PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Polymorphism of amyloid-like fibrils can be defined by the concentration of seeds
items: Winter Aconite (Eranthis hyemalis) Lectin as a cytotoxic effector in the lifecycle of Caenorhabditis elegans
items: Low relative error in consumer-grade GPS units make them ideal for measuring small-scale animal movement patterns
items: Neutering of cats and dogs in Ireland; pet owner self-reported perceptions of enabling and disabling factors in the decision to neuter
items: Personality and intelligence: persistence, not self-directedness, cooperativeness or self-transcendence, is related to twins’ cognitive abilities
items: A glacial survivor of the alpine Mediterranean region: phylogenetic and phylogeographic insights into Silene ciliata Pourr. (Caryophyllaceae)
items: A specimen of Rhamphorhynchus with soft tissue preservation, stomach contents and a putative coprolite
items: Irrigation and avifaunal change in coastal Northwest Mexico: has irrigated habit attracted threatened migratory species?
items: Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA)
items: The effects of leaf litter nutrient pulses on Alliaria petiolata performance

Polymorphism of amyloid-like fibrils can be defined by the concentration of seeds
type: item
type: AcademicArticle
description: Prions are infectious proteins where the same protein may express distinct strains. The strains are enciphered by different misfolded conformations. Strain-like phenomena have also been reported in a number of other amyloid-forming proteins. One of the features of amyloid strains is the ability to self-propagate, maintaining a constant set of physical properties despite being propagated under conditions different from those that allowed initial formation of the strain. Here we report a cross-seeding experiment using strains formed under different conditions. Using high concentrations of seeds results in rapid elongation and new fibrils preserve the properties of the seeding fibrils. At low seed concentrations, secondary nucleation plays the major role and new fibrils gain properties predicted by the environment rather than the structure of the seeds. Our findings could explain conformational switching between amyloid strains observed in a wide variety of in vivo and in vitro experiments.
format: application/pdf
format: text/html
creator: Tomas Sneideris
creator: Katažyna Milto
creator: Vytautas Smirnovas
subject: Biochemistry
subject: Biophysics
description: doi:10.7717/peerj.1207
publisher: PeerJ Inc.
rights: © 2015 Sneideris et al.
abstract: Prions are infectious proteins where the same protein may express distinct strains. The strains are enciphered by different misfolded conformations. Strain-like phenomena have also been reported in a number of other amyloid-forming proteins. One of the features of amyloid strains is the ability to self-propagate, maintaining a constant set of physical properties despite being propagated under conditions different from those that allowed initial formation of the strain. Here we report a cross-seeding experiment using strains formed under different conditions. Using high concentrations of seeds results in rapid elongation and new fibrils preserve the properties of the seeding fibrils. At low seed concentrations, secondary nucleation plays the major role and new fibrils gain properties predicted by the environment rather than the structure of the seeds. Our findings could explain conformational switching between amyloid strains observed in a wide variety of in vivo and in vitro experiments.
bibliographic citation: Sneideris et al. (2015) Polymorphism of amyloid-like fibrils can be defined by the concentration of seeds. PeerJ 3:e1207 https://doi.org/10.7717/peerj.1207
date submitted: 2015-05-19
date accepted: 2015-08-01
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sneideris
  given name: Tomas
author list: Agent
  family name: Milto
  given name: Katažyna
author list: Agent
  family name: Smirnovas
  given name: Vytautas
doi: 10.7717/peerj.1207
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Sneideris et al.
attribution name: Sneideris et al.

Winter Aconite (Eranthis hyemalis) Lectin as a cytotoxic effector in the lifecycle of Caenorhabditis elegans
type: item
type: AcademicArticle
description: The lectin found in the tubers of the Winter Aconite (Eranthis hyemalis) plant is an N-acetyl-D-galactosamine specific Type II Ribosome Inactivating Protein (RIP); Type II RIPs have shown anti-cancer properties, and hence have potential as therapeutic agents. Here we present a modified protocol for the extraction and purification of the E. hyemalis lectin (EHL) using affinity chromatography. De novo amino acid sequencing of EHL confirms its classification as a Type II Ribosome Inactivating Protein. The biocidal properties of EHL have been investigated against the nematode Caenorhabditis elegans. Arrested first stage larvae treated with EHL have shown some direct mortality, with surviving larvae subsequently showing a range of phenotypes including food avoidance, reduced fecundity, developmental delay and constitutive dauer larvae formation. Both inappropriate dauer larvae development and failure to locate to bacterial food source are consistent with the disruption of chemosensory function and the ablation of amphid neurons. Further investigation indicates that mutations that disrupt normal amphid formation can block the EHL-induced dauer larvae formation. In combination, these phenotypes indicate that EHL is cytotoxic and suggest a cell specific activity against the amphid neurons of C. elegans.
