PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Discovery of novel astrovirus genotype species in small ruminants
items: TLR2 polymorphism (rs650082970) is associated with somatic cell count in goat milk
items: Functional and evolutionary perspectives on gill structures of an obligate air-breathing, aquatic snail
items: A 3-mRNA-based prognostic signature of survival in oral squamous cell carcinoma
items: The use of biochar in animal feeding
items: Long-term warming results in species-specific shifts in seed mass in alpine communities
items: Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples
items: Three-dimensional facial development of children with unilateral cleft lip and palate during the first year of life in comparison with normative average faces
items: Characterization of the karyotype and accumulation of repetitive sequences in Australian Darling hardyhead Craterocephalus amniculus (Atheriniformes, Teleostei)
items: Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue–green damselfish (Chromis viridis)

Discovery of novel astrovirus genotype species in small ruminants
type: item
type: AcademicArticle
description: Astroviruses (AstV) are single-stranded, positive-sense RNA viruses, best known for causing diarrhea in humans and are also found in many other mammals; in those, the relevance in gastroenteritis remains unclear. Recently described neurotropic AstV showed associations with encephalitis in humans as well as in other mammals. In Switzerland, two different neurotropic AstV were identified in cattle, as well as one in a sheep. The high genetic similarity between the ovine and one of the bovine AstV strengthens the hypothesis of an interspecies transmission. In humans, AstV associated with encephalitis were found also in human stool samples, suggesting that in these patients the infection spreads from the gastrointestinal tract to the brain under certain conditions, such as immunosuppression. Whether a similar pathogenesis occurs in ruminants remains unknown. The aims of this study were (1) the investigation of the potential occurrence of neurotropic AstV in feces samples, (2) the discovery and analysis of so far unknown AstV in small ruminants and other ruminant species’ fecal samples and (3) the examination of a potential interspecies transmission of AstV. To achieve these aims, RNA extraction out of 164 fecal samples from different ruminant species was performed and all samples were screened for known neurotropic AstV occurring in Switzerland, as well as for various AstV using RT-PCR. Positive tested samples were submitted to next generation sequencing. The generated sequences were compared to nucleotide- and amino acid databases, virus properties were identified, and phylogenetic analyses as well as recombination analysis were performed. The excretion of neurotropic AstV in small ruminants’ feces could not be demonstrated, but this work suggests the first identification of AstV in goats as well as the discovery of multiple and highly diverse new genetic variants in small ruminants, which lead to a classification into novel genotype-species. Additionally, the predicti…
format: application/pdf
format: text/html
creator: Ronja V. Kauer
creator: Michel C. Koch
creator: Melanie M. Hierweger
creator: Simea Werder
creator: Céline L. Boujon
creator: Torsten Seuberlich
subject: Veterinary Medicine
subject: Virology
description: doi:10.7717/peerj.7338
publisher: PeerJ Inc.
rights: © 2019 Kauer et al.
abstract: Astroviruses (AstV) are single-stranded, positive-sense RNA viruses, best known for causing diarrhea in humans and are also found in many other mammals; in those, the relevance in gastroenteritis remains unclear. Recently described neurotropic AstV showed associations with encephalitis in humans as well as in other mammals. In Switzerland, two different neurotropic AstV were identified in cattle, as well as one in a sheep. The high genetic similarity between the ovine and one of the bovine AstV strengthens the hypothesis of an interspecies transmission. In humans, AstV associated with encephalitis were found also in human stool samples, suggesting that in these patients the infection spreads from the gastrointestinal tract to the brain under certain conditions, such as immunosuppression. Whether a similar pathogenesis occurs in ruminants remains unknown. The aims of this study were (1) the investigation of the potential occurrence of neurotropic AstV in feces samples, (2) the discovery and analysis of so far unknown AstV in small ruminants and other ruminant species’ fecal samples and (3) the examination of a potential interspecies transmission of AstV. To achieve these aims, RNA extraction out of 164 fecal samples from different ruminant species was performed and all samples were screened for known neurotropic AstV occurring in Switzerland, as well as for various AstV using RT-PCR. Positive tested samples were submitted to next generation sequencing. The generated sequences were compared to nucleotide- and amino acid databases, virus properties were identified, and phylogenetic analyses as well as recombination analysis were performed. The excretion of neurotropic AstV in small ruminants’ feces could not be demonstrated, but this work suggests the first identification of AstV in goats as well as the discovery of multiple and highly diverse new genetic variants in small ruminants, which lead to a classification into novel genotype-species. Additionally, the predicti…
bibliographic citation: Kauer et al. (2019) Discovery of novel astrovirus genotype species in small ruminants. PeerJ 7:e7338 https://doi.org/10.7717/peerj.7338
date submitted: 2019-02-27
date accepted: 2019-06-23
issued: 2019-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kauer
  given name: Ronja V.
author list: Agent
  family name: Koch
  given name: Michel C.
author list: Agent
  family name: Hierweger
  given name: Melanie M.
author list: Agent
  family name: Werder
  given name: Simea
author list: Agent
  family name: Boujon
  given name: Céline L.
author list: Agent
  family name: Seuberlich
  given name: Torsten
doi: 10.7717/peerj.7338
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-07-31
copyright: © 2019 Kauer et al.
attribution name: Kauer et al.

