PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Functional characterisation of phagocytes in the Pacific oyster Crassostrea gigas
items: Age-congruency and contact effects in body expression recognition from point-light displays (PLD)
items: Species interactions in an Andean bird–flowering plant network: phenology is more important than abundance or morphology
items: One-year mortality after severe COPD exacerbation in Bulgaria
items: Diet of the endangered big-headed turtle Platysternon megacephalum
items: Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America
items: A large and unusually colored new snake species of the genus Tantilla (Squamata; Colubridae) from the Peruvian Andes
items: Using a thermistor flowmeter with attached video camera for monitoring sponge excurrent speed and oscular behaviour
items: Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA
items: Biodiversity data obsolescence and land uses changes

Functional characterisation of phagocytes in the Pacific oyster Crassostrea gigas
type: item
type: AcademicArticle
description: Invertebrates lack canonical adaptive immunity and mainly rely on innate immune system to fight against pathogens. The phagocytes, which could engulf and kill microbial pathogens, are likely to be of great importance and have to undertake significant roles in invertebrate immune defense. In the present study, flow cytometry combined with histological and lectin staining was employed to characterise functional features of phagocytes in the Pacific oyster Crassostrea gigas. Based on the cell size and cellular contents, haemocytes were categorised into three cell types, i.e., granulocytes, semigranulocytes and agranulocytes. Agranulocytes with smaller cell volume and lower cytoplasmic-to-nuclear ratio did not show phagocytic activity, while semigranulocytes and agranulocytes exhibited larger cell volume, higher cytoplasmic-to-nuclear ratio and phagocytic activity. In addition, granulocytes with higher side scatter (SSC) exhibited higher phagocytic activity than that of semigranulocytes. When β-integrin and lectin-like receptors were blocked by RGD tripeptide and carbohydrates, respectively, the phagocytic activity of both granulocytes and semigranulocytes was significantly inhibited, indicating that β-integrin and certain lectin-like receptors were involved in phagocytosis towards microbes. Moreover, lipopolysaccharide but not peptidylglycan could enhance phagocytic activity of granulocytes and semigranulocytes towards Vibrio splendidus and Staphylococcus aureus. Lectin staining analysis revealed that Lycopersicon esculentum lectin (LEL), binding the epitope polylactosamine, was highly distributed on the extracellular cell surface of phagocytes, and could be utilized as a potential molecular marker to differentiate phagocytes from non-phagocytic haemocytes. The results, collectively, provide knowledge on the functional characters of oyster phagocytes, which would contribute to deep investigation of cell typing and cellular immunity in bivalves.
format: application/pdf
format: text/html
creator: Shuai Jiang
creator: Zhihao Jia
creator: Tao Zhang
creator: Lingling Wang
creator: Limei Qiu
creator: Jinsheng Sun
creator: Linsheng Song
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.2590
publisher: PeerJ Inc.
rights: © 2016 Jiang et al.
abstract: Invertebrates lack canonical adaptive immunity and mainly rely on innate immune system to fight against pathogens. The phagocytes, which could engulf and kill microbial pathogens, are likely to be of great importance and have to undertake significant roles in invertebrate immune defense. In the present study, flow cytometry combined with histological and lectin staining was employed to characterise functional features of phagocytes in the Pacific oyster Crassostrea gigas. Based on the cell size and cellular contents, haemocytes were categorised into three cell types, i.e., granulocytes, semigranulocytes and agranulocytes. Agranulocytes with smaller cell volume and lower cytoplasmic-to-nuclear ratio did not show phagocytic activity, while semigranulocytes and agranulocytes exhibited larger cell volume, higher cytoplasmic-to-nuclear ratio and phagocytic activity. In addition, granulocytes with higher side scatter (SSC) exhibited higher phagocytic activity than that of semigranulocytes. When β-integrin and lectin-like receptors were blocked by RGD tripeptide and carbohydrates, respectively, the phagocytic activity of both granulocytes and semigranulocytes was significantly inhibited, indicating that β-integrin and certain lectin-like receptors were involved in phagocytosis towards microbes. Moreover, lipopolysaccharide but not peptidylglycan could enhance phagocytic activity of granulocytes and semigranulocytes towards Vibrio splendidus and Staphylococcus aureus. Lectin staining analysis revealed that Lycopersicon esculentum lectin (LEL), binding the epitope polylactosamine, was highly distributed on the extracellular cell surface of phagocytes, and could be utilized as a potential molecular marker to differentiate phagocytes from non-phagocytic haemocytes. The results, collectively, provide knowledge on the functional characters of oyster phagocytes, which would contribute to deep investigation of cell typing and cellular immunity in bivalves.