format: application/pdf
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creator: Marie-Therese McConnell
creator: David R. Lisgarten
creator: Lee J. Byrne
creator: Simon C. Harvey
creator: Emilia Bertolo
subject: Biochemistry
subject: Developmental Biology
subject: Genetics
subject: Toxicology
description: doi:10.7717/peerj.1206
publisher: PeerJ Inc.
rights: © 2015 McConnell et al.
abstract: The lectin found in the tubers of the Winter Aconite (Eranthis hyemalis) plant is an N-acetyl-D-galactosamine specific Type II Ribosome Inactivating Protein (RIP); Type II RIPs have shown anti-cancer properties, and hence have potential as therapeutic agents. Here we present a modified protocol for the extraction and purification of the E. hyemalis lectin (EHL) using affinity chromatography. De novo amino acid sequencing of EHL confirms its classification as a Type II Ribosome Inactivating Protein. The biocidal properties of EHL have been investigated against the nematode Caenorhabditis elegans. Arrested first stage larvae treated with EHL have shown some direct mortality, with surviving larvae subsequently showing a range of phenotypes including food avoidance, reduced fecundity, developmental delay and constitutive dauer larvae formation. Both inappropriate dauer larvae development and failure to locate to bacterial food source are consistent with the disruption of chemosensory function and the ablation of amphid neurons. Further investigation indicates that mutations that disrupt normal amphid formation can block the EHL-induced dauer larvae formation. In combination, these phenotypes indicate that EHL is cytotoxic and suggest a cell specific activity against the amphid neurons of C. elegans.
bibliographic citation: McConnell et al. (2015) Winter Aconite (Eranthis hyemalis) Lectin as a cytotoxic effector in the lifecycle of Caenorhabditis elegans. PeerJ 3:e1206 https://doi.org/10.7717/peerj.1206
date submitted: 2015-05-29
date accepted: 2015-07-31
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McConnell
  given name: Marie-Therese
author list: Agent
  family name: Lisgarten
  given name: David R.
author list: Agent
  family name: Byrne
  given name: Lee J.
author list: Agent
  family name: Harvey
  given name: Simon C.
author list: Agent
  family name: Bertolo
  given name: Emilia
doi: 10.7717/peerj.1206
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 McConnell et al.
attribution name: McConnell et al.

Low relative error in consumer-grade GPS units make them ideal for measuring small-scale animal movement patterns
type: item
type: AcademicArticle
description: Consumer-grade GPS units are a staple of modern field ecology, but the relatively large error radii reported by manufacturers (up to 10 m) ostensibly precludes their utility in measuring fine-scale movement of small animals such as insects. Here we demonstrate that for data collected at fine spatio-temporal scales, these devices can produce exceptionally accurate data on step-length and movement patterns of small animals. With an understanding of the properties of GPS error and how it arises, it is possible, using a simple field protocol, to use consumer grade GPS units to collect step-length data for the movement of small animals that introduces a median error as small as 11 cm. These small error rates were measured in controlled observations of real butterfly movement. Similar conclusions were reached using a ground-truth test track prepared with a field tape and compass and subsequently measured 20 times using the same methodology as the butterfly tracking. Median error in the ground-truth track was slightly higher than the field data, mostly between 20 and 30 cm, but even for the smallest ground-truth step (70 cm), this is still a signal-to-noise ratio of 3:1, and for steps of 3 m or more, the ratio is greater than 10:1. Such small errors relative to the movements being measured make these inexpensive units useful for measuring insect and other small animal movements on small to intermediate scales with budgets orders of magnitude lower than survey-grade units used in past studies. As an additional advantage, these units are simpler to operate, and insect or other small animal trackways can be collected more quickly than either survey-grade units or more traditional ruler/gird approaches.
format: application/pdf
format: text/html
creator: Greg A. Breed
creator: Paul M. Severns
subject: Animal Behavior
subject: Bioengineering
subject: Ecology
subject: Entomology
subject: Computational Science
description: doi:10.7717/peerj.1205
publisher: PeerJ Inc.