TLR2 polymorphism (rs650082970) is associated with somatic cell count in goat milk
type: item
type: AcademicArticle
description: Pathogens invading the mammary gland are recognized through a range of pattern recognition receptors (PRRs), residing on the plasma membrane of mammary epithelial cells. Toll-like receptor 2 (TLR2) signalling is responsible for recognition of Gram-positive bacteria, which are the most common mastitis-causing pathogens in goats. Somatic cell counts (SCC) in milk are routinely determined in goat dairy flocks and serve as an indicator of milk quality, which is highly correlated to intramammary infections. Recently, a single nucleotide polymorphism of the TLR2 was suggested to be associated with SCC in goat milk. To further test the suggested association, we genotyped 61 Slovenian Alpine goats included in the dataset. The effect of the genotype was analysed using the general linear model (GLM) procedure of SAS/STAT software. We found the TLR2 genotypes significantly (p = 0.0007) associated with milk SCC. Animals with the A/G genotype had significantly (p ≤ 0.05) lower SCC value in milk compared to the G/G genotype. Our data suggest that the A allele is the minor one and is associated with lower milk SCC. In the current study, we provide a validated PCR-RFLP based genotyping assay for the TLR2 SNP (rs650082970) and confirm its association with milk SCC. Further studies to confirm the association on a larger number of animals of different breeds and to explain functional consequences of the polymorphism in relation to SCC are encouraged.
format: application/pdf
format: text/html
creator: Jernej Ogorevc
creator: Mojca Simčič
creator: Minja Zorc
creator: Monika Škrjanc
creator: Peter Dovč
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.7340
publisher: PeerJ Inc.
rights: © 2019 Ogorevc et al.
abstract: Pathogens invading the mammary gland are recognized through a range of pattern recognition receptors (PRRs), residing on the plasma membrane of mammary epithelial cells. Toll-like receptor 2 (TLR2) signalling is responsible for recognition of Gram-positive bacteria, which are the most common mastitis-causing pathogens in goats. Somatic cell counts (SCC) in milk are routinely determined in goat dairy flocks and serve as an indicator of milk quality, which is highly correlated to intramammary infections. Recently, a single nucleotide polymorphism of the TLR2 was suggested to be associated with SCC in goat milk. To further test the suggested association, we genotyped 61 Slovenian Alpine goats included in the dataset. The effect of the genotype was analysed using the general linear model (GLM) procedure of SAS/STAT software. We found the TLR2 genotypes significantly (p = 0.0007) associated with milk SCC. Animals with the A/G genotype had significantly (p ≤ 0.05) lower SCC value in milk compared to the G/G genotype. Our data suggest that the A allele is the minor one and is associated with lower milk SCC. In the current study, we provide a validated PCR-RFLP based genotyping assay for the TLR2 SNP (rs650082970) and confirm its association with milk SCC. Further studies to confirm the association on a larger number of animals of different breeds and to explain functional consequences of the polymorphism in relation to SCC are encouraged.
bibliographic citation: Ogorevc et al. (2019) TLR2 polymorphism (rs650082970) is associated with somatic cell count in goat milk. PeerJ 7:e7340 https://doi.org/10.7717/peerj.7340
date submitted: 2019-03-18
date accepted: 2019-06-23
issued: 2019-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ogorevc
  given name: Jernej
author list: Agent
  family name: Simčič
  given name: Mojca
author list: Agent
  family name: Zorc
  given name: Minja
author list: Agent
  family name: Škrjanc
  given name: Monika
author list: Agent
  family name: Dovč
  given name: Peter
doi: 10.7717/peerj.7340
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-07-31
copyright: ©2019 Ogorevc et al.
attribution name: Ogorevc et al.

Functional and evolutionary perspectives on gill structures of an obligate air-breathing, aquatic snail
type: item
type: AcademicArticle
description: Ampullariids are freshwater gastropods bearing a gill and a lung, thus showing different degrees of amphibiousness. In particular, Pomacea canaliculata (Caenogastropoda, Ampullariidae) is an obligate air-breather that relies mainly or solely on the lung for dwelling in poorly oxygenated water, for avoiding predators, while burying in the mud during aestivation, and for oviposition above water level. In this paper, we studied the morphological peculiarities of the gill in this species. We found (1) the gill and lung vasculature and innervation are intimately related, allowing alternation between water and air respiration; (2) the gill epithelium has features typical of a transporting rather than a respiratory epithelium; and (3) the gill has resident granulocytes within intraepithelial spaces that may serve a role for immune defence. Thus, the role in oxygen uptake may be less significant than the roles in ionic/osmotic regulation and immunity. Also, our results provide a morphological background to understand the dependence on aerial respiration of Pomacea canaliculata. Finally, we consider these findings from a functional perspective in the light of the evolution of amphibiousness in the Ampullariidae, and discuss that master regulators may explain the phenotypic convergence of gill structures amongst this molluscan species and those in other phyla.
