PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Re-positive of SARS-CoV-2 test is common in COVID-19 patients after hospital discharge. Data from high standard post-discharge quarantined patients in Macao SAR, China
items: A molecular dynamics simulation study of the ACE2 receptor with screened natural inhibitors to identify novel drug candidate against COVID-19
items: Marine microalgae co-cultured with floc-forming bacterium: Insight into growth and lipid productivity
items: Subterranean movement inferred by temporary emigration in Barton Springs salamanders (Eurycea sosorum)
items: Planktonic associations between medusae (classes Scyphozoa and Hydrozoa) and epifaunal crustaceans
items: Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision
items: Bloom evenness modulates the influence of bloom abundance on insect community structure in suburban gardens
items: Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity
items: The biosonar of the boto: evidence of differences among species of river dolphins (Inia spp.) from the Amazon
items: Commercial arbuscular mycorrhizal fungal inoculant failed to establish in a vineyard despite priority advantage

Re-positive of SARS-CoV-2 test is common in COVID-19 patients after hospital discharge. Data from high standard post-discharge quarantined patients in Macao SAR, China
type: item
type: AcademicArticle
description: During the pandemic of COVID-19, Macau faces tremendous pressure because it is a famous gambling and tourism city with the world’s highest population density. The Macau government implemented decisive public health intervention to control the transmission of COVID-19, and there were only two independent outbreaks in Macau. In the second outbreak, all 35 cases were infected in foreign countries. They were quarantined in airborne infection isolation rooms for at least 14 days with reverse transcription-polymerase chain reaction (RT-PCR) tests after hospital discharge. Twelve (34.3%) of them had re-positive SARS-CoV-2 test results, and none of them presented any COVID-19 signs or symptoms during the entire quarantine period. In this study, the re-positive patients were more likely to be diagnosed in the early stage of the disease with a longer hospital stay. Virus re-infection is impossible in this high standard isolation setting, and reactivation is also unlikely, so that residual virus nucleic acid should be the possible reason for this phenomenon. Due to limited data about the risk of re-positive patients, it is better to quarantine patients after discharge for a prolonged period with repeat RT-PCR tests to minimize the community’s potential risk, particularly in the regions with relative plenty of resources and low community infection rate such as Macau.
format: application/pdf
format: text/html
creator: Chi Leong Wong
creator: Sao Kuan Lei
creator: Chin Ion Lei
creator: Iek Long Lo
creator: Chong Lam
creator: Iek Hou Leong
subject: Molecular Biology
subject: Virology
subject: Health Policy
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.11170
publisher: PeerJ Inc.
rights: © 2021 Wong et al.
abstract: During the pandemic of COVID-19, Macau faces tremendous pressure because it is a famous gambling and tourism city with the world’s highest population density. The Macau government implemented decisive public health intervention to control the transmission of COVID-19, and there were only two independent outbreaks in Macau. In the second outbreak, all 35 cases were infected in foreign countries. They were quarantined in airborne infection isolation rooms for at least 14 days with reverse transcription-polymerase chain reaction (RT-PCR) tests after hospital discharge. Twelve (34.3%) of them had re-positive SARS-CoV-2 test results, and none of them presented any COVID-19 signs or symptoms during the entire quarantine period. In this study, the re-positive patients were more likely to be diagnosed in the early stage of the disease with a longer hospital stay. Virus re-infection is impossible in this high standard isolation setting, and reactivation is also unlikely, so that residual virus nucleic acid should be the possible reason for this phenomenon. Due to limited data about the risk of re-positive patients, it is better to quarantine patients after discharge for a prolonged period with repeat RT-PCR tests to minimize the community’s potential risk, particularly in the regions with relative plenty of resources and low community infection rate such as Macau.
bibliographic citation: Wong et al. (2021) Re-positive of SARS-CoV-2 test is common in COVID-19 patients after hospital discharge. Data from high standard post-discharge quarantined patients in Macao SAR, China. PeerJ 9:e11170 https://doi.org/10.7717/peerj.11170
date submitted: 2020-12-13
date accepted: 2021-03-07
issued: 2021-04-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wong
  given name: Chi Leong
author list: Agent
  family name: Lei
  given name: Sao Kuan
author list: Agent
  family name: Lei
  given name: Chin Ion
author list: Agent
  family name: Lo
  given name: Iek Long
author list: Agent
  family name: Lam
  given name: Chong
author list: Agent
  family name: Leong
  given name: Iek Hou
doi: 10.7717/peerj.11170
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-23
copyright: ©2021 Wong et al.
attribution name: Wong et al.