rights: © 2015 Breed and Severns
abstract: Consumer-grade GPS units are a staple of modern field ecology, but the relatively large error radii reported by manufacturers (up to 10 m) ostensibly precludes their utility in measuring fine-scale movement of small animals such as insects. Here we demonstrate that for data collected at fine spatio-temporal scales, these devices can produce exceptionally accurate data on step-length and movement patterns of small animals. With an understanding of the properties of GPS error and how it arises, it is possible, using a simple field protocol, to use consumer grade GPS units to collect step-length data for the movement of small animals that introduces a median error as small as 11 cm. These small error rates were measured in controlled observations of real butterfly movement. Similar conclusions were reached using a ground-truth test track prepared with a field tape and compass and subsequently measured 20 times using the same methodology as the butterfly tracking. Median error in the ground-truth track was slightly higher than the field data, mostly between 20 and 30 cm, but even for the smallest ground-truth step (70 cm), this is still a signal-to-noise ratio of 3:1, and for steps of 3 m or more, the ratio is greater than 10:1. Such small errors relative to the movements being measured make these inexpensive units useful for measuring insect and other small animal movements on small to intermediate scales with budgets orders of magnitude lower than survey-grade units used in past studies. As an additional advantage, these units are simpler to operate, and insect or other small animal trackways can be collected more quickly than either survey-grade units or more traditional ruler/gird approaches.
bibliographic citation: Breed et al. (2015) Low relative error in consumer-grade GPS units make them ideal for measuring small-scale animal movement patterns. PeerJ 3:e1205 https://doi.org/10.7717/peerj.1205
date submitted: 2015-06-03
date accepted: 2015-07-31
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Breed
  given name: Greg A.
author list: Agent
  family name: Severns
  given name: Paul M.
doi: 10.7717/peerj.1205
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Breed and Severns
attribution name: Breed and Severns

Neutering of cats and dogs in Ireland; pet owner self-reported perceptions of enabling and disabling factors in the decision to neuter
type: item
type: AcademicArticle
description: Background. Failure among pet owners to neuter their pets results in increased straying and overpopulation problems. Variations in neutering levels can be explained by cultural differences, differences in economic status in rural and urban locations, and owner perceptions about their pet. There are also differences between male and female pet owners. There is no research pertaining to Irish pet owner attitudes towards neutering their pets. This paper identified the perceptions of a sample of Irish cat and dog owners that influenced their decisions on pet neutering. Methods. This study was conducted using social science (qualitative) methods, including an interview-administered survey questionnaire and focus group discussions. Data was coded and managed using Nvivo 8 qualitative data analysis software. Results. Focus groups were conducted with 43 pet (cats and dogs) owners. Two major categories relating to the decision to neuter were identified: (1) enabling perceptions in the decision to neuter (subcategories were: controlling unwanted pet behaviour; positive perceptions regarding pet health and welfare outcomes; perceived owner responsibility; pet function; and the influence of veterinary advice), and (2) disabling perceptions in the decision to neuter (subcategories were: perceived financial cost of neutering; perceived adequacy of existing controls; and negative perceptions regarding pet health and welfare outcomes). Discussion. Pet owner sense of responsibility and control are two central issues to the decision to neuter their pets. Understanding how pet owners feel about topics such as pet neutering, can help improve initiatives aimed at emphasising the responsibility of population control of cats and dogs.
format: application/pdf
format: text/html
creator: Martin J. Downes
creator: Catherine Devitt
creator: Marie T. Downes
creator: Simon J. More
subject: Animal Behavior
subject: Veterinary Medicine
subject: Science and Medical Education
description: doi:10.7717/peerj.1196
publisher: PeerJ Inc.
rights: © 2015 Downes et al.
abstract: Background. Failure among pet owners to neuter their pets results in increased straying and overpopulation problems. Variations in neutering levels can be explained by cultural differences, differences in economic status in rural and urban locations, and owner perceptions about their pet. There are also differences between male and female pet owners. There is no research pertaining to Irish pet owner attitudes towards neutering their pets. This paper identified the perceptions of a sample of Irish cat and dog owners that influenced their decisions on pet neutering. Methods. This study was conducted using social science (qualitative) methods, including an interview-administered survey questionnaire and focus group discussions. Data was coded and managed using Nvivo 8 qualitative data analysis software. Results. Focus groups were conducted with 43 pet (cats and dogs) owners. Two major categories relating to the decision to neuter were identified: (1) enabling perceptions in the decision to neuter (subcategories were: controlling unwanted pet behaviour; positive perceptions regarding pet health and welfare outcomes; perceived owner responsibility; pet function; and the influence of veterinary advice), and (2) disabling perceptions in the decision to neuter (subcategories were: perceived financial cost of neutering; perceived adequacy of existing controls; and negative perceptions regarding pet health and welfare outcomes). Discussion. Pet owner sense of responsibility and control are two central issues to the decision to neuter their pets. Understanding how pet owners feel about topics such as pet neutering, can help improve initiatives aimed at emphasising the responsibility of population control of cats and dogs.
