PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Transfer of intestinal bacterial components to mammary secretions in the cow
items: Cyclic nucleotide binding and structural changes in the isolated GAF domain of Anabaena adenylyl cyclase, CyaB2
items: The influences of N-acetyl cysteine (NAC) on the cytotoxicity and mechanical properties of Poly-methylmethacrylate (PMMA)-based dental resin
items: Does the sex difference in competitiveness decrease in selective sub-populations? A test with intercollegiate distance runners
items: Validation of the Emotiv EPOC EEG system for research quality auditory event-related potentials in children
items: The first occurrence of the enigmatic archosauriform Crosbysaurus Heckert 2004 from the Chinle Formation of southern Utah
items: Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species
items: Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)
items: Water availability as an agent of selection in introduced populations of Arabidopsis thaliana: impacts on flowering time evolution
items: Co-father relationships among the Suruí (Paiter) of Brazil

Transfer of intestinal bacterial components to mammary secretions in the cow
type: item
type: AcademicArticle
description: Results from large multicentre epidemiological studies suggest an association between the consumption of raw milk and a reduced incidence of allergy and asthma in children. Although the underlying mechanisms for this association are yet to be confirmed, researchers have investigated whether bacteria or bacterial components that naturally occur in cow’s milk are responsible for modulating the immune system to reduce the risk of allergic diseases. Previous research in human and mice suggests that bacterial components derived from the maternal intestine are transported to breast milk through the bloodstream. The aim of our study was to assess whether a similar mechanism of bacterial trafficking could occur in the cow. Through the application of culture-independent methodology, we investigated the microbial composition and diversity of milk, blood and feces of healthy lactating cows. We found that a small number of bacterial OTUs belonging to the genera Ruminococcus and Bifidobacterium, and the Peptostreptococcaceae family were present in all three samples from the same individual animals. Although these results do not confirm the hypothesis that trafficking of intestinal bacteria into mammary secretions does occur in the cow, they support the existence of an endogenous entero-mammary pathway for some bacterial components during lactation in the cow. Further research is required to define the specific mechanisms by which gut bacteria are transported into the mammary gland of the cow, and the health implications of such bacteria being present in milk.
format: application/pdf
format: text/html
creator: Wayne Young
creator: Brad C. Hine
creator: Olivia A.M. Wallace
creator: Megan Callaghan
creator: Rodrigo Bibiloni
subject: Biotechnology
subject: Genetics
subject: Microbiology
description: doi:10.7717/peerj.888
publisher: PeerJ Inc.
rights: © 2015 Young et al.
abstract: Results from large multicentre epidemiological studies suggest an association between the consumption of raw milk and a reduced incidence of allergy and asthma in children. Although the underlying mechanisms for this association are yet to be confirmed, researchers have investigated whether bacteria or bacterial components that naturally occur in cow’s milk are responsible for modulating the immune system to reduce the risk of allergic diseases. Previous research in human and mice suggests that bacterial components derived from the maternal intestine are transported to breast milk through the bloodstream. The aim of our study was to assess whether a similar mechanism of bacterial trafficking could occur in the cow. Through the application of culture-independent methodology, we investigated the microbial composition and diversity of milk, blood and feces of healthy lactating cows. We found that a small number of bacterial OTUs belonging to the genera Ruminococcus and Bifidobacterium, and the Peptostreptococcaceae family were present in all three samples from the same individual animals. Although these results do not confirm the hypothesis that trafficking of intestinal bacteria into mammary secretions does occur in the cow, they support the existence of an endogenous entero-mammary pathway for some bacterial components during lactation in the cow. Further research is required to define the specific mechanisms by which gut bacteria are transported into the mammary gland of the cow, and the health implications of such bacteria being present in milk.
bibliographic citation: Young et al. (2015) Transfer of intestinal bacterial components to mammary secretions in the cow. PeerJ 3:e888 https://doi.org/10.7717/peerj.888
date submitted: 2014-11-21
date accepted: 2015-03-20
issued: 2015-04-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Young
  given name: Wayne
author list: Agent
  family name: Hine
  given name: Brad C.
author list: Agent
  family name: Wallace
  given name: Olivia A.M.
author list: Agent
  family name: Callaghan
  given name: Megan
author list: Agent
  family name: Bibiloni
  given name: Rodrigo
doi: 10.7717/peerj.888
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-23
copyright: © 2015 Young et al.
attribution name: Young et al.

