator: Shan-Shan Sun
creator: Paul F. Gugger
creator: Qing-Feng Wang
creator: Jin-Ming Chen
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.2369
publisher: PeerJ Inc.
rights: © 2016 Sun et al.
abstract: The lotus (Nelumbonaceae: Nelumbo Adans.) is a highly desired ornamental plant, comprising only two extant species, the sacred lotus (N. nucifera Gaerten.) with red flowers and the American lotus (N. lutea Willd.) with yellow flowers. Flower color is the most obvious difference of two species. To better understand the mechanism of flower color differentiation, the content of anthocyanins and the expression levels of four key structural genes (e.g., DFR, ANS, UFGT and GST) were analyzed in two species. Our results revealed that anthocyanins were detected in red flowers, not yellow flowers. Expression analysis showed that no transcripts of GST gene and low expression level of three UFGT genes were detected in yellow flowers. In addition, three regulatory genes (NnMYB5, NnbHLH1 and NnTTG1) were isolated from red flowers and showed a high similarity to corresponding regulatory genes of other species. Sequence analysis of MYB5, bHLH1 and TTG1 in two species revealed striking differences in coding region and promoter region of MYB5 gene. Population analysis identified three MYB5 variants in Nelumbo: a functional allele existed in red flowers and two inactive forms existed in yellow flowers. This result revealed that there was an association between allelic variation in MYB5 gene and flower color difference. Yeast two-hybrid experiments showed that NnMYB5 interacts with NnbHLH1, NlbHLH1 and NnTTG1, and NnTTG1 also interacts with NnbHLH1 and NlbHLH1. The over-expression of NnMYB5 led to anthocyanin accumulation in immature seeds and flower stalks and up-regulation of expression of TT19 in Arabidopsis. Therefore, NnMYB5 is a transcription activator of anthocyanin synthesis. This study helps to elucidate the function of NnMYB5 and will contribute to clarify the mechanism of flower coloration and genetic engineering of flower color in lotus.
bibliographic citation: Sun et al. (2016) Identification of a R2R3-MYB gene regulating anthocyanin biosynthesis and relationships between its variation and flower color difference in lotus (Nelumbo Adans.). PeerJ 4:e2369 https://doi.org/10.7717/peerj.2369
date submitted: 2016-05-13
date accepted: 2016-07-26
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Shan-Shan
author list: Agent
  family name: Gugger
  given name: Paul F.
author list: Agent
  family name: Wang
  given name: Qing-Feng
author list: Agent
  family name: Chen
  given name: Jin-Ming
doi: 10.7717/peerj.2369
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: © 2016 Sun et al.
attribution name: Sun et al.

Specific carotenoid pigments in the diet and a bit of oxidative stress in the recipe for producing red carotenoid-based signals
type: item
type: AcademicArticle
description: Colorful ornaments have been the focus of sexual selection studies since the work of Darwin. Yellow to red coloration is often produced by carotenoid pigments. Different hypotheses have been formulated to explain the evolution of these traits as signals of individual quality. Many of these hypotheses involve the existence of a signal production cost. The carotenoids necessary for signaling can only be obtained from food. In this line, carotenoid-based signals could reveal an individual’s capacity to find sufficient dietary pigments. However, the ingested carotenoids are often yellow and became transformed by the organism to produce pigments of more intense color (red ketocarotenoids). Biotransformation should involve oxidation reactions, although the exact mechanism is poorly known. We tested the hypothesis that carotenoid biotransformation could be costly because a certain level of oxidative stress is required to correctly perform the conversion. The carotenoid-based signals could thus reveal the efficiency of the owner in successfully managing this challenge. In a bird with ketocarotenoid-based ornaments (the red-legged partridge; Alectoris rufa), the availability of different carotenoids in the diet (i.e. astaxanthin, zeaxanthin and lutein) and oxidative stress were manipulated. The carotenoid composition was analyzed and quantified in the ornaments, blood, liver and fat. A number of oxidative stress biomarkers were also measured in the same tissues. First, we found that color and pigment levels in the ornaments depended on food levels of those carotenoids used as substrates in biotransformation. Second, we found that birds exposed to mild levels of a free radical generator (diquat) developed redder bills and deposited higher amounts of ketocarotenoids (astaxanthin) in ornaments. Moreover, the same diquat-exposed birds also showed a weaker resistance to hemolysis when their erythrocytes were exposed to free radicals, with females also enduring higher oxidative da…
format: application/pdf
format: text/html
creator: Esther García-de Blas
creator: Rafael Mateo
creator: Carlos Alonso-Alvarez
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.2237
publisher: PeerJ Inc.
