PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Proteomic profiling analysis reveals that glutathione system plays important roles responding to osmotic stress in wheat (Triticum aestivum L.) roots
items: Effects of origin, seasons and storage under different temperatures on germination of Senecio vulgaris (Asteraceae) seeds
items: Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds
items: MOST: a modified MLST typing tool based on short read sequencing
items: Detection of a Yersinia pestis gene homologue in rodent samples
items: Arktocara yakataga, a new fossil odontocete (Mammalia, Cetacea) from the Oligocene of Alaska and the antiquity of Platanistoidea
items: Ancient phylogenetic divergence of the enigmatic African rodent Zenkerella and the origin of anomalurid gliding
items: The adder (Vipera berus) in Southern Altay Mountains: population characteristics, distribution, morphology and phylogenetic position
items: Evolution of morphological and climatic adaptations in Veronica L. (Plantaginaceae)
items: The health care and life sciences community profile for dataset descriptions

Proteomic profiling analysis reveals that glutathione system plays important roles responding to osmotic stress in wheat (Triticum aestivum L.) roots
type: item
type: AcademicArticle
description: Wheat is one of the most important crops in the world, and osmotic stress has become one of the main factors affecting wheat production. Understanding the mechanism of the response of wheat to osmotic stress would be greatly significant. In the present study, isobaric tag for relative and absolute quantification (iTRAQ) was used to analyze the changes of protein expression in the wheat roots exposed to different osmotic stresses. A total of 2,228 expressed proteins, including 81 differentially expressed proteins, between osmotic stress and control, were found. The comprehensive analysis of these differentially expressed proteins revealed that osmotic stress increased the variety of expressed proteins and suppressed the quantity of expressed proteins in wheat roots. Furthermore, the proteins for detoxifying and reactive oxygen species scavenging, especially the glutathione system, played important roles in maintaining organism balance in response to osmotic stress in wheat roots. Thus, the present study comprehensively describes the protein expression changes in wheat roots in response to osmotic stress, providing firmer foundation to further study the mechanism of osmotic resistance in wheat.
format: application/pdf
format: text/html
creator: Jianhui Ma
creator: Wen Dong
creator: Daijing Zhang
creator: Xiaolong Gao
creator: Lina Jiang
creator: Yun Shao
creator: Doudou Tong
creator: Chunxi Li
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.2334
publisher: PeerJ Inc.
rights: © 2016 Ma et al.
abstract: Wheat is one of the most important crops in the world, and osmotic stress has become one of the main factors affecting wheat production. Understanding the mechanism of the response of wheat to osmotic stress would be greatly significant. In the present study, isobaric tag for relative and absolute quantification (iTRAQ) was used to analyze the changes of protein expression in the wheat roots exposed to different osmotic stresses. A total of 2,228 expressed proteins, including 81 differentially expressed proteins, between osmotic stress and control, were found. The comprehensive analysis of these differentially expressed proteins revealed that osmotic stress increased the variety of expressed proteins and suppressed the quantity of expressed proteins in wheat roots. Furthermore, the proteins for detoxifying and reactive oxygen species scavenging, especially the glutathione system, played important roles in maintaining organism balance in response to osmotic stress in wheat roots. Thus, the present study comprehensively describes the protein expression changes in wheat roots in response to osmotic stress, providing firmer foundation to further study the mechanism of osmotic resistance in wheat.
bibliographic citation: Ma et al. (2016) Proteomic profiling analysis reveals that glutathione system plays important roles responding to osmotic stress in wheat (Triticum aestivum L.) roots. PeerJ 4:e2334 https://doi.org/10.7717/peerj.2334
date submitted: 2015-11-16
date accepted: 2016-07-16
issued: 2016-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Jianhui
author list: Agent
  family name: Dong
  given name: Wen
author list: Agent
  family name: Zhang
  given name: Daijing
author list: Agent
  family name: Gao
  given name: Xiaolong
author list: Agent
  family name: Jiang
  given name: Lina
author list: Agent
  family name: Shao
  given name: Yun
author list: Agent
  family name: Tong
  given name: Doudou
author list: Agent
  family name: Li
  given name: Chunxi
doi: 10.7717/peerj.2334
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-17
copyright: ©2016 Ma et al.
attribution name: Ma et al.

