PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genetic diversity of indigenous guinea fowl (Numida meleagris) using microsatellite markers in northern Togo
items: Galapagos land iguanas as ecosystem engineers
items: Ecosystem design as an avenue for improving services provided by carbonate producing marine ecosystems
items: Should I use fixed effects or random effects when I have fewer than five levels of a grouping factor in a mixed-effects model?
items: Knockdown of GmD53a confers strigolactones mediated rhizobia interaction and promotes nodulation in soybean
items: Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants
items: Fast, low-memory detection and localization of large, polymorphic inversions from SNPs
items: Exploring the relationship between ADHD, its common comorbidities, and their relationship to organizational skills
items: Effect of fire on the palatability of plants in an African woodland savanna: varying impacts depending on plant functional groups
items: Effective asexual reproduction of a widespread soft coral: comparative assessment of four different fragmentation methods

Genetic diversity of indigenous guinea fowl (Numida meleagris) using microsatellite markers in northern Togo
type: item
type: AcademicArticle
description: Indigenous guinea fowl is an important animal resource for improving rural household income. In order to provide molecular data for a sustainable management of this poultry resource, an assessment of the genetic diversity and phylogenic relationships was undertaken on seven guinea fowl phenotypes from two agroecological zones (Dry Savannah and Atakora) of Togo. Genotyping was carried out using 18 microsatellite markers on 94 individuals from Dry Savannah (59) and Atakora (35) zones. The results obtained showed a high genetic diversity, with six as an average alleles per locus and an observed heterozygosity of 0.512. However, the FIS values varied from 0.047 (Lavender) to 0.257 (Albino), reflecting a deficit of heterozygotes, which suggests low to moderate inbreeding levels. The genetic distances between phenotypes are low, ranging from 0.0068 (Bonaparte-Pearl grey) to 0.1559 (Lavender-Albino), unlike the strong genetic identities that reflect a strong genetic similarity between the seven phenotypes of indigenous guinea fowl studied. These results indicate the existence of a single indigenous guinea fowl population, derived from three probable parental populations, with a high within population genetic diversity (phenotypic or agroecological zone). These results could be of use to conservation and improvement programs aiming at the maintenance and sustainable exploitation of this important socio-cultural and economic resource in Togo.
format: application/pdf
format: text/html
creator: Aïcha Edith Soara
creator: Essodina Talaki
creator: Guiguigbaza-Kossigan Dayo
creator: Isidore Houaga
creator: Kokou Tona
creator: Mohammed Bakkali
subject: Biodiversity
subject: Genetics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12637
publisher: PeerJ Inc.
rights: © 2022 Soara et al.
abstract: Indigenous guinea fowl is an important animal resource for improving rural household income. In order to provide molecular data for a sustainable management of this poultry resource, an assessment of the genetic diversity and phylogenic relationships was undertaken on seven guinea fowl phenotypes from two agroecological zones (Dry Savannah and Atakora) of Togo. Genotyping was carried out using 18 microsatellite markers on 94 individuals from Dry Savannah (59) and Atakora (35) zones. The results obtained showed a high genetic diversity, with six as an average alleles per locus and an observed heterozygosity of 0.512. However, the FIS values varied from 0.047 (Lavender) to 0.257 (Albino), reflecting a deficit of heterozygotes, which suggests low to moderate inbreeding levels. The genetic distances between phenotypes are low, ranging from 0.0068 (Bonaparte-Pearl grey) to 0.1559 (Lavender-Albino), unlike the strong genetic identities that reflect a strong genetic similarity between the seven phenotypes of indigenous guinea fowl studied. These results indicate the existence of a single indigenous guinea fowl population, derived from three probable parental populations, with a high within population genetic diversity (phenotypic or agroecological zone). These results could be of use to conservation and improvement programs aiming at the maintenance and sustainable exploitation of this important socio-cultural and economic resource in Togo.
bibliographic citation: Soara et al. (2022) Genetic diversity of indigenous guinea fowl (Numida meleagris) using microsatellite markers in northern Togo. PeerJ 10:e12637 https://doi.org/10.7717/peerj.12637
date submitted: 2021-06-18
date accepted: 2021-11-23
issued: 2022-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soara
  given name: Aïcha Edith
author list: Agent
  family name: Talaki
  given name: Essodina
author list: Agent
  family name: Dayo
  given name: Guiguigbaza-Kossigan
author list: Agent
  family name: Houaga
  given name: Isidore
author list: Agent
  family name: Tona
  given name: Kokou
author list: Agent
  family name: Bakkali
  given name: Mohammed
doi: 10.7717/peerj.12637
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-20
copyright: ©2022 Soara et al.
attribution name: Soara et al.

