PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Environmentally relevant levels of four psychoactive compounds vary in their effects on freshwater fish condition: a brain concentration evidence approach
items: Access to scientific literature by the conservation community
items: Molecular phylogenetics and evolutionary history of the endemic land snail genus Everettia in northern Borneo
items: A collection of hexactinellids (Porifera) from the deep South Atlantic and North Pacific: new genus, new species and new records
items: Sharing for science: high-resolution trophic interactions revealed rapidly by social media
items: Prognostic value of complementary biomarkers of neurodegeneration in a mixed memory clinic cohort
items: Very few sites can reshape the inferred phylogenetic tree
items: Effect of predation risk and ectoparasitic louse flies on physiological stress condition of the red-tailed tropicbird (Phaethon rubricauda) from Rapa Nui and Salas & Gómez islands
items: Low frequencies in the display vocalization of the Western Capercaillie (Tetrao urogallus)
items: ?Amphictis (Carnivora, Ailuridae) from the Belgrade Formation of North Carolina, USA

Environmentally relevant levels of four psychoactive compounds vary in their effects on freshwater fish condition: a brain concentration evidence approach
type: item
type: AcademicArticle
description: Background The aquatic environment has been contaminated with various anthropogenic pollutants, including psychoactive compounds that may alter the physiology and behavior of free-living organisms. The present study focused on the condition and related mortality of the juvenile chub (Squalius cephalus). The aim of the study was to test whether the adverse effects of the antidepressants sertraline and citalopram, the analgesic tramadol and the illicit drug methamphetamine, on fish condition exist under environmentally relevant concentrations and whether these effects persist after a depuration period. Innovative analyses of the fish brain concentrations of these compounds were performed with the aim to show relationship between compound brain tissue concentration and fish condition. Methods The laboratory experiment consisted of 42 days of exposure and a subsequent 14-day depuration period with regular monitoring of the condition and mortality of exposed and control fish. Identical methodology, including individual brain concentration analyses for the tested compounds, was applied for all substances. Additional study on feeding under sertraline exposure was also conducted. The feeding was measured from the 28th day of the exposure, three times in a week, by observation of food intake during 15 minutes in social environment. Results The effects of particular psychoactive compounds on chub condition varied. While sertraline induced a lower condition and increased mortality, the effects of methamphetamine were inverse, and tramadol and citalopram had no significant effect at all. Individual brain concentrations of the tested compounds showed that the effects of sertraline and methamphetamine on fish condition were increased with brain concentration increases. Additionally, the food intake was reduced in case of sertraline. In contrast, there was no relationship between tramadol and citalopram brain tissue concentration and fish condition, suggesting that the concentrati…
format: application/pdf
format: text/html
creator: Pavla Hubená
creator: Pavel Horký
creator: Roman Grabic
creator: Kateřina Grabicová
creator: Ondřej Slavík
creator: Tomáš Randák
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Toxicology
subject: Ecotoxicology
description: doi:10.7717/peerj.9356
publisher: PeerJ Inc.
rights: © 2020 Hubená et al.
abstract: Background The aquatic environment has been contaminated with various anthropogenic pollutants, including psychoactive compounds that may alter the physiology and behavior of free-living organisms. The present study focused on the condition and related mortality of the juvenile chub (Squalius cephalus). The aim of the study was to test whether the adverse effects of the antidepressants sertraline and citalopram, the analgesic tramadol and the illicit drug methamphetamine, on fish condition exist under environmentally relevant concentrations and whether these effects persist after a depuration period. Innovative analyses of the fish brain concentrations of these compounds were performed with the aim to show relationship between compound brain tissue concentration and fish condition. Methods The laboratory experiment consisted of 42 days of exposure and a subsequent 14-day depuration period with regular monitoring of the condition and mortality of exposed and control fish. Identical methodology, including individual brain concentration analyses for the tested compounds, was applied for all substances. Additional study on feeding under sertraline exposure was also conducted. The feeding was measured from the 28th day of the exposure, three times in a week, by observation of food intake during 15 minutes in social environment. Results The effects of particular psychoactive compounds on chub condition varied. While sertraline induced a lower condition and increased mortality, the effects of methamphetamine were inverse, and tramadol and citalopram had no significant effect at all. Individual brain concentrations of the tested compounds showed that the effects of sertraline and methamphetamine on fish condition were increased with brain concentration increases. Additionally, the food intake was reduced in case of sertraline. In contrast, there was no relationship between tramadol and citalopram brain tissue concentration and fish condition, suggesting that the concentrati…
bibliographic citation: Hubená et al. (2020) Environmentally relevant levels of four psychoactive compounds vary in their effects on freshwater fish condition: a brain concentration evidence approach. PeerJ 8:e9356 https://doi.org/10.7717/peerj.9356
date submitted: 2019-12-19
date accepted: 2020-05-24
issued: 2020-07-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hubená
  given name: Pavla
author list: Agent
  family name: Horký
  given name: Pavel
author list: Agent
  family name: Grabic
  given name: Roman
author list: Agent
  family name: Grabicová
  given name: Kateřina
author list: Agent
  family name: Slavík
  given name: Ondřej
author list: Agent
  family name: Randák
  given name: Tomáš
doi: 10.7717/peerj.9356
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-09
copyright: ©2020 Hubená et al.
