Topical Collection "Tools for Population and Evolutionary Genetics"

A topical collection in Genes (ISSN 2073-4425). This collection belongs to the section "Population and Evolutionary Genetics and Genomics".

Editors

Dr. David Alvarez-Ponce
E-Mail Website
Collection Editor
Department of Biology, University of Nevada, Reno, NV 89557, USA
Interests: molecular evolution; comparative genomics; natural selection; rates of protein evolution
Special Issues, Collections and Topics in MDPI journals
Dr. Julie M. Allen
E-Mail Website
Collection Editor
Department of Biology, University of Nevada, Reno, NV, USA
Interests: co-evolution; phylogenomics; bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Won C. Yim
E-Mail Website
Collection Editor
Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV, USA
Interests: genomics; comparative genomics; crop genetics; bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Marco Fondi
E-Mail Website
Collection Editor
Department of Biology, University of Florence, 50019 Florence, Italy
Interests: systems biology; evolutionary genomics; metabolic modelling
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

In recent years, the development of next-generation sequencing (NGS) techniques has fueled an explosion in the pace at which genomic data sets are generated, while dramatically decreasing the costs of genome sequencing. A comparison of these datasets can uncover remarkable information about the evolution of organisms. The availability of datasets of ever-increasing size and complexity has resulted in a growing need for computational tools that allow their effective and efficient analysis.

This Collection focuses on tools for population and evolutionary genetics, including, but not limited to, bioinformatic approaches, computational tools and models, algorithms, databases, NGS pipelines and other genetic and genomic resources.

A previous edition in form of Special Issue has already been edited in Genes here: https://www.mdpi.com/journal/genes/special_issues/tools_evo.

We continue to welcome submissions of reviews, research articles, and short communications. We also encourage the submission of manuscripts describing new tools, in the form of “concept papers”.

Dr. David Alvarez-Ponce
Dr. Julie M. Allen
Dr. Won C. Yim
Dr. Marco Fondi
Collection Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the collection website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • bioinformatics
  • comparative genomics
  • population genomics
  • phylogenomics
  • evolution

Published Papers (2 papers)

2021

Jump to: 2020

Article
Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography
Genes 2021, 12(1), 97; https://doi.org/10.3390/genes12010097 - 14 Jan 2021
Viewed by 768
Abstract
The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, [...] Read more.
The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (~100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography. Full article
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Figure 1

2020

Jump to: 2021

Article
Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population
Genes 2020, 11(7), 775; https://doi.org/10.3390/genes11070775 - 10 Jul 2020
Viewed by 863
Abstract
A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the [...] Read more.
A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. FST ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainland Japanese population has a higher T allele frequency than other populations. We found that haplotypes harboring the C allele are composed of two subhaplotypes. We detected that positive selection on both subhaplotypes has occurred in the East Asian lineage. However, the selection on one of the subhaplotypes in JPT seems to have been relaxed or ceased after divergence from the continental population; this may have caused the elevation of T allele frequency. Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese. Full article
Show Figures

Figure 1

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