Tracing evolutionary history and admixture in mixed‐ploidy systems

Kolář, Filip

doi:10.1111/1755-0998.13390

Cited by 5 publications

(6 citation statements)

References 11 publications

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“…Issues more specific to plants include escalating costs of sequencing of genomic‐scale data for taxa with big genomes, widespread hybridization, polyploidization, and various mating systems (Stebbins, 1950), and the difficulty of developing analytical tools that accommodate these complexities (Blischak et al, 2023; but see Garrison and Marth, 2012 [preprint]; Serang et al, 2012; Gerard et al, 2018; Blischak et al, 2018b; Clark et al, 2019 for genotyping tools that enable ploidy specification and algorithms for genotype likelihood estimation). Other challenges include the identification of paralogous and orthologous loci prior to phylogenetic inference (Yang and Smith, 2014; Johnson et al, 2016; Gardner et al, 2021; Morales‐Briones et al, 2022; Freyman et al, 2023; Mendez‐Reneau et al, 2023), a scarcity of resources for analysis of shared ancestry in polyploids (but see Kolář, 2021; Shastry et al, 2021), and demographic modeling under various ploidy and mating systems scenarios (but see Roux and Pannell, 2015; Blischak et al, 2023; Roux et al, 2023). Simulation studies testing the effect of strategies and violations of model assumptions in plant geogenomics research (Schenk, 2016; Stift et al, 2019) are critical to better constrain and propose plausible geological scenarios from biological data in light of uncertainty.…”

Section: Why and How To Shift The Paradigm?mentioning

confidence: 99%

Botany and geogenomics: Constraining geological hypotheses in the neotropics with large‐scale genetic data derived from plants

Bedoya

2024

American J of Botany

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Decades of empirical research have revealed how the geological history of our planet shaped plant evolution by establishing well‐known patterns (e.g., how mountain uplift resulted in high rates of diversification and replicate radiations in montane plant taxa). This follows a traditional approach where botanical data are interpreted in light of geological events. In this synthesis, I instead describe how by integrating natural history, phylogenetics, and population genetics, botanical research can be applied alongside geology and paleontology to inform our understanding of past geological and climatic processes. This conceptual shift aligns with the goals of the emerging field of geogenomics. In the neotropics, plant geogenomics is a powerful tool for the reciprocal exploration of two long standing questions in biology and geology: how the dynamic landscape of the region came to be and how it shaped the evolution of the richest flora. Current challenges that are specific to analytical approaches for plant geogenomics are discussed. I describe the scale at which various geological questions can be addressed from biological data and what makes some groups of plants excellent model systems for geogenomics research. Although plant geogenomics is discussed with reference to the neotropics, the recommendations given here for approaches to plant geogenomics can and should be expanded to exploring long‐standing questions on how the earth evolved with the use of plant DNA.

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Section: Why and How To Shift The Paradigm?mentioning

confidence: 99%

Botany and geogenomics: Constraining geological hypotheses in the neotropics with large‐scale genetic data derived from plants

Bedoya

2024

American J of Botany

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“…Another application requiring sequencing depth to be high enough to accurately estimate allele frequencies and distinguish between different homologues is the genotyping of mixed ploidy populations due to the presence of multiple inheritance patterns and allelic dosages (Dufresne et al, 2014;Kolář, 2021;McKinney et al, 2017). Although these populations may involve lower ploidy individuals, e.g.…”

Section: Moder Ate S Equen Cing Dep Th Requirementsmentioning

confidence: 99%

When do autopolyploids need poly‐sequencing data?

Jighly

2021

Molecular Ecology

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The sequencing depth required to genotype autopolyploid populations is a very controversial topic. Different studies have adopted variable depth values without a clear guide on the optimal sequencing depth value. Many studies suggest high depth thresholds for different ploidies that may not be practical and substantially increase the overall genotyping cost for different projects. However, such conservative thresholds may not be required to achieve the most common research goals. In fact, some recent reports in the field of quantitative genetics found that much lower sequencing depth thresholds could achieve the same accuracy as high depth thresholds. In this manuscript, I discuss when researchers need to use stringent sequencing depth thresholds and when they can use more relaxed ones. I support my argument by calculating the probabilities of sampling different homologues at a given sequencing depth. I also discuss the uses and the uncertainty in calculating a continuous allelic dosage as the proportion of sequencing reads that hold the alternative allele, which is becoming a common method now in quantitative genetics to replace discrete dosage estimation.

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“…There were also multiple articles providing guidance for biodiversity monitoring with eDNA (Bensch et al, 2021;Jurburg et al, 2021;Rodríguez-Ezpeleta et al, 2021). Kolář, 2021). There was also an emphasis to improve de novo transcriptome assemblies (Freedman et al, 2021; Perspective by Hölzer, 2021) and genome assemblies for an arcticalpine plant (Nowak et al, 2021;Perspective by Pyhäjärvi, & Mattila, 2021) and vaquita (Morin et al, 2021;Perspective by Whibley, 2021).…”

Section: Top Content Pub Lis Hed In Molecul Ar Ecology Re Source Smentioning

confidence: 99%

“…In the last year, From the Cover and Perspective articles highlighted advances in several study areas. This included novel approaches and study design resources for reduced‐representation sequencing (Rivera‐Colón et al, 2021; Perspective by Choquet, 2021) and polyploid and mixed‐ploidy individuals (Shastry et al, 2021; Perspective by Kolář, 2021). There was also an emphasis to improve de novo transcriptome assemblies (Freedman et al, 2021; Perspective by Hölzer, 2021) and genome assemblies for an arctic‐alpine plant (Nowak et al, 2021; Perspective by Pyhäjärvi, & Mattila, 2021) and vaquita (Morin et al, 2021; Perspective by Whibley, 2021).…”

Section: Top Content Published In Molecular Ecology Resourcesmentioning

confidence: 99%