attribution name: Hubená et al.

Access to scientific literature by the conservation community
type: item
type: AcademicArticle
description: Access to the scientific literature is perceived to be a challenge to the biodiversity conservation community, but actual level of literature access relative to needs has never been assessed globally. We examined this question by surveying the constituency of the International Union for Conservation of Nature (IUCN) as a proxy for the conservation community, generating 2,285 responses. Of these respondents, ∼97% need to use the scientific literature in order to support their IUCN-related conservation work, with ∼50% needing to do so at least once per week. The crux of the survey revolved around the question, “How easy is it for you currently to obtain the scientific literature you need to carry out your IUCN-related work?” and revealed that roughly half (49%) of the respondents find it not easy or not at all easy to access scientific literature. We fitted a binary logistic regression model to explore factors predicting ease of literature access. Whether the respondent had institutional literature access (55% do) is the strongest predictor, with region (Western Europe, the United States, Canada, Australia and New Zealand) and sex (male) also significant predictors. Approximately 60% of respondents from Western Europe, the United States, Canada, Australia and New Zealand have institutional access compared to ∼50% in Asia and Latin America, and ∼40% in Eastern Europe and in Africa. Nevertheless, accessing free online material is a popular means of accessing literature for both those with and without institutional access. The four journals most frequently mentioned when asked which journal access would deliver the greatest improvements to the respondent’s IUCN-related work were Conservation Biology, Biological Conservation, Nature, and Science. The majority prefer to read journal articles on screen but books in hard copy. Overall, it is apparent that access to the literature is a challenge facing roughly half of the conservation community worldwide.
format: application/pdf
format: text/html
creator: Daisy Larios
creator: Thomas M. Brooks
creator: Nicholas B.W. Macfarlane
creator: Sugoto Roy
subject: Biodiversity
subject: Conservation Biology
subject: Science Policy
description: doi:10.7717/peerj.9404
publisher: PeerJ Inc.
rights: © 2020 Larios et al.
abstract: Access to the scientific literature is perceived to be a challenge to the biodiversity conservation community, but actual level of literature access relative to needs has never been assessed globally. We examined this question by surveying the constituency of the International Union for Conservation of Nature (IUCN) as a proxy for the conservation community, generating 2,285 responses. Of these respondents, ∼97% need to use the scientific literature in order to support their IUCN-related conservation work, with ∼50% needing to do so at least once per week. The crux of the survey revolved around the question, “How easy is it for you currently to obtain the scientific literature you need to carry out your IUCN-related work?” and revealed that roughly half (49%) of the respondents find it not easy or not at all easy to access scientific literature. We fitted a binary logistic regression model to explore factors predicting ease of literature access. Whether the respondent had institutional literature access (55% do) is the strongest predictor, with region (Western Europe, the United States, Canada, Australia and New Zealand) and sex (male) also significant predictors. Approximately 60% of respondents from Western Europe, the United States, Canada, Australia and New Zealand have institutional access compared to ∼50% in Asia and Latin America, and ∼40% in Eastern Europe and in Africa. Nevertheless, accessing free online material is a popular means of accessing literature for both those with and without institutional access. The four journals most frequently mentioned when asked which journal access would deliver the greatest improvements to the respondent’s IUCN-related work were Conservation Biology, Biological Conservation, Nature, and Science. The majority prefer to read journal articles on screen but books in hard copy. Overall, it is apparent that access to the literature is a challenge facing roughly half of the conservation community worldwide.
bibliographic citation: Larios et al. (2020) Access to scientific literature by the conservation community. PeerJ 8:e9404 https://doi.org/10.7717/peerj.9404
date submitted: 2019-12-17
date accepted: 2020-06-01
issued: 2020-07-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Larios
  given name: Daisy
author list: Agent
  family name: Brooks
  given name: Thomas M.
author list: Agent
  family name: Macfarlane
  given name: Nicholas B.W.
author list: Agent
  family name: Roy
  given name: Sugoto
doi: 10.7717/peerj.9404
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-09
copyright: ©2020 Larios et al.
attribution name: Larios et al.