bibliographic citation: Downes et al. (2015) Neutering of cats and dogs in Ireland; pet owner self-reported perceptions of enabling and disabling factors in the decision to neuter. PeerJ 3:e1196 https://doi.org/10.7717/peerj.1196
date submitted: 2015-01-05
date accepted: 2015-07-28
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Downes
  given name: Martin J.
author list: Agent
  family name: Devitt
  given name: Catherine
author list: Agent
  family name: Downes
  given name: Marie T.
author list: Agent
  family name: More
  given name: Simon J.
doi: 10.7717/peerj.1196
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Downes et al.
attribution name: Downes et al.

Personality and intelligence: persistence, not self-directedness, cooperativeness or self-transcendence, is related to twins’ cognitive abilities
type: item
type: AcademicArticle
description: Background. A person-centered approach focusing on the interaction of an individual’s temperament-character-life events is essential in the path of individuals’ well-being. In this context, three character traits, Self-directedness (e.g., self-acceptance, self-control, goal-directed behavior), Cooperativeness (e.g., social affiliation, social tolerance, empathy and helpfulness) and Self-transcendence (e.g., spiritual acceptance, transpersonal identification), measured using Cloninger’s model of personality are suggested to help the individual to regulate and resolve the conflicts derived from her/his temperament combinations as a reaction to life events. However, if character is related to the individual’s cognitive ability, then this association might limit any intervention that focuses on character development. We used data from the Child and Adolescent Twin Study in Sweden (CATSS) to investigate the relationship between personality and cognitive ability. Method. The sample consisted of 370 15-year-old twins (159 girls/211 boys), 192 of whom screen-positive with various types of mental health problems. We used the Temperament and Character Inventory to measure personality and the Wechsler Intelligence Scales for Children (WISC-IV) to measure intelligence. The relationship was investigated using correlation analyses using random-selected twins from each dyad and separately for monozygotic and dizygotic twins. Additional analyses investigated the genetic and environmental effects on personality and cognitive ability in this specific sample. Results. There were no significant correlations between the WISC-IV indices and any of the character traits (i.e., Self-directedness, Cooperativeness, and Self-transcendence). Persistence was significantly related, if weak, to four WISC-IV indices: Verbal Comprehension, Perceptual Reasoning, Working Memory, and the Full WISC-IV Scale. Post-hoc cross-twin/cross-trait analyses showed that the Persistence-cognitive ability correlati…
format: application/pdf
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creator: Fariba Mousavi
creator: Sandor Rozsa
creator: Thomas Nilsson
creator: Trevor Archer
creator: Henrik Anckarsäter
creator: Danilo Garcia
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.1195
publisher: PeerJ Inc.
rights: © 2015 Mousavi et al.
