Biology subjects

Whibley, A.

Publications and source records attributed to Whibley, A..

14 recordsLinked to original sources

bioRxiv2025

Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species

Bird genomes are among the most stable in terms of synteny and gene content across vertebrates. However, germline-restricted chromosomes (GRCs) represent a striking exception where programmed DNA elimination confines large-scale genomic changes to the germline. GRCs are known to occur in songbirds (oscines), but have been studied only in a few species of Passerides such as the zebra finch, the key model for passerine genomics. Their presence and evolutionary dynamics in most major passerine lineages remain largely unexplored, with suboscines entirely unexamined by cytogenetic or genomic methods. Here, we present the most comprehensive comparative analysis of GRCs to date, spanning 44 million years of passerine evolution. By generating the first germline reference genomes of an oscine and a suboscine, 22 novel germline draft genomes spanning nearly all major passerine lineages and a germline draft genome of a parrot outgroup, we show that the GRC is likely present in 6,700 passerine species. Our results reveal that the GRC evolves rapidly and distinctly from the standard A chromosomes (autosomes and sex chromosomes), yet retains functionally important, selectively maintained genes. We observed gene and repeat turnover occuring orders of magnitude faster than on the A chromosomes. Some GRC genes, such as cpeb1 and pim1, are widespread from an ancient duplication. In contrast, other GRC genes, like mfsd2b and bmp15, have been independently duplicated onto the GRC multiple times, suggesting adaptive constraints. The discovery of zglp1 on the zebra finch GRC, initially copied from chromosome 30 and subsequently lost from it, indicates functional replacement, where the GRC permits gene loss from the standard genome. As the GRC harbors the only zglp1 copy in most of the [~]4000 Passerides species, GRC loss would compromise essential germline functions. Our findings establish the GRC as a genomic innovator driving rapid germline evolution. This fact highlights its evolutionary significance for passerine diversification and suggests that programmed DNA elimination may be an overlooked yet phylogenetically widespread mechanism in many understudied animal lineages.

genomics↗

bioRxiv2025

Shaping of developmental gradients through selection on multiple loci in Antirrhinum

Development depends on precise shaping of molecular gradients, but how natural selection acts to establish precision is unknown. Here we analyse genes that control differences in the gradient of yellow flower colour between two varieties of snapdragon (Antirrhinum). We show that these differences depend, in part, on cis regulatory variation in the pigment biosynthetic gene, FLAVIA (FLA). FLA interacts multiplicatively with three other loci, one of which is a trans-acting regulator of FLA, to further shape the yellow gradient. All the loci exhibit clines at a hybrid zone, with widths that correlate with phenotypic effect, showing how selection can hone gradient shape with remarkable precision by acting on cis and trans variation at multiple loci.

evolutionary biology↗

bioRxiv2025

Genomic tree scans identify loci underlying adaptive peaks in Antirrhinum

A key question in evolutionary biology is how barriers to gene flow operate and arise between populations, leading to speciation. Barriers are typically identified by comparing populations distinguished by phenotype, geographical location and/or environment. However, such prior classifications may bias recovery towards features obvious to the human eye, influencing mechanistic interpretations. Here we develop a method blind to prior classifications. We apply it to 18 Antirrhinum populations occupying habitats from coastal to alpine. By scanning the genome for regions with deeply rooted similar trees, we identify a single multi-locus partition, comprising less than 0.5% of the genome. It derives from eight genes, three newly identified here, which interact to generate complementary pollinator guides, likely corresponding to two adaptive peaks in a fitness landscape. Hybrid genotypes fall in a fitness valley, allowing the partition to be maintained through hybrid incompatibility and creating steep clines in allele frequency at a hybrid zone. Another partition derives from a single locus linked to a gene controlling plant height. The locus exhibits a shallow cline in allele frequency across an eco-geographic barrier and may be eco-adaptive. Our results suggest that two ancestral subspecies underwent extensive gene flow except at a few barrier loci, showing how both hybrid incompatibility and eco-adaptation can operate to maintain diversity.

evolutionary biology↗

bioRxiv2024

Low-pass nanopore sequencing for measurement of global methylation levels in plants