A molecular dynamics simulation study of the ACE2 receptor with screened natural inhibitors to identify novel drug candidate against COVID-19
type: item
type: AcademicArticle
description: Background & Objectives The massive outbreak of Novel Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has turned out to be a serious global health issue worldwide. Currently, no drugs or vaccines are available for the treatment of COVID-19. The current computational study was attempted to identify a novel therapeutic inhibitor against novel SARS-CoV-2 using in silico drug discovery pipeline. Methods In the present study, the human angiotensin-converting enzyme 2 (ACE2) receptor was the target for the designing of drugs against the deadly virus. The 3D structure of the receptor was modeled & validated using a Swiss-model, Procheck & Errat server. A molecular docking study was performed between a group of natural & synthetic compounds having proven anti-viral activity with ACE2 receptor using Autodock tool 1.5.6. The molecular dynamics simulation study was performed using Desmond v 12 to evaluate the stability and interaction of the ACE2 receptor with a ligand. Results Based on the lowest binding energy, confirmation, and H-bond interaction, cinnamic acid (−5.20 kcal/mol), thymoquinone (−4.71 kcal/mol), and andrographolide (Kalmegh) (−4.00 kcal/mol) were screened out showing strong binding affinity to the active site of ACE2 receptor. MD simulations suggest that cinnamic acid, thymoquinone, and andrographolide (Kalmegh) could efficiently activate the biological pathway without changing the conformation in the binding site of the ACE2 receptor. The bioactivity and drug-likeness properties of compounds show their better pharmacological property and safer to use. Interpretation & Conclusions The study concludes the high potential of cinnamic acid, thymoquinone, and andrographolide against the SARS-CoV-2 ACE2 receptor protein. Thus, the molecular docking and MD simulation study will aid in understanding the molecular interaction between ligand and receptor binding site, thereby leading to novel therapeutic intervention.
format: application/pdf
format: text/html
creator: Neha Srivastava
creator: Prekshi Garg
creator: Prachi Srivastava
creator: Prahlad Kishore Seth
subject: Bioinformatics
subject: Computational Biology
subject: Virology
subject: Infectious Diseases
description: doi:10.7717/peerj.11171
publisher: PeerJ Inc.
rights: © 2021 Srivastava et al.
abstract: Background & Objectives The massive outbreak of Novel Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has turned out to be a serious global health issue worldwide. Currently, no drugs or vaccines are available for the treatment of COVID-19. The current computational study was attempted to identify a novel therapeutic inhibitor against novel SARS-CoV-2 using in silico drug discovery pipeline. Methods In the present study, the human angiotensin-converting enzyme 2 (ACE2) receptor was the target for the designing of drugs against the deadly virus. The 3D structure of the receptor was modeled & validated using a Swiss-model, Procheck & Errat server. A molecular docking study was performed between a group of natural & synthetic compounds having proven anti-viral activity with ACE2 receptor using Autodock tool 1.5.6. The molecular dynamics simulation study was performed using Desmond v 12 to evaluate the stability and interaction of the ACE2 receptor with a ligand. Results Based on the lowest binding energy, confirmation, and H-bond interaction, cinnamic acid (−5.20 kcal/mol), thymoquinone (−4.71 kcal/mol), and andrographolide (Kalmegh) (−4.00 kcal/mol) were screened out showing strong binding affinity to the active site of ACE2 receptor. MD simulations suggest that cinnamic acid, thymoquinone, and andrographolide (Kalmegh) could efficiently activate the biological pathway without changing the conformation in the binding site of the ACE2 receptor. The bioactivity and drug-likeness properties of compounds show their better pharmacological property and safer to use. Interpretation & Conclusions The study concludes the high potential of cinnamic acid, thymoquinone, and andrographolide against the SARS-CoV-2 ACE2 receptor protein. Thus, the molecular docking and MD simulation study will aid in understanding the molecular interaction between ligand and receptor binding site, thereby leading to novel therapeutic intervention.
bibliographic citation: Srivastava et al. (2021) A molecular dynamics simulation study of the ACE2 receptor with screened natural inhibitors to identify novel drug candidate against COVID-19. PeerJ 9:e11171 https://doi.org/10.7717/peerj.11171
date submitted: 2020-09-15
date accepted: 2021-03-07
issued: 2021-04-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Srivastava
  given name: Neha
author list: Agent
  family name: Garg
  given name: Prekshi
author list: Agent
  family name: Srivastava
  given name: Prachi
author list: Agent
  family name: Seth
  given name: Prahlad Kishore
doi: 10.7717/peerj.11171
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-23
copyright: © 2021 Srivastava et al.
attribution name: Srivastava et al.