Galapagos land iguanas as ecosystem engineers
type: item
type: AcademicArticle
description: Background Declines of large-bodied herbivorous reptiles are well documented, but the consequences for ecosystem function are not. Understanding how large-bodied herbivorous reptiles engineer ecosystems is relevant given the current interest in restoration of tropical islands where extinction rates are disproportionately high and reptiles are prominent as herbivores. Methods In this study, we measured the ecosystem-level outcomes of long-term quasi-experiment represented by two adjacent islands within the Galapagos Archipelago, one with and the other without Galapagos land iguanas (Conolophus subcristatus), large-bodied herbivores known to feed on many plant species. We characterized plant communities on each island by developing high-resolution (<1 cm2) aerial imagery and delineating extent of plant associations and counting individual plants on each. Results In the presence of iguanas there was dramatically less woody plant cover, more area with seasonal grasses, and many fewer cacti. Cacti had a more clumped distribution where iguanas were absent than where iguanas were present. Discussion This study provided strong evidence that Galapagos land iguanas can substantially engineer the structure of terrestrial plant communities; therefore, restoration of large-bodied reptilian herbivores, such as land iguanas and giant tortoises, should be regarded as an important component of overall ecosystem restoration, especially for tropical islands from which they have been extirpated.
format: application/pdf
format: text/html
creator: Washington Tapia
creator: James P. Gibbs
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Natural Resource Management
description: doi:10.7717/peerj.12711
publisher: PeerJ Inc.
rights: © 2022 Tapia and Gibbs
abstract: Background Declines of large-bodied herbivorous reptiles are well documented, but the consequences for ecosystem function are not. Understanding how large-bodied herbivorous reptiles engineer ecosystems is relevant given the current interest in restoration of tropical islands where extinction rates are disproportionately high and reptiles are prominent as herbivores. Methods In this study, we measured the ecosystem-level outcomes of long-term quasi-experiment represented by two adjacent islands within the Galapagos Archipelago, one with and the other without Galapagos land iguanas (Conolophus subcristatus), large-bodied herbivores known to feed on many plant species. We characterized plant communities on each island by developing high-resolution (<1 cm2) aerial imagery and delineating extent of plant associations and counting individual plants on each. Results In the presence of iguanas there was dramatically less woody plant cover, more area with seasonal grasses, and many fewer cacti. Cacti had a more clumped distribution where iguanas were absent than where iguanas were present. Discussion This study provided strong evidence that Galapagos land iguanas can substantially engineer the structure of terrestrial plant communities; therefore, restoration of large-bodied reptilian herbivores, such as land iguanas and giant tortoises, should be regarded as an important component of overall ecosystem restoration, especially for tropical islands from which they have been extirpated.
bibliographic citation: Tapia et al. (2022) Galapagos land iguanas as ecosystem engineers. PeerJ 10:e12711 https://doi.org/10.7717/peerj.12711
date submitted: 2021-06-02
date accepted: 2021-12-09
issued: 2022-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tapia
  given name: Washington
author list: Agent
  family name: Gibbs
  given name: James P.
doi: 10.7717/peerj.12711
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-20
copyright: ©2022 Tapia and Gibbs
attribution name: Tapia and Gibbs

Ecosystem design as an avenue for improving services provided by carbonate producing marine ecosystems
type: item
type: AcademicArticle
description: Ecosystem Design (ED) is an approach for constructing habitats that places human needs for ecosystem services at the center of intervention, with the overarching goal of establishing self-sustaining habitats which require limited management. This concept was originally developed for use in mangrove ecosystems, and is understandably controversial, as it markedly diverges from other protection approaches that assign human use a minor priority or exclude it. However, the advantage of ED lies within the considered implementation of these designed ecosystems, thus preserving human benefits from potential later disturbances. Here, we outline the concept of ED in tropical carbonate depositional systems and discuss potential applications to aid ecosystem services such as beach nourishment and protection of coastlines and reef islands at risk from environmental and climate change, CO2 sequestration, food production, and tourism. Biological carbonate sediment production is a crucial source of stability of reef islands and reef-rimmed coastlines. Careful implementation of designed carbonate depositional ecosystems could help counterbalance sea-level rise and manage documented erosion effects of coastal constructions. Importantly, adhering to the core ethos of ED, careful dynamic assessments which provide a balanced approach to maximizing ecosystem services (e.g., carbonate production), should identify and avoid any potential damages to existing functioning ecosystems.
