PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A comprehensive investigation of mesophotic coral ecosystems in the Hawaiian Archipelago
items: Age, growth, and natural mortality of schoolmaster (Lutjanus apodus) from the southeastern United States
items: Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae)
items: Did the 1918 influenza cause the twentieth century cardiovascular mortality epidemic in the United States?
items: Transcriptome response to elevated atmospheric CO2 concentration in the Formosan subterranean termite, Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae)
items: Geographical and altitudinal distribution of Brachycephalus (Anura: Brachycephalidae) endemic to the Brazilian Atlantic Rainforest
items: Performance of maximum likelihood mixture models to estimate nursery habitat contributions to fish stocks: a case study on sea bream Sparus aurata
items: The complete chloroplast genome sequence of Gentiana lawrencei var. farreri (Gentianaceae) and comparative analysis with its congeneric species
items: Deer herbivory reduces web-building spider abundance by simplifying forest vegetation structure
items: The relationship between mobile phone location sensor data and depressive symptom severity

A comprehensive investigation of mesophotic coral ecosystems in the Hawaiian Archipelago
type: item
type: AcademicArticle
description: Although the existence of coral-reef habitats at depths to 165 m in tropical regions has been known for decades, the richness, diversity, and ecological importance of mesophotic coral ecosystems (MCEs) has only recently become widely acknowledged. During an interdisciplinary effort spanning more than two decades, we characterized the most expansive MCEs ever recorded, with vast macroalgal communities and areas of 100% coral cover between depths of 50–90 m extending for tens of km2 in the Hawaiian Archipelago. We used a variety of sensors and techniques to establish geophysical characteristics. Biodiversity patterns were established from visual and video observations and collected specimens obtained from submersible, remotely operated vehicles and mixed-gas SCUBA and rebreather dives. Population dynamics based on age, growth and fecundity estimates of selected fish species were obtained from laser-videogrammetry, specimens, and otolith preparations. Trophic dynamics were determined using carbon and nitrogen stable isotopic analyses on more than 750 reef fishes. MCEs are associated with clear water and suitable substrate. In comparison to shallow reefs in the Hawaiian Archipelago, inhabitants of MCEs have lower total diversity, harbor new and unique species, and have higher rates of endemism in fishes. Fish species present in shallow and mesophotic depths have similar population and trophic (except benthic invertivores) structures and high genetic connectivity with lower fecundity at mesophotic depths. MCEs in Hawai‘i are widespread but associated with specific geophysical characteristics. High genetic, ecological and trophic connectivity establish the potential for MCEs to serve as refugia for some species, but our results question the premise that MCEs are more resilient than shallow reefs. We found that endemism within MCEs increases with depth, and our results do not support suggestions of a global faunal break at 60 m. Our findings enhance the scientific foundati…
format: application/pdf
format: text/html
creator: Richard L. Pyle
creator: Raymond Boland
creator: Holly Bolick
creator: Brian W. Bowen
creator: Christina J. Bradley
creator: Corinne Kane
creator: Randall K. Kosaki
creator: Ross Langston
creator: Ken Longenecker
creator: Anthony Montgomery
creator: Frank A. Parrish
creator: Brian N. Popp
creator: John Rooney
creator: Celia M. Smith
creator: Daniel Wagner
creator: Heather L. Spalding
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.2475
publisher: PeerJ Inc.
rights: © 2016 Pyle et al.
abstract: Although the existence of coral-reef habitats at depths to 165 m in tropical regions has been known for decades, the richness, diversity, and ecological importance of mesophotic coral ecosystems (MCEs) has only recently become widely acknowledged. During an interdisciplinary effort spanning more than two decades, we characterized the most expansive MCEs ever recorded, with vast macroalgal communities and areas of 100% coral cover between depths of 50–90 m extending for tens of km2 in the Hawaiian Archipelago. We used a variety of sensors and techniques to establish geophysical characteristics. Biodiversity patterns were established from visual and video observations and collected specimens obtained from submersible, remotely operated vehicles and mixed-gas SCUBA and rebreather dives. Population dynamics based on age, growth and fecundity estimates of selected fish species were obtained from laser-videogrammetry, specimens, and otolith preparations. Trophic dynamics were determined using carbon and nitrogen stable isotopic analyses on more than 750 reef fishes. MCEs are associated with clear water and suitable substrate. In comparison to shallow reefs in the Hawaiian Archipelago, inhabitants of MCEs have lower total diversity, harbor new and unique species, and have higher rates of endemism in fishes. Fish species present in shallow and mesophotic depths have similar population and trophic (except benthic invertivores) structures and high genetic connectivity with lower fecundity at mesophotic depths. MCEs in Hawai‘i are widespread but associated with specific geophysical characteristics. High genetic, ecological and trophic connectivity establish the potential for MCEs to serve as refugia for some species, but our results question the premise that MCEs are more resilient than shallow reefs. We found that endemism within MCEs increases with depth, and our results do not support suggestions of a global faunal break at 60 m. Our findings enhance the scientific foundati…
bibliographic citation: Pyle et al. (2016) A comprehensive investigation of mesophotic coral ecosystems in the Hawaiian Archipelago. PeerJ 4:e2475 https://doi.org/10.7717/peerj.2475
date submitted: 2015-11-10
date accepted: 2016-08-23
issued: 2016-10-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pyle
  given name: Richard L.