abstract: Background. A person-centered approach focusing on the interaction of an individual’s temperament-character-life events is essential in the path of individuals’ well-being. In this context, three character traits, Self-directedness (e.g., self-acceptance, self-control, goal-directed behavior), Cooperativeness (e.g., social affiliation, social tolerance, empathy and helpfulness) and Self-transcendence (e.g., spiritual acceptance, transpersonal identification), measured using Cloninger’s model of personality are suggested to help the individual to regulate and resolve the conflicts derived from her/his temperament combinations as a reaction to life events. However, if character is related to the individual’s cognitive ability, then this association might limit any intervention that focuses on character development. We used data from the Child and Adolescent Twin Study in Sweden (CATSS) to investigate the relationship between personality and cognitive ability. Method. The sample consisted of 370 15-year-old twins (159 girls/211 boys), 192 of whom screen-positive with various types of mental health problems. We used the Temperament and Character Inventory to measure personality and the Wechsler Intelligence Scales for Children (WISC-IV) to measure intelligence. The relationship was investigated using correlation analyses using random-selected twins from each dyad and separately for monozygotic and dizygotic twins. Additional analyses investigated the genetic and environmental effects on personality and cognitive ability in this specific sample. Results. There were no significant correlations between the WISC-IV indices and any of the character traits (i.e., Self-directedness, Cooperativeness, and Self-transcendence). Persistence was significantly related, if weak, to four WISC-IV indices: Verbal Comprehension, Perceptual Reasoning, Working Memory, and the Full WISC-IV Scale. Post-hoc cross-twin/cross-trait analyses showed that the Persistence-cognitive ability correlati…
bibliographic citation: Mousavi et al. (2015) Personality and intelligence: persistence, not self-directedness, cooperativeness or self-transcendence, is related to twins’ cognitive abilities. PeerJ 3:e1195 https://doi.org/10.7717/peerj.1195
date submitted: 2015-04-01
date accepted: 2015-07-28
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mousavi
  given name: Fariba
author list: Agent
  family name: Rozsa
  given name: Sandor
author list: Agent
  family name: Nilsson
  given name: Thomas
author list: Agent
  family name: Archer
  given name: Trevor
author list: Agent
  family name: Anckarsäter
  given name: Henrik
author list: Agent
  family name: Garcia
  given name: Danilo
doi: 10.7717/peerj.1195
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Mousavi et al.
attribution name: Mousavi et al.

A glacial survivor of the alpine Mediterranean region: phylogenetic and phylogeographic insights into Silene ciliata Pourr. (Caryophyllaceae)
type: item
type: AcademicArticle
description: Silene ciliata Pourr. (Caryophyllaceae) is a species with a highly disjunct distribution which inhabits the alpine mountains of the Mediterranean Basin. We investigated the phylogeny and phylogeography of the species to (a) clarify the long-suggested division of S. ciliata into two subspecies, (b) evaluate its phylogenetic origin and (c) assess whether the species’ diversification patterns were affected by the Mediterranean relief. For this purpose, we collected DNA from 25 populations of the species that inhabit the mountains of Portugal, Spain, France, Italy, former Yugoslav Republic of Macedonia, Bulgaria and Greece and studied the plastid regions rbcL, rps16 and trnL. Major intraspecific variation was supported by all analyses, while the possibility of the existence of more varieties or subspecies was not favoured. Plastid DNA (cpDNA) evidence was in accordance with the division of S. ciliata into the two subspecies, one spreading west (Iberian Peninsula and Central Massif) and the other east of the Alps region (Italian and Balkan Peninsula). This study proposes that the species’ geographically disconnected distribution has probably derived from vicariance processes and from the Alps acting as a barrier to the species’ dispersal. The monophyletic origin of the species is highly supported. cpDNA patterns were shown independent of the chromosome evolution in the populations and could have resulted from a combination of geographic factors providing links and barriers, climatic adversities and evolutionary processes that took place during Quaternary glaciations.
format: application/pdf
format: text/html
creator: Ifigeneia Kyrkou
creator: José María Iriondo
creator: Alfredo García-Fernández
subject: Biogeography
subject: Evolutionary Studies
subject: Genetics
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.1193
publisher: PeerJ Inc.
rights: © 2015 Kyrkou et al.
abstract: Silene ciliata Pourr. (Caryophyllaceae) is a species with a highly disjunct distribution which inhabits the alpine mountains of the Mediterranean Basin. We investigated the phylogeny and phylogeography of the species to (a) clarify the long-suggested division of S. ciliata into two subspecies, (b) evaluate its phylogenetic origin and (c) assess whether the species’ diversification patterns were affected by the Mediterranean relief. For this purpose, we collected DNA from 25 populations of the species that inhabit the mountains of Portugal, Spain, France, Italy, former Yugoslav Republic of Macedonia, Bulgaria and Greece and studied the plastid regions rbcL, rps16 and trnL. Major intraspecific variation was supported by all analyses, while the possibility of the existence of more varieties or subspecies was not favoured. Plastid DNA (cpDNA) evidence was in accordance with the division of S. ciliata into the two subspecies, one spreading west (Iberian Peninsula and Central Massif) and the other east of the Alps region (Italian and Balkan Peninsula). This study proposes that the species’ geographically disconnected distribution has probably derived from vicariance processes and from the Alps acting as a barrier to the species’ dispersal. The monophyletic origin of the species is highly supported. cpDNA patterns were shown independent of the chromosome evolution in the populations and could have resulted from a combination of geographic factors providing links and barriers, climatic adversities and evolutionary processes that took place during Quaternary glaciations.
bibliographic citation: Kyrkou et al. (2015) A glacial survivor of the alpine Mediterranean region: phylogenetic and phylogeographic insights into Silene ciliata Pourr. (Caryophyllaceae). PeerJ 3:e1193 https://doi.org/10.7717/peerj.1193
date submitted: 2015-03-11
date accepted: 2015-07-26
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kyrkou
  given name: Ifigeneia
author list: Agent
  family name: Iriondo
  given name: José María
author list: Agent
  family name: García-Fernández
  given name: Alfredo
doi: 10.7717/peerj.1193
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Kyrkou et al.
attribution name: Kyrkou et al.

