PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Domestic sewage dispersion scenarios as a subsidy to the design of urban sewage systems in the Lower Amazon River, Amapá, Brazil
items: Sporting tournaments and changed birth rates 9 months later: a systematic review
items: The decline and fall of the mammalian stem
items: Retrospective study and implementation of a low-cost LAMP-turbidimetric assay for screening α0-thalassemia (SEA deletion): preventing and controlling Hb Bart’s hydrops fetalis syndrome in Thailand
items: Vestibulospinal reflexes elicited with a tone burst method are dependent on spatial orientation
items: How to account for behavioral states in step-selection analysis: a model comparison
items: Metabarcoding is (usually) more cost effective than seining or qPCR for detecting tidewater gobies and other estuarine fishes
items: Conservation gaps and priorities of range-restricted birds in the Northern Andes
items: The first gladius-bearing coleoid cephalopods from the lower Toarcian “Schistes Cartons” Formation of the Causses Basin (southeastern France)
items: Mathematical modelling of antibiotic interaction on evolution of antibiotic resistance: an analytical approach

Domestic sewage dispersion scenarios as a subsidy to the design of urban sewage systems in the Lower Amazon River, Amapá, Brazil
type: item
type: AcademicArticle
description: The final in natura discharge of urban domestic sewage in rivers in the Amazon is a widespread practice. In addition, there is an evident lack of knowledge about the self-depurative characteristics of the receiving water bodies in these rivers. This problem is a challenge for designing sanitary sewage system (SSS) projects in the region. We aimed to numerically simulate hydrodynamic scenarios to study pollutant dispersion processes in an urban stretch impacted by domestic sewage in the Lower Amazon River (Amapá, Brazil) using a hydrodynamic model calibrated and coupled to a dispersive model (Lagrangian) (SisBaHiA). The following methodological steps were performed: (a) bathymetric and liquid discharge experimental campaigns using acoustic techniques (acoustic doppler current profiler—ADCP); (b) identification of point and diffuse sources of pollution in the Santana Channel (CSA) and North Channel of the Amazon River (NCM) in Macapá; (c) calibration of the hydrodynamic model and simulation of the dispersive process of domestic sewage plumes; (d) simulation of dispersive process scenarios in two seasonal hydrological periods and different tidal phases. The results of the simulations indicated significant spatiotemporal variations in the plumes, suggesting critical restriction of water quality in the dry period. The hotspot water collection supply station for ETA-CAESA was found to be the most threatened site by diffuse and point source loads. The simulated impacts showed that concentration variation worsens seasonally, restricting the multiple uses of water in both seasonal periods, regardless of tide phase. The pollutant plumes near the coastal-urban zone were apparently more inhibited by the influence of currents, and, due to the greater dilution capacity in the center of the channel, by the effect reversing with the approximation to the riverbank. The research hypotheses were supported: (a) the process of self-depuration of pollutants in the NCM has considerable li…
format: application/pdf
format: text/html
creator: Carlos Henrique Medeiros de Abreu
creator: Elizandra Perez Araújo
creator: Helenilza Ferreira Albuquerque Cunha
creator: Marcelo Teixeira
creator: Alan Cavalcanti da Cunha
subject: Computational Science
subject: Natural Resource Management
subject: Ecohydrology
subject: Environmental Impacts
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.16933
publisher: PeerJ Inc.
rights: © 2024 Medeiros de Abreu et al.
abstract: The final in natura discharge of urban domestic sewage in rivers in the Amazon is a widespread practice. In addition, there is an evident lack of knowledge about the self-depurative characteristics of the receiving water bodies in these rivers. This problem is a challenge for designing sanitary sewage system (SSS) projects in the region. We aimed to numerically simulate hydrodynamic scenarios to study pollutant dispersion processes in an urban stretch impacted by domestic sewage in the Lower Amazon River (Amapá, Brazil) using a hydrodynamic model calibrated and coupled to a dispersive model (Lagrangian) (SisBaHiA). The following methodological steps were performed: (a) bathymetric and liquid discharge experimental campaigns using acoustic techniques (acoustic doppler current profiler—ADCP); (b) identification of point and diffuse sources of pollution in the Santana Channel (CSA) and North Channel of the Amazon River (NCM) in Macapá; (c) calibration of the hydrodynamic model and simulation of the dispersive process of domestic sewage plumes; (d) simulation of dispersive process scenarios in two seasonal hydrological periods and different tidal phases. The results of the simulations indicated significant spatiotemporal variations in the plumes, suggesting critical restriction of water quality in the dry period. The hotspot water collection supply station for ETA-CAESA was found to be the most threatened site by diffuse and point source loads. The simulated impacts showed that concentration variation worsens seasonally, restricting the multiple uses of water in both seasonal periods, regardless of tide phase. The pollutant plumes near the coastal-urban zone were apparently more inhibited by the influence of currents, and, due to the greater dilution capacity in the center of the channel, by the effect reversing with the approximation to the riverbank. The research hypotheses were supported: (a) the process of self-depuration of pollutants in the NCM has considerable li…
bibliographic citation: Medeiros de Abreu et al. (2024) Domestic sewage dispersion scenarios as a subsidy to the design of urban sewage systems in the Lower Amazon River, Amapá, Brazil. PeerJ 12:e16933 https://doi.org/10.7717/peerj.16933
date submitted: 2023-07-18
date accepted: 2024-01-22
issued: 2024-02-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Medeiros de Abreu
  given name: Carlos Henrique
author list: Agent
  family name: Perez Araújo
  given name: Elizandra
author list: Agent
  family name: Ferreira Albuquerque Cunha
  given name: Helenilza
author list: Agent
  family name: Teixeira
  given name: Marcelo
author list: Agent
  family name: Cavalcanti da Cunha
  given name: Alan
doi: 10.7717/peerj.16933
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-27
copyright: ©2024 Medeiros de Abreu et al.