Effects of origin, seasons and storage under different temperatures on germination of Senecio vulgaris (Asteraceae) seeds
type: item
type: AcademicArticle
description: Invasive plants colonize new environments, become pests and cause biodiversity loss, economic loss and health damage. Senecio vulgaris L. (Common groundsel, Asteraceae), a widely distributing cosmopolitan weed in the temperate area, is reported with large populations in the north–eastern and south–western part, but not in southern, central, or north-western parts of China. We studied the germination behavior of S. vulgaris to explain the distribution and the biological invasion of this species in China. We used seeds originating from six native and six invasive populations to conduct germination experiments in a climate chamber and under outdoor condition. When incubated in a climate chamber (15 °C), seeds from the majority of the populations showed >90% germination percentage (GP) and the GP was equal for seeds with a native and invasive origin. The mean germination time (MGT) was significantly different among the populations. Under outdoor conditions, significant effects of origin, storage conditions (stored at 4 °C or ambient room temperature, ca. 27 °C) and seasons (in summer or autumn) were observed on the GP while the MGT was only affected by the season. In autumn, the GP (38.6%) was higher and the MGT was slightly longer than that in summer. In autumn, seeds stored at 4 °C showed higher GP than those stored at ambient room temperature (ca.27 °C), and seeds from invasive populations revealed higher GP than those from native populations. The results implied that the high temperature in summer has a negative impact on the germination and might cause viability loss or secondary dormancy to S. vulgaris seeds. Our study offers a clue to exploring what factor limits the distribution of S. vulgaris in China by explaining why, in the cities in South-East China and central China such as Wuhan, S. vulgaris cannot establish natural and viable populations.
format: application/pdf
format: text/html
creator: Noel Ndihokubwayo
creator: Viet-Thang Nguyen
creator: Dandan Cheng
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.2346
publisher: PeerJ Inc.
rights: © 2016 Ndihokubwayo et al.
abstract: Invasive plants colonize new environments, become pests and cause biodiversity loss, economic loss and health damage. Senecio vulgaris L. (Common groundsel, Asteraceae), a widely distributing cosmopolitan weed in the temperate area, is reported with large populations in the north–eastern and south–western part, but not in southern, central, or north-western parts of China. We studied the germination behavior of S. vulgaris to explain the distribution and the biological invasion of this species in China. We used seeds originating from six native and six invasive populations to conduct germination experiments in a climate chamber and under outdoor condition. When incubated in a climate chamber (15 °C), seeds from the majority of the populations showed >90% germination percentage (GP) and the GP was equal for seeds with a native and invasive origin. The mean germination time (MGT) was significantly different among the populations. Under outdoor conditions, significant effects of origin, storage conditions (stored at 4 °C or ambient room temperature, ca. 27 °C) and seasons (in summer or autumn) were observed on the GP while the MGT was only affected by the season. In autumn, the GP (38.6%) was higher and the MGT was slightly longer than that in summer. In autumn, seeds stored at 4 °C showed higher GP than those stored at ambient room temperature (ca.27 °C), and seeds from invasive populations revealed higher GP than those from native populations. The results implied that the high temperature in summer has a negative impact on the germination and might cause viability loss or secondary dormancy to S. vulgaris seeds. Our study offers a clue to exploring what factor limits the distribution of S. vulgaris in China by explaining why, in the cities in South-East China and central China such as Wuhan, S. vulgaris cannot establish natural and viable populations.
bibliographic citation: Ndihokubwayo et al. (2016) Effects of origin, seasons and storage under different temperatures on germination of Senecio vulgaris (Asteraceae) seeds. PeerJ 4:e2346 https://doi.org/10.7717/peerj.2346
date submitted: 2016-02-03
date accepted: 2016-07-19
issued: 2016-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ndihokubwayo
  given name: Noel
author list: Agent
  family name: Nguyen
  given name: Viet-Thang
author list: Agent
  family name: Cheng
  given name: Dandan
doi: 10.7717/peerj.2346
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-17
copyright: ©2016 Ndihokubwayo et al.
attribution name: Ndihokubwayo et al.

Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds
type: item
type: AcademicArticle
description: Food availability and diet selection are important factors influencing the abundance and distribution of wild waterbirds. In order to better understand changes in waterbird population, it is essential to figure out what they feed on. However, analyzing their diet could be difficult and inefficient using traditional methods such as microhistologic observation. Here, we addressed this gap of knowledge by investigating the diet of greater white-fronted goose Anser albifrons and bean goose Anser fabalis, which are obligate herbivores wintering in China, mostly in the Middle and Lower Yangtze River floodplain. First, we selected a suitable and high-resolution marker gene for wetland plants that these geese would consume during the wintering period. Eight candidate genes were included: rbcL, rpoC1, rpoB, matK, trnH-psbA, trnL (UAA), atpF-atpH, and psbK-psbI. The selection was performed via analysis of representative sequences from NCBI and comparison of amplification efficiency and resolution power of plant samples collected from the wintering area. The trnL gene was chosen at last with c/h primers, and a local plant reference library was constructed with this gene. Then, utilizing DNA metabarcoding, we discovered 15 food items in total from the feces of these birds. Of the 15 unique dietary sequences, 10 could be identified at specie level. As for greater white-fronted goose, 73% of sequences belonged to Poaceae spp., and 26% belonged to Carex spp. In contrast, almost all sequences of bean goose belonged to Carex spp. (99%). Using the same samples, microhistology provided consistent food composition with metabarcoding results for greater white-fronted goose, while 13% of Poaceae was recovered for bean goose. In addition, two other taxa were discovered only through microhistologic analysis. Although most of the identified taxa matched relatively well between the two methods, DNA metabarcoding gave taxonomically more detailed information. Discrepancies were likely due to b…
format: application/pdf
format: text/html
creator: Yuzhan Yang
creator: Aibin Zhan
creator: Lei Cao
creator: Fanjuan Meng
creator: Wenbin Xu
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.2345
publisher: PeerJ Inc.
rights: © 2016 Yang et al.
abstract: Food availability and diet selection are important factors influencing the abundance and distribution of wild waterbirds. In order to better understand changes in waterbird population, it is essential to figure out what they feed on. However, analyzing their diet could be difficult and inefficient using traditional methods such as microhistologic observation. Here, we addressed this gap of knowledge by investigating the diet of greater white-fronted goose Anser albifrons and bean goose Anser fabalis, which are obligate herbivores wintering in China, mostly in the Middle and Lower Yangtze River floodplain. First, we selected a suitable and high-resolution marker gene for wetland plants that these geese would consume during the wintering period. Eight candidate genes were included: rbcL, rpoC1, rpoB, matK, trnH-psbA, trnL (UAA), atpF-atpH, and psbK-psbI. The selection was performed via analysis of representative sequences from NCBI and comparison of amplification efficiency and resolution power of plant samples collected from the wintering area. The trnL gene was chosen at last with c/h primers, and a local plant reference library was constructed with this gene. Then, utilizing DNA metabarcoding, we discovered 15 food items in total from the feces of these birds. Of the 15 unique dietary sequences, 10 could be identified at specie level. As for greater white-fronted goose, 73% of sequences belonged to Poaceae spp., and 26% belonged to Carex spp. In contrast, almost all sequences of bean goose belonged to Carex spp. (99%). Using the same samples, microhistology provided consistent food composition with metabarcoding results for greater white-fronted goose, while 13% of Poaceae was recovered for bean goose. In addition, two other taxa were discovered only through microhistologic analysis. Although most of the identified taxa matched relatively well between the two methods, DNA metabarcoding gave taxonomically more detailed information. Discrepancies were likely due to b…
bibliographic citation: Yang et al. (2016) Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds. PeerJ 4:e2345 https://doi.org/10.7717/peerj.2345
date submitted: 2016-04-12
date accepted: 2016-07-19
issued: 2016-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yuzhan
author list: Agent
  family name: Zhan
  given name: Aibin
author list: Agent
  family name: Cao
  given name: Lei
author list: Agent
  family name: Meng
  given name: Fanjuan
author list: Agent
  family name: Xu
  given name: Wenbin
doi: 10.7717/peerj.2345
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-17
copyright: ©2016 Yang et al.
attribution name: Yang et al.