Molecular phylogenetics and evolutionary history of the endemic land snail genus Everettia in northern Borneo
type: item
type: AcademicArticle
description: Borneo has gone through dramatic changes in geology and topography from the early Eocene until the early Pliocene and experienced climatic cycling during the Pleistocene. However, how these changes have shaped the present-day patterns of high diversity and complex distribution are still poorly understood. In this study, we use integrative approaches by estimating phylogenetic relationships, divergence time, and current and past niche suitability for the Bornean endemic land snail genus Everettia to provide additional insight into the evolutionary history of this genus in northern Borneo in the light of the geological vicariance events and climatic fluctuations in the Pleistocene. Our results show that northern Borneo Everettia species belong to two deeply divergent lineages: one contains the species that inhabit high elevation at the central mountain range, while the other contains lowland species. Species diversification in these lineages has taken place before the Pliocene. Climate changes during the Pleistocene did not play a significant role in species diversification but could have shaped contemporary species distribution patterns. Our results also show that the species-rich highland habitats have acted as interglacial refugia for highland species. This study of a relatively sedentary invertebrate supports and enhances the growing understanding of the evolutionary history of Borneo. Species diversification in Everettia is caused by geological vicariance events between the early Miocene and the Pliocene, and the distribution patterns were subsequently determined by climatic fluctuations in the Pleistocene.
format: application/pdf
format: text/html
creator: Thor-Seng Liew
creator: Mohammad Effendi Marzuki
creator: Menno Schilthuizen
creator: Yansen Chen
creator: Jaap J. Vermeulen
creator: Jayasilan Mohd-Azlan
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.9416
publisher: PeerJ Inc.
rights: © 2020 Liew et al.
abstract: Borneo has gone through dramatic changes in geology and topography from the early Eocene until the early Pliocene and experienced climatic cycling during the Pleistocene. However, how these changes have shaped the present-day patterns of high diversity and complex distribution are still poorly understood. In this study, we use integrative approaches by estimating phylogenetic relationships, divergence time, and current and past niche suitability for the Bornean endemic land snail genus Everettia to provide additional insight into the evolutionary history of this genus in northern Borneo in the light of the geological vicariance events and climatic fluctuations in the Pleistocene. Our results show that northern Borneo Everettia species belong to two deeply divergent lineages: one contains the species that inhabit high elevation at the central mountain range, while the other contains lowland species. Species diversification in these lineages has taken place before the Pliocene. Climate changes during the Pleistocene did not play a significant role in species diversification but could have shaped contemporary species distribution patterns. Our results also show that the species-rich highland habitats have acted as interglacial refugia for highland species. This study of a relatively sedentary invertebrate supports and enhances the growing understanding of the evolutionary history of Borneo. Species diversification in Everettia is caused by geological vicariance events between the early Miocene and the Pliocene, and the distribution patterns were subsequently determined by climatic fluctuations in the Pleistocene.
bibliographic citation: Liew et al. (2020) Molecular phylogenetics and evolutionary history of the endemic land snail genus Everettia in northern Borneo. PeerJ 8:e9416 https://doi.org/10.7717/peerj.9416
date submitted: 2019-10-30
date accepted: 2020-06-03
issued: 2020-07-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liew
  given name: Thor-Seng
author list: Agent
  family name: Marzuki
  given name: Mohammad Effendi
author list: Agent
  family name: Schilthuizen
  given name: Menno
author list: Agent
  family name: Chen
  given name: Yansen
author list: Agent
  family name: Vermeulen
  given name: Jaap J.
author list: Agent
  family name: Mohd-Azlan
  given name: Jayasilan
doi: 10.7717/peerj.9416
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-09
copyright: © 2020 Liew et al.
attribution name: Liew et al.

A collection of hexactinellids (Porifera) from the deep South Atlantic and North Pacific: new genus, new species and new records
type: item
type: AcademicArticle
description: This article describes or redescribes four hexactinellid sponges, namely Poliopogon amadou, Euplectella sanctipauli sp. nov., Bolosoma perezi sp. nov. and Advhena magnifica gen. et sp. nov. P. amadou, E. sanctipauli sp. nov. and B. perezi sp. nov. represent new findings for the South Atlantic deep-sea fauna, including the first record of Bolosoma for this ocean. Advhena magnifica gen. et sp. nov., on the other hand, was collected by NOAA oceanographic expeditions in the North Pacific (Pigafetta Guyot).
format: application/pdf
format: text/html
creator: Cristiana Castello-Branco
creator: Allen G. Collins
creator: Eduardo Hajdu
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9431
publisher: PeerJ Inc.