format: application/pdf
format: text/html
creator: Hildegard Westphal
creator: Gary N. Murphy
creator: Steve S. Doo
creator: Thomas Mann
creator: Alexander Petrovic
creator: Christiane Schmidt
creator: Marleen Stuhr
subject: Conservation Biology
subject: Ecosystem Science
subject: Marine Biology
subject: Climate Change Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.12785
publisher: PeerJ Inc.
rights: © 2022 Westphal et al.
abstract: Ecosystem Design (ED) is an approach for constructing habitats that places human needs for ecosystem services at the center of intervention, with the overarching goal of establishing self-sustaining habitats which require limited management. This concept was originally developed for use in mangrove ecosystems, and is understandably controversial, as it markedly diverges from other protection approaches that assign human use a minor priority or exclude it. However, the advantage of ED lies within the considered implementation of these designed ecosystems, thus preserving human benefits from potential later disturbances. Here, we outline the concept of ED in tropical carbonate depositional systems and discuss potential applications to aid ecosystem services such as beach nourishment and protection of coastlines and reef islands at risk from environmental and climate change, CO2 sequestration, food production, and tourism. Biological carbonate sediment production is a crucial source of stability of reef islands and reef-rimmed coastlines. Careful implementation of designed carbonate depositional ecosystems could help counterbalance sea-level rise and manage documented erosion effects of coastal constructions. Importantly, adhering to the core ethos of ED, careful dynamic assessments which provide a balanced approach to maximizing ecosystem services (e.g., carbonate production), should identify and avoid any potential damages to existing functioning ecosystems.
bibliographic citation: Westphal et al. (2022) Ecosystem design as an avenue for improving services provided by carbonate producing marine ecosystems. PeerJ 10:e12785 https://doi.org/10.7717/peerj.12785
date submitted: 2021-07-26
date accepted: 2021-12-21
issued: 2022-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Westphal
  given name: Hildegard
author list: Agent
  family name: Murphy
  given name: Gary N.
author list: Agent
  family name: Doo
  given name: Steve S.
author list: Agent
  family name: Mann
  given name: Thomas
author list: Agent
  family name: Petrovic
  given name: Alexander
author list: Agent
  family name: Schmidt
  given name: Christiane
author list: Agent
  family name: Stuhr
  given name: Marleen
doi: 10.7717/peerj.12785
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-20
copyright: ©2022 Westphal et al.
attribution name: Westphal et al.

Should I use fixed effects or random effects when I have fewer than five levels of a grouping factor in a mixed-effects model?
type: item
type: AcademicArticle
description: As linear mixed-effects models (LMMs) have become a widespread tool in ecology, the need to guide the use of such tools is increasingly important. One common guideline is that one needs at least five levels of the grouping variable associated with a random effect. Having so few levels makes the estimation of the variance of random effects terms (such as ecological sites, individuals, or populations) difficult, but it need not muddy one’s ability to estimate fixed effects terms—which are often of primary interest in ecology. Here, I simulate datasets and fit simple models to show that having few random effects levels does not strongly influence the parameter estimates or uncertainty around those estimates for fixed effects terms—at least in the case presented here. Instead, the coverage probability of fixed effects estimates is sample size dependent. LMMs including low-level random effects terms may come at the expense of increased singular fits, but this did not appear to influence coverage probability or RMSE, except in low sample size (N = 30) scenarios. Thus, it may be acceptable to use fewer than five levels of random effects if one is not interested in making inferences about the random effects terms (i.e. when they are ‘nuisance’ parameters used to group non-independent data), but further work is needed to explore alternative scenarios. Given the widespread accessibility of LMMs in ecology and evolution, future simulation studies and further assessments of these statistical methods are necessary to understand the consequences both of violating and of routinely following simple guidelines.
format: application/pdf
format: text/html
creator: Dylan G.E. Gomes
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Evolutionary Studies
subject: Statistics
description: doi:10.7717/peerj.12794
publisher: PeerJ Inc.