author list: Agent
  family name: Boland
  given name: Raymond
author list: Agent
  family name: Bolick
  given name: Holly
author list: Agent
  family name: Bowen
  given name: Brian W.
author list: Agent
  family name: Bradley
  given name: Christina J.
author list: Agent
  family name: Kane
  given name: Corinne
author list: Agent
  family name: Kosaki
  given name: Randall K.
author list: Agent
  family name: Langston
  given name: Ross
author list: Agent
  family name: Longenecker
  given name: Ken
author list: Agent
  family name: Montgomery
  given name: Anthony
author list: Agent
  family name: Parrish
  given name: Frank A.
author list: Agent
  family name: Popp
  given name: Brian N.
author list: Agent
  family name: Rooney
  given name: John
author list: Agent
  family name: Smith
  given name: Celia M.
author list: Agent
  family name: Wagner
  given name: Daniel
author list: Agent
  family name: Spalding
  given name: Heather L.
doi: 10.7717/peerj.2475
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-04
copyright: ©2016 Pyle et al.
attribution name: Pyle et al.

Age, growth, and natural mortality of schoolmaster (Lutjanus apodus) from the southeastern United States
type: item
type: AcademicArticle
description: Ages of schoolmaster (n = 136) from the southeastern Florida coast from 1981–2015 were determined using sectioned sagittal otoliths. Opaque zones were annular, forming March–July (peaking in May–June). Schoolmaster ranged in age from 1–42 years; the largest fish measured 505 mm total length (TL) and was 19 years old. The oldest fish measured 440 mm TL. Estimated body size relationships for schoolmaster were: W = 9.26 × 10−6 TL3.11 (n = 256, r2 = 0.95); W = 2.13 × 10−5 FL2.99 (n = 161, r2 = 0.95); TL = 1.03 FL + 10.36 (n = 143, r2 = 0.99); and FL = 0.96 TL − 8.41 (n = 143, r2 = 0.99), where W = whole weight in g, FL = fork length in mm, and TL in mm. The fitted von Bertalanffy growth equation was: Lt = 482 (1 − e−0.12(t+2.79)) (n = 136). Based on published life history relationships, a point estimate of natural mortality for schoolmaster was M = 0.10, while age-specific estimates of M ranged from 1.57–0.18 for ages 1–42.
format: application/pdf
format: text/html
creator: Jennifer C. Potts
creator: Michael L. Burton
creator: Amanda R. Myers
subject: Aquaculture, Fisheries and Fish Science
subject: Ecosystem Science
subject: Marine Biology
description: doi:10.7717/peerj.2543
publisher: PeerJ Inc.
rights: © 2016
abstract: Ages of schoolmaster (n = 136) from the southeastern Florida coast from 1981–2015 were determined using sectioned sagittal otoliths. Opaque zones were annular, forming March–July (peaking in May–June). Schoolmaster ranged in age from 1–42 years; the largest fish measured 505 mm total length (TL) and was 19 years old. The oldest fish measured 440 mm TL. Estimated body size relationships for schoolmaster were: W = 9.26 × 10−6 TL3.11 (n = 256, r2 = 0.95); W = 2.13 × 10−5 FL2.99 (n = 161, r2 = 0.95); TL = 1.03 FL + 10.36 (n = 143, r2 = 0.99); and FL = 0.96 TL − 8.41 (n = 143, r2 = 0.99), where W = whole weight in g, FL = fork length in mm, and TL in mm. The fitted von Bertalanffy growth equation was: Lt = 482 (1 − e−0.12(t+2.79)) (n = 136). Based on published life history relationships, a point estimate of natural mortality for schoolmaster was M = 0.10, while age-specific estimates of M ranged from 1.57–0.18 for ages 1–42.
bibliographic citation: Potts et al. (2016) Age, growth, and natural mortality of schoolmaster (Lutjanus apodus) from the southeastern United States. PeerJ 4:e2543 https://doi.org/10.7717/peerj.2543
date submitted: 2016-04-01
date accepted: 2016-09-08
issued: 2016-10-04
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Potts
  given name: Jennifer C.
author list: Agent
  family name: Burton
  given name: Michael L.
author list: Agent
  family name: Myers
  given name: Amanda R.
doi: 10.7717/peerj.2543
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-04

Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae)
type: item
type: AcademicArticle
description: Bioluminescence, which living organisms such as fireflies emit light, has been studied extensively for over half a century. This intriguing reaction, having its origins in nature where glowing insects can signal things such as attraction or defense, is now widely used in biotechnology with applications of bioluminescence and chemiluminescence. Luciferase, a key enzyme in this reaction, has been well characterized; however, the enzymes involved in the biosynthetic pathway of its substrate, luciferin, remains unsolved at present. To elucidate the luciferin metabolism, we performed a de novo transcriptome analysis using larvae of the firefly species, Luciola aquatilis. Here, a comparative analysis is performed with the model coleopteran insect Tribolium casteneum to elucidate the metabolic pathways in L. aquatilis. Based on a template luciferin biosynthetic pathway, combined with a range of protein and pathway databases, and various prediction tools for functional annotation, the candidate genes, enzymes, and biochemical reactions involved in luciferin metabolism are proposed for L. aquatilis. The candidate gene expression is validated in the adult L. aquatilis using reverse transcription PCR (RT-PCR). This study provides useful information on the bio-production of luciferin in the firefly and will benefit to future applications of the valuable firefly bioluminescence system.