attribution name: Medeiros de Abreu et al.

Sporting tournaments and changed birth rates 9 months later: a systematic review
type: item
type: AcademicArticle
description: Introduction Major sporting tournaments may be associated with increased birth rates 9 months afterwards, possibly due to celebratory sex. The influence of major sporting tournaments on birth patterns remains to be fully explored. Methods Studies that examined the relationship between such events and altered birth metrics (number of births and/or birth sex ratio (male/total live births)) 9(±1) months later were sought in PubMed and Scopus and reported via standard guidelines. Database searches were conducted up to 7 November 2022. Results Five events led to increased birth metrics 9(±1) months later and these included the Super Bowl, the 2009 UEFA Champions League, the 2010 FIFA World Cup, the 2016 UEFA Euros and the 2019 Rugby World Cup. Several la Liga soccer matches also had effects. With a few exceptions, major American football, Association football (soccer) and Rugby apex tournaments in Africa, North America, Asia and Europe were associated with increases in the number of babies born and/or in the birth sex ratio 9(±1) months following notable team wins and/or hosting the tournament. Furthermore, unexpected losses by teams from a premier soccer league were associated with a decline in births 9 months on. Conclusions This systematic review establishes that major sporting tournaments have a notable impact on birth patterns, influencing both birth rates and sex ratios. Emotional intensification during these events likely triggers hormonal shifts, driving changes in sexual activity and subsequently shaping birth rates, often positively, about 9 months later. The context is crucial, especially when a region/country hosts a major single-sport tournament or participates for the first time, as population excitement is likely to be at its peak. These findings hold significance for healthcare planning and highlight the role of societal events in shaping demographic trends. PROSPERO registration CRD42022382971.
format: application/pdf
format: text/html
creator: Gwinyai Masukume
creator: Victor Grech
creator: Margaret Ryan
subject: Epidemiology
subject: Gynecology and Obstetrics
subject: Pediatrics
subject: Sports Medicine
description: doi:10.7717/peerj.16993
publisher: PeerJ Inc.
rights: © 2024 Masukume et al.
abstract: Introduction Major sporting tournaments may be associated with increased birth rates 9 months afterwards, possibly due to celebratory sex. The influence of major sporting tournaments on birth patterns remains to be fully explored. Methods Studies that examined the relationship between such events and altered birth metrics (number of births and/or birth sex ratio (male/total live births)) 9(±1) months later were sought in PubMed and Scopus and reported via standard guidelines. Database searches were conducted up to 7 November 2022. Results Five events led to increased birth metrics 9(±1) months later and these included the Super Bowl, the 2009 UEFA Champions League, the 2010 FIFA World Cup, the 2016 UEFA Euros and the 2019 Rugby World Cup. Several la Liga soccer matches also had effects. With a few exceptions, major American football, Association football (soccer) and Rugby apex tournaments in Africa, North America, Asia and Europe were associated with increases in the number of babies born and/or in the birth sex ratio 9(±1) months following notable team wins and/or hosting the tournament. Furthermore, unexpected losses by teams from a premier soccer league were associated with a decline in births 9 months on. Conclusions This systematic review establishes that major sporting tournaments have a notable impact on birth patterns, influencing both birth rates and sex ratios. Emotional intensification during these events likely triggers hormonal shifts, driving changes in sexual activity and subsequently shaping birth rates, often positively, about 9 months later. The context is crucial, especially when a region/country hosts a major single-sport tournament or participates for the first time, as population excitement is likely to be at its peak. These findings hold significance for healthcare planning and highlight the role of societal events in shaping demographic trends. PROSPERO registration CRD42022382971.
bibliographic citation: Masukume et al. (2024) Sporting tournaments and changed birth rates 9 months later: a systematic review. PeerJ 12:e16993 https://doi.org/10.7717/peerj.16993
date submitted: 2023-09-01
date accepted: 2024-02-01
issued: 2024-02-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Masukume
  given name: Gwinyai
author list: Agent
  family name: Grech
  given name: Victor
author list: Agent
  family name: Ryan
  given name: Margaret
doi: 10.7717/peerj.16993
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-27
copyright: © 2024 Masukume et al.
attribution name: Masukume et al.