Cyclic nucleotide binding and structural changes in the isolated GAF domain of Anabaena adenylyl cyclase, CyaB2
type: item
type: AcademicArticle
description: GAF domains are a large family of regulatory domains, and a subset are found associated with enzymes involved in cyclic nucleotide (cNMP) metabolism such as adenylyl cyclases and phosphodiesterases. CyaB2, an adenylyl cyclase from Anabaena, contains two GAF domains in tandem at the N-terminus and an adenylyl cyclase domain at the C-terminus. Cyclic AMP, but not cGMP, binding to the GAF domains of CyaB2 increases the activity of the cyclase domain leading to enhanced synthesis of cAMP. Here we show that the isolated GAFb domain of CyaB2 can bind both cAMP and cGMP, and enhanced specificity for cAMP is observed only when both the GAFa and the GAFb domains are present in tandem (GAFab domain). In silico docking and mutational analysis identified distinct residues important for interaction with either cAMP or cGMP in the GAFb domain. Structural changes associated with ligand binding to the GAF domains could not be detected by bioluminescence resonance energy transfer (BRET) experiments. However, amide hydrogen-deuterium exchange mass spectrometry (HDXMS) experiments provided insights into the structural basis for cAMP-induced allosteric regulation of the GAF domains, and differences in the changes induced by cAMP and cGMP binding to the GAF domain. Thus, our findings could allow the development of molecules that modulate the allosteric regulation by GAF domains present in pharmacologically relevant proteins.
format: application/pdf
format: text/html
creator: Kabir Hassan Biswas
creator: Suguna Badireddy
creator: Abinaya Rajendran
creator: Ganesh Srinivasan Anand
creator: Sandhya S. Visweswariah
subject: Biochemistry
description: doi:10.7717/peerj.882
publisher: PeerJ Inc.
rights: © 2015 Biswas et al.
abstract: GAF domains are a large family of regulatory domains, and a subset are found associated with enzymes involved in cyclic nucleotide (cNMP) metabolism such as adenylyl cyclases and phosphodiesterases. CyaB2, an adenylyl cyclase from Anabaena, contains two GAF domains in tandem at the N-terminus and an adenylyl cyclase domain at the C-terminus. Cyclic AMP, but not cGMP, binding to the GAF domains of CyaB2 increases the activity of the cyclase domain leading to enhanced synthesis of cAMP. Here we show that the isolated GAFb domain of CyaB2 can bind both cAMP and cGMP, and enhanced specificity for cAMP is observed only when both the GAFa and the GAFb domains are present in tandem (GAFab domain). In silico docking and mutational analysis identified distinct residues important for interaction with either cAMP or cGMP in the GAFb domain. Structural changes associated with ligand binding to the GAF domains could not be detected by bioluminescence resonance energy transfer (BRET) experiments. However, amide hydrogen-deuterium exchange mass spectrometry (HDXMS) experiments provided insights into the structural basis for cAMP-induced allosteric regulation of the GAF domains, and differences in the changes induced by cAMP and cGMP binding to the GAF domain. Thus, our findings could allow the development of molecules that modulate the allosteric regulation by GAF domains present in pharmacologically relevant proteins.
bibliographic citation: Biswas et al. (2015) Cyclic nucleotide binding and structural changes in the isolated GAF domain of Anabaena adenylyl cyclase, CyaB2. PeerJ 3:e882 https://doi.org/10.7717/peerj.882
date submitted: 2014-11-13
date accepted: 2015-03-18
issued: 2015-04-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Biswas
  given name: Kabir Hassan
author list: Agent
  family name: Badireddy
  given name: Suguna
author list: Agent
  family name: Rajendran
  given name: Abinaya
author list: Agent
  family name: Anand
  given name: Ganesh Srinivasan
author list: Agent
  family name: Visweswariah
  given name: Sandhya S.
doi: 10.7717/peerj.882
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-23
copyright: © 2015 Biswas et al.
attribution name: Biswas et al.

The influences of N-acetyl cysteine (NAC) on the cytotoxicity and mechanical properties of Poly-methylmethacrylate (PMMA)-based dental resin
type: item
type: AcademicArticle
description: Objectives. This study aimed to investigate the influences of N-acetyl cysteine (NAC) on cytotoxicity and mechanical properties of Poly-methylmethacrylate (PMMA) dental resins. Methods. Experimental PMMA resin was prepared by incorporating various concentrations of NAC (0, 0.15, 0.3, 0.6 and 0.9 wt.%). MTT assay was performed to investigate viability of human dental pulp cells after exposure to extract of PMMA resin with or without NAC. Cell adhesion on resin specimens was examined with scanning electron microscopy. Degree of conversion was studied with Fourier Transform Infrared Spectroscopy (FTIR). Flexural strength, microhardness and surface roughness was evaluated using a universal testing machine, microhardness tester and optical profilometer, respectively. Results. Incorporation of NAC into PMMA resin significantly reduced its cytotoxicity and enhanced cell adhesion on its surface. NAC induced negative influences on the mechanical and physical properties of PMMA resin in a dose-dependent manner. The degree of conversion for all experimental PMMA resins reached as high as 72% after 24 h of polymerization. All the tested properties were maintained when the concentration of incorporated NAC was 0.15 wt.%. Conclusion. The addition of 0.15 wt.% NAC remarkably improved biocompatibility of PMMA resin without exerting significant negative influence on its mechanical and physical properties.