rights: © 2022 Gomes
abstract: As linear mixed-effects models (LMMs) have become a widespread tool in ecology, the need to guide the use of such tools is increasingly important. One common guideline is that one needs at least five levels of the grouping variable associated with a random effect. Having so few levels makes the estimation of the variance of random effects terms (such as ecological sites, individuals, or populations) difficult, but it need not muddy one’s ability to estimate fixed effects terms—which are often of primary interest in ecology. Here, I simulate datasets and fit simple models to show that having few random effects levels does not strongly influence the parameter estimates or uncertainty around those estimates for fixed effects terms—at least in the case presented here. Instead, the coverage probability of fixed effects estimates is sample size dependent. LMMs including low-level random effects terms may come at the expense of increased singular fits, but this did not appear to influence coverage probability or RMSE, except in low sample size (N = 30) scenarios. Thus, it may be acceptable to use fewer than five levels of random effects if one is not interested in making inferences about the random effects terms (i.e. when they are ‘nuisance’ parameters used to group non-independent data), but further work is needed to explore alternative scenarios. Given the widespread accessibility of LMMs in ecology and evolution, future simulation studies and further assessments of these statistical methods are necessary to understand the consequences both of violating and of routinely following simple guidelines.
bibliographic citation: Gomes (2022) Should I use fixed effects or random effects when I have fewer than five levels of a grouping factor in a mixed-effects model?. PeerJ 10:e12794 https://doi.org/10.7717/peerj.12794
date submitted: 2021-04-20
date accepted: 2021-12-22
issued: 2022-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gomes
  given name: Dylan G.E.
doi: 10.7717/peerj.12794
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-20
copyright: © 2022 Gomes
attribution name: Gomes

Knockdown of GmD53a confers strigolactones mediated rhizobia interaction and promotes nodulation in soybean
type: item
type: AcademicArticle
description: Background Strigolactones (SLs) play a key role in modulating plant root growth, shoot branching, and plant-symbiont interaction. However, despite their significance, the components of SL biosynthesis and signaling in soybean and their role in soybean-rhizobia interaction is unknown. Methods In this study, we identified and functionally characterized the GmD53a from soybean. The GmD53a ORFs were amplified from root cDNA using primers for GmD53a RNA interference. To induce transgenic hairy roots of soybean, electric shock was used to transform pB7WG1WG2 vectors containing GmD53a knockdown and GUS into K599 strains of Agrobacterium rhizogenes. The hairy roots and nodules were collected and examined for root nodules ratio and RNA was extracted after 4 weeks of rhizobia inoculation. Results A tissue-specific expression assay showed that GmD53a was differentially expressed in plant parts, predominantly in the stem and nodule. Furthermore, its expression was significantly up-regulated during rhizobia infection and varied with nodule formation. The GmD53a-knockdown chimerical plants were produced to further check its role in soybean nodulation in comparison with control GUS. In knockdown lines, the GmD53a (suppressor of strigolactone MAX2) has a higher number of nodules compared to control lines. Furthermore, the expression levels of several nodulation genes essential for initiation and formation of nodules were altered in GmD53a-knockdown lines. Conclusion The results revealed that SL biosynthesis and signaling are not conserved but also have close interaction between SL and legume rhizobia.
format: application/pdf
format: text/html
creator: Naveed Rehman
creator: Fahim Ullah Khan
creator: Muhammad Imran
creator: Shahid Ali Rajput
creator: Yiming Li
creator: Ihteram Ullah
creator: Rana waseem Akhtar
creator: Arwa Abdulkreem AL-Huqail
creator: Ahmad El Askary
creator: Amany Salah Khalifa
creator: Muhammad Tehseen Azhar
subject: Agricultural Science
subject: Bioinformatics
subject: Biotechnology
subject: Plant Science
description: doi:10.7717/peerj.12815
publisher: PeerJ Inc.
rights: © 2022 Rehman et al.
