PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins
items: Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives
items: Ciprofloxacin reduces tenocyte viability and proteoglycan synthesis in short-term explant cultures of equine tendon
items: The distribution of benthic amphipod crustaceans in Indonesian seas
items: Wedge-tailed Shearwater (Ardenna pacifica) nesting success in human-dominated coastal environments
items: When size matters: the first comprehensive anatomical study of a species of “Condylocardiidae”, an extremely miniaturized bivalve
items: Anti-clustering in the national SARS-CoV-2 daily infection counts
items: Genetic diversity and structure of one of the most endangered freshwater fish species in Mexico: Tlaloc hildebrandi (Miller, 1950) and recognition of its evolutionarily significant units
items: Low winter precipitation, but not warm autumns and springs, threatens mountain butterflies in middle-high mountains
items: The stability of soil organic carbon across topographies in a tropical rainforest

Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins
type: item
type: AcademicArticle
description: Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species’ guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent.
format: application/pdf
format: text/html
creator: Ruber Rodríguez-Barreras
creator: Eduardo L. Tosado-Rodríguez
creator: Filipa Godoy-Vitorino
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Zoology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.12084
publisher: PeerJ Inc.
rights: © 2021 Rodríguez-Barreras et al.
abstract: Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species’ guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent.
bibliographic citation: Rodríguez-Barreras et al. (2021) Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins. PeerJ 9:e12084 https://doi.org/10.7717/peerj.12084
date submitted: 2021-03-24
date accepted: 2021-08-07
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodríguez-Barreras
  given name: Ruber
author list: Agent
  family name: Tosado-Rodríguez
  given name: Eduardo L.
author list: Agent
  family name: Godoy-Vitorino
  given name: Filipa
doi: 10.7717/peerj.12084
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: ©2021 Rodríguez-Barreras et al.
attribution name: Rodríguez-Barreras et al.

Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives
type: item
type: AcademicArticle
description: The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.
format: application/pdf
format: text/html
creator: Mikhail I. Schelkunov
creator: Maxim S. Nuraliev
creator: Maria D. Logacheva
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.12106
publisher: PeerJ Inc.
rights: © 2021 Schelkunov et al.
abstract: The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.
bibliographic citation: Schelkunov et al. (2021) Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives. PeerJ 9:e12106 https://doi.org/10.7717/peerj.12106
date submitted: 2020-10-07
date accepted: 2021-08-11
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schelkunov
  given name: Mikhail I.
author list: Agent
  family name: Nuraliev
  given name: Maxim S.
author list: Agent
  family name: Logacheva
  given name: Maria D.
doi: 10.7717/peerj.12106
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: © 2021 Schelkunov et al.
attribution name: Schelkunov et al.

Ciprofloxacin reduces tenocyte viability and proteoglycan synthesis in short-term explant cultures of equine tendon
type: item
type: AcademicArticle
description: Fluoroquinolones are an effective, broad-spectrum antibiotic used to treat an array of bacterial infections. However, they are associated with an increased risk of tendinopathy and tendon rupture even after discontinuation of treatment. This condition is known as fluoroquinolone-associated tendinopathy, the underlying mechanisms of which are poorly understood. While many factors may be involved in the pathophysiology of tendinopathies in general, changes in tenocyte metabolism and viability, as well as alteration of proteoglycan metabolism are prominent findings in the scientific literature. This study investigated the effects of ciprofloxacin, a common fluoroquinolone, on cell viability, proteoglycan synthesis, and proteoglycan mRNA expression in equine superficial digital flexor tendon explants after 96 h treatment with between 1–300 µg/mL ciprofloxacin, and again after 8 days discontinuation of treatment. Ciprofloxacin caused significant reductions in cell viability by between 25–33% at all dosages except 10 µg/mL, and viability decreased further after 8 days discontinuation of treatment. Proteoglycan synthesis significantly decreased by approximately 50% in explants treated with 100 µg/mL and 300 µg/mL, however this effect reversed after 8 days in the absence of treatment. No significant mRNA expression changes were observed after the treatment period with the exception of versican which was down-regulated at the highest concentration of ciprofloxacin. After the recovery period, aggrecan, biglycan and versican genes were all significantly downregulated in explants initially treated with 1–100 µg/mL. Results from this study corroborate previously reported findings of reduced cell viability and proteoglycan synthesis in a whole tissue explant model and provide further insight into the mechanisms underlying fluoroquinolone-associated tendinopathy and rupture. This study further demonstrates that certain ciprofloxacin induced cellular changes are not rapidly reverse…
format: application/pdf
format: text/html
creator: Stuart James
creator: Johannes Schuijers
creator: John Daffy
creator: Jill Cook
creator: Tom Samiric
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.12003
publisher: PeerJ Inc.