format: application/pdf
format: text/html
creator: Cristian Rodriguez
creator: Guido I. Prieto
creator: Israel A. Vega
creator: Alfredo Castro-Vazquez
subject: Aquaculture, Fisheries and Fish Science
subject: Zoology
subject: Anatomy and Physiology
subject: Histology
subject: Freshwater Biology
description: doi:10.7717/peerj.7342
publisher: PeerJ Inc.
rights: © 2019 Rodriguez et al.
abstract: Ampullariids are freshwater gastropods bearing a gill and a lung, thus showing different degrees of amphibiousness. In particular, Pomacea canaliculata (Caenogastropoda, Ampullariidae) is an obligate air-breather that relies mainly or solely on the lung for dwelling in poorly oxygenated water, for avoiding predators, while burying in the mud during aestivation, and for oviposition above water level. In this paper, we studied the morphological peculiarities of the gill in this species. We found (1) the gill and lung vasculature and innervation are intimately related, allowing alternation between water and air respiration; (2) the gill epithelium has features typical of a transporting rather than a respiratory epithelium; and (3) the gill has resident granulocytes within intraepithelial spaces that may serve a role for immune defence. Thus, the role in oxygen uptake may be less significant than the roles in ionic/osmotic regulation and immunity. Also, our results provide a morphological background to understand the dependence on aerial respiration of Pomacea canaliculata. Finally, we consider these findings from a functional perspective in the light of the evolution of amphibiousness in the Ampullariidae, and discuss that master regulators may explain the phenotypic convergence of gill structures amongst this molluscan species and those in other phyla.
bibliographic citation: Rodriguez et al. (2019) Functional and evolutionary perspectives on gill structures of an obligate air-breathing, aquatic snail. PeerJ 7:e7342 https://doi.org/10.7717/peerj.7342
date submitted: 2019-02-01
date accepted: 2019-06-24
issued: 2019-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodriguez
  given name: Cristian
author list: Agent
  family name: Prieto
  given name: Guido I.
author list: Agent
  family name: Vega
  given name: Israel A.
author list: Agent
  family name: Castro-Vazquez
  given name: Alfredo
doi: 10.7717/peerj.7342
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-07-31
copyright: © 2019 Rodriguez et al.
attribution name: Rodriguez et al.

A 3-mRNA-based prognostic signature of survival in oral squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Oral squamous cell carcinoma (OSCC) is the most common type of head and neck squamous cell carcinoma with an unsatisfactory prognosis. The aim of this study was to identify potential prognostic mRNA biomarkers of OSCC based on analysis of The Cancer Genome Atlas (TCGA). Methods Expression profiles and clinical data of OSCC patients were collected from TCGA database. Univariate Cox analysis and the least absolute shrinkage and selection operator Cox (LASSO Cox) regression were used to primarily screen prognostic biomarkers. Then multivariate Cox analysis was performed to build a prognostic model based on the selected prognostic mRNAs. Nomograms were generated to predict the individual’s overall survival at 3 and 5 years. The model performance was assessed by the time-dependent receiver operating characteristic (ROC) curve and calibration plot in both training cohort and validation cohort (GSE41613 from NCBI GEO databases). In addition, machine learning was used to assess the importance of risk factors of OSCC. Finally, in order to explore the potential mechanisms of OSCC, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was completed. Results Three mRNAs (CLEC3B, C6 and CLCN1) were finally identified as a prognostic biomarker pattern. The risk score was imputed as: (−0.38602 × expression level of CLEC3B) + (−0.20632 × expression level of CLCN1) + (0.31541 × expression level of C6). In the TCGA training cohort, the area under the curve (AUC) was 0.705 and 0.711 for 3- and 5-year survival, respectively. In the validation cohort, AUC was 0.718 and 0.717 for 3- and 5-year survival. A satisfactory agreement between predictive values and observation values was demonstrated by the calibration curve in the probabilities of 3- and 5- year survival in both cohorts. Furthermore, machine learning identified the 3-mRNA signature as the most important risk factor to survival of OSCC. Neuroactive ligand-receptor interaction was most enriched mostly in KEGG…
format: application/pdf
format: text/html
creator: Ruoyan Cao
creator: Qiqi Wu
creator: Qiulan Li
creator: Mianfeng Yao
creator: Hongbo Zhou
subject: Bioinformatics
subject: Dentistry
subject: Oncology
description: doi:10.7717/peerj.7360
publisher: PeerJ Inc.
rights: © 2019 Cao et al.
