Biology subjects

Whitney, K. D.

Publications and source records attributed to Whitney, K. D..

7 recordsLinked to original sources

bioRxiv2024

Shared selection and genetic architecture drive strikingly repeatable evolution in long-term experimental hybrid populations

The degree to which evolution repeats itself has implications regarding the major forces driving evolution and the potential for evolutionary biology to be a predictive (versus solely historical) science. To understand the factors that control evolutionary repeatability, we experimentally evolved four replicate hybrid populations of sunflowers at natural sites for up to 14 years and tracked ancestry across the genome. We found that there was very strong negative selection against introgressed ancestry in several chromosomes, but positive selection for introgressed ancestry in one chromosome. Further, the strength of selection was influenced by recombination rate. High recombination regions had lower selection against introgressed ancestry due to more frequent recombination away from incompatible backgrounds. Strikingly, evolution was highly parallel across replicates, with shared selection driving 88% of variance in introgressed allele frequency change. Parallel evolution was driven by both high levels of sustained linkage in introgressed alleles and strong selection on large-effect quantitative trait loci. This work highlights the repeatability of evolution through hybridization and confirms the central roles that natural selection, genomic architecture, and recombination play in the process.

evolutionary biology↗

bioRxiv2022

Differentiation of rhizosphere fungal assemblages by host ploidy level in mixed-ploidy Larrea tridentata populations

Polyploidy--whole genome duplication--is common in plants. Studies over the last several decades have documented numerous mixed-ploidy populations. Whether arising via recurrent whole genome duplication events within a population, or from secondary contact, the persistence of mixed populations depends on the ability of the minority cytotype to overcome the negative frequency dependent effects of outcrossing with other ploidies, known as Minority Cytotype Exclusion. One mechanism of overcoming Minority Cytotype Exclusion is microbially-mediated niche differentiation (MMND), wherein cytotypes occupy different niches via interactions with different sets of microbes. Inherently cryptic, MMND is underexplored in polyploid plant populations. Here, we search for evidence of MMND in creosotebush (Larrea tridentata), a dominant desert shrub of the southwestern U.S. and northern Mexico. We sequenced fungi from rhizosphere soils of diploid, autotetraploid, and autohexaploid plants growing in two naturally-occurring mixed-cytotype populations. Within populations, we found substantial fungal assemblage overlap across host plant cytotypes. However, using indicator species analysis, we identified some fungi that are differentiated by host plant cytotype, satisfying a precondition for MMND. Future study is needed to determine the degree of niche differentiation conferred, if any, and whether the identified fungi play a role in the long-term persistence of multiple cytotypes within populations.

evolutionary biology↗

bioRxiv2020

An unexpected donor in the adaptive introgression candidate Helianthus annuus subsp. texanus.

Hybridization is widely acknowledged as an important mechanism of acquiring adaptive variation. In Texas, the sunflower Helianthus annuus subsp. texanus is thought to have acquired herbivore resistance and morphological traits via introgression from a local congener, H. debilis. Here we test this hypothesis using whole genome sequencing data from across the entire range of H. annuus and possible donor species, as well as phenotypic data from a common garden study. We find that although it is morphologically convergent with H. debilis, H. a. texanus has conflicting signals of introgression. Genome wide tests (Pattersons D and TreeMix) only find evidence of introgression from H. argophyllus (sister species to H. annuus and also sympatric), but not H. debilis, with the exception of one individual of 109 analysed. We further scanned the genome for localized signals of introgression using PCAdmix and found minimal but non-zero introgression from H. debilis and significant introgression from H. argophyllus. Putative introgressions mainly occur in high recombination regions as predicted by theory if introgressed ancestry contains maladaptive alleles. To reconcile the disparate findings of our analyses, we discuss potential test-specific confounding features, including introgression from other taxa. Given the paucity of introgression from H. debilis, we argue that the morphological convergence observed in Texas is likely independent of introgression.

evolutionary biology↗

bioRxiv2019

Patterns, predictors, and consequences of dominance in hybrids

Are first-generation (F1) hybrids typically intermediate for all traits that differentiate their parents? Or are they similar to one parent for most traits, or even mismatched for divergent traits? Although the phenotype of otherwise viable and fertile hybrids determines their fate, little is known about the general patterns, predictors, and consequences of phenotype expression in hybrids. To address this empirical gap, we compiled data from nearly 200 studies where traits were measured in a common environment for two parent populations and F1 hybrids. We find that individual traits are typically halfway between the parental midpoint and one parental value (i.e., hybrid trait values are typically 0.25 or 0.75 if parents values are 0 & 1). When considering pairs of traits together, a hybrids multivariate phenotype tends to resemble one parent (pairwise parent-bias) about 50 % more than the other while also exhibiting a similar magnitude of trait mismatch due to different traits having dominance in conflicting directions. We detect no phylogenetic signal nor an effect of parental genetic distance on dominance or mismatch. Using data from an experimental field planting of recombinant hybrid sunflowers--where there is among-individual variation in dominance and mismatch due to segregation of divergent alleles--we illustrate that pairwise parent-bias improves fitness while mismatch reduces fitness. Importantly, the effect of mismatch on fitness was stronger than that of pairwise parent-bias. In sum, our study has three major conclusions. First, hybrids between ecologically divergent natural populations are typically not phenotypically intermediate but rather exhibit substantial mismatch while also resembling one parent more than the other. Second, dominance and mismatch are likely determined by population-specific processes rather than general rules. Finally, selection against hybrids likely results from both selection against somewhat intermediate phenotypes and against mismatched trait combinations.