rights: © 2016 García-de Blas Alguacil et al.
abstract: Colorful ornaments have been the focus of sexual selection studies since the work of Darwin. Yellow to red coloration is often produced by carotenoid pigments. Different hypotheses have been formulated to explain the evolution of these traits as signals of individual quality. Many of these hypotheses involve the existence of a signal production cost. The carotenoids necessary for signaling can only be obtained from food. In this line, carotenoid-based signals could reveal an individual’s capacity to find sufficient dietary pigments. However, the ingested carotenoids are often yellow and became transformed by the organism to produce pigments of more intense color (red ketocarotenoids). Biotransformation should involve oxidation reactions, although the exact mechanism is poorly known. We tested the hypothesis that carotenoid biotransformation could be costly because a certain level of oxidative stress is required to correctly perform the conversion. The carotenoid-based signals could thus reveal the efficiency of the owner in successfully managing this challenge. In a bird with ketocarotenoid-based ornaments (the red-legged partridge; Alectoris rufa), the availability of different carotenoids in the diet (i.e. astaxanthin, zeaxanthin and lutein) and oxidative stress were manipulated. The carotenoid composition was analyzed and quantified in the ornaments, blood, liver and fat. A number of oxidative stress biomarkers were also measured in the same tissues. First, we found that color and pigment levels in the ornaments depended on food levels of those carotenoids used as substrates in biotransformation. Second, we found that birds exposed to mild levels of a free radical generator (diquat) developed redder bills and deposited higher amounts of ketocarotenoids (astaxanthin) in ornaments. Moreover, the same diquat-exposed birds also showed a weaker resistance to hemolysis when their erythrocytes were exposed to free radicals, with females also enduring higher oxidative da…
bibliographic citation: García-de Blas et al. (2016) Specific carotenoid pigments in the diet and a bit of oxidative stress in the recipe for producing red carotenoid-based signals. PeerJ 4:e2237 https://doi.org/10.7717/peerj.2237
date submitted: 2016-03-16
date accepted: 2016-06-20
issued: 2016-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-de Blas
  given name: Esther
author list: Agent
  family name: Mateo
  given name: Rafael
author list: Agent
  family name: Alonso-Alvarez
  given name: Carlos
doi: 10.7717/peerj.2237
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-01
copyright: © 2016 García-de Blas Alguacil et al.
attribution name: García-de Blas Alguacil et al.

Continent-wide survey reveals massive decline in African savannah elephants
type: item
type: AcademicArticle
description: African elephants (Loxodonta africana) are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC), the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants’ downward trajectory by preventing poaching and protecting habitat.
format: application/pdf
format: text/html
creator: Michael J. Chase
creator: Scott Schlossberg
creator: Curtice R. Griffin
creator: Philippe J.C. Bouché
creator: Sintayehu W. Djene
creator: Paul W. Elkan
creator: Sam Ferreira
creator: Falk Grossman
creator: Edward Mtarima Kohi
creator: Kelly Landen
creator: Patrick Omondi
creator: Alexis Peltier
creator: S.A. Jeanetta Selier
creator: Robert Sutcliffe
subject: Biosphere Interactions
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.2354
publisher: PeerJ Inc.
rights: © 2016 Chase et al.
abstract: African elephants (Loxodonta africana) are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC), the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants’ downward trajectory by preventing poaching and protecting habitat.
bibliographic citation: Chase et al. (2016) Continent-wide survey reveals massive decline in African savannah elephants. PeerJ 4:e2354 https://doi.org/10.7717/peerj.2354
date submitted: 2016-06-09
date accepted: 2016-07-21
issued: 2016-08-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chase
  given name: Michael J.
author list: Agent
  family name: Schlossberg
  given name: Scott
author list: Agent
  family name: Griffin
  given name: Curtice R.
author list: Agent
  family name: Bouché
  given name: Philippe J.C.
author list: Agent
  family name: Djene
  given name: Sintayehu W.
author list: Agent
  family name: Elkan
  given name: Paul W.
author list: Agent
  family name: Ferreira
  given name: Sam
author list: Agent
  family name: Grossman
  given name: Falk
author list: Agent
  family name: Kohi
  given name: Edward Mtarima
author list: Agent
  family name: Landen
  given name: Kelly
author list: Agent
  family name: Omondi
  given name: Patrick
author list: Agent
  family name: Peltier
  given name: Alexis
author list: Agent
  family name: Selier
  given name: S.A. Jeanetta
author list: Agent
  family name: Sutcliffe
  given name: Robert
doi: 10.7717/peerj.2354
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-31
copyright: ©2016 Chase et al.
attribution name: Chase et al.

Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification
type: item
type: AcademicArticle
description: Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.
format: application/pdf
format: text/html
creator: Laura Taillebois
creator: Christine Dudgeon
creator: Safia Maher
creator: David A. Crook
creator: Thor M. Saunders
creator: Diane P. Barton
creator: Jonathan A. Taylor
creator: David J. Welch
creator: Stephen J. Newman
creator: Michael J. Travers
creator: Richard J. Saunders
creator: Jennifer Ovenden
subject: Aquaculture, Fisheries and Fish Science
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.2418
publisher: PeerJ Inc.
rights: © 2016 Taillebois et al.
abstract: Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.
bibliographic citation: Taillebois et al. (2016) Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification. PeerJ 4:e2418 https://doi.org/10.7717/peerj.2418
date submitted: 2016-06-27
date accepted: 2016-08-06
issued: 2016-08-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Taillebois
  given name: Laura
author list: Agent
  family name: Dudgeon
  given name: Christine
author list: Agent
  family name: Maher
  given name: Safia
author list: Agent
  family name: Crook
  given name: David A.
author list: Agent
  family name: Saunders
  given name: Thor M.
author list: Agent
  family name: Barton
  given name: Diane P.
author list: Agent
  family name: Taylor
  given name: Jonathan A.
author list: Agent
  family name: Welch
  given name: David J.
author list: Agent
  family name: Newman
  given name: Stephen J.
author list: Agent
  family name: Travers
  given name: Michael J.
author list: Agent
  family name: Saunders
  given name: Richard J.
author list: Agent
  family name: Ovenden
  given name: Jennifer
doi: 10.7717/peerj.2418
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-31
copyright: ©2016 Taillebois et al.
attribution name: Taillebois et al.

Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement
type: item
type: AcademicArticle
description: The Pomacentridae (damselfish) and Apogonidae (cardinalfish) are among the most common fish families on coral reefs and in the aquarium trade. Members of both families undergo a pelagic larvae phase prior to settlement on the reef, where adults play key roles in benthic habitat structuring and trophic interactions. Fish-associated microbial communities (microbiomes) significantly influence fish health and ecology, yet little is known of how microbiomes change with life stage. We quantified the taxonomic (16S rRNA gene) composition of whole gut microbiomes from ten species of damselfish and two species of cardinalfish from Lizard Island, Australia, focusing specifically on comparisons between pelagic larvae prior to settlement on the reef versus post-settlement juvenile and adult individuals. On average, microbiome phylogenetic diversity increased from pre- to post-settlement, and was unrelated to the microbial composition in the surrounding water column. However, this trend varied among species, suggesting stochasticity in fish microbiome assembly. Pre-settlement fish were enriched with bacteria of the Endozoicomonaceae, Shewanellaceae, and Fusobacteriaceae, whereas settled fish harbored higher abundances of Vibrionaceae and Pasteurellaceae. Several individual operational taxonomic units, including ones related to Vibrio harveyi, Shewanella sp., and uncultured Endozoicomonas bacteria, were shared between both pre and post-settlement stages and may be of central importance in the intestinal niche across development. Richness of the core microbiome shared among pre-settlement fish was comparable to that of settled individuals, suggesting that changes in diversity with adulthood are due to the acquisition or loss of host-specific microbes. These results identify a key transition in microbiome structure across host life stage, suggesting changes in the functional contribution of microbiomes over development in two ecologically dominant reef fish families.
format: application/pdf
format: text/html
creator: Darren J. Parris
creator: Rohan M. Brooker
creator: Michael A. Morgan
creator: Danielle L. Dixson
creator: Frank J. Stewart
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.2412
publisher: PeerJ Inc.
