PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Some like it hot: factors impacting thermal preferences of two Ponto-Caspian amphipods Dikerogammarus villosus (Sovinsky, 1894) and Dikerogammarus haemobaphes (Eichwald, 1841)
items: Current knowledge on bioacoustics of the subfamily Lophyohylinae (Hylidae, Anura) and description of Ocellated treefrog Itapotihyla langsdorffii vocalizations
items: The smallest biggest theropod dinosaur: a tiny pedal ungual of a juvenile Spinosaurus from the Cretaceous of Morocco
items: Assessment of the ecotoxicity of urban estuarine sediment using benthic and pelagic copepod bioassays
items: Urbanization alters small rodent community composition but not abundance
items: A new species of spotted leaf frog, genus Phasmahyla (Amphibia, Phyllomedusidae) from Southeast Brazil
items: Top-down and bottom-up controls on southern New England salt marsh crab populations
items: Multi-dimensional Precision Livestock Farming: a potential toolbox for sustainable rangeland management
items: Characterization of tumor heterogeneity by latent haplotypes: a sequential Monte Carlo approach
items: Potent antibacterial, antioxidant and toxic activities of extracts from Passiflora suberosa L. leaves

Some like it hot: factors impacting thermal preferences of two Ponto-Caspian amphipods Dikerogammarus villosus (Sovinsky, 1894) and Dikerogammarus haemobaphes (Eichwald, 1841)
type: item
type: AcademicArticle
description: Temperature is a crucial factor determining biology and ecology of poikilothermic animals. It often constitutes an important barrier for invasive species originating from different climate zones but, on the other hand, may facilitate the invasion process of animals with wide thermal preferences and high resistance to extreme temperatures. In our experimental study, we investigated the thermal behaviour of two Ponto-Caspian amphipod crustaceans—Dikerogammarus villosus and Dikerogammarus haemobaphes. Both species are known to live under a wide range of thermal conditions which may promote their invasion. Moreover, both these amphipods are hosts for microsporidian parasites which co-evolved with them within the Ponto-Caspian region and spread in European waters. As the presence of a parasite may influence the thermal preferences of its host, we expected to observe behavioural changes in infected individuals of the studied amphipods leading to (1) behavioural fever (selecting a warmer habitat) or (2) anapyrexia (selecting a colder habitat). The experiment (N = 20) was carried out for 30 min in a 100 cm. 20 cm from boths sides were not avaliable for amphipods long thermal gradient (0–40 °C), using 30 randomly selected adult amphipod individuals of one species. At the end of each trial, we checked the position of amphipods along the gradient and determined their sex and infection status (uninfected or infected by one of microsporidium species). D. villosus was infected with Cucumispora dikerogammari whereas D. haemobaphes was a host for C. dikerogammari, Dictyocoela muelleri or D. berillonum. Thermal preferences of amphipods depended on their species and sex. Females of D. villosus preferred warmer microhabitats (often much above 30 °C) than conspecific males and females of D. haemobaphes, whereas no significant differences were found among males of both species and both sexes of D. haemobaphes. Moreover, infected males of D. villosus stayed in warmer water more often tha…
format: application/pdf
format: text/html
creator: Michał Rachalewski
creator: Jarosław Kobak
creator: Eliza Szczerkowska-Majchrzak
creator: Karolina Bącela-Spychalska
subject: Animal Behavior
subject: Ecology
subject: Parasitology
subject: Freshwater Biology
description: doi:10.7717/peerj.4871
publisher: PeerJ Inc.
rights: © 2018 Rachalewski et al.
abstract: Temperature is a crucial factor determining biology and ecology of poikilothermic animals. It often constitutes an important barrier for invasive species originating from different climate zones but, on the other hand, may facilitate the invasion process of animals with wide thermal preferences and high resistance to extreme temperatures. In our experimental study, we investigated the thermal behaviour of two Ponto-Caspian amphipod crustaceans—Dikerogammarus villosus and Dikerogammarus haemobaphes. Both species are known to live under a wide range of thermal conditions which may promote their invasion. Moreover, both these amphipods are hosts for microsporidian parasites which co-evolved with them within the Ponto-Caspian region and spread in European waters. As the presence of a parasite may influence the thermal preferences of its host, we expected to observe behavioural changes in infected individuals of the studied amphipods leading to (1) behavioural fever (selecting a warmer habitat) or (2) anapyrexia (selecting a colder habitat). The experiment (N = 20) was carried out for 30 min in a 100 cm. 20 cm from boths sides were not avaliable for amphipods long thermal gradient (0–40 °C), using 30 randomly selected adult amphipod individuals of one species. At the end of each trial, we checked the position of amphipods along the gradient and determined their sex and infection status (uninfected or infected by one of microsporidium species). D. villosus was infected with Cucumispora dikerogammari whereas D. haemobaphes was a host for C. dikerogammari, Dictyocoela muelleri or D. berillonum. Thermal preferences of amphipods depended on their species and sex. Females of D. villosus preferred warmer microhabitats (often much above 30 °C) than conspecific males and females of D. haemobaphes, whereas no significant differences were found among males of both species and both sexes of D. haemobaphes. Moreover, infected males of D. villosus stayed in warmer water more often tha…
bibliographic citation: Rachalewski et al. (2018) Some like it hot: factors impacting thermal preferences of two Ponto-Caspian amphipods Dikerogammarus villosus (Sovinsky, 1894) and Dikerogammarus haemobaphes (Eichwald, 1841). PeerJ 6:e4871 https://doi.org/10.7717/peerj.4871
date submitted: 2018-03-13
date accepted: 2018-05-10
issued: 2018-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rachalewski
  given name: Michał
author list: Agent
  family name: Kobak
  given name: Jarosław
author list: Agent
  family name: Szczerkowska-Majchrzak
  given name: Eliza
author list: Agent
  family name: Bącela-Spychalska
  given name: Karolina
doi: 10.7717/peerj.4871
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-31
copyright: ©2018 Rachalewski et al.
