PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Experimental moose reduction lowers wolf density and stops decline of endangered caribou
items: High incidence of cervical ribs indicates vulnerable condition in Late Pleistocene woolly rhinoceroses
items: Prevalence of bacterial vaginosis in Portuguese pregnant women and vaginal colonization by Gardnerella vaginalis
items: Relying on known or exploring for new? Movement patterns and reproductive resource use in a tadpole-transporting frog
items: The Brazilian version of the 20-item rapid estimate of adult literacy in medicine and dentistry
items: Distribution and biological implications of plastic pollution on the fringing reef of Mo’orea, French Polynesia
items: Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology
items: The microbial biosphere of the coral Acropora cervicornis in Northeastern Puerto Rico
items: Dinosaur origin of egg color: oviraptors laid blue-green eggs
items: Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients

Experimental moose reduction lowers wolf density and stops decline of endangered caribou
type: item
type: AcademicArticle
description: The expansion of moose into southern British Columbia caused the decline and extirpation of woodland caribou due to their shared predators, a process commonly referred to as apparent competition. Using an adaptive management experiment, we tested the hypothesis that reducing moose to historic levels would reduce apparent competition and therefor recover caribou populations. Nested within this broad hypothesis were three specific hypotheses: (1) sport hunting could be used to substantially reduce moose numbers to an ecological target; (2) wolves in this ecosystem were primarily limited by moose abundance; and (3) caribou were limited by wolf predation. These hypotheses were evaluated with a before-after control-impact (BACI) design that included response metrics such as population trends and vital rates of caribou, moose, and wolves. Three caribou subpopulations were subject to the moose reduction treatment and two were in a reference area where moose were not reduced. When the moose harvest was increased, the moose population declined substantially in the treatment area (by 70%) but not the reference area, suggesting that the policy had the desired effect and was not caused by a broader climatic process. Wolf numbers subsequently declined in the treatment area, with wolf dispersal rates 2.5× greater, meaning that dispersal was the likely mechanism behind the wolf numerical response, though reduced recruitment and starvation was also documented in the treatment area. Caribou adult survival increased from 0.78 to 0.88 in the treatment area, but declined in the reference. Caribou recruitment was unaffected by the treatment. The largest caribou subpopulation stabilized in the treatment area, but declined in the reference area. The observed population stability is comparable to other studies that used intensive wolf control, but is insufficient to achieve recovery, suggesting that multiple limiting factors and corresponding management tools must be addressed simultaneous…
format: application/pdf
format: text/html
creator: Robert Serrouya
creator: Bruce N. McLellan
creator: Harry van Oort
creator: Garth Mowat
creator: Stan Boutin
subject: Conservation Biology
subject: Ecology
subject: Natural Resource Management
description: doi:10.7717/peerj.3736
publisher: PeerJ Inc.
rights: © 2017 Serrouya et al.
abstract: The expansion of moose into southern British Columbia caused the decline and extirpation of woodland caribou due to their shared predators, a process commonly referred to as apparent competition. Using an adaptive management experiment, we tested the hypothesis that reducing moose to historic levels would reduce apparent competition and therefor recover caribou populations. Nested within this broad hypothesis were three specific hypotheses: (1) sport hunting could be used to substantially reduce moose numbers to an ecological target; (2) wolves in this ecosystem were primarily limited by moose abundance; and (3) caribou were limited by wolf predation. These hypotheses were evaluated with a before-after control-impact (BACI) design that included response metrics such as population trends and vital rates of caribou, moose, and wolves. Three caribou subpopulations were subject to the moose reduction treatment and two were in a reference area where moose were not reduced. When the moose harvest was increased, the moose population declined substantially in the treatment area (by 70%) but not the reference area, suggesting that the policy had the desired effect and was not caused by a broader climatic process. Wolf numbers subsequently declined in the treatment area, with wolf dispersal rates 2.5× greater, meaning that dispersal was the likely mechanism behind the wolf numerical response, though reduced recruitment and starvation was also documented in the treatment area. Caribou adult survival increased from 0.78 to 0.88 in the treatment area, but declined in the reference. Caribou recruitment was unaffected by the treatment. The largest caribou subpopulation stabilized in the treatment area, but declined in the reference area. The observed population stability is comparable to other studies that used intensive wolf control, but is insufficient to achieve recovery, suggesting that multiple limiting factors and corresponding management tools must be addressed simultaneous…
bibliographic citation: Serrouya et al. (2017) Experimental moose reduction lowers wolf density and stops decline of endangered caribou. PeerJ 5:e3736 https://doi.org/10.7717/peerj.3736
date submitted: 2017-05-02
date accepted: 2017-08-04
issued: 2017-08-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Serrouya
  given name: Robert
author list: Agent
  family name: McLellan
  given name: Bruce N.
author list: Agent
  family name: van Oort
  given name: Harry
author list: Agent
  family name: Mowat
  given name: Garth
author list: Agent
  family name: Boutin
  given name: Stan
doi: 10.7717/peerj.3736
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-29
copyright: ©2017 Serrouya et al.
attribution name: Serrouya et al.

