Biology subjects

Peake, A. L.

Publications and source records attributed to Peake, A. L..

6 recordsLinked to original sources

bioRxiv2026

GxE and changes to the genetic architecture of flowering time in an overwintering environment

Characterizing how the expression of genetic variation changes across environments is essential for understanding evolution in complex environments, the evolution of phenotypic plasticity, and the genetic architecture of adaptation. We investigated how the phenotypic distribution, large-effect loci, and polygenetic architecture of flowering time in Arabidopsis thaliana changes when grown in an ecologically realistic environment compared to standard chamber conditions. We grew 479 A. thaliana accessions in an overwintering common garden that have previously been phenotyped in growth chambers by the 1001 Genomes Project (2016). Our findings suggest there is extensive GxE for flowering time between the overwintering common garden and the growth chamber environments. None of the large effect loci that we identified using a multivariate Genome Wide Association Study (GWAS) were shared across growth conditions. We find evidence of allelic differential sensitivity, conditional neutrality, and antagonistic pleiotropy contributing to GxE for flowering time between growth conditions. Our results also suggest that the effects of genetic variation across multiple flowering time regulatory pathways is revealed when grown in a more ecologically realistic environment. The effect sizes for the most significant 1% of SNPs are moderately correlated between the outdoor and growth chamber conditions which indicates a partially shared genetic basis. Overall, our findings highlight how making inferences about the genetic basis and evolution of complex traits may be dependent on conducting experiments in ecologically realistic environments.

genetics↗

bioRxiv2026

The genetic basis of extra-lobed leaves in ivyleaf morning glory (Ipomoea hederacea)

Intraspecific leaf shape variation is common among angiosperms. Ivyleaf morning glory (Ipomoea hederacea) has become a useful system for studying the genetics and ecology of leaf shape variation as this species exhibits two leaf shapes: leaves with entire margins, and 3-lobed leaves. It is known that these phenotypes are controlled by a single locus, and differ in their ecophysiology, geographic distribution, ecology, and fitness. However, individuals producing leaves with 1-2 extra lobes have also been observed, but the genetic basis of these phenotypes have not been described. To investigate the genetic basis of extra-lobing, we compared phenotypic distributions of leaf shapes of an F2 generation to Mendelian ratios for a single locus trait, and conducted a bulked segregant analysis to uncover quantitative trait loci. Our results suggest that producing extra-lobed leaves has a complex genetic basis and that there are multiple QTLs underlying this phenotype containing potential candidate genes involved with auxin distribution and leaf development. Whether these extra-lobed phenotypes also differ in terms of their physiology and ecology remains unexplored.

plant biology↗

bioRxiv2026

A rare deletion of BZ1 in the ivy-leaf morning glory eliminates anthocyanin-based pigmentation.

Anthocyanin biosynthesis is a highly branched network with upstream mutations leading to the loss of many other branches beyond just anthocyanins like flavonols, isoflavonoids, and proanthocyanidins. Consequently, disentangling the specific effects of anthocyanins on plant fitness from those of other branches is difficult unless a mutant impacting the terminal step of anthocyanin biosynthesis can be found. We discovered an Ipomoea hederacea plant (ivy-leaf morning glory) lacking anthocyanins due to a genetic deletion in the terminal step of the anthocyanin biosynthetic pathway. Anthocyanin loss follows a recessive, Mendelian inheritance pattern. Anthocyanin loss is perfectly correlated with a lack of expression of the anthocyanin biosynthesis gene IhUF3GT1 (anthocyanidin-3-O-glucosyltransferase). IhUF3GT1 is the gene most strongly and consistently differentially expressed between unpigmented and pigmented flowers in F2 siblings. A deletion of half of the IhUF3GT1 gene which includes the start codon is the genetic basis underlying a loss of IhUF3GT1 expression and, consequently, anthocyanins in unpigmented plants. The IhUF3GT1 deletion is rare and unique to the unpigmented line. Genome coverage analyses demonstrate that no other pigmented I. hederacea line (of 123 screened) has a loss-of-function mutation in IhUF3GT1. Furthermore, we confirm cosegregation of the IhUF3GT1 deletion with the unpigmented phenotype in F3 progeny from a cross where all unpigmented plants are homozygous for the IhUF3GT1 deletion. Taken together, we describe the genetic basis of a novel unpigmented mutant in I. hederacea, creating a potentially important model for studying the fitness effects of anthocyanin loss.