MOST: a modified MLST typing tool based on short read sequencing
type: item
type: AcademicArticle
description: Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR) amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS). This paper reports the comparison of the reliability of MLST results derived from WGS data, comparing mapping and assembly-based approaches to conventional methods using 323 bacterial genomes of diverse species. The sensitivity of the two WGS based methods were further investigated with 26 mixed and 29 low coverage genomic data sets from Salmonella enteridis and Streptococcus pneumoniae. Of the 323 samples, 92.9% (n = 300), 97.5% (n = 315) and 99.7% (n = 322) full MLST profiles were derived by the conventional method, assembly- and mapping-based approaches, respectively. The concordance between samples that were typed by conventional (92.9%) and both WGS methods was 100%. From the 55 mixed and low coverage genomes, 89.1% (n = 49) and 67.3% (n = 37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. In conclusion, deriving MLST from WGS data is more sensitive than the conventional method. When comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the mapping based approach described here derives quality metrics, which are difficult to determine quantitatively using conventional and WGS-assembly based approaches.
format: application/pdf
format: text/html
creator: Rediat Tewolde
creator: Timothy Dallman
creator: Ulf Schaefer
creator: Carmen L. Sheppard
creator: Philip Ashton
creator: Bruno Pichon
creator: Matthew Ellington
creator: Craig Swift
creator: Jonathan Green
creator: Anthony Underwood
subject: Bioinformatics
subject: Microbiology
description: doi:10.7717/peerj.2308
publisher: PeerJ Inc.
rights: © 2016 Tewolde et al.
abstract: Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR) amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS). This paper reports the comparison of the reliability of MLST results derived from WGS data, comparing mapping and assembly-based approaches to conventional methods using 323 bacterial genomes of diverse species. The sensitivity of the two WGS based methods were further investigated with 26 mixed and 29 low coverage genomic data sets from Salmonella enteridis and Streptococcus pneumoniae. Of the 323 samples, 92.9% (n = 300), 97.5% (n = 315) and 99.7% (n = 322) full MLST profiles were derived by the conventional method, assembly- and mapping-based approaches, respectively. The concordance between samples that were typed by conventional (92.9%) and both WGS methods was 100%. From the 55 mixed and low coverage genomes, 89.1% (n = 49) and 67.3% (n = 37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. In conclusion, deriving MLST from WGS data is more sensitive than the conventional method. When comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the mapping based approach described here derives quality metrics, which are difficult to determine quantitatively using conventional and WGS-assembly based approaches.
bibliographic citation: Tewolde et al. (2016) MOST: a modified MLST typing tool based on short read sequencing. PeerJ 4:e2308 https://doi.org/10.7717/peerj.2308
date submitted: 2016-04-19
date accepted: 2016-07-10
issued: 2016-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tewolde
  given name: Rediat
author list: Agent
  family name: Dallman
  given name: Timothy
author list: Agent
  family name: Schaefer
  given name: Ulf
author list: Agent
  family name: Sheppard
  given name: Carmen L.
author list: Agent
  family name: Ashton
  given name: Philip
author list: Agent
  family name: Pichon
  given name: Bruno
author list: Agent
  family name: Ellington
  given name: Matthew
author list: Agent
  family name: Swift
  given name: Craig
author list: Agent
  family name: Green
  given name: Jonathan
author list: Agent
  family name: Underwood
  given name: Anthony
doi: 10.7717/peerj.2308
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-17
copyright: ©2016 Tewolde et al.
attribution name: Tewolde et al.

Detection of a Yersinia pestis gene homologue in rodent samples
type: item
type: AcademicArticle
description: A homologue to a widely used genetic marker, pla, for Yersinia pestis has been identified in tissue samples of two species of rat (Rattus rattus and Rattus norvegicus) and of mice (Mus musculus and Apodemus sylvaticus) using a microarray based platform to screen for zoonotic pathogens of interest. Samples were from urban locations in the UK (Liverpool) and Canada (Vancouver). The results indicate the presence of an unknown bacterium that shares a homologue for the pla gene of Yersinia pestis, so caution should be taken when using this gene as a diagnostic marker.
format: application/pdf
format: text/html
creator: Timothy A. Giles
creator: Alex D. Greenwood
creator: Kyriakos Tsangaras
creator: Tom C. Giles
creator: Paul A. Barrow
creator: Duncan Hannant
creator: Abu-Bakr Abu-Median
creator: Lisa Yon
subject: Genetics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.2216
publisher: PeerJ Inc.
rights: © 2016 Giles et al.
abstract: A homologue to a widely used genetic marker, pla, for Yersinia pestis has been identified in tissue samples of two species of rat (Rattus rattus and Rattus norvegicus) and of mice (Mus musculus and Apodemus sylvaticus) using a microarray based platform to screen for zoonotic pathogens of interest. Samples were from urban locations in the UK (Liverpool) and Canada (Vancouver). The results indicate the presence of an unknown bacterium that shares a homologue for the pla gene of Yersinia pestis, so caution should be taken when using this gene as a diagnostic marker.
bibliographic citation: Giles et al. (2016) Detection of a Yersinia pestis gene homologue in rodent samples. PeerJ 4:e2216 https://doi.org/10.7717/peerj.2216
date submitted: 2016-03-16
date accepted: 2016-06-14
issued: 2016-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giles
  given name: Timothy A.
author list: Agent
  family name: Greenwood
  given name: Alex D.
author list: Agent
  family name: Tsangaras
  given name: Kyriakos
author list: Agent
  family name: Giles
  given name: Tom C.
author list: Agent
  family name: Barrow
  given name: Paul A.
author list: Agent
  family name: Hannant
  given name: Duncan
author list: Agent
  family name: Abu-Median
  given name: Abu-Bakr
author list: Agent
  family name: Yon
  given name: Lisa
doi: 10.7717/peerj.2216
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-17
copyright: ©2016 Giles et al.
attribution name: Giles et al.