The decline and fall of the mammalian stem
type: item
type: AcademicArticle
description: The mammalian crown originated during the Mesozoic and subsequently radiated into the substantial array of forms now extant. However, for about 100 million years before the crown’s origin, a diverse array of stem mammalian lineages dominated terrestrial ecosystems. Several of these stem lineages overlapped temporally and geographically with the crown mammals during the Mesozoic, but by the end of the Cretaceous crown mammals make up the overwhelming majority of the fossil record. The progress of this transition between ecosystems dominated by stem mammals and those dominated by crown mammals is not entirely clear, in part due to a distinct separation of analyses and datasets. Analyses of macroevolutionary patterns tend to focus on either the Mammaliaformes or the non-mammalian cynodonts, with little overlap in the datasets, preventing direct comparison of the diversification trends. Here I analyse species richness and biogeography of Synapsida as a whole during the Mesozoic, allowing comparison of the patterns in the mammalian crown and stem within a single framework. The analysis reveals the decline of the stem mammals occurred in two discrete phases. The first phase occurred between the Triassic and Middle Jurassic, during which the stem mammals were more restricted in their geographic range than the crown mammals, although within localities their species richness remained at levels seen previously. The second phase was a decline in species richness, which occurred during the Lower Cretaceous. The results show the decline of stem mammals, including tritylodontids and several mammaliaform groups, was not tied to a specific event, nor a gradual decline, but was instead a multiphase transition.
format: application/pdf
format: text/html
creator: Neil Brocklehurst
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.17004
publisher: PeerJ Inc.
rights: © 2024 Brocklehurst
abstract: The mammalian crown originated during the Mesozoic and subsequently radiated into the substantial array of forms now extant. However, for about 100 million years before the crown’s origin, a diverse array of stem mammalian lineages dominated terrestrial ecosystems. Several of these stem lineages overlapped temporally and geographically with the crown mammals during the Mesozoic, but by the end of the Cretaceous crown mammals make up the overwhelming majority of the fossil record. The progress of this transition between ecosystems dominated by stem mammals and those dominated by crown mammals is not entirely clear, in part due to a distinct separation of analyses and datasets. Analyses of macroevolutionary patterns tend to focus on either the Mammaliaformes or the non-mammalian cynodonts, with little overlap in the datasets, preventing direct comparison of the diversification trends. Here I analyse species richness and biogeography of Synapsida as a whole during the Mesozoic, allowing comparison of the patterns in the mammalian crown and stem within a single framework. The analysis reveals the decline of the stem mammals occurred in two discrete phases. The first phase occurred between the Triassic and Middle Jurassic, during which the stem mammals were more restricted in their geographic range than the crown mammals, although within localities their species richness remained at levels seen previously. The second phase was a decline in species richness, which occurred during the Lower Cretaceous. The results show the decline of stem mammals, including tritylodontids and several mammaliaform groups, was not tied to a specific event, nor a gradual decline, but was instead a multiphase transition.
bibliographic citation: Brocklehurst (2024) The decline and fall of the mammalian stem. PeerJ 12:e17004 https://doi.org/10.7717/peerj.17004
date submitted: 2023-10-23
date accepted: 2024-02-05
issued: 2024-02-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brocklehurst
  given name: Neil
doi: 10.7717/peerj.17004
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-27
copyright: ©2024 Brocklehurst
attribution name: Brocklehurst

Retrospective study and implementation of a low-cost LAMP-turbidimetric assay for screening α0-thalassemia (SEA deletion): preventing and controlling Hb Bart’s hydrops fetalis syndrome in Thailand
type: item
type: AcademicArticle
description: Homozygous α0-thalassemia (SEA deletion) or Hb Bart’s hydrops fetalis syndrome is a significant public health issue in Thailand and Southeast Asia. A prevention and control program has been implemented in this region. This study focuses on retrospective laboratory data collected between January 2021 and April 2023 at a single center. Additionally, we developed a low-cost LAMP-turbidimetric assay to propose in the screening strategy. A total of 3,623 samples underwent screening tests (MCV, MCH, and DCIP), including 1,658 couple screenings (84.25%) and 310 single pregnant screenings (15.75%). Negative screenings, which did not require further investigation, were found in 75.51% for couple screenings and 46.58% for single pregnant screenings. At hemoglobin (Hb) analysis identified 129 couples which had fetuses at risk of severe thalassemia, whereas molecular analysis during the retrospective period revealed 210 samples with different genotypes. These remaining samples were validated using the low-cost LAMP-turbidimetric assay to detect α0-thalassemia (SEA deletion). The developed LAMP turbidimetric assay demonstrated a sensitivity and specificity of 100% (36/36 × 100) and 97.7% (170/174 × 100), respectively, when compared with gap-PCR. Furthermore, we propose a strategy involving the addition of the low-cost LAMP-turbidimetric assay before performing the gold standard. This strategy represents a cost-saving of USD 2,608 based on 210 samples that required DNA analysis. Finally, the developed LAMP turbidimetric assays offer advantages such as reduced time, workload, cost savings, no need for highly developed instruments, and a straightforward interpreting process. Therefore, implementation of LAMP assays into routine settings would be improve the efficiency of prevention and control program for severe thalassemia disease in this region.