attribution name: Rachalewski et al.

Current knowledge on bioacoustics of the subfamily Lophyohylinae (Hylidae, Anura) and description of Ocellated treefrog Itapotihyla langsdorffii vocalizations
type: item
type: AcademicArticle
description: Background Anuran vocalizations, such as advertisement and release calls, are informative for taxonomy because species recognition can be based on those signals. Thus, a proper acoustic description of the calls may support taxonomic decisions and may contribute to knowledge about amphibian phylogeny. Methods Here we present a perspective on advertisement call descriptions of the frog subfamily Lophyohylinae, through a literature review and a spatial analysis presenting bioacoustic coldspots (sites with high diversity of species lacking advertisement call descriptions) for this taxonomic group. Additionally, we describe the advertisement and release calls of the still poorly known treefrog, Itapotihyla langsdorffii. We analyzed recordings of six males using the software Raven Pro 1.4 and calculated the coefficient of variation for classifying static and dynamic acoustic properties. Results and Discussion We found that more than half of the species within the subfamily do not have their vocalizations described yet. Most of these species are distributed in the western and northern Amazon, where recording sampling effort should be strengthened in order to fill these gaps. The advertisement call of I. langsdorffii is composed of 3–18 short unpulsed notes (mean of 13 ms long), presents harmonic structure, and has a peak dominant frequency of about 1.4 kHz. This call usually presents amplitude modulation, with decreasing intensity along the sequence of notes. The release call is a simple unpulsed note with an average duration of 9 ms, and peak dominant frequency around 1.8 kHz. Temporal properties presented higher variations than spectral properties at both intra- and inter-individual levels. However, only peak dominant frequency was static at intra-individual level. High variability in temporal properties and lower variations related to spectral ones is usual for anurans; The first set of variables is determined by social environment or temperature, while the second is us…
format: application/pdf
format: text/html
creator: Lucas Rodriguez Forti
creator: Roseli Maria Foratto
creator: Rafael Márquez
creator: Vânia Rosa Pereira
creator: Luís Felipe Toledo
subject: Animal Behavior
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.4813
publisher: PeerJ Inc.
rights: © 2018 Forti et al.
abstract: Background Anuran vocalizations, such as advertisement and release calls, are informative for taxonomy because species recognition can be based on those signals. Thus, a proper acoustic description of the calls may support taxonomic decisions and may contribute to knowledge about amphibian phylogeny. Methods Here we present a perspective on advertisement call descriptions of the frog subfamily Lophyohylinae, through a literature review and a spatial analysis presenting bioacoustic coldspots (sites with high diversity of species lacking advertisement call descriptions) for this taxonomic group. Additionally, we describe the advertisement and release calls of the still poorly known treefrog, Itapotihyla langsdorffii. We analyzed recordings of six males using the software Raven Pro 1.4 and calculated the coefficient of variation for classifying static and dynamic acoustic properties. Results and Discussion We found that more than half of the species within the subfamily do not have their vocalizations described yet. Most of these species are distributed in the western and northern Amazon, where recording sampling effort should be strengthened in order to fill these gaps. The advertisement call of I. langsdorffii is composed of 3–18 short unpulsed notes (mean of 13 ms long), presents harmonic structure, and has a peak dominant frequency of about 1.4 kHz. This call usually presents amplitude modulation, with decreasing intensity along the sequence of notes. The release call is a simple unpulsed note with an average duration of 9 ms, and peak dominant frequency around 1.8 kHz. Temporal properties presented higher variations than spectral properties at both intra- and inter-individual levels. However, only peak dominant frequency was static at intra-individual level. High variability in temporal properties and lower variations related to spectral ones is usual for anurans; The first set of variables is determined by social environment or temperature, while the second is us…
bibliographic citation: Forti et al. (2018) Current knowledge on bioacoustics of the subfamily Lophyohylinae (Hylidae, Anura) and description of Ocellated treefrog Itapotihyla langsdorffii vocalizations. PeerJ 6:e4813 https://doi.org/10.7717/peerj.4813
date submitted: 2018-02-24
date accepted: 2018-04-30
issued: 2018-05-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Forti
  given name: Lucas Rodriguez
author list: Agent
  family name: Foratto
  given name: Roseli Maria
author list: Agent
  family name: Márquez
  given name: Rafael
author list: Agent
  family name: Pereira
  given name: Vânia Rosa
author list: Agent
  family name: Toledo
  given name: Luís Felipe
doi: 10.7717/peerj.4813
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-31
copyright: ©2018 Forti et al.
attribution name: Forti et al.