Marine microalgae co-cultured with floc-forming bacterium: Insight into growth and lipid productivity
type: item
type: AcademicArticle
description: This study investigated the effect of co-culturing microalgae with a floc-forming bacterium. Of the six microalgae isolated from a biofloc sample, only Thalassiosira weissflogii, Chlamydomonas sp. and Chlorella vulgaris were propagated successfully in Conway medium. Hence, these species were selected for the experiment comparing microalgae axenic culture and co-culture with the floc-forming bacterium, Bacillus infantis. Results obtained showed that the co-culture had higher microalgae biomass compared to the axenic culture. A similar trend was also observed concerning the lipid content of the microalgae-bacterium co-cultures. The cell number of B. infantis co-cultured with T. weissflogii increased during the exponential stage until the sixth day, but the other microalgae species experienced a significant early reduction in cell density of the bacteria at the exponential stage. This study represents the first attempt at co-culturing microalgae with B. infantis, a floc-forming bacterium, and observed increased biomass growth and lipid accumulation compared to the axenic culture.
format: application/pdf
format: text/html
creator: Chin Sze Yee
creator: Victor Tosin Okomoda
creator: Fakriah Hashim
creator: Khor Waiho
creator: Siti Rozaimah Sheikh Abdullah
creator: Cosmas Alamanjo
creator: Hassimi Abu Hasan
creator: Emienour Muzalina Mustafa
creator: Nor Azman Kasan
subject: Aquaculture, Fisheries and Fish Science
subject: Biotechnology
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.11217
publisher: PeerJ Inc.
rights: © 2021 Yee et al.
abstract: This study investigated the effect of co-culturing microalgae with a floc-forming bacterium. Of the six microalgae isolated from a biofloc sample, only Thalassiosira weissflogii, Chlamydomonas sp. and Chlorella vulgaris were propagated successfully in Conway medium. Hence, these species were selected for the experiment comparing microalgae axenic culture and co-culture with the floc-forming bacterium, Bacillus infantis. Results obtained showed that the co-culture had higher microalgae biomass compared to the axenic culture. A similar trend was also observed concerning the lipid content of the microalgae-bacterium co-cultures. The cell number of B. infantis co-cultured with T. weissflogii increased during the exponential stage until the sixth day, but the other microalgae species experienced a significant early reduction in cell density of the bacteria at the exponential stage. This study represents the first attempt at co-culturing microalgae with B. infantis, a floc-forming bacterium, and observed increased biomass growth and lipid accumulation compared to the axenic culture.
bibliographic citation: Yee et al. (2021) Marine microalgae co-cultured with floc-forming bacterium: Insight into growth and lipid productivity. PeerJ 9:e11217 https://doi.org/10.7717/peerj.11217
date submitted: 2020-12-13
date accepted: 2021-03-15
issued: 2021-04-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yee
  given name: Chin Sze
author list: Agent
  family name: Okomoda
  given name: Victor Tosin
author list: Agent
  family name: Hashim
  given name: Fakriah
author list: Agent
  family name: Waiho
  given name: Khor
author list: Agent
  family name: Sheikh Abdullah
  given name: Siti Rozaimah
author list: Agent
  family name: Alamanjo
  given name: Cosmas
author list: Agent
  family name: Abu Hasan
  given name: Hassimi
author list: Agent
  family name: Muzalina Mustafa
  given name: Emienour
author list: Agent
  family name: Kasan
  given name: Nor Azman
doi: 10.7717/peerj.11217
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-23
copyright: © 2021 Yee et al.
attribution name: Yee et al.