High incidence of cervical ribs indicates vulnerable condition in Late Pleistocene woolly rhinoceroses
type: item
type: AcademicArticle
description: Mammals as a rule have seven cervical vertebrae, a number that remains remarkably constant. Changes of this number are associated with major congenital abnormalities (pleiotropic effects) that are, at least in humans, strongly selected against. Recently, it was found that Late Pleistocene mammoths (Mammuthus primigenius) from the North Sea have an unusually high incidence of abnormal cervical vertebral numbers, approximately ten times higher than that of extant elephants. Abnormal numbers were due to the presence of large cervical ribs on the seventh vertebra, indicating a homeotic change from a cervical rib-less vertebra into a thoracic rib-bearing vertebra. The high incidence of cervical ribs indicates a vulnerable condition and is thought to be due to inbreeding and adverse conditions that may have impacted early pregnancies in declining populations. In this study we investigated the incidence of cervical ribs in another extinct Late Pleistocene megaherbivore from the North Sea and the Netherlands, the woolly rhinoceros (Coelodonta antiquitatis). We show that the incidence of abnormal cervical vertebral numbers in the woolly rhinoceros is unusually high for mammals (15,6%, n = 32) and much higher than in extant Rhinoceratidae (0%, n = 56). This indicates that woolly rhinoceros lived under vulnerable conditions, just like woolly mammoths. The vulnerable condition may well have contributed to their eventual extinction.
format: application/pdf
format: text/html
creator: Alexandra A.E. van der Geer
creator: Frietson Galis
subject: Ecology
subject: Evolutionary Studies
subject: Paleontology
subject: Veterinary Medicine
subject: Pathology
description: doi:10.7717/peerj.3684
publisher: PeerJ Inc.
rights: © 2017 Van der Geer and Galis
abstract: Mammals as a rule have seven cervical vertebrae, a number that remains remarkably constant. Changes of this number are associated with major congenital abnormalities (pleiotropic effects) that are, at least in humans, strongly selected against. Recently, it was found that Late Pleistocene mammoths (Mammuthus primigenius) from the North Sea have an unusually high incidence of abnormal cervical vertebral numbers, approximately ten times higher than that of extant elephants. Abnormal numbers were due to the presence of large cervical ribs on the seventh vertebra, indicating a homeotic change from a cervical rib-less vertebra into a thoracic rib-bearing vertebra. The high incidence of cervical ribs indicates a vulnerable condition and is thought to be due to inbreeding and adverse conditions that may have impacted early pregnancies in declining populations. In this study we investigated the incidence of cervical ribs in another extinct Late Pleistocene megaherbivore from the North Sea and the Netherlands, the woolly rhinoceros (Coelodonta antiquitatis). We show that the incidence of abnormal cervical vertebral numbers in the woolly rhinoceros is unusually high for mammals (15,6%, n = 32) and much higher than in extant Rhinoceratidae (0%, n = 56). This indicates that woolly rhinoceros lived under vulnerable conditions, just like woolly mammoths. The vulnerable condition may well have contributed to their eventual extinction.
bibliographic citation: van der Geer et al. (2017) High incidence of cervical ribs indicates vulnerable condition in Late Pleistocene woolly rhinoceroses. PeerJ 5:e3684 https://doi.org/10.7717/peerj.3684
date submitted: 2017-03-04
date accepted: 2017-07-22
issued: 2017-08-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van der Geer
  given name: Alexandra A.E.
author list: Agent
  family name: Galis
  given name: Frietson
doi: 10.7717/peerj.3684
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-29
copyright: ©2017 Van der Geer and Galis
attribution name: Van der Geer and Galis

Prevalence of bacterial vaginosis in Portuguese pregnant women and vaginal colonization by Gardnerella vaginalis
type: item
type: AcademicArticle
description: Background We aimed to determine the prevalence of vaginal colonization by Gardnerella vaginalis and of bacterial vaginosis (BV) in Portuguese pregnant women, and to identify risk factors for BV and G. vaginalis colonization in pregnancy. Methods A cross-sectional study was conducted among pregnant women aged ≥ 18 years who were attending in two public hospitals of the Northwest region of Portugal. Epidemiological data was collected by anonymous questionnaire. BV was diagnosed by Nugent criteria and G. vaginalis presence was identified by polymerase chain reaction. Crude associations between the study variables and BV or G. vaginalis colonization were quantified by odds ratios (ORs) and their 95% confidence intervals (CIs). Results The prevalences of BV and of G. vaginalis colonization among Portuguese pregnant women were 3.88% and 67.48%, respectively. Previous preterm delivery and colonization by G. vaginalis were factors with very high OR, but only statistically significant for a 90% CI. Conversely, higher rates of G. vaginalis colonization were found in women with basic educational level (OR = 2.77, 95% CI [1.33–5.78]), during the second trimester of pregnancy (OR = 6.12, 95% CI [1.80–20.85]) and with BV flora (OR = 8.73, 95% CI [0.50–153.60]). Discussion Despite the lower number of women with BV, prevalence ratios and association with risk factors were similar to recent European studies. However, the percentage of healthy women colonized by G. vaginalis was significantly higher than many previous studies, confirming that G. vaginalis colonization does not always lead to BV development.
format: application/pdf
format: text/html
creator: Daniela Machado
creator: Joana Castro
creator: José Martinez-de-Oliveira
creator: Cristina Nogueira-Silva
creator: Nuno Cerca
subject: Epidemiology
subject: Gynecology and Obstetrics
subject: Infectious Diseases
subject: Women's Health
description: doi:10.7717/peerj.3750
publisher: PeerJ Inc.
rights: © 2017 Machado et al.