The smallest biggest theropod dinosaur: a tiny pedal ungual of a juvenile Spinosaurus from the Cretaceous of Morocco
type: item
type: AcademicArticle
description: We describe a nearly complete pedal ungual phalanx, discovered in the Kem Kem Beds (Cenomanian) of Tafilalt region, south-eastern Morocco. The bone is symmetric, pointed, low, elongate, and almost flat ventrally in lateral aspect. This peculiar morphology allows to refer the specimen to the smallest known individual of the genus Spinosaurus. The bone belongs to an early juvenile individual and it is proportionally identical to the ungual of the third digit of a large partial skeleton recently found, suggesting an isometric growth for this part of the pes and the retention of peculiar locomotor adaptations—such as traversing soft substrates or paddling—during the entire lifespan.
format: application/pdf
format: text/html
creator: Simone Maganuco
creator: Cristiano Dal Sasso
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.4785
publisher: PeerJ Inc.
rights: © 2018 Maganuco et al.
abstract: We describe a nearly complete pedal ungual phalanx, discovered in the Kem Kem Beds (Cenomanian) of Tafilalt region, south-eastern Morocco. The bone is symmetric, pointed, low, elongate, and almost flat ventrally in lateral aspect. This peculiar morphology allows to refer the specimen to the smallest known individual of the genus Spinosaurus. The bone belongs to an early juvenile individual and it is proportionally identical to the ungual of the third digit of a large partial skeleton recently found, suggesting an isometric growth for this part of the pes and the retention of peculiar locomotor adaptations—such as traversing soft substrates or paddling—during the entire lifespan.
bibliographic citation: Maganuco et al. (2018) The smallest biggest theropod dinosaur: a tiny pedal ungual of a juvenile Spinosaurus from the Cretaceous of Morocco. PeerJ 6:e4785 https://doi.org/10.7717/peerj.4785
date submitted: 2018-01-08
date accepted: 2018-04-27
issued: 2018-05-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maganuco
  given name: Simone
author list: Agent
  family name: Dal Sasso
  given name: Cristiano
doi: 10.7717/peerj.4785
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-30
copyright: © 2018 Maganuco and Dal Sasso
attribution name: Maganuco et al.

Assessment of the ecotoxicity of urban estuarine sediment using benthic and pelagic copepod bioassays
type: item
type: AcademicArticle
description: Urban estuarine sediments are sinks to a range of contaminants of anthropogenic origin, and a key challenge is to characterize the risk of these compounds to receiving environments. In this study, the toxicity of urban estuarine sediments was tested using acute and chronic bioassays in the benthic harpacticoid Quinquelaophonte sp., and in the planktonic calanoid Gladioferens pectinatus, two New Zealand copepod species. The sediment samples from the estuary tributary sites significantly impacted reproduction in Quinquelaophonte sp. However, results from one of the estuary sites were not significantly different to those from the tributaries sites, suggesting that chemicals other than trace metals, polycyclic aromatic hydrocarbons and ammonia may be the causative stressors. Sediment elutriate samples had significant effects on reproductive endpoints in G. pectinatus, and on the induction of DNA damage in cells, as shown by the comet assay. The results indicate that sediment contamination at the Ahuriri Estuary has the potential to impact biological processes of benthic and pelagic organisms. The approach used provides a standardized methodology to assess the toxicity of estuarine sediments.
format: application/pdf
format: text/html
creator: Maria P. Charry
creator: Vaughan Keesing
creator: Mark Costello
creator: Louis A. Tremblay
subject: Ecology
subject: Marine Biology
subject: Ecotoxicology
subject: Aquatic and Marine Chemistry
subject: Environmental Impacts
description: doi:10.7717/peerj.4936
publisher: PeerJ Inc.
rights: © 2018 Charry et al.
abstract: Urban estuarine sediments are sinks to a range of contaminants of anthropogenic origin, and a key challenge is to characterize the risk of these compounds to receiving environments. In this study, the toxicity of urban estuarine sediments was tested using acute and chronic bioassays in the benthic harpacticoid Quinquelaophonte sp., and in the planktonic calanoid Gladioferens pectinatus, two New Zealand copepod species. The sediment samples from the estuary tributary sites significantly impacted reproduction in Quinquelaophonte sp. However, results from one of the estuary sites were not significantly different to those from the tributaries sites, suggesting that chemicals other than trace metals, polycyclic aromatic hydrocarbons and ammonia may be the causative stressors. Sediment elutriate samples had significant effects on reproductive endpoints in G. pectinatus, and on the induction of DNA damage in cells, as shown by the comet assay. The results indicate that sediment contamination at the Ahuriri Estuary has the potential to impact biological processes of benthic and pelagic organisms. The approach used provides a standardized methodology to assess the toxicity of estuarine sediments.