format: application/pdf
format: text/html
creator: Wanwipa Vongsangnak
creator: Pramote Chumnanpuen
creator: Ajaraporn Sriboonlert
subject: Entomology
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.2534
publisher: PeerJ Inc.
rights: © 2016 Vongsangnak et al.
abstract: Bioluminescence, which living organisms such as fireflies emit light, has been studied extensively for over half a century. This intriguing reaction, having its origins in nature where glowing insects can signal things such as attraction or defense, is now widely used in biotechnology with applications of bioluminescence and chemiluminescence. Luciferase, a key enzyme in this reaction, has been well characterized; however, the enzymes involved in the biosynthetic pathway of its substrate, luciferin, remains unsolved at present. To elucidate the luciferin metabolism, we performed a de novo transcriptome analysis using larvae of the firefly species, Luciola aquatilis. Here, a comparative analysis is performed with the model coleopteran insect Tribolium casteneum to elucidate the metabolic pathways in L. aquatilis. Based on a template luciferin biosynthetic pathway, combined with a range of protein and pathway databases, and various prediction tools for functional annotation, the candidate genes, enzymes, and biochemical reactions involved in luciferin metabolism are proposed for L. aquatilis. The candidate gene expression is validated in the adult L. aquatilis using reverse transcription PCR (RT-PCR). This study provides useful information on the bio-production of luciferin in the firefly and will benefit to future applications of the valuable firefly bioluminescence system.
bibliographic citation: Vongsangnak et al. (2016) Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae). PeerJ 4:e2534 https://doi.org/10.7717/peerj.2534
date submitted: 2016-05-29
date accepted: 2016-09-06
issued: 2016-10-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vongsangnak
  given name: Wanwipa
author list: Agent
  family name: Chumnanpuen
  given name: Pramote
author list: Agent
  family name: Sriboonlert
  given name: Ajaraporn
doi: 10.7717/peerj.2534
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-04
copyright: ©2016 Vongsangnak et al.
attribution name: Vongsangnak et al.

Did the 1918 influenza cause the twentieth century cardiovascular mortality epidemic in the United States?
type: item
type: AcademicArticle
description: During most of the twentieth century, cardiovascular mortality increased in the United States while other causes of death declined. By 1958, the age-standardized death rate (ASDR) for cardiovascular causes for females was 1.84 times that for all other causes, combined (and, for males, 1.79×). Although contemporary observers believed that cardiovascular mortality would remain high, the late 1950s and early 1960s turned out to be the peak of a roughly 70-year epidemic. By 1988 for females (1986 for males), a spectacular decline had occurred, wherein the ASDR for cardiovascular causes was less than that for other causes combined. We discuss this phenomenon from a demographic point of view. We also test a hypothesis from the literature, that the 1918 influenza pandemic caused the cardiovascular mortality epidemic; we fail to find support.
format: application/pdf
format: text/html
creator: Steven Tate
creator: Jamie J. Namkung
creator: Andrew Noymer
subject: Virology
subject: Cardiology
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.2531
publisher: PeerJ Inc.
rights: © 2016 Tate et al.
abstract: During most of the twentieth century, cardiovascular mortality increased in the United States while other causes of death declined. By 1958, the age-standardized death rate (ASDR) for cardiovascular causes for females was 1.84 times that for all other causes, combined (and, for males, 1.79×). Although contemporary observers believed that cardiovascular mortality would remain high, the late 1950s and early 1960s turned out to be the peak of a roughly 70-year epidemic. By 1988 for females (1986 for males), a spectacular decline had occurred, wherein the ASDR for cardiovascular causes was less than that for other causes combined. We discuss this phenomenon from a demographic point of view. We also test a hypothesis from the literature, that the 1918 influenza pandemic caused the cardiovascular mortality epidemic; we fail to find support.
bibliographic citation: Tate et al. (2016) Did the 1918 influenza cause the twentieth century cardiovascular mortality epidemic in the United States?. PeerJ 4:e2531 https://doi.org/10.7717/peerj.2531
date submitted: 2016-05-02
date accepted: 2016-09-06
issued: 2016-10-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tate
  given name: Steven
author list: Agent
  family name: Namkung
  given name: Jamie J.
author list: Agent
  family name: Noymer
  given name: Andrew
doi: 10.7717/peerj.2531
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-04
copyright: ©2016 Tate et al.
attribution name: Tate et al.