bibliographic citation: Jiang et al. (2016) Functional characterisation of phagocytes in the Pacific oyster Crassostrea gigas. PeerJ 4:e2590 https://doi.org/10.7717/peerj.2590
date submitted: 2016-06-29
date accepted: 2016-09-21
issued: 2016-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Shuai
author list: Agent
  family name: Jia
  given name: Zhihao
author list: Agent
  family name: Zhang
  given name: Tao
author list: Agent
  family name: Wang
  given name: Lingling
author list: Agent
  family name: Qiu
  given name: Limei
author list: Agent
  family name: Sun
  given name: Jinsheng
author list: Agent
  family name: Song
  given name: Linsheng
doi: 10.7717/peerj.2590
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-14
copyright: ©2016 Jiang et al.
attribution name: Jiang et al.

Age-congruency and contact effects in body expression recognition from point-light displays (PLD)
type: item
type: AcademicArticle
description: Recognition of older people’s body expressions is a crucial social skill. We here investigate how age, not just of the observer, but also of the observed individual, affects this skill. Age may influence the ability to recognize other people’s body expressions by changes in one’s own ability to perform certain action over the life-span (i.e., an own-age bias may occur, with best recognition for one’s own age). Whole body point light displays of children, young adults and older adults (>70 years) expressing six different emotions were presented to observers of the same three age-groups. Across two variations of the paradigm, no evidence for the predicted own-age bias (a cross-over interaction between one’s own age and the observed person’s age) was found. Instead, experience effects were found with children better recognizing older actors’ expressions of ‘active emotions,’ such as anger and happiness with greater exposure in daily life. Together, the findings suggest that age-related changes in one own’s mobility only influences body expression categorization in young children who interact frequently with older adults.
format: application/pdf
format: text/html
creator: Petra M.J. Pollux
creator: Frouke Hermens
creator: Alexander P. Willmott
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2796
publisher: PeerJ Inc.
rights: © 2016 Pollux et al.
abstract: Recognition of older people’s body expressions is a crucial social skill. We here investigate how age, not just of the observer, but also of the observed individual, affects this skill. Age may influence the ability to recognize other people’s body expressions by changes in one’s own ability to perform certain action over the life-span (i.e., an own-age bias may occur, with best recognition for one’s own age). Whole body point light displays of children, young adults and older adults (>70 years) expressing six different emotions were presented to observers of the same three age-groups. Across two variations of the paradigm, no evidence for the predicted own-age bias (a cross-over interaction between one’s own age and the observed person’s age) was found. Instead, experience effects were found with children better recognizing older actors’ expressions of ‘active emotions,’ such as anger and happiness with greater exposure in daily life. Together, the findings suggest that age-related changes in one own’s mobility only influences body expression categorization in young children who interact frequently with older adults.
bibliographic citation: Pollux et al. (2016) Age-congruency and contact effects in body expression recognition from point-light displays (PLD). PeerJ 4:e2796 https://doi.org/10.7717/peerj.2796
date submitted: 2016-06-22
date accepted: 2016-11-15
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pollux
  given name: Petra M.J.
author list: Agent
  family name: Hermens
  given name: Frouke
author list: Agent
  family name: Willmott
  given name: Alexander P.
doi: 10.7717/peerj.2796
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Pollux et al.
attribution name: Pollux et al.