rights: © 2021 James et al.
abstract: Fluoroquinolones are an effective, broad-spectrum antibiotic used to treat an array of bacterial infections. However, they are associated with an increased risk of tendinopathy and tendon rupture even after discontinuation of treatment. This condition is known as fluoroquinolone-associated tendinopathy, the underlying mechanisms of which are poorly understood. While many factors may be involved in the pathophysiology of tendinopathies in general, changes in tenocyte metabolism and viability, as well as alteration of proteoglycan metabolism are prominent findings in the scientific literature. This study investigated the effects of ciprofloxacin, a common fluoroquinolone, on cell viability, proteoglycan synthesis, and proteoglycan mRNA expression in equine superficial digital flexor tendon explants after 96 h treatment with between 1–300 µg/mL ciprofloxacin, and again after 8 days discontinuation of treatment. Ciprofloxacin caused significant reductions in cell viability by between 25–33% at all dosages except 10 µg/mL, and viability decreased further after 8 days discontinuation of treatment. Proteoglycan synthesis significantly decreased by approximately 50% in explants treated with 100 µg/mL and 300 µg/mL, however this effect reversed after 8 days in the absence of treatment. No significant mRNA expression changes were observed after the treatment period with the exception of versican which was down-regulated at the highest concentration of ciprofloxacin. After the recovery period, aggrecan, biglycan and versican genes were all significantly downregulated in explants initially treated with 1–100 µg/mL. Results from this study corroborate previously reported findings of reduced cell viability and proteoglycan synthesis in a whole tissue explant model and provide further insight into the mechanisms underlying fluoroquinolone-associated tendinopathy and rupture. This study further demonstrates that certain ciprofloxacin induced cellular changes are not rapidly reverse…
bibliographic citation: James et al. (2021) Ciprofloxacin reduces tenocyte viability and proteoglycan synthesis in short-term explant cultures of equine tendon. PeerJ 9:e12003 https://doi.org/10.7717/peerj.12003
date submitted: 2021-03-17
date accepted: 2021-07-27
issued: 2021-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: James
  given name: Stuart
author list: Agent
  family name: Schuijers
  given name: Johannes
author list: Agent
  family name: Daffy
  given name: John
author list: Agent
  family name: Cook
  given name: Jill
author list: Agent
  family name: Samiric
  given name: Tom
doi: 10.7717/peerj.12003
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-30
copyright: © 2021 James et al.
attribution name: James et al.

The distribution of benthic amphipod crustaceans in Indonesian seas
type: item
type: AcademicArticle
description: Amphipod crustaceans are an essential component of tropical marine biodiversity. However, their distribution and biogeography have not been analysed in one of the world’s largest tropical countries nested in the Coral Triangle, Indonesia. We collected and identified amphipod crustaceans from eight sites in Indonesian waters and combined the results with data from 32 additional sites in the literature. We analysed the geographic distribution of 147 benthic amphipod crustaceans using cluster analysis and the ‘Bioregions Infomaps’ neural network method of biogeographic discrimination. We found five groups of benthic amphipod crustaceans which show relationships with sampling methods, depth, and substrata. Neural network biogeographic analysis indicated there was only one biogeographic region that matched with the global amphipod regions and marine biogeographic realms defined for all marine taxa. There was no support for Wallaces or other lines being marine biogeographic boundaries in the region. Species richness was lower than expected considering the region is within the Coral Triangle. We hypothesise that this low richness might be due to the intense fish predation which may have limited amphipod diversification. The results indicated that habitat rather than biogeography determines amphipod distribution in Indonesia. Therefore, future research needs to sample more habitats, and consider habitat in conservation planning.
format: application/pdf
format: text/html
creator: Tri Arfianti
creator: Mark John Costello
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12054
publisher: PeerJ Inc.