abstract: Background Strigolactones (SLs) play a key role in modulating plant root growth, shoot branching, and plant-symbiont interaction. However, despite their significance, the components of SL biosynthesis and signaling in soybean and their role in soybean-rhizobia interaction is unknown. Methods In this study, we identified and functionally characterized the GmD53a from soybean. The GmD53a ORFs were amplified from root cDNA using primers for GmD53a RNA interference. To induce transgenic hairy roots of soybean, electric shock was used to transform pB7WG1WG2 vectors containing GmD53a knockdown and GUS into K599 strains of Agrobacterium rhizogenes. The hairy roots and nodules were collected and examined for root nodules ratio and RNA was extracted after 4 weeks of rhizobia inoculation. Results A tissue-specific expression assay showed that GmD53a was differentially expressed in plant parts, predominantly in the stem and nodule. Furthermore, its expression was significantly up-regulated during rhizobia infection and varied with nodule formation. The GmD53a-knockdown chimerical plants were produced to further check its role in soybean nodulation in comparison with control GUS. In knockdown lines, the GmD53a (suppressor of strigolactone MAX2) has a higher number of nodules compared to control lines. Furthermore, the expression levels of several nodulation genes essential for initiation and formation of nodules were altered in GmD53a-knockdown lines. Conclusion The results revealed that SL biosynthesis and signaling are not conserved but also have close interaction between SL and legume rhizobia.
bibliographic citation: Rehman et al. (2022) Knockdown of GmD53a confers strigolactones mediated rhizobia interaction and promotes nodulation in soybean. PeerJ 10:e12815 https://doi.org/10.7717/peerj.12815
date submitted: 2021-09-27
date accepted: 2021-12-29
issued: 2022-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rehman
  given name: Naveed
author list: Agent
  family name: Khan
  given name: Fahim Ullah
author list: Agent
  family name: Imran
  given name: Muhammad
author list: Agent
  family name: Rajput
  given name: Shahid Ali
author list: Agent
  family name: Li
  given name: Yiming
author list: Agent
  family name: Ullah
  given name: Ihteram
author list: Agent
  family name: Akhtar
  given name: Rana waseem
author list: Agent
  family name: Imran
  given name: Muhammad
author list: Agent
  family name: AL-Huqail
  given name: Arwa Abdulkreem
author list: Agent
  family name: Askary
  given name: Ahmad El
author list: Agent
  family name: Khalifa
  given name: Amany Salah
author list: Agent
  family name: Azhar
  given name: Muhammad Tehseen
doi: 10.7717/peerj.12815
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-20
copyright: ©2022 Rehman et al.
attribution name: Rehman et al.

Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants
type: item
type: AcademicArticle
description: Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C4 photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C4 and CAM plants and shed light on the adaptation of plants in dry, hot environments.
format: application/pdf
format: text/html
creator: Jiang-Ping Shu
creator: Yue-Hong Yan
creator: Rui-Jiang Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.12828
publisher: PeerJ Inc.
rights: © 2022 Shu et al.
abstract: Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C4 photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C4 and CAM plants and shed light on the adaptation of plants in dry, hot environments.
bibliographic citation: Shu et al. (2022) Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants. PeerJ 10:e12828 https://doi.org/10.7717/peerj.12828
date submitted: 2021-07-08
date accepted: 2022-01-03
issued: 2022-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shu
  given name: Jiang-Ping
author list: Agent
  family name: Yan
  given name: Yue-Hong
author list: Agent
  family name: Wang
  given name: Rui-Jiang
doi: 10.7717/peerj.12828
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-20
copyright: ©2022 Shu et al.
attribution name: Shu et al.

Fast, low-memory detection and localization of large, polymorphic inversions from SNPs
type: item
type: AcademicArticle
description: Background Large (>1 Mb), polymorphic inversions have substantial impacts on population structure and maintenance of genotypes. These large inversions can be detected from single nucleotide polymorphism (SNP) data using unsupervised learning techniques like PCA. Construction and analysis of a feature matrix from millions of SNPs requires large amount of memory and limits the sizes of data sets that can be analyzed. Methods We propose using feature hashing construct a feature matrix from a VCF file of SNPs for reducing memory usage. The matrix is constructed in a streaming fashion such that the entire VCF file is never loaded into memory at one time. Results When evaluated on Anopheles mosquito and Drosophila fly data sets, our approach reduced memory usage by 97% with minimal reductions in accuracy for inversion detection and localization tasks. Conclusion With these changes, inversions in larger data sets can be analyzed easily and efficiently on common laptop and desktop computers. Our method is publicly available through our open-source inversion analysis software, Asaph.
format: application/pdf
format: text/html
creator: Ronald J. Nowling
creator: Fabian Fallas-Moya
creator: Amir Sadovnik
creator: Scott Emrich
creator: Matthew Aleck
creator: Daniel Leskiewicz
creator: John G. Peters
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.12831
publisher: PeerJ Inc.
