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Article ; Online: Are we paying-to-play? A quantitative assessment of Canadian open access research in ecology and evolution

Aaron B.A. Shafer

FACETS, Vol 6, Iss 1, Pp 537-

2021 Volume 544

Abstract: Open access (OA) allows for peer-reviewed research to be freely accessed and there has been a collective shift from both researchers and publishers towards more OA publishing. OA typically occurs either through article-processing charges (the gold road) ... ...

Abstract	Open access (OA) allows for peer-reviewed research to be freely accessed and there has been a collective shift from both researchers and publishers towards more OA publishing. OA typically occurs either through article-processing charges (the gold road) or via self-archiving (the green road); the former can be expensive, while the latter has seen minimal uptake. The gold road of OA has led to predatory publishers and, to some, questionable publications. Here, I used publicly available grant information in Canada and combined this with individual publishing statistics to test a variety of factors and their influence on OA publishing. I showed that an individual’s award amount, H-index, and gender did not influence the proportion of OA articles they published, but an individual’s H-index scaled with the number of OA publications. Institute size influenced OA publishing patterns, with researchers at large universities (i.e., >20 000 full-time students) publishing proportionately more OA articles than medium and small institutes. I discuss the potential for this pattern to build on pre-existing systemic biases when it comes to funding and publishing.
Keywords	publishing ; article processing charges ; journals ; bibliometrics ; h-index ; Education ; L ; Science ; Q
Subject code	070
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Canadian Science Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Development of an environmental DNA metabarcoding assay for aquatic vascular plant communities

Stephanie A. Coghlan / Aaron B. A. Shafer / Joanna R. Freeland

Environmental DNA, Vol 3, Iss 2, Pp 372-

2021 Volume 387

Abstract: Abstract Environmental DNA (eDNA) metabarcodes allow for the simultaneous detection of multiple taxa if the barcode regions meet several key requirements including conserved primer‐binding sites, interspecific variability that exceeds intraspecific ... ...

Abstract	Abstract Environmental DNA (eDNA) metabarcodes allow for the simultaneous detection of multiple taxa if the barcode regions meet several key requirements including conserved primer‐binding sites, interspecific variability that exceeds intraspecific variability, and relatively short amplicons. Currently, there are no established metabarcoding assays for aquatic vascular plants, which could limit biodiversity assessments and the early detection of alien species. We used a combination of novel and pre‐existing primers to generate eDNA metabarcodes from three gene regions that are commonly used for plant barcoding: two regions of chloroplast DNA (rbcL and matK) plus a segment of an internal transcribed spacer (ITS2). We optimized the assay on a mock community of 25 known species and then applied it to wild samples collected from two waterbodies in southern Ontario, Canada (Black River and Seymour Lake). Our novel rbcL primers, which amplify a fragment of ~220 bp, provided the most comprehensive description of the mock community, identifying all but one of the taxa to species or genus. In addition, after pooling data from five sites within each sampled waterbody, metabarcodes generated by this same primer pair identified more taxa than all other primer pairs; more specifically, 20 and 26 taxa were identified from Black River and Seymour Lake, respectively, to species or genus. Across the two sites, nine of the identified taxa are alien invasive aquatic plants. Five of these invasive species have no previous reports from our sites, and in some cases have no known established Ontario populations; our data therefore suggest an urgent need to increase surveillance for these aliens. Overall, our study showed that eDNA metabarcoding with a novel rbcL primer pair provides a cost‐effective method for simultaneously detecting multiple aquatic vascular plant taxa and is a valuable tool for the early detection of invasive species.
Keywords	aquatic plants ; biodiversity ; chloroplast DNA ; high‐throughput sequencing ; internal transcribed spacer ; matK ; Environmental sciences ; GE1-350 ; Microbial ecology ; QR100-130
Subject code	580
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The Peril of Gene-Targeted Conservation

Kardos, Marty / Aaron B.A. Shafer

Trends in ecology & evolution. 2018 Nov., v. 33, no. 11

2018

Abstract: The genomics revolution has sparked interest in using our increased understanding of the loci involved in phenotypic variation and adaptation to advance the conservation of biodiversity. Despite much interest and discussion, it remains unclear whether, ... ...