A specimen of Rhamphorhynchus with soft tissue preservation, stomach contents and a putative coprolite
type: item
type: AcademicArticle
description: Despite being known for nearly two centuries, new specimens of the derived non-pterodactyloid pterosaur Rhamphorhynchus continue to be discovered and reveal new information about their anatomy and palaeobiology. Here we describe a specimen held in the collections of the Royal Tyrrell Museum of Palaeontology, Alberta, Canada that shows both preservation and impressions of soft tissues, and also preserves material interpreted as stomach contents of vertebrate remains and, uniquely, a putative coprolite. The specimen also preserves additional evidence for fibers in the uropatagium.
format: application/pdf
format: text/html
creator: David Hone
creator: Donald M. Henderson
creator: François Therrien
creator: Michael B. Habib
subject: Paleontology
description: doi:10.7717/peerj.1191
publisher: PeerJ Inc.
rights: © 2015 Hone et al.
abstract: Despite being known for nearly two centuries, new specimens of the derived non-pterodactyloid pterosaur Rhamphorhynchus continue to be discovered and reveal new information about their anatomy and palaeobiology. Here we describe a specimen held in the collections of the Royal Tyrrell Museum of Palaeontology, Alberta, Canada that shows both preservation and impressions of soft tissues, and also preserves material interpreted as stomach contents of vertebrate remains and, uniquely, a putative coprolite. The specimen also preserves additional evidence for fibers in the uropatagium.
bibliographic citation: Hone et al. (2015) A specimen of Rhamphorhynchus with soft tissue preservation, stomach contents and a putative coprolite. PeerJ 3:e1191 https://doi.org/10.7717/peerj.1191
date submitted: 2015-03-29
date accepted: 2015-07-26
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hone
  given name: David
author list: Agent
  family name: Henderson
  given name: Donald M.
author list: Agent
  family name: Therrien
  given name: François
author list: Agent
  family name: Habib
  given name: Michael B.
doi: 10.7717/peerj.1191
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Hone et al.
attribution name: Hone et al.

Irrigation and avifaunal change in coastal Northwest Mexico: has irrigated habit attracted threatened migratory species?
type: item
type: AcademicArticle
description: Irrigation in desert ecosystems can either reduce or increase species diversity. Groundwater pumping often lowers water tables and reduces natural wetlands, whereas canal irrigation often creates mesic habitat, resulting in great increases in avian diversity from irrigation. Here we compare a dataset of potential natural vegetation to recent datasets from areal and satellite imagery to show that 60% of the land in the coastal plain of southern Sonora and northern Sinaloa lying below 200 m elevation has been converted by irrigation to more mesic habitats. We then use the record of bird specimens in the world’s museums from this same region of Mexico to examine the avian community before and after the development of extensive irrigation. In general these museum records show an increase in the abundance and diversity of breeding birds associated with mesic habitats. Although thorn forest birds have likely decreased in total numbers, most are common enough in the remaining thorn forest that collection records did not indicate their probable decline. Four migrants having most of their breeding ranges in the US or Canada, Yellow-billed Cuckoo, Cliff Swallow, Bell’s Vireo, and Orchard Oriole, apparently have increased dramatically as breeders in irrigated habitats of NW Mexico. Because these species have decreased or even largely disappeared as breeding birds in parts of the US or Canada, further research should assess whether their increases in new mesic habitats of NW Mexico are linked to their declines as breeding birds in Canada and the US For Bell’s Vireo recent specimens from Sinaloa suggest its new breeding population in NW Mexico may be composed partly of the endangered Least Bell’s Vireo.
format: application/pdf
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creator: Sievert Rohwer
creator: Emily Grason
creator: Adolfo G. Navarro-Sigüenza
subject: Animal Behavior
subject: Biosphere Interactions
subject: Conservation Biology
subject: Coupled Natural and Human Systems
subject: Ecology
description: doi:10.7717/peerj.1187
publisher: PeerJ Inc.
