PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Post-fledging habitat use in a declining songbird
items: Echinoids from the Tesero Member (Werfen Formation) of the Dolomites (Italy): implications for extinction and survival of echinoids in the aftermath of the end-Permian mass extinction
items: Age, growth, reproduction and management of Southwestern Atlantic’s largest and endangered herbivorous reef fish, Scarus trispinosus Valenciennes, 1840
items: The adipokinetic hormones and their cognate receptor from the desert locust, Schistocerca gregaria: solution structure of endogenous peptides and models of their binding to the receptor
items: Expansion of sandhill cranes (Grus canadensis) in east Asia during the non-breeding period
items: Sargassum blooms in the Caribbean alter the trophic structure of the sea urchin Diadema antillarum
items: The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene
items: Two salamander species respond differently to timber harvests in a managed New England forest
items: Comparative and evolutionary analysis of the reptilian hedgehog gene family (Shh, Dhh, and Ihh)
items: Microbial community dynamics during aerobic granulation in a sequencing batch reactor (SBR)

Post-fledging habitat use in a declining songbird
type: item
type: AcademicArticle
description: Background Fledglings of many mature forest-dependent Neotropical songbirds move from mature forest habitats into areas of thick vegetation such as regenerating clearcuts. The Cerulean Warbler (Setophaga cerulea), a Neotropical migratory songbird, is a species of conservation concern across its range and it is listed as endangered in Indiana. This species has declined faster than any other species of wood-warbler in North America. Most prior research on Cerulean Warblers has examined the breeding biology, but there are no data on habitat use by fledgling Cerulean Warblers. Our research aimed to determine where fledgling Cerulean Warblers dispersed after they left their nest, but before they migrated to their wintering grounds. Methods Since 2007, Cerulean Warbler breeding populations have been monitored in Yellowwood and Morgan–Monroe state forests in southern Indiana as part of a 100-year study called the Hardwood Ecosystem Experiment. To identify habitats used by fledgling Cerulean Warblers, we captured by hand or mist-nets, adult and juvenile Cerulean Warblers once young had fledged from a nest. We attached radio-transmitters to individuals and tracked each bird daily using radio-telemetry. Radio-telemetry data were collected from May to July 2015–2017, and microhabitat data on fledgling locations and random locations were collected during the same years in the month of July. Results Fledgling presence, when compared to random non-use sites, was positively correlated to presence of grapevines, greater vertical vegetation density, and greater ground and canopy cover. Fledgling presence was negatively correlated with white oak abundance, aspect, basal area, and the abundance of mature trees that Cerulean Warbler adults use for nesting. Conclusions Our study is the first to demonstrate that Cerulean Warbler fledglings occupy habitats that are characterized by specific habitat components. Fledgling sites were located in areas with high vegetation density, such as clu…
format: application/pdf
format: text/html
creator: Clayton D. Delancey
creator: Kamal Islam
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.7358
publisher: PeerJ Inc.
rights: © 2019 Delancey and Islam
abstract: Background Fledglings of many mature forest-dependent Neotropical songbirds move from mature forest habitats into areas of thick vegetation such as regenerating clearcuts. The Cerulean Warbler (Setophaga cerulea), a Neotropical migratory songbird, is a species of conservation concern across its range and it is listed as endangered in Indiana. This species has declined faster than any other species of wood-warbler in North America. Most prior research on Cerulean Warblers has examined the breeding biology, but there are no data on habitat use by fledgling Cerulean Warblers. Our research aimed to determine where fledgling Cerulean Warblers dispersed after they left their nest, but before they migrated to their wintering grounds. Methods Since 2007, Cerulean Warbler breeding populations have been monitored in Yellowwood and Morgan–Monroe state forests in southern Indiana as part of a 100-year study called the Hardwood Ecosystem Experiment. To identify habitats used by fledgling Cerulean Warblers, we captured by hand or mist-nets, adult and juvenile Cerulean Warblers once young had fledged from a nest. We attached radio-transmitters to individuals and tracked each bird daily using radio-telemetry. Radio-telemetry data were collected from May to July 2015–2017, and microhabitat data on fledgling locations and random locations were collected during the same years in the month of July. Results Fledgling presence, when compared to random non-use sites, was positively correlated to presence of grapevines, greater vertical vegetation density, and greater ground and canopy cover. Fledgling presence was negatively correlated with white oak abundance, aspect, basal area, and the abundance of mature trees that Cerulean Warbler adults use for nesting. Conclusions Our study is the first to demonstrate that Cerulean Warbler fledglings occupy habitats that are characterized by specific habitat components. Fledgling sites were located in areas with high vegetation density, such as clu…
bibliographic citation: Delancey et al. (2019) Post-fledging habitat use in a declining songbird. PeerJ 7:e7358 https://doi.org/10.7717/peerj.7358
date submitted: 2019-02-13
date accepted: 2019-06-26
issued: 2019-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Delancey
  given name: Clayton D.