rights: © 2021 Arfianti and Costello
abstract: Amphipod crustaceans are an essential component of tropical marine biodiversity. However, their distribution and biogeography have not been analysed in one of the world’s largest tropical countries nested in the Coral Triangle, Indonesia. We collected and identified amphipod crustaceans from eight sites in Indonesian waters and combined the results with data from 32 additional sites in the literature. We analysed the geographic distribution of 147 benthic amphipod crustaceans using cluster analysis and the ‘Bioregions Infomaps’ neural network method of biogeographic discrimination. We found five groups of benthic amphipod crustaceans which show relationships with sampling methods, depth, and substrata. Neural network biogeographic analysis indicated there was only one biogeographic region that matched with the global amphipod regions and marine biogeographic realms defined for all marine taxa. There was no support for Wallaces or other lines being marine biogeographic boundaries in the region. Species richness was lower than expected considering the region is within the Coral Triangle. We hypothesise that this low richness might be due to the intense fish predation which may have limited amphipod diversification. The results indicated that habitat rather than biogeography determines amphipod distribution in Indonesia. Therefore, future research needs to sample more habitats, and consider habitat in conservation planning.
bibliographic citation: Arfianti et al. (2021) The distribution of benthic amphipod crustaceans in Indonesian seas. PeerJ 9:e12054 https://doi.org/10.7717/peerj.12054
date submitted: 2021-04-27
date accepted: 2021-08-04
issued: 2021-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arfianti
  given name: Tri
author list: Agent
  family name: Costello
  given name: Mark John
doi: 10.7717/peerj.12054
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-30
copyright: ©2021 Arfianti and Costello
attribution name: Arfianti and Costello

Wedge-tailed Shearwater (Ardenna pacifica) nesting success in human-dominated coastal environments
type: item
type: AcademicArticle
description: Many seabird populations are declining globally, but successful conservation efforts have led to population expansion of some species into human-dominated landscapes. Thus, there is an increased potential for direct human and seabird interactions for certain species in human-occupied areas, with nest-site characteristics potentially affecting the susceptibility of nests to human disturbance. We assessed the effect of human activity and nest-site characteristics on Wedge-tailed Shearwater (Ardenna pacifica, ʻuaʻu kani) nesting success at two breeding colonies, one with human exposure and one without, located in Kailua, Oʻahu, Hawaiʻi. Human activity was measured by recording the frequency of people who entered a 5 m buffer around each nest. Nests were checked every two to three days to monitor nest success. The effect of human activity and nest-site characteristics on nesting success was determined using a variety of combinations of variables within binomial logistic regression models and AICc model selection. Nest-site characteristics among nests at both sites and human activity at the human-exposed site did not show a significant effect on nesting success. Our results suggest Wedge-tailed Shearwaters may experience some tolerance of human activity immediately around their nests—as long as burrow collapse does not occur. Given the small sample sizes and a single season of data collection, additional studies are needed to better understand the effect of human disturbance on Wedge-tailed Shearwaters. Infrastructure, such as fencing and signage, may be effective at reducing human-caused nest failure and may allow humans and disturbance-tolerant seabird species to coexist in shared coastal environments.
format: application/pdf
format: text/html
creator: Jessica L. Idle
creator: Chad J. Wilhite
creator: Kristen C. Harmon
creator: Brooke Friswold
creator: Melissa R. Price
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.12096
publisher: PeerJ Inc.
rights: © 2021 Idle et al.
abstract: Many seabird populations are declining globally, but successful conservation efforts have led to population expansion of some species into human-dominated landscapes. Thus, there is an increased potential for direct human and seabird interactions for certain species in human-occupied areas, with nest-site characteristics potentially affecting the susceptibility of nests to human disturbance. We assessed the effect of human activity and nest-site characteristics on Wedge-tailed Shearwater (Ardenna pacifica, ʻuaʻu kani) nesting success at two breeding colonies, one with human exposure and one without, located in Kailua, Oʻahu, Hawaiʻi. Human activity was measured by recording the frequency of people who entered a 5 m buffer around each nest. Nests were checked every two to three days to monitor nest success. The effect of human activity and nest-site characteristics on nesting success was determined using a variety of combinations of variables within binomial logistic regression models and AICc model selection. Nest-site characteristics among nests at both sites and human activity at the human-exposed site did not show a significant effect on nesting success. Our results suggest Wedge-tailed Shearwaters may experience some tolerance of human activity immediately around their nests—as long as burrow collapse does not occur. Given the small sample sizes and a single season of data collection, additional studies are needed to better understand the effect of human disturbance on Wedge-tailed Shearwaters. Infrastructure, such as fencing and signage, may be effective at reducing human-caused nest failure and may allow humans and disturbance-tolerant seabird species to coexist in shared coastal environments.