Transcriptome response to elevated atmospheric CO2 concentration in the Formosan subterranean termite, Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae)
type: item
type: AcademicArticle
description: Background Carbon dioxide (CO2) is a pervasive chemical stimulus that plays a critical role in insect life, eliciting behavioral and physiological responses across different species. High CO2 concentration is a major feature of termite nests, which may be used as a cue for locating their nests. Termites also survive under an elevated CO2 concentration. However, the mechanism by which elevated CO2 concentration influences gene expression in termites is poorly understood. Methods To gain a better understanding of the molecular basis involved in the adaptation to CO2 concentration, a transcriptome of Coptotermes formosanus Shiraki was constructed to assemble the reference genes, followed by comparative transcriptomic analyses across different CO2 concentration (0.04%, 0.4%, 4% and 40%) treatments. Results (1) Based on a high throughput sequencing platform, we obtained approximately 20 GB of clean data and revealed 189,421 unigenes, with a mean length and an N50 length of 629 bp and 974 bp, respectively. (2) The transcriptomic response of C. formosanus to elevated CO2 levels presented discontinuous changes. Comparative analysis of the transcriptomes revealed 2,936 genes regulated among 0.04%, 0.4%, 4% and 40% CO2 concentration treatments, 909 genes derived from termites and 2,027 from gut symbionts. Genes derived from termites appears selectively activated under 4% CO2 level. In 40% CO2 level, most of the down-regulated genes were derived from symbionts. (3) Through similarity searches to data from other species, a number of protein sequences putatively involved in chemosensory reception were identified and characterized in C. formosanus, including odorant receptors, gustatory receptors, ionotropic receptors, odorant binding proteins, and chemosensory proteins. Discussion We found that most genes associated with carbohydrate metabolism, energy metabolism, and genetic information processing were regulated under different CO2 concentrations. Results suggested that termite…
format: application/pdf
format: text/html
creator: Wenjing Wu
creator: Zhiqiang Li
creator: Shijun Zhang
creator: Yunling Ke
creator: Yahui Hou
subject: Bioinformatics
subject: Entomology
subject: Molecular Biology
subject: Statistics
description: doi:10.7717/peerj.2527
publisher: PeerJ Inc.
rights: © 2016 Wu et al.
abstract: Background Carbon dioxide (CO2) is a pervasive chemical stimulus that plays a critical role in insect life, eliciting behavioral and physiological responses across different species. High CO2 concentration is a major feature of termite nests, which may be used as a cue for locating their nests. Termites also survive under an elevated CO2 concentration. However, the mechanism by which elevated CO2 concentration influences gene expression in termites is poorly understood. Methods To gain a better understanding of the molecular basis involved in the adaptation to CO2 concentration, a transcriptome of Coptotermes formosanus Shiraki was constructed to assemble the reference genes, followed by comparative transcriptomic analyses across different CO2 concentration (0.04%, 0.4%, 4% and 40%) treatments. Results (1) Based on a high throughput sequencing platform, we obtained approximately 20 GB of clean data and revealed 189,421 unigenes, with a mean length and an N50 length of 629 bp and 974 bp, respectively. (2) The transcriptomic response of C. formosanus to elevated CO2 levels presented discontinuous changes. Comparative analysis of the transcriptomes revealed 2,936 genes regulated among 0.04%, 0.4%, 4% and 40% CO2 concentration treatments, 909 genes derived from termites and 2,027 from gut symbionts. Genes derived from termites appears selectively activated under 4% CO2 level. In 40% CO2 level, most of the down-regulated genes were derived from symbionts. (3) Through similarity searches to data from other species, a number of protein sequences putatively involved in chemosensory reception were identified and characterized in C. formosanus, including odorant receptors, gustatory receptors, ionotropic receptors, odorant binding proteins, and chemosensory proteins. Discussion We found that most genes associated with carbohydrate metabolism, energy metabolism, and genetic information processing were regulated under different CO2 concentrations. Results suggested that termite…
bibliographic citation: Wu et al. (2016) Transcriptome response to elevated atmospheric CO2 concentration in the Formosan subterranean termite, Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae). PeerJ 4:e2527 https://doi.org/10.7717/peerj.2527
date submitted: 2016-06-21
date accepted: 2016-09-04
issued: 2016-10-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Wenjing
author list: Agent
  family name: Li
  given name: Zhiqiang
author list: Agent
  family name: Zhang
  given name: Shijun
author list: Agent
  family name: Ke
  given name: Yunling
author list: Agent
  family name: Hou
  given name: Yahui
doi: 10.7717/peerj.2527
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-04
copyright: ©2016 Wu et al.
attribution name: Wu et al.

Geographical and altitudinal distribution of Brachycephalus (Anura: Brachycephalidae) endemic to the Brazilian Atlantic Rainforest
type: item
type: AcademicArticle
description: Mountains of the Brazilian Atlantic Forest can act as islands of cold and wet climate, leading to the isolation and speciation of species with low dispersal capacity, such as the toadlet species of the genus Brachycephalus. This genus is composed primarily by diurnal species, with miniaturized body sizes (<2.5 cm), inhabiting microhabitats in the leaf litter of montane forests. Still, little is known about the geographical distribution, altitudinal range, and ecological limits of most Brachycephalus species. In this study, we review the available data on the geographical and altitudinal distribution of Brachycephalus based on occurrence records compiled from literature and museums, both for the genus as a whole and separately for the three recently proposed groups of species (ephippium, didactylus, and pernix). The final ensemble dataset comprised 333 records, 120 localities, 28 described species, and six undescribed ones. Species were recorded in six relief units, the richest of which being the Serra do Mar, with 30 species. When the Serra do Mar is subdivided into three subunits, Northern, Central and Southern Serra do Mar, the number of species increase from north to the south, with records of six, nine, and 16 species, respectively. We were able to estimate the extent of occurrence of nearly half of the described species, and the resulting estimates indicate that many of them show remarkably small ranges, some of which less than 50 ha. Brachycephalus species are present from sea level to roughly 1,900 m a.s.l., with the highest richness being found between 751 and 1,000 m a.s.l. (21 spp.). The species with the broadest altitudinal range were B. didactylus (1,075 m) and Brachycephalus sp. 1 (1,035 m), both in the didactylus group, and B. ephippium (1,050 m), of the ephippium group. The broadest altitudinal amplitude for species of the pernix group was recorded for B. brunneus (535 m). The lowest altitudinal records for the pernix group were at 845 m a.s.l. in the…
format: application/pdf
format: text/html
creator: Marcos R. Bornschein
creator: Carina R. Firkowski
creator: Ricardo Belmonte-Lopes
creator: Leandro Corrêa
creator: Luiz F. Ribeiro
creator: Sérgio A.A. Morato
creator: Reuber L. Antoniazzi-Jr.
