Biology subjects

Larson, D. A.

Publications and source records attributed to Larson, D. A..

5 recordsLinked to original sources

bioRxiv2026

Resolving the oak tree of life: comparing RADseq and whole genome resequencing methods for oak phylogenetics

Forest trees pose numerous potential challenges to phylogenomic inference. Their large effective population sizes and relatively long generation times lead to deep allele coalescence and consequently incomplete lineage sorting (ILS), which biases inferences of divergence times toward older ages and introduces gene tree discordance. Deep phylogenetic divergences, reaching back into the Paleocene, introduce reference-mapping biases. Introgression--the movement of genes between lineages--may result in different phylogenies being inferred depending on which individuals are included in analysis, even if the plurality of the genome favors the divergence history unaffected by introgression. These factors influence phylogenetic inference across the Tree of Life but are particularly prevalent in forest trees. Oaks (Quercus) are notable for all three influences. In addition, our knowledge of the oak phylogeny is currently based strongly on restriction site associated DNA sequencing (RADseq) datasets published over the past decade, which may introduce additional sources of uncertainty. In this chapter, we analyze a 322-species RADseq dataset and genome resequencing data from across the genus to address sources of uncertainty in our understanding of the global oak phylogeny, which we hope will serve as a model for other research groups working on comparable woody plant groups.

evolutionary biology↗

bioRxiv2025

Herbaria provide a valuable resource for obtaining informative mRNA

While DNA has built the framework for molecular insights from museum collections, the utility of archival RNA remains largely unexplored. Likely a consequence of the known instability of RNA relative to DNA, this has effectively precluded the use of herbaria for transcriptomics. Here, we challenge the assumption that herbaria cannot be used for transcriptomics by assembling transcriptomes from RNA extracted from herbarium specimens. Through systematic comparison of transcriptomes from fresh-collected, silica-dried, and archival specimens, we demonstrate the suitability of herbarium-derived RNA for transcriptomics. We show the practical applicability of archival mRNA by functionally validating a plant immune receptor synthesized from a specimen collected in 1956. These results contradict the community consensus regarding archival RNA and open the door to subsequent transcriptomic explorations of rare and extinct plant species. Our findings highlight the importance of preserving and utilizing the diversity embedded within herbarium collections.

plant biology↗

bioRxiv2024

A haplotype-resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks

O_LIWhite oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. C_LIO_LIWe report the first haplotype-resolved chromosome-scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. In addition, we probe the genetic diversity of this widespread species and investigate its phylogenetic relationships with other oaks using whole-genome data. C_LIO_LIOur genome assembly comprises two haplotypes each consisting of 12 chromosomes. We found that the species has high genetic diversity, much of which predates the divergence of Q. alba from other oak species and likely impacts divergence time estimation in Quercus. Our phylogenetic results highlight phylogenetic discordance across the genus and suggest different relationships among North American oaks than have been reported previously. Despite a high preservation of chromosome synteny and genome size across the Quercus phylogeny, certain gene families have undergone rapid changes in size including resistance genes (R genes). C_LIO_LIThe white oak genome represents a major new resource for studying genome diversity and evolution in Quercus and forest trees more generally. Future research will continue to reveal the full scope of genomic diversity across the white oak clade. C_LI

genomics↗

bioRxiv2019

A consensus phylogenomic approach highlights the ancient rapid radiation of Ericales

Premise of studyLarge genomic datasets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications. MethodsWe used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods and is summarized in a consensus framework. Key ResultsOur consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships due to lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole genome duplication before the radiation of all or most ericalean families and demonstrate that tree topology and heterogeneous evolutionary rates impact the inferred placement of genome duplications. ConclusionsOur approach provides a novel hypothesis regarding the history of Ericales and confidently resolves most nodes. We demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

evolutionary biology↗

bioRxiv2019

Characterizing gene tree conflict in plastome-inferred phylogenies

Premise of the studyEvolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict.\n\nMethodsUsing a broad sampling of angiosperm plastomes, we characterized gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type).\n\nKey resultsWe uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find gene length is the strongest correlate to concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes.\n\nConclusionsOur results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given the documented cases of heteroplasmic recombination. We suggest rpoC2 as a useful marker for reconstructing angiosperm phylogeny, reducing the effort and expense of assembling and analyzing entire plastomes.

evolutionary biology↗