author list: Agent
  family name: Islam
  given name: Kamal
doi: 10.7717/peerj.7358
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-30
copyright: ©2019 Delancey and Islam
attribution name: Delancey and Islam

Echinoids from the Tesero Member (Werfen Formation) of the Dolomites (Italy): implications for extinction and survival of echinoids in the aftermath of the end-Permian mass extinction
type: item
type: AcademicArticle
description: The end-Permian mass extinction (∼252 Ma) was responsible for high rates of extinction and evolutionary bottlenecks in a number of animal groups. Echinoids, or sea urchins, were no exception, and the Permian to Triassic represents one of the most significant intervals of time in their macroevolutionary history. The extinction event was responsible for significant turnover, with the Permian–Triassic representing the transition from stem group echinoid-dominated faunas in the Palaeozoic to Mesozoic faunas dominated by crown group echinoids. This turnover is well-known, however, the environmental and taxonomic distribution of echinoids during the latest Permian and Early Triassic is not. Here we report on an echinoid fauna from the Tesero Member, Werfen Formation (latest Permian to Early Triassic) of the Dolomites (northern Italy). The fauna is largely known from disarticulated ossicles, but consists of both stem group taxa, and a new species of crown group echinoid, Eotiaris teseroensis n. sp. That these stem group echinoids were present in the Tesero Member indicates that stem group echinoids did not go extinct in the Dolomites coincident with the onset of extinction, further supporting other recent work indicating that stem group echinoids survived the end-Permian extinction. Furthermore, the presence of Eotiaris across a number of differing palaeoenvironments in the Early Triassic may have had implications for the survival of cidaroid echinoids during the extinction event.
format: application/pdf
format: text/html
creator: Jeffrey R. Thompson
creator: Renato Posenato
creator: David J. Bottjer
creator: Elizabeth Petsios
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Biosphere Interactions
description: doi:10.7717/peerj.7361
publisher: PeerJ Inc.
rights: © 2019 Thompson et al.
abstract: The end-Permian mass extinction (∼252 Ma) was responsible for high rates of extinction and evolutionary bottlenecks in a number of animal groups. Echinoids, or sea urchins, were no exception, and the Permian to Triassic represents one of the most significant intervals of time in their macroevolutionary history. The extinction event was responsible for significant turnover, with the Permian–Triassic representing the transition from stem group echinoid-dominated faunas in the Palaeozoic to Mesozoic faunas dominated by crown group echinoids. This turnover is well-known, however, the environmental and taxonomic distribution of echinoids during the latest Permian and Early Triassic is not. Here we report on an echinoid fauna from the Tesero Member, Werfen Formation (latest Permian to Early Triassic) of the Dolomites (northern Italy). The fauna is largely known from disarticulated ossicles, but consists of both stem group taxa, and a new species of crown group echinoid, Eotiaris teseroensis n. sp. That these stem group echinoids were present in the Tesero Member indicates that stem group echinoids did not go extinct in the Dolomites coincident with the onset of extinction, further supporting other recent work indicating that stem group echinoids survived the end-Permian extinction. Furthermore, the presence of Eotiaris across a number of differing palaeoenvironments in the Early Triassic may have had implications for the survival of cidaroid echinoids during the extinction event.
bibliographic citation: Thompson et al. (2019) Echinoids from the Tesero Member (Werfen Formation) of the Dolomites (Italy): implications for extinction and survival of echinoids in the aftermath of the end-Permian mass extinction. PeerJ 7:e7361 https://doi.org/10.7717/peerj.7361
date submitted: 2019-01-17
date accepted: 2019-06-27
issued: 2019-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thompson
  given name: Jeffrey R.
author list: Agent
  family name: Posenato
  given name: Renato
author list: Agent
  family name: Bottjer
  given name: David J.
author list: Agent
  family name: Petsios
  given name: Elizabeth
doi: 10.7717/peerj.7361
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-30
copyright: ©2019 Thompson et al.
attribution name: Thompson et al.

Age, growth, reproduction and management of Southwestern Atlantic’s largest and endangered herbivorous reef fish, Scarus trispinosus Valenciennes, 1840
type: item
type: AcademicArticle
description: The Brazilian-endemic greenbeack parrotfish, Scarus trispinosus Valenciennes, 1840, is the largest herbivorous reef fish in the South Atlantic. Following the sharp decline of large carnivorous reef fishes, parrotfishes (Labridae: Scarinae) were progressively targeted by commercial fisheries in Brazil, resulting in a global population decline of 50% for S. trispinosus. Most of its remnant population is concentrated in the Abrolhos Bank, where the present study was conducted. We present novel information on age, growth and the reproductive cycle of S. trispinosus, based on 814 individuals obtained from commercial fisheries’ landings and scientific collections, between 2010 and 2013. Sex ratio was biased toward females (1:8), and spawning occurred year-round with discrete peaks in February-March and June-December. Increment analysis indicated annual deposition of growth rings in otoliths, which presented 1–22 rings. The asymptotic length at which growth is zero (L∞) was estimated from a Bayesian logistic regression at 85.28 cm, growth rate (K) at 0.14 year−1, and the theoretical age at zero size (t0) at 0.16. Subregional demographic structuring was detected, with predominance of slower-growing individuals in shallower inshore reefs and predominance of faster-growing and older individuals in deeper offshore sites. We demonstrate that S. trispinosus is highly vulnerable to over-exploitation due to its large size, long live and slow-growth, and review the management measures proposed since its Red List assessment in 2012.