Abstract	The genomics revolution has sparked interest in using our increased understanding of the loci involved in phenotypic variation and adaptation to advance the conservation of biodiversity. Despite much interest and discussion, it remains unclear whether, when, and how such analyses should be used to guide conservation action. Such ‘gene-targeted’ conservation strategies, while promising, are complicated by several factors including the complex genomic architecture of phenotypic variation and the strong potential for undesirable outcomes such as the loss of genome-wide genetic variation and evolutionary potential. We caution against relying on gene-targeted approaches as a conservation silver bullet and propose rigorous criteria to identify situations where gene-targeted approaches are likely to benefit conservation.
Keywords	biodiversity ; genetic variation ; genomics ; loci ; phenotypic variation
Language	English
Dates of publication	2018-11
Size	p. 827-839.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	284965-3
ISSN	1872-8383 ; 0169-5347
ISSN (online)	1872-8383
ISSN	0169-5347
DOI	10.1016/j.tree.2018.08.011
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genomic Insights Into the Molecular Basis of Sexual Selection in Birds

Shubham K. Jaiswal / Ankit Gupta / Aaron B. A. Shafer / Vishnu Prasoodanan P. K. / Nagarjun Vijay / Vineet K. Sharma

Frontiers in Ecology and Evolution, Vol

2021 Volume 9

Abstract: Sexual selection is a well-known biological process, yet the genomic basis and patterns of sexual selection are not fully understood. The extravagant ornamental plumage of peacock (Pavo cristatus) was instrumental in shaping Charles Darwin's theory of ... ...

Abstract	Sexual selection is a well-known biological process, yet the genomic basis and patterns of sexual selection are not fully understood. The extravagant ornamental plumage of peacock (Pavo cristatus) was instrumental in shaping Charles Darwin's theory of sexual selection and is considered to be an honest signal of its immunocompetence. Here, we used the recently generated draft genome sequence of peafowl (Pavo cristatus) and carried out a comparative analysis across 11 bird genomes that encompass a range of sexual selection and also had high-quality genomic and phenotypic data publically available to study the genomic basis of sexual selection. We found that varying degree of purifying selection was the predominant mechanism of action for sexual selection at the genome-wide scale and observed that sexual selection mostly influences genes regulating gene expression and protein processing. Specifically, the genome-wide phylogenetically corrected regression analysis supported the continuous or ongoing model of sexual selection. Genes involved in nucleic acid binding and gene expression regulation, including a specific regulator of sex-determination known as TRA2A to be under positive selection in the species with high post-copulatory sexual selection manifested as high sperm competition. We also detected specific feather-related and immune-related gene-pairs evolving under similar selection pressures across the 11 species, including peacock (Pavo cristatus), which is consistent with the Hamilton-Zuk hypothesis. The comparative genomics analysis of 11 avian taxa has provided new insights on the molecular underpinnings of sexual selection and identifies specific genomic regions for future in-depth analysis.
Keywords	sexual selection ; avian evolution ; comparative genomics ; purifying selection ; dN/dS (ω) ; turnover ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
Subject code	612
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The importance of non-academic coauthors in bridging the conservation genetics gap

Britt, Meghan / Sarah E. Haworth / Justin B. Johnson / Daria Martchenko / Aaron B.A. Shafer

Biological conservation. 2018 Feb., v. 218

2018

Abstract: DNA sequence data from genetic (traditional) and genomic (high-throughput) instruments have been highlighted as important information for biodiversity conservation. Despite a high number of publications, a gap has emerged between fundamental research and ...

Abstract	DNA sequence data from genetic (traditional) and genomic (high-throughput) instruments have been highlighted as important information for biodiversity conservation. Despite a high number of publications, a gap has emerged between fundamental research and real-world application, meaning genetic studies often do not have a substantive link to policy or conservation science. We conducted a meta-analysis on conservation studies using genetic and genomic datasets and found the majority of publications were on species that were data deficient or of low conservation priority (66%); only 38% of studies specifically identified how the data could inform conservation or management through clearly stated recommendations for action or policy. Importantly, our mixed-model found a 2.5-fold increase in the odds of a publication making a specific recommendation when non-academic affiliated authors were included. This suggests the conservation genetics gap has arisen, in part, by academic authors failing to make explicit links to policy and conservation outcomes. Conservation geneticists should refrain from hyperbole and collaborate with agency and non-government scientists to accelerate development and implementation, and ultmately help bridge the conservation genetics gap.
Keywords	DNA ; biodiversity conservation ; conservation genetics ; data collection ; geneticists ; genomics ; issues and policy ; meta-analysis ; nucleotide sequences ; statistical models
Language	English
Dates of publication	2018-02
Size	p. 118-123.
Publishing place	Elsevier Ltd
Document type	Article
ISSN	0006-3207
DOI	10.1016/j.biocon.2017.12.019
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Forecasting Ecological Genomics