abstract: Background Oral squamous cell carcinoma (OSCC) is the most common type of head and neck squamous cell carcinoma with an unsatisfactory prognosis. The aim of this study was to identify potential prognostic mRNA biomarkers of OSCC based on analysis of The Cancer Genome Atlas (TCGA). Methods Expression profiles and clinical data of OSCC patients were collected from TCGA database. Univariate Cox analysis and the least absolute shrinkage and selection operator Cox (LASSO Cox) regression were used to primarily screen prognostic biomarkers. Then multivariate Cox analysis was performed to build a prognostic model based on the selected prognostic mRNAs. Nomograms were generated to predict the individual’s overall survival at 3 and 5 years. The model performance was assessed by the time-dependent receiver operating characteristic (ROC) curve and calibration plot in both training cohort and validation cohort (GSE41613 from NCBI GEO databases). In addition, machine learning was used to assess the importance of risk factors of OSCC. Finally, in order to explore the potential mechanisms of OSCC, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was completed. Results Three mRNAs (CLEC3B, C6 and CLCN1) were finally identified as a prognostic biomarker pattern. The risk score was imputed as: (−0.38602 × expression level of CLEC3B) + (−0.20632 × expression level of CLCN1) + (0.31541 × expression level of C6). In the TCGA training cohort, the area under the curve (AUC) was 0.705 and 0.711 for 3- and 5-year survival, respectively. In the validation cohort, AUC was 0.718 and 0.717 for 3- and 5-year survival. A satisfactory agreement between predictive values and observation values was demonstrated by the calibration curve in the probabilities of 3- and 5- year survival in both cohorts. Furthermore, machine learning identified the 3-mRNA signature as the most important risk factor to survival of OSCC. Neuroactive ligand-receptor interaction was most enriched mostly in KEGG…
bibliographic citation: Cao et al. (2019) A 3-mRNA-based prognostic signature of survival in oral squamous cell carcinoma. PeerJ 7:e7360 https://doi.org/10.7717/peerj.7360
date submitted: 2019-03-06
date accepted: 2019-06-26
issued: 2019-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Ruoyan
author list: Agent
  family name: Wu
  given name: Qiqi
author list: Agent
  family name: Li
  given name: Qiulan
author list: Agent
  family name: Yao
  given name: Mianfeng
author list: Agent
  family name: Zhou
  given name: Hongbo
doi: 10.7717/peerj.7360
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-07-31
copyright: ©2019 Cao et al.
attribution name: Cao et al.

The use of biochar in animal feeding
type: item
type: AcademicArticle
description: Biochar, that is, carbonized biomass similar to charcoal, has been used in acute medical treatment of animals for many centuries. Since 2010, livestock farmers increasingly use biochar as a regular feed supplement to improve animal health, increase nutrient intake efficiency and thus productivity. As biochar gets enriched with nitrogen-rich organic compounds during the digestion process, the excreted biochar-manure becomes a more valuable organic fertilizer causing lower nutrient losses and greenhouse gas emissions during storage and soil application. Scientists only recently started to investigate the mechanisms of biochar in the different stages of animal digestion and thus most published results on biochar feeding are based so far on empirical studies. This review summarizes the state of knowledge up to the year 2019 by evaluating 112 relevant scientific publications on the topic to derive initial insights, discuss potential mechanisms behind observations and identify important knowledge gaps and future research needs. The literature analysis shows that in most studies and for all investigated farm animal species, positive effects on different parameters such as toxin adsorption, digestion, blood values, feed efficiency, meat quality and/or greenhouse gas emissions could be found when biochar was added to feed. A considerable number of studies provided statistically non-significant results, though tendencies were mostly positive. Rare negative effects were identified in regard to the immobilization of liposoluble feed ingredients (e.g., vitamin E or Carotenoids) which may limit long-term biochar feeding. We found that most of the studies did not systematically investigate biochar properties (which may vastly differ) and dosage, which is a major drawback for generalizing results. Our review demonstrates that the use of biochar as a feed additive has the potential to improve animal health, feed efficiency and livestock housing climate, to reduce nutrient losses and…
format: application/pdf
format: text/html
creator: Hans-Peter Schmidt
creator: Nikolas Hagemann
creator: Kathleen Draper
creator: Claudia Kammann
subject: Agricultural Science
subject: Ecology
subject: Soil Science
subject: Veterinary Medicine
subject: Environmental Impacts
description: doi:10.7717/peerj.7373
publisher: PeerJ Inc.
rights: © 2019 Schmidt et al.
