Biology subjects

Berner, D.

Publications and source records attributed to Berner, D..

5 recordsLinked to original sources

bioRxiv2025

Hybridization but minimal introgression: ecologically-based divergent selection maintains a steep hybrid zone in parapatric stickleback fish

Steep hybrid zones provide key insights into the mechanisms of speciation by reflecting incomplete reproductive isolation between diverging populations. However, the specific reproductive barriers preventing the fusion of such populations generally remain unclear, particularly the role of ecologically-based divergent selection. To address the latter, we here investigate a steep hybrid zone between lake and stream ecotypes of threespine stickleback fish inhabiting contiguous habitats within a single watershed. Given the spatial proximity of these habitats and the systems postglacial age, historical allopatry is unlikely to have contributed to the evolution of reproductive isolation. Using individual whole-genome sequencing from clinal sampling sites, we find that hybridization occurs within a narrow zone - just a few hundred meters long - at the transition between lake and stream habitat. Individuals in this contact zone exhibit strongly bimodal genome-wide ancestry, with a rapid shift toward the stream ecotypes genomic background, consistent with strong selection against lake-derived alleles in the stream habitat. Individual-based simulations tailored to this system demonstrate that divergent ecological selection alone can maintain the observed sharp cline, and illustrate the sustained antagonism between gene flow and selection near the habitat transition. Our findings underscore the power of ecological divergence to generate and maintain reproductive isolation, even in the absence of historical separation, and motivate further empirical work on the ecological underpinnings of steep hybrid zones.

evolutionary biology↗

bioRxiv2025

Developmental genetic basis of dorsal spine reduction in acidic-adapted threespine stickleback fish

The repeated emergence of similar phenotypes in independent populations is a widespread feature of evolution, yet the extent to which repeated evolution reflects shared molecular mechanisms, and the factors that determine this similarity, remain unclear. Here, we investigate the genetic basis of dorsal spine reduction in threespine stickleback fish, an adaptive trait that has evolved repeatedly in freshwater populations. Phenotypic analyses of crosses between a spine-reduced population from Scotland and the ancestral marine form reveal a major-effect locus, with the spine-reducing allele acting dominantly and influencing body patterning. Bulk segregant analysis maps this effect to a single region on chromosome VI that overlaps the hoxdb gene cluster. Transcriptomic analyses of larval stages show a gain of hoxdb expression in the developing spine region of spine-reduced fish, consistent with the dominance of the derived allele. Together, these results indicate dorsal spine reduction in threespine stickleback through cis-regulatory changes at hoxdb, a mechanism found to mediate dorsal spine evolution in a different species of stickleback fish too. These findings highlight the role of hox genes in adaptive divergence between natural populations within a species and provide a clear example of parallel evolution at the molecular level between species.

evolutionary biology↗

bioRxiv2023

Chromosome-level assemblies of the Pieris mannii butterfly genome suggest Z-origin and rapid evolution of the W chromosome

The insect order Lepidoptera (butterflies and moth) represents the largest group of organisms with ZW/ZZ sex determination. While the origin of the Z chromosome predates the evolution of the Lepidoptera, the W chromosome is considered younger, but its origin is debated. To shed light on the origin of the lepidopteran W, we here produce chromosome-level genome assemblies for the butterfly Pieris mannii, and compare the sex chromosomes within and between P. mannii and its sister species P. rapae. Our analyses clearly indicate a common origin of the W chromosomes of the two Pieris species, and reveal similarity between the Z and W in chromosome sequence and structure. This supports the view that the W originates from Z-autosome fusion rather than from a redundant B chromosome. We further demonstrate the extremely rapid evolution of the W relative to the other chromosomes and argue that this may preclude reliable conclusions about the origin of the W based on comparisons among distantly related Lepidoptera. Finally, we find that sequence similarity between the Z and W chromosomes is greatest toward the chromosome ends, perhaps reflecting selection for the maintenance of recognition sites essential to chromosome segregation. Our study highlights the utility of long-read sequencing technology for illuminating chromosome evolution. SignificanceLepidoptera (butterflies and moths) typically exhibit a ZW/ZZ sex determination system, but the origin of the W chromosome is controversial. Based on a chromosome-level reference genome for the Southern Small white butterfly and comparative genomic analyses, we propose that the W chromosome in this group of butterflies derives from the Z chromosome and evolves extremely rapidly.

genomics↗

bioRxiv2020

Analysis of Genetically Determined Gene Expression Suggests Role of Inflammatory Processes in Exfoliation Syndrome

Exfoliation syndrome (XFS) is an age-related systemic disorder characterized by excessive production and progressive accumulation of abnormal extracellular material, with pathognomonic ocular manifestations. It is the most common cause of secondary glaucoma, resulting in widespread global blindness. We performed Transcriptomic Wide Association Studies (TWAS) using PrediXcan models trained in 48 GTEx tissues to identify genetically- determined gene expression changes associated with XFS risk, leveraging on results from a global GWAS that included 123,457 individuals from 24 countries. We observed twenty-eight genes in a three-Megabase chr15q22-25 region that showed statistically significant associations, which were further whittled down to ten genes after additional statistical validations. In experimental analysist of these ten genes, mRNA transcript levels for ARID3B, CD276, LOXL1, NEO1, SCAMP2, and UBL7 were significantly decreased in iris tissues from XFS patients compared to control samples. Genes with genetically determined expression changes in XFS were significantly enriched for genes associated with inflammatory conditions. We further explored the health consequences of high susceptibility to XFS using a large electronic health record and observed a higher incidence of XFS comorbidity with inflammatory and connective tissue diseases. Our results implicate a role for connective tissues and inflammation in the etiology of XFS. Targeting the inflammatory pathway may be a potential therapeutic option to reduce progression in XFS.

genetics↗

bioRxiv2020

Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish

How ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback population pair adapted to contiguous, ecologically different lake and stream habitats. Dense clinal whole-genome sequence data reveal numerous regions fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow because a steep cline in allele frequencies is observed across the entire genome, and because the cline center co-localizes with the habitat transition. Simulations confirm that such strong reproductive isolation can be maintained by polygenic selection despite high dispersal and small per-locus selection coefficients. Finally, comparing samples from the cline center before and after an unusual ecological perturbation demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale.

evolutionary biology↗