bibliographic citation: Charry et al. (2018) Assessment of the ecotoxicity of urban estuarine sediment using benthic and pelagic copepod bioassays. PeerJ 6:e4936 https://doi.org/10.7717/peerj.4936
date submitted: 2018-03-07
date accepted: 2018-05-21
issued: 2018-05-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Charry
  given name: Maria P.
author list: Agent
  family name: Keesing
  given name: Vaughan
author list: Agent
  family name: Costello
  given name: Mark
author list: Agent
  family name: Tremblay
  given name: Louis A.
doi: 10.7717/peerj.4936
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-30
copyright: © 2018 Charry et al.
attribution name: Charry et al.

Urbanization alters small rodent community composition but not abundance
type: item
type: AcademicArticle
description: Desert ecosystems are one of the fastest urbanizing areas on the planet. This rapid shift has the potential to alter the abundances and species richness of herbivore and plant communities. Herbivores, for example, are expected to be more abundant within urban desert remnant parks located within cities due to anthropogenic activities that concentrate food resources and reduce native predator populations. Despite this assumption, previous research conducted around Phoenix, AZ, USA has shown that top-down herbivory led to equally reduced plant biomass in both urban and outlying locations. It is unclear if this insignificant difference in herbivory at urban and outlying sites is due to unaltered desert herbivore populations or altered activity levels that counteract abundance differences. Small rodent herbivore/granivore populations were surveyed at four sites inside and four sites outside of the core of Phoenix during fall 2014 and spring 2015 in order to determine whether abundances and richness differ significantly between urban and rural sites. In order to survey species composition and abundance at these sites, 100 Sherman traps and eight larger wire traps that are designed to attract and capture small vertebrates such as mice, rats, and squirrels were set at each site for two consecutive trap nights. Results suggest that the commonly assumed effect of urbanization on herbivore abundances does not apply to small rodent populations in a desert city, as overall small rodent abundances were statistically similar regardless of location. Though a significant difference was not found for species richness, a significant difference between small rodent genus richness at these sites was observed, with altered community composition. The compositional differences likely reflect the altered vegetative community and may impact ecological interactions at these sites.
format: application/pdf
format: text/html
creator: Jessica N. Alvarez Guevara
creator: Becky A. Ball
subject: Biodiversity
subject: Ecology
subject: Environmental Impacts
description: doi:10.7717/peerj.4885
publisher: PeerJ Inc.
rights: © 2018 Alvarez Guevara and Ball
abstract: Desert ecosystems are one of the fastest urbanizing areas on the planet. This rapid shift has the potential to alter the abundances and species richness of herbivore and plant communities. Herbivores, for example, are expected to be more abundant within urban desert remnant parks located within cities due to anthropogenic activities that concentrate food resources and reduce native predator populations. Despite this assumption, previous research conducted around Phoenix, AZ, USA has shown that top-down herbivory led to equally reduced plant biomass in both urban and outlying locations. It is unclear if this insignificant difference in herbivory at urban and outlying sites is due to unaltered desert herbivore populations or altered activity levels that counteract abundance differences. Small rodent herbivore/granivore populations were surveyed at four sites inside and four sites outside of the core of Phoenix during fall 2014 and spring 2015 in order to determine whether abundances and richness differ significantly between urban and rural sites. In order to survey species composition and abundance at these sites, 100 Sherman traps and eight larger wire traps that are designed to attract and capture small vertebrates such as mice, rats, and squirrels were set at each site for two consecutive trap nights. Results suggest that the commonly assumed effect of urbanization on herbivore abundances does not apply to small rodent populations in a desert city, as overall small rodent abundances were statistically similar regardless of location. Though a significant difference was not found for species richness, a significant difference between small rodent genus richness at these sites was observed, with altered community composition. The compositional differences likely reflect the altered vegetative community and may impact ecological interactions at these sites.
bibliographic citation: Alvarez Guevara et al. (2018) Urbanization alters small rodent community composition but not abundance. PeerJ 6:e4885 https://doi.org/10.7717/peerj.4885
date submitted: 2018-01-18
date accepted: 2018-05-12
issued: 2018-05-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alvarez Guevara
  given name: Jessica N.
author list: Agent
  family name: Ball
  given name: Becky A.