format: application/pdf
format: text/html
creator: Yang Jiao
creator: Sai Ma
creator: Jing Li
creator: Lequn Shan
creator: Yanwei Yang
creator: Meng Li
creator: Jihua Chen
subject: Dentistry
description: doi:10.7717/peerj.868
publisher: PeerJ Inc.
rights: © 2015 Jiao et al.
abstract: Objectives. This study aimed to investigate the influences of N-acetyl cysteine (NAC) on cytotoxicity and mechanical properties of Poly-methylmethacrylate (PMMA) dental resins. Methods. Experimental PMMA resin was prepared by incorporating various concentrations of NAC (0, 0.15, 0.3, 0.6 and 0.9 wt.%). MTT assay was performed to investigate viability of human dental pulp cells after exposure to extract of PMMA resin with or without NAC. Cell adhesion on resin specimens was examined with scanning electron microscopy. Degree of conversion was studied with Fourier Transform Infrared Spectroscopy (FTIR). Flexural strength, microhardness and surface roughness was evaluated using a universal testing machine, microhardness tester and optical profilometer, respectively. Results. Incorporation of NAC into PMMA resin significantly reduced its cytotoxicity and enhanced cell adhesion on its surface. NAC induced negative influences on the mechanical and physical properties of PMMA resin in a dose-dependent manner. The degree of conversion for all experimental PMMA resins reached as high as 72% after 24 h of polymerization. All the tested properties were maintained when the concentration of incorporated NAC was 0.15 wt.%. Conclusion. The addition of 0.15 wt.% NAC remarkably improved biocompatibility of PMMA resin without exerting significant negative influence on its mechanical and physical properties.
bibliographic citation: Jiao et al. (2015) The influences of N-acetyl cysteine (NAC) on the cytotoxicity and mechanical properties of Poly-methylmethacrylate (PMMA)-based dental resin. PeerJ 3:e868 https://doi.org/10.7717/peerj.868
date submitted: 2015-01-06
date accepted: 2015-03-10
issued: 2015-04-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiao
  given name: Yang
author list: Agent
  family name: Ma
  given name: Sai
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Shan
  given name: Lequn
author list: Agent
  family name: Yang
  given name: Yanwei
author list: Agent
  family name: Li
  given name: Meng
author list: Agent
  family name: Chen
  given name: Jihua
doi: 10.7717/peerj.868
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-23
copyright: © 2015 Jiao et al.
attribution name: Jiao et al.

Does the sex difference in competitiveness decrease in selective sub-populations? A test with intercollegiate distance runners
type: item
type: AcademicArticle
description: Sex differences in some preferences and motivations are well established, but it is unclear whether they persist in selective sub-populations, such as expert financial decision makers, top scientists, or elite athletes. We addressed this issue by studying competitiveness in 1,147 varsity intercollegiate distance runners. As expected, across all runners, men reported greater competitiveness with two previously validated instruments, greater competitiveness on a new elite competitiveness scale, and greater training volume, a known correlate of competitiveness. Among faster runners, the sex difference decreased for one measure of competitiveness but did not decrease for the two other competitiveness measures or either measure of training volume. Across NCAA athletic divisions (DI, DII, DIII), the sex difference did not decrease for any competitiveness or training measure. Further analyses showed that these sex differences could not be attributed to women suffering more injuries or facing greater childcare responsibilities. However, women did report greater commitment than men to their academic studies, suggesting a sex difference in priorities. Therefore, policies aiming to provide men and women with equal opportunities to flourish should acknowledge that sex differences in some kinds of preferences and motivation may persist even in selective sub-populations.
format: application/pdf
format: text/html
creator: Robert O. Deaner
creator: Aaron Lowen
creator: William Rogers
creator: Eric Saksa
subject: Anthropology
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.884
publisher: PeerJ Inc.
rights: © 2015 Deaner et al.
