Biology subjects

Gibson, M. J.

Publications and source records attributed to Gibson, M. J..

7 recordsLinked to original sources

bioRxiv2024

Gene expression and pollen performance indicate altered postmating selection between Solanum species with different mating systems

Postmating prezygotic (PMPZ) traits play an important role in mating success, especially in species where gametes from multiple males compete. Despite this, the effect of mating system transitions, and attendant shifts in the intensity of sexual selection, on specific PMPZ traits and their underlying loci is still poorly understood. Here we assessed differences in pollen PMPZ traits and tissue-specific gene expression (in leaf, pollen, and style) between two closely related plant species with different mating systems--Solanum lycopersicum (selfing) & Solanum pennellii (outcrossing). We focused on species differences in loci with known roles in pollen tube growth rate, including pectin methylesterases (PMEs) and their inhibitors (PMEIs), and in- vitro & in-vivo pollen tube growth rates. Among the gene expression differences observed between species, we found that the expression domain of pollen-biased genes was much narrower in the selfing species S. lycopersicum compared to the outcrossing species S. pennellii, including for most reproductive PMEs and PMEIs. In addition, S. pennellii had faster pollen tube growth rates in-vivo, while S. lycopersicum had faster in-vitro pollen tube growth rates. We propose that the lower expression of pollen tube development genes in S. lycopersicum style tissue, and reduced in-vivo pollen performance, is a result of reduced allocation to stylar mechanisms that modulate pollen tube growth, potentially consistent with relaxed selection on cryptic female choice in the selfing species. Article SummaryThis study investigates the evidence for differential postmating sexual selection in plants, by analyzing reproductive gene expression and pollen performance in two Solanum species with different mating systems. It finds that species differ systematically in pollen tube growth rates, and that pollen ( male)-biased genes have higher secondary expression in stylar ( female) tissues in the outcrossing species. These observations are consistent with the outcrossing species experiencing stronger selection on female reproductive tract traits that influence male postmating performance. This study evaluates key expectations of sexual selection on postmating traits but does so in the uncommon context of flowering plants.

evolutionary biology↗

bioRxiv2024

A comparison between low-cost library preparation kits for low coverage sequencing

In the fields of human health and agricultural research, low coverage whole-genome sequencing followed by imputation to a large haplotype reference panel has emerged as a cost-effective alternative to genotyping arrays for assaying large numbers of samples. However, a systematic comparison of library preparation methods tailored for low coverage sequencing remains absent in the existing literature. In this study, we evaluated one full sized kit from IDT and miniaturized and evaluated three Illumina-compatible library preparation kits--the KAPA HyperPlus kit (Roche), the DNA Prep kit (Illumina), and an IDT kit--using 96 human DNA samples. Metrics evaluated included imputation concordance with high-depth genotypes, coverage, duplication rates, time for library preparation, and additional optimization requirements. Despite slightly elevated duplication rates in IDT kits, we find that all four kits perform well in terms of imputation accuracy, with IDT kits being only marginally less performant than Illumina and Roche kits. Laboratory handling of the kits was similar: thus, the choice of a kit will largely depend on (1) existing or planned infrastructure, such as liquid handling capabilities, (2) whether a specific characteristic is desired, such as the use of full-length adapters, shorter processing times, or (3) use case, for instance, long vs short read sequencing. Our findings offer a comprehensive resource for both commercial and research workflows of low-cost library preparation methods suitable for high-throughput low coverage whole genome sequencing.

genomics↗

bioRxiv2023

The effects of reference panel perturbations on the accuracy of genotype imputation

Reference-based genotype imputation is a standard technique that has become increasingly popular in large-scale studies involving genomic data. The two key elements involved in the process of genotype imputation are (1) the haplotype reference panel to which a target individual is being imputed, and (2) the imputation algorithm used to infer missing genotypes in the target individual. The imputation literature has historically focused mainly on (2), with a typical comparative study investigating the relative performance of various imputation algorithms while holding the reference panel constant. However, the role of the reference panel itself (1) on overall imputation performance is equally, if not more, important than the choice among many high-performing algorithms. Even though it is intuitive that the quality of a reference panel should play a role in the accuracy of imputation, it is nonetheless unclear to what extent common errors during panel creation (e.g., genotyping and phase error) lead to suboptimal imputation performance. In this study, we investigate the effects of applying three distinct modes of perturbations to a widely used haplotype reference panel in human genetics on the resulting imputation accuracy. Specifically, we perturb the reference panel by (1) randomly introducing phase errors, (2) randomly introducing genotype errors, and (3) randomly pruning variants from the panel (all at varying magnitudes). We then impute a set of diverse individuals at various sequencing coverages (0.5x, 1.0x, and 2.0x) to these various perturbed panels and evaluate imputation accuracy using the r2 metric for the entire cohort as well as ancestry-stratified subsets. We observe that both phase- and genotype-perturbations can dramatically affect imputation accuracy, particularly at very low allele frequencies, while pruning variants has a far smaller effect. We then empirically verified that our simulations reliably predict the impact of potential filtering techniques in a real-world dataset. In the context of haplotype reference panels, these results suggest that phasing and genotyping accuracy are far more important than the density of a reference panel used for imputation.

genomics↗

bioRxiv2020

Reconstructing the history and biological consequences of a plant invasion on the Galapagos islands