Species interactions in an Andean bird–flowering plant network: phenology is more important than abundance or morphology
type: item
type: AcademicArticle
description: Biological constraints and neutral processes have been proposed to explain the properties of plant–pollinator networks. Using interactions between nectarivorous birds (hummingbirds and flowerpiercers) and flowering plants in high elevation forests (i.e., “elfin” forests) of the Andes, we explore the importance of biological constraints and neutral processes (random interactions) to explain the observed species interactions and network metrics, such as connectance, specialization, nestedness and asymmetry. In cold environments of elfin forests, which are located at the top of the tropical montane forest zone, many plants are adapted for pollination by birds, making this an ideal system to study plant–pollinator networks. To build the network of interactions between birds and plants, we used direct field observations. We measured abundance of birds using mist-nets and flower abundance using transects, and phenology by scoring presence of birds and flowers over time. We compared the length of birds’ bills to flower length to identify “forbidden interactions”—those interactions that could not result in legitimate floral visits based on mis-match in morphology. Diglossa flowerpiercers, which are characterized as “illegitimate” flower visitors, were relatively abundant. We found that the elfin forest network was nested with phenology being the factor that best explained interaction frequencies and nestedness, providing support for biological constraints hypothesis. We did not find morphological constraints to be important in explaining observed interaction frequencies and network metrics. Other network metrics (connectance, evenness and asymmetry), however, were better predicted by abundance (neutral process) models. Flowerpiercers, which cut holes and access flowers at their base and, consequently, facilitate nectar access for other hummingbirds, explain why morphological mis-matches were relatively unimportant in this system. Future work should focus on how changes in a…
format: application/pdf
format: text/html
creator: Oscar Gonzalez
creator: Bette A. Loiselle
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.2789
publisher: PeerJ Inc.
rights: © 2016 Gonzalez and Loiselle
abstract: Biological constraints and neutral processes have been proposed to explain the properties of plant–pollinator networks. Using interactions between nectarivorous birds (hummingbirds and flowerpiercers) and flowering plants in high elevation forests (i.e., “elfin” forests) of the Andes, we explore the importance of biological constraints and neutral processes (random interactions) to explain the observed species interactions and network metrics, such as connectance, specialization, nestedness and asymmetry. In cold environments of elfin forests, which are located at the top of the tropical montane forest zone, many plants are adapted for pollination by birds, making this an ideal system to study plant–pollinator networks. To build the network of interactions between birds and plants, we used direct field observations. We measured abundance of birds using mist-nets and flower abundance using transects, and phenology by scoring presence of birds and flowers over time. We compared the length of birds’ bills to flower length to identify “forbidden interactions”—those interactions that could not result in legitimate floral visits based on mis-match in morphology. Diglossa flowerpiercers, which are characterized as “illegitimate” flower visitors, were relatively abundant. We found that the elfin forest network was nested with phenology being the factor that best explained interaction frequencies and nestedness, providing support for biological constraints hypothesis. We did not find morphological constraints to be important in explaining observed interaction frequencies and network metrics. Other network metrics (connectance, evenness and asymmetry), however, were better predicted by abundance (neutral process) models. Flowerpiercers, which cut holes and access flowers at their base and, consequently, facilitate nectar access for other hummingbirds, explain why morphological mis-matches were relatively unimportant in this system. Future work should focus on how changes in a…
bibliographic citation: Gonzalez et al. (2016) Species interactions in an Andean bird–flowering plant network: phenology is more important than abundance or morphology. PeerJ 4:e2789 https://doi.org/10.7717/peerj.2789
date submitted: 2016-06-14
date accepted: 2016-11-12
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gonzalez
  given name: Oscar
author list: Agent
  family name: Loiselle
  given name: Bette A.