abstract: Sex differences in some preferences and motivations are well established, but it is unclear whether they persist in selective sub-populations, such as expert financial decision makers, top scientists, or elite athletes. We addressed this issue by studying competitiveness in 1,147 varsity intercollegiate distance runners. As expected, across all runners, men reported greater competitiveness with two previously validated instruments, greater competitiveness on a new elite competitiveness scale, and greater training volume, a known correlate of competitiveness. Among faster runners, the sex difference decreased for one measure of competitiveness but did not decrease for the two other competitiveness measures or either measure of training volume. Across NCAA athletic divisions (DI, DII, DIII), the sex difference did not decrease for any competitiveness or training measure. Further analyses showed that these sex differences could not be attributed to women suffering more injuries or facing greater childcare responsibilities. However, women did report greater commitment than men to their academic studies, suggesting a sex difference in priorities. Therefore, policies aiming to provide men and women with equal opportunities to flourish should acknowledge that sex differences in some kinds of preferences and motivation may persist even in selective sub-populations.
bibliographic citation: Deaner et al. (2015) Does the sex difference in competitiveness decrease in selective sub-populations? A test with intercollegiate distance runners. PeerJ 3:e884 https://doi.org/10.7717/peerj.884
date submitted: 2015-01-28
date accepted: 2015-03-19
issued: 2015-04-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deaner
  given name: Robert O.
author list: Agent
  family name: Lowen
  given name: Aaron
author list: Agent
  family name: Rogers
  given name: William
author list: Agent
  family name: Saksa
  given name: Eric
doi: 10.7717/peerj.884
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-21
copyright: © 2015 Deaner et al.
attribution name: Deaner et al.

Validation of the Emotiv EPOC EEG system for research quality auditory event-related potentials in children
type: item
type: AcademicArticle
description: Background. Previous work has demonstrated that a commercial gaming electroencephalography (EEG) system, Emotiv EPOC, can be adjusted to provide valid auditory event-related potentials (ERPs) in adults that are comparable to ERPs recorded by a research-grade EEG system, Neuroscan. The aim of the current study was to determine if the same was true for children. Method. An adapted Emotiv EPOC system and Neuroscan system were used to make simultaneous EEG recordings in nineteen 6- to 12-year-old children under “passive” and “active” listening conditions. In the passive condition, children were instructed to watch a silent DVD and ignore 566 standard (1,000 Hz) and 100 deviant (1,200 Hz) tones. In the active condition, they listened to the same stimuli, and were asked to count the number of ‘high’ (i.e., deviant) tones. Results. Intraclass correlations (ICCs) indicated that the ERP morphology recorded with the two systems was very similar for the P1, N1, P2, N2, and P3 ERP peaks (r = .82 to .95) in both passive and active conditions, and less so, though still strong, for mismatch negativity ERP component (MMN; r = .67 to .74). There were few differences between peak amplitude and latency estimates for the two systems. Conclusions. An adapted EPOC EEG system can be used to index children’s late auditory ERP peaks (i.e., P1, N1, P2, N2, P3) and their MMN ERP component.
format: application/pdf
format: text/html
creator: Nicholas A. Badcock
creator: Kathryn A. Preece
creator: Bianca de Wit
creator: Katharine Glenn
creator: Nora Fieder
creator: Johnson Thie
creator: Genevieve McArthur
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.907
publisher: PeerJ Inc.
rights: © 2015 Badcock et al.
abstract: Background. Previous work has demonstrated that a commercial gaming electroencephalography (EEG) system, Emotiv EPOC, can be adjusted to provide valid auditory event-related potentials (ERPs) in adults that are comparable to ERPs recorded by a research-grade EEG system, Neuroscan. The aim of the current study was to determine if the same was true for children. Method. An adapted Emotiv EPOC system and Neuroscan system were used to make simultaneous EEG recordings in nineteen 6- to 12-year-old children under “passive” and “active” listening conditions. In the passive condition, children were instructed to watch a silent DVD and ignore 566 standard (1,000 Hz) and 100 deviant (1,200 Hz) tones. In the active condition, they listened to the same stimuli, and were asked to count the number of ‘high’ (i.e., deviant) tones. Results. Intraclass correlations (ICCs) indicated that the ERP morphology recorded with the two systems was very similar for the P1, N1, P2, N2, and P3 ERP peaks (r = .82 to .95) in both passive and active conditions, and less so, though still strong, for mismatch negativity ERP component (MMN; r = .67 to .74). There were few differences between peak amplitude and latency estimates for the two systems. Conclusions. An adapted EPOC EEG system can be used to index children’s late auditory ERP peaks (i.e., P1, N1, P2, N2, P3) and their MMN ERP component.
