Botany and Geogenomics: constraining geological hypotheses with large-scale genetic data derived from plants

  1. Ana Maria Bedoya

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Abstract

Past studies in plant phylogenetics have shed light on 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). Under this approach, information is transferred from geology to botany, by interpreting data in light of geological processes. In this synthesis, I propose a conceptual shift in this traditional approach to specifically transfer information from botany to geology. This conceptual shift follows the goals of the emerging field of geogenomics and emphasizes that plant phylogenetics can go beyond investigating patterns in light of landscape change, to reduce the inherent uncertainty in models of paleotopography, river system structure, and land connections through time. 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. This synthesis highlights the critical role of classical botanical knowledge in identifying good study systems to unveil long-standing questions on how the earth evolved with the use of plant DNA.

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  1. PREreview

    This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/11511961.

    Concise, but informative summary of the preprint

    The author proposes a paradigm shift in which geogenomic data would help us define timestamps of geological events. This is based on the understanding that population dynamics and speciation events in plants are very closely related to geological events. The author defends an integrative approach that combines genetic information and geological data to understand species distribution in space and time.

    Big-picture comments

    Good/Excellent things

    • Figures! Visually compelling, clean and easy to understand.

    • We like the way the text is broken down into sections. The breaks make sense to us.

    • Overall, the writing is quite clear, and we like the level of detail in this paper. It feels like a general paper that has many specific examples and points to specific evidence, which is compelling!

    Things to be improved

    • We could use more figures! We think they could help us understand most of the new ideas on the paper.

    • Maybe the figures could've helped, but it was not clear how genetic fluctuation rates could be a trustworthy marker for geological events, which seem to have a much lower fluctuation rate.

    • Although it is alluded in the text, we think it might be beneficial to explicitly highlight what makes a 'good' system where this type of genomic-focused approach would help us understand geologic history e.g. timescale, the species life history that lends us to being able to make these inferences. Although this would by no means be extensive it would help to give an idea of what people should think about.

    Small-picture things

    The first paragraph could be reworked to feel lighter and to read more smoothly, to make it easier to be introduced to the subject. The enumeration of examples of diversification specifically could be broken up to be more fluid. The examples are interesting to include, but it is difficult to assimilate all the patterns of diversification because the flow is interrupted with parentheses - which makes it difficult to dive into the introduction.

    Competing interests

    The authors declare that they have no competing interests.

  2. PREreview

    This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/10199060.

    This review was made as part of a community of practice supported by ASAPbio and BIOS2. One of the authors, GH, is a signatory of Publish Your Reviews, and has committed to publish her peer reviews alongside the preprint version of an article. For more information, see publishyourreviews.org.

    Authors' background:

    Open science, open data, network ecology, plant ecology, conservation biology, taxonomy, ecological modelling, plant biology, seed science and technology, agronomy, urban evolutionary biology, biodiversity change, indicators, population dynamics, island biogeography, computational and quantitative ecology, prediction, community ecology, eDNA, metacommunity.

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    Summary:

    The author proposes a paradigm shift in which geogenomic data would help us define timestamps of geological events. This is based on the understanding that population dynamics and speciation events in plants are very closely related to geological events. The author defends an integrative approach that combines genetic information and geological data to understand species distribution in space and time.

    Big-picture comments

    Good/Excellent things

    Overall, the writing is quite clear, and we appreciate the level of detail in this paper. It feels like a general paper that has many specific examples and points to specific evidence, which is compelling! Specifically, we liked the way the text is broken down into sections and the figures, which are visually compelling, clean and easy to understand.

    Things to be improved

    Although it is alluded in the text, it might be beneficial to explicitly highlight what makes a 'good' system where this type of genomic-focused approach would help us understand geologic history e.g. timescale, the species life history that lends us to being able to make these inferences. Although this would by no means be extensive it would help to give an idea of what people should think about.

    Additionally, the paper could use more figures. It could potentially have helped to clarify, for example, how genetic fluctuation rates could be a trustworthy marker for geological events, which seem to have a much lower fluctuation rate.

    Small-picture things

    To be improved

    • The first paragraph could be reworked to feel lighter and to read more smoothly, to make it easier to be introduced to the subject.

    • The enumeration of examples of diversification specifically could be broken up to be more fluid.

    • The examples are interesting to include, but it is difficult to assimilate all the patterns of diversification because the flow is interrupted with parentheses - which makes it difficult to dive into the introduction.

    Competing interests

    The author declares that they have no competing interests.

  3. Version published to 10.32942/x2w02f