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format: text/html
creator: Matheus O. Freitas
creator: Marília Previero
creator: Jonas R. Leite
creator: Ronaldo B. Francini-Filho
creator: Carolina V. Minte-Vera
creator: Rodrigo L. Moura
subject: Ecology
subject: Environmental Impacts
subject: Biological Oceanography
description: doi:10.7717/peerj.7459
publisher: PeerJ Inc.
rights: © 2019 Freitas et al.
abstract: The Brazilian-endemic greenbeack parrotfish, Scarus trispinosus Valenciennes, 1840, is the largest herbivorous reef fish in the South Atlantic. Following the sharp decline of large carnivorous reef fishes, parrotfishes (Labridae: Scarinae) were progressively targeted by commercial fisheries in Brazil, resulting in a global population decline of 50% for S. trispinosus. Most of its remnant population is concentrated in the Abrolhos Bank, where the present study was conducted. We present novel information on age, growth and the reproductive cycle of S. trispinosus, based on 814 individuals obtained from commercial fisheries’ landings and scientific collections, between 2010 and 2013. Sex ratio was biased toward females (1:8), and spawning occurred year-round with discrete peaks in February-March and June-December. Increment analysis indicated annual deposition of growth rings in otoliths, which presented 1–22 rings. The asymptotic length at which growth is zero (L∞) was estimated from a Bayesian logistic regression at 85.28 cm, growth rate (K) at 0.14 year−1, and the theoretical age at zero size (t0) at 0.16. Subregional demographic structuring was detected, with predominance of slower-growing individuals in shallower inshore reefs and predominance of faster-growing and older individuals in deeper offshore sites. We demonstrate that S. trispinosus is highly vulnerable to over-exploitation due to its large size, long live and slow-growth, and review the management measures proposed since its Red List assessment in 2012.
bibliographic citation: Freitas et al. (2019) Age, growth, reproduction and management of Southwestern Atlantic’s largest and endangered herbivorous reef fish, Scarus trispinosus Valenciennes, 1840. PeerJ 7:e7459 https://doi.org/10.7717/peerj.7459
date submitted: 2018-04-18
date accepted: 2019-07-11
issued: 2019-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Freitas
  given name: Matheus O.
author list: Agent
  family name: Previero
  given name: Marília
author list: Agent
  family name: Leite
  given name: Jonas R.
author list: Agent
  family name: Francini-Filho
  given name: Ronaldo B.
author list: Agent
  family name: Minte-Vera
  given name: Carolina V.
author list: Agent
  family name: Moura
  given name: Rodrigo L.
doi: 10.7717/peerj.7459
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-30
copyright: ©2019 Freitas et al.
attribution name: Freitas et al.

The adipokinetic hormones and their cognate receptor from the desert locust, Schistocerca gregaria: solution structure of endogenous peptides and models of their binding to the receptor
type: item
type: AcademicArticle
description: Background Neuropeptides exert their activity through binding to G protein-coupled receptors (GPCRs). GPCRs are well-known drug targets in the pharmaceutical industry and are currently discussed as targets to control pest insects. Here, we investigate the neuropeptide adipokinetic hormone (AKH) system of the desert locust Schistocerca gregaria. The desert locust is known for its high reproduction, and for forming devastating swarms consisting of billions of individual insects. It is also known that S. gregaria produces three different AKHs as ligands but has only one AKH receptor (AKHR). The AKH system is known to be essential for metabolic regulation, which is necessary for reproduction and flight activity. Methods Nuclear magnetic resonance techniques (NMR) in a dodecylphosphocholin (DPC) micelle solution were used to determine the structure of the three AKHs. The primary sequence of the S. gregaria AKHR was used to construct a 3D molecular model. Next, the three AKHs were individually docked to the receptor, and dynamic simulation of the whole ligand–receptor complex in a model membrane was performed. Results Although the three endogenous AKHs of S. gregaria have quite different amino acids sequences and chain length (two octa- and one decapeptide), NMR experiments assigned a turn structure in DPC micelle solution for all. The GPCR-ModSim program identified human kappa opioid receptor to be the best template after which the S. gregaria AKHR was modeled. All three AKHs were found to have the same binding site on this receptor, interact with similar residues of the receptor and have comparable binding constants. Molecular switches were also identified; the movement of the receptor could be visually shown when ligands (AKHs) were docked and the receptor was activated. Conclusions The study proposes a model of binding of the three endogenous ligands to the one existing AKHR in the desert locust and paves the way to use such a model for the design of peptide analogs a…
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creator: Graham E. Jackson
creator: Elumalai Pavadai
creator: Gerd Gäde
creator: Niels H. Andersen
subject: Computational Biology
subject: Entomology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.7514
publisher: PeerJ Inc.