rights: © 2022 Nowling et al.
abstract: Background Large (>1 Mb), polymorphic inversions have substantial impacts on population structure and maintenance of genotypes. These large inversions can be detected from single nucleotide polymorphism (SNP) data using unsupervised learning techniques like PCA. Construction and analysis of a feature matrix from millions of SNPs requires large amount of memory and limits the sizes of data sets that can be analyzed. Methods We propose using feature hashing construct a feature matrix from a VCF file of SNPs for reducing memory usage. The matrix is constructed in a streaming fashion such that the entire VCF file is never loaded into memory at one time. Results When evaluated on Anopheles mosquito and Drosophila fly data sets, our approach reduced memory usage by 97% with minimal reductions in accuracy for inversion detection and localization tasks. Conclusion With these changes, inversions in larger data sets can be analyzed easily and efficiently on common laptop and desktop computers. Our method is publicly available through our open-source inversion analysis software, Asaph.
bibliographic citation: Nowling et al. (2022) Fast, low-memory detection and localization of large, polymorphic inversions from SNPs. PeerJ 10:e12831 https://doi.org/10.7717/peerj.12831
date submitted: 2021-09-02
date accepted: 2022-01-04
issued: 2022-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nowling
  given name: Ronald J.
author list: Agent
  family name: Fallas-Moya
  given name: Fabian
author list: Agent
  family name: Sadovnik
  given name: Amir
author list: Agent
  family name: Emrich
  given name: Scott
author list: Agent
  family name: Aleck
  given name: Matthew
author list: Agent
  family name: Leskiewicz
  given name: Daniel
author list: Agent
  family name: Peters
  given name: John G.
doi: 10.7717/peerj.12831
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-20
copyright: © 2022 Nowling et al.
attribution name: Nowling et al.

Exploring the relationship between ADHD, its common comorbidities, and their relationship to organizational skills
type: item
type: AcademicArticle
description: Background Attention Deficit Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder affecting numerous executive functioning skills, such as organizational skills. While the relationship between the inattention aspect of ADHD and poor organizational skills is well documented, it is still unclear if lower organizational skills are only associated with ADHD or if they are also associated with other comorbid disorders commonly diagnosed in conjunction with ADHD. The purpose of the present study is to investigate the relationship between organizational skills and ADHD in adults, as well as the impact of comorbid disorders on ADHD in relation to organizational skills. Methods Four hundred seven (n = 201 with a diagnosis of ADHD) adults from the general population were recruited online. Participants completed a measure of organizational skills, measures assessing levels of ADHD, depression, and anxiety, and extensive demographic information related to their diagnosis of ADHD or other possible diagnosis. Results Participants with a diagnosis of ADHD were significantly more likely to have a comorbid diagnosis of depression and/or anxiety. Organizational skills were significantly lower in individuals who reported having received a diagnosis of ADHD, but not in those with a past diagnosis of depression and anxiety. However, organizational skills were lower in individuals currently experiencing higher levels of depression and anxiety. The results of regression analyses suggest that levels of organizational skills are most strongly predicted by inattention and more weakly predicted by comorbid disorders. Discussion These results highlight the centrality of organizational skills deficit in ADHD as well as the influence of the inattention component over other components commonly observed in ADHD on organizational skills. Suggestions for treatment of ADHD in adults are discussed.
format: application/pdf
format: text/html
creator: Guillaume Durand
creator: Ioana-Smarandita Arbone
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12836
publisher: PeerJ Inc.
rights: © 2022 Durand and Arbone
abstract: Background Attention Deficit Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder affecting numerous executive functioning skills, such as organizational skills. While the relationship between the inattention aspect of ADHD and poor organizational skills is well documented, it is still unclear if lower organizational skills are only associated with ADHD or if they are also associated with other comorbid disorders commonly diagnosed in conjunction with ADHD. The purpose of the present study is to investigate the relationship between organizational skills and ADHD in adults, as well as the impact of comorbid disorders on ADHD in relation to organizational skills. Methods Four hundred seven (n = 201 with a diagnosis of ADHD) adults from the general population were recruited online. Participants completed a measure of organizational skills, measures assessing levels of ADHD, depression, and anxiety, and extensive demographic information related to their diagnosis of ADHD or other possible diagnosis. Results Participants with a diagnosis of ADHD were significantly more likely to have a comorbid diagnosis of depression and/or anxiety. Organizational skills were significantly lower in individuals who reported having received a diagnosis of ADHD, but not in those with a past diagnosis of depression and anxiety. However, organizational skills were lower in individuals currently experiencing higher levels of depression and anxiety. The results of regression analyses suggest that levels of organizational skills are most strongly predicted by inattention and more weakly predicted by comorbid disorders. Discussion These results highlight the centrality of organizational skills deficit in ADHD as well as the influence of the inattention component over other components commonly observed in ADHD on organizational skills. Suggestions for treatment of ADHD in adults are discussed.