bibliographic citation: Badcock et al. (2015) Validation of the Emotiv EPOC EEG system for research quality auditory event-related potentials in children. PeerJ 3:e907 https://doi.org/10.7717/peerj.907
date submitted: 2014-11-06
date accepted: 2015-04-01
issued: 2015-04-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Badcock
  given name: Nicholas A.
author list: Agent
  family name: Preece
  given name: Kathryn A.
author list: Agent
  family name: de Wit
  given name: Bianca
author list: Agent
  family name: Glenn
  given name: Katharine
author list: Agent
  family name: Fieder
  given name: Nora
author list: Agent
  family name: Thie
  given name: Johnson
author list: Agent
  family name: McArthur
  given name: Genevieve
doi: 10.7717/peerj.907
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-21
copyright: © 2015 Badcock et al.
attribution name: Badcock et al.

The first occurrence of the enigmatic archosauriform Crosbysaurus Heckert 2004 from the Chinle Formation of southern Utah
type: item
type: AcademicArticle
description: Originally identified as an ornithischian dinosaur, Crosbysaurus harrisae has been found in New Mexico, Arizona, and its type locality in Texas, as well as in North Carolina. The genus has been reassessed by other workers in light of reinterpretations about the postcrania of another putative Triassic ornithischian, Revueltosaurus. The understanding of Triassic dental faunas has become more complicated by the extreme convergence between pseudosuchian archosaurs and ornithischian dinosaur dental morphologies. We report here on a new specimen of Crosbysaurus (MNA V10666) from the Chinle Formation at Comb Ridge in southeastern Utah. This new specimen is assigned to Crosbysaurus sp. on the basis of the unique compound posterior denticles, labiolingual width, and curvature. While MNA V10666 does not help resolve the affinities of Crosbysaurus, it does represent the extension of the geographic range of this taxon for approximately 250 kilometers. This is the first record of the genus Crosbysaurus in Utah and as such it represents the northernmost known record of this taxon. This indicates that Crosbysaurus was not limited to the southern area of the Chinle/Dockum deposition but instead was widespread across the Late Triassic paleoriver systems of western Pangea. The reported specimen was found in close association with a typical Late Triassic Chinle fauna, including phytosaurs, metoposaurs, and dinosauromorphs.
format: application/pdf
format: text/html
creator: Robert J. Gay
creator: Isabella St. Aude
subject: Paleontology
description: doi:10.7717/peerj.905
publisher: PeerJ Inc.
rights: © 2015 Gay and Aude
abstract: Originally identified as an ornithischian dinosaur, Crosbysaurus harrisae has been found in New Mexico, Arizona, and its type locality in Texas, as well as in North Carolina. The genus has been reassessed by other workers in light of reinterpretations about the postcrania of another putative Triassic ornithischian, Revueltosaurus. The understanding of Triassic dental faunas has become more complicated by the extreme convergence between pseudosuchian archosaurs and ornithischian dinosaur dental morphologies. We report here on a new specimen of Crosbysaurus (MNA V10666) from the Chinle Formation at Comb Ridge in southeastern Utah. This new specimen is assigned to Crosbysaurus sp. on the basis of the unique compound posterior denticles, labiolingual width, and curvature. While MNA V10666 does not help resolve the affinities of Crosbysaurus, it does represent the extension of the geographic range of this taxon for approximately 250 kilometers. This is the first record of the genus Crosbysaurus in Utah and as such it represents the northernmost known record of this taxon. This indicates that Crosbysaurus was not limited to the southern area of the Chinle/Dockum deposition but instead was widespread across the Late Triassic paleoriver systems of western Pangea. The reported specimen was found in close association with a typical Late Triassic Chinle fauna, including phytosaurs, metoposaurs, and dinosauromorphs.
bibliographic citation: Gay et al. (2015) The first occurrence of the enigmatic archosauriform Crosbysaurus Heckert 2004 from the Chinle Formation of southern Utah. PeerJ 3:e905 https://doi.org/10.7717/peerj.905
date submitted: 2014-11-13
date accepted: 2015-03-31
issued: 2015-04-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gay
  given name: Robert J.
author list: Agent
  family name: Aude
  given name: Isabella St.
