Biology subjects

Gaynor, M. L.

Publications and source records attributed to Gaynor, M. L..

5 recordsLinked to original sources

bioRxiv2026

All detectable ancient whole-genome duplications involve hybridization

Whole-genome duplication (WGD), or polyploidy, is a major evolutionary force throughout the tree of life. Ancient WGDs are commonly inferred from the distribution of synonymous substitutions per synonymous site () between duplicated genes. Here, we argue that the standard interpretation of these distributions is incomplete. Using haplotype-phased genome assemblies spanning canonical autopolyploid and allopolyploid systems, we find that accumulates primarily between gene copies on non-recombining chromosomes. Thus, -based WGD detection depends not simply on WGD, but on whether duplicated copies evolve independently. This distinction reframes many inferences of ancient WGD as signatures of hybridization and the evolution of meiotic isolation and alters how we interpret the origin, detectability, and evolutionary consequences of polyploidy across the tree of life.

evolutionary biology↗

bioRxiv2025

The frequency and importance of polyploidy in tropical rainforest tree radiations

O_LIThe presence of two or more copies of the genome in an organism, termed polyploidy, is a crucial force in plant evolution, generating genetic, phenotypic and ecological diversity. The Amazonian tree flora is the most species-rich on Earth, and largely arose as a result of rapid evolutionary radiations. While polyploidy is an important catalyst of rapid radiations, it remains poorly studied in tropical tree radiations. C_LIO_LIWe examined ploidy variation across Inga (Fabaceae), a characteristic Amazonian tree radiation, using DNA sequence data from 1305 loci for 189/282 Inga species. We then tested whether polyploid species experience more positive selection than diploids, particularly in loci underlying chemical defence against herbivory, which is a key ecological pressure affecting rainforest tree diversification. C_LIO_LIWe show that tetraploidy occurs in 14% (N=27) of the Inga species we sequenced, with several widespread species showing geographical ploidy variation, alongside minimal phylogenetic signal in ploidy which suggests recurrent polyploidisation. Interestingly, we found more loci under selection in polyploids than diploids, most notably in chemical defence loci. C_LIO_LIOur results show that polyploidy has arisen independently in several Inga species, and that polyploidisation can lead to elevated selection in chemical defence, helping to shape ecological interactions and influence diversification in Inga. C_LI

evolutionary biology↗

bioRxiv2024

nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity

PremiseTraditional methods of ploidal level estimation are tedious; leveraging sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage DNA sequence data for ploidy prediction based on site-based heterozygosity have been developed. However, these approaches may require high-coverage sequence data, use improper probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open-source R package, that addresses the main shortcomings of current methods. Methods and ResultsnQuack performs model selection for improved ploidy predictions. Here, we implement expected maximization algorithms with normal, beta, and beta-binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack. ConclusionInferring ploidal level based on site-based heterozygosity alone is discouraged due to the low accuracy of pattern-based inference.

bioinformatics↗

bioRxiv2023

Dynamics of mixed-ploidy populations under demographic and environmental stochasticities

The theoretical population dynamics of autopolyploids - organisms with more than two genome copies of a single ancestral species - and their diploid progenitors have been extensively studied. The acquisition of multiple genome copies, being in essence a stochastic process, strongly suggests a probabilistic approach to examine the long-term dynamics of a population with multiple cytotypes. Yet, our current understanding of empirical evidence on the dynamics of autopolyploid populations has not incorporated stochastic population dynamics. To investigate the factors contributing to the probability and stability of coexisting cytotypes, we designed a new population dynamics model with demographic and environmental stochasticities to simulate the formation, establishment, and persistence of diploids, triploids, and autotetraploids over time when gene flow is allowed among cytotypes. Contrary to previous research, increased selfing rates and pronounced reproductive isolation stabilized the long-run coexistence of multiple cyto-types. In stressful environments, these dynamics become much more complex, and our stochastic modeling approach helped reveal the resulting intricacies that give tetraploids competitive advantage over their diploid progenitors. Our work is fundamental to a better understanding of the dynamics of coexistence of multiple cytotypes and is a necessary step for further work modeling the dynamics between an autopolyploid and its diploid progenitor.

evolutionary biology↗

bioRxiv2022

Identifying climatic drivers of hybridization in Heuchereae (Saxifragaceae)

Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and ultimately confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization.

evolutionary biology↗