rights: © 2020 Castello-Branco et al.
abstract: This article describes or redescribes four hexactinellid sponges, namely Poliopogon amadou, Euplectella sanctipauli sp. nov., Bolosoma perezi sp. nov. and Advhena magnifica gen. et sp. nov. P. amadou, E. sanctipauli sp. nov. and B. perezi sp. nov. represent new findings for the South Atlantic deep-sea fauna, including the first record of Bolosoma for this ocean. Advhena magnifica gen. et sp. nov., on the other hand, was collected by NOAA oceanographic expeditions in the North Pacific (Pigafetta Guyot).
bibliographic citation: Castello-Branco et al. (2020) A collection of hexactinellids (Porifera) from the deep South Atlantic and North Pacific: new genus, new species and new records. PeerJ 8:e9431 https://doi.org/10.7717/peerj.9431
date submitted: 2019-10-21
date accepted: 2020-06-06
issued: 2020-07-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Castello-Branco
  given name: Cristiana
author list: Agent
  family name: Collins
  given name: Allen G.
author list: Agent
  family name: Hajdu
  given name: Eduardo
doi: 10.7717/peerj.9431
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-09
copyright: © 2020 Castello-Branco et al.
attribution name: Castello-Branco et al.

Sharing for science: high-resolution trophic interactions revealed rapidly by social media
type: item
type: AcademicArticle
description: Discrete, ephemeral natural phenomena with low spatial or temporal predictability are incredibly challenging to study systematically. In ecology, species interactions, which constitute the functional backbone of ecological communities, can be notoriously difficult to characterise especially when taxa are inconspicuous and the interactions of interest (e.g., trophic events) occur infrequently, rapidly, or variably in space and time. Overcoming such issues has historically required significant time and resource investment to collect sufficient data, precluding the answering of many ecological and evolutionary questions. Here, we show the utility of social media for rapidly collecting observations of ephemeral ecological phenomena with low spatial and temporal predictability by using a Facebook group dedicated to collecting predation events involving reptiles and amphibians in sub-Saharan Africa. We collected over 1900 independent feeding observations using Facebook from 2015 to 2019 involving 83 families of predators and 129 families of prey. Feeding events by snakes were particularly well-represented with close to 1,100 feeding observations recorded. Relative to an extensive literature review spanning 226 sources and 138 years, we found that social media has provided snake dietary records faster than ever before in history with prey being identified to a finer taxonomic resolution and showing only modest concordance with the literature due to the number of novel interactions that were detected. Finally, we demonstrate that social media can outperform other citizen science image-based approaches (iNaturalist and Google Images) highlighting the versatility of social media and its ability to function as a citizen science platform.
format: application/pdf
format: text/html
creator: Robin A. Maritz
creator: Bryan Maritz
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.9485
publisher: PeerJ Inc.
rights: © 2020 Maritz and Maritz
abstract: Discrete, ephemeral natural phenomena with low spatial or temporal predictability are incredibly challenging to study systematically. In ecology, species interactions, which constitute the functional backbone of ecological communities, can be notoriously difficult to characterise especially when taxa are inconspicuous and the interactions of interest (e.g., trophic events) occur infrequently, rapidly, or variably in space and time. Overcoming such issues has historically required significant time and resource investment to collect sufficient data, precluding the answering of many ecological and evolutionary questions. Here, we show the utility of social media for rapidly collecting observations of ephemeral ecological phenomena with low spatial and temporal predictability by using a Facebook group dedicated to collecting predation events involving reptiles and amphibians in sub-Saharan Africa. We collected over 1900 independent feeding observations using Facebook from 2015 to 2019 involving 83 families of predators and 129 families of prey. Feeding events by snakes were particularly well-represented with close to 1,100 feeding observations recorded. Relative to an extensive literature review spanning 226 sources and 138 years, we found that social media has provided snake dietary records faster than ever before in history with prey being identified to a finer taxonomic resolution and showing only modest concordance with the literature due to the number of novel interactions that were detected. Finally, we demonstrate that social media can outperform other citizen science image-based approaches (iNaturalist and Google Images) highlighting the versatility of social media and its ability to function as a citizen science platform.
bibliographic citation: Maritz et al. (2020) Sharing for science: high-resolution trophic interactions revealed rapidly by social media. PeerJ 8:e9485 https://doi.org/10.7717/peerj.9485
date submitted: 2020-03-26
date accepted: 2020-06-15
issued: 2020-07-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maritz
  given name: Robin A.