doi: 10.7717/peerj.905
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-21
copyright: © 2015 Gay and Aude
attribution name: Gay and Aude

Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species
type: item
type: AcademicArticle
description: Comparing inferences among datasets generated using short read sequencing may provide insight into the concerted impacts of divergence, gene flow and selection across organisms, but comparisons are complicated by biases introduced during dataset assembly. Sequence similarity thresholds allow the de novo assembly of short reads into clusters of alleles representing different loci, but the resulting datasets are sensitive to both the similarity threshold used and to the variation naturally present in the organism under study. Thresholds that require high sequence similarity among reads for assembly (stringent thresholds) as well as highly variable species may result in datasets in which divergent alleles are lost or divided into separate loci (‘over-splitting’), whereas liberal thresholds increase the risk of paralogous loci being combined into a single locus (‘under-splitting’). Comparisons among datasets or species are therefore potentially biased if different similarity thresholds are applied or if the species differ in levels of within-lineage genetic variation. We examine the impact of a range of similarity thresholds on assembly of empirical short read datasets from populations of four different non-model bird lineages (species or species pairs) with different levels of genetic divergence. We find that, in all species, stringent similarity thresholds result in fewer alleles per locus than more liberal thresholds, which appears to be the result of high levels of over-splitting. The frequency of putative under-splitting, conversely, is low at all thresholds. Inferred genetic distances between individuals, gene tree depths, and estimates of the ancestral mutation-scaled effective population size (θ) differ depending upon the similarity threshold applied. Relative differences in inferences across species differ even when the same threshold is applied, but may be dramatically different when datasets assembled under different thresholds are compared. These differences…
format: application/pdf
format: text/html
creator: Michael G. Harvey
creator: Caroline Duffie Judy
creator: Glenn F. Seeholzer
creator: James M. Maley
creator: Gary R. Graves
creator: Robb T. Brumfield
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.895
publisher: PeerJ Inc.
rights: © 2015 Harvey et al.
abstract: Comparing inferences among datasets generated using short read sequencing may provide insight into the concerted impacts of divergence, gene flow and selection across organisms, but comparisons are complicated by biases introduced during dataset assembly. Sequence similarity thresholds allow the de novo assembly of short reads into clusters of alleles representing different loci, but the resulting datasets are sensitive to both the similarity threshold used and to the variation naturally present in the organism under study. Thresholds that require high sequence similarity among reads for assembly (stringent thresholds) as well as highly variable species may result in datasets in which divergent alleles are lost or divided into separate loci (‘over-splitting’), whereas liberal thresholds increase the risk of paralogous loci being combined into a single locus (‘under-splitting’). Comparisons among datasets or species are therefore potentially biased if different similarity thresholds are applied or if the species differ in levels of within-lineage genetic variation. We examine the impact of a range of similarity thresholds on assembly of empirical short read datasets from populations of four different non-model bird lineages (species or species pairs) with different levels of genetic divergence. We find that, in all species, stringent similarity thresholds result in fewer alleles per locus than more liberal thresholds, which appears to be the result of high levels of over-splitting. The frequency of putative under-splitting, conversely, is low at all thresholds. Inferred genetic distances between individuals, gene tree depths, and estimates of the ancestral mutation-scaled effective population size (θ) differ depending upon the similarity threshold applied. Relative differences in inferences across species differ even when the same threshold is applied, but may be dramatically different when datasets assembled under different thresholds are compared. These differences…
bibliographic citation: Harvey et al. (2015) Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species. PeerJ 3:e895 https://doi.org/10.7717/peerj.895
date submitted: 2015-02-27
date accepted: 2015-03-27
issued: 2015-04-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harvey
  given name: Michael G.
author list: Agent
  family name: Judy
  given name: Caroline Duffie
author list: Agent
  family name: Seeholzer
  given name: Glenn F.
author list: Agent
  family name: Maley
  given name: James M.
author list: Agent
  family name: Graves
  given name: Gary R.
author list: Agent
  family name: Brumfield
  given name: Robb T.
doi: 10.7717/peerj.895
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-21
copyright: © 2015 Harvey et al.
attribution name: Harvey et al.

Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)
type: item
type: AcademicArticle
description: The teosinte branched1(tb1) gene is a major QTL controlling branching differences between maize and its wild progenitor, teosinte. The insertion of a transposable element (Hopscotch) upstream of tb1 is known to enhance the gene’s expression, causing reduced tillering in maize. Observations of the maize tb1 allele in teosinte and estimates of an insertion age of the Hopscotch that predates domestication led us to investigate its prevalence and potential role in teosinte. We assessed the prevalence of the Hopscotch element across an Americas-wide sample of 837 maize and teosinte individuals using a co-dominant PCR assay. Additionally, we calculated population genetic summaries using sequence data from a subset of individuals from four teosinte populations and collected phenotypic data using seed from a single teosinte population where Hopscotch was found segregating at high frequency. Genotyping results indicate the Hopscotch element is found in a number of teosinte populations and linkage disequilibrium near tb1 does not support recent introgression from maize. Population genetic signatures are consistent with selection on the tb1 locus, revealing a potential ecological role, but a greenhouse experiment does not detect a strong association between the Hopscotch and tillering in teosinte. Our findings suggest the role of Hopscotch differs between maize and teosinte. Future work should assess tb1 expression levels in teosinte with and without the Hopscotch and more comprehensively phenotype teosinte to assess the ecological significance of the Hopscotch insertion and, more broadly, the tb1 locus in teosinte.
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creator: Laura Vann
creator: Thomas Kono
creator: Tanja Pyhäjärvi
creator: Matthew B. Hufford
creator: Jeffrey Ross-Ibarra
subject: Agricultural Science
subject: Ecology
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.900
publisher: PeerJ Inc.
rights: © 2015 Vann et al.
abstract: The teosinte branched1(tb1) gene is a major QTL controlling branching differences between maize and its wild progenitor, teosinte. The insertion of a transposable element (Hopscotch) upstream of tb1 is known to enhance the gene’s expression, causing reduced tillering in maize. Observations of the maize tb1 allele in teosinte and estimates of an insertion age of the Hopscotch that predates domestication led us to investigate its prevalence and potential role in teosinte. We assessed the prevalence of the Hopscotch element across an Americas-wide sample of 837 maize and teosinte individuals using a co-dominant PCR assay. Additionally, we calculated population genetic summaries using sequence data from a subset of individuals from four teosinte populations and collected phenotypic data using seed from a single teosinte population where Hopscotch was found segregating at high frequency. Genotyping results indicate the Hopscotch element is found in a number of teosinte populations and linkage disequilibrium near tb1 does not support recent introgression from maize. Population genetic signatures are consistent with selection on the tb1 locus, revealing a potential ecological role, but a greenhouse experiment does not detect a strong association between the Hopscotch and tillering in teosinte. Our findings suggest the role of Hopscotch differs between maize and teosinte. Future work should assess tb1 expression levels in teosinte with and without the Hopscotch and more comprehensively phenotype teosinte to assess the ecological significance of the Hopscotch insertion and, more broadly, the tb1 locus in teosinte.
bibliographic citation: Vann et al. (2015) Natural variation in teosinte at the domestication locus teosinte branched1 (tb1). PeerJ 3:e900 https://doi.org/10.7717/peerj.900
date submitted: 2014-12-10
date accepted: 2015-03-30
issued: 2015-04-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vann
  given name: Laura
author list: Agent
  family name: Kono
  given name: Thomas
author list: Agent
  family name: Pyhäjärvi
  given name: Tanja
author list: Agent
  family name: Hufford
  given name: Matthew B.
author list: Agent
  family name: Ross-Ibarra
  given name: Jeffrey
doi: 10.7717/peerj.900
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-16
copyright: © 2015 Vann et al.
attribution name: Vann et al.

Water availability as an agent of selection in introduced populations of Arabidopsis thaliana: impacts on flowering time evolution
type: item
type: AcademicArticle
description: Flowering is one of the most influential events in the life history of a plant and one of the main determinants of reproductive investment and lifetime fitness. It is also a highly complex trait controlled by dozens of genes. Understanding the selective pressures influencing time to flowering, and being able to reliably predict how it will evolve in novel environments, are unsolved challenges for plant evolutionary geneticists. Using the model plant species, Arabidopsis thaliana, we examined the impact of simulated high and low winter precipitation levels on the flowering time of naturalized lines from across the eastern portion of the introduced North American range, and the fitness consequences of early versus late flowering. Flowering time order was significantly correlated across two environments—in a previous common garden experiment and in environmental chambers set to mimic mid-range photoperiod and temperature conditions. Plants in low water flowered earlier, had fewer basal branches and produced fewer fruits. Selection in both treatments favored earlier flowering and more basal branches. Our analyses revealed an interaction between flowering time and water treatment for fitness, where flowering later was more deleterious for fitness in the low water treatment. Our results are consistent with the hypothesis that differences in winter precipitation levels are one of the selective agents underlying a flowering time cline in introduced A. thaliana populations.
format: application/pdf
format: text/html
creator: Amanda J. Stock
creator: Brechann V. McGoey
creator: John R. Stinchcombe
subject: Ecology
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.898
publisher: PeerJ Inc.
rights: © 2015 Stock et al.