format: application/pdf
format: text/html
creator: Wittaya Jomoui
creator: Kanokkorn Saknava
creator: Kanokpron Prechatrammaruch
creator: Yanticha Ondee
subject: Biochemistry
subject: Genetics
subject: Molecular Biology
subject: Hematology
subject: Medical Genetics
description: doi:10.7717/peerj.17054
publisher: PeerJ Inc.
rights: © 2024 Jomoui et al.
abstract: Homozygous α0-thalassemia (SEA deletion) or Hb Bart’s hydrops fetalis syndrome is a significant public health issue in Thailand and Southeast Asia. A prevention and control program has been implemented in this region. This study focuses on retrospective laboratory data collected between January 2021 and April 2023 at a single center. Additionally, we developed a low-cost LAMP-turbidimetric assay to propose in the screening strategy. A total of 3,623 samples underwent screening tests (MCV, MCH, and DCIP), including 1,658 couple screenings (84.25%) and 310 single pregnant screenings (15.75%). Negative screenings, which did not require further investigation, were found in 75.51% for couple screenings and 46.58% for single pregnant screenings. At hemoglobin (Hb) analysis identified 129 couples which had fetuses at risk of severe thalassemia, whereas molecular analysis during the retrospective period revealed 210 samples with different genotypes. These remaining samples were validated using the low-cost LAMP-turbidimetric assay to detect α0-thalassemia (SEA deletion). The developed LAMP turbidimetric assay demonstrated a sensitivity and specificity of 100% (36/36 × 100) and 97.7% (170/174 × 100), respectively, when compared with gap-PCR. Furthermore, we propose a strategy involving the addition of the low-cost LAMP-turbidimetric assay before performing the gold standard. This strategy represents a cost-saving of USD 2,608 based on 210 samples that required DNA analysis. Finally, the developed LAMP turbidimetric assays offer advantages such as reduced time, workload, cost savings, no need for highly developed instruments, and a straightforward interpreting process. Therefore, implementation of LAMP assays into routine settings would be improve the efficiency of prevention and control program for severe thalassemia disease in this region.
bibliographic citation: Jomoui et al. (2024) Retrospective study and implementation of a low-cost LAMP-turbidimetric assay for screening α0-thalassemia (SEA deletion): preventing and controlling Hb Bart’s hydrops fetalis syndrome in Thailand. PeerJ 12:e17054 https://doi.org/10.7717/peerj.17054
date submitted: 2023-12-14
date accepted: 2024-02-14
issued: 2024-02-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jomoui
  given name: Wittaya
author list: Agent
  family name: Saknava
  given name: Kanokkorn
author list: Agent
  family name: Prechatrammaruch
  given name: Kanokpron
author list: Agent
  family name: Ondee
  given name: Yanticha
doi: 10.7717/peerj.17054
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-27
copyright: ©2024 Jomoui et al.
attribution name: Jomoui et al.

Vestibulospinal reflexes elicited with a tone burst method are dependent on spatial orientation
type: item
type: AcademicArticle
description: Balance involves several sensory modalities including vision, proprioception and the vestibular system. This study aims to investigate vestibulospinal activation elicited by tone burst stimulation in various muscles and how head position influences these responses. We recorded electromyogram (EMG) responses in different muscles (sternocleidomastoid-SCM, cervical erector spinae-ES-C, lumbar erector spinae-ES-L, gastrocnemius-G, and tibialis anterior-TA) of healthy participants using tone burst stimulation applied to the vestibular system. We also evaluated how head position affected the responses. Tone burst stimulation elicited reproducible vestibulospinal reflexes in the SCM and ES-C muscles, while responses in the distal muscles (ES-L, G, and TA) were less consistent among participants. The magnitude and polarity of the responses were influenced by the head position relative to the cervical spine. When the head was rotated or tilted, the polarity of the vestibulospinal responses changed, indicating the integration of vestibular and proprioceptive inputs in generating these reflexes. Overall, our study provides valuable insights into the complexity of vestibulospinal reflexes and their modulation by head position. However, the high variability in responses in some muscles limits their clinical application. These findings may have implications for future research in understanding vestibular function and its role in posture and movement control.
format: application/pdf
format: text/html
creator: Vincent Jecko
creator: Léa Garcia
creator: Emilie Doat
creator: Vincent Leconte
creator: Dominique Liguoro
creator: Jean-René Cazalets
creator: Etienne Guillaud
subject: Neuroscience
subject: Kinesiology
subject: Otorhinolaryngology
subject: Sports Medicine
description: doi:10.7717/peerj.17056
publisher: PeerJ Inc.
rights: © 2024 Jecko et al.