abstract: Biochar, that is, carbonized biomass similar to charcoal, has been used in acute medical treatment of animals for many centuries. Since 2010, livestock farmers increasingly use biochar as a regular feed supplement to improve animal health, increase nutrient intake efficiency and thus productivity. As biochar gets enriched with nitrogen-rich organic compounds during the digestion process, the excreted biochar-manure becomes a more valuable organic fertilizer causing lower nutrient losses and greenhouse gas emissions during storage and soil application. Scientists only recently started to investigate the mechanisms of biochar in the different stages of animal digestion and thus most published results on biochar feeding are based so far on empirical studies. This review summarizes the state of knowledge up to the year 2019 by evaluating 112 relevant scientific publications on the topic to derive initial insights, discuss potential mechanisms behind observations and identify important knowledge gaps and future research needs. The literature analysis shows that in most studies and for all investigated farm animal species, positive effects on different parameters such as toxin adsorption, digestion, blood values, feed efficiency, meat quality and/or greenhouse gas emissions could be found when biochar was added to feed. A considerable number of studies provided statistically non-significant results, though tendencies were mostly positive. Rare negative effects were identified in regard to the immobilization of liposoluble feed ingredients (e.g., vitamin E or Carotenoids) which may limit long-term biochar feeding. We found that most of the studies did not systematically investigate biochar properties (which may vastly differ) and dosage, which is a major drawback for generalizing results. Our review demonstrates that the use of biochar as a feed additive has the potential to improve animal health, feed efficiency and livestock housing climate, to reduce nutrient losses and…
bibliographic citation: Schmidt et al. (2019) The use of biochar in animal feeding. PeerJ 7:e7373 https://doi.org/10.7717/peerj.7373
date submitted: 2019-05-07
date accepted: 2019-06-28
issued: 2019-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schmidt
  given name: Hans-Peter
author list: Agent
  family name: Hagemann
  given name: Nikolas
author list: Agent
  family name: Draper
  given name: Kathleen
author list: Agent
  family name: Kammann
  given name: Claudia
doi: 10.7717/peerj.7373
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-07-31
copyright: © 2019 Schmidt et al.
attribution name: Schmidt et al.

Long-term warming results in species-specific shifts in seed mass in alpine communities
type: item
type: AcademicArticle
description: Background Global warming can cause variation in plant functional traits due to phenotypic plasticity or rapid microevolutionary change. Seed mass represents a fundamental axis of trait variation in plants, from an individual to a community scale. Here, we hypothesize that long-term warming can shift the mean seed mass of species. Methods We tested our hypothesis in plots that had been warmed over 18 years in alpine meadow communities with a history of light grazing (LG) and heavy grazing (HG) on the Qinghai-Tibet plateau. In this study, seeds were collected during the growing season of 2015. Results We found that warming increased the mean seed mass of 4 (n = 19) species in the LG meadow and 6 (n = 20) species in the HG meadow, while decreasing the mean seed mass of 6 species in the LG and HG meadows, respectively. For 7 species, grazing history modified the effect of warming on seed mass. Therefore, we concluded that long-term warming can shift the mean seed mass at the species level. However, the direction of this variation is species-specific. Our study suggests that mean seed mass of alpine plant species appears to decrease in warmer (less stressful) habitats based on life-history theory, but it also suggests there may be an underlying trade-off in which mean seed mass may increase due to greater thermal energy inputs into seed development. Furthermore, the physical and biotic environment modulating this trade-off result in complex patterns of variation in mean seed mass of alpine plant species facing global warming.
format: application/pdf
format: text/html
creator: Chunhui Zhang
creator: Zhen Ma
creator: Huakun Zhou
creator: Xinquan Zhao
subject: Ecology
description: doi:10.7717/peerj.7416
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background Global warming can cause variation in plant functional traits due to phenotypic plasticity or rapid microevolutionary change. Seed mass represents a fundamental axis of trait variation in plants, from an individual to a community scale. Here, we hypothesize that long-term warming can shift the mean seed mass of species. Methods We tested our hypothesis in plots that had been warmed over 18 years in alpine meadow communities with a history of light grazing (LG) and heavy grazing (HG) on the Qinghai-Tibet plateau. In this study, seeds were collected during the growing season of 2015. Results We found that warming increased the mean seed mass of 4 (n = 19) species in the LG meadow and 6 (n = 20) species in the HG meadow, while decreasing the mean seed mass of 6 species in the LG and HG meadows, respectively. For 7 species, grazing history modified the effect of warming on seed mass. Therefore, we concluded that long-term warming can shift the mean seed mass at the species level. However, the direction of this variation is species-specific. Our study suggests that mean seed mass of alpine plant species appears to decrease in warmer (less stressful) habitats based on life-history theory, but it also suggests there may be an underlying trade-off in which mean seed mass may increase due to greater thermal energy inputs into seed development. Furthermore, the physical and biotic environment modulating this trade-off result in complex patterns of variation in mean seed mass of alpine plant species facing global warming.