abstract: Background We aimed to determine the prevalence of vaginal colonization by Gardnerella vaginalis and of bacterial vaginosis (BV) in Portuguese pregnant women, and to identify risk factors for BV and G. vaginalis colonization in pregnancy. Methods A cross-sectional study was conducted among pregnant women aged ≥ 18 years who were attending in two public hospitals of the Northwest region of Portugal. Epidemiological data was collected by anonymous questionnaire. BV was diagnosed by Nugent criteria and G. vaginalis presence was identified by polymerase chain reaction. Crude associations between the study variables and BV or G. vaginalis colonization were quantified by odds ratios (ORs) and their 95% confidence intervals (CIs). Results The prevalences of BV and of G. vaginalis colonization among Portuguese pregnant women were 3.88% and 67.48%, respectively. Previous preterm delivery and colonization by G. vaginalis were factors with very high OR, but only statistically significant for a 90% CI. Conversely, higher rates of G. vaginalis colonization were found in women with basic educational level (OR = 2.77, 95% CI [1.33–5.78]), during the second trimester of pregnancy (OR = 6.12, 95% CI [1.80–20.85]) and with BV flora (OR = 8.73, 95% CI [0.50–153.60]). Discussion Despite the lower number of women with BV, prevalence ratios and association with risk factors were similar to recent European studies. However, the percentage of healthy women colonized by G. vaginalis was significantly higher than many previous studies, confirming that G. vaginalis colonization does not always lead to BV development.
bibliographic citation: Machado et al. (2017) Prevalence of bacterial vaginosis in Portuguese pregnant women and vaginal colonization by Gardnerella vaginalis. PeerJ 5:e3750 https://doi.org/10.7717/peerj.3750
date submitted: 2017-06-21
date accepted: 2017-08-08
issued: 2017-08-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Machado
  given name: Daniela
author list: Agent
  family name: Castro
  given name: Joana
author list: Agent
  family name: Martinez-de-Oliveira
  given name: José
author list: Agent
  family name: Nogueira-Silva
  given name: Cristina
author list: Agent
  family name: Cerca
  given name: Nuno
doi: 10.7717/peerj.3750
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-29
copyright: ©2017 Machado et al.
attribution name: Machado et al.

Relying on known or exploring for new? Movement patterns and reproductive resource use in a tadpole-transporting frog
type: item
type: AcademicArticle
description: Animals relying on uncertain, ephemeral and patchy resources have to regularly update their information about profitable sites. For many tropical amphibians, widespread, scattered breeding pools constitute such fluctuating resources. Among tropical amphibians, poison frogs (Dendrobatidae) exhibit some of the most complex spatial and parental behaviors—including territoriality and tadpole transport from terrestrial clutches to ephemeral aquatic deposition sites. Recent studies have revealed that poison frogs rely on spatial memory to successfully navigate through their environment. This raises the question of when and how these frogs gain information about the area and suitable reproductive resources. To investigate the spatial patterns of pool use and to reveal potential explorative behavior, we used telemetry to follow males of the territorial dendrobatid frog Allobates femoralis during tadpole transport and subsequent homing. To elicit exploration, we reduced resource availability experimentally by simulating desiccated deposition sites. We found that tadpole transport is strongly directed towards known deposition sites and that frogs take similar direct paths when returning to their home territory. Frogs move faster during tadpole transport than when homing after the deposition, which probably reflects different risks and costs during these two movement phases. We found no evidence for exploration, neither during transport nor homing, and independent of the availability of deposition sites. We suggest that prospecting during tadpole transport is too risky for the transported offspring as well as for the transporting male. Relying on spatial memory of multiple previously discovered pools appears to be the predominant and successful strategy for the exploitation of reproductive resources in A. femoralis. Our study provides for the first time a detailed description of poison frog movement patterns during tadpole transport and corroborates recent findings on the sign…
format: application/pdf
format: text/html
creator: Kristina B. Beck
creator: Matthias-Claudio Loretto
creator: Max Ringler
creator: Walter Hödl
creator: Andrius Pašukonis
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.3745
publisher: PeerJ Inc.
rights: © 2017 Beck et al.
abstract: Animals relying on uncertain, ephemeral and patchy resources have to regularly update their information about profitable sites. For many tropical amphibians, widespread, scattered breeding pools constitute such fluctuating resources. Among tropical amphibians, poison frogs (Dendrobatidae) exhibit some of the most complex spatial and parental behaviors—including territoriality and tadpole transport from terrestrial clutches to ephemeral aquatic deposition sites. Recent studies have revealed that poison frogs rely on spatial memory to successfully navigate through their environment. This raises the question of when and how these frogs gain information about the area and suitable reproductive resources. To investigate the spatial patterns of pool use and to reveal potential explorative behavior, we used telemetry to follow males of the territorial dendrobatid frog Allobates femoralis during tadpole transport and subsequent homing. To elicit exploration, we reduced resource availability experimentally by simulating desiccated deposition sites. We found that tadpole transport is strongly directed towards known deposition sites and that frogs take similar direct paths when returning to their home territory. Frogs move faster during tadpole transport than when homing after the deposition, which probably reflects different risks and costs during these two movement phases. We found no evidence for exploration, neither during transport nor homing, and independent of the availability of deposition sites. We suggest that prospecting during tadpole transport is too risky for the transported offspring as well as for the transporting male. Relying on spatial memory of multiple previously discovered pools appears to be the predominant and successful strategy for the exploitation of reproductive resources in A. femoralis. Our study provides for the first time a detailed description of poison frog movement patterns during tadpole transport and corroborates recent findings on the sign…
bibliographic citation: Beck et al. (2017) Relying on known or exploring for new? Movement patterns and reproductive resource use in a tadpole-transporting frog. PeerJ 5:e3745 https://doi.org/10.7717/peerj.3745
date submitted: 2017-05-31
date accepted: 2017-08-07
issued: 2017-08-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beck
  given name: Kristina B.
author list: Agent
  family name: Loretto
  given name: Matthias-Claudio
author list: Agent
  family name: Ringler
  given name: Max
author list: Agent
  family name: Hödl
  given name: Walter
author list: Agent
  family name: Pašukonis
  given name: Andrius
doi: 10.7717/peerj.3745
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-29
copyright: ©2017 Beck et al.
attribution name: Beck et al.