bibliographic citation: Idle et al. (2021) Wedge-tailed Shearwater (Ardenna pacifica) nesting success in human-dominated coastal environments. PeerJ 9:e12096 https://doi.org/10.7717/peerj.12096
date submitted: 2020-09-14
date accepted: 2021-08-10
issued: 2021-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Idle
  given name: Jessica L.
author list: Agent
  family name: Wilhite
  given name: Chad J.
author list: Agent
  family name: Harmon
  given name: Kristen C.
author list: Agent
  family name: Friswold
  given name: Brooke
author list: Agent
  family name: Price
  given name: Melissa R.
doi: 10.7717/peerj.12096
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-30
copyright: ©2021 Idle et al.
attribution name: Idle et al.

When size matters: the first comprehensive anatomical study of a species of “Condylocardiidae”, an extremely miniaturized bivalve
type: item
type: AcademicArticle
description: ‘Miniaturization’ is a widespread phenomenon among the Metazoa. In the molluscan class Bivalvia, records of miniaturization are numerous. Among the Archiheterodonta, Warrana besnardi (Klappenbach, 1963) has attracted attention for its tiny size, which does not exceed 1.5 mm in shell length, and because it belongs to a group with limited anatomical information and often-debated status, the “Condylocardiidae” (which recent molecular studies place deeply nested within the family Carditidae). All species of Warrana Laseron, 1953 are small-bodied, and so miniaturization presumably occurred from a large-bodied ancestor within the Carditidae sensu lato. South American W. besnardi is here studied in detail. Its small size and the enlargement of the anterodorsal region during growth, reflects (and likely led) to infaunal habit, living as a burrowing bivalve that passively feeds on deposit particles entering the pallial cavity anteriorly. Mantle glands, previously reported as a common feature of other archiheterodonts, are missing in W. besnardi, but spongiform tissue in the antero-ventral portion of the mantle lobes presumably represents a blood sinus that might compensate for the great reduction of the ctenidia. Lecithotrophy is reported, with yolky oocytes bearing a thick non-cellular capsule layer; brooding was not observed, and it is here hypothesized that the extreme miniaturization, with the great reduction of ctenidia, is responsible for a shift in the reproductive mode of condylocardiids, contrasting with the commonly reported ovoviviparity of the carditids.
format: application/pdf
format: text/html
creator: Flávio Dias Passos
creator: Alan Rodrigo Batistão
creator: Rüdiger Bieler
subject: Biodiversity
subject: Marine Biology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.12108
publisher: PeerJ Inc.
rights: © 2021 Passos et al.
abstract: ‘Miniaturization’ is a widespread phenomenon among the Metazoa. In the molluscan class Bivalvia, records of miniaturization are numerous. Among the Archiheterodonta, Warrana besnardi (Klappenbach, 1963) has attracted attention for its tiny size, which does not exceed 1.5 mm in shell length, and because it belongs to a group with limited anatomical information and often-debated status, the “Condylocardiidae” (which recent molecular studies place deeply nested within the family Carditidae). All species of Warrana Laseron, 1953 are small-bodied, and so miniaturization presumably occurred from a large-bodied ancestor within the Carditidae sensu lato. South American W. besnardi is here studied in detail. Its small size and the enlargement of the anterodorsal region during growth, reflects (and likely led) to infaunal habit, living as a burrowing bivalve that passively feeds on deposit particles entering the pallial cavity anteriorly. Mantle glands, previously reported as a common feature of other archiheterodonts, are missing in W. besnardi, but spongiform tissue in the antero-ventral portion of the mantle lobes presumably represents a blood sinus that might compensate for the great reduction of the ctenidia. Lecithotrophy is reported, with yolky oocytes bearing a thick non-cellular capsule layer; brooding was not observed, and it is here hypothesized that the extreme miniaturization, with the great reduction of ctenidia, is responsible for a shift in the reproductive mode of condylocardiids, contrasting with the commonly reported ovoviviparity of the carditids.
bibliographic citation: Passos et al. (2021) When size matters: the first comprehensive anatomical study of a species of “Condylocardiidae”, an extremely miniaturized bivalve. PeerJ 9:e12108 https://doi.org/10.7717/peerj.12108
date submitted: 2021-03-29
date accepted: 2021-08-12
issued: 2021-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Passos
  given name: Flávio Dias
author list: Agent
  family name: Batistão
  given name: Alan Rodrigo
author list: Agent
  family name: Bieler
  given name: Rüdiger
doi: 10.7717/peerj.12108
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-30
copyright: © 2021 Passos et al.
attribution name: Passos et al.