author list: Agent
  family name: Maritz
  given name: Bryan
doi: 10.7717/peerj.9485
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-09
copyright: ©2020 Maritz and Maritz
attribution name: Maritz and Maritz

Prognostic value of complementary biomarkers of neurodegeneration in a mixed memory clinic cohort
type: item
type: AcademicArticle
description: Background Biomarkers of neurodegeneration, e.g. MRI brain atrophy and [18F]FDG-PET hypometabolism, are often evaluated in patients suspected of neurodegenerative disease. Objective Our primary objective was to investigate prognostic properties of atrophy and hypometabolism. Methods From March 2015-June 2016, 149 patients referred to a university hospital memory clinic were included. The primary outcome was progression/stable disease course as assessed by a clinician at 12 months follow-up. Intracohort defined z-scores of baseline MRI automatic quantified volume and [18F]FDG-PET standardized uptake value ratios were calculated for all unilaterally defined brain lobes and dichotomized as pronounced atrophy (+A)/ pronounced hypometabolism (+H) at z-score <0. A logistic regression model with progression status as the outcome was carried out with number of lobes with the patterns +A/-H, -A/+H, +A/+H respectively as predictors. The model was mutually adjusted along with adjustment for age and sex. A sensitivity analysis with a z-score dichotomization at −0.1 and −0.5 and dichotomization regarding number of lobes affected at one and three lobes was done. Results Median follow-up time was 420 days [IQR: 387-461 days] and 50 patients progressed. Patients with two or more lobes affected by the pattern +A/+H compared to patients with 0–1 lobes affected had a statistically significant increased risk of progression (odds ratio, 95 % confidence interval: 4.33, 1.90–9.86) in a multivariable model. The model was partially robust to the applied sensitivity analysis. Conclusion Combined atrophy and hypometabolism as assessed by MRI and [18F]FDG-PET in patients under suspicion of neurodegenerative disease predicts progression over 1 year.
format: application/pdf
format: text/html
creator: Mathias Holsey Gramkow
creator: Le Gjerum
creator: Juha Koikkalainen
creator: Jyrki Lötjönen
creator: Ian Law
creator: Steen Gregers Hasselbalch
creator: Gunhild Waldemar
creator: Kristian Steen Frederiksen
subject: Neuroscience
subject: Cognitive Disorders
subject: Neurology
subject: Radiology and Medical Imaging
subject: Translational Medicine
description: doi:10.7717/peerj.9498
publisher: PeerJ Inc.
rights: © 2020 Gramkow et al.
abstract: Background Biomarkers of neurodegeneration, e.g. MRI brain atrophy and [18F]FDG-PET hypometabolism, are often evaluated in patients suspected of neurodegenerative disease. Objective Our primary objective was to investigate prognostic properties of atrophy and hypometabolism. Methods From March 2015-June 2016, 149 patients referred to a university hospital memory clinic were included. The primary outcome was progression/stable disease course as assessed by a clinician at 12 months follow-up. Intracohort defined z-scores of baseline MRI automatic quantified volume and [18F]FDG-PET standardized uptake value ratios were calculated for all unilaterally defined brain lobes and dichotomized as pronounced atrophy (+A)/ pronounced hypometabolism (+H) at z-score <0. A logistic regression model with progression status as the outcome was carried out with number of lobes with the patterns +A/-H, -A/+H, +A/+H respectively as predictors. The model was mutually adjusted along with adjustment for age and sex. A sensitivity analysis with a z-score dichotomization at −0.1 and −0.5 and dichotomization regarding number of lobes affected at one and three lobes was done. Results Median follow-up time was 420 days [IQR: 387-461 days] and 50 patients progressed. Patients with two or more lobes affected by the pattern +A/+H compared to patients with 0–1 lobes affected had a statistically significant increased risk of progression (odds ratio, 95 % confidence interval: 4.33, 1.90–9.86) in a multivariable model. The model was partially robust to the applied sensitivity analysis. Conclusion Combined atrophy and hypometabolism as assessed by MRI and [18F]FDG-PET in patients under suspicion of neurodegenerative disease predicts progression over 1 year.
bibliographic citation: Gramkow et al. (2020) Prognostic value of complementary biomarkers of neurodegeneration in a mixed memory clinic cohort. PeerJ 8:e9498 https://doi.org/10.7717/peerj.9498
date submitted: 2020-02-04
date accepted: 2020-06-17
issued: 2020-07-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gramkow
  given name: Mathias Holsey
author list: Agent
  family name: Gjerum
  given name: Le
author list: Agent
  family name: Koikkalainen
  given name: Juha
author list: Agent
  family name: Lötjönen
  given name: Jyrki
author list: Agent
  family name: Law
  given name: Ian
author list: Agent
  family name: Hasselbalch
  given name: Steen Gregers
author list: Agent
  family name: Waldemar
  given name: Gunhild
author list: Agent
  family name: Frederiksen
  given name: Kristian Steen
doi: 10.7717/peerj.9498
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-09
copyright: ©2020 Gramkow et al.
attribution name: Gramkow et al.