abstract: Balance involves several sensory modalities including vision, proprioception and the vestibular system. This study aims to investigate vestibulospinal activation elicited by tone burst stimulation in various muscles and how head position influences these responses. We recorded electromyogram (EMG) responses in different muscles (sternocleidomastoid-SCM, cervical erector spinae-ES-C, lumbar erector spinae-ES-L, gastrocnemius-G, and tibialis anterior-TA) of healthy participants using tone burst stimulation applied to the vestibular system. We also evaluated how head position affected the responses. Tone burst stimulation elicited reproducible vestibulospinal reflexes in the SCM and ES-C muscles, while responses in the distal muscles (ES-L, G, and TA) were less consistent among participants. The magnitude and polarity of the responses were influenced by the head position relative to the cervical spine. When the head was rotated or tilted, the polarity of the vestibulospinal responses changed, indicating the integration of vestibular and proprioceptive inputs in generating these reflexes. Overall, our study provides valuable insights into the complexity of vestibulospinal reflexes and their modulation by head position. However, the high variability in responses in some muscles limits their clinical application. These findings may have implications for future research in understanding vestibular function and its role in posture and movement control.
bibliographic citation: Jecko et al. (2024) Vestibulospinal reflexes elicited with a tone burst method are dependent on spatial orientation. PeerJ 12:e17056 https://doi.org/10.7717/peerj.17056
date submitted: 2023-09-07
date accepted: 2024-02-15
issued: 2024-02-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jecko
  given name: Vincent
author list: Agent
  family name: Garcia
  given name: Léa
author list: Agent
  family name: Doat
  given name: Emilie
author list: Agent
  family name: Leconte
  given name: Vincent
author list: Agent
  family name: Liguoro
  given name: Dominique
author list: Agent
  family name: Cazalets
  given name: Jean-René
author list: Agent
  family name: Guillaud
  given name: Etienne
doi: 10.7717/peerj.17056
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-27
copyright: ©2024 Jecko et al.
attribution name: Jecko et al.

How to account for behavioral states in step-selection analysis: a model comparison
type: item
type: AcademicArticle
description: Step-selection models are widely used to study animals’ fine-scale habitat selection based on movement data. Resource preferences and movement patterns, however, often depend on the animal’s unobserved behavioral states, such as resting or foraging. As this is ignored in standard (integrated) step-selection analyses (SSA, iSSA), different approaches have emerged to account for such states in the analysis. The performance of these approaches and the consequences of ignoring the states in step-selection analysis, however, have rarely been quantified. We evaluate the recent idea of combining iSSAs with hidden Markov models (HMMs), which allows for a joint estimation of the unobserved behavioral states and the associated state-dependent habitat selection. Besides theoretical considerations, we use an extensive simulation study and a case study on fine-scale interactions of simultaneously tracked bank voles (Myodes glareolus) to compare this HMM-iSSA empirically to both the standard and a widely used classification-based iSSA (i.e., a two-step approach based on a separate prior state classification). Moreover, to facilitate its use, we implemented the basic HMM-iSSA approach in the R package HMMiSSA available on GitHub.
format: application/pdf
format: text/html
creator: Jennifer Pohle
creator: Johannes Signer
creator: Jana A. Eccard
creator: Melanie Dammhahn
creator: Ulrike E. Schlägel
subject: Animal Behavior
subject: Bioinformatics
subject: Ecology
subject: Zoology
subject: Statistics
description: doi:10.7717/peerj.16509
publisher: PeerJ Inc.
rights: © 2024 Pohle et al.
abstract: Step-selection models are widely used to study animals’ fine-scale habitat selection based on movement data. Resource preferences and movement patterns, however, often depend on the animal’s unobserved behavioral states, such as resting or foraging. As this is ignored in standard (integrated) step-selection analyses (SSA, iSSA), different approaches have emerged to account for such states in the analysis. The performance of these approaches and the consequences of ignoring the states in step-selection analysis, however, have rarely been quantified. We evaluate the recent idea of combining iSSAs with hidden Markov models (HMMs), which allows for a joint estimation of the unobserved behavioral states and the associated state-dependent habitat selection. Besides theoretical considerations, we use an extensive simulation study and a case study on fine-scale interactions of simultaneously tracked bank voles (Myodes glareolus) to compare this HMM-iSSA empirically to both the standard and a widely used classification-based iSSA (i.e., a two-step approach based on a separate prior state classification). Moreover, to facilitate its use, we implemented the basic HMM-iSSA approach in the R package HMMiSSA available on GitHub.
bibliographic citation: Pohle et al. (2024) How to account for behavioral states in step-selection analysis: a model comparison. PeerJ 12:e16509 https://doi.org/10.7717/peerj.16509
date submitted: 2023-06-19
date accepted: 2023-11-01
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pohle
  given name: Jennifer
author list: Agent
  family name: Signer
  given name: Johannes
author list: Agent
  family name: Eccard
  given name: Jana A.
author list: Agent
  family name: Dammhahn
  given name: Melanie
author list: Agent
  family name: Schlägel
  given name: Ulrike E.
doi: 10.7717/peerj.16509
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: ©2024 Pohle et al.
attribution name: Pohle et al.