rights: © 2019 Jackson et al.
abstract: Background Neuropeptides exert their activity through binding to G protein-coupled receptors (GPCRs). GPCRs are well-known drug targets in the pharmaceutical industry and are currently discussed as targets to control pest insects. Here, we investigate the neuropeptide adipokinetic hormone (AKH) system of the desert locust Schistocerca gregaria. The desert locust is known for its high reproduction, and for forming devastating swarms consisting of billions of individual insects. It is also known that S. gregaria produces three different AKHs as ligands but has only one AKH receptor (AKHR). The AKH system is known to be essential for metabolic regulation, which is necessary for reproduction and flight activity. Methods Nuclear magnetic resonance techniques (NMR) in a dodecylphosphocholin (DPC) micelle solution were used to determine the structure of the three AKHs. The primary sequence of the S. gregaria AKHR was used to construct a 3D molecular model. Next, the three AKHs were individually docked to the receptor, and dynamic simulation of the whole ligand–receptor complex in a model membrane was performed. Results Although the three endogenous AKHs of S. gregaria have quite different amino acids sequences and chain length (two octa- and one decapeptide), NMR experiments assigned a turn structure in DPC micelle solution for all. The GPCR-ModSim program identified human kappa opioid receptor to be the best template after which the S. gregaria AKHR was modeled. All three AKHs were found to have the same binding site on this receptor, interact with similar residues of the receptor and have comparable binding constants. Molecular switches were also identified; the movement of the receptor could be visually shown when ligands (AKHs) were docked and the receptor was activated. Conclusions The study proposes a model of binding of the three endogenous ligands to the one existing AKHR in the desert locust and paves the way to use such a model for the design of peptide analogs a…
bibliographic citation: Jackson et al. (2019) The adipokinetic hormones and their cognate receptor from the desert locust, Schistocerca gregaria: solution structure of endogenous peptides and models of their binding to the receptor. PeerJ 7:e7514 https://doi.org/10.7717/peerj.7514
date submitted: 2019-04-05
date accepted: 2019-07-18
issued: 2019-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jackson
  given name: Graham E.
author list: Agent
  family name: Pavadai
  given name: Elumalai
author list: Agent
  family name: Gäde
  given name: Gerd
author list: Agent
  family name: Andersen
  given name: Niels H.
doi: 10.7717/peerj.7514
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-30
copyright: © 2019 Jackson et al.
attribution name: Jackson et al.

Expansion of sandhill cranes (Grus canadensis) in east Asia during the non-breeding period
type: item
type: AcademicArticle
description: Aim Historically, the distribution of Sandhill Cranes included much of North America and extending in summer into northeast Russia. In recent years, observations of sandhill cranes in Asia during the non-breeding period have been frequently reported. However, the distribution and abundance of sandhill cranes during the non-breeding period in Asia have rarely been summarized and studied. Our study aimed to analyze the status of sandhill cranes that have spread south into East Asia during the non-breeding period and to assess the possible impacts of their potential spread. Methods Based on opportunistic data collected in the field and occurrence data collected online over the past half century, we used Geographic Information System to visualize the spatial distribution changes and regression analysis to analyze and visualize the changes in the amount of individuals over time. Results In the last 50 years, the distribution of sandhill cranes during the non-breeding season in Asia spanned 31 degrees in longitude to the west and 15 degrees in latitude to the south. Their distribution in Asia has expanded to 17 provinces and municipalities in China, Japan and South Korea. The amount of cranes in the non-breeding period in Asia increased significantly from 1963 to 2017. According to the historical records in East Asia, sandhill cranes were mixed with five other species of crane groups. Main conclusions These results indicate that the range and amount of sandhill cranes have expanded. Sandhill cranes were mixed with five other crane species, which indicate their adaptability to a range of habitat types and food resources. The implications of these trends in sandhill cranes in East Asia for this and other crane species warrants further research.
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creator: Linqiang Gao
creator: Chunrong Mi
creator: Yumin Guo
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.7545
publisher: PeerJ Inc.
rights: © 2019 Gao et al.