rights: © 2016 Parris et al.
abstract: The Pomacentridae (damselfish) and Apogonidae (cardinalfish) are among the most common fish families on coral reefs and in the aquarium trade. Members of both families undergo a pelagic larvae phase prior to settlement on the reef, where adults play key roles in benthic habitat structuring and trophic interactions. Fish-associated microbial communities (microbiomes) significantly influence fish health and ecology, yet little is known of how microbiomes change with life stage. We quantified the taxonomic (16S rRNA gene) composition of whole gut microbiomes from ten species of damselfish and two species of cardinalfish from Lizard Island, Australia, focusing specifically on comparisons between pelagic larvae prior to settlement on the reef versus post-settlement juvenile and adult individuals. On average, microbiome phylogenetic diversity increased from pre- to post-settlement, and was unrelated to the microbial composition in the surrounding water column. However, this trend varied among species, suggesting stochasticity in fish microbiome assembly. Pre-settlement fish were enriched with bacteria of the Endozoicomonaceae, Shewanellaceae, and Fusobacteriaceae, whereas settled fish harbored higher abundances of Vibrionaceae and Pasteurellaceae. Several individual operational taxonomic units, including ones related to Vibrio harveyi, Shewanella sp., and uncultured Endozoicomonas bacteria, were shared between both pre and post-settlement stages and may be of central importance in the intestinal niche across development. Richness of the core microbiome shared among pre-settlement fish was comparable to that of settled individuals, suggesting that changes in diversity with adulthood are due to the acquisition or loss of host-specific microbes. These results identify a key transition in microbiome structure across host life stage, suggesting changes in the functional contribution of microbiomes over development in two ecologically dominant reef fish families.
bibliographic citation: Parris et al. (2016) Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement. PeerJ 4:e2412 https://doi.org/10.7717/peerj.2412
date submitted: 2016-05-09
date accepted: 2016-08-04
issued: 2016-08-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Parris
  given name: Darren J.
author list: Agent
  family name: Brooker
  given name: Rohan M.
author list: Agent
  family name: Morgan
  given name: Michael A.
author list: Agent
  family name: Dixson
  given name: Danielle L.
author list: Agent
  family name: Stewart
  given name: Frank J.
doi: 10.7717/peerj.2412
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-31
copyright: ©2016 Parris et al.
attribution name: Parris et al.

Male foraging efficiency, but not male problem-solving performance, influences female mating preferences in zebra finches
type: item
type: AcademicArticle
description: Experimental evidence suggests that females would prefer males with better cognitive abilities as mates. However, little is known about the traits reflecting enhanced cognitive skills on which females might base their mate-choice decisions. In particular, it has been suggested that male foraging performance could be used as an indicator of cognitive capacity, but convincing evidence for this hypothesis is still lacking. In the present study, we investigated whether female zebra finches (Taeniopygia guttata) modify their mating preferences after having observed the performance of males on a problem-solving task. Specifically, we measured the females’ preferences between two males once before and once after an observation period, during which their initially preferred male was incapable of solving the task contrary to their initially less-preferred male. We also conducted a control treatment to test whether the shift in female preferences was attributable to differences between the two stimulus males in their foraging efficiency. Finally, we assessed each bird’s performance in a color associative task to check whether females can discriminate among males based on their learning speed. We found that females significantly increased their preference toward the most efficient male in both treatments. Yet, there was no difference between the two treatments and we found no evidence that females assess male cognitive ability indirectly via morphological traits. Thus, our results suggest that females would not use the males’ problem-solving performance as an indicator of general cognitive ability to gain indirect fitness benefits (i.e., good genes) but rather to assess their foraging efficiency and gain direct benefits.
format: application/pdf
format: text/html
creator: Véronique Chantal
creator: Julie Gibelli
creator: Frédérique Dubois
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.2409
publisher: PeerJ Inc.
rights: © 2016 Chantal et al.