Aaron B A Shafer / Joseph M Northrup / Martin Wikelski / George Wittemyer / Jochen B W Wolf

PLoS Biology, Vol 14, Iss 1, p e

High-Tech Animal Instrumentation Meets High-Throughput Sequencing.

2016 Volume 1002350

Abstract: Recent advancements in animal tracking technology and high-throughput sequencing are rapidly changing the questions and scope of research in the biological sciences. The integration of genomic data with high-tech animal instrumentation comes as a natural ...

Abstract	Recent advancements in animal tracking technology and high-throughput sequencing are rapidly changing the questions and scope of research in the biological sciences. The integration of genomic data with high-tech animal instrumentation comes as a natural progression of traditional work in ecological genetics, and we provide a framework for linking the separate data streams from these technologies. Such a merger will elucidate the genetic basis of adaptive behaviors like migration and hibernation and advance our understanding of fundamental ecological and evolutionary processes such as pathogen transmission, population responses to environmental change, and communication in natural populations.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Does learning or instinct shape habitat selection?

Scott E Nielsen / Aaron B A Shafer / Mark S Boyce / Gordon B Stenhouse

PLoS ONE, Vol 8, Iss 1, p e

2013 Volume 53721

Abstract: Habitat selection is an important behavioural process widely studied for its population-level effects. Models of habitat selection are, however, often fit without a mechanistic consideration. Here, we investigated whether patterns in habitat selection ... ...

Abstract	Habitat selection is an important behavioural process widely studied for its population-level effects. Models of habitat selection are, however, often fit without a mechanistic consideration. Here, we investigated whether patterns in habitat selection result from instinct or learning for a population of grizzly bears (Ursus arctos) in Alberta, Canada. We found that habitat selection and relatedness were positively correlated in female bears during the fall season, with a trend in the spring, but not during any season for males. This suggests that habitat selection is a learned behaviour because males do not participate in parental care: a genetically predetermined behaviour (instinct) would have resulted in habitat selection and relatedness correlations for both sexes. Geographic distance and home range overlap among animals did not alter correlations indicating that dispersal and spatial autocorrelation had little effect on the observed trends. These results suggest that habitat selection in grizzly bears are partly learned from their mothers, which could have implications for the translocation of wildlife to novel environments.
Keywords	Medicine ; R ; Science ; Q
Subject code	590
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Blood transcriptomics of captive forest musk deer (Moschus berezovskii) and possible associations with the immune response to abscesses

Xiaoning Sun / Ruibo Cai / Xuelin Jin / Aaron B. A. Shafer / Xiaolong Hu / Shuang Yang / Yimeng Li / Lei Qi / Shuqiang Liu / Defu Hu

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 9

Abstract: Abstract Forest musk deer (Moschus berezovskii; FMD) are both economically valuable and highly endangered. A problem for FMD captive breeding programs has been the susceptibility of FMD to abscesses. To investigate the mechanisms of abscess development ... ...

Abstract	Abstract Forest musk deer (Moschus berezovskii; FMD) are both economically valuable and highly endangered. A problem for FMD captive breeding programs has been the susceptibility of FMD to abscesses. To investigate the mechanisms of abscess development in FMD, the blood transcriptomes of three purulent and three healthy individuals were generated. A total of ~39.68 Gb bases were generated using Illumina HiSeq 4000 sequencing technology and 77,752 unigenes were identified after assembling. All the unigenes were annotated, with 63,531 (81.71%) mapping to at least one database. Based on these functional annotations, 45,798 coding sequences (CDS) were detected, along with 12,697 simple sequence repeats (SSRs) and 65,536 single nucleotide polymorphisms (SNPs). A total of 113 unigenes were found to be differentially expressed between healthy and purulent individuals. Functional annotation indicated that most of these differentially expressed genes were involved in the regulation of immune system processes, particularly those associated with parasitic and bacterial infection pathways.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome Sequence of Indian Peacock Reveals the Peculiar Case of a Glittering Bird