Very few sites can reshape the inferred phylogenetic tree
type: item
type: AcademicArticle
description: The history of animal evolution, and the relative placement of extant animal phyla in this history is, in principle, testable from phylogenies derived from molecular sequence data. Though datasets have increased in size and quality in the past years, the contribution of individual genes (and ultimately amino acid sites) to the final phylogeny is unequal across genes. Here we demonstrate that removing a small fraction of sites strongly favoring one topology can produce a highly-supported tree of an alternate topology. We explore this approach using a dataset for animal phylogeny, and create a highly-supported tree with a monophyletic group of sponges and ctenophores, a topology not usually recovered. Because of the high sensitivity of such an analysis to gene selection, and because most gene sets are neither standardized nor representative of the entire genome, researchers should be diligent about making intermediate analyses available with their phylogenetic studies. Effort is needed to ensure these datasets are maximally informative, by ensuring all genes are systematically sampled across relevant species. From there, it could be determined whether any gene or gene sets introduce bias, and then deal with those biases appropriately.
format: application/pdf
format: text/html
creator: Warren R. Francis
creator: Donald E. Canfield
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Taxonomy
description: doi:10.7717/peerj.8865
publisher: PeerJ Inc.
rights: © 2020 Francis and Canfield
abstract: The history of animal evolution, and the relative placement of extant animal phyla in this history is, in principle, testable from phylogenies derived from molecular sequence data. Though datasets have increased in size and quality in the past years, the contribution of individual genes (and ultimately amino acid sites) to the final phylogeny is unequal across genes. Here we demonstrate that removing a small fraction of sites strongly favoring one topology can produce a highly-supported tree of an alternate topology. We explore this approach using a dataset for animal phylogeny, and create a highly-supported tree with a monophyletic group of sponges and ctenophores, a topology not usually recovered. Because of the high sensitivity of such an analysis to gene selection, and because most gene sets are neither standardized nor representative of the entire genome, researchers should be diligent about making intermediate analyses available with their phylogenetic studies. Effort is needed to ensure these datasets are maximally informative, by ensuring all genes are systematically sampled across relevant species. From there, it could be determined whether any gene or gene sets introduce bias, and then deal with those biases appropriately.
bibliographic citation: Francis et al. (2020) Very few sites can reshape the inferred phylogenetic tree. PeerJ 8:e8865 https://doi.org/10.7717/peerj.8865
date submitted: 2018-09-20
date accepted: 2020-03-08
issued: 2020-07-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Francis
  given name: Warren R.
author list: Agent
  family name: Canfield
  given name: Donald E.
doi: 10.7717/peerj.8865
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-08
copyright: ©2020 Francis and Canfield
attribution name: Francis and Canfield

Effect of predation risk and ectoparasitic louse flies on physiological stress condition of the red-tailed tropicbird (Phaethon rubricauda) from Rapa Nui and Salas & Gómez islands
type: item
type: AcademicArticle
description: Background Introduced predators at seabird colonies and parasites may have lethal and/or sub-lethal consequences for bird populations. We assessed the potential sub-lethal negative effects of these stressors in a native seabird listed as vulnerable in its south-eastern pacific distribution. This study was conducted in two red-tailed tropicbird (Phaethon rubricauda) colonies, one located in Rapa Nui Island, which is threatened by the presence of introduced predators, and the other located in Salas & Gómez Island, which has no introduced predators, but birds are infested by ectoparasitic louse flies. Methods The effects on physiological stress traits of both, predation risk on different nest types (protected and exposed) on Rapa Nui, and different levels of louse flies’ parasitic loads on Salas & Gómez were studied. Three variables were analyzed: the heterophil/lymphocyte (H/L) ratio, the transcriptional levels of mRNA HSP70 in blood, and the body condition. These stress indicators and leukocyte counts were compared between colonies. Results No significant differences were found in any stress indicator between different nest types within Rapa Nui, showing that the effect of predator’s presence was the same for adults nesting in both, protected and exposed nests. No significant correlation was found between louse flies’ parasitic loads and any stress indicators in the birds of Salas & Gómez. Also, there was no difference in any stress indicator between islands. However, a significant opposite trend between islands was found in the eosinophil, lymphocyte, and monocyte counts when related to body condition. Conclusions We found a lack of significant differentiation in all the stress level indicators assessed within and between islands. The presence of louse flies in Salas & Gómez vs. the absence of this parasite at Rapa Nui may be the cause for the significant difference in the trend of eosinophil, lymphocyte and monocyte counts between the islands. However, further stud…
format: application/pdf
format: text/html
creator: Nicolas Luna
creator: Andrea I. Varela
creator: Guillermo Luna-Jorquera
creator: Katherina Brokordt
subject: Conservation Biology
subject: Genetics
subject: Marine Biology
subject: Parasitology
description: doi:10.7717/peerj.9088
publisher: PeerJ Inc.
