Biology subjects

Manicki, A.

Publications and source records attributed to Manicki, A..

4 recordsLinked to original sources

bioRxiv2026

Dispersal, gene flow and adaptive differentiation in hierarchically structured populations

The balance between local adaptation and gene flow is rarely quantified when populations are hierarchically differentiated across multiple spatial scales. We addressed this gap in Atlantic salmon (Salmo salar) at its southern range edge, using 1342 individuals from 21 rivers along the French Atlantic and Channel coasts with a 60k SNP array, and combining estimates of dispersal with genome-wide scans for adaptive differentiation across spatial scales. Population structure was hierarchical, resolving five genetic clusters with differentiation among groups five times higher than among populations within them. Assignment tests revealed a marked contrast between clusters, but unassigned individuals reached very high proportions within some clusters, indicating that gene flow has already blurred among-populations differences. Adaptive differentiation was detected among and within clusters, but the loci involved overlapped only partially across scales and among clusters, indicating that adaptation at each hierarchical level relies on distinct sets of variants. Dispersal was a poor guide to where this signal persisted: retaining putative dispersers reduced the candidate set more than threefold, showing that immigrant genotypes could dilute among-populations allele-frequency contrasts within a single generation. Yet differentiation among populations remained strong, as expected if dispersers reproduce poorly. Resolving the balance between local adaptation and gene flow therefore requires accounting for dispersal and adaptive differentiation at different spatial scales, with direct implications for conserving hierarchically structured populations at climatically vulnerable range edges.

evolutionary biology↗

bioRxiv2026

Telomere length can be estimated from fish scales

Telomeres, repetitive DNA sequences at the ends of chromosomes, are increasingly studied as biomarkers of physiological stress as well as ageing processes. In ichthyology, fish scales provide valuable information regarding life history and ageing and are thus often preserved in substantial collections. This study aims to adapt a quantitative Polymerase Chain Reaction (qPCR) method to estimate relative telomere length (RTL) from fish scales archived in such collections. Using the brown trout (Salmo trutta) as a model species, we show that archived scales contain enough DNA to perform qPCR-based RTL measurement. RTLs in scales are on average higher than in fins, however we found no significant correlation between RTL values of both tissues at the individual level. Analysing archived scales originating from the subantarctic Kerguelen Islands introduced brown trout populations, we find substantial variation in RTL between rivers, age classes and body size.

molecular biology↗

bioRxiv2025

Selection against dispersers: Sex, age and origin-dependent fitness differences in wild Atlantic salmon

Local adaptation is often portrayed as uniform fitness disadvantages of immigrants relative to residents. Yet dispersal costs vary with origin, sex, and life-history traits, shaping the balance between gene flow and adaptation. We quantified these heterogeneous costs by comparing the reproductive success of local and immigrant individuals using a 15-year genetic pedigree of Atlantic salmon (Salmo salar), including over 1,100 adults and 3,400 juveniles. Immigrants represented 19.5% of adults, showed male-biased dispersal, and averaged 15% lower reproductive success than locals. However, outcomes were strongly origin-dependent: immigrants from some populations suffered severe fitness costs while others matched or exceeded locals. Sex and life-history further modulated reproductive success: male immigrants underperformed local males, whereas multi-sea-winter females often equaled or outperformed female residents. Immigrant males partially compensated their fitness offset by acquiring more mates. These findings highlight that, while local adaptation promotes philopatry, immigrants origin effects should be considered in gene-flow adaptation dynamics.

evolutionary biology↗

bioRxiv2019

Fast sequence-based microsatellite genotyping development workflow for any non-model species

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20 to 40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence, quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

genetics↗