creator: Bianca L. Reinert
creator: Andreas L.S. Meyer
creator: Felipe A. Cini
creator: Marcio R. Pie
subject: Biodiversity
subject: Biogeography
subject: Zoology
description: doi:10.7717/peerj.2490
publisher: PeerJ Inc.
rights: © 2016 Bornschein et al.
abstract: Mountains of the Brazilian Atlantic Forest can act as islands of cold and wet climate, leading to the isolation and speciation of species with low dispersal capacity, such as the toadlet species of the genus Brachycephalus. This genus is composed primarily by diurnal species, with miniaturized body sizes (<2.5 cm), inhabiting microhabitats in the leaf litter of montane forests. Still, little is known about the geographical distribution, altitudinal range, and ecological limits of most Brachycephalus species. In this study, we review the available data on the geographical and altitudinal distribution of Brachycephalus based on occurrence records compiled from literature and museums, both for the genus as a whole and separately for the three recently proposed groups of species (ephippium, didactylus, and pernix). The final ensemble dataset comprised 333 records, 120 localities, 28 described species, and six undescribed ones. Species were recorded in six relief units, the richest of which being the Serra do Mar, with 30 species. When the Serra do Mar is subdivided into three subunits, Northern, Central and Southern Serra do Mar, the number of species increase from north to the south, with records of six, nine, and 16 species, respectively. We were able to estimate the extent of occurrence of nearly half of the described species, and the resulting estimates indicate that many of them show remarkably small ranges, some of which less than 50 ha. Brachycephalus species are present from sea level to roughly 1,900 m a.s.l., with the highest richness being found between 751 and 1,000 m a.s.l. (21 spp.). The species with the broadest altitudinal range were B. didactylus (1,075 m) and Brachycephalus sp. 1 (1,035 m), both in the didactylus group, and B. ephippium (1,050 m), of the ephippium group. The broadest altitudinal amplitude for species of the pernix group was recorded for B. brunneus (535 m). The lowest altitudinal records for the pernix group were at 845 m a.s.l. in the…
bibliographic citation: Bornschein et al. (2016) Geographical and altitudinal distribution of Brachycephalus (Anura: Brachycephalidae) endemic to the Brazilian Atlantic Rainforest. PeerJ 4:e2490 https://doi.org/10.7717/peerj.2490
date submitted: 2015-09-24
date accepted: 2016-08-25
issued: 2016-10-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bornschein
  given name: Marcos R.
author list: Agent
  family name: Firkowski
  given name: Carina R.
author list: Agent
  family name: Belmonte-Lopes
  given name: Ricardo
author list: Agent
  family name: Corrêa
  given name: Leandro
author list: Agent
  family name: Ribeiro
  given name: Luiz F.
author list: Agent
  family name: Morato
  given name: Sérgio A.A.
author list: Agent
  family name: Antoniazzi-Jr.
  given name: Reuber L.
author list: Agent
  family name: Reinert
  given name: Bianca L.
author list: Agent
  family name: Meyer
  given name: Andreas L.S.
author list: Agent
  family name: Cini
  given name: Felipe A.
author list: Agent
  family name: Pie
  given name: Marcio R.
doi: 10.7717/peerj.2490
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-04
copyright: ©2016 Bornschein et al.
attribution name: Bornschein et al.

Performance of maximum likelihood mixture models to estimate nursery habitat contributions to fish stocks: a case study on sea bream Sparus aurata
type: item
type: AcademicArticle
description: Background Mixture models (MM) can be used to describe mixed stocks considering three sets of parameters: the total number of contributing sources, their chemical baseline signatures and their mixing proportions. When all nursery sources have been previously identified and sampled for juvenile fish to produce baseline nursery-signatures, mixing proportions are the only unknown set of parameters to be estimated from the mixed-stock data. Otherwise, the number of sources, as well as some/all nursery-signatures may need to be also estimated from the mixed-stock data. Our goal was to assess bias and uncertainty in these MM parameters when estimated using unconditional maximum likelihood approaches (ML-MM), under several incomplete sampling and nursery-signature separation scenarios. Methods We used a comprehensive dataset containing otolith elemental signatures of 301 juvenile Sparus aurata, sampled in three contrasting years (2008, 2010, 2011), from four distinct nursery habitats. (Mediterranean lagoons) Artificial nursery-source and mixed-stock datasets were produced considering: five different sampling scenarios where 0–4 lagoons were excluded from the nursery-source dataset and six nursery-signature separation scenarios that simulated data separated 0.5, 1.5, 2.5, 3.5, 4.5 and 5.5 standard deviations among nursery-signature centroids. Bias (BI) and uncertainty (SE) were computed to assess reliability for each of the three sets of MM parameters. Results Both bias and uncertainty in mixing proportion estimates were low (BI ≤ 0.14, SE ≤ 0.06) when all nursery-sources were sampled but exhibited large variability among cohorts and increased with the number of non-sampled sources up to BI = 0.24 and SE = 0.11. Bias and variability in baseline signature estimates also increased with the number of non-sampled sources, but tended to be less biased, and more uncertain than mixing proportion ones, across all sampling scenarios (BI < 0.13, SE < 0.29). Increasing separation amon…
format: application/pdf
format: text/html
creator: Edwin J. Niklitschek
creator: Audrey M. Darnaude
subject: Aquaculture, Fisheries and Fish Science
subject: Computational Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.2415
publisher: PeerJ Inc.