abstract: Aim Historically, the distribution of Sandhill Cranes included much of North America and extending in summer into northeast Russia. In recent years, observations of sandhill cranes in Asia during the non-breeding period have been frequently reported. However, the distribution and abundance of sandhill cranes during the non-breeding period in Asia have rarely been summarized and studied. Our study aimed to analyze the status of sandhill cranes that have spread south into East Asia during the non-breeding period and to assess the possible impacts of their potential spread. Methods Based on opportunistic data collected in the field and occurrence data collected online over the past half century, we used Geographic Information System to visualize the spatial distribution changes and regression analysis to analyze and visualize the changes in the amount of individuals over time. Results In the last 50 years, the distribution of sandhill cranes during the non-breeding season in Asia spanned 31 degrees in longitude to the west and 15 degrees in latitude to the south. Their distribution in Asia has expanded to 17 provinces and municipalities in China, Japan and South Korea. The amount of cranes in the non-breeding period in Asia increased significantly from 1963 to 2017. According to the historical records in East Asia, sandhill cranes were mixed with five other species of crane groups. Main conclusions These results indicate that the range and amount of sandhill cranes have expanded. Sandhill cranes were mixed with five other crane species, which indicate their adaptability to a range of habitat types and food resources. The implications of these trends in sandhill cranes in East Asia for this and other crane species warrants further research.
bibliographic citation: Gao et al. (2019) Expansion of sandhill cranes (Grus canadensis) in east Asia during the non-breeding period. PeerJ 7:e7545 https://doi.org/10.7717/peerj.7545
date submitted: 2019-04-07
date accepted: 2019-07-24
issued: 2019-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Linqiang
author list: Agent
  family name: Mi
  given name: Chunrong
author list: Agent
  family name: Guo
  given name: Yumin
doi: 10.7717/peerj.7545
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-30
copyright: ©2019 Gao et al.
attribution name: Gao et al.

Sargassum blooms in the Caribbean alter the trophic structure of the sea urchin Diadema antillarum
type: item
type: AcademicArticle
description: The arrival of large masses of drifting Sargassum since 2011 has caused changes in the natural dynamics of Caribbean coastal ecosystems. In the summer of 2015, unprecedented and massive mats of S. fluitans and S. natans have been observed throughout the Mexican Caribbean including exceptional accumulations ashore. This study uses stable isotopes to assess the impact of Sargassum blooms on the trophic dynamics of the Diadema antillarum sea urchin, a keystone herbivore on many Caribbean reefs. Bayesian models were used to estimate the variations in the relative proportions of carbon and nitrogen of assimilated algal resources. At three lagoon reef sites, the niche breadth of D. antillarum was analysed and compared under massive influx of drifting Sargassum spp. vs. no influx of Sargassum blooms. The effects of the leachates generated by the decomposition of Sargassum led to hypoxic conditions on these reefs and reduced the taxonomic diversity of macroalgal food sources available to D. antillarum. Our trophic data support the hypothesis that processes of assimilation of carbon and nitrogen were modified under Sargassum effect. Isotopic signatures of macroalgae associated with the reef sites exhibited significantly lower values of δ15N altering the natural herbivory of D. antillarum. The Stable Isotopes Analysis in R (SIAR) indicated that, under the influence of Sargassum blooms, certain algal resources (Dictyota, Halimeda and Udotea) were more assimilated due to a reduction in available algal resources. Despite being an abundant available resource, pelagic Sargassum was a negligible contributor to sea urchin diet. The Stable Isotope Bayesian Ellipses in R (SIBER) analysis displayed differences between sites, and suggests a reduction in trophic niche breadth, particularly in a protected reef lagoon. Our findings reveal that Sargassum blooms caused changes in trophic characteristics of D. antillarum with a negative impact by hypoxic conditions. These dynamics, coupled wi…
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format: text/html
creator: Nancy Cabanillas-Terán
creator: Héctor A. Hernández-Arana
creator: Miguel-Ángel Ruiz-Zárate
creator: Alejandro Vega-Zepeda
creator: Alberto Sanchez-Gonzalez
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.7589
publisher: PeerJ Inc.
rights: © 2019 Cabanillas-Terán et al.
abstract: The arrival of large masses of drifting Sargassum since 2011 has caused changes in the natural dynamics of Caribbean coastal ecosystems. In the summer of 2015, unprecedented and massive mats of S. fluitans and S. natans have been observed throughout the Mexican Caribbean including exceptional accumulations ashore. This study uses stable isotopes to assess the impact of Sargassum blooms on the trophic dynamics of the Diadema antillarum sea urchin, a keystone herbivore on many Caribbean reefs. Bayesian models were used to estimate the variations in the relative proportions of carbon and nitrogen of assimilated algal resources. At three lagoon reef sites, the niche breadth of D. antillarum was analysed and compared under massive influx of drifting Sargassum spp. vs. no influx of Sargassum blooms. The effects of the leachates generated by the decomposition of Sargassum led to hypoxic conditions on these reefs and reduced the taxonomic diversity of macroalgal food sources available to D. antillarum. Our trophic data support the hypothesis that processes of assimilation of carbon and nitrogen were modified under Sargassum effect. Isotopic signatures of macroalgae associated with the reef sites exhibited significantly lower values of δ15N altering the natural herbivory of D. antillarum. The Stable Isotopes Analysis in R (SIAR) indicated that, under the influence of Sargassum blooms, certain algal resources (Dictyota, Halimeda and Udotea) were more assimilated due to a reduction in available algal resources. Despite being an abundant available resource, pelagic Sargassum was a negligible contributor to sea urchin diet. The Stable Isotope Bayesian Ellipses in R (SIBER) analysis displayed differences between sites, and suggests a reduction in trophic niche breadth, particularly in a protected reef lagoon. Our findings reveal that Sargassum blooms caused changes in trophic characteristics of D. antillarum with a negative impact by hypoxic conditions. These dynamics, coupled wi…
bibliographic citation: Cabanillas-Terán et al. (2019) Sargassum blooms in the Caribbean alter the trophic structure of the sea urchin Diadema antillarum. PeerJ 7:e7589 https://doi.org/10.7717/peerj.7589
date submitted: 2019-03-06
date accepted: 2019-07-30
issued: 2019-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cabanillas-Terán
  given name: Nancy
author list: Agent
  family name: Hernández-Arana
  given name: Héctor A.