Anti-clustering in the national SARS-CoV-2 daily infection counts
type: item
type: AcademicArticle
description: The noise in daily infection counts of an epidemic should be super-Poissonian due to intrinsic epidemiological and administrative clustering. Here, we use this clustering to classify the official national SARS-CoV-2 daily infection counts and check for infection counts that are unusually anti-clustered. We adopt a one-parameter model of $\phi _i^{\prime}$ϕi′ infections per cluster, dividing any daily count ni into $n_i/ _i^{\prime}$ni/ϕi′ ‘clusters’, for ‘country’ i. We assume that ${n_i}/\phi _i^{\prime}$ni/ϕi′ on a given day j is drawn from a Poisson distribution whose mean is robustly estimated from the four neighbouring days, and calculate the inferred Poisson probability $P_{ij}^{\prime}$Pij′ of the observation. The $P_{ij}^{\prime}$Pij′ values should be uniformly distributed. We find the value $\phi_i$ϕi that minimises the Kolmogorov–Smirnov distance from a uniform distribution. We investigate the (ϕi, Ni) distribution, for total infection count Ni. We consider consecutive count sequences above a threshold of 50 daily infections. We find that most of the daily infection count sequences are inconsistent with a Poissonian model. Most are found to be consistent with the ϕi model. The 28-, 14- and 7-day least noisy sequences for several countries are best modelled as sub-Poissonian, suggesting a distinct epidemiological family. The 28-day least noisy sequence of Algeria has a preferred model that is strongly sub-Poissonian, with $\phi _i^{28} < 0.1$ϕi28<0.1 . Tajikistan, Turkey, Russia, Belarus, Albania, United Arab Emirates and Nicaragua have preferred models that are also sub-Poissonian, with $\phi _i^{28} < 0.5$ϕi28<0.5 . A statistically significant (Pτ < 0.05) correlation was found between the lack of media freedom in a country, as represented by a high Reporters sans frontieres Press Freedom Index (PFI2020), and the lack of statistical noise in the country’s daily counts. The ϕi model appears to be an effective detector of suspiciously low statistical noise i…
format: application/pdf
format: text/html
creator: Boudewijn F. Roukema
subject: Epidemiology
subject: Infectious Diseases
subject: Statistics
subject: Data Science
description: doi:10.7717/peerj.11856
publisher: PeerJ Inc.
rights: © 2021 Roukema
abstract: The noise in daily infection counts of an epidemic should be super-Poissonian due to intrinsic epidemiological and administrative clustering. Here, we use this clustering to classify the official national SARS-CoV-2 daily infection counts and check for infection counts that are unusually anti-clustered. We adopt a one-parameter model of $\phi _i^{\prime}$ϕi′ infections per cluster, dividing any daily count ni into $n_i/ _i^{\prime}$ni/ϕi′ ‘clusters’, for ‘country’ i. We assume that ${n_i}/\phi _i^{\prime}$ni/ϕi′ on a given day j is drawn from a Poisson distribution whose mean is robustly estimated from the four neighbouring days, and calculate the inferred Poisson probability $P_{ij}^{\prime}$Pij′ of the observation. The $P_{ij}^{\prime}$Pij′ values should be uniformly distributed. We find the value $\phi_i$ϕi that minimises the Kolmogorov–Smirnov distance from a uniform distribution. We investigate the (ϕi, Ni) distribution, for total infection count Ni. We consider consecutive count sequences above a threshold of 50 daily infections. We find that most of the daily infection count sequences are inconsistent with a Poissonian model. Most are found to be consistent with the ϕi model. The 28-, 14- and 7-day least noisy sequences for several countries are best modelled as sub-Poissonian, suggesting a distinct epidemiological family. The 28-day least noisy sequence of Algeria has a preferred model that is strongly sub-Poissonian, with $\phi _i^{28} < 0.1$ϕi28<0.1 . Tajikistan, Turkey, Russia, Belarus, Albania, United Arab Emirates and Nicaragua have preferred models that are also sub-Poissonian, with $\phi _i^{28} < 0.5$ϕi28<0.5 . A statistically significant (Pτ < 0.05) correlation was found between the lack of media freedom in a country, as represented by a high Reporters sans frontieres Press Freedom Index (PFI2020), and the lack of statistical noise in the country’s daily counts. The ϕi model appears to be an effective detector of suspiciously low statistical noise i…
bibliographic citation: Roukema (2021) Anti-clustering in the national SARS-CoV-2 daily infection counts. PeerJ 9:e11856 https://doi.org/10.7717/peerj.11856
date submitted: 2021-01-26
date accepted: 2021-07-04
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roukema
  given name: Boudewijn F.