The Brazilian version of the 20-item rapid estimate of adult literacy in medicine and dentistry
type: item
type: AcademicArticle
description: Background The misunderstanding of specific vocabulary may hamper the patient-health provider communication. The 20-item Rapid Estimate Adult Literacy in Medicine and Dentistry (REALMD-20) was constructed to screen patients by their ability in reading medical/dental terminologies in a simple and rapid way. This study aimed to perform the cross-cultural adaptation and validation of this instrument for its application in Brazilian dental patients. Methods The cross-cultural adaptation was performed through conceptual equivalence, verbatim translation, semantic, item and operational equivalence, and back-translation. After that, 200 participants responded the adapted version of the REALMD-20, the Brazilian version of the Rapid Estimate of Adult Literacy in Dentistry (BREALD-30), ten questions of the Brazilian National Functional Literacy Index (BNFLI), and a questionnaire with socio-demographic and oral health-related questions. Statistical analysis was conducted to assess the reliability and validity of the REALMD-20 (P < 0.05). Results The sample was composed predominantly by women (55.5%) and white/brown (76%) individuals, with an average age of 39.02 years old (±15.28). The average REALMD-20 score was 17.48 (±2.59, range 8–20). It displayed a good internal consistency (Cronbach’s alpha = 0.789) and test-retest reliability (ICC = 0.73; 95% CI [0.66 − 0.79]). In the exploratory factor analysis, six factors were extracted according to Kaiser’s criterion. The factor I (eigenvalue = 4.53) comprised four terms— “Jaundice”, “Amalgam”, “Periodontitis” and “Abscess”—accounted for 25.18% of total variance, while the factor II (eigenvalue = 1.88) comprised other four terms—“Gingivitis”, “Instruction”, “Osteoporosis” and “Constipation”—accounted for 10.46% of total variance. The first four factors accounted for 52.1% of total variance. The REALMD-20 was positively correlated with the BREALD-30 (Rs = 0.73, P < 0.001) and BNFLI (Rs = 0.60, P < 0.001). The scores were significant…
format: application/pdf
format: text/html
creator: Agnes Fátima P. Cruvinel
creator: Daniela Alejandra C. Méndez
creator: Juliana G. Oliveira
creator: Eliézer Gutierres
creator: Matheus Lotto
creator: Maria Aparecida A.M. Machado
creator: Thaís M. Oliveira
creator: Thiago Cruvinel
subject: Dentistry
subject: Health Policy
subject: Science and Medical Education
description: doi:10.7717/peerj.3744
publisher: PeerJ Inc.
rights: © 2017 Cruvinel et al.
abstract: Background The misunderstanding of specific vocabulary may hamper the patient-health provider communication. The 20-item Rapid Estimate Adult Literacy in Medicine and Dentistry (REALMD-20) was constructed to screen patients by their ability in reading medical/dental terminologies in a simple and rapid way. This study aimed to perform the cross-cultural adaptation and validation of this instrument for its application in Brazilian dental patients. Methods The cross-cultural adaptation was performed through conceptual equivalence, verbatim translation, semantic, item and operational equivalence, and back-translation. After that, 200 participants responded the adapted version of the REALMD-20, the Brazilian version of the Rapid Estimate of Adult Literacy in Dentistry (BREALD-30), ten questions of the Brazilian National Functional Literacy Index (BNFLI), and a questionnaire with socio-demographic and oral health-related questions. Statistical analysis was conducted to assess the reliability and validity of the REALMD-20 (P < 0.05). Results The sample was composed predominantly by women (55.5%) and white/brown (76%) individuals, with an average age of 39.02 years old (±15.28). The average REALMD-20 score was 17.48 (±2.59, range 8–20). It displayed a good internal consistency (Cronbach’s alpha = 0.789) and test-retest reliability (ICC = 0.73; 95% CI [0.66 − 0.79]). In the exploratory factor analysis, six factors were extracted according to Kaiser’s criterion. The factor I (eigenvalue = 4.53) comprised four terms— “Jaundice”, “Amalgam”, “Periodontitis” and “Abscess”—accounted for 25.18% of total variance, while the factor II (eigenvalue = 1.88) comprised other four terms—“Gingivitis”, “Instruction”, “Osteoporosis” and “Constipation”—accounted for 10.46% of total variance. The first four factors accounted for 52.1% of total variance. The REALMD-20 was positively correlated with the BREALD-30 (Rs = 0.73, P < 0.001) and BNFLI (Rs = 0.60, P < 0.001). The scores were significant…
bibliographic citation: Cruvinel et al. (2017) The Brazilian version of the 20-item rapid estimate of adult literacy in medicine and dentistry. PeerJ 5:e3744 https://doi.org/10.7717/peerj.3744
date submitted: 2017-04-14
date accepted: 2017-08-07
issued: 2017-08-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cruvinel
  given name: Agnes Fátima P.
author list: Agent
  family name: Méndez
  given name: Daniela Alejandra C.
author list: Agent
  family name: Oliveira
  given name: Juliana G.
author list: Agent
  family name: Gutierres
  given name: Eliézer
author list: Agent
  family name: Lotto
  given name: Matheus
author list: Agent
  family name: Machado
  given name: Maria Aparecida A.M.
author list: Agent
  family name: Oliveira
  given name: Thaís M.
author list: Agent
  family name: Cruvinel
  given name: Thiago
doi: 10.7717/peerj.3744
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-29
copyright: ©2017 Cruvinel et al.
attribution name: Cruvinel et al.