evolutionary biology↗

bioRxiv2026

Newly arisen indel governs a leaf shape polymorphism in the Ivy Leaf Morning Glory (Ipomoea hederacea)

Leaf shape varies widely across plant taxa and has repeatedly been shown to affect ecophysiology, interspecific interactions, and fitness. We used population genomics, genome wide association studies (GWAS), and comparative genomics to determine the genetic basis and evolutionary history of an uncharacterized Mendelian leaf shape polymorphism in Ipomoea hederacea. To do so, we assembled a reference genome and generated whole genome sequencing for 123 individuals from 55 populations. We identified a 117 kb indel that perfectly co-segregates with leaf shape by conducting a GWAS and assessing differences in coverage. Syntenic orthologs for genes on the indel were present in five other Ipomoea species with various leaf shapes, indicating the indel is a newly arisen deletion in I. hederacea despite similar leaf shape phenotypes in the other species. More broadly, these results illustrate how a range of leaf shape phenotypes can be produced by distinct genetic mechanisms even in closely related species. Although none of the genes on the indel itself are known leaf shape candidates, there are multiple leaf shape candidate genes in close proximity that are involved in the auxin biosynthesis pathway. Additionally, the genes within the indel have gene functions that could affect other potentially ecologically relevant traits that have previously been shown to be associated with leaf shape in I. hederacea. Therefore, the pleiotropic effects of the indel polymorphism can have important implications for understanding the ecological mechanisms influencing a well-documented leaf shape latitudinal cline in I. hederacea. Significance StatementIpomoea hederacea has been used to investigate the ecological and evolutionary effects of leaf shape because of a well-documented latitudinal leaf shape cline governed by an uncharacterized Mendelian polymorphism in this species. We identified a 117 kb indel that perfectly co-segregates with leaf shape in I. hederacea. The indel appears to be a distinct genetic mechanism than those governing similar leaf shapes in other closely related Ipomoea species. Additionally, possible pleiotropic effects of the indel on other traits has important implications for understanding the ecology and evolution of leaf shape variation in I. hederacea. Therefore, the results and the new genomic resources that we developed will facilitate future work understanding the genetic, developmental, and ecological mechanisms governing leaf shape variation.

plant biology↗

bioRxiv2025

High-throughput developmental assay of cold tolerance in Caenorhabditis elegans

Temperature can impose strong selection causing thermal tolerance variation between individuals, populations, and species. We developed a high-throughput larval development assay for cold tolerance in the model organism Caenorhabditis elegans. We exposed animals to 4{degrees}C cold treatments for either 12 or 24 hours. Animals exposed to the 24-hour cold treatment exhibited greater variation and heritability in cold tolerance during the L1 larval stage. The high-throughput approach that we developed is easily scalable to simultaneously measure a large number of strains, which makes it ideal for studying the genetics and evolution of cold tolerance in Caenorhabditis nematodes.

evolutionary biology↗

bioRxiv2022

Genomic signatures of hybridization on the neo-X chromosome of Rumex hastatulus

Natural hybrid zones provide opportunities for studies of the evolution of reproductive isolation in wild populations. Although several recent investigations have found that the formation of neo-sex chromosomes is associated with reproductive isolation, the mechanisms remain unclear in most cases. Here, we assess the contemporary structure of gene flow in the contact zone between largely allopatric cytotypes of the dioecious plant Rumex hastatulus, a species in which there is evidence of sex chromosome turn-over. Males to the west of the Mississippi river, USA, have an X and a single Y chromosome, whereas populations to the east of the river have undergone a chromosomal rearrangement giving rise to a larger X and two Y chromosomes. Using reduced-representation sequencing, we provide evidence that hybrids form readily and survive multiple backcross generations in the field, demonstrating the potential for ongoing gene flow between the cytotypes. At the scale of chromosomes, cline analysis of each chromosome separately captured no signals of difference in cline shape between chromosomes. However, when comparing SNPs, principal component regression revealed a significant increase in the contribution of individual SNPs to inter-cytotype differentiation on the neo-X, but no correlation with recombination rate. Cline analysis revealed that the only SNPs with significantly shallower clines than the genome-average were located on the neo-X. Our data are consistent with a role for the neo-sex chromosome in reproductive isolation between R. hastatulus cytotypes. Our investigation highlights the importance of studying plant hybrid zones in species with sex chromosomes for understanding mechanisms of reproductive isolation and for understanding the role of gene flow in governing the spread of the neo-X chromosomes.

evolutionary biology↗