Shubham K. Jaiswal / Ankit Gupta / Rituja Saxena / P. K. Vishnu Prasoodanan / Ashok K. Sharma / Parul Mittal / Ankita Roy / Aaron B.A. Shafer / Nagarjun Vijay / Vineet K. Sharma

Abstract: ABSTRACTThe unique ornamental features and extreme sexual traits of Peacock have always intrigued the scientists. However, the genomic evidence to explain its phenotype are yet unknown. Thus, we report the first genome sequence and comparative analysis ... ...

Abstract	ABSTRACTThe unique ornamental features and extreme sexual traits of Peacock have always intrigued the scientists. However, the genomic evidence to explain its phenotype are yet unknown. Thus, we report the first genome sequence and comparative analysis of peacock with the available high-quality genomes of chicken, turkey, duck, flycatcher and zebra finch. The candidate genes involved in early developmental pathways including TGF-β, BMP, and Wnt signaling pathway, which are also involved in feather patterning, bone morphogenesis, and skeletal muscle development, showed signs of adaptive evolution and provided useful clues on the phenotype of peacock. The innate and adaptive immune components such as complement system and T-cell response also showed signs of adaptive evolution in peacock suggesting their possible role in building a robust immune system which is consistent with the between species predictions of Hamilton-Zuk hypothesis. This study provides novel genomic and evolutionary insights into the molecular understanding towards the phenotypic evolution of Indian peacock.
Keywords	covid19
Publisher	biorxiv
Document type	Article ; Online
DOI	10.1101/315457
Database	COVID19

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Article: Genetic structure and population history of wintering Asian Great Bustard (Otis tarda dybowskii) in China: implications for conservation

Liu, Gang / Xiaolong Hu / Aaron B. A. Shafer / Minghao Gong / Morigen Han / Changjiang Yu / Jingying Zhou / Jie Bai / Derong Meng / Guohai Yu / Dapeng Dang

Journal of ornithology. 2017 July, v. 158, no. 3

2017

Abstract: Wintering areas affect population processes and genetic structuring of many bird species. The Asian Great Bustard (Otis tarda dybowskii) is declining across its range as its breeding and wintering grounds become more fragmented. No genetic information ... ...

Abstract	Wintering areas affect population processes and genetic structuring of many bird species. The Asian Great Bustard (Otis tarda dybowskii) is declining across its range as its breeding and wintering grounds become more fragmented. No genetic information for this vulnerable subspecies in the wild exists. We used noninvasive fecal sampling and mitochondrial sequencing to quantify the level of genetic diversity and the extent of genetic differentiation within and among the wintering populations. Bayesian skyline plot (BSP) analysis was conducted to assess changes in population size over the last several thousand years. Overall, 17 haplotypes were identified in 101 individuals from six wintering grounds, with mean haplotype diversity of 0.90Â Â±Â 0.02. Significant population differentiation among wintering grounds was observed [population pairwise test (Î¦ ST)Â =Â 0.13, pÂ <Â 0.001], with genetic differentiation associated with geographical distance (R Â²Â =Â 0.26, pÂ <Â 0.05) and pairwise tests consistent with some degree of population admixture. The BSP exhibited a gradual increase in effective population size beginning around 28,000Â years ago, but a decrease starting approximately 4000Â years ago. Given that China has the most important wintering grounds for the Asian Great Bustard, and that these are becoming increasingly fragmented, it is likely necessary to establish more protected areas to facilitate the protection and monitoring of wintering Great Bustards.
Keywords	Otis tarda ; birds ; breeding ; conservation areas ; effective population size ; genetic variation ; haplotypes ; mitochondria ; monitoring ; wintering grounds ; China
Language	English
Dates of publication	2017-07
Size	p. 761-772.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ISSN	2193-7192
DOI	10.1007/s10336-017-1448-5
Database	NAL-Catalogue (AGRICOLA)

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