Distribution and biological implications of plastic pollution on the fringing reef of Mo’orea, French Polynesia
type: item
type: AcademicArticle
description: Coral reef ecosystems of the South Pacific are extremely vulnerable to plastic pollution from oceanic gyres and land-based sources. To describe the extent and impact of plastic pollution, the distribution of both macro- (>5 mm) and microplastic (plastic < 5 mm) of the fringing reef of an isolated South Pacific island, Mo’orea, French Polynesia was quantified. Macroplastic was found on every beach on the island that was surveyed. The distribution of this plastic was categorized by site type and by the presence of Turbinaria ornata, a common macroalgae on Mo’orea. Microplastics were discovered in the water column of the fringing reef of the island, at a concentration of 0.74 pieces m−2. Additionally, this study reports for the first time the ingestion of microplastic by the corallimorpha Discosoma nummiforme. Microplastics were made available to corallimorph polyps in a laboratory setting over the course of 108 h. Positively and negatively buoyant microplastics were ingested, and a microplastic particle that was not experimentally introduced was also discovered in the stomach cavity of one organism. This study indicates that plastic pollution has the potential to negatively impact coral reef ecosystems of the South Pacific, and warrants further study to explore the broader potential impacts of plastic pollution on coral reef ecosystems.
format: application/pdf
format: text/html
creator: Elizabeth J. Connors
subject: Biosphere Interactions
subject: Conservation Biology
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
subject: Marine Biology
description: doi:10.7717/peerj.3733
publisher: PeerJ Inc.
rights: © 2017 Connors
abstract: Coral reef ecosystems of the South Pacific are extremely vulnerable to plastic pollution from oceanic gyres and land-based sources. To describe the extent and impact of plastic pollution, the distribution of both macro- (>5 mm) and microplastic (plastic < 5 mm) of the fringing reef of an isolated South Pacific island, Mo’orea, French Polynesia was quantified. Macroplastic was found on every beach on the island that was surveyed. The distribution of this plastic was categorized by site type and by the presence of Turbinaria ornata, a common macroalgae on Mo’orea. Microplastics were discovered in the water column of the fringing reef of the island, at a concentration of 0.74 pieces m−2. Additionally, this study reports for the first time the ingestion of microplastic by the corallimorpha Discosoma nummiforme. Microplastics were made available to corallimorph polyps in a laboratory setting over the course of 108 h. Positively and negatively buoyant microplastics were ingested, and a microplastic particle that was not experimentally introduced was also discovered in the stomach cavity of one organism. This study indicates that plastic pollution has the potential to negatively impact coral reef ecosystems of the South Pacific, and warrants further study to explore the broader potential impacts of plastic pollution on coral reef ecosystems.
bibliographic citation: Connors (2017) Distribution and biological implications of plastic pollution on the fringing reef of Mo’orea, French Polynesia. PeerJ 5:e3733 https://doi.org/10.7717/peerj.3733
date submitted: 2017-01-02
date accepted: 2017-08-04
issued: 2017-08-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Connors
  given name: Elizabeth J.
doi: 10.7717/peerj.3733
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-29
copyright: ©2017 Connors
attribution name: Connors

Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology
type: item
type: AcademicArticle
description: While methods for genetic species delimitation have noticeably improved in the last decade, this remains a work in progress. Ideally, model based approaches should be applied and considered jointly with other lines of evidence, primarily morphology and geography, in an integrative taxonomy framework. Deep phylogeographic divergences have been reported for several species of Carlia skinks, but only for some eastern taxa have species boundaries been formally tested. The present study does this and revises the taxonomy for two species from northern Australia, Carlia johnstonei and C. triacantha. We introduce an approach that is based on the recently published method StarBEAST2, which uses multilocus data to explore the support for alternative species delimitation hypotheses using Bayes Factors (BFD). We apply this method, jointly with two other multispecies coalescent methods, using an extensive (from 2,163 exons) data set along with measures of 11 morphological characters. We use this integrated approach to evaluate two new candidate species previously revealed in phylogeographic analyses of rainbow skinks (genus Carlia) in Western Australia. The results based on BFD StarBEAST2, BFD* SNAPP and BPP genetic delimitation, together with morphology, support each of the four recently identified Carlia lineages as separate species. The BFD StarBEAST2 approach yielded results highly congruent with those from BFD* SNAPP and BPP. This supports use of the robust multilocus multispecies coalescent StarBEAST2 method for species delimitation, which does not require a priori resolved species or gene trees. Compared to the situation in C. triacantha, morphological divergence was greater between the two lineages within Kimberley endemic C. johnstonei, which also had deeper divergent histories. This congruence supports recognition of two species within C. johnstonei. Nevertheless, the combined evidence also supports recognition of two taxa within the more widespread C. triacantha. With…
format: application/pdf
format: text/html
creator: Ana C. Afonso Silva
creator: Natali Santos
creator: Huw A. Ogilvie
creator: Craig Moritz
subject: Genomics
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.3724
publisher: PeerJ Inc.