rights: © 2016 Niklitschek & Darnaude
abstract: Background Mixture models (MM) can be used to describe mixed stocks considering three sets of parameters: the total number of contributing sources, their chemical baseline signatures and their mixing proportions. When all nursery sources have been previously identified and sampled for juvenile fish to produce baseline nursery-signatures, mixing proportions are the only unknown set of parameters to be estimated from the mixed-stock data. Otherwise, the number of sources, as well as some/all nursery-signatures may need to be also estimated from the mixed-stock data. Our goal was to assess bias and uncertainty in these MM parameters when estimated using unconditional maximum likelihood approaches (ML-MM), under several incomplete sampling and nursery-signature separation scenarios. Methods We used a comprehensive dataset containing otolith elemental signatures of 301 juvenile Sparus aurata, sampled in three contrasting years (2008, 2010, 2011), from four distinct nursery habitats. (Mediterranean lagoons) Artificial nursery-source and mixed-stock datasets were produced considering: five different sampling scenarios where 0–4 lagoons were excluded from the nursery-source dataset and six nursery-signature separation scenarios that simulated data separated 0.5, 1.5, 2.5, 3.5, 4.5 and 5.5 standard deviations among nursery-signature centroids. Bias (BI) and uncertainty (SE) were computed to assess reliability for each of the three sets of MM parameters. Results Both bias and uncertainty in mixing proportion estimates were low (BI ≤ 0.14, SE ≤ 0.06) when all nursery-sources were sampled but exhibited large variability among cohorts and increased with the number of non-sampled sources up to BI = 0.24 and SE = 0.11. Bias and variability in baseline signature estimates also increased with the number of non-sampled sources, but tended to be less biased, and more uncertain than mixing proportion ones, across all sampling scenarios (BI < 0.13, SE < 0.29). Increasing separation amon…
bibliographic citation: Niklitschek et al. (2016) Performance of maximum likelihood mixture models to estimate nursery habitat contributions to fish stocks: a case study on sea bream Sparus aurata. PeerJ 4:e2415 https://doi.org/10.7717/peerj.2415
date submitted: 2016-05-03
date accepted: 2016-08-05
issued: 2016-10-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niklitschek
  given name: Edwin J.
author list: Agent
  family name: Darnaude
  given name: Audrey M.
doi: 10.7717/peerj.2415
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-04
copyright: © 2016 Niklitschek & Darnaude
attribution name: Niklitschek & Darnaude

The complete chloroplast genome sequence of Gentiana lawrencei var. farreri (Gentianaceae) and comparative analysis with its congeneric species
type: item
type: AcademicArticle
description: Background The chloroplast (cp) genome is useful in plant systematics, genetic diversity analysis, molecular identification and divergence dating. The genus Gentiana contains 362 species, but there are only two valuable complete cp genomes. The purpose of this study is to report the characterization of complete cp genome of G. lawrencei var. farreri, which is endemic to the Qinghai-Tibetan Plateau (QTP). Methods Using high throughput sequencing technology, we got the complete nucleotide sequence of the G. lawrencei var. farreri cp genome. The comparison analysis including genome difference and gene divergence was performed with its congeneric species G. straminea. The simple sequence repeats (SSRs) and phylogenetics were studied as well. Results The cp genome of G. lawrencei var. farreri is a circular molecule of 138,750 bp, containing a pair of 24,653 bp inverted repeats which are separated by small and large single-copy regions of 11,365 and 78,082 bp, respectively. The cp genome contains 130 known genes, including 85 protein coding genes (PCGs), eight ribosomal RNA genes and 37 tRNA genes. Comparative analyses indicated that G. lawrencei var. farreri is 10,241 bp shorter than its congeneric species G. straminea. Four large gaps were detected that are responsible for 85% of the total sequence loss. Further detailed analyses revealed that 10 PCGs were included in the four gaps that encode nine NADH dehydrogenase subunits. The cp gene content, order and orientation are similar to those of its congeneric species, but with some variation among the PCGs. Three genes, ndhB, ndhF and clpP, have high nonsynonymous to synonymous values. There are 34 SSRs in the G. lawrencei var. farreri cp genome, of which 25 are mononucleotide repeats: no dinucleotide repeats were detected. Comparison with the G. straminea cp genome indicated that five SSRs have length polymorphisms and 23 SSRs are species-specific. The phylogenetic analysis of 48 PCGs from 12 Gentianales taxa cp genomes …
format: application/pdf
format: text/html
creator: Peng-Cheng Fu
creator: Yan-Zhao Zhang
creator: Hui-Min Geng
creator: Shi-Long Chen
subject: Evolutionary Studies
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.2540
publisher: PeerJ Inc.