doi: 10.7717/peerj.11856
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: © 2021 Roukema
attribution name: Roukema

Genetic diversity and structure of one of the most endangered freshwater fish species in Mexico: Tlaloc hildebrandi (Miller, 1950) and recognition of its evolutionarily significant units
type: item
type: AcademicArticle
description: The endangered Chiapas killifish Tlaloc hildebrandi is an endemic freshwater species that lives in four subbasins of the Grijalva and Usumacinta basins, and one of the most geographically restricted species of the Produndulidae family. The species was originally described as endemic to springs in the high limestone plateau in San Cristóbal de Las Casas in the Río Amarillo subbasin (upper Grijalva basin). However, it was recently recorded in the Jataté and Tzaconejá subbasins in the upper Usumacinta basin, thereby expanding its known distribution range. The discovery of these populations is relevant not only for the conservation of the species but also for a better understanding of its evolutionary history. Currently, the scarce populations of T. hildebrandi, found in only a few localities in the Grijalva and Usumacinta basins, are fragmented and living under unfavorable conditions. Here, we analyzed three mitochondrial (mt-atp8&6 and mt-nd2) and one nuclear (nuc-s7) marker in order to assess the genetic diversity and population structure of T. hildebrandi. We found that, in comparison with other endangered freshwater fish species from Mexico, T. hildebrandi showed a lower level of genetic diversity (mt-nd2: h = 0.469, π = 0.0009; mt-atp8&6: h = 0.398, π = 0.001; and nuc-S7: h = 0.433, π = 0.001). Moreover, the analyzed populations exhibited a strong genetic structure in accordance with their geographic distribution, and can be placed into three genetic clusters: (1) Amarillo plus Chenhaló in the upper Grijalva basin, (2) Jataté, and (3) Tzaconejá, both in the upper Usumacinta basin. On the basis of our results, we propose the recognition of at least three evolutionarily significant units (ESUs) for the species and the urgent implementation of ex situ and in situ conservation and management efforts that consider the genetic background of the species.
format: application/pdf
format: text/html
creator: Rosa G. Beltrán-López
creator: Alfonso A. González-Díaz
creator: Miriam Soria-Barreto
creator: Marco Antonio Garduño-Sánchez
creator: Carmela Xochitla-Castrejón
creator: Rocío Rodiles-Hernández
creator: Claudia Patricia Ornelas-García
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.11952
publisher: PeerJ Inc.
rights: © 2021 Beltrán-López et al.
abstract: The endangered Chiapas killifish Tlaloc hildebrandi is an endemic freshwater species that lives in four subbasins of the Grijalva and Usumacinta basins, and one of the most geographically restricted species of the Produndulidae family. The species was originally described as endemic to springs in the high limestone plateau in San Cristóbal de Las Casas in the Río Amarillo subbasin (upper Grijalva basin). However, it was recently recorded in the Jataté and Tzaconejá subbasins in the upper Usumacinta basin, thereby expanding its known distribution range. The discovery of these populations is relevant not only for the conservation of the species but also for a better understanding of its evolutionary history. Currently, the scarce populations of T. hildebrandi, found in only a few localities in the Grijalva and Usumacinta basins, are fragmented and living under unfavorable conditions. Here, we analyzed three mitochondrial (mt-atp8&6 and mt-nd2) and one nuclear (nuc-s7) marker in order to assess the genetic diversity and population structure of T. hildebrandi. We found that, in comparison with other endangered freshwater fish species from Mexico, T. hildebrandi showed a lower level of genetic diversity (mt-nd2: h = 0.469, π = 0.0009; mt-atp8&6: h = 0.398, π = 0.001; and nuc-S7: h = 0.433, π = 0.001). Moreover, the analyzed populations exhibited a strong genetic structure in accordance with their geographic distribution, and can be placed into three genetic clusters: (1) Amarillo plus Chenhaló in the upper Grijalva basin, (2) Jataté, and (3) Tzaconejá, both in the upper Usumacinta basin. On the basis of our results, we propose the recognition of at least three evolutionarily significant units (ESUs) for the species and the urgent implementation of ex situ and in situ conservation and management efforts that consider the genetic background of the species.