rights: © 2015 Rohwer et al.
abstract: Irrigation in desert ecosystems can either reduce or increase species diversity. Groundwater pumping often lowers water tables and reduces natural wetlands, whereas canal irrigation often creates mesic habitat, resulting in great increases in avian diversity from irrigation. Here we compare a dataset of potential natural vegetation to recent datasets from areal and satellite imagery to show that 60% of the land in the coastal plain of southern Sonora and northern Sinaloa lying below 200 m elevation has been converted by irrigation to more mesic habitats. We then use the record of bird specimens in the world’s museums from this same region of Mexico to examine the avian community before and after the development of extensive irrigation. In general these museum records show an increase in the abundance and diversity of breeding birds associated with mesic habitats. Although thorn forest birds have likely decreased in total numbers, most are common enough in the remaining thorn forest that collection records did not indicate their probable decline. Four migrants having most of their breeding ranges in the US or Canada, Yellow-billed Cuckoo, Cliff Swallow, Bell’s Vireo, and Orchard Oriole, apparently have increased dramatically as breeders in irrigated habitats of NW Mexico. Because these species have decreased or even largely disappeared as breeding birds in parts of the US or Canada, further research should assess whether their increases in new mesic habitats of NW Mexico are linked to their declines as breeding birds in Canada and the US For Bell’s Vireo recent specimens from Sinaloa suggest its new breeding population in NW Mexico may be composed partly of the endangered Least Bell’s Vireo.
bibliographic citation: Rohwer et al. (2015) Irrigation and avifaunal change in coastal Northwest Mexico: has irrigated habit attracted threatened migratory species?. PeerJ 3:e1187 https://doi.org/10.7717/peerj.1187
date submitted: 2015-03-20
date accepted: 2015-07-24
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rohwer
  given name: Sievert
author list: Agent
  family name: Grason
  given name: Emily
author list: Agent
  family name: Navarro-Sigüenza
  given name: Adolfo G.
doi: 10.7717/peerj.1187
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Rohwer et al.
attribution name: Rohwer et al.

Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA)
type: item
type: AcademicArticle
description: Within highly diverse ecosystems, the majority of bacterial taxa are present in low abundance as members of the rare biosphere. The rationale for the occurrence and maintenance of the rare biosphere, and the putative ecological role(s) and dynamics of its members within a specific ecosystem is currently debated. We hypothesized that in highly diverse ecosystems, a fraction of the rare biosphere acts as a backup system that readily responds to environmental disturbances. We tested this hypothesis by subjecting sediments from Zodletone spring, a sulfide- and sulfur-rich spring in Southwestern OK, to incremental levels of salinity (1, 2, 3, 4, and 10% NaCl), or temperature (28°, 30°, 32°, and 70 °C), and traced the trajectories of rare members of the community in response to these manipulations using 16S rRNA gene analysis. Our results indicate that multiple rare bacterial taxa are promoted from rare to abundant members of the community following such manipulations and that, in general, the magnitude of such recruitment is directly proportional to the severity of the applied manipulation. Rare members that are phylogenetically distinct from abundant taxa in the original sample (unique rare biosphere) played a more important role in the microbial community response to environmental disturbances, compared to rare members that are phylogenetically similar to abundant taxa in the original sample (non-unique rare biosphere). The results emphasize the dynamic nature of the rare biosphere, and highlight its complexity and non-monolithic nature.
format: application/pdf
format: text/html
creator: Suzanne Coveley
creator: Mostafa S. Elshahed
creator: Noha H. Youssef
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.1182
publisher: PeerJ Inc.
rights: © 2015 Coveley et al.
abstract: Within highly diverse ecosystems, the majority of bacterial taxa are present in low abundance as members of the rare biosphere. The rationale for the occurrence and maintenance of the rare biosphere, and the putative ecological role(s) and dynamics of its members within a specific ecosystem is currently debated. We hypothesized that in highly diverse ecosystems, a fraction of the rare biosphere acts as a backup system that readily responds to environmental disturbances. We tested this hypothesis by subjecting sediments from Zodletone spring, a sulfide- and sulfur-rich spring in Southwestern OK, to incremental levels of salinity (1, 2, 3, 4, and 10% NaCl), or temperature (28°, 30°, 32°, and 70 °C), and traced the trajectories of rare members of the community in response to these manipulations using 16S rRNA gene analysis. Our results indicate that multiple rare bacterial taxa are promoted from rare to abundant members of the community following such manipulations and that, in general, the magnitude of such recruitment is directly proportional to the severity of the applied manipulation. Rare members that are phylogenetically distinct from abundant taxa in the original sample (unique rare biosphere) played a more important role in the microbial community response to environmental disturbances, compared to rare members that are phylogenetically similar to abundant taxa in the original sample (non-unique rare biosphere). The results emphasize the dynamic nature of the rare biosphere, and highlight its complexity and non-monolithic nature.