doi: 10.7717/peerj.2789
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Gonzalez and Loiselle
attribution name: Gonzalez and Loiselle

One-year mortality after severe COPD exacerbation in Bulgaria
type: item
type: AcademicArticle
description: Introduction One-year mortality in COPD patients is reported to be between 4% and 43%, depending on the group examined. Aim To examine the one-year mortality in COPD patients after severe exacerbation and the correlation between mortality and patients’ characteristics and comorbidities. Methods A total of 152 COPD patients hospitalized for severe exacerbation were assessed for vitamin D status, diabetes mellitus (DM), arterial hypertension (AH), and metabolic syndrome (MS). Data were gathered about smoking status and number of exacerbations in previous year. CAT and mMRC questionnaires were completed by all patients. Pre- and post-bronchodilatory spirometry was performed. One-year mortality was established from national death register. Results One-year mortality is 7.2%. DM, MS, and VD are not predictors for one-year mortality. However there is a trend for increased mortality in patients with AH (9.5% vs. 2.1%, p = 0.107). There is increased mortality in patients with mMRC > 2 (11.1 vs. 0%, p = 0.013). The presence of severe exacerbation in the previous year is a risk factor for mortality (12.5% vs. 1.4%, p = 0.009). There is a trend for increased mortality in the group with FEV1 < 50% (11.5 vs. 4.4%, p = 0.094). Cox regression shows 3.7% increase in mortality rate for 1% decrease in FEV1, 5.2% for 1% decrease in PEF, 7.8% for one year age increase and 8.1% for 1 CAT point increase (all p < 0.05). Conclusions This study finds relatively low one-year mortality in COPD patients after surviving severe exacerbation. Grade C and FEV1 > 80% may be factors for good prognosis. Risk factors for increased mortality are age, FEV1 value, severe exacerbation in previous year and reduced quality of life.
format: application/pdf
format: text/html
creator: Evgeni Mekov
creator: Yanina Slavova
creator: Adelina Tsakova
creator: Marianka P. Genova
creator: Dimitar T. Kostadinov
creator: Delcho Minchev
creator: Dora Marinova
creator: Mihail A. Boyanov
subject: Epidemiology
subject: Internal Medicine
subject: Respiratory Medicine
description: doi:10.7717/peerj.2788
publisher: PeerJ Inc.
rights: © 2016 Mekov et al.
abstract: Introduction One-year mortality in COPD patients is reported to be between 4% and 43%, depending on the group examined. Aim To examine the one-year mortality in COPD patients after severe exacerbation and the correlation between mortality and patients’ characteristics and comorbidities. Methods A total of 152 COPD patients hospitalized for severe exacerbation were assessed for vitamin D status, diabetes mellitus (DM), arterial hypertension (AH), and metabolic syndrome (MS). Data were gathered about smoking status and number of exacerbations in previous year. CAT and mMRC questionnaires were completed by all patients. Pre- and post-bronchodilatory spirometry was performed. One-year mortality was established from national death register. Results One-year mortality is 7.2%. DM, MS, and VD are not predictors for one-year mortality. However there is a trend for increased mortality in patients with AH (9.5% vs. 2.1%, p = 0.107). There is increased mortality in patients with mMRC > 2 (11.1 vs. 0%, p = 0.013). The presence of severe exacerbation in the previous year is a risk factor for mortality (12.5% vs. 1.4%, p = 0.009). There is a trend for increased mortality in the group with FEV1 < 50% (11.5 vs. 4.4%, p = 0.094). Cox regression shows 3.7% increase in mortality rate for 1% decrease in FEV1, 5.2% for 1% decrease in PEF, 7.8% for one year age increase and 8.1% for 1 CAT point increase (all p < 0.05). Conclusions This study finds relatively low one-year mortality in COPD patients after surviving severe exacerbation. Grade C and FEV1 > 80% may be factors for good prognosis. Risk factors for increased mortality are age, FEV1 value, severe exacerbation in previous year and reduced quality of life.