Nanopore sequencing enables detection of DNA methylation at the same time as identification of canonical sequence. A recent study validated low pass nanopore sequencing to accurately estimate global methylation levels in vertebrates with sequencing coverage as low as 0.01x. We investigated the applicability of this approach to plants by testing three plant species and analysed the effect of technical and biological parameters on estimate precision and accuracy. Our results indicate that a higher coverage (0.1x) is required to assess plant global methylation at an equivalent accuracy to vertebrates. Shorter read length and a closer sequence match between sample and reference genome improved measurement accuracy. Application of this method in Vitis vinifera showed consistent global methylation levels across different leaf sizes, and different sample preservation and DNA extraction methods, whereas different varieties and tissue types did exhibit methylation differences. Similarly, distinct methylation patterns could be observed in different genomic features. Our findings suggest the suitability of this method as a low-cost screening tool for validation of experimental parameters, developmental time courses and to assess methylation status for different modification types and sequence contexts at the level of whole genome or for abundant genomic features such as transposable elements.

genomics↗

bioRxiv2024

A Cry For Kelp: Evidence for Polyphenolic Inhibition of Oxford Nanopore Sequencing of Brown Algae

Genomic resources for macroalgae are increasingly important for conservation and commercial management, however the generation of such resources continues to be hampered by difficulties in the isolation of suitable DNA. Even when DNA has been isolated that otherwise appears high quality, such samples may not perform well during the sequencing process. We here compare Oxford Nanopore long-read sequencing results for three species of macroalgae to those of non-macroalgal species and find that macroalgal samples tend to lead to rapid decline in the number of available sequencing pores resulting in reduced sequencing yield. LC-MS analysis of macroalgal DNA that would be considered suitable for sequencing reveals that DNA derived from dried macroalgae is enriched for polyphenol-DNA adducts - which may lead to sequencing inhibition. Our findings have wide-ranging implications for the generation of genomic resources from macroalgae, for example long read sequencing of dried herbarium specimens, and suggest a need to use fresh tissue wherever possible for genome sequencing.

molecular biology↗

bioRxiv2024

A High-quality Oxford Nanopore Assembly of the Hourglass Dolphin (Sagmatias cruciger) Genome

The hourglass dolphin (Lagenorhynchus cruciger) is a small cetacean species of the Southern Ocean, with significance to iwi M[a]ori (M[a]ori tribes) of Aotearoa New Zealand as taonga (treasured/valued). Due to the remoteness and difficulty of surveying Antarctic waters, it remains one of the least-studied dolphin species. A recent stranding of an hourglass dolphin represented a rare opportunity to generate a genome assembly as a resource for future study into the conservation and evolutionary biology of this species. In this study, we present a high-quality genome assembly of an hourglass dolphin individual using a single sequencing platform, Oxford Nanopore Technologies, coupled with computationally efficient assembly methods. Our assembly strategy yielded a genome of high contiguity (N50 of 8.07 Mbp) and quality (98.3% BUSCO completeness). Compared to other Delphinoidea reference genomes, this assembly has fewer missing BUSCOs than any except Orcinus orca, more single-copy complete BUSCOs than any except Phocoena sinus, and 20% fewer duplicated BUSCOs than the average Delphinoidea reference genome. This suggests that it is one of the most complete and accurate marine mammal genomes to date. This study showcases the feasibility of a cost-effective mammalian genome assembly method, allowing for genomic data generation outside the traditional confines of academia and/or resource-rich genome assembly hubs, and facilitating the ability to uphold Indigenous data sovereignty. In the future the genome assembly presented here will allow valuable insights into the past population size changes, adaptation, vulnerability to future climate change of the hourglass dolphin and related species.

genomics↗

bioRxiv2023

The genome of a globally invasive passerine, the common myna (Acridotheres tristis)

In an era of global climate change and massive environmental disturbance, biodiversity conservation is receiving increased attention. Conservation efforts are being greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions around adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with the novel selection regime of the invaded range to drive rapid evolution. The common myna (Acridotheres tristis) is a globally invasive passerine, which has undergone multiple concurrent and sequential bottlenecks across its globally invasive range, and yet has established itself across a diverse array of ecological conditions. It is therefore an excellent model species for research both into the persistence of low-diversity populations and the mechanics of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna, assembled using a backbone of Oxford Nanopore Technologies long reads, alongside an RNA-seq based transcriptome and genome annotation. To provide genomic context for future studies, we describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family expansions and contractions. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, but also reveal artefactual impacts of genetic bottlenecks on demographic analysis.