abstract: Flowering is one of the most influential events in the life history of a plant and one of the main determinants of reproductive investment and lifetime fitness. It is also a highly complex trait controlled by dozens of genes. Understanding the selective pressures influencing time to flowering, and being able to reliably predict how it will evolve in novel environments, are unsolved challenges for plant evolutionary geneticists. Using the model plant species, Arabidopsis thaliana, we examined the impact of simulated high and low winter precipitation levels on the flowering time of naturalized lines from across the eastern portion of the introduced North American range, and the fitness consequences of early versus late flowering. Flowering time order was significantly correlated across two environments—in a previous common garden experiment and in environmental chambers set to mimic mid-range photoperiod and temperature conditions. Plants in low water flowered earlier, had fewer basal branches and produced fewer fruits. Selection in both treatments favored earlier flowering and more basal branches. Our analyses revealed an interaction between flowering time and water treatment for fitness, where flowering later was more deleterious for fitness in the low water treatment. Our results are consistent with the hypothesis that differences in winter precipitation levels are one of the selective agents underlying a flowering time cline in introduced A. thaliana populations.
bibliographic citation: Stock et al. (2015) Water availability as an agent of selection in introduced populations of Arabidopsis thaliana: impacts on flowering time evolution. PeerJ 3:e898 https://doi.org/10.7717/peerj.898
date submitted: 2015-01-19
date accepted: 2015-03-28
issued: 2015-04-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stock
  given name: Amanda J.
author list: Agent
  family name: McGoey
  given name: Brechann V.
author list: Agent
  family name: Stinchcombe
  given name: John R.
doi: 10.7717/peerj.898
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-16
copyright: © 2015 Stock et al.
attribution name: Stock et al.

Co-father relationships among the Suruí (Paiter) of Brazil
type: item
type: AcademicArticle
description: Partible paternity refers to the conception belief that children can have multiple fathers (“co-fathers”) and is common to indigenous cultures of lowland South America. The nature of social relationships observed between co-fathers reveals information about the reproductive strategies underlying partible paternity. Here we analyze clan, genealogical, and social relationships between co-fathers for the Suruí, an indigenous horticultural population in Brazil. We show that co-fathers roughly assort into two separate categories. In the affiliative category, co-father relationships are amicable when they are between close kin, namely brothers and father-son. In the competitive category, relationships are more likely of avoidance or open hostility when between more distant kin such as cousins or unrelated men of different clans. Results therefore imply multiple types of relationships, including both cooperative and competitive contexts, under the rubric of partible paternity. These complexities of partible paternity institutions add to our knowledge of the full range of cross-cultural variation in human mating/marriage arrangements and speak to the debate on whether or not humans should be classified as cooperative breeders.
format: application/pdf
format: text/html
creator: Robert S. Walker
creator: Cédric Yvinec
creator: Ryan M. Ellsworth
creator: Drew H. Bailey
subject: Anthropology
description: doi:10.7717/peerj.899
publisher: PeerJ Inc.
rights: © 2015 Walker et al.
abstract: Partible paternity refers to the conception belief that children can have multiple fathers (“co-fathers”) and is common to indigenous cultures of lowland South America. The nature of social relationships observed between co-fathers reveals information about the reproductive strategies underlying partible paternity. Here we analyze clan, genealogical, and social relationships between co-fathers for the Suruí, an indigenous horticultural population in Brazil. We show that co-fathers roughly assort into two separate categories. In the affiliative category, co-father relationships are amicable when they are between close kin, namely brothers and father-son. In the competitive category, relationships are more likely of avoidance or open hostility when between more distant kin such as cousins or unrelated men of different clans. Results therefore imply multiple types of relationships, including both cooperative and competitive contexts, under the rubric of partible paternity. These complexities of partible paternity institutions add to our knowledge of the full range of cross-cultural variation in human mating/marriage arrangements and speak to the debate on whether or not humans should be classified as cooperative breeders.
bibliographic citation: Walker et al. (2015) Co-father relationships among the Suruí (Paiter) of Brazil. PeerJ 3:e899 https://doi.org/10.7717/peerj.899
date submitted: 2015-02-18
date accepted: 2015-03-29
issued: 2015-04-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Walker
  given name: Robert S.
author list: Agent
  family name: Yvinec
  given name: Cédric
author list: Agent
  family name: Ellsworth
  given name: Ryan M.
author list: Agent
  family name: Bailey
  given name: Drew H.
doi: 10.7717/peerj.899
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-04-14
copyright: © 2015 Walker et al.
attribution name: Walker et al.

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