author list: Agent
  family name: Ruiz-Zárate
  given name: Miguel-Ángel
author list: Agent
  family name: Vega-Zepeda
  given name: Alejandro
author list: Agent
  family name: Sanchez-Gonzalez
  given name: Alberto
doi: 10.7717/peerj.7589
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-30
copyright: ©2019 Cabanillas-Terán et al.
attribution name: Cabanillas-Terán et al.

The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene
type: item
type: AcademicArticle
description: Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China, and it has become an emerging economic crop that is rapidly developing. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (83,981 bp), and a small single-copy region (18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. A total of 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased toward A/T bases. A total of 32 SSRs were distributed in the non-coding regions. A comparative analysis of the chloroplast genome sequence of the Jerusalem artichoke and other species of the composite family revealed that the chloroplast genome sequences of plants of the composite family were highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. A phylogenetic analysis showed that H. petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in…
format: application/pdf
format: text/html
creator: Qiwen Zhong
creator: Shipeng Yang
creator: Xuemei Sun
creator: Lihui Wang
creator: Yi Li
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.7596
publisher: PeerJ Inc.
rights: © 2019 Zhong et al.
abstract: Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China, and it has become an emerging economic crop that is rapidly developing. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (83,981 bp), and a small single-copy region (18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. A total of 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased toward A/T bases. A total of 32 SSRs were distributed in the non-coding regions. A comparative analysis of the chloroplast genome sequence of the Jerusalem artichoke and other species of the composite family revealed that the chloroplast genome sequences of plants of the composite family were highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. A phylogenetic analysis showed that H. petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in…
bibliographic citation: Zhong et al. (2019) The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene. PeerJ 7:e7596 https://doi.org/10.7717/peerj.7596
date submitted: 2019-02-06
date accepted: 2019-07-31
issued: 2019-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Qiwen
author list: Agent
  family name: Yang
  given name: Shipeng
author list: Agent
  family name: Sun
  given name: Xuemei
author list: Agent
  family name: Wang
  given name: Lihui
author list: Agent
  family name: Li
  given name: Yi
doi: 10.7717/peerj.7596
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-30
copyright: © 2019 Zhong et al.
attribution name: Zhong et al.

Two salamander species respond differently to timber harvests in a managed New England forest
type: item
type: AcademicArticle
description: Background Managing forests for timber while protecting wildlife habitat is of increasing concern. Amphibians may be particularly sensitive to forest management practices due to their unique biology; however, it is not clear how different species respond to timber harvest practices—particularly over longer time scales. Methods Here we report on the differential responses of two salamander species—the eastern red-backed salamander (Plethodon cinereus Green) and the eastern newt (Notophthalmus viridescens Rafinesque)—to forest harvesting, by examining communities across a 25-year chronosequence of regenerating shelterwood harvests. Results Populations of both species were lowest immediately after harvest, but increased at substantially different rates. Red-backed salamander populations were highest in 20–25 year-old shelterwoods—significantly higher than in mature, unharvested, control (100–120 year old) stands. Eastern newt populations, however, were greatest in unharvested control stands and still had not recovered to population levels found in mature stands in the 25 years since harvest. Red-backed salamander abundances were strongly tied to stand age as well as abundance of decayed coarse woody debris, suggesting that timber harvests influence some wildlife species by affecting a suite of interacting habitat variables that change over time. In contrast, newt abundances were not directly related to stand age but were more related to downed wood and vegetation characteristics. Our results highlight markedly variable responses by two common salamander species to forest harvesting—species with markedly different life histories and reproductive patterns—and that time since harvest may be useful in predicting abundance.
format: application/pdf
format: text/html
creator: Angus Mossman
creator: Max R. Lambert
creator: Mark S. Ashton
creator: Jessica Wikle
creator: Marlyse C. Duguid
subject: Conservation Biology
subject: Forestry
description: doi:10.7717/peerj.7604
publisher: PeerJ Inc.
rights: © 2019 Mossman et al.