bibliographic citation: Mekov et al. (2016) One-year mortality after severe COPD exacerbation in Bulgaria. PeerJ 4:e2788 https://doi.org/10.7717/peerj.2788
date submitted: 2016-08-01
date accepted: 2016-11-11
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mekov
  given name: Evgeni
author list: Agent
  family name: Slavova
  given name: Yanina
author list: Agent
  family name: Tsakova
  given name: Adelina
author list: Agent
  family name: Genova
  given name: Marianka P.
author list: Agent
  family name: Kostadinov
  given name: Dimitar T.
author list: Agent
  family name: Minchev
  given name: Delcho
author list: Agent
  family name: Marinova
  given name: Dora
author list: Agent
  family name: Boyanov
  given name: Mihail A.
doi: 10.7717/peerj.2788
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Mekov et al.
attribution name: Mekov et al.

Diet of the endangered big-headed turtle Platysternon megacephalum
type: item
type: AcademicArticle
description: Populations of the big-headed turtle Platysternon megacephalum are declining at unprecedented rates across most of its distribution in Southeast Asia owing to unsustainable harvest for pet, food, and Chinese medicine markets. Research on Asian freshwater turtles becomes more challenging as populations decline and basic ecological information is needed to inform conservation efforts. We examined fecal samples collected from P. megacephalum in five streams in Hong Kong to quantify the diet, and we compared the germination success of ingested and uningested seeds. Fruits, primarily of Machilus spp., were most frequently consumed, followed by insects, plant matter, crabs and mollusks. The niche breadth of adults was wider than that of juveniles. Diet composition differed between sites, which may be attributable to the history of illegal trapping at some sites, which reduced the proportion of larger and older individuals. Digestion of Machilus spp. fruits by P. megacephalum enhanced germination success of seeds by about 30%. However, most digested seeds are likely defecated in water in this highly aquatic species, which limits the potential benefit to dispersal. The results of our study can be used by conservation-related captive breeding programs to ensure a more optimal diet is provided to captive P. megacephalum.
format: application/pdf
format: text/html
creator: Yik-Hei Sung
creator: Billy C.H. Hau
creator: Nancy E. Karraker
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.2784
publisher: PeerJ Inc.
rights: © 2016 Sung et al.
abstract: Populations of the big-headed turtle Platysternon megacephalum are declining at unprecedented rates across most of its distribution in Southeast Asia owing to unsustainable harvest for pet, food, and Chinese medicine markets. Research on Asian freshwater turtles becomes more challenging as populations decline and basic ecological information is needed to inform conservation efforts. We examined fecal samples collected from P. megacephalum in five streams in Hong Kong to quantify the diet, and we compared the germination success of ingested and uningested seeds. Fruits, primarily of Machilus spp., were most frequently consumed, followed by insects, plant matter, crabs and mollusks. The niche breadth of adults was wider than that of juveniles. Diet composition differed between sites, which may be attributable to the history of illegal trapping at some sites, which reduced the proportion of larger and older individuals. Digestion of Machilus spp. fruits by P. megacephalum enhanced germination success of seeds by about 30%. However, most digested seeds are likely defecated in water in this highly aquatic species, which limits the potential benefit to dispersal. The results of our study can be used by conservation-related captive breeding programs to ensure a more optimal diet is provided to captive P. megacephalum.
bibliographic citation: Sung et al. (2016) Diet of the endangered big-headed turtle Platysternon megacephalum. PeerJ 4:e2784 https://doi.org/10.7717/peerj.2784
date submitted: 2016-08-05
date accepted: 2016-11-11
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sung
  given name: Yik-Hei
author list: Agent
  family name: Hau
  given name: Billy C.H.
author list: Agent
  family name: Karraker
  given name: Nancy E.
doi: 10.7717/peerj.2784
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Sung et al.
attribution name: Sung et al.

Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America
type: item
type: AcademicArticle
description: Background Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth’s most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte–saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest. Methods We cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3–4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolated only from non-living leaves. Results Across the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activity in vitro. Cellulolytic activity differed…
format: application/pdf
format: text/html
creator: Jana M. U’Ren
creator: A. Elizabeth Arnold
subject: Ecology
subject: Microbiology
subject: Mycology
description: doi:10.7717/peerj.2768
publisher: PeerJ Inc.
rights: © 2016 U’Ren and Arnold
abstract: Background Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth’s most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte–saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest. Methods We cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3–4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolated only from non-living leaves. Results Across the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activity in vitro. Cellulolytic activity differed…
bibliographic citation: U’Ren et al. (2016) Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America. PeerJ 4:e2768 https://doi.org/10.7717/peerj.2768
date submitted: 2016-04-17
date accepted: 2016-11-07
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: U’Ren
  given name: Jana M.
author list: Agent
  family name: Arnold
  given name: A. Elizabeth
doi: 10.7717/peerj.2768
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 U’Ren and Arnold
attribution name: U’Ren and Arnold

A large and unusually colored new snake species of the genus Tantilla (Squamata; Colubridae) from the Peruvian Andes
type: item
type: AcademicArticle
description: A new colubrid species of the genus Tantilla from the dry forest of the northern Peruvian Andes is described on the basis of two specimens, which exhibit a conspicuous sexual dimorphism. Tantilla tjiasmantoi sp. nov. represents the third species of the genus in Peru. The new species is easily distinguished from its congeners by the combination of scalation characteristics and the unusual transversely-banded color pattern on the dorsum. A detailed description of the skull morphology of the new species is given based on micro-computed tomography images. The habitat of this new species is gravely threatened due to human interventions. Conservation efforts are urgently needed in the inter-Andean valley of the Maranon River.
format: application/pdf
format: text/html
creator: Claudia Koch
creator: Pablo J. Venegas
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2767
publisher: PeerJ Inc.
rights: © 2016 Koch and Venegas
abstract: A new colubrid species of the genus Tantilla from the dry forest of the northern Peruvian Andes is described on the basis of two specimens, which exhibit a conspicuous sexual dimorphism. Tantilla tjiasmantoi sp. nov. represents the third species of the genus in Peru. The new species is easily distinguished from its congeners by the combination of scalation characteristics and the unusual transversely-banded color pattern on the dorsum. A detailed description of the skull morphology of the new species is given based on micro-computed tomography images. The habitat of this new species is gravely threatened due to human interventions. Conservation efforts are urgently needed in the inter-Andean valley of the Maranon River.
bibliographic citation: Koch et al. (2016) A large and unusually colored new snake species of the genus Tantilla (Squamata; Colubridae) from the Peruvian Andes. PeerJ 4:e2767 https://doi.org/10.7717/peerj.2767
date submitted: 2016-08-25
date accepted: 2016-11-07
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koch
  given name: Claudia
author list: Agent
  family name: Venegas
  given name: Pablo J.
doi: 10.7717/peerj.2767
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Koch and Venegas
attribution name: Koch and Venegas

Using a thermistor flowmeter with attached video camera for monitoring sponge excurrent speed and oscular behaviour
type: item
type: AcademicArticle
description: A digital, four-channel thermistor flowmeter integrated with time-lapse cameras was developed as an experimental tool for measuring pumping rates in marine sponges, particularly those with small excurrent openings (oscula). Combining flowmeters with time-lapse imagery yielded valuable insights into the contractile behaviour of oscula in Cliona orientalis. Osculum cross-sectional area (OSA) was positively correlated to measured excurrent speeds (ES), indicating that sponge pumping and osculum contraction are coordinated behaviours. Both OSA and ES were positively correlated to pumping rate (Q). Diel trends in pumping activity and osculum contraction were also observed, with sponges increasing their pumping activity to peak at midday and decreasing pumping and contracting oscula at night. Short-term elevation of the suspended sediment concentration (SSC) within the seawater initially decreased pumping rates by up to 90%, ultimately resulting in closure of the oscula and cessation of pumping.
format: application/pdf
format: text/html
creator: Brian W. Strehlow
creator: Damien Jorgensen
creator: Nicole S. Webster
creator: Mari-Carmen Pineda
creator: Alan Duckworth
subject: Animal Behavior
subject: Marine Biology
description: doi:10.7717/peerj.2761
publisher: PeerJ Inc.