doi: 10.7717/peerj.4885
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-30
copyright: ©2018 Alvarez Guevara and Ball
attribution name: Alvarez Guevara and Ball

A new species of spotted leaf frog, genus Phasmahyla (Amphibia, Phyllomedusidae) from Southeast Brazil
type: item
type: AcademicArticle
description: Based on concordant differences in male advertisement call, tadpole morphology, and absence of haplotype sharing in the barcoding 16S mitochondrial DNA, we describe here a new species of spotted leaf frog of the genus Phasmahyla from Atlantic Forest, State of Rio de Janeiro, Southeast Brazil. The new species is most similar to P. cochranae (type locality) and P. spectabilis (type locality). It differs from these species by the size of the calcar, moderate-sized body (snout-vent length 30.4–34.4 mm in adult eight males), and in the advertisement call. The tadpoles of Phasmahyla lisbella sp. nov. differ from P. exilis, P. spectabilis, P. timbo, P. guttata and P. jandaia because they do not have row of teeth in the anterior part; differ from P. cruzi by the shape of the anterior end of the oral disc. Through genetic data (phylogenetic distance and haplotype genealogy) we diagnosed the new species where the genetic divergences among its congeners is about 3–6% in a fragment of the 16S rRNA gene, which is above the threshold typically characterizing distinct species of anurans. However, the new species can be distinguished from other congeneric species based on an integrative approach (molecular, bioacoustics, larval, and adult morphology).
format: application/pdf
format: text/html
creator: Elvis Almeida Pereira
creator: Lucas Custódio Lomba Rocha
creator: Henrique Folly
creator: Hélio Ricardo da Silva
creator: Diego José Santana
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.4900
publisher: PeerJ Inc.
rights: © 2018 Pereira et al.
abstract: Based on concordant differences in male advertisement call, tadpole morphology, and absence of haplotype sharing in the barcoding 16S mitochondrial DNA, we describe here a new species of spotted leaf frog of the genus Phasmahyla from Atlantic Forest, State of Rio de Janeiro, Southeast Brazil. The new species is most similar to P. cochranae (type locality) and P. spectabilis (type locality). It differs from these species by the size of the calcar, moderate-sized body (snout-vent length 30.4–34.4 mm in adult eight males), and in the advertisement call. The tadpoles of Phasmahyla lisbella sp. nov. differ from P. exilis, P. spectabilis, P. timbo, P. guttata and P. jandaia because they do not have row of teeth in the anterior part; differ from P. cruzi by the shape of the anterior end of the oral disc. Through genetic data (phylogenetic distance and haplotype genealogy) we diagnosed the new species where the genetic divergences among its congeners is about 3–6% in a fragment of the 16S rRNA gene, which is above the threshold typically characterizing distinct species of anurans. However, the new species can be distinguished from other congeneric species based on an integrative approach (molecular, bioacoustics, larval, and adult morphology).
bibliographic citation: Pereira et al. (2018) A new species of spotted leaf frog, genus Phasmahyla (Amphibia, Phyllomedusidae) from Southeast Brazil. PeerJ 6:e4900 https://doi.org/10.7717/peerj.4900
date submitted: 2018-03-02
date accepted: 2018-05-14
issued: 2018-05-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pereira
  given name: Elvis Almeida
author list: Agent
  family name: Rocha
  given name: Lucas Custódio Lomba
author list: Agent
  family name: Folly
  given name: Henrique
author list: Agent
  family name: da Silva
  given name: Hélio Ricardo
author list: Agent
  family name: Santana
  given name: Diego José
doi: 10.7717/peerj.4900
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-30
copyright: © 2018 Pereira et al.
attribution name: Pereira et al.

Top-down and bottom-up controls on southern New England salt marsh crab populations
type: item
type: AcademicArticle
description: Southern New England salt marsh vegetation and habitats are changing rapidly in response to sea-level rise. At the same time, fiddler crab (Uca spp.) distributions have expanded and purple marsh crab (Sesarma reticulatum) grazing on creekbank vegetation has increased. Sea-level rise and reduced predation pressure drive these changing crab populations but most studies focus on one species; there is a need for community-level assessments of impacts from multiple crab species. There is also a need to identify additional factors that can affect crab populations. We sampled crabs and environmental parameters in four Rhode Island salt marshes in 2014 and compiled existing data to quantify trends in crab abundance and multiple factors that potentially affect crabs. Crab communities were dominated by fiddler and green crabs (Carcinus maenas); S. reticulatum was much less abundant. Burrow sizes suggest that Uca is responsible for most burrows. On the marsh platform, burrows and Carcinus abundance were negatively correlated with elevation, soil moisture, and soil percent organic matter and positively correlated with soil bulk density. Uca abundance was negatively correlated with Spartina patens cover and height and positively correlated with Spartina alterniflora cover and soil shear strength. Creekbank burrow density increased dramatically between 1998 and 2016. During the same time, fishing effort and the abundance of birds that prey on crabs decreased, and water levels increased. Unlike in other southern New England marshes where recreational overfishing is hypothesized to drive increasing marsh crab abundance, we propose that changes in crab abundance were likely unrelated to recreational finfish over-harvest; instead, they better track sea-level rise and changing abundances of alternate predators, such as birds. We predict that marsh crab abundance will continue to expand with ongoing sea-level rise, at least until inundation thresholds for crab survival are exceeded.
format: application/pdf
format: text/html
creator: Kenneth B. Raposa
creator: Richard A. McKinney
creator: Cathleen Wigand
creator: Jeffrey W. Hollister
creator: Cassie Lovall
creator: Katelyn Szura
creator: John A. Gurak, Jr.