bibliographic citation: Beltrán-López et al. (2021) Genetic diversity and structure of one of the most endangered freshwater fish species in Mexico: Tlaloc hildebrandi (Miller, 1950) and recognition of its evolutionarily significant units. PeerJ 9:e11952 https://doi.org/10.7717/peerj.11952
date submitted: 2021-01-08
date accepted: 2021-07-20
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beltrán-López
  given name: Rosa G.
author list: Agent
  family name: González-Díaz
  given name: Alfonso A.
author list: Agent
  family name: Soria-Barreto
  given name: Miriam
author list: Agent
  family name: Garduño-Sánchez
  given name: Marco Antonio
author list: Agent
  family name: Xochitla-Castrejón
  given name: Carmela
author list: Agent
  family name: Rodiles-Hernández
  given name: Rocío
author list: Agent
  family name: Ornelas-García
  given name: Claudia Patricia
doi: 10.7717/peerj.11952
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: © 2021 Beltrán-López et al.
attribution name: Beltrán-López et al.

Low winter precipitation, but not warm autumns and springs, threatens mountain butterflies in middle-high mountains
type: item
type: AcademicArticle
description: Low-elevation mountains represent unique model systems to study species endangered by climate warming, such as subalpine and alpine species of butterflies. We aimed to test the effect of climate variables experienced by Erebia butterflies during their development on adult abundances and phenology, targeting the key climate factors determining the population dynamics of mountain insects. We analysed data from a long-term monitoring of adults of two subalpine and alpine butterfly species, Erebia epiphron and E. sudetica (Nymphalidae: Satyrinae) in the Jeseník Mts and Krkonoše Mts (Czech Republic). Our data revealed consistent patterns in their responses to climatic conditions. Lower precipitation (i.e., less snow cover) experienced by overwintering larvae decreases subsequent adult abundances. Conversely, warmer autumns and warmer and drier springs during the active larval phase increase adult abundances and lead to earlier onset and extended duration of the flight season. The population trends of these mountain butterflies are stable or even increasing. On the background of generally increasing temperatures within the mountain ranges, population stability indicates dynamic equilibrium of positive and detrimental consequences of climate warming among different life history stages. These contradictory effects warn against simplistic predictions of climate change consequences on mountain species based only on predicted increases in average temperature. Microclimate variability may facilitate the survival of mountain insect populations, however the availability of suitable habitats will strongly depend on the management of mountain grasslands.
format: application/pdf
format: text/html
creator: Martin Konvicka
creator: Tomas Kuras
creator: Jana Liparova
creator: Vit Slezak
creator: Dita Horázná
creator: Jan Klečka
creator: Irena Kleckova
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.12021
publisher: PeerJ Inc.
rights: © 2021 Konvicka et al.
abstract: Low-elevation mountains represent unique model systems to study species endangered by climate warming, such as subalpine and alpine species of butterflies. We aimed to test the effect of climate variables experienced by Erebia butterflies during their development on adult abundances and phenology, targeting the key climate factors determining the population dynamics of mountain insects. We analysed data from a long-term monitoring of adults of two subalpine and alpine butterfly species, Erebia epiphron and E. sudetica (Nymphalidae: Satyrinae) in the Jeseník Mts and Krkonoše Mts (Czech Republic). Our data revealed consistent patterns in their responses to climatic conditions. Lower precipitation (i.e., less snow cover) experienced by overwintering larvae decreases subsequent adult abundances. Conversely, warmer autumns and warmer and drier springs during the active larval phase increase adult abundances and lead to earlier onset and extended duration of the flight season. The population trends of these mountain butterflies are stable or even increasing. On the background of generally increasing temperatures within the mountain ranges, population stability indicates dynamic equilibrium of positive and detrimental consequences of climate warming among different life history stages. These contradictory effects warn against simplistic predictions of climate change consequences on mountain species based only on predicted increases in average temperature. Microclimate variability may facilitate the survival of mountain insect populations, however the availability of suitable habitats will strongly depend on the management of mountain grasslands.
bibliographic citation: Konvicka et al. (2021) Low winter precipitation, but not warm autumns and springs, threatens mountain butterflies in middle-high mountains. PeerJ 9:e12021 https://doi.org/10.7717/peerj.12021
date submitted: 2021-05-25
date accepted: 2021-07-29
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Konvicka
  given name: Martin
author list: Agent
  family name: Kuras
  given name: Tomas
author list: Agent
  family name: Liparova
  given name: Jana
author list: Agent
  family name: Slezak
  given name: Vit
author list: Agent
  family name: Horázná
  given name: Dita
author list: Agent
  family name: Klečka
  given name: Jan
author list: Agent
  family name: Kleckova
  given name: Irena
doi: 10.7717/peerj.12021
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: © 2021 Konvicka et al.
attribution name: Konvicka et al.