Subterranean movement inferred by temporary emigration in Barton Springs salamanders (Eurycea sosorum)
type: item
type: AcademicArticle
description: Movement behavior is an important aspect of animal ecology but is challenging to study in species that are unobservable for some portion of their lives, such as those inhabiting subterranean environments. Using four years of robust-design capture-recapture data, we examined the probability of movement into subterranean habitat by a population of endangered Barton Springs salamanders (Eurycea sosorum), a species that inhabits both surface and subterranean groundwater habitats. We tested the effects of environmental variables and body size on survival and temporary emigration, using the latter as a measure of subterranean habitat use. Based on 2,046 observations of 1,578 individuals, we found that temporary emigration was higher for larger salamanders, 79% of which temporarily emigrated into subterranean habitat between primary sampling intervals, on average. Body size was a better predictor of temporary emigration and survival compared to environmental covariates, although coefficients from lower ranked models suggested turbidity and dissolved oxygen may influence salamander movement between the surface and subsurface. Surface population dynamics are partly driven by movement below ground and therefore surface abundance estimates represent a fraction of the superpopulation. As such, while surface habitat management remains an important conservation strategy for this species, periodic declines in apparent surface abundance do not necessarily indicate declines of the superpopulation associated with the spring habitat.
format: application/pdf
format: text/html
creator: Nathan F. Bendik
creator: Dee Ann Chamberlain
creator: Thomas J. Devitt
creator: Sarah E. Donelson
creator: Bradley Nissen
creator: Jacob D. Owen
creator: Donelle Robinson
creator: Blake N. Sissel
creator: Kenneth Sparks
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Freshwater Biology
subject: Population Biology
description: doi:10.7717/peerj.11246
publisher: PeerJ Inc.
rights: ©
abstract: Movement behavior is an important aspect of animal ecology but is challenging to study in species that are unobservable for some portion of their lives, such as those inhabiting subterranean environments. Using four years of robust-design capture-recapture data, we examined the probability of movement into subterranean habitat by a population of endangered Barton Springs salamanders (Eurycea sosorum), a species that inhabits both surface and subterranean groundwater habitats. We tested the effects of environmental variables and body size on survival and temporary emigration, using the latter as a measure of subterranean habitat use. Based on 2,046 observations of 1,578 individuals, we found that temporary emigration was higher for larger salamanders, 79% of which temporarily emigrated into subterranean habitat between primary sampling intervals, on average. Body size was a better predictor of temporary emigration and survival compared to environmental covariates, although coefficients from lower ranked models suggested turbidity and dissolved oxygen may influence salamander movement between the surface and subsurface. Surface population dynamics are partly driven by movement below ground and therefore surface abundance estimates represent a fraction of the superpopulation. As such, while surface habitat management remains an important conservation strategy for this species, periodic declines in apparent surface abundance do not necessarily indicate declines of the superpopulation associated with the spring habitat.
bibliographic citation: Bendik et al. (2021) Subterranean movement inferred by temporary emigration in Barton Springs salamanders (Eurycea sosorum). PeerJ 9:e11246 https://doi.org/10.7717/peerj.11246
date submitted: 2020-12-14
date accepted: 2021-03-18
issued: 2021-04-23
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Bendik
  given name: Nathan F.
author list: Agent
  family name: Chamberlain
  given name: Dee Ann
author list: Agent
  family name: Devitt
  given name: Thomas J.
author list: Agent
  family name: Donelson
  given name: Sarah E.
author list: Agent
  family name: Nissen
  given name: Bradley
author list: Agent
  family name: Owen
  given name: Jacob D.
author list: Agent
  family name: Robinson
  given name: Donelle
author list: Agent
  family name: Sissel
  given name: Blake N.
author list: Agent
  family name: Sparks
  given name: Kenneth
doi: 10.7717/peerj.11246
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-23

Planktonic associations between medusae (classes Scyphozoa and Hydrozoa) and epifaunal crustaceans
type: item
type: AcademicArticle
description: Jellyfish are known to carry various epibionts, including many of the subphylum Crustacea. However, the associations between gelatinous zooplankton and other invertebrates have been chronically overlooked. Crustacea, a massive clade of economically, ecologically, and culturally important species, includes many taxa that utilize gelatinous zooplankton for food, transport, and protection as both adults and juveniles. Here we compile 211 instances of epifaunal crustaceans recorded on Hydromedusae and Scyphomedusae from a century of literature. These include 78 identified crustacean species in 65 genera across nine orders found upon 37 Hydromedusa species and 48 Scyphomedusae. The crustacean life stage, location, nature of the association with the medusa, years, months, and depths are compiled to form a comprehensive view of the current state of the literature. Additionally, this review highlights areas where the current literature is lacking, particularly noting our poor understanding of the relationships between juvenile crabs of commercially valuable species and medusae.
format: application/pdf
format: text/html
creator: Kaden Muffett
creator: Maria Pia Miglietta
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.11281
publisher: PeerJ Inc.