rights: © 2020 Luna et al.
abstract: Background Introduced predators at seabird colonies and parasites may have lethal and/or sub-lethal consequences for bird populations. We assessed the potential sub-lethal negative effects of these stressors in a native seabird listed as vulnerable in its south-eastern pacific distribution. This study was conducted in two red-tailed tropicbird (Phaethon rubricauda) colonies, one located in Rapa Nui Island, which is threatened by the presence of introduced predators, and the other located in Salas & Gómez Island, which has no introduced predators, but birds are infested by ectoparasitic louse flies. Methods The effects on physiological stress traits of both, predation risk on different nest types (protected and exposed) on Rapa Nui, and different levels of louse flies’ parasitic loads on Salas & Gómez were studied. Three variables were analyzed: the heterophil/lymphocyte (H/L) ratio, the transcriptional levels of mRNA HSP70 in blood, and the body condition. These stress indicators and leukocyte counts were compared between colonies. Results No significant differences were found in any stress indicator between different nest types within Rapa Nui, showing that the effect of predator’s presence was the same for adults nesting in both, protected and exposed nests. No significant correlation was found between louse flies’ parasitic loads and any stress indicators in the birds of Salas & Gómez. Also, there was no difference in any stress indicator between islands. However, a significant opposite trend between islands was found in the eosinophil, lymphocyte, and monocyte counts when related to body condition. Conclusions We found a lack of significant differentiation in all the stress level indicators assessed within and between islands. The presence of louse flies in Salas & Gómez vs. the absence of this parasite at Rapa Nui may be the cause for the significant difference in the trend of eosinophil, lymphocyte and monocyte counts between the islands. However, further stud…
bibliographic citation: Luna et al. (2020) Effect of predation risk and ectoparasitic louse flies on physiological stress condition of the red-tailed tropicbird (Phaethon rubricauda) from Rapa Nui and Salas & Gómez islands. PeerJ 8:e9088 https://doi.org/10.7717/peerj.9088
date submitted: 2019-07-17
date accepted: 2020-04-08
issued: 2020-07-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luna
  given name: Nicolas
author list: Agent
  family name: Varela
  given name: Andrea I.
author list: Agent
  family name: Luna-Jorquera
  given name: Guillermo
author list: Agent
  family name: Brokordt
  given name: Katherina
doi: 10.7717/peerj.9088
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-08
copyright: © 2020 Luna et al.
attribution name: Luna et al.

Low frequencies in the display vocalization of the Western Capercaillie (Tetrao urogallus)
type: item
type: AcademicArticle
description: Only a few bird species are known to produce low-frequency vocalizations. We analyzed the display vocalizations of Western Capercaillie males kept in breeding centers and identified harmonically structured signals with a fundamental frequency of 28.7 ± 1.2 Hz (25.6–31.6 Hz). These low-frequency components temporally overlap with the Whetting phase (96% of its duration) and they significantly contribute to the distinct vocal expression between individuals. The resulting model of discrimination analysis classified 67.6% vocalizations (63%, cross-validated result) correctly to the specific individual in comparison to the probability by chance of 12.5%. We discuss a possible function of low-frequency components that remains unclear. The occurrence of such low frequencies is surprising as this grouse is substantially smaller than cassowaries (Southern cassowary Casuarius casuarius and Dwarf cassowary Casuarius bennetti) , the species that produces similarly low frequencies. Because these low frequency components temporarily overlap with the Whetting phase, they are hardly audible from a distance larger than several meters.
format: application/pdf
format: text/html
creator: Vlastimil Hart
creator: Richard Policht
creator: Vojtěch Jandák
creator: Marek Brothánek
creator: Hynek Burda
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.9189
publisher: PeerJ Inc.
rights: © 2020 Hart et al.