bibliographic citation: Zhang et al. (2019) Long-term warming results in species-specific shifts in seed mass in alpine communities. PeerJ 7:e7416 https://doi.org/10.7717/peerj.7416
date submitted: 2018-10-17
date accepted: 2019-07-05
issued: 2019-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Chunhui
author list: Agent
  family name: Ma
  given name: Zhen
author list: Agent
  family name: Zhou
  given name: Huakun
author list: Agent
  family name: Zhao
  given name: Xinquan
doi: 10.7717/peerj.7416
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-07-31
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples
type: item
type: AcademicArticle
description: Background Biological invasions are major drivers of environmental change that can significantly alter ecosystem function and diversity. In plants, soil microbes play an important role in plant establishment and growth; however, relatively little is known about the role they might play in biological invasions. A first step to assess whether root microbes may be playing a role in the invasion process is to find out if invasive plants host different microbes than neighbouring native plant species. Methods In this study we investigated differences in root associated microbes of native sugar maple (Acer saccharum Marsh.) and exotic Norway maple (A. platanoides L.) collected from a forested reserve in eastern Canada. We used microscopy to examine root fungi and high-throughput sequencing to characterize the bacterial, fungal and arbuscular mycorrhizal communities of both maple species over one growing season. Results We found differences in root associated bacterial and fungal communities between host species. Norway maple had a higher bacterial and fungal OTU (operational taxonomic units) richness compared to sugar maple, and the indicator species analysis revealed that nine fungal OTUs and three bacterial OTUs had a significant preference for sugar maple. The dominant bacterial phyla found on the roots of both maple species were Actinobacteria and Proteobacteria. The most common fungal orders associated with the Norway maple roots (in descending order) were Helotiales, Agaricales, Pleosporales, Hypocreales, Trechisporales while the Agaricales, Pleosporales, Helotiales, Capnodiales and Hypocreales were the dominant orders present in the sugar maple roots. Dark septate fungi colonization levels were higher in the sugar maple, but no differences in arbuscular mycorrhizal fungal communities and colonization rates were detected between maple species. Discussion Our findings show that two congeneric plant species grown in close proximity can harbor distinct root microbial co…
format: application/pdf
format: text/html
creator: Tonia DeBellis
creator: Steven W. Kembel
creator: Jean-Philippe Lessard
subject: Ecology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.7295
publisher: PeerJ Inc.
rights: © 2019 DeBellis et al.
abstract: Background Biological invasions are major drivers of environmental change that can significantly alter ecosystem function and diversity. In plants, soil microbes play an important role in plant establishment and growth; however, relatively little is known about the role they might play in biological invasions. A first step to assess whether root microbes may be playing a role in the invasion process is to find out if invasive plants host different microbes than neighbouring native plant species. Methods In this study we investigated differences in root associated microbes of native sugar maple (Acer saccharum Marsh.) and exotic Norway maple (A. platanoides L.) collected from a forested reserve in eastern Canada. We used microscopy to examine root fungi and high-throughput sequencing to characterize the bacterial, fungal and arbuscular mycorrhizal communities of both maple species over one growing season. Results We found differences in root associated bacterial and fungal communities between host species. Norway maple had a higher bacterial and fungal OTU (operational taxonomic units) richness compared to sugar maple, and the indicator species analysis revealed that nine fungal OTUs and three bacterial OTUs had a significant preference for sugar maple. The dominant bacterial phyla found on the roots of both maple species were Actinobacteria and Proteobacteria. The most common fungal orders associated with the Norway maple roots (in descending order) were Helotiales, Agaricales, Pleosporales, Hypocreales, Trechisporales while the Agaricales, Pleosporales, Helotiales, Capnodiales and Hypocreales were the dominant orders present in the sugar maple roots. Dark septate fungi colonization levels were higher in the sugar maple, but no differences in arbuscular mycorrhizal fungal communities and colonization rates were detected between maple species. Discussion Our findings show that two congeneric plant species grown in close proximity can harbor distinct root microbial co…
bibliographic citation: DeBellis et al. (2019) Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples. PeerJ 7:e7295 https://doi.org/10.7717/peerj.7295
date submitted: 2019-02-11
date accepted: 2019-06-14
issued: 2019-07-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: DeBellis
  given name: Tonia
author list: Agent
  family name: Kembel
  given name: Steven W.
author list: Agent
  family name: Lessard
  given name: Jean-Philippe
doi: 10.7717/peerj.7295
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-07-30
copyright: ©2019 DeBellis et al.
attribution name: DeBellis et al.

Three-dimensional facial development of children with unilateral cleft lip and palate during the first year of life in comparison with normative average faces
type: item
type: AcademicArticle
description: Background Stereophotogrammetry can be used to study facial morphology in both healthy individuals as well as subjects with orofacial clefts because it shows good reliability, ability to capture images rapidly, archival capabilities, and high resolution, and does not require ionizing radiation. This study aimed to compare the three-dimensional (3D) facial morphology of infants born with unilateral cleft lip and palate (UCLP) with an age-matched normative 3D average face before and after primary closure of the lip and soft palate. Methods Thirty infants with a non-syndromic complete unilateral cleft lip, alveolus, and palate participated in the study. Three-dimensional images were acquired at 3, 6, 9, and 12 months of age. All subjects were treated according to the primary surgical protocol consisting of surgical closure of the lip and the soft palate at 6 months of age. Three-dimensional images of UCLP patients at 3, 6 (pre-treatment), 9, and 12 months of age were superimposed on normative datasets of average facial morphology using the children’s reference frame. Distance maps of the complete 3D facial surface and the nose, upper lip, chin, forehead, and cheek regions were developed. Results Assessments of the facial morphology of UCLP and control subjects by using color-distance maps showed large differences in the upper lip region at the location of the cleft defect and an asymmetry at the nostrils at 3 and 6 months of age. At 9 months of age, the labial symmetry was completely restored although the tip of the nose towards the unaffected side showed some remnant asymmetry. At 12 months of age, the symmetry of the nose improved, with only some remnant asymmetry noted on both sides of the nasal tip. At all ages, the mandibular and chin regions of the UCLP patients were 2.5–5 mm posterior to those in the average controls. Conclusion In patients with UCLP deviations from the normative average 3D facial morphology of age-matched control subjects existed for the upper …
format: application/pdf
format: text/html
creator: Sander Brons
creator: Jene W. Meulstee
creator: Tom G.J. Loonen
creator: Rania M. Nada
creator: Mette A.R. Kuijpers
creator: Ewald M. Bronkhorst
creator: Stefaan J. Bergé
creator: Thomas J.J. Maal
creator: Anne Marie Kuijpers-Jagtman
subject: Anatomy and Physiology
subject: Dentistry
subject: Pediatrics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.7302
publisher: PeerJ Inc.