rights: © 2021 Muffett and Miglietta
abstract: Jellyfish are known to carry various epibionts, including many of the subphylum Crustacea. However, the associations between gelatinous zooplankton and other invertebrates have been chronically overlooked. Crustacea, a massive clade of economically, ecologically, and culturally important species, includes many taxa that utilize gelatinous zooplankton for food, transport, and protection as both adults and juveniles. Here we compile 211 instances of epifaunal crustaceans recorded on Hydromedusae and Scyphomedusae from a century of literature. These include 78 identified crustacean species in 65 genera across nine orders found upon 37 Hydromedusa species and 48 Scyphomedusae. The crustacean life stage, location, nature of the association with the medusa, years, months, and depths are compiled to form a comprehensive view of the current state of the literature. Additionally, this review highlights areas where the current literature is lacking, particularly noting our poor understanding of the relationships between juvenile crabs of commercially valuable species and medusae.
bibliographic citation: Muffett et al. (2021) Planktonic associations between medusae (classes Scyphozoa and Hydrozoa) and epifaunal crustaceans. PeerJ 9:e11281 https://doi.org/10.7717/peerj.11281
date submitted: 2020-12-17
date accepted: 2021-03-24
issued: 2021-04-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Muffett
  given name: Kaden
author list: Agent
  family name: Miglietta
  given name: Maria Pia
doi: 10.7717/peerj.11281
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-23
copyright: © 2021 Muffett and Miglietta
attribution name: Muffett and Miglietta

Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision
type: item
type: AcademicArticle
description: Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).
format: application/pdf
format: text/html
creator: Petr G. Garibian
creator: Dmitry P. Karabanov
creator: Anna N. Neretina
creator: Derek J. Taylor
creator: Alexey A. Kotov
subject: Biodiversity
subject: Biogeography
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.11310
publisher: PeerJ Inc.
rights: © 2021 Garibian et al.
abstract: Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).
bibliographic citation: Garibian et al. (2021) Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision. PeerJ 9:e11310 https://doi.org/10.7717/peerj.11310
date submitted: 2021-01-21
date accepted: 2021-03-29
issued: 2021-04-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garibian
  given name: Petr G.
author list: Agent
  family name: Karabanov
  given name: Dmitry P.
author list: Agent
  family name: Neretina
  given name: Anna N.
author list: Agent
  family name: Taylor
  given name: Derek J.
author list: Agent
  family name: Kotov
  given name: Alexey A.
doi: 10.7717/peerj.11310
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-23
copyright: © 2021 Garibian et al.
attribution name: Garibian et al.

Bloom evenness modulates the influence of bloom abundance on insect community structure in suburban gardens
type: item
type: AcademicArticle
description: As land use change drives global insect declines, the value of enhancing habitat in urban and suburban landscapes has become increasingly important for flower-visiting insects. In order to help identify best landscaping practices, we conducted plant surveys and insect bowl-trap surveys in 34 suburban yards for 21 months in Gainesville, FL, USA, which resulted in 274 paired days of plant and insect survey data. We assessed the impact of nearest greenspace size, distance to greenspace, yard area, plant richness, plant type, bloom abundance, bloom richness and bloom evenness on insect abundance and richness. Our samples include 34,972 insects captured, 485,827 blooms counted and 774 species of plants recorded. We found that bloom evenness had a modulating effect on bloom abundance—a more even sample of the same number of blooms would have a disproportionately greater positive impact on flower visitor richness, insect richness and insect abundance. Bloom abundance was also highly significant and positively associated with flower visitor abundance, but nearest greenspace size, distance to greenspace, plant type (native vs. non-native vs. Florida Friendly), and yard area were not found to be important factors. Plant richness was a highly significant factor, but its effect size was very small.
format: application/pdf
format: text/html
creator: Elizabeth Y. Braatz
creator: Zachariah J. Gezon
creator: Kristin Rossetti
creator: Lily T. Maynard
creator: Jonathan S. Bremer
creator: Geena M. Hill
creator: Marissa A. Streifel
creator: Jaret C. Daniels
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.11132
publisher: PeerJ Inc.
rights: © 2021 Braatz et al.