creator: Jason McNamee
creator: Christopher Raithel
creator: Elizabeth B. Watson
subject: Ecology
subject: Marine Biology
subject: Climate Change Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.4876
publisher: PeerJ Inc.
rights: © 2018 Raposa et al.
abstract: Southern New England salt marsh vegetation and habitats are changing rapidly in response to sea-level rise. At the same time, fiddler crab (Uca spp.) distributions have expanded and purple marsh crab (Sesarma reticulatum) grazing on creekbank vegetation has increased. Sea-level rise and reduced predation pressure drive these changing crab populations but most studies focus on one species; there is a need for community-level assessments of impacts from multiple crab species. There is also a need to identify additional factors that can affect crab populations. We sampled crabs and environmental parameters in four Rhode Island salt marshes in 2014 and compiled existing data to quantify trends in crab abundance and multiple factors that potentially affect crabs. Crab communities were dominated by fiddler and green crabs (Carcinus maenas); S. reticulatum was much less abundant. Burrow sizes suggest that Uca is responsible for most burrows. On the marsh platform, burrows and Carcinus abundance were negatively correlated with elevation, soil moisture, and soil percent organic matter and positively correlated with soil bulk density. Uca abundance was negatively correlated with Spartina patens cover and height and positively correlated with Spartina alterniflora cover and soil shear strength. Creekbank burrow density increased dramatically between 1998 and 2016. During the same time, fishing effort and the abundance of birds that prey on crabs decreased, and water levels increased. Unlike in other southern New England marshes where recreational overfishing is hypothesized to drive increasing marsh crab abundance, we propose that changes in crab abundance were likely unrelated to recreational finfish over-harvest; instead, they better track sea-level rise and changing abundances of alternate predators, such as birds. We predict that marsh crab abundance will continue to expand with ongoing sea-level rise, at least until inundation thresholds for crab survival are exceeded.
bibliographic citation: Raposa et al. (2018) Top-down and bottom-up controls on southern New England salt marsh crab populations. PeerJ 6:e4876 https://doi.org/10.7717/peerj.4876
date submitted: 2017-12-22
date accepted: 2018-05-10
issued: 2018-05-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Raposa
  given name: Kenneth B.
author list: Agent
  family name: McKinney
  given name: Richard A.
author list: Agent
  family name: Wigand
  given name: Cathleen
author list: Agent
  family name: Hollister
  given name: Jeffrey W.
author list: Agent
  family name: Lovall
  given name: Cassie
author list: Agent
  family name: Szura
  given name: Katelyn
author list: Agent
  family name: Gurak, Jr.
  given name: John A.
author list: Agent
  family name: McNamee
  given name: Jason
author list: Agent
  family name: Raithel
  given name: Christopher
author list: Agent
  family name: Watson
  given name: Elizabeth B.
doi: 10.7717/peerj.4876
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-30
copyright: ©2018 Raposa et al.
attribution name: Raposa et al.

Multi-dimensional Precision Livestock Farming: a potential toolbox for sustainable rangeland management
type: item
type: AcademicArticle
description: Background Precision Livestock Farming (PLF) is a promising approach to minimize the conflicts between socio-economic activities and landscape conservation. However, its application on extensive systems of livestock production can be challenging. The main difficulties arise because animals graze on large natural pastures where they are exposed to competition with wild herbivores for heterogeneous and scarce resources, predation risk, adverse weather, and complex topography. Considering that the 91% of the world’s surface devoted to livestock production is composed of extensive systems (i.e., rangelands), our general aim was to develop a PLF methodology that quantifies: (i) detailed behavioural patterns, (ii) feeding rate, and (iii) costs associated with different behaviours and landscape traits. Methods For this, we used Merino sheep in Patagonian rangelands as a case study. We combined data from an animal-attached multi-sensor tag (tri-axial acceleration, tri-axial magnetometry, temperature sensor and Global Positioning System) with landscape layers from a Geographical Information System to acquire data. Then, we used high accuracy decision trees, dead reckoning methods and spatial data processing techniques to show how this combination of tools could be used to assess energy balance, predation risk and competition experienced by livestock through time and space. Results The combination of methods proposed here are a useful tool to assess livestock behaviour and the different factors that influence extensive livestock production, such as topography, environmental temperature, predation risk and competition for heterogeneous resources. We were able to quantify feeding rate continuously through time and space with high accuracy and show how it could be used to estimate animal production and the intensity of grazing on the landscape. We also assessed the effects of resource heterogeneity (inferred through search times), and the potential costs associated with predatio…
format: application/pdf
format: text/html
creator: Agustina di Virgilio
creator: Juan M. Morales
creator: Sergio A. Lambertucci
creator: Emily L.C. Shepard
creator: Rory P. Wilson
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.4867
publisher: PeerJ Inc.
rights: © 2018 di Virgilio et al.