abstract: Background Managing forests for timber while protecting wildlife habitat is of increasing concern. Amphibians may be particularly sensitive to forest management practices due to their unique biology; however, it is not clear how different species respond to timber harvest practices—particularly over longer time scales. Methods Here we report on the differential responses of two salamander species—the eastern red-backed salamander (Plethodon cinereus Green) and the eastern newt (Notophthalmus viridescens Rafinesque)—to forest harvesting, by examining communities across a 25-year chronosequence of regenerating shelterwood harvests. Results Populations of both species were lowest immediately after harvest, but increased at substantially different rates. Red-backed salamander populations were highest in 20–25 year-old shelterwoods—significantly higher than in mature, unharvested, control (100–120 year old) stands. Eastern newt populations, however, were greatest in unharvested control stands and still had not recovered to population levels found in mature stands in the 25 years since harvest. Red-backed salamander abundances were strongly tied to stand age as well as abundance of decayed coarse woody debris, suggesting that timber harvests influence some wildlife species by affecting a suite of interacting habitat variables that change over time. In contrast, newt abundances were not directly related to stand age but were more related to downed wood and vegetation characteristics. Our results highlight markedly variable responses by two common salamander species to forest harvesting—species with markedly different life histories and reproductive patterns—and that time since harvest may be useful in predicting abundance.
bibliographic citation: Mossman et al. (2019) Two salamander species respond differently to timber harvests in a managed New England forest. PeerJ 7:e7604 https://doi.org/10.7717/peerj.7604
date submitted: 2019-05-20
date accepted: 2019-08-01
issued: 2019-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mossman
  given name: Angus
author list: Agent
  family name: Lambert
  given name: Max R.
author list: Agent
  family name: Ashton
  given name: Mark S.
author list: Agent
  family name: Wikle
  given name: Jessica
author list: Agent
  family name: Duguid
  given name: Marlyse C.
doi: 10.7717/peerj.7604
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-30
copyright: ©2019 Mossman et al.
attribution name: Mossman et al.

Comparative and evolutionary analysis of the reptilian hedgehog gene family (Shh, Dhh, and Ihh)
type: item
type: AcademicArticle
description: The hedgehog signaling pathway plays a vital role in human and animal patterning and cell proliferation during the developmental process. The hedgehog gene family of vertebrate species includes three genes, Shh, Dhh, and Ihh, which possess different functions and expression patterns. Despite the importance of hedgehog genes, genomic evidence of this gene family in reptiles is lacking. In this study, the available genomes of a number of representative reptile species were explored by utilizing adaptive evolutionary analysis methods to characterize the evolutionary patterns of the hedgehog gene family. Altogether, 33 sonic hedgehog (Shh), 25 desert hedgehog (Dhh), and 20 Indian hedgehog (Ihh) genes were obtained from reptiles, and six avian and five mammalian sequences were added to the analysis. The phylogenetic maximum likelihood (ML) tree of the Shh, Dhh, and Ihh genes revealed a similar topology, which is approximately consistent with the traditional taxonomic group. No shared positive selection site was identified by the PAML site model or the three methods in the Data Monkey Server. Branch model and Clade model C analyses revealed that the Dhh and Ihh genes experienced different evolutionary forces in reptiles and other vertebrates, while the Shh gene was not significantly different in terms of selection pressure. The different evolutionary rates of the Dhh and Ihh genes suggest that these genes may be potential contributors to the discrepant sperm and body development of different clades. The different adaptive evolutionary history of the Shh, Dhh, and Ihh genes among reptiles may be due to their different functions in regulating cellular events of development from the embryonic stages to adulthood. Overall, this study has provided meaningful information regarding the evolution of the hedgehog gene family in reptiles and a theoretical foundation for further analyses on the functional and molecular mechanisms that have shaped the reptilian hedgehog genes.
format: application/pdf
format: text/html
creator: Tian Xia
creator: Honghai Zhang
creator: Lei Zhang
creator: Xiufeng Yang
creator: Guolei Sun
creator: Jun Chen
creator: Dajie Xu
creator: Chao Zhao
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.7613
publisher: PeerJ Inc.
rights: © 2019 Xia et al.
abstract: The hedgehog signaling pathway plays a vital role in human and animal patterning and cell proliferation during the developmental process. The hedgehog gene family of vertebrate species includes three genes, Shh, Dhh, and Ihh, which possess different functions and expression patterns. Despite the importance of hedgehog genes, genomic evidence of this gene family in reptiles is lacking. In this study, the available genomes of a number of representative reptile species were explored by utilizing adaptive evolutionary analysis methods to characterize the evolutionary patterns of the hedgehog gene family. Altogether, 33 sonic hedgehog (Shh), 25 desert hedgehog (Dhh), and 20 Indian hedgehog (Ihh) genes were obtained from reptiles, and six avian and five mammalian sequences were added to the analysis. The phylogenetic maximum likelihood (ML) tree of the Shh, Dhh, and Ihh genes revealed a similar topology, which is approximately consistent with the traditional taxonomic group. No shared positive selection site was identified by the PAML site model or the three methods in the Data Monkey Server. Branch model and Clade model C analyses revealed that the Dhh and Ihh genes experienced different evolutionary forces in reptiles and other vertebrates, while the Shh gene was not significantly different in terms of selection pressure. The different evolutionary rates of the Dhh and Ihh genes suggest that these genes may be potential contributors to the discrepant sperm and body development of different clades. The different adaptive evolutionary history of the Shh, Dhh, and Ihh genes among reptiles may be due to their different functions in regulating cellular events of development from the embryonic stages to adulthood. Overall, this study has provided meaningful information regarding the evolution of the hedgehog gene family in reptiles and a theoretical foundation for further analyses on the functional and molecular mechanisms that have shaped the reptilian hedgehog genes.