bibliographic citation: Durand et al. (2022) Exploring the relationship between ADHD, its common comorbidities, and their relationship to organizational skills. PeerJ 10:e12836 https://doi.org/10.7717/peerj.12836
date submitted: 2021-06-26
date accepted: 2022-01-05
issued: 2022-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Durand
  given name: Guillaume
author list: Agent
  family name: Arbone
  given name: Ioana-Smarandita
doi: 10.7717/peerj.12836
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-20
copyright: ©2022 Durand and Arbone
attribution name: Durand and Arbone

Effect of fire on the palatability of plants in an African woodland savanna: varying impacts depending on plant functional groups
type: item
type: AcademicArticle
description: Fire and herbivores are two important drivers of changes in vegetation composition, quality and dynamics and both are highly related to each other. Herbivores are known to respond to fire both in terms of foraging decisions and distribution. However, little is known about the actual changes in plant chemistry following a fire event and how long these changes will last. We investigated the effect of fire on two different plant functional groups (grasses and woody species) in a woodland savanna of southern Africa. We studied chemical compounds known to be important for palatability of five perennial grass and seven woody species (trees and shrubs) common in the woodland savanna and known to be utilized by herbivores. We wanted to know if plant chemistry differs between a recently burned site (burned 2 years ago) and a control site, burned 16 years ago, and if grasses and woody species show similar relative differences between sites (i.e., the plants’ response to fire). We found a clear difference in chemical composition patterns between the plant functional groups, with an almost homogenous response to fire among woody species, but higher variability in response among grass species. Furthermore, we found that woody species maintained a higher nutritional value even 2 years after burning, whereas grasses did not show clear differences among the two investigated sites. Hence, few years after burning, woody plants might still serve as an attraction for herbivores, especially browsers, in contrast to grasses. The knowledge about these differences between the two functional groups in response to fire is beneficial for the development of management strategies for large herbivores whether domestic or wild.
format: application/pdf
format: text/html
creator: Caroline Stolter
creator: David F. Joubert
creator: Nekulilo Uunona
creator: Elise Nghalipo
creator: Vistorina Amputu
creator: Annika M. Felton
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.12721
publisher: PeerJ Inc.
rights: © 2022 Stolter et al.
abstract: Fire and herbivores are two important drivers of changes in vegetation composition, quality and dynamics and both are highly related to each other. Herbivores are known to respond to fire both in terms of foraging decisions and distribution. However, little is known about the actual changes in plant chemistry following a fire event and how long these changes will last. We investigated the effect of fire on two different plant functional groups (grasses and woody species) in a woodland savanna of southern Africa. We studied chemical compounds known to be important for palatability of five perennial grass and seven woody species (trees and shrubs) common in the woodland savanna and known to be utilized by herbivores. We wanted to know if plant chemistry differs between a recently burned site (burned 2 years ago) and a control site, burned 16 years ago, and if grasses and woody species show similar relative differences between sites (i.e., the plants’ response to fire). We found a clear difference in chemical composition patterns between the plant functional groups, with an almost homogenous response to fire among woody species, but higher variability in response among grass species. Furthermore, we found that woody species maintained a higher nutritional value even 2 years after burning, whereas grasses did not show clear differences among the two investigated sites. Hence, few years after burning, woody plants might still serve as an attraction for herbivores, especially browsers, in contrast to grasses. The knowledge about these differences between the two functional groups in response to fire is beneficial for the development of management strategies for large herbivores whether domestic or wild.
bibliographic citation: Stolter et al. (2022) Effect of fire on the palatability of plants in an African woodland savanna: varying impacts depending on plant functional groups. PeerJ 10:e12721 https://doi.org/10.7717/peerj.12721
date submitted: 2021-07-27
date accepted: 2021-12-09
issued: 2022-01-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stolter
  given name: Caroline
author list: Agent
  family name: Joubert
  given name: David F.
author list: Agent
  family name: Uunona
  given name: Nekulilo
author list: Agent
  family name: Nghalipo
  given name: Elise
author list: Agent
  family name: Amputu
  given name: Vistorina
author list: Agent
  family name: Felton
  given name: Annika M.
doi: 10.7717/peerj.12721
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-19
copyright: © 2022 Stolter et al.
attribution name: Stolter et al.