abstract: As land use change drives global insect declines, the value of enhancing habitat in urban and suburban landscapes has become increasingly important for flower-visiting insects. In order to help identify best landscaping practices, we conducted plant surveys and insect bowl-trap surveys in 34 suburban yards for 21 months in Gainesville, FL, USA, which resulted in 274 paired days of plant and insect survey data. We assessed the impact of nearest greenspace size, distance to greenspace, yard area, plant richness, plant type, bloom abundance, bloom richness and bloom evenness on insect abundance and richness. Our samples include 34,972 insects captured, 485,827 blooms counted and 774 species of plants recorded. We found that bloom evenness had a modulating effect on bloom abundance—a more even sample of the same number of blooms would have a disproportionately greater positive impact on flower visitor richness, insect richness and insect abundance. Bloom abundance was also highly significant and positively associated with flower visitor abundance, but nearest greenspace size, distance to greenspace, plant type (native vs. non-native vs. Florida Friendly), and yard area were not found to be important factors. Plant richness was a highly significant factor, but its effect size was very small.
bibliographic citation: Braatz et al. (2021) Bloom evenness modulates the influence of bloom abundance on insect community structure in suburban gardens. PeerJ 9:e11132 https://doi.org/10.7717/peerj.11132
date submitted: 2020-08-24
date accepted: 2021-03-01
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Braatz
  given name: Elizabeth Y.
author list: Agent
  family name: Gezon
  given name: Zachariah J.
author list: Agent
  family name: Rossetti
  given name: Kristin
author list: Agent
  family name: Maynard
  given name: Lily T.
author list: Agent
  family name: Bremer
  given name: Jonathan S.
author list: Agent
  family name: Hill
  given name: Geena M.
author list: Agent
  family name: Streifel
  given name: Marissa A.
author list: Agent
  family name: Daniels
  given name: Jaret C.
doi: 10.7717/peerj.11132
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: © 2021 Braatz et al.
attribution name: Braatz et al.

Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity
type: item
type: AcademicArticle
description: Phylogenomic studies can provide insights into speciation, adaptation, and extinction, while providing a roadmap for conservation. Hawaiian tree snails are a model system for an adaptive radiation facing an extinction crisis. In the last 5 years, nearly all populations of Hawaiian tree snails across the 30 remaining species in the subfamily Achatinellinae (Achatinellidae) have declined from hundreds or thousands in the wild down to undetectable levels. Nearly 100 species historically occurred across dramatic environmental gradients on five of the Hawaiian Islands, but habitat loss, overcollection, and predation by invasive species have decimated populations. As such, this system offers the opportunity to integrate efforts to conserve evolutionary potential into conservation planning for a rapidly declining subfamily. Here, we used genome-wide, restriction-site associated DNA sequencing (RADseq), along with mitochondrial genome reconstruction, to resolve evolutionary relationships to inform conservation efforts. Phylogenetic analysis of nearly 400k genome-wide SNPs from 59 populations and 25 species across six genera in the family Achatinellidae, was generally concordant with taxonomy, geography, and mtDNA with several notable exceptions; mtDNA was unable to resolve some deeper nodes (e.g., the monophyly of Achatinella), while SNP data did not resolve as many shallow nodes. Both phylogenetic and coalescent analysis revealed deep divergences between populations within Achatinella mustelina that were consistent with species-level differences. Given cryptic species-level divergence within populations that are geographically proximate, they are at higher risk of extirpation from invasive predators and climate change than previously assumed. This study clarifies evolutionary relationships within this model system for adaptive radiation, forming the basis for conservation strategies such as translocation, captive rearing, and hybridization trials to prevent the loss of cap…
format: application/pdf
format: text/html
creator: Melissa R. Price
creator: Michael G. Hadfield
creator: Ingrid S.S. Knapp
creator: Robert J. Toonen
creator: Zac H. Forsman
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genomics
subject: Natural Resource Management
description: doi:10.7717/peerj.10993
publisher: PeerJ Inc.
rights: © 2021 Price et al.