bibliographic citation: Xia et al. (2019) Comparative and evolutionary analysis of the reptilian hedgehog gene family (Shh, Dhh, and Ihh). PeerJ 7:e7613 https://doi.org/10.7717/peerj.7613
date submitted: 2019-03-13
date accepted: 2019-08-05
issued: 2019-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xia
  given name: Tian
author list: Agent
  family name: Zhang
  given name: Honghai
author list: Agent
  family name: Zhang
  given name: Lei
author list: Agent
  family name: Yang
  given name: Xiufeng
author list: Agent
  family name: Sun
  given name: Guolei
author list: Agent
  family name: Chen
  given name: Jun
author list: Agent
  family name: Xu
  given name: Dajie
author list: Agent
  family name: Zhao
  given name: Chao
doi: 10.7717/peerj.7613
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-30
copyright: © 2019 Xia et al.
attribution name: Xia et al.

Microbial community dynamics during aerobic granulation in a sequencing batch reactor (SBR)
type: item
type: AcademicArticle
description: Microorganisms in aerobic granules formed in sequencing batch reactors (SBR) remove contaminants, such as xenobiotics or dyes, from wastewater. The granules, however, are not stable over time, decreasing the removal of the pollutant. A better understanding of the granule formation and the dynamics of the microorganisms involved will help to optimize the removal of contaminants from wastewater in a SBR. Sequencing the 16S rRNA gene and internal transcribed spacer PCR amplicons revealed that during the acclimation phase the relative abundance of Acinetobacter reached 70.8%. At the start of the granulation phase the relative abundance of Agrobacterium reached 35.9% and that of Dipodascus 89.7% during the mature granule phase. Fluffy granules were detected on day 43. The granules with filamentous overgrowth were not stable and they lysed on day 46 resulting in biomass wash-out. It was found that the reactor operation strategy resulted in stable aerobic granules for 46 days. As the reactor operations remained the same from the mature granule phase to the end of the experiment, the disintegration of the granules after day 46 was due to changes in the microbial community structure and not by the reactor operation.
format: application/pdf
format: text/html
creator: Fabiola Gómez-Basurto
creator: Miguel Vital-Jácome
creator: Elizabeth Selene Gómez-Acata
creator: Frederic Thalasso
creator: Marco Luna-Guido
creator: Luc Dendooven
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.7152
publisher: PeerJ Inc.
rights: © 2019 Gómez-Basurto et al.
abstract: Microorganisms in aerobic granules formed in sequencing batch reactors (SBR) remove contaminants, such as xenobiotics or dyes, from wastewater. The granules, however, are not stable over time, decreasing the removal of the pollutant. A better understanding of the granule formation and the dynamics of the microorganisms involved will help to optimize the removal of contaminants from wastewater in a SBR. Sequencing the 16S rRNA gene and internal transcribed spacer PCR amplicons revealed that during the acclimation phase the relative abundance of Acinetobacter reached 70.8%. At the start of the granulation phase the relative abundance of Agrobacterium reached 35.9% and that of Dipodascus 89.7% during the mature granule phase. Fluffy granules were detected on day 43. The granules with filamentous overgrowth were not stable and they lysed on day 46 resulting in biomass wash-out. It was found that the reactor operation strategy resulted in stable aerobic granules for 46 days. As the reactor operations remained the same from the mature granule phase to the end of the experiment, the disintegration of the granules after day 46 was due to changes in the microbial community structure and not by the reactor operation.
bibliographic citation: Gómez-Basurto et al. (2019) Microbial community dynamics during aerobic granulation in a sequencing batch reactor (SBR). PeerJ 7:e7152 https://doi.org/10.7717/peerj.7152
date submitted: 2018-12-06
date accepted: 2019-05-20
issued: 2019-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gómez-Basurto
  given name: Fabiola
author list: Agent
  family name: Vital-Jácome
  given name: Miguel
author list: Agent
  family name: Gómez-Acata
  given name: Elizabeth Selene
author list: Agent
  family name: Thalasso
  given name: Frederic
author list: Agent
  family name: Luna-Guido
  given name: Marco
author list: Agent
  family name: Dendooven
  given name: Luc
doi: 10.7717/peerj.7152
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-29
copyright: © 2019 Gómez-Basurto et al.
attribution name: Gómez-Basurto et al.

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