Arktocara yakataga, a new fossil odontocete (Mammalia, Cetacea) from the Oligocene of Alaska and the antiquity of Platanistoidea
type: item
type: AcademicArticle
description: The diversification of crown cetacean lineages (i.e., crown Odontoceti and crown Mysticeti) occurred throughout the Oligocene, but it remains an ongoing challenge to resolve the phylogenetic pattern of their origins, especially with respect to stem lineages. One extant monotypic lineage, Platanista gangetica (the Ganges and Indus river dolphin), is the sole surviving member of the broader group Platanistoidea, with many fossil relatives that range from Oligocene to Miocene in age. Curiously, the highly threatened Platanista is restricted today to freshwater river systems of South Asia, yet nearly all fossil platanistoids are known globally from marine rocks, suggesting a marine ancestry for this group. In recent years, studies on the phylogenetic relationships in Platanistoidea have reached a general consensus about the membership of different sub-clades and putative extinct groups, although the position of some platanistoid groups (e.g., Waipatiidae) has been contested. Here we describe a new genus and species of fossil platanistoid, Arktocara yakataga, gen. et sp. nov. from the Oligocene of Alaska, USA. The type and only known specimen was collected from the marine Poul Creek Formation, a unit known to include Oligocene strata, exposed in the Yakutat City and Borough of Southeast Alaska. In our phylogenetic analysis of stem and node-based Platanistoidea, Arktocara falls within the node-based sub-clade Allodelphinidae as the sister taxon to Allodelphis pratti. With a geochronologic age between ∼29–24 million years old, Arktocara is among the oldest crown Odontoceti, reinforcing the long-standing view that the diversification for crown lineages must have occurred no later than the early Oligocene.
format: application/pdf
format: text/html
creator: Alexandra T. Boersma
creator: Nicholas D. Pyenson
subject: Ecology
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.2321
publisher: PeerJ Inc.
rights: © 2016 Boersma and Pyenson
abstract: The diversification of crown cetacean lineages (i.e., crown Odontoceti and crown Mysticeti) occurred throughout the Oligocene, but it remains an ongoing challenge to resolve the phylogenetic pattern of their origins, especially with respect to stem lineages. One extant monotypic lineage, Platanista gangetica (the Ganges and Indus river dolphin), is the sole surviving member of the broader group Platanistoidea, with many fossil relatives that range from Oligocene to Miocene in age. Curiously, the highly threatened Platanista is restricted today to freshwater river systems of South Asia, yet nearly all fossil platanistoids are known globally from marine rocks, suggesting a marine ancestry for this group. In recent years, studies on the phylogenetic relationships in Platanistoidea have reached a general consensus about the membership of different sub-clades and putative extinct groups, although the position of some platanistoid groups (e.g., Waipatiidae) has been contested. Here we describe a new genus and species of fossil platanistoid, Arktocara yakataga, gen. et sp. nov. from the Oligocene of Alaska, USA. The type and only known specimen was collected from the marine Poul Creek Formation, a unit known to include Oligocene strata, exposed in the Yakutat City and Borough of Southeast Alaska. In our phylogenetic analysis of stem and node-based Platanistoidea, Arktocara falls within the node-based sub-clade Allodelphinidae as the sister taxon to Allodelphis pratti. With a geochronologic age between ∼29–24 million years old, Arktocara is among the oldest crown Odontoceti, reinforcing the long-standing view that the diversification for crown lineages must have occurred no later than the early Oligocene.
bibliographic citation: Boersma et al. (2016) Arktocara yakataga, a new fossil odontocete (Mammalia, Cetacea) from the Oligocene of Alaska and the antiquity of Platanistoidea. PeerJ 4:e2321 https://doi.org/10.7717/peerj.2321
date submitted: 2016-05-16
date accepted: 2016-07-13
issued: 2016-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boersma
  given name: Alexandra T.
author list: Agent
  family name: Pyenson
  given name: Nicholas D.
doi: 10.7717/peerj.2321
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-16
copyright: ©2016 Boersma and Pyenson
attribution name: Boersma and Pyenson