rights: © 2019 Brons et al.
abstract: Background Stereophotogrammetry can be used to study facial morphology in both healthy individuals as well as subjects with orofacial clefts because it shows good reliability, ability to capture images rapidly, archival capabilities, and high resolution, and does not require ionizing radiation. This study aimed to compare the three-dimensional (3D) facial morphology of infants born with unilateral cleft lip and palate (UCLP) with an age-matched normative 3D average face before and after primary closure of the lip and soft palate. Methods Thirty infants with a non-syndromic complete unilateral cleft lip, alveolus, and palate participated in the study. Three-dimensional images were acquired at 3, 6, 9, and 12 months of age. All subjects were treated according to the primary surgical protocol consisting of surgical closure of the lip and the soft palate at 6 months of age. Three-dimensional images of UCLP patients at 3, 6 (pre-treatment), 9, and 12 months of age were superimposed on normative datasets of average facial morphology using the children’s reference frame. Distance maps of the complete 3D facial surface and the nose, upper lip, chin, forehead, and cheek regions were developed. Results Assessments of the facial morphology of UCLP and control subjects by using color-distance maps showed large differences in the upper lip region at the location of the cleft defect and an asymmetry at the nostrils at 3 and 6 months of age. At 9 months of age, the labial symmetry was completely restored although the tip of the nose towards the unaffected side showed some remnant asymmetry. At 12 months of age, the symmetry of the nose improved, with only some remnant asymmetry noted on both sides of the nasal tip. At all ages, the mandibular and chin regions of the UCLP patients were 2.5–5 mm posterior to those in the average controls. Conclusion In patients with UCLP deviations from the normative average 3D facial morphology of age-matched control subjects existed for the upper …
bibliographic citation: Brons et al. (2019) Three-dimensional facial development of children with unilateral cleft lip and palate during the first year of life in comparison with normative average faces. PeerJ 7:e7302 https://doi.org/10.7717/peerj.7302
date submitted: 2019-03-06
date accepted: 2019-06-17
issued: 2019-07-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brons
  given name: Sander
author list: Agent
  family name: Meulstee
  given name: Jene W.
author list: Agent
  family name: Loonen
  given name: Tom G.J.
author list: Agent
  family name: Nada
  given name: Rania M.
author list: Agent
  family name: Kuijpers
  given name: Mette A.R.
author list: Agent
  family name: Bronkhorst
  given name: Ewald M.
author list: Agent
  family name: Bergé
  given name: Stefaan J.
author list: Agent
  family name: Maal
  given name: Thomas J.J.
author list: Agent
  family name: Kuijpers-Jagtman
  given name: Anne Marie
doi: 10.7717/peerj.7302
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-07-30
copyright: © 2019 Brons et al.
attribution name: Brons et al.

Characterization of the karyotype and accumulation of repetitive sequences in Australian Darling hardyhead Craterocephalus amniculus (Atheriniformes, Teleostei)
type: item
type: AcademicArticle
description: Belonging to the order Atheriniformes, Craterocephalus is one of the most widespread genera of freshwater fishes in Australia, spanning along the northern coast from central Western Australia to central New South Wales and across the Murray-Darling and Lake Eyre basins. In this study, both conventional cytogenetic techniques (Giemsa, C-banding, CMA3/DAPI staining), and fluorescence in situ hybridization (FISH) with telomeric DNA and rDNA probes were used to examine the karyotypes and other chromosomal characteristics of Darling hardyhead (Craterocephalus amniculus) from New South Wales, Australia. We identified a diploid chromosome number 2n = 48 (NF = 58) in all studied individuals. FISH with rDNA probes showed a nonsyntenic pattern, with signals on one pair of subtelocentric chromosomes for 5S rDNA and one pair of submetacentric chromosomes for 28S rDNA. C-banding displayed the accumulation of constitutive heterochromatin in the centromeric regions of approximately 40 chromosomes. CMA3/DAPI fluorescence staining revealed extremely GC-rich signals in the pericentromeric region of one submetacentric chromosomal pair with size polymorphism. We detected telomeric signals at the end of all chromosomes and no interstitial signals.