The stability of soil organic carbon across topographies in a tropical rainforest
type: item
type: AcademicArticle
description: Mechanisms of soil organic carbon (SOC) stability are still unclear in forest ecosystems. In order to unveil the influences of topography on the SOC stability, a 60ha dynamic plot of a tropical montane rainforest was selected in Jianfengling, in Hainan Island, China and soil was sampled from 60 quadrats. The chemical fractions of the SOC were detected with 13C CPMAS/NMR and path analyses explore the mechanisms of SOC stability in different topographies. The chemical fractions of the SOC comprised alkyl carbon > O-alkyl carbon > carboxyl carbon > aromatic carbon. The decomposition index (DI) values were greater than 1 in the different topographies, with an average DI value was 1.29, which indicated that the SOC in the study area was stable. Flat and top areas (together named RF) had more favorable nutrients and silt contents compared with steep and slight steep areas (together named RS). The influencing factors of SOC stability varied across the topographies, where SOC, soil moisture (SM) and ammoniacal nitrogen (NH4+-N, AN) were the main influencing factors in the RF, while SM and AN were the main factors in the RS. Greater SOC and AN strengthened the SOC stability, while higher soil moisture lowered SOC stability. The inertia index was higher in the RS than the RF areas, indicating that local topography significantly affects SOC content and SOC stability by changing soil environmental factors. Topography cannot be neglected in considering SOC stability and future C budgets.
format: application/pdf
format: text/html
creator: Yamin Jiang
creator: Huai Yang
creator: Qiu Yang
creator: Wenjie Liu
creator: Zhaolei Li
creator: Wei Mao
creator: Xu Wang
creator: Zhenghong Tan
subject: Ecology
subject: Soil Science
subject: Climate Change Biology
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.12057
publisher: PeerJ Inc.
rights: © 2021 Jiang et al.
abstract: Mechanisms of soil organic carbon (SOC) stability are still unclear in forest ecosystems. In order to unveil the influences of topography on the SOC stability, a 60ha dynamic plot of a tropical montane rainforest was selected in Jianfengling, in Hainan Island, China and soil was sampled from 60 quadrats. The chemical fractions of the SOC were detected with 13C CPMAS/NMR and path analyses explore the mechanisms of SOC stability in different topographies. The chemical fractions of the SOC comprised alkyl carbon > O-alkyl carbon > carboxyl carbon > aromatic carbon. The decomposition index (DI) values were greater than 1 in the different topographies, with an average DI value was 1.29, which indicated that the SOC in the study area was stable. Flat and top areas (together named RF) had more favorable nutrients and silt contents compared with steep and slight steep areas (together named RS). The influencing factors of SOC stability varied across the topographies, where SOC, soil moisture (SM) and ammoniacal nitrogen (NH4+-N, AN) were the main influencing factors in the RF, while SM and AN were the main factors in the RS. Greater SOC and AN strengthened the SOC stability, while higher soil moisture lowered SOC stability. The inertia index was higher in the RS than the RF areas, indicating that local topography significantly affects SOC content and SOC stability by changing soil environmental factors. Topography cannot be neglected in considering SOC stability and future C budgets.
bibliographic citation: Jiang et al. (2021) The stability of soil organic carbon across topographies in a tropical rainforest. PeerJ 9:e12057 https://doi.org/10.7717/peerj.12057
date submitted: 2021-04-21
date accepted: 2021-08-04
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Yamin
author list: Agent
  family name: Yang
  given name: Huai
author list: Agent
  family name: Yang
  given name: Qiu
author list: Agent
  family name: Liu
  given name: Wenjie
author list: Agent
  family name: Li
  given name: Zhaolei
author list: Agent
  family name: Mao
  given name: Wei
author list: Agent
  family name: Wang
  given name: Xu
author list: Agent
  family name: Tan
  given name: Zhenghong
doi: 10.7717/peerj.12057
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: ©2021 Jiang et al.
attribution name: Jiang et al.

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