Biology subjects

McKibben, M. T. W.

Publications and source records attributed to McKibben, M. T. W..

5 recordsLinked to original sources

bioRxiv2026

The Genomic Legacy of Ancient Polyploidy in Crop Domestication

Species that have an ancestry of whole-genome duplications (WGDs) are more likely to be domesticated, but the underlying mechanisms remain unclear. We tested whether paleologs--genes duplicated during ancient WGDs--are enriched in candidate domestication lists across 22 crop species spanning 17 genera. Paleologs were significantly enriched in 14 species, with single-copy paleologs showing the most consistent overrepresentation. In contrast, genes from small-scale duplications were consistently underrepresented among domestication candidates. This enrichment was independent of WGD age and degree of gene loss, indicating that constraint on copy number does not preclude selection on gene function. Several non-mutually exclusive processes could explain this pattern, including accumulated genetic diversity becoming available upon return to single-copy, selection to maintain essential functions, and greater selection efficiency on unmasked loci. Ancient WGDs thus provide a persistent genomic substrate for crop evolution millions of years later.

bioinformatics↗

bioRxiv2024

A comprehensive examination of Chelicerate genomes reveals no evidence for a whole genome duplication among spiders and scorpions

Whole genome duplications (WGDs) can be a key event in evolution, playing a role in both adaptation and speciation. While WGDs are common throughout the history of plants, only a few examples have been proposed in metazoans. Among these, recent proposals of WGD events in Chelicerates, the group of Arthropods that includes horseshoe crabs, ticks, scorpions, and spiders, include several rounds in the history of horseshoe crabs, with an additional WGD proposed in the ancestor of spiders and scorpions. However, many of these inferences are based on evidence from only a small portion of the genome (in particular, the Hox gene cluster); therefore, genome-wide inferences with broader species sampling may give a clearer picture of WGDs in this clade. Here, we investigate signals of WGD in Chelicerates using whole genomes from 17 species. We employ multiple methods to look for these signals, including gene tree analysis of thousands of gene families, comparisons of synteny, and signals of divergence among within-species paralogs. We test several scenarios of WGD in Chelicerates using multiple species trees as a backbone for all hypotheses. While we do find support for at least one WGD in the ancestral horseshoe crab lineage, we find no evidence for a WGD in the history of spiders and scorpions using any genome-scale method. This study not only sheds light on genome evolution and phylogenetics within Chelicerates, but also demonstrates how a combination of comparative methods can be used to investigate signals of ancient WGDs.

evolutionary biology↗

bioRxiv2024

Species Tree Topology Impacts the Inference of Ancient Whole-Genome Duplications Across the Angiosperm Phylogeny

PremiseThe history of angiosperms is marked by repeated rounds of ancient whole-genome duplications (WGDs). Here we use state of the art methods to provide an up-to-date view of the distribution of WGDs in the history of angiosperms that considers both the uncertainty introduced by inference methods and alternative phylogenetic hypotheses. MethodsTranscriptomic and genomic data were used to infer and place WGDs across two hypothesized angiosperm phylogenies. Initial WGD hypotheses were made using rate corrections to the distribution of synonymous divergences (Ks) of paralogs and orthologs. WGD hypotheses were tested using syntenic inferences and Bayesian models of duplicate gene gain and loss across the phylogeny. Key resultsThe number of ancient WGDs in the history of angiosperms ([~]170) is largely similar across different inference methods, but there is often variation in the precise placement of WGDs on the phylogeny. Ks based methods often yield alternative hypothesized WGD placements largely due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation, allowing for post hoc testing of WGD hypotheses. However, errors in species tree inference can still produce spurious WGD hypotheses regardless of method used. ConclusionsHere we show that different WGD inference methods largely agree on an average of 3.5 WGD in the history of angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods.

evolutionary biology↗

bioRxiv2022

Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits

Invasive species offer outstanding opportunities to identify the genomic sources of variation that contribute to rapid adaptation, as well as the genetic mechanisms facilitating invasions. The Eurasian plant yellow starthistle (Centaurea solstitialis) is highly invasive in North and South American grasslands and known to have evolved increased growth and reproduction during invasion. Here we develop new genomic resources for C. solstitialis and map the genetic basis of invasiveness traits. We present a chromosome-scale (1N = 8) reference genome using PacBio CLR and Dovetail Omni-C technologies, and functional gene annotation using RNAseq. We find repeat structure typical of the family Asteraceae, with over 25% of gene content derived from ancestral whole genome duplications (paleologs). Using an F2 mapping population derived from a cross between native and invading parents, with a restriction site-associated DNA (RAD)-based genetic map, we validate the assembly and identify 13 QTL underpinning size traits that have evolved during invasion. We find evidence that large effect QTL may be associated with structural variants between native and invading genotypes, including a variant with an overdominant and pleiotropic effect on key invader traits. We also find evidence of significant paleolog enrichment under two QTL. Our results add to growing evidence of the importance of structural variants in evolution, and to understanding of the rapid evolution of invaders. Significance StatementInvasive species often evolve rapidly in new environments, potentially informing our understanding of the genomic basis of adaptation, but genomic studies of these non-model systems are limited. We provide a chromosome-scale reference genome, annotation, and genetic map for the invasive plant yellow starthistle, and we investigate the genetic basis of invader trait evolution in this system. We find regions of the genome with large effects on traits that differ between native and invading genotypes, and evidence suggesting genome structural variants and past genome duplications could play a role in rapid adaptation of invading populations. These genomic resources and evolutionary insights aid in our understanding of the sources of genomic variation for adaptation, and how their evolution facilitates invasion.

genomics↗

bioRxiv2021

Applying Machine Learning to Classify the Origins of Gene Duplications

Nearly all lineages of land plants have experienced at least one whole genome duplication (WGD) in their history. The legacy of these ancient WGDs is still observable in the diploidized genomes of extant plants. Genes originating from WGD--paleologs--can be maintained in diploidized genomes for millions of years. These paleologs have the potential to shape plant evolution through sub- and neofunctionalization, increased genetic diversity, and reciprocal gene loss among lineages. Current methods for classifying paleologs often rely on only a subset of potential genomic features, have varying levels of accuracy, and often require significant data and/or computational time. Here we developed a supervised machine learning approach to classify paleologs from a target WGD in diploidized genomes across a broad range of different duplication histories. We collected empirical data on syntenic block sizes and other genomic features from 27 plant species each with a different history of paleopolyploidy. Features from these genomes were used to develop simulations of syntenic blocks and paleologs to train a gradient boosted decision tree. Using this approach, Frackify (Fractionation Classify), we were able to accurately identify and classify paleologs across a broad range of parameter space, including cases with multiple overlapping WGDs. We then compared Frackify with other paleolog inference approaches in six species with paleotetraploid and paleohexaploid ancestries. Frackify provides a way to combine multiple genomic features to quickly classify paleologs while providing a high degree of consistency with existing approaches.

bioinformatics↗