evolutionary biology↗

bioRxiv2019

Predicting changes in bee assemblages following state transitions in North American drylands

Drylands worldwide are experiencing ecosystem state transitions: the expansion of some ecosystem types at the expense of others. Bees in drylands are particularly abundant and diverse, with potential for large compositional differences and seasonal turnover across ecotones. To better understand how future ecosystem state transitions may influence bees, we compared bee assemblages and their seasonality among sites at the Sevilleta National Wildlife Refuge (NM, USA) that represent three dryland ecosystem types (and two ecotones) of the southwestern U.S. (Plains grassland, Chihuahuan Desert grassland, and Chihuahuan Desert shrubland). Using passive traps, we caught bees during two-week intervals from March - October, 2002 - 2014. The resulting dataset included 302 bee species and 56 genera. Bee abundance, composition, and diversity differed among ecosystems, indicating that future state transitions could alter bee assemblage composition in our system. We found strong seasonal bee species turnover, suggesting that bee phenological shifts may accompany state transitions. Common species drove the observed trends, and both specialist and generalist bee species were indicators of ecosystem types or months; these species could be sentinels of community-wide responses to future shifts. Our work suggests that predicting the consequences of global change for bee assemblages requires accounting for both within-year and among-ecosystem variation.

ecology↗

bioRxiv2019

Correlates of hybridization in plants

Hybridization is a biological phenomenon increasingly recognized as an important evolutionary process in both plants and animals, as it is linked to speciation, radiation, extinction, range expansion and invasion, and allows for increased trait diversity in agricultural and horticultural systems. Estimates of hybridization frequency vary across taxonomic groups, and previous work has demonstrated that some plant groups hybridize more frequently than others. Here, we ask on a global scale whether hybridization is linked to any of 11 traits related to plant life history, reproduction, genetic predisposition, and environment or opportunity. Given that hybridization is not evenly distributed across the plant tree of life, we use phylogenetic generalized least squares regression models and phylogenetic path analysis to detect statistical associations between hybridization and plant traits at both the family and genus levels. We find that perenniality and woodiness are each associated with an increased frequency of hybridization in univariate analyses, but path analysis suggests that the direct linkage is between perenniality and increased hybridization (with woodiness having only an indirect relationship with hybridization via perenniality). Associations between higher rates of hybridization and higher outcrossing rates, abiotic pollination syndromes, vegetative reproductive modes, larger genomes, and less variable genome sizes are detectable in some cases but not others. We argue that correlational evidence at the global scale, such as that presented here, provides a robust framework for forming hypotheses to examine and test drivers of hybridization at a more mechanistic level.\n\nIMPACT SUMMARYAlthough historically thought of as rare, inter-specific mating is increasingly recognized as an important evolutionary process. Hybridization can generate increased genetic and morphological variation and has been tied to increased diversification and other biological phenomena such as geographic range expansion and the success of invasive species. Here, we examine hybridization of plants on a global scale. Previous work has demonstrated that some plant groups hybridize more than others, but the reasons for this pattern remain unclear. We combine data from eight regional floras with trait data to test for associations between hybridization and different aspects of plant biology, such as life history, growth form, reproduction, and opportunity, all while accounting for the fact that plant lineages are related to each other.\n\nWe find that plant groups that are dominated by perennial species and species with woody growth forms tend to hybridize more than those dominated by annual or herbaceous species. We also find some evidence that frequent hybridization is found in plant families that are predominantly pollinated abiotically (such as by wind or water) or have higher rates of outcrossing, plant genera that have less variable genome sizes, and plant groups (both genera and families) that can reproduce asexually and have larger genome sizes. This study provides the first analysis of the global correlates of hybridization in plants. Although this correlational evidence does not provide any mechanistic explanations for these patterns, the trends we find are novel in terms of both geographic and taxonomic sale. The correlations detected provide robust hypotheses for understanding the conditions for hybridization and its contributions to evolution.

evolutionary biology↗

bioRxiv2019

Hybridization and diversification are positively correlated across vascular plant families

Hybridization has experimental and observational ties to evolutionary processes and outcomes such as adaptation, speciation, and radiation. Although it has been hypothesized that hybridization and diversification are correlated, this idea remains largely untested empirically. Here, we use a hybridization database on 195 plant families, life history information, and a time-calibrated family-level phylogeny to test for phylogenetically-corrected associations between hybridization and diversification rates, while also taking into account life-history traits that may be correlated with both processes. We show that diversification and hybridization are positively correlated using three different methods to estimate diversification rates and two different metrics of hybridization. Moreover, the relationship remains detectable when incorporating the correlations between diversification and two other life history characteristics, perenniality and woodiness. We further provide potential mechanisms for this association under three different scenarios: hybridization may drive diversification, diversification may drive hybridization, or both hybridization and diversification may jointly be driven by other factors. We suggest future studies to disentangle the causal structure.

evolutionary biology↗