Dataset Information

Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography.

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, 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.

SUBMITTER: Sacks BN

PROVIDER: S-EPMC7828831 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Publications

Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography.

Sacks Benjamin N BN Lounsberry Zachary T ZT Rando Halie M HM Kluepfel Kristopher K Fain Steven R SR Brown Sarah K SK Kukekova Anna V AV

Genes 20210114 1

The red fox (<i>Vulpes vulpes</i>) 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 wit ...[more]

PMID: 33466657

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Project description:BackgroundHigh-throughput sequencing of phylogenetically informative marker genes is a widely used method to assess the diversity and composition of microbial communities. Taxonomic assignment of sampled marker gene sequences (referred to as amplicon sequence variants, or ASVs) imparts ecological significance to these genetic data. To assign taxonomy to an ASV, a taxonomic assignment algorithm compares the ASV to a collection of reference sequences (a reference database) with known taxonomic affiliations. However, many taxonomic assignment algorithms and reference databases are available, and the optimal algorithm and database for a particular scientific question is often unclear. Here, we present the ensembleTax R package, which provides an efficient framework for integrating taxonomic assignments predicted with any number of taxonomic assignment algorithms and reference databases to determine ensemble taxonomic assignments for ASVs.MethodsThe ensembleTax R package relies on two core algorithms: taxmapper and assign.ensembleTax. The taxmapper algorithm maps taxonomic assignments derived from one reference database onto the taxonomic nomenclature (a set of taxonomic naming and ranking conventions) of another reference database. The assign.ensembleTax algorithm computes ensemble taxonomic assignments for each ASV in a data set based on any number of taxonomic assignments determined with independent methods. Various parameters allow analysts to prioritize obtaining either more ASVs with more predicted clade names or more robust clade name predictions supported by multiple independent methods in ensemble taxonomic assignments.ResultsThe ensembleTax R package is used to compute two sets of ensemble taxonomic assignments for a collection of protistan ASVs sampled from the coastal ocean. Comparisons of taxonomic assignments predicted by individual methods with those predicted by ensemble methods show that conservative implementations of the ensembleTax package minimize disagreements between taxonomic assignments predicted by individual and ensemble methods, but result in ASVs with fewer ranks assigned taxonomy. Less conservative implementations of the ensembleTax package result in an increased fraction of ASVs classified at all taxonomic ranks, but increase the number of ASVs for which ensemble assignments disagree with those predicted by individual methods.DiscussionWe discuss how implementation of the ensembleTax R package may be optimized to address specific scientific objectives based on the results of the application of the ensembleTax package to marine protist communities. While further work is required to evaluate the accuracy of ensemble taxonomic assignments relative to taxonomic assignments predicted by individual methods, we also discuss scenarios where ensemble methods are expected to improve the accuracy of taxonomy prediction for ASVs.

Dataset Information

Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography.

Publications

Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography.

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