genomics↗

bioRxiv2023

Genetic control of cell layer interactions in plants via tissue mechanics

Plant development depends on coordination of growth between different cell layers. Coordination may be mediated by molecular signalling or mechanical connectivity between cells, but evidence for genetic control via direct mechanics has been lacking. We show that a brassinosteroid-deficient dwarf mutant of the aquatic plant Utricularia gibba has twisted internal tissue, likely caused by a mechanical constraint from a slow-growing epidermis creating tissue stresses. This conclusion is supported by showing that inhibition of brassinosteroid action in an Arabidopsis mutant compromised for cell adhesion, enhances epidermal crack formation, an indicator of increased tissue tension. Thus, genes driving brassinosteroid synthesis can promote growth of internal tissue by reducing mechanical epidermal constraint, showing that tissue mechanics plays a key role in coordinating growth between cell layers. One-Sentence SummaryInternal twists in a mutant carnivorous plant reveal how genes control growth via tissue mechanics.

plant biology↗

bioRxiv2022

Subtle introgression footprints at the end of the speciation continuum in a clade of Heliconius butterflies

Quantifying gene flow between lineages at different stages of the speciation continuum is central to understanding speciation. Heliconius butterflies have undergone an adaptive radiation in wing colour patterns driven partly by natural selection for local mimicry. Colour patterns are also known to be used as assortative mating cues. Therefore, wing pattern divergence is considered to play a role in speciation. A corollary is that mimicry between closely-related species may be associated with hybridization and interfere with reproductive isolation. Here, we take a multifaceted approach to explore speciation history, species boundaries, and traits involved in species differentiation between the two closely-related species H. hecale and H. ismenius. We focus on geographic regions where the two species mimic each other, and contrast this with geographic regions where they do not mimic each other. To examine population history and patterns of gene flow, we tested and compared a four-population model accounting for linked selection. This model suggests that the two species have remained isolated for a large part of their history, yet with a small amount of gene exchange. Accordingly, signatures of genomic introgression were small except at a major wing pattern allele and chemosensing genes, and stronger in the mimetic populations compared to non-mimetic populations. Behavioural assays confirm that visual confusion exists but that short-range cues determine strong sexual isolation. Tests for chemical differentiation between species identified major differences in putative pheromones which likely mediate mate choice and the maintenance of species differences.

evolutionary biology↗

bioRxiv2021

Dissecting supergene: evidence for recombination suppression among multiple functional loci within inversions.

Supergenes are genetic architectures associated with discrete and concerted variation in multiple traits. It has long been suggested that supergenes control these complex polymorphisms by suppressing recombination between set of coadapted genes. However, because recombination suppression hinders the dissociation of the individual effects of genes within supergenes, there is still little evidence that supergenes evolve by tightening linkage between coadapted genes. Here, combining an landmark-free phenotyping algorithm with multivariate genome wide association studies, we dissected the genetic basis of wing pattern variation in the butterfly Heliconius numata. We showed that the supergene controlling the striking wing-pattern polymorphism displayed by this species contains many independent loci associated with different features of wing patterns. The three chromosomal inversions of this supergene suppress recombination between these loci, supporting the hypothesis that they may have evolved because they captured beneficial combinations of alleles. Some of these loci are associated with colour variations only in morphs controlled by inversions, indicating that they were recruited after the formation of these inversions. Our study shows that supergenes and clusters of adaptive loci in general may form via the evolution of chromosomal rearrangements suppressing recombination between co-adapted loci but also via the subsequent recruitment of linked adaptive mutations.

evolutionary biology↗

bioRxiv2021

Supergene formation is associated with a major shift in genome-wide patterns of diversity in a butterfly