abstract: Phylogenomic studies can provide insights into speciation, adaptation, and extinction, while providing a roadmap for conservation. Hawaiian tree snails are a model system for an adaptive radiation facing an extinction crisis. In the last 5 years, nearly all populations of Hawaiian tree snails across the 30 remaining species in the subfamily Achatinellinae (Achatinellidae) have declined from hundreds or thousands in the wild down to undetectable levels. Nearly 100 species historically occurred across dramatic environmental gradients on five of the Hawaiian Islands, but habitat loss, overcollection, and predation by invasive species have decimated populations. As such, this system offers the opportunity to integrate efforts to conserve evolutionary potential into conservation planning for a rapidly declining subfamily. Here, we used genome-wide, restriction-site associated DNA sequencing (RADseq), along with mitochondrial genome reconstruction, to resolve evolutionary relationships to inform conservation efforts. Phylogenetic analysis of nearly 400k genome-wide SNPs from 59 populations and 25 species across six genera in the family Achatinellidae, was generally concordant with taxonomy, geography, and mtDNA with several notable exceptions; mtDNA was unable to resolve some deeper nodes (e.g., the monophyly of Achatinella), while SNP data did not resolve as many shallow nodes. Both phylogenetic and coalescent analysis revealed deep divergences between populations within Achatinella mustelina that were consistent with species-level differences. Given cryptic species-level divergence within populations that are geographically proximate, they are at higher risk of extirpation from invasive predators and climate change than previously assumed. This study clarifies evolutionary relationships within this model system for adaptive radiation, forming the basis for conservation strategies such as translocation, captive rearing, and hybridization trials to prevent the loss of cap…
bibliographic citation: Price et al. (2021) Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity. PeerJ 9:e10993 https://doi.org/10.7717/peerj.10993
date submitted: 2019-12-21
date accepted: 2021-02-01
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Price
  given name: Melissa R.
author list: Agent
  family name: Hadfield
  given name: Michael G.
author list: Agent
  family name: Knapp
  given name: Ingrid S.S.
author list: Agent
  family name: Toonen
  given name: Robert J.
author list: Agent
  family name: Forsman
  given name: Zac H.
doi: 10.7717/peerj.10993
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: © 2021 Price et al.
attribution name: Price et al.

The biosonar of the boto: evidence of differences among species of river dolphins (Inia spp.) from the Amazon
type: item
type: AcademicArticle
description: Echolocation clicks can reflect the anatomy of the vocalizing animal, enabling the distinction of species. River dolphins from the family Iniidae are formally represented by one species and two subspecies (Inia geoffrensis geoffrensis and I. g. humboldtiana). Additionally, two other species have been proposed (I. boliviensis and I. araguaiaensis) regarding its level of restricted distribution and morph-genetics differences. For the Committee on Taxonomy of the Society for Marine Mammalogy, the specific status of the proposed species relies on further knowledge on morphology, ecology, and genetics. Given that species-specific status is required for conservation efforts, we described and compared the echolocation clicks of Inia spp., searching for specific differences on their vocalizations. The sounds were captured with a Cetacean Research ™ C54XRS (+3/−20 dB, −185 dB re: 1V/μPa) in Guaviare River (Orinoco basin), Madeira River (Madeira basin), Xingu River (Amazon Basin), and Araguaia River (Tocantins-Araguaia basin). We found significant differences in all analyzed parameters (peak frequency, 3 dB bandwidth, 10 dB bandwidth and inter-click interval) for all species and subspecies. Differences in acoustical parameters of clicks are mainly related to the animal’s internal morphology, thus this study may potentially support with information for the species-level classification mostly of I. araguaiaensis (the Araguaian boto). Classifying the Araguaian boto separately from I. geoffrensis has important implications for the species in terms of conservation status, since it is restricted to a highly impacted river system.
format: application/pdf
format: text/html
creator: Jéssica F. Melo
creator: Thiago O. S. Amorim
creator: Mariana Paschoalini
creator: Artur Andriolo
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.11105
publisher: PeerJ Inc.
rights: © 2021 Melo et al.
abstract: Echolocation clicks can reflect the anatomy of the vocalizing animal, enabling the distinction of species. River dolphins from the family Iniidae are formally represented by one species and two subspecies (Inia geoffrensis geoffrensis and I. g. humboldtiana). Additionally, two other species have been proposed (I. boliviensis and I. araguaiaensis) regarding its level of restricted distribution and morph-genetics differences. For the Committee on Taxonomy of the Society for Marine Mammalogy, the specific status of the proposed species relies on further knowledge on morphology, ecology, and genetics. Given that species-specific status is required for conservation efforts, we described and compared the echolocation clicks of Inia spp., searching for specific differences on their vocalizations. The sounds were captured with a Cetacean Research ™ C54XRS (+3/−20 dB, −185 dB re: 1V/μPa) in Guaviare River (Orinoco basin), Madeira River (Madeira basin), Xingu River (Amazon Basin), and Araguaia River (Tocantins-Araguaia basin). We found significant differences in all analyzed parameters (peak frequency, 3 dB bandwidth, 10 dB bandwidth and inter-click interval) for all species and subspecies. Differences in acoustical parameters of clicks are mainly related to the animal’s internal morphology, thus this study may potentially support with information for the species-level classification mostly of I. araguaiaensis (the Araguaian boto). Classifying the Araguaian boto separately from I. geoffrensis has important implications for the species in terms of conservation status, since it is restricted to a highly impacted river system.