bibliographic citation: Coveley et al. (2015) Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA). PeerJ 3:e1182 https://doi.org/10.7717/peerj.1182
date submitted: 2015-05-14
date accepted: 2015-07-23
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coveley
  given name: Suzanne
author list: Agent
  family name: Elshahed
  given name: Mostafa S.
author list: Agent
  family name: Youssef
  given name: Noha H.
doi: 10.7717/peerj.1182
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Coveley et al.
attribution name: Coveley et al.

The effects of leaf litter nutrient pulses on Alliaria petiolata performance
type: item
type: AcademicArticle
description: Nutrient pulses can facilitate species establishment and spread in new habitats, particularly when one species more effectively uses that nutrient pulse. Biological differences in nutrient acquisition between native and exotic species may facilitate invasions into a variety of habitats including deciduous forest understories. Alliaria petiolata (Bieb.) Cavara & Grande is an important invader of deciduous forest understories throughout much of North America. These understory communities contain many species which perform the majority of their growth and reproduction before canopy closure in spring. Because A. petiolata is a wintergreen biennial that can be active during autumn and winter, it may utilize nutrients released from decaying leaf litter before its competitors. To investigate this we manipulated the timing of leaf litter addition (fall or spring) and experimentally simulated the nutrient pulse from decaying leaves using artificial fertilizer. To determine whether A. petiolata affected the abundance of understory competitors, we also removed A. petiolata from one treatment. A. petiolata that received early nutrients exhibited greater growth. Treatments receiving fall leaf litter or artificial nutrients had greater A. petiolata adult biomass than plots receiving spring nutrient additions (leaf litter or artificial nutrients). However, fall leaf litter addition had no effect on the richness of competitor species. Thus, wintergreen phenology may contribute to the spread of A. petiolata through deciduous forest understories, but may not explain community-level impacts of A. petiolata in deciduous forests.
format: application/pdf
format: text/html
creator: Robert W. Heckman
creator: David E. Carr
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Plant Science
description: doi:10.7717/peerj.1166
publisher: PeerJ Inc.
rights: © 2015 Heckman and Carr
abstract: Nutrient pulses can facilitate species establishment and spread in new habitats, particularly when one species more effectively uses that nutrient pulse. Biological differences in nutrient acquisition between native and exotic species may facilitate invasions into a variety of habitats including deciduous forest understories. Alliaria petiolata (Bieb.) Cavara & Grande is an important invader of deciduous forest understories throughout much of North America. These understory communities contain many species which perform the majority of their growth and reproduction before canopy closure in spring. Because A. petiolata is a wintergreen biennial that can be active during autumn and winter, it may utilize nutrients released from decaying leaf litter before its competitors. To investigate this we manipulated the timing of leaf litter addition (fall or spring) and experimentally simulated the nutrient pulse from decaying leaves using artificial fertilizer. To determine whether A. petiolata affected the abundance of understory competitors, we also removed A. petiolata from one treatment. A. petiolata that received early nutrients exhibited greater growth. Treatments receiving fall leaf litter or artificial nutrients had greater A. petiolata adult biomass than plots receiving spring nutrient additions (leaf litter or artificial nutrients). However, fall leaf litter addition had no effect on the richness of competitor species. Thus, wintergreen phenology may contribute to the spread of A. petiolata through deciduous forest understories, but may not explain community-level impacts of A. petiolata in deciduous forests.
bibliographic citation: Heckman et al. (2015) The effects of leaf litter nutrient pulses on Alliaria petiolata performance. PeerJ 3:e1166 https://doi.org/10.7717/peerj.1166
date submitted: 2015-06-01
date accepted: 2015-07-18
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heckman
  given name: Robert W.
author list: Agent
  family name: Carr
  given name: David E.
doi: 10.7717/peerj.1166
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Heckman and Carr
attribution name: Heckman and Carr

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