Metabarcoding is (usually) more cost effective than seining or qPCR for detecting tidewater gobies and other estuarine fishes
type: item
type: AcademicArticle
description: Many studies have shown that environmental DNA (eDNA) sampling can be more sensitive than traditional sampling. For instance, past studies found a specific qPCR probe of a water sample is better than a seine for detecting the endangered northern tidewater goby, Eucyclogobius newberryi. Furthermore, a metabarcoding sample often detects more fish species than a seine detects. Less consideration has been given to sampling costs. To help managers choose the best sampling method for their budget, I estimated detectability and costs per sample to compare the cost effectiveness of seining, qPCR and metabarcoding for detecting endangered tidewater gobies as well as the associated estuarine fish community in California. Five samples were enough for eDNA methods to confidently detect tidewater gobies, whereas seining took twice as many samples. Fixed program costs can be high for qPCR and seining, whereas metabarcoding had high per-sample costs, which led to changes in relative cost-effectiveness with the number of locations sampled. Under some circumstances (multiple locations visited or an already validated assay), qPCR was a bit more cost effective than metabarcoding for detecting tidewater gobies. Under all assumptions, seining was the least cost-effective method for detecting tidewater gobies or other fishes. Metabarcoding was the most cost-effective sampling method for multiple species detection. Despite its advantages, metabarcoding has gaps in sequence databases, can yield vague results for some species, and can lead novices to serious errors. Seining remains the only way to rapidly assess densities, size distributions, and fine-scale spatial distributions.
format: application/pdf
format: text/html
creator: Kevin Lafferty
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
subject: Science Policy
description: doi:10.7717/peerj.16847
publisher: PeerJ Inc.
rights: © 2024 Lafferty
abstract: Many studies have shown that environmental DNA (eDNA) sampling can be more sensitive than traditional sampling. For instance, past studies found a specific qPCR probe of a water sample is better than a seine for detecting the endangered northern tidewater goby, Eucyclogobius newberryi. Furthermore, a metabarcoding sample often detects more fish species than a seine detects. Less consideration has been given to sampling costs. To help managers choose the best sampling method for their budget, I estimated detectability and costs per sample to compare the cost effectiveness of seining, qPCR and metabarcoding for detecting endangered tidewater gobies as well as the associated estuarine fish community in California. Five samples were enough for eDNA methods to confidently detect tidewater gobies, whereas seining took twice as many samples. Fixed program costs can be high for qPCR and seining, whereas metabarcoding had high per-sample costs, which led to changes in relative cost-effectiveness with the number of locations sampled. Under some circumstances (multiple locations visited or an already validated assay), qPCR was a bit more cost effective than metabarcoding for detecting tidewater gobies. Under all assumptions, seining was the least cost-effective method for detecting tidewater gobies or other fishes. Metabarcoding was the most cost-effective sampling method for multiple species detection. Despite its advantages, metabarcoding has gaps in sequence databases, can yield vague results for some species, and can lead novices to serious errors. Seining remains the only way to rapidly assess densities, size distributions, and fine-scale spatial distributions.
bibliographic citation: Lafferty (2024) Metabarcoding is (usually) more cost effective than seining or qPCR for detecting tidewater gobies and other estuarine fishes. PeerJ 12:e16847 https://doi.org/10.7717/peerj.16847
date submitted: 2023-11-09
date accepted: 2024-01-07
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Lafferty
  given name: Kevin
doi: 10.7717/peerj.16847
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: ©2024 Lafferty
attribution name: Lafferty

Conservation gaps and priorities of range-restricted birds in the Northern Andes
type: item
type: AcademicArticle
description: The ongoing destruction of habitats in the tropics accelerates the current rate of species extinction. Range-restricted species are exceptionally vulnerable, yet we have insufficient knowledge about their protection. Species’ current distributions, range sizes, and protection gaps are crucial to determining conservation priorities. Here, we identified priority range-restricted bird species and their conservation hotspots in the Northern Andes. We employed maps of the Area of Habitat (AOH), that better reflect their current distributions than existing maps. AOH provides unprecedented resolution and maps a species in the detail essential for practical conservation actions. We estimated protection within each species’ AOH and for the cumulative distribution of all 335 forest-dependent range-restricted birds across the Northern Andes. For the latter, we also calculated protection across the elevational gradient. We estimated how much additional protection community lands (Indigenous and Afro-Latin American lands) would contribute if they were conservation-focused. AOHs ranged from 8 to 141,000 km2. We identified four conservation priorities based on cumulative species richness: the number of AOHs stacked per unit area. These priorities are high-resolution mapped representations of Endemic Bird Areas for the Tropical Andes that we consider critically important. Protected areas cover only 31% of the cumulative AOH, but community lands could add 19% more protection. Sixty-two per cent of the 335 species have ranges smaller than their published estimates, yet IUCN designates only 23% of these as Threatened. We identified 50 species as top conservation priorities. Most of these concentrate in areas of low protection near community lands and at middle elevations where, on average, only 34% of the land is protected. We highlight the importance of collaborative efforts among stakeholders: governments should support private and community-based conservation practices to protect t…
format: application/pdf
format: text/html
creator: Wilderson Medina
creator: Stuart L. Pimm
creator: Ryan M. Huang
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.16893
publisher: PeerJ Inc.