abstract: Background Precision Livestock Farming (PLF) is a promising approach to minimize the conflicts between socio-economic activities and landscape conservation. However, its application on extensive systems of livestock production can be challenging. The main difficulties arise because animals graze on large natural pastures where they are exposed to competition with wild herbivores for heterogeneous and scarce resources, predation risk, adverse weather, and complex topography. Considering that the 91% of the world’s surface devoted to livestock production is composed of extensive systems (i.e., rangelands), our general aim was to develop a PLF methodology that quantifies: (i) detailed behavioural patterns, (ii) feeding rate, and (iii) costs associated with different behaviours and landscape traits. Methods For this, we used Merino sheep in Patagonian rangelands as a case study. We combined data from an animal-attached multi-sensor tag (tri-axial acceleration, tri-axial magnetometry, temperature sensor and Global Positioning System) with landscape layers from a Geographical Information System to acquire data. Then, we used high accuracy decision trees, dead reckoning methods and spatial data processing techniques to show how this combination of tools could be used to assess energy balance, predation risk and competition experienced by livestock through time and space. Results The combination of methods proposed here are a useful tool to assess livestock behaviour and the different factors that influence extensive livestock production, such as topography, environmental temperature, predation risk and competition for heterogeneous resources. We were able to quantify feeding rate continuously through time and space with high accuracy and show how it could be used to estimate animal production and the intensity of grazing on the landscape. We also assessed the effects of resource heterogeneity (inferred through search times), and the potential costs associated with predatio…
bibliographic citation: di Virgilio et al. (2018) Multi-dimensional Precision Livestock Farming: a potential toolbox for sustainable rangeland management. PeerJ 6:e4867 https://doi.org/10.7717/peerj.4867
date submitted: 2018-01-24
date accepted: 2018-05-09
issued: 2018-05-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: di Virgilio
  given name: Agustina
author list: Agent
  family name: Morales
  given name: Juan M.
author list: Agent
  family name: Lambertucci
  given name: Sergio A.
author list: Agent
  family name: Shepard
  given name: Emily L.C.
author list: Agent
  family name: Wilson
  given name: Rory P.
doi: 10.7717/peerj.4867
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-30
copyright: ©2018 di Virgilio et al.
attribution name: di Virgilio et al.

Characterization of tumor heterogeneity by latent haplotypes: a sequential Monte Carlo approach
type: item
type: AcademicArticle
description: Tumor samples obtained from a single cancer patient spatially or temporally often consist of varying cell populations, each harboring distinct mutations that uniquely characterize its genome. Thus, in any given samples of a tumor having more than two haplotypes, defined as a scaffold of single nucleotide variants (SNVs) on the same homologous genome, is evidence of heterogeneity because humans are diploid and we would therefore only observe up to two haplotypes if all cells in a tumor sample were genetically homogeneous. We characterize tumor heterogeneity by latent haplotypes and present state-space formulation of the feature allocation model for estimating the haplotypes and their proportions in the tumor samples. We develop an efficient sequential Monte Carlo (SMC) algorithm that estimates the states and the parameters of our proposed state-space model, which are equivalently the haplotypes and their proportions in the tumor samples. The sequential algorithm produces more accurate estimates of the model parameters when compared with existing methods. Also, because our algorithm processes the variant allele frequency (VAF) of a locus as the observation at a single time-step, VAF from newly sequenced candidate SNVs from next-generation sequencing (NGS) can be analyzed to improve existing estimates without re-analyzing the previous datasets, a feature that existing solutions do not possess.
format: application/pdf
format: text/html
creator: Oyetunji E. Ogundijo
creator: Xiaodong Wang
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.4838
publisher: PeerJ Inc.
rights: © 2018 Ogundijo and Wang
abstract: Tumor samples obtained from a single cancer patient spatially or temporally often consist of varying cell populations, each harboring distinct mutations that uniquely characterize its genome. Thus, in any given samples of a tumor having more than two haplotypes, defined as a scaffold of single nucleotide variants (SNVs) on the same homologous genome, is evidence of heterogeneity because humans are diploid and we would therefore only observe up to two haplotypes if all cells in a tumor sample were genetically homogeneous. We characterize tumor heterogeneity by latent haplotypes and present state-space formulation of the feature allocation model for estimating the haplotypes and their proportions in the tumor samples. We develop an efficient sequential Monte Carlo (SMC) algorithm that estimates the states and the parameters of our proposed state-space model, which are equivalently the haplotypes and their proportions in the tumor samples. The sequential algorithm produces more accurate estimates of the model parameters when compared with existing methods. Also, because our algorithm processes the variant allele frequency (VAF) of a locus as the observation at a single time-step, VAF from newly sequenced candidate SNVs from next-generation sequencing (NGS) can be analyzed to improve existing estimates without re-analyzing the previous datasets, a feature that existing solutions do not possess.
bibliographic citation: Ogundijo et al. (2018) Characterization of tumor heterogeneity by latent haplotypes: a sequential Monte Carlo approach. PeerJ 6:e4838 https://doi.org/10.7717/peerj.4838
date submitted: 2018-02-12
date accepted: 2018-05-02
issued: 2018-05-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ogundijo
  given name: Oyetunji E.