The introduction of non-native species into new habitats is one of the foremost risks to global biodiversity. Here, we evaluate a recent invasion of wild tomato (Solanum pimpinellifolium) onto the Galapagos islands from a population genomic perspective, using a large panel of novel collections from the archipelago as well as historical accessions from mainland Ecuador and Peru. We infer a recent invasion of S. pimpinellifolium on the islands, largely the result of a single event from central Ecuador which, despite its recency, has rapidly spread onto several islands in the Galapagos. By reconstructing patterns of local ancestry throughout the genomes of invasive plants, we uncover evidence for recent hybridization and introgression between S. pimpinellifolium and the closely related endemic species Solanum cheesmaniae. Two large introgressed regions overlap with known fruit color loci involved in carotenoid biosynthesis. Instead of red fruits, admixed individuals with endemic haplotypes at these loci have orange fruit colors that are typically characteristic of the endemic species. We therefore infer that introgression explains the observed trait convergence. Moreover, we infer roles for two independent loci in driving this pattern, and a likely history of selection favoring the repeated phenotypic transition from red to orange fruits. Together, our data reconstruct a complex history of invasion, expansion, and gene flow among wild tomatoes on the Galapagos islands. These findings provide critical data on the evolutionary importance of hybridization during colonization and its role in influencing conservation outcomes. Significance StatementThe isolation and unique diversity of the Galapagos Islands provide numerous natural experiments that have enriched our understanding of evolutionary biology. Here we use population genomic sequencing to reconstruct the timing, path, and consequences of a biological invasion by wild tomato onto the Galapagos. We infer that invasive populations originated from a recent human-mediated migration event from central Ecuador. Our data also indicate that invasive populations are hybridizing with endemic populations, and that this has led to some invasive individuals adopting both fruit color genes and the fruit color characteristic of the endemic island species. Our results demonstrate how hybridization can shape patterns of trait evolution over very short time scales, and characterize genetic factors underlying invasive success.

evolutionary biology↗

bioRxiv2019

Local extirpation is pervasive among populations of Galapagos endemic tomatoes

The Galapagos Islands are home to incredible endemic biodiversity that is of high conservation interest. Two such endemic species are the Galapagos tomatoes: Solanum cheesmaniae and Solanum galapagense. Both are known from historical location records, but like many endemic plant species on the Galapagos, their current conservation status is unclear. We revisited previously documented sites of endemic species on San Cristobal, Santa Cruz, and Isabela, and document the disappearance of >80% of these populations. In contrast, we find that two invasive relatives (Solanum pimpinellifolium and Solanum lycopersicum) are now highly abundant, and in some cases--based on morphological observations--might be hybridizing with endemics. Our findings suggest that expanding human developments and putative interspecific hybridization are among the major factors affecting the prevalence of invasives and the threatened persistence of the endemic populations.

evolutionary biology↗

bioRxiv2019

Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species

The wild currant tomato Solanum pimpinellifolium inhabits a wide range of abiotic habitats across its native range of Ecuador and Peru. Although it has served as a key genetic resource for the improvement of domestic cultivars, little is known about the genetic basis of traits underlying local adaptation in this species, nor what abiotic variables are most important for driving differentiation. Here we use redundancy analysis (RDA) and other multivariate statistical methods (structural equation modeling (SEM) and generalized dissimilarity modeling (GDM)) to quantify the relationship of genomic variation (6,830 single nucleotide polymorphisms) with climate and geography, among 140 wild accessions. RDA, SEM, and GDM each identified environment as explaining more genomic variation than geography, suggesting that local adaptation to heterogeneous abiotic habitats may be an important source of genetic diversity in this species. Environmental factors describing temporal variation in precipitation and evaporative demand explained the most SNP variation among accessions, indicating that these forces may represent key selective agents. Lastly, by studying how SNP-environment associations vary throughout the genome (44,064 SNPs), we mapped the location and investigated the functions of loci putatively contributing to climatic adaptations. Together our findings indicate an important role for selection imposed by the abiotic environment in driving genomic differentiation between populations.

evolutionary biology↗

bioRxiv2019

Intraspecific genetic variation underlying postmating reproductive barriers between species in the wild tomato clade (Solanum sect. Lycopersicon)

A goal of speciation genetics is to understand how the genetic components underlying interspecific reproductive barriers originate within species. Unilateral incompatibility (UI) is a postmating prezygotic barrier in which pollen rejection in the female reproductive tract (style) occurs in only one direction of an interspecific cross. Natural variation in the strength of UI has been observed among populations within species in the wild tomato clade. In some cases, molecular loci underlying self-incompatibility (SI) are associated with this variation in UI, but the mechanistic connection between these intra- and inter-specific pollen rejection behaviors is poorly understood in most instances. We generated an F2 population between SI and SC genotypes of a single species, Solanum pennellii, to examine the genetic basis of intraspecific variation in the strength of UI against other species, and to determine whether loci underlying SI are genetically associated with this variation. We found that F2 individuals vary in the rate at which UI rejection occurs. One large effect QTL detected for this trait co-localized with the SI-determining S-locus. Moreover, individuals that expressed S-RNase--the S-locus protein involved in SI pollen rejection--in their styles had much more rapid UI responses compared to those without S-RNase protein. Our analysis shows that intraspecific variation at mate choice loci--in this case at loci that prevent self-fertilization--can contribute to variation in the strength of interspecific isolation, including postmating prezygotic barriers. Understanding the nature of such standing variation can provide insight into the accumulation of these barriers between diverging lineages.

evolutionary biology↗