rights: © 2016 Fu et al.
abstract: Background The chloroplast (cp) genome is useful in plant systematics, genetic diversity analysis, molecular identification and divergence dating. The genus Gentiana contains 362 species, but there are only two valuable complete cp genomes. The purpose of this study is to report the characterization of complete cp genome of G. lawrencei var. farreri, which is endemic to the Qinghai-Tibetan Plateau (QTP). Methods Using high throughput sequencing technology, we got the complete nucleotide sequence of the G. lawrencei var. farreri cp genome. The comparison analysis including genome difference and gene divergence was performed with its congeneric species G. straminea. The simple sequence repeats (SSRs) and phylogenetics were studied as well. Results The cp genome of G. lawrencei var. farreri is a circular molecule of 138,750 bp, containing a pair of 24,653 bp inverted repeats which are separated by small and large single-copy regions of 11,365 and 78,082 bp, respectively. The cp genome contains 130 known genes, including 85 protein coding genes (PCGs), eight ribosomal RNA genes and 37 tRNA genes. Comparative analyses indicated that G. lawrencei var. farreri is 10,241 bp shorter than its congeneric species G. straminea. Four large gaps were detected that are responsible for 85% of the total sequence loss. Further detailed analyses revealed that 10 PCGs were included in the four gaps that encode nine NADH dehydrogenase subunits. The cp gene content, order and orientation are similar to those of its congeneric species, but with some variation among the PCGs. Three genes, ndhB, ndhF and clpP, have high nonsynonymous to synonymous values. There are 34 SSRs in the G. lawrencei var. farreri cp genome, of which 25 are mononucleotide repeats: no dinucleotide repeats were detected. Comparison with the G. straminea cp genome indicated that five SSRs have length polymorphisms and 23 SSRs are species-specific. The phylogenetic analysis of 48 PCGs from 12 Gentianales taxa cp genomes …
bibliographic citation: Fu et al. (2016) The complete chloroplast genome sequence of Gentiana lawrencei var. farreri (Gentianaceae) and comparative analysis with its congeneric species. PeerJ 4:e2540 https://doi.org/10.7717/peerj.2540
date submitted: 2016-06-01
date accepted: 2016-09-07
issued: 2016-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Peng-Cheng
author list: Agent
  family name: Zhang
  given name: Yan-Zhao
author list: Agent
  family name: Geng
  given name: Hui-Min
author list: Agent
  family name: Chen
  given name: Shi-Long
doi: 10.7717/peerj.2540
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-29
copyright: ©2016 Fu et al.
attribution name: Fu et al.

Deer herbivory reduces web-building spider abundance by simplifying forest vegetation structure
type: item
type: AcademicArticle
description: Indirect ecological effects are a common feature of ecological systems, arising when one species affects interactions among two or more other species. We examined how browsing by white-tailed deer (Odocoileus virginianus) indirectly affected the abundance and composition of a web-building spider guild through their effects on the structure of the ground and shrub layers of northern hardwood forests. We examined paired plots consisting of deer-free and control plots in the Allegheny Plateau region Pennsylvania and Northern Highlands region of Wisconsin. We recorded the abundance of seven types of webs, each corresponding to a family of web-building spiders. We quantified vegetation structure and habitat suitability for the spiders by computing a web scaffold availability index (WSAI) at 0.5 m and 1.0 m above the ground. At Northern Highlands sites, we recorded prey availability. Spider webs were twice as abundant in deer-free plots compared to control plots, while WSAI was 7–12 times greater in deerfree plots. Prey availability was lower in deer-free plots. With the exception of funnel web-builders, all spider web types were significantly more abundant in deer-free plots. Both deer exclusion and the geographic region of plots were significant predictors of spider community structure. In closed canopy forests with high browsing pressure, the low density of tree saplings and shrubs provides few locations for web-building spiders to anchor webs. Recruitment of these spiders may become coupled with forest disturbance events that increase tree and shrub recruitment. By modifying habitat structure, deer appear to indirectly modify arthropod food web interactions. As deer populations have increased in eastern North America over the past several decades, the effects of deer on web-building spiders may be widespread.
format: application/pdf
format: text/html
creator: Elizabeth J. Roberson
creator: Michael J. Chips
creator: Walter P. Carson
creator: Thomas P. Rooney
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.2538
publisher: PeerJ Inc.
rights: © 2016 Roberson et al.