format: application/pdf
format: text/html
creator: Zuzana Majtánová
creator: Karl G. Moy
creator: Peter J. Unmack
creator: Petr Ráb
creator: Tariq Ezaz
subject: Aquaculture, Fisheries and Fish Science
subject: Genetics
subject: Molecular Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.7347
publisher: PeerJ Inc.
rights: © 2019 Majtánová et al.
abstract: Belonging to the order Atheriniformes, Craterocephalus is one of the most widespread genera of freshwater fishes in Australia, spanning along the northern coast from central Western Australia to central New South Wales and across the Murray-Darling and Lake Eyre basins. In this study, both conventional cytogenetic techniques (Giemsa, C-banding, CMA3/DAPI staining), and fluorescence in situ hybridization (FISH) with telomeric DNA and rDNA probes were used to examine the karyotypes and other chromosomal characteristics of Darling hardyhead (Craterocephalus amniculus) from New South Wales, Australia. We identified a diploid chromosome number 2n = 48 (NF = 58) in all studied individuals. FISH with rDNA probes showed a nonsyntenic pattern, with signals on one pair of subtelocentric chromosomes for 5S rDNA and one pair of submetacentric chromosomes for 28S rDNA. C-banding displayed the accumulation of constitutive heterochromatin in the centromeric regions of approximately 40 chromosomes. CMA3/DAPI fluorescence staining revealed extremely GC-rich signals in the pericentromeric region of one submetacentric chromosomal pair with size polymorphism. We detected telomeric signals at the end of all chromosomes and no interstitial signals.
bibliographic citation: Majtánová et al. (2019) Characterization of the karyotype and accumulation of repetitive sequences in Australian Darling hardyhead Craterocephalus amniculus (Atheriniformes, Teleostei). PeerJ 7:e7347 https://doi.org/10.7717/peerj.7347
date submitted: 2019-04-18
date accepted: 2019-06-25
issued: 2019-07-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Majtánová
  given name: Zuzana
author list: Agent
  family name: Moy
  given name: Karl G.
author list: Agent
  family name: Unmack
  given name: Peter J.
author list: Agent
  family name: Ráb
  given name: Petr
author list: Agent
  family name: Ezaz
  given name: Tariq
doi: 10.7717/peerj.7347
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-07-30
copyright: ©2019 Majtánová et al.
attribution name: Majtánová et al.

Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue–green damselfish (Chromis viridis)
type: item
type: AcademicArticle
description: Species delimitation is challenging in sibling species/cryptic lineages because of the absence of clear diagnostic traits. However, integration of different approaches such as phylogeography and ecological niche comparison offers one potential approach to tease apart recently diverged lineages. In this study, we estimate the ecological niche divergence among lineages in Chromis viridis in a broad-scale phylogeographic framework to test whether the combination of these two approaches can effectively distinguish recently diverged lineages. Results from Cytb and Rag2 analyses identified two cryptic lineages (C. viridis A and C. viridis B) that diverged ∼3 Myr ago. Estimates of ecological niche divergence with 11 environmental parameters across the broad geographic range of these lineages showed overlapping ecological niches and niche conservatism. However, regardless of the incongruence between genetic and ecological niche divergence, the substantial genetic divergence between the two clades of C. viridis in both mtDNA and nuclear loci strong suggest that they are cryptic taxa.
format: application/pdf
format: text/html
creator: Shang Yin Vanson Liu
creator: Mao-Ning Tuanmu
creator: Rita Rachmawati
creator: Gusti Ngurah Mahardika
creator: Paul H. Barber
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Evolutionary Studies
subject: Marine Biology
description: doi:10.7717/peerj.7384
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Species delimitation is challenging in sibling species/cryptic lineages because of the absence of clear diagnostic traits. However, integration of different approaches such as phylogeography and ecological niche comparison offers one potential approach to tease apart recently diverged lineages. In this study, we estimate the ecological niche divergence among lineages in Chromis viridis in a broad-scale phylogeographic framework to test whether the combination of these two approaches can effectively distinguish recently diverged lineages. Results from Cytb and Rag2 analyses identified two cryptic lineages (C. viridis A and C. viridis B) that diverged ∼3 Myr ago. Estimates of ecological niche divergence with 11 environmental parameters across the broad geographic range of these lineages showed overlapping ecological niches and niche conservatism. However, regardless of the incongruence between genetic and ecological niche divergence, the substantial genetic divergence between the two clades of C. viridis in both mtDNA and nuclear loci strong suggest that they are cryptic taxa.
bibliographic citation: Liu et al. (2019) Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue–green damselfish (Chromis viridis). PeerJ 7:e7384 https://doi.org/10.7717/peerj.7384
date submitted: 2019-05-29
date accepted: 2019-06-30
issued: 2019-07-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Shang Yin Vanson
author list: Agent
  family name: Tuanmu
  given name: Mao-Ning
author list: Agent
  family name: Rachmawati
  given name: Rita
author list: Agent
  family name: Mahardika
  given name: Gusti Ngurah
author list: Agent
  family name: Barber
  given name: Paul H.
doi: 10.7717/peerj.7384
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-07-30
copyright: © 2019 Liu et al.
attribution name: Liu et al.

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