bibliographic citation: Melo et al. (2021) The biosonar of the boto: evidence of differences among species of river dolphins (Inia spp.) from the Amazon. PeerJ 9:e11105 https://doi.org/10.7717/peerj.11105
date submitted: 2020-09-02
date accepted: 2021-02-22
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Melo
  given name: Jéssica F.
author list: Agent
  family name: Amorim
  given name: Thiago O. S.
author list: Agent
  family name: Paschoalini
  given name: Mariana
author list: Agent
  family name: Andriolo
  given name: Artur
doi: 10.7717/peerj.11105
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: © 2021 Melo et al.
attribution name: Melo et al.

Commercial arbuscular mycorrhizal fungal inoculant failed to establish in a vineyard despite priority advantage
type: item
type: AcademicArticle
description: Background Arbuscular mycorrhizal (AM) fungi associate with most plants and can increase nutrient uptake. As a result, commercial inoculants called “biofertilizers” containing AM fungi have been developed and marketed to increase plant performance. However, successful establishment of these inoculants remains a challenge, and may be negatively impacted by competition with fungi already present (priority effects). Perennial agriculture may be more amenable if inoculants can be successfully established on crops prior to field planting. Methods Here, we inoculate grapevine (Vitis vinifera) with a commercial inoculant in three treatments designed to manipulate the strength and direction of priority effects and quantified the abundance of the fungal strain before and after introduction using droplet digital PCR (ddPCR). Results We found that the introduced strain did not establish in any treatment, even with priority advantage, and inoculated vines did not differ in performance from non-inoculated vines. Fungal abundance was not greater than in pre-inoculation soil samples during any of the five years sampled and may have been impaired by high available phosphorus levels in the soil. This study highlights the need to understand and evaluate how the management of the agricultural system will affect establishment before introduction of “biofertilizers”, which is often unpredictable.
format: application/pdf
format: text/html
creator: Corrina Thomsen
creator: Laura Loverock
creator: Vasilis Kokkoris
creator: Taylor Holland
creator: Patricia A. Bowen
creator: Miranda Hart
subject: Agricultural Science
subject: Ecology
subject: Mycology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.11119
publisher: PeerJ Inc.
rights: © 2021 Thomsen et al.
abstract: Background Arbuscular mycorrhizal (AM) fungi associate with most plants and can increase nutrient uptake. As a result, commercial inoculants called “biofertilizers” containing AM fungi have been developed and marketed to increase plant performance. However, successful establishment of these inoculants remains a challenge, and may be negatively impacted by competition with fungi already present (priority effects). Perennial agriculture may be more amenable if inoculants can be successfully established on crops prior to field planting. Methods Here, we inoculate grapevine (Vitis vinifera) with a commercial inoculant in three treatments designed to manipulate the strength and direction of priority effects and quantified the abundance of the fungal strain before and after introduction using droplet digital PCR (ddPCR). Results We found that the introduced strain did not establish in any treatment, even with priority advantage, and inoculated vines did not differ in performance from non-inoculated vines. Fungal abundance was not greater than in pre-inoculation soil samples during any of the five years sampled and may have been impaired by high available phosphorus levels in the soil. This study highlights the need to understand and evaluate how the management of the agricultural system will affect establishment before introduction of “biofertilizers”, which is often unpredictable.
bibliographic citation: Thomsen et al. (2021) Commercial arbuscular mycorrhizal fungal inoculant failed to establish in a vineyard despite priority advantage. PeerJ 9:e11119 https://doi.org/10.7717/peerj.11119
date submitted: 2020-11-26
date accepted: 2021-02-25
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thomsen
  given name: Corrina
author list: Agent
  family name: Loverock
  given name: Laura
author list: Agent
  family name: Kokkoris
  given name: Vasilis
author list: Agent
  family name: Holland
  given name: Taylor
author list: Agent
  family name: Bowen
  given name: Patricia A.
author list: Agent
  family name: Hart
  given name: Miranda
doi: 10.7717/peerj.11119
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: ©2021 Thomsen et al.
attribution name: Thomsen et al.

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