rights: © 2017 Afonso Silva et al.
abstract: While methods for genetic species delimitation have noticeably improved in the last decade, this remains a work in progress. Ideally, model based approaches should be applied and considered jointly with other lines of evidence, primarily morphology and geography, in an integrative taxonomy framework. Deep phylogeographic divergences have been reported for several species of Carlia skinks, but only for some eastern taxa have species boundaries been formally tested. The present study does this and revises the taxonomy for two species from northern Australia, Carlia johnstonei and C. triacantha. We introduce an approach that is based on the recently published method StarBEAST2, which uses multilocus data to explore the support for alternative species delimitation hypotheses using Bayes Factors (BFD). We apply this method, jointly with two other multispecies coalescent methods, using an extensive (from 2,163 exons) data set along with measures of 11 morphological characters. We use this integrated approach to evaluate two new candidate species previously revealed in phylogeographic analyses of rainbow skinks (genus Carlia) in Western Australia. The results based on BFD StarBEAST2, BFD* SNAPP and BPP genetic delimitation, together with morphology, support each of the four recently identified Carlia lineages as separate species. The BFD StarBEAST2 approach yielded results highly congruent with those from BFD* SNAPP and BPP. This supports use of the robust multilocus multispecies coalescent StarBEAST2 method for species delimitation, which does not require a priori resolved species or gene trees. Compared to the situation in C. triacantha, morphological divergence was greater between the two lineages within Kimberley endemic C. johnstonei, which also had deeper divergent histories. This congruence supports recognition of two species within C. johnstonei. Nevertheless, the combined evidence also supports recognition of two taxa within the more widespread C. triacantha. With…
bibliographic citation: Afonso Silva et al. (2017) Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology. PeerJ 5:e3724 https://doi.org/10.7717/peerj.3724
date submitted: 2017-02-08
date accepted: 2017-08-01
issued: 2017-08-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Afonso Silva
  given name: Ana C.
author list: Agent
  family name: Santos
  given name: Natali
author list: Agent
  family name: Ogilvie
  given name: Huw A.
author list: Agent
  family name: Moritz
  given name: Craig
doi: 10.7717/peerj.3724
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-29
copyright: ©2017 Afonso Silva et al.
attribution name: Afonso Silva et al.

The microbial biosphere of the coral Acropora cervicornis in Northeastern Puerto Rico
type: item
type: AcademicArticle
description: Background Coral reefs are the most biodiverse ecosystems in the marine realm, and they not only contribute a plethora of ecosystem services to other marine organisms, but they also are beneficial to humankind via, for instance, their role as nurseries for commercially important fish species. Corals are considered holobionts (host + symbionts) since they are composed not only of coral polyps, but also algae, other microbial eukaryotes and prokaryotes. In recent years, Caribbean reef corals, including the once-common scleractinian coral Acropora cervicornis, have suffered unprecedented mortality due to climate change-related stressors. Unfortunately, our basic knowledge of the molecular ecophysiology of reef corals, particularly with respect to their complex bacterial microbiota, is currently too poor to project how climate change will affect this species. For instance, we do not know how light influences microbial communities of A. cervicornis, arguably the most endangered of all Caribbean coral species. To this end, we characterized the microbiota of A. cervicornis inhabiting water depths with different light regimes. Methods Six A. cervicornis fragments from different individuals were collected at two different depths (three at 1.5 m and three at 11 m) from a reef 3.2 km off the northeastern coast of Puerto Rico. We characterized the microbial communities by sequencing the 16S rRNA gene region V4 with the Illumina platform. Results A total of 173,137 good-quality sequences were binned into 803 OTUs with a 97% similarity. We uncovered eight bacterial phyla at both depths with a dominance of 725 Rickettsiales OTUs (Proteobacteria). A fewer number (38) of low dominance OTUs varied by depth and taxa enriched in shallow water corals included Proteobacteria (e.g. Rhodobacteraceae and Serratia) and Firmicutes (Streptococcus). Those enriched in deeper water corals featured different Proteobacterial taxa (Campylobacterales and Bradyrhizobium) and Firmicutes (Lactobacillus)…
format: application/pdf
format: text/html
creator: Filipa Godoy-Vitorino
creator: Claudia P. Ruiz-Diaz
creator: Abigail Rivera-Seda
creator: Juan S. Ramírez-Lugo
creator: Carlos Toledo-Hernández
subject: Biodiversity
subject: Marine Biology
description: doi:10.7717/peerj.3717
publisher: PeerJ Inc.
rights: © 2017 Godoy-Vitorino et al.