rights: © 2024 Medina et al.
abstract: The ongoing destruction of habitats in the tropics accelerates the current rate of species extinction. Range-restricted species are exceptionally vulnerable, yet we have insufficient knowledge about their protection. Species’ current distributions, range sizes, and protection gaps are crucial to determining conservation priorities. Here, we identified priority range-restricted bird species and their conservation hotspots in the Northern Andes. We employed maps of the Area of Habitat (AOH), that better reflect their current distributions than existing maps. AOH provides unprecedented resolution and maps a species in the detail essential for practical conservation actions. We estimated protection within each species’ AOH and for the cumulative distribution of all 335 forest-dependent range-restricted birds across the Northern Andes. For the latter, we also calculated protection across the elevational gradient. We estimated how much additional protection community lands (Indigenous and Afro-Latin American lands) would contribute if they were conservation-focused. AOHs ranged from 8 to 141,000 km2. We identified four conservation priorities based on cumulative species richness: the number of AOHs stacked per unit area. These priorities are high-resolution mapped representations of Endemic Bird Areas for the Tropical Andes that we consider critically important. Protected areas cover only 31% of the cumulative AOH, but community lands could add 19% more protection. Sixty-two per cent of the 335 species have ranges smaller than their published estimates, yet IUCN designates only 23% of these as Threatened. We identified 50 species as top conservation priorities. Most of these concentrate in areas of low protection near community lands and at middle elevations where, on average, only 34% of the land is protected. We highlight the importance of collaborative efforts among stakeholders: governments should support private and community-based conservation practices to protect t…
bibliographic citation: Medina et al. (2024) Conservation gaps and priorities of range-restricted birds in the Northern Andes. PeerJ 12:e16893 https://doi.org/10.7717/peerj.16893
date submitted: 2023-05-25
date accepted: 2024-01-16
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Medina
  given name: Wilderson
author list: Agent
  family name: Pimm
  given name: Stuart L.
author list: Agent
  family name: Huang
  given name: Ryan M.
doi: 10.7717/peerj.16893
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: ©2024 Medina et al.
attribution name: Medina et al.

The first gladius-bearing coleoid cephalopods from the lower Toarcian “Schistes Cartons” Formation of the Causses Basin (southeastern France)
type: item
type: AcademicArticle
description: The fossil record of gladius-bearing coleoids is scarce and based only on a few localities with geological horizons particularly favourable to their preservation (the so-called Konservat-Lagerstätten), which naturally leads to strongly limited data on geographical distributions. This emphasizes the importance of every new locality providing gladius-bearing coleoids. Here, we assess for the first time the gladius-bearing coleoid taxonomic diversity within the lower Toarcian “Schistes Cartons” of the Causses Basin (southeastern France). The material includes two fragmentary gladii, identified as Paraplesioteuthis sagittata and ?Loligosepia sp. indet. Just with these two specimens, two (Prototeuthina and Loligosepiina) of the three (Prototeuthina, Loligosepiina and Teudopseina) suborders of Mesozoic gladius-bearing coleoids are represented. Thus, our results hint at a rich early Toarcian gladius-bearing coleoid diversity in the Causses Basin and point out the need for further field investigations in the lower Toarcian “Schistes Cartons” in this area. This new record of Paraplesioteuthis sagittata is only the second one in Europe and the third in the world (western Canada, Germany and now France). Based on these occurrences, we tentatively suggest that P. sagittata originated in the Mediterranean domain and moved to the Arctic realm through the Viking Corridor to eventually move even farther to North America.
format: application/pdf
format: text/html
creator: Romain Jattiot
creator: Nathalie Coquel-Poussy
creator: Isabelle Kruta
creator: Isabelle Rouget
creator: Alison J. Rowe
creator: Jean-David Moreau
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.16894
publisher: PeerJ Inc.
rights: © 2024 Jattiot et al.
abstract: The fossil record of gladius-bearing coleoids is scarce and based only on a few localities with geological horizons particularly favourable to their preservation (the so-called Konservat-Lagerstätten), which naturally leads to strongly limited data on geographical distributions. This emphasizes the importance of every new locality providing gladius-bearing coleoids. Here, we assess for the first time the gladius-bearing coleoid taxonomic diversity within the lower Toarcian “Schistes Cartons” of the Causses Basin (southeastern France). The material includes two fragmentary gladii, identified as Paraplesioteuthis sagittata and ?Loligosepia sp. indet. Just with these two specimens, two (Prototeuthina and Loligosepiina) of the three (Prototeuthina, Loligosepiina and Teudopseina) suborders of Mesozoic gladius-bearing coleoids are represented. Thus, our results hint at a rich early Toarcian gladius-bearing coleoid diversity in the Causses Basin and point out the need for further field investigations in the lower Toarcian “Schistes Cartons” in this area. This new record of Paraplesioteuthis sagittata is only the second one in Europe and the third in the world (western Canada, Germany and now France). Based on these occurrences, we tentatively suggest that P. sagittata originated in the Mediterranean domain and moved to the Arctic realm through the Viking Corridor to eventually move even farther to North America.