Ancient phylogenetic divergence of the enigmatic African rodent Zenkerella and the origin of anomalurid gliding
type: item
type: AcademicArticle
description: The “scaly-tailed squirrels” of the rodent family Anomaluridae have a long evolutionary history in Africa, and are now represented by two gliding genera (Anomalurus and Idiurus) and a rare and obscure genus (Zenkerella) that has never been observed alive by mammalogists. Zenkerella shows no anatomical adaptations for gliding, but has traditionally been grouped with the glider Idiurus on the basis of craniodental similarities, implying that either the Zenkerella lineage lost its gliding adaptations, or that Anomalurus and Idiurus evolved theirs independently. Here we present the first nuclear and mitochondrial DNA sequences of Zenkerella, based on recently recovered whole-body specimens from Bioko Island (Equatorial Guinea), which show unambiguously that Zenkerella is the sister taxon of Anomalurus and Idiurus. These data indicate that gliding likely evolved only once within Anomaluridae, and that there were no subsequent evolutionary reversals. We combine this new molecular evidence with morphological data from living and extinct anomaluromorph rodents and estimate that the lineage leading to Zenkerella has been evolving independently in Africa since the early Eocene, approximately 49 million years ago. Recently discovered fossils further attest to the antiquity of the lineage leading to Zenkerella, which can now be recognized as a classic example of a “living fossil,” about which we know remarkably little. The osteological markers of gliding are estimated to have evolved along the stem lineage of the Anomalurus–Idiurus clade by the early Oligocene, potentially indicating that this adaptation evolved in response to climatic perturbations at the Eocene–Oligocene boundary (∼34 million years ago).
format: application/pdf
format: text/html
creator: Steven Heritage
creator: David Fernández
creator: Hesham M. Sallam
creator: Drew T. Cronin
creator: José Manuel Esara Echube
creator: Erik R. Seiffert
subject: Evolutionary Studies
subject: Genetics
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2320
publisher: PeerJ Inc.
rights: © 2016 Heritage et al.
abstract: The “scaly-tailed squirrels” of the rodent family Anomaluridae have a long evolutionary history in Africa, and are now represented by two gliding genera (Anomalurus and Idiurus) and a rare and obscure genus (Zenkerella) that has never been observed alive by mammalogists. Zenkerella shows no anatomical adaptations for gliding, but has traditionally been grouped with the glider Idiurus on the basis of craniodental similarities, implying that either the Zenkerella lineage lost its gliding adaptations, or that Anomalurus and Idiurus evolved theirs independently. Here we present the first nuclear and mitochondrial DNA sequences of Zenkerella, based on recently recovered whole-body specimens from Bioko Island (Equatorial Guinea), which show unambiguously that Zenkerella is the sister taxon of Anomalurus and Idiurus. These data indicate that gliding likely evolved only once within Anomaluridae, and that there were no subsequent evolutionary reversals. We combine this new molecular evidence with morphological data from living and extinct anomaluromorph rodents and estimate that the lineage leading to Zenkerella has been evolving independently in Africa since the early Eocene, approximately 49 million years ago. Recently discovered fossils further attest to the antiquity of the lineage leading to Zenkerella, which can now be recognized as a classic example of a “living fossil,” about which we know remarkably little. The osteological markers of gliding are estimated to have evolved along the stem lineage of the Anomalurus–Idiurus clade by the early Oligocene, potentially indicating that this adaptation evolved in response to climatic perturbations at the Eocene–Oligocene boundary (∼34 million years ago).
bibliographic citation: Heritage et al. (2016) Ancient phylogenetic divergence of the enigmatic African rodent Zenkerella and the origin of anomalurid gliding. PeerJ 4:e2320 https://doi.org/10.7717/peerj.2320
date submitted: 2016-04-21
date accepted: 2016-07-13
issued: 2016-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heritage
  given name: Steven
author list: Agent
  family name: Fernández
  given name: David
author list: Agent
  family name: Sallam
  given name: Hesham M.
author list: Agent
  family name: Cronin
  given name: Drew T.
author list: Agent
  family name: Esara Echube
  given name: José Manuel
author list: Agent
  family name: Seiffert
  given name: Erik R.
doi: 10.7717/peerj.2320
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-16
copyright: ©2016 Heritage et al.
attribution name: Heritage et al.