Effective asexual reproduction of a widespread soft coral: comparative assessment of four different fragmentation methods
type: item
type: AcademicArticle
description: Background Many coral reefs worldwide are experiencing declines in hard corals, resulting in other benthic organisms, e.g., soft corals, becoming more dominant. As such, more studies on the ecophysiology of soft corals are needed. Despite many methods for asexual reproduction of hard corals, effective methods for soft corals, i.e., without a hard skeleton, are scarce. This study, thus, assessed four fragmentation methods, the glue, rubber band, tunnel mesh, and plug mesh method for the pulsating soft coral Xenia umbellata that is widely distributed in the tropical Indo-Pacific. Methods Methods were comparatively assessed by determining the required time and labor for the fragmentation plus the health status of the fragmented corals by measuring their oxygen fluxes and pulsation rates, i.e., a special feature of this soft coral that can be used as a proxy for its health. Results There were no significant health status differences between methods. This was indicated by similar gross photosynthesis (between 7.4 to 9.7 μg O2 polyp−1 h−1) and pulsating rates (between 35 and 44 pulses min−1) among methods. In terms of time/labor intensity and success rates, i.e., the percentage of fragments attached to the desired surface, the plug mesh method was the most efficient method with a significantly higher success rate (95 ± 5%), while the others had a success rate between 5 ± 5 and 45 ± 15%. The time needed for fragmentation, though not significant, was also the shortest (78 ± 11 s fragment−1), while other methods required between 84 ± 14 and 126 ± 8 s frag−1. The plug mesh method may thus be a valuable tool related to the reproduction of soft corals for use in subsequent experimental work.
format: application/pdf
format: text/html
creator: Sohyoung Kim
creator: Christian Wild
creator: Arjen Tilstra
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12589
publisher: PeerJ Inc.
rights: © 2022 Kim et al.
abstract: Background Many coral reefs worldwide are experiencing declines in hard corals, resulting in other benthic organisms, e.g., soft corals, becoming more dominant. As such, more studies on the ecophysiology of soft corals are needed. Despite many methods for asexual reproduction of hard corals, effective methods for soft corals, i.e., without a hard skeleton, are scarce. This study, thus, assessed four fragmentation methods, the glue, rubber band, tunnel mesh, and plug mesh method for the pulsating soft coral Xenia umbellata that is widely distributed in the tropical Indo-Pacific. Methods Methods were comparatively assessed by determining the required time and labor for the fragmentation plus the health status of the fragmented corals by measuring their oxygen fluxes and pulsation rates, i.e., a special feature of this soft coral that can be used as a proxy for its health. Results There were no significant health status differences between methods. This was indicated by similar gross photosynthesis (between 7.4 to 9.7 μg O2 polyp−1 h−1) and pulsating rates (between 35 and 44 pulses min−1) among methods. In terms of time/labor intensity and success rates, i.e., the percentage of fragments attached to the desired surface, the plug mesh method was the most efficient method with a significantly higher success rate (95 ± 5%), while the others had a success rate between 5 ± 5 and 45 ± 15%. The time needed for fragmentation, though not significant, was also the shortest (78 ± 11 s fragment−1), while other methods required between 84 ± 14 and 126 ± 8 s frag−1. The plug mesh method may thus be a valuable tool related to the reproduction of soft corals for use in subsequent experimental work.
bibliographic citation: Kim et al. (2022) Effective asexual reproduction of a widespread soft coral: comparative assessment of four different fragmentation methods. PeerJ 10:e12589 https://doi.org/10.7717/peerj.12589
date submitted: 2021-06-04
date accepted: 2021-11-12
issued: 2022-01-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Sohyoung
author list: Agent
  family name: Wild
  given name: Christian
author list: Agent
  family name: Tilstra
  given name: Arjen
doi: 10.7717/peerj.12589
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-19
copyright: © 2022 Kim et al.
attribution name: Kim et al.

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