author list: Agent
  family name: Wang
  given name: Xiaodong
doi: 10.7717/peerj.4838
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-30
copyright: ©2018 Ogundijo and Wang
attribution name: Ogundijo and Wang

Potent antibacterial, antioxidant and toxic activities of extracts from Passiflora suberosa L. leaves
type: item
type: AcademicArticle
description: Passiflora suberosa L. belonging to the family Passifloraceae is an important medicinal plant used in traditional medicinal system in Sri Lanka to treat diabetes, hypertension and skin diseases. We extracted P. suberosa leaves under reflux conditions using different solvents (hexane, chloroform, methanol and water), then subjected to phytochemical screening. Alkaloids, flavonoids and saponins and saponins and anthraquinones were present in hexane and chloroform extracts. Alkaloids, unsaturated sterols, triterpenes, saponins, flavonoids and tannins were observed in both methanol and aqueous extracts. Proanthocyanidins were observed only in the aqueous extract. Hence, aqueous and methanol extracts with most classes of phytochemicals present were subjected to antimicrobial, antioxidant, antihaemolytic activities and Brine shrimp lethality studies. Antibacterial activity and minimum inhibition concentrations were evaluated using three Gram-positive (Bacillus subtilis, Staphylococcus aureus and Enterococcus faecium) and three Gram-negative bacteria (Pseudumonas aeruginosa, Salmonella typhimuriam and Escherichia coli). The results indicated that only the methanol extract of P. suberosa exhibited antibacterial activities against all the strains of Gram-negative and Gram-positive bacterial with stronger activity against Gram-negative bacteria. DPHH (2,2-diphenyl-1-picrylhydrazy) scavenging assay was adopted to evaluate antioxidant properties while antihaemolytic and toxic activities were studied respectively using cow blood and Brine shrimp lethality assay. The IC50 values of the aqueous extract in both antioxidant and antihaemolytic assays were significantly lower than the standard ascorbic acid. Similar results were observed in the Brine shrimp lethality assay. In conclusion both aqueous and methanol extracts of P. suberosa leaves showed the presence of majority of phytochemicals including proanthocyanidins. Antibacterial activity was obtained only for methanol extract wi…
format: application/pdf
format: text/html
creator: Kumudu R.V. Bandara
creator: Chayanika Padumadasa
creator: Dinithi C. Peiris
subject: Microbiology
subject: Plant Science
subject: Pharmacology
description: doi:10.7717/peerj.4804
publisher: PeerJ Inc.
rights: © 2018 Bandara et al.
abstract: Passiflora suberosa L. belonging to the family Passifloraceae is an important medicinal plant used in traditional medicinal system in Sri Lanka to treat diabetes, hypertension and skin diseases. We extracted P. suberosa leaves under reflux conditions using different solvents (hexane, chloroform, methanol and water), then subjected to phytochemical screening. Alkaloids, flavonoids and saponins and saponins and anthraquinones were present in hexane and chloroform extracts. Alkaloids, unsaturated sterols, triterpenes, saponins, flavonoids and tannins were observed in both methanol and aqueous extracts. Proanthocyanidins were observed only in the aqueous extract. Hence, aqueous and methanol extracts with most classes of phytochemicals present were subjected to antimicrobial, antioxidant, antihaemolytic activities and Brine shrimp lethality studies. Antibacterial activity and minimum inhibition concentrations were evaluated using three Gram-positive (Bacillus subtilis, Staphylococcus aureus and Enterococcus faecium) and three Gram-negative bacteria (Pseudumonas aeruginosa, Salmonella typhimuriam and Escherichia coli). The results indicated that only the methanol extract of P. suberosa exhibited antibacterial activities against all the strains of Gram-negative and Gram-positive bacterial with stronger activity against Gram-negative bacteria. DPHH (2,2-diphenyl-1-picrylhydrazy) scavenging assay was adopted to evaluate antioxidant properties while antihaemolytic and toxic activities were studied respectively using cow blood and Brine shrimp lethality assay. The IC50 values of the aqueous extract in both antioxidant and antihaemolytic assays were significantly lower than the standard ascorbic acid. Similar results were observed in the Brine shrimp lethality assay. In conclusion both aqueous and methanol extracts of P. suberosa leaves showed the presence of majority of phytochemicals including proanthocyanidins. Antibacterial activity was obtained only for methanol extract wi…
bibliographic citation: Bandara et al. (2018) Potent antibacterial, antioxidant and toxic activities of extracts from Passiflora suberosa L. leaves. PeerJ 6:e4804 https://doi.org/10.7717/peerj.4804
date submitted: 2018-02-27
date accepted: 2018-04-29
issued: 2018-05-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bandara
  given name: Kumudu R.V.
author list: Agent
  family name: Padumadasa
  given name: Chayanika
author list: Agent
  family name: Peiris
  given name: Dinithi C.
doi: 10.7717/peerj.4804
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-30
copyright: ©2018 Bandara et al.
attribution name: Bandara et al.

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