The adder (Vipera berus) in Southern Altay Mountains: population characteristics, distribution, morphology and phylogenetic position
type: item
type: AcademicArticle
description: As the most widely distributed snake in Eurasia, the adder (Vipera berus) has been extensively investigated in Europe but poorly understood in Asia. The Southern Altay Mountains represent the adder’s southern distribution limit in Central Asia, whereas its population status has never been assessed. We conducted, for the first time, field surveys for the adder at two areas of Southern Altay Mountains using a combination of line transects and random searches. We also described the morphological characteristics of the collected specimens and conducted analyses of external morphology and molecular phylogeny. The results showed that the adder distributed in both survey sites and we recorded a total of 34 sightings. In Kanas river valley, the estimated encounter rate over a total of 137 km transects was 0.15 ± 0.05 sightings/km. The occurrence of melanism was only 17%. The small size was typical for the adders in Southern Altay Mountains in contrast to other geographic populations of the nominate subspecies. A phylogenetic tree obtained by Bayesian Inference based on DNA sequences of the mitochondrial cytochrome b (1,023 bp) grouped them within the Northern clade of the species but failed to separate them from the subspecies V. b. sachalinensis. Our discovery extends the distribution range of V. berus and provides a basis for further researches. We discuss the hypothesis that the adder expands its distribution border to the southwest along the mountains’ elevation gradient, but the population abundance declines gradually due to a drying climate.
format: application/pdf
format: text/html
creator: Shaopeng Cui
creator: Xiao Luo
creator: Daiqiang Chen
creator: Jizhou Sun
creator: Hongjun Chu
creator: Chunwang Li
creator: Zhigang Jiang
subject: Biodiversity
subject: Ecology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2342
publisher: PeerJ Inc.
rights: © 2016 Cui et al.
abstract: As the most widely distributed snake in Eurasia, the adder (Vipera berus) has been extensively investigated in Europe but poorly understood in Asia. The Southern Altay Mountains represent the adder’s southern distribution limit in Central Asia, whereas its population status has never been assessed. We conducted, for the first time, field surveys for the adder at two areas of Southern Altay Mountains using a combination of line transects and random searches. We also described the morphological characteristics of the collected specimens and conducted analyses of external morphology and molecular phylogeny. The results showed that the adder distributed in both survey sites and we recorded a total of 34 sightings. In Kanas river valley, the estimated encounter rate over a total of 137 km transects was 0.15 ± 0.05 sightings/km. The occurrence of melanism was only 17%. The small size was typical for the adders in Southern Altay Mountains in contrast to other geographic populations of the nominate subspecies. A phylogenetic tree obtained by Bayesian Inference based on DNA sequences of the mitochondrial cytochrome b (1,023 bp) grouped them within the Northern clade of the species but failed to separate them from the subspecies V. b. sachalinensis. Our discovery extends the distribution range of V. berus and provides a basis for further researches. We discuss the hypothesis that the adder expands its distribution border to the southwest along the mountains’ elevation gradient, but the population abundance declines gradually due to a drying climate.
bibliographic citation: Cui et al. (2016) The adder (Vipera berus) in Southern Altay Mountains: population characteristics, distribution, morphology and phylogenetic position. PeerJ 4:e2342 https://doi.org/10.7717/peerj.2342
date submitted: 2016-04-21
date accepted: 2016-07-18
issued: 2016-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cui
  given name: Shaopeng
author list: Agent
  family name: Luo
  given name: Xiao
author list: Agent
  family name: Chen
  given name: Daiqiang
author list: Agent
  family name: Sun
  given name: Jizhou
author list: Agent
  family name: Chu
  given name: Hongjun
author list: Agent
  family name: Li
  given name: Chunwang
author list: Agent
  family name: Jiang
  given name: Zhigang
doi: 10.7717/peerj.2342
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-16
copyright: ©2016 Cui et al.
attribution name: Cui et al.

Evolution of morphological and climatic adaptations in Veronica L. (Plantaginaceae)
type: item
type: AcademicArticle
description: Perennials and annuals apply different strategies to adapt to the adverse environment, based on ‘tolerance’ and ‘avoidance’, respectively. To understand lifespan evolution and its impact on plant adaptability, we carried out a comparative study of perennials and annuals in the genus Veronica from a phylogenetic perspective. The results showed that ancestors of the genus Veronicawere likely to be perennial plants. Annual life history of Veronica has evolved multiple times and subtrees with more annual species have a higher substitution rate. Annuals can adapt to more xeric habitats than perennials. This indicates that annuals are more drought-resistant than their perennial relatives. Due to adaptation to similar selective pressures, parallel evolution occurs in morphological characters among annual species of Veronica.
format: application/pdf
format: text/html
creator: Jian-Cheng Wang
creator: Bo-Rong Pan
creator: Dirk C. Albach
subject: Ecology
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.2333
publisher: PeerJ Inc.
rights: © 2016 Wang et al.
abstract: Perennials and annuals apply different strategies to adapt to the adverse environment, based on ‘tolerance’ and ‘avoidance’, respectively. To understand lifespan evolution and its impact on plant adaptability, we carried out a comparative study of perennials and annuals in the genus Veronica from a phylogenetic perspective. The results showed that ancestors of the genus Veronicawere likely to be perennial plants. Annual life history of Veronica has evolved multiple times and subtrees with more annual species have a higher substitution rate. Annuals can adapt to more xeric habitats than perennials. This indicates that annuals are more drought-resistant than their perennial relatives. Due to adaptation to similar selective pressures, parallel evolution occurs in morphological characters among annual species of Veronica.
bibliographic citation: Wang et al. (2016) Evolution of morphological and climatic adaptations in Veronica L. (Plantaginaceae). PeerJ 4:e2333 https://doi.org/10.7717/peerj.2333
date submitted: 2016-05-09
date accepted: 2016-07-14
issued: 2016-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jian-Cheng
author list: Agent
  family name: Pan
  given name: Bo-Rong
author list: Agent
  family name: Albach
  given name: Dirk C.
doi: 10.7717/peerj.2333
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-16
copyright: ©2016 Wang et al.
attribution name: Wang et al.