abstract: Only a few bird species are known to produce low-frequency vocalizations. We analyzed the display vocalizations of Western Capercaillie males kept in breeding centers and identified harmonically structured signals with a fundamental frequency of 28.7 ± 1.2 Hz (25.6–31.6 Hz). These low-frequency components temporally overlap with the Whetting phase (96% of its duration) and they significantly contribute to the distinct vocal expression between individuals. The resulting model of discrimination analysis classified 67.6% vocalizations (63%, cross-validated result) correctly to the specific individual in comparison to the probability by chance of 12.5%. We discuss a possible function of low-frequency components that remains unclear. The occurrence of such low frequencies is surprising as this grouse is substantially smaller than cassowaries (Southern cassowary Casuarius casuarius and Dwarf cassowary Casuarius bennetti) , the species that produces similarly low frequencies. Because these low frequency components temporarily overlap with the Whetting phase, they are hardly audible from a distance larger than several meters.
bibliographic citation: Hart et al. (2020) Low frequencies in the display vocalization of the Western Capercaillie (Tetrao urogallus). PeerJ 8:e9189 https://doi.org/10.7717/peerj.9189
date submitted: 2019-11-12
date accepted: 2020-04-23
issued: 2020-07-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hart
  given name: Vlastimil
author list: Agent
  family name: Policht
  given name: Richard
author list: Agent
  family name: Jandák
  given name: Vojtěch
author list: Agent
  family name: Brothánek
  given name: Marek
author list: Agent
  family name: Burda
  given name: Hynek
doi: 10.7717/peerj.9189
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-08
copyright: ©2020 Hart et al.
attribution name: Hart et al.

?Amphictis (Carnivora, Ailuridae) from the Belgrade Formation of North Carolina, USA
type: item
type: AcademicArticle
description: Miocene terrestrial mammals are poorly known from the Atlantic Coastal Plain. Fossils of the Order Carnivora from this time and region are especially rare. We describe a carnivoran mandible with a p4 from the late Oligocene or early early Miocene Belgrade Formation in Jones County, North Carolina. Comparisons are made with carnivoran jaws with similar premolar and molar lengths from the late Oligocene and Miocene of North America and Eurasia. These indicate that the North Carolina jaw is assignable to the Ailuridae, a family whose only living member is the red panda. The jaw is tentatively referred to Amphictis, a genus known elsewhere from the late Oligocene and early Miocene of Europe and the early Miocene (Hemingfordian) of North America. The North Carolina mandible compares best with the late Oligocene (MP 28) Amphictis ambiguus from Pech du Fraysse, France, the oldest known member of the Family Ailuridae, and with the early Miocene (MN 1–MN 2a) A. schlosseri from southwestern Germany. This identification is compatible with a late late Arikareean (Ar4, early Miocene, MN 2-3 equivalent) age assignment for the other terrestrial mammals of the Belgrade Formation.
format: application/pdf
format: text/html
creator: Jon Baskin
creator: Edwin Dickinson
creator: John DuBois
creator: Henry Galiano
creator: Adam Hartstone-Rose
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9284
publisher: PeerJ Inc.
rights: © 2020 Baskin et al.
abstract: Miocene terrestrial mammals are poorly known from the Atlantic Coastal Plain. Fossils of the Order Carnivora from this time and region are especially rare. We describe a carnivoran mandible with a p4 from the late Oligocene or early early Miocene Belgrade Formation in Jones County, North Carolina. Comparisons are made with carnivoran jaws with similar premolar and molar lengths from the late Oligocene and Miocene of North America and Eurasia. These indicate that the North Carolina jaw is assignable to the Ailuridae, a family whose only living member is the red panda. The jaw is tentatively referred to Amphictis, a genus known elsewhere from the late Oligocene and early Miocene of Europe and the early Miocene (Hemingfordian) of North America. The North Carolina mandible compares best with the late Oligocene (MP 28) Amphictis ambiguus from Pech du Fraysse, France, the oldest known member of the Family Ailuridae, and with the early Miocene (MN 1–MN 2a) A. schlosseri from southwestern Germany. This identification is compatible with a late late Arikareean (Ar4, early Miocene, MN 2-3 equivalent) age assignment for the other terrestrial mammals of the Belgrade Formation.
bibliographic citation: Baskin et al. (2020) ?Amphictis (Carnivora, Ailuridae) from the Belgrade Formation of North Carolina, USA. PeerJ 8:e9284 https://doi.org/10.7717/peerj.9284
date submitted: 2020-03-18
date accepted: 2020-05-12
issued: 2020-07-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baskin
  given name: Jon
author list: Agent
  family name: Dickinson
  given name: Edwin
author list: Agent
  family name: DuBois
  given name: John
author list: Agent
  family name: Galiano
  given name: Henry
author list: Agent
  family name: Hartstone-Rose
  given name: Adam
doi: 10.7717/peerj.9284
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-08
copyright: ©2020 Baskin et al.
attribution name: Baskin et al.

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