abstract: Background Coral reefs are the most biodiverse ecosystems in the marine realm, and they not only contribute a plethora of ecosystem services to other marine organisms, but they also are beneficial to humankind via, for instance, their role as nurseries for commercially important fish species. Corals are considered holobionts (host + symbionts) since they are composed not only of coral polyps, but also algae, other microbial eukaryotes and prokaryotes. In recent years, Caribbean reef corals, including the once-common scleractinian coral Acropora cervicornis, have suffered unprecedented mortality due to climate change-related stressors. Unfortunately, our basic knowledge of the molecular ecophysiology of reef corals, particularly with respect to their complex bacterial microbiota, is currently too poor to project how climate change will affect this species. For instance, we do not know how light influences microbial communities of A. cervicornis, arguably the most endangered of all Caribbean coral species. To this end, we characterized the microbiota of A. cervicornis inhabiting water depths with different light regimes. Methods Six A. cervicornis fragments from different individuals were collected at two different depths (three at 1.5 m and three at 11 m) from a reef 3.2 km off the northeastern coast of Puerto Rico. We characterized the microbial communities by sequencing the 16S rRNA gene region V4 with the Illumina platform. Results A total of 173,137 good-quality sequences were binned into 803 OTUs with a 97% similarity. We uncovered eight bacterial phyla at both depths with a dominance of 725 Rickettsiales OTUs (Proteobacteria). A fewer number (38) of low dominance OTUs varied by depth and taxa enriched in shallow water corals included Proteobacteria (e.g. Rhodobacteraceae and Serratia) and Firmicutes (Streptococcus). Those enriched in deeper water corals featured different Proteobacterial taxa (Campylobacterales and Bradyrhizobium) and Firmicutes (Lactobacillus)…
bibliographic citation: Godoy-Vitorino et al. (2017) The microbial biosphere of the coral Acropora cervicornis in Northeastern Puerto Rico. PeerJ 5:e3717 https://doi.org/10.7717/peerj.3717
date submitted: 2017-02-08
date accepted: 2017-07-29
issued: 2017-08-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Godoy-Vitorino
  given name: Filipa
author list: Agent
  family name: Ruiz-Diaz
  given name: Claudia P.
author list: Agent
  family name: Rivera-Seda
  given name: Abigail
author list: Agent
  family name: Ramírez-Lugo
  given name: Juan S.
author list: Agent
  family name: Toledo-Hernández
  given name: Carlos
doi: 10.7717/peerj.3717
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-29
copyright: ©2017 Godoy-Vitorino et al.
attribution name: Godoy-Vitorino et al.

Dinosaur origin of egg color: oviraptors laid blue-green eggs
type: item
type: AcademicArticle
description: Protoporphyrin (PP) and biliverdin (BV) give rise to the enormous diversity in avian egg coloration. Egg color serves several ecological purposes, including post-mating signaling and camouflage. Egg camouflage represents a major character of open-nesting birds which accomplish protection of their unhatched offspring against visually oriented predators by cryptic egg coloration. Cryptic coloration evolved to match the predominant shades of color found in the nesting environment. Such a selection pressure for the evolution of colored or cryptic eggs should be present in all open nesting birds and relatives. Many birds are open-nesting, but protect their eggs by continuous brooding, and thus exhibit no or minimal eggshell pigmentation. Their closest extant relatives, crocodiles, protect their eggs by burial and have unpigmented eggs. This phylogenetic pattern led to the assumption that colored eggs evolved within crown birds. The mosaic evolution of supposedly avian traits in non-avian theropod dinosaurs, however, such as the supposed evolution of partially open nesting behavior in oviraptorids, argues against this long-established theory. Using a double-checking liquid chromatography ESI-Q-TOF mass spectrometry routine, we traced the origin of colored eggs to their non-avian dinosaur ancestors by providing the first record of the avian eggshell pigments protoporphyrin and biliverdin in the eggshells of Late Cretaceous oviraptorid dinosaurs. The eggshell parataxon Macroolithus yaotunensis can be assigned to the oviraptor Heyuannia huangi based on exceptionally preserved, late developmental stage embryo remains. The analyzed eggshells are from three Late Cretaceous fluvial deposits ranging from eastern to southernmost China. Reevaluation of these taphonomic settings, and a consideration of patterns in the porosity of completely preserved eggs support an at least partially open nesting behavior for oviraptorosaurs. Such a nest arrangement corresponds with our reconstruct…
format: application/pdf
format: text/html
creator: Jasmina Wiemann
creator: Tzu-Ruei Yang
creator: Philipp N. Sander
creator: Marion Schneider
creator: Marianne Engeser
creator: Stephanie Kath-Schorr
creator: Christa E. Müller
creator: P. Martin Sander
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.3706
publisher: PeerJ Inc.
rights: © 2017 Wiemann et al.
abstract: Protoporphyrin (PP) and biliverdin (BV) give rise to the enormous diversity in avian egg coloration. Egg color serves several ecological purposes, including post-mating signaling and camouflage. Egg camouflage represents a major character of open-nesting birds which accomplish protection of their unhatched offspring against visually oriented predators by cryptic egg coloration. Cryptic coloration evolved to match the predominant shades of color found in the nesting environment. Such a selection pressure for the evolution of colored or cryptic eggs should be present in all open nesting birds and relatives. Many birds are open-nesting, but protect their eggs by continuous brooding, and thus exhibit no or minimal eggshell pigmentation. Their closest extant relatives, crocodiles, protect their eggs by burial and have unpigmented eggs. This phylogenetic pattern led to the assumption that colored eggs evolved within crown birds. The mosaic evolution of supposedly avian traits in non-avian theropod dinosaurs, however, such as the supposed evolution of partially open nesting behavior in oviraptorids, argues against this long-established theory. Using a double-checking liquid chromatography ESI-Q-TOF mass spectrometry routine, we traced the origin of colored eggs to their non-avian dinosaur ancestors by providing the first record of the avian eggshell pigments protoporphyrin and biliverdin in the eggshells of Late Cretaceous oviraptorid dinosaurs. The eggshell parataxon Macroolithus yaotunensis can be assigned to the oviraptor Heyuannia huangi based on exceptionally preserved, late developmental stage embryo remains. The analyzed eggshells are from three Late Cretaceous fluvial deposits ranging from eastern to southernmost China. Reevaluation of these taphonomic settings, and a consideration of patterns in the porosity of completely preserved eggs support an at least partially open nesting behavior for oviraptorosaurs. Such a nest arrangement corresponds with our reconstruct…
bibliographic citation: Wiemann et al. (2017) Dinosaur origin of egg color: oviraptors laid blue-green eggs. PeerJ 5:e3706 https://doi.org/10.7717/peerj.3706
date submitted: 2015-09-18
date accepted: 2017-07-27
issued: 2017-08-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wiemann
  given name: Jasmina
author list: Agent
  family name: Yang
  given name: Tzu-Ruei
author list: Agent
  family name: Sander
  given name: Philipp N.