The health care and life sciences community profile for dataset descriptions
type: item
type: AcademicArticle
description: Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets.
format: application/pdf
format: text/html
creator: Michel Dumontier
creator: Alasdair J.G. Gray
creator: M. Scott Marshall
creator: Vladimir Alexiev
creator: Peter Ansell
creator: Gary Bader
creator: Joachim Baran
creator: Jerven T. Bolleman
creator: Alison Callahan
creator: José Cruz-Toledo
creator: Pascale Gaudet
creator: Erich A. Gombocz
creator: Alejandra N. Gonzalez-Beltran
creator: Paul Groth
creator: Melissa Haendel
creator: Maori Ito
creator: Simon Jupp
creator: Nick Juty
creator: Toshiaki Katayama
creator: Norio Kobayashi
creator: Kalpana Krishnaswami
creator: Camille Laibe
creator: Nicolas Le Novère
creator: Simon Lin
creator: James Malone
creator: Michael Miller
creator: Christopher J. Mungall
creator: Laurens Rietveld
creator: Sarala M. Wimalaratne
creator: Atsuko Yamaguchi
subject: Bioinformatics
subject: Taxonomy
subject: Computational Science
description: doi:10.7717/peerj.2331
publisher: PeerJ Inc.
rights: © 2016 Dumontier et al.
abstract: Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets.
bibliographic citation: Dumontier et al. (2016) The health care and life sciences community profile for dataset descriptions. PeerJ 4:e2331 https://doi.org/10.7717/peerj.2331
date submitted: 2016-04-15
date accepted: 2016-07-14
issued: 2016-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dumontier
  given name: Michel
author list: Agent
  family name: Gray
  given name: Alasdair J.G.
author list: Agent
  family name: Marshall
  given name: M. Scott
author list: Agent
  family name: Alexiev
  given name: Vladimir
author list: Agent
  family name: Ansell
  given name: Peter
author list: Agent
  family name: Bader
  given name: Gary
author list: Agent
  family name: Baran
  given name: Joachim
author list: Agent
  family name: Bolleman
  given name: Jerven T.
author list: Agent
  family name: Callahan
  given name: Alison
author list: Agent
  family name: Cruz-Toledo
  given name: José
author list: Agent
  family name: Gaudet
  given name: Pascale
author list: Agent
  family name: Gombocz
  given name: Erich A.
author list: Agent
  family name: Gonzalez-Beltran
  given name: Alejandra N.
author list: Agent
  family name: Groth
  given name: Paul
author list: Agent
  family name: Haendel
  given name: Melissa
author list: Agent
  family name: Ito
  given name: Maori
author list: Agent
  family name: Jupp
  given name: Simon
author list: Agent
  family name: Juty
  given name: Nick
author list: Agent
  family name: Katayama
  given name: Toshiaki
author list: Agent
  family name: Kobayashi
  given name: Norio
author list: Agent
  family name: Krishnaswami
  given name: Kalpana
author list: Agent
  family name: Laibe
  given name: Camille
author list: Agent
  family name: Le Novère
  given name: Nicolas
author list: Agent
  family name: Lin
  given name: Simon
author list: Agent
  family name: Malone
  given name: James
doi: 10.7717/peerj.2331
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-16
copyright: ©2016 Dumontier et al.
attribution name: Dumontier et al.

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

Agent
family name: Miller
given name: Michael

Agent
family name: Mungall
given name: Christopher J.

Agent
family name: Rietveld
given name: Laurens

Agent
family name: Wimalaratne
given name: Sarala M.

Agent
family name: Yamaguchi
given name: Atsuko