bibliographic citation: Jattiot et al. (2024) The first gladius-bearing coleoid cephalopods from the lower Toarcian “Schistes Cartons” Formation of the Causses Basin (southeastern France). PeerJ 12:e16894 https://doi.org/10.7717/peerj.16894
date submitted: 2023-11-24
date accepted: 2024-01-16
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jattiot
  given name: Romain
author list: Agent
  family name: Coquel-Poussy
  given name: Nathalie
author list: Agent
  family name: Kruta
  given name: Isabelle
author list: Agent
  family name: Rouget
  given name: Isabelle
author list: Agent
  family name: Rowe
  given name: Alison J.
author list: Agent
  family name: Moreau
  given name: Jean-David
doi: 10.7717/peerj.16894
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: ©2024 Jattiot et al.
attribution name: Jattiot et al.

Mathematical modelling of antibiotic interaction on evolution of antibiotic resistance: an analytical approach
type: item
type: AcademicArticle
description: Background The emergence and spread of antibiotic-resistant pathogens have led to the exploration of antibiotic combinations to enhance clinical effectiveness and counter resistance development. Synergistic and antagonistic interactions between antibiotics can intensify or diminish the combined therapy’s impact. Moreover, these interactions can evolve as bacteria transition from wildtype to mutant (resistant) strains. Experimental studies have shown that the antagonistically interacting antibiotics against wildtype bacteria slow down the evolution of resistance. Interestingly, other studies have shown that antibiotics that interact antagonistically against mutants accelerate resistance. However, it is unclear if the beneficial effect of antagonism in the wildtype bacteria is more critical than the detrimental effect of antagonism in the mutants. This study aims to illuminate the importance of antibiotic interactions against wildtype bacteria and mutants on the deacceleration of antimicrobial resistance. Methods To address this, we developed and analyzed a mathematical model that explores the population dynamics of wildtype and mutant bacteria under the influence of interacting antibiotics. The model investigates the relationship between synergistic and antagonistic antibiotic interactions with respect to the growth rate of mutant bacteria acquiring resistance. Stability analysis was conducted for equilibrium points representing bacteria-free conditions, all-mutant scenarios, and coexistence of both types. Numerical simulations corroborated the analytical findings, illustrating the temporal dynamics of wildtype and mutant bacteria under different combination therapies. Results Our analysis provides analytical clarification and numerical validation that antibiotic interactions against wildtype bacteria exert a more significant effect on reducing the rate of resistance development than interactions against mutants. Specifically, our findings highlight the crucial role …
format: application/pdf
format: text/html
creator: Ramin Nashebi
creator: Murat Sari
creator: Seyfullah Enes Kotil
subject: Bioinformatics
subject: Computational Biology
subject: Mathematical Biology
subject: Microbiology
description: doi:10.7717/peerj.16917
publisher: PeerJ Inc.
rights: © 2024 Nashebi et al.
abstract: Background The emergence and spread of antibiotic-resistant pathogens have led to the exploration of antibiotic combinations to enhance clinical effectiveness and counter resistance development. Synergistic and antagonistic interactions between antibiotics can intensify or diminish the combined therapy’s impact. Moreover, these interactions can evolve as bacteria transition from wildtype to mutant (resistant) strains. Experimental studies have shown that the antagonistically interacting antibiotics against wildtype bacteria slow down the evolution of resistance. Interestingly, other studies have shown that antibiotics that interact antagonistically against mutants accelerate resistance. However, it is unclear if the beneficial effect of antagonism in the wildtype bacteria is more critical than the detrimental effect of antagonism in the mutants. This study aims to illuminate the importance of antibiotic interactions against wildtype bacteria and mutants on the deacceleration of antimicrobial resistance. Methods To address this, we developed and analyzed a mathematical model that explores the population dynamics of wildtype and mutant bacteria under the influence of interacting antibiotics. The model investigates the relationship between synergistic and antagonistic antibiotic interactions with respect to the growth rate of mutant bacteria acquiring resistance. Stability analysis was conducted for equilibrium points representing bacteria-free conditions, all-mutant scenarios, and coexistence of both types. Numerical simulations corroborated the analytical findings, illustrating the temporal dynamics of wildtype and mutant bacteria under different combination therapies. Results Our analysis provides analytical clarification and numerical validation that antibiotic interactions against wildtype bacteria exert a more significant effect on reducing the rate of resistance development than interactions against mutants. Specifically, our findings highlight the crucial role …
bibliographic citation: Nashebi et al. (2024) Mathematical modelling of antibiotic interaction on evolution of antibiotic resistance: an analytical approach. PeerJ 12:e16917 https://doi.org/10.7717/peerj.16917
date submitted: 2022-11-11
date accepted: 2024-01-18
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nashebi
  given name: Ramin
author list: Agent
  family name: Sari
  given name: Murat
author list: Agent
  family name: Kotil
  given name: Seyfullah Enes
doi: 10.7717/peerj.16917
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: © 2024 Nashebi et al.
attribution name: Nashebi et al.

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