Selection shapes genetic diversity around target mutations, yet little is known about how selection on specific loci affects the genetic trajectories of populations, including their genome-wide patterns of diversity and demographic responses. Here we study the patterns of genetic variation and geographic structure in a neotropical butterfly, Heliconius numata, and its closely related allies in the so-called melpomene-silvaniform clade. H. numata is known to have evolved an inversion supergene which controls variation in wing patterns involved in mimicry associations with distinct groups of co-mimics whereas it is associated to disassortative mate preferences and heterozygote advantage at this locus. We contrasted patterns of genetic diversity and structure 1) among extant polymorphic and monomorphic populations of H. numata, 2) between H. numata and its close relatives, and 3) between ancestral lineages. We show that H. numata populations which carry the inversions as a balanced polymorphism show markedly distinct patterns of diversity compared to all other taxa. They show the highest genetic diversity and effective population size estimates in the entire clade, as well as a low level of geographic structure and isolation by distance across the entire Amazon basin. By contrast, monomorphic populations of H. numata as well as its sister species and their ancestral lineages all show lower effective population sizes and genetic diversity, and higher levels of geographical structure across the continent. One hypothesis is that the large effective population size of polymorphic populations could be caused by the shift to a regime of balancing selection due to the genetic load and disassortative preferences associated with inversions. Testing this hypothesis with forward simulations supported the observation of increased diversity in populations with the supergene. Our results are consistent with the hypothesis that the formation of the supergene triggered a change in gene flow, causing a general increase in genetic diversity and the homogenisation of genomes at the continental scale.

evolutionary biology↗

bioRxiv2019

Mutation accumulation in chromosomal inversions maintains wing pattern polymorphism in a butterfly

While natural selection favours the fittest genotype, polymorphisms are maintained over evolutionary timescales in numerous species. Why these long-lived polymorphisms are often associated with chromosomal rearrangements remains obscure. Combining genome assemblies, population genomic analyses, and fitness assays, we studied the factors maintaining multiple mimetic morphs in the butterfly Heliconius numata. We show that the polymorphism is maintained because three chromosomal inversions controlling wing patterns express a recessive mutational load, which prevents their fixation despite their ecological advantage. Since inversions suppress recombination and hamper genetic purging, their formation fostered the capture and accumulation of deleterious variants. This suggests that many complex polymorphisms, instead of representing adaptations to the existence of alternative ecological optima, could be maintained primarily because chromosomal rearrangements are prone to carrying recessive harmful mutations.

evolutionary biology↗

bioRxiv2018

Genome structure and evolution of Antirrhnum majus L.

Snapdragon (Antirrhinum majus L.), a member of Plantaginaceae, is an important model for plant genetics and molecular studies on plant growth and development, transposon biology and self-incompatibility. Here we report a high-quality genome assembly of A. majus cultivated JI7 (A. majus cv.JI7) of a 510 Mb with 37,714 annotated protein-coding genes. The scaffolds covering 97.12% of the assembled genome were anchored on 8 chromosomes. Comparative and evolutionary analyses revealed that Plantaginaceae and Solanaceae diverged from their most recent ancestor around 62 million years ago (MYA). We also revealed the genetic architectures associated with complex traits such as flower asymmetry and self-incompatibility including a unique TCP duplication around 46-49 MYA and a near complete{psi} S-locus of ca.2 Mb. The genome sequence obtained in this study not only provides the first genome sequenced from Plantaginaceae but also bring the popular plant model system of Antirrhinum into a genomic age.

genomics↗

bioRxiv2017

Supergene evolution triggered by the introgression of a chromosomal inversion

Supergenes are groups of tightly linked loci whose variation is inherited as a single Mendelian locus and are a common genetic architecture for complex traits under balancing selection1. Supergene alleles are long-range haplotypes with numerous mutations underlying distinct adaptive strategies, often maintained in linkage disequilibrium through the suppression of recombination by chromosomal rearrangements2-5. However, the mechanism governing the formation of supergenes is not well understood, and poses the paradox of establishing divergent functional haplotypes in face of recombination1,6. Here, we show that the formation of the supergene alleles encoding mimicry polymorphism in the butterfly Heliconius numata is associated with the introgression of a divergent, inverted chromosomal segment. Haplotype divergence and linkage disequilibrium indicate that supergene alleles, each allowing precise wing-pattern resemblance to distinct butterfly models, originate from over a million years of independent chromosomal evolution in separate lineages. These \"superalleles\" have evolved from a chromosomal inversion captured by introgression and maintained in balanced polymorphism, triggering supergene inheritance. This mode of evolution is likely to be a common feature of complex structural polymorphisms associated with the coexistence of distinct adaptive syndromes, and shows that the reticulation of genealogies may have a powerful influence on the evolution of genetic architectures in nature.

evolutionary biology↗