rights: © 2016 Strehlow et al.
abstract: A digital, four-channel thermistor flowmeter integrated with time-lapse cameras was developed as an experimental tool for measuring pumping rates in marine sponges, particularly those with small excurrent openings (oscula). Combining flowmeters with time-lapse imagery yielded valuable insights into the contractile behaviour of oscula in Cliona orientalis. Osculum cross-sectional area (OSA) was positively correlated to measured excurrent speeds (ES), indicating that sponge pumping and osculum contraction are coordinated behaviours. Both OSA and ES were positively correlated to pumping rate (Q). Diel trends in pumping activity and osculum contraction were also observed, with sponges increasing their pumping activity to peak at midday and decreasing pumping and contracting oscula at night. Short-term elevation of the suspended sediment concentration (SSC) within the seawater initially decreased pumping rates by up to 90%, ultimately resulting in closure of the oscula and cessation of pumping.
bibliographic citation: Strehlow et al. (2016) Using a thermistor flowmeter with attached video camera for monitoring sponge excurrent speed and oscular behaviour. PeerJ 4:e2761 https://doi.org/10.7717/peerj.2761
date submitted: 2016-06-15
date accepted: 2016-11-05
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Strehlow
  given name: Brian W.
author list: Agent
  family name: Jorgensen
  given name: Damien
author list: Agent
  family name: Webster
  given name: Nicole S.
author list: Agent
  family name: Pineda
  given name: Mari-Carmen
author list: Agent
  family name: Duckworth
  given name: Alan
doi: 10.7717/peerj.2761
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Strehlow et al.
attribution name: Strehlow et al.

Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA
type: item
type: AcademicArticle
description: There is only one exception to strict maternal inheritance of mitochondrial DNA (mtDNA) in the animal kingdom: a system named doubly uniparental inheritance (DUI), which is found in several bivalve species. Why and how such a radically different system of mitochondrial transmission evolved in bivalve remains obscure. Obtaining a more complete taxonomic distribution of DUI in the Bivalvia may help to better understand its origin and function. In this study we provide evidence for the presence of sex-linked heteroplasmy (thus the possible presence of DUI) in two bivalve species, i.e., the nuculanoid Yoldia hyperborea(Gould, 1841)and the veneroid Scrobicularia plana(Da Costa,1778), increasing the number of families in which DUI has been found by two. An update on the taxonomic distribution of DUI in the Bivalvia is also presented.
format: application/pdf
format: text/html
creator: Arthur Gusman
creator: Sophia Lecomte
creator: Donald T. Stewart
creator: Marco Passamonti
creator: Sophie Breton
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.2760
publisher: PeerJ Inc.
rights: © 2016 Gusman et al.
abstract: There is only one exception to strict maternal inheritance of mitochondrial DNA (mtDNA) in the animal kingdom: a system named doubly uniparental inheritance (DUI), which is found in several bivalve species. Why and how such a radically different system of mitochondrial transmission evolved in bivalve remains obscure. Obtaining a more complete taxonomic distribution of DUI in the Bivalvia may help to better understand its origin and function. In this study we provide evidence for the presence of sex-linked heteroplasmy (thus the possible presence of DUI) in two bivalve species, i.e., the nuculanoid Yoldia hyperborea(Gould, 1841)and the veneroid Scrobicularia plana(Da Costa,1778), increasing the number of families in which DUI has been found by two. An update on the taxonomic distribution of DUI in the Bivalvia is also presented.
bibliographic citation: Gusman et al. (2016) Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA. PeerJ 4:e2760 https://doi.org/10.7717/peerj.2760
date submitted: 2016-09-04
date accepted: 2016-11-05
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gusman
  given name: Arthur
author list: Agent
  family name: Lecomte
  given name: Sophia
author list: Agent
  family name: Stewart
  given name: Donald T.
author list: Agent
  family name: Passamonti
  given name: Marco
author list: Agent
  family name: Breton
  given name: Sophie
doi: 10.7717/peerj.2760
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Gusman et al.
attribution name: Gusman et al.