author list: Agent
  family name: Schneider
  given name: Marion
author list: Agent
  family name: Engeser
  given name: Marianne
author list: Agent
  family name: Kath-Schorr
  given name: Stephanie
author list: Agent
  family name: Müller
  given name: Christa E.
author list: Agent
  family name: Sander
  given name: P. Martin
doi: 10.7717/peerj.3706
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-29
copyright: ©2017 Wiemann et al.
attribution name: Wiemann et al.

Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients
type: item
type: AcademicArticle
description: Host-associated microbial communities are ubiquitous among animals, and serve important functions. For example, the bacterial skin microbiome of amphibians can play a role in preventing or reducing infection by the amphibian chytrid fungus, Batrachochytrium dendrobatidis. Evidence suggests that environmental bacteria likely serve as a source pool for at least some of the members of the amphibian skin bacterial community, underscoring the potential for local environmental changes to disrupt microbial community source pools that could be critical to the health of host organisms. However, few studies have assessed variation in the amphibian skin microbiome along clear environmental gradients, and so we know relatively little about how local environmental conditions influence microbiome diversity. We sampled the skin bacterial communities of Coqui frogs, Eleutherodactylus coqui (N = 77), along an elevational gradient in eastern Puerto Rico (0–875 m), with transects in two land use types: intact forest (N = 4 sites) and disturbed (N = 3 sites) forest. We found that alpha diversity (as assessed by Shannon, Simpson, and Phylogenetic Diversity indices) varied across sites, but this variation was not correlated with elevation or land use. Beta diversity (community structure), on the other hand, varied with site, elevation and land use, primarily due to changes in the relative abundance of certain bacterial OTUs (∼species) within these communities. Importantly, although microbiome diversity varied, E. coqui maintained a common core microbiota across all sites. Thus, our findings suggest that environmental conditions can influence the composition of the skin microbiome of terrestrial amphibians, but that some aspects of the microbiome remain consistent despite environmental variation.
format: application/pdf
format: text/html
creator: Myra C. Hughey
creator: Janelle A. Pena
creator: Roberto Reyes
creator: Daniel Medina
creator: Lisa K. Belden
creator: Patricia A. Burrowes
subject: Ecology
subject: Environmental Impacts
subject: Environmental Sciences
subject: Microbiology
description: doi:10.7717/peerj.3688
publisher: PeerJ Inc.
rights: © 2017 Hughey et al.
abstract: Host-associated microbial communities are ubiquitous among animals, and serve important functions. For example, the bacterial skin microbiome of amphibians can play a role in preventing or reducing infection by the amphibian chytrid fungus, Batrachochytrium dendrobatidis. Evidence suggests that environmental bacteria likely serve as a source pool for at least some of the members of the amphibian skin bacterial community, underscoring the potential for local environmental changes to disrupt microbial community source pools that could be critical to the health of host organisms. However, few studies have assessed variation in the amphibian skin microbiome along clear environmental gradients, and so we know relatively little about how local environmental conditions influence microbiome diversity. We sampled the skin bacterial communities of Coqui frogs, Eleutherodactylus coqui (N = 77), along an elevational gradient in eastern Puerto Rico (0–875 m), with transects in two land use types: intact forest (N = 4 sites) and disturbed (N = 3 sites) forest. We found that alpha diversity (as assessed by Shannon, Simpson, and Phylogenetic Diversity indices) varied across sites, but this variation was not correlated with elevation or land use. Beta diversity (community structure), on the other hand, varied with site, elevation and land use, primarily due to changes in the relative abundance of certain bacterial OTUs (∼species) within these communities. Importantly, although microbiome diversity varied, E. coqui maintained a common core microbiota across all sites. Thus, our findings suggest that environmental conditions can influence the composition of the skin microbiome of terrestrial amphibians, but that some aspects of the microbiome remain consistent despite environmental variation.
bibliographic citation: Hughey et al. (2017) Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients. PeerJ 5:e3688 https://doi.org/10.7717/peerj.3688
date submitted: 2017-05-27
date accepted: 2017-07-24
issued: 2017-08-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hughey
  given name: Myra C.
author list: Agent
  family name: Pena
  given name: Janelle A.
author list: Agent
  family name: Reyes
  given name: Roberto
author list: Agent
  family name: Medina
  given name: Daniel
author list: Agent
  family name: Belden
  given name: Lisa K.
author list: Agent
  family name: Burrowes
  given name: Patricia A.
doi: 10.7717/peerj.3688
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-29
copyright: ©2017 Hughey et al.
attribution name: Hughey et al.

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