abstract: Indirect ecological effects are a common feature of ecological systems, arising when one species affects interactions among two or more other species. We examined how browsing by white-tailed deer (Odocoileus virginianus) indirectly affected the abundance and composition of a web-building spider guild through their effects on the structure of the ground and shrub layers of northern hardwood forests. We examined paired plots consisting of deer-free and control plots in the Allegheny Plateau region Pennsylvania and Northern Highlands region of Wisconsin. We recorded the abundance of seven types of webs, each corresponding to a family of web-building spiders. We quantified vegetation structure and habitat suitability for the spiders by computing a web scaffold availability index (WSAI) at 0.5 m and 1.0 m above the ground. At Northern Highlands sites, we recorded prey availability. Spider webs were twice as abundant in deer-free plots compared to control plots, while WSAI was 7–12 times greater in deerfree plots. Prey availability was lower in deer-free plots. With the exception of funnel web-builders, all spider web types were significantly more abundant in deer-free plots. Both deer exclusion and the geographic region of plots were significant predictors of spider community structure. In closed canopy forests with high browsing pressure, the low density of tree saplings and shrubs provides few locations for web-building spiders to anchor webs. Recruitment of these spiders may become coupled with forest disturbance events that increase tree and shrub recruitment. By modifying habitat structure, deer appear to indirectly modify arthropod food web interactions. As deer populations have increased in eastern North America over the past several decades, the effects of deer on web-building spiders may be widespread.
bibliographic citation: Roberson et al. (2016) Deer herbivory reduces web-building spider abundance by simplifying forest vegetation structure. PeerJ 4:e2538 https://doi.org/10.7717/peerj.2538
date submitted: 2016-06-23
date accepted: 2016-09-07
issued: 2016-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roberson
  given name: Elizabeth J.
author list: Agent
  family name: Chips
  given name: Michael J.
author list: Agent
  family name: Carson
  given name: Walter P.
author list: Agent
  family name: Rooney
  given name: Thomas P.
doi: 10.7717/peerj.2538
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-29
copyright: ©2016 Roberson et al.
attribution name: Roberson et al.

The relationship between mobile phone location sensor data and depressive symptom severity
type: item
type: AcademicArticle
description: Background Smartphones offer the hope that depression can be detected using passively collected data from the phone sensors. The aim of this study was to replicate and extend previous work using geographic location (GPS) sensors to identify depressive symptom severity. Methods We used a dataset collected from 48 college students over a 10-week period, which included GPS phone sensor data and the Patient Health Questionnaire 9-item (PHQ-9) to evaluate depressive symptom severity at baseline and end-of-study. GPS features were calculated over the entire study, for weekdays and weekends, and in 2-week blocks. Results The results of this study replicated our previous findings that a number of GPS features, including location variance, entropy, and circadian movement, were significantly correlated with PHQ-9 scores (r’s ranging from −0.43 to −0.46, p-values < .05). We also found that these relationships were stronger when GPS features were calculated from weekend, compared to weekday, data. Although the correlation between baseline PHQ-9 scores with 2-week GPS features diminished as we moved further from baseline, correlations with the end-of-study scores remained significant regardless of the time point used to calculate the features. Discussion Our findings were consistent with past research demonstrating that GPS features may be an important and reliable predictor of depressive symptom severity. The varying strength of these relationships on weekends and weekdays suggests the role of weekend/weekday as a moderating variable. The finding that GPS features predict depressive symptom severity up to 10 weeks prior to assessment suggests that GPS features may have the potential as early warning signals of depression.
format: application/pdf
format: text/html
creator: Sohrab Saeb
creator: Emily G. Lattie
creator: Stephen M. Schueller
creator: Konrad P. Kording
creator: David C. Mohr
subject: Bioinformatics
subject: Psychiatry and Psychology
subject: Public Health
subject: Computational Science
description: doi:10.7717/peerj.2537
publisher: PeerJ Inc.
rights: © 2016 Saeb et al.
abstract: Background Smartphones offer the hope that depression can be detected using passively collected data from the phone sensors. The aim of this study was to replicate and extend previous work using geographic location (GPS) sensors to identify depressive symptom severity. Methods We used a dataset collected from 48 college students over a 10-week period, which included GPS phone sensor data and the Patient Health Questionnaire 9-item (PHQ-9) to evaluate depressive symptom severity at baseline and end-of-study. GPS features were calculated over the entire study, for weekdays and weekends, and in 2-week blocks. Results The results of this study replicated our previous findings that a number of GPS features, including location variance, entropy, and circadian movement, were significantly correlated with PHQ-9 scores (r’s ranging from −0.43 to −0.46, p-values < .05). We also found that these relationships were stronger when GPS features were calculated from weekend, compared to weekday, data. Although the correlation between baseline PHQ-9 scores with 2-week GPS features diminished as we moved further from baseline, correlations with the end-of-study scores remained significant regardless of the time point used to calculate the features. Discussion Our findings were consistent with past research demonstrating that GPS features may be an important and reliable predictor of depressive symptom severity. The varying strength of these relationships on weekends and weekdays suggests the role of weekend/weekday as a moderating variable. The finding that GPS features predict depressive symptom severity up to 10 weeks prior to assessment suggests that GPS features may have the potential as early warning signals of depression.
bibliographic citation: Saeb et al. (2016) The relationship between mobile phone location sensor data and depressive symptom severity. PeerJ 4:e2537 https://doi.org/10.7717/peerj.2537
date submitted: 2016-06-23
date accepted: 2016-09-07
issued: 2016-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saeb
  given name: Sohrab
author list: Agent
  family name: Lattie
  given name: Emily G.
author list: Agent
  family name: Schueller
  given name: Stephen M.
author list: Agent
  family name: Kording
  given name: Konrad P.
author list: Agent
  family name: Mohr
  given name: David C.
doi: 10.7717/peerj.2537
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-29
copyright: ©2016 Saeb et al.
attribution name: Saeb et al.

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