Biodiversity data obsolescence and land uses changes
type: item
type: AcademicArticle
description: Background Primary biodiversity records (PBR) are essential in many areas of scientific research as they document the biodiversity through time and space. However, concerns about PBR quality and fitness-for-use have grown, especially as derived from taxonomical, geographical and sampling effort biases. Nonetheless, the temporal bias stemming from data ageing has received less attention. We examine the effect of changes in land use in the information currentness, and therefore data obsolescence, in biodiversity databases. Methods We created maps of land use changes for three periods (1956–1985, 1985–2000 and 2000–2012) at 5-kilometres resolution. For each cell we calculated the percentage of land use change within each period. We then overlaid distribution data about small mammals, and classified each data as ‘non-obsolete or ‘obsolete,’ depending on both the amount of land use changes in the cell, and whether changes occurred at or after the data sampling’s date. Results A total of 14,528 records out of the initial 59,677 turned out to be non-obsolete after taking into account the changes in the land uses in Navarra. These obsolete data existed in 115 of the 156 cells analysed. Furthermore, more than one half of the remaining cells holding non-obsolete records had not been visited at least for the last fifteen years. Conclusion Land use changes challenge the actual information obtainable from biodiversity datasets and therefore its potential uses. With the passage of time, one can expect a steady increase in the availability and use of biological records—but not without them becoming older and likely to be obsolete by land uses changes. Therefore, it becomes necessary to assess records’ obsolescence, as it may jeopardize the knowledge and perception of biodiversity patterns.
format: application/pdf
format: text/html
creator: Nora Escribano
creator: Arturo H. Ariño
creator: David Galicia
subject: Biodiversity
subject: Biogeography
subject: Bioinformatics
subject: Ecosystem Science
subject: Zoology
description: doi:10.7717/peerj.2743
publisher: PeerJ Inc.
rights: © 2016 Escribano et al.
abstract: Background Primary biodiversity records (PBR) are essential in many areas of scientific research as they document the biodiversity through time and space. However, concerns about PBR quality and fitness-for-use have grown, especially as derived from taxonomical, geographical and sampling effort biases. Nonetheless, the temporal bias stemming from data ageing has received less attention. We examine the effect of changes in land use in the information currentness, and therefore data obsolescence, in biodiversity databases. Methods We created maps of land use changes for three periods (1956–1985, 1985–2000 and 2000–2012) at 5-kilometres resolution. For each cell we calculated the percentage of land use change within each period. We then overlaid distribution data about small mammals, and classified each data as ‘non-obsolete or ‘obsolete,’ depending on both the amount of land use changes in the cell, and whether changes occurred at or after the data sampling’s date. Results A total of 14,528 records out of the initial 59,677 turned out to be non-obsolete after taking into account the changes in the land uses in Navarra. These obsolete data existed in 115 of the 156 cells analysed. Furthermore, more than one half of the remaining cells holding non-obsolete records had not been visited at least for the last fifteen years. Conclusion Land use changes challenge the actual information obtainable from biodiversity datasets and therefore its potential uses. With the passage of time, one can expect a steady increase in the availability and use of biological records—but not without them becoming older and likely to be obsolete by land uses changes. Therefore, it becomes necessary to assess records’ obsolescence, as it may jeopardize the knowledge and perception of biodiversity patterns.
bibliographic citation: Escribano et al. (2016) Biodiversity data obsolescence and land uses changes. PeerJ 4:e2743 https://doi.org/10.7717/peerj.2743
date submitted: 2016-08-06
date accepted: 2016-11-01
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Escribano
  given name: Nora
author list: Agent
  family name: Ariño
  given name: Arturo H.
author list: Agent
  family name: Galicia
  given name: David
doi: 10.7717/peerj.2743
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Escribano et al.
attribution name: Escribano et al.

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