abstract: Experimental evidence suggests that females would prefer males with better cognitive abilities as mates. However, little is known about the traits reflecting enhanced cognitive skills on which females might base their mate-choice decisions. In particular, it has been suggested that male foraging performance could be used as an indicator of cognitive capacity, but convincing evidence for this hypothesis is still lacking. In the present study, we investigated whether female zebra finches (Taeniopygia guttata) modify their mating preferences after having observed the performance of males on a problem-solving task. Specifically, we measured the females’ preferences between two males once before and once after an observation period, during which their initially preferred male was incapable of solving the task contrary to their initially less-preferred male. We also conducted a control treatment to test whether the shift in female preferences was attributable to differences between the two stimulus males in their foraging efficiency. Finally, we assessed each bird’s performance in a color associative task to check whether females can discriminate among males based on their learning speed. We found that females significantly increased their preference toward the most efficient male in both treatments. Yet, there was no difference between the two treatments and we found no evidence that females assess male cognitive ability indirectly via morphological traits. Thus, our results suggest that females would not use the males’ problem-solving performance as an indicator of general cognitive ability to gain indirect fitness benefits (i.e., good genes) but rather to assess their foraging efficiency and gain direct benefits.
bibliographic citation: Chantal et al. (2016) Male foraging efficiency, but not male problem-solving performance, influences female mating preferences in zebra finches. PeerJ 4:e2409 https://doi.org/10.7717/peerj.2409
date submitted: 2016-06-17
date accepted: 2016-08-04
issued: 2016-08-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chantal
  given name: Véronique
author list: Agent
  family name: Gibelli
  given name: Julie
author list: Agent
  family name: Dubois
  given name: Frédérique
doi: 10.7717/peerj.2409
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-31
copyright: © 2016 Chantal et al.
attribution name: Chantal et al.

Influence of droplet coverage on the electrochemical response of planar microelectrodes and potential solving strategies based on nesting concept
type: item
type: AcademicArticle
description: Recently, biosensors have been widely used for the detection of bacteria, viruses and other toxins. Electrodes, as commonly used transducers, are a vital part of electrochemical biosensors. The coverage of the droplets can change significantly based on the hydrophobicity of the microelectrode surface materials. In the present research, screen-printed interdigitated microelectrodes (SPIMs), as one type of planar microelectrode, were applied to investigate the influence of droplet coverage on electrochemical response. Furthermore, three dimensional (3D) printing technology was employed to print smart devices with different diameters based on the nesting concept. Theoretical explanations were proposed to elucidate the influence of the droplet coverage on the electrochemical response. 3D-printed ring devices were used to incubate the SPIMs and the analytical performances of the SPIMs were tested. According to the results obtained, our device successfully improved the stability of the signal responses and eliminated irregular signal changes to a large extent. Our proposed method based on the nesting concept provides a promising method for the fabrication of stable electrochemical biosensors. We also introduced two types of electrode bases to improve the signal stability.
format: application/pdf
format: text/html
creator: Yue Yu
creator: Zhanming Li
subject: Biochemistry
subject: Bioengineering
subject: Biophysics
subject: Biotechnology
subject: Food Science and Technology
description: doi:10.7717/peerj.2400
publisher: PeerJ Inc.
rights: © 2016 Yu and Li
abstract: Recently, biosensors have been widely used for the detection of bacteria, viruses and other toxins. Electrodes, as commonly used transducers, are a vital part of electrochemical biosensors. The coverage of the droplets can change significantly based on the hydrophobicity of the microelectrode surface materials. In the present research, screen-printed interdigitated microelectrodes (SPIMs), as one type of planar microelectrode, were applied to investigate the influence of droplet coverage on electrochemical response. Furthermore, three dimensional (3D) printing technology was employed to print smart devices with different diameters based on the nesting concept. Theoretical explanations were proposed to elucidate the influence of the droplet coverage on the electrochemical response. 3D-printed ring devices were used to incubate the SPIMs and the analytical performances of the SPIMs were tested. According to the results obtained, our device successfully improved the stability of the signal responses and eliminated irregular signal changes to a large extent. Our proposed method based on the nesting concept provides a promising method for the fabrication of stable electrochemical biosensors. We also introduced two types of electrode bases to improve the signal stability.
bibliographic citation: Yu et al. (2016) Influence of droplet coverage on the electrochemical response of planar microelectrodes and potential solving strategies based on nesting concept. PeerJ 4:e2400 https://doi.org/10.7717/peerj.2400
date submitted: 2016-05-10
date accepted: 2016-08-03
issued: 2016-08-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Yue
author list: Agent
  family name: Li
  given name: Zhanming
doi: 10.7717/peerj.2400
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-31
copyright: ©2016 Yu and Li
attribution name: Yu and Li

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