Biology subjects

Ivanovic, A.

Publications and source records attributed to Ivanovic, A..

4 recordsLinked to original sources

bioRxiv2026

Ancient whole genomes reveal regional selection during adaptation to Neolithic lifestyle in Western Eurasia

The introduction of agriculture in Western Eurasia during the Mesolithic-Neolithic transition reshaped human lifestyle, demography and pathogen exposure. Yet, the associated selective pressures remain incompletely resolved because previous ancient DNA studies relied on targeted SNP panels and yielded non-overlapping results. Here, using high-coverage whole-genome data from 152 ancient individuals, including 12 newly sequenced genomes from the Iron Gates, we show that adaptation during this transition was geographically structured and involved selection of both Early Farmer and Hunter-Gatherer alleles. By combining scans of population differentiation, extended haplotype homozygosity, and adaptive admixture, we identify candidate loci under selection in ancestral and admixed populations. Extending the analysis beyond SNPs, we also detect differential copy-number variants, ancestry-associated shifts in transposable-element abundance, and an early Neolithic hepatitis B infection. Functional analyses including effects on gene expression suggested selection on immune, metabolic, reproductive, sensory, and behavioural processes. Taken together, our results reveal a broader and more regionally variable adaptive landscape than previously appreciated.

evolutionary biology↗

bioRxiv2024

Identification of Y-chromosome turnover in newts fails to support a sex chromosome origin for the Triturus balanced lethal system

Non-recombining regions of the genome often have profound effects on evolution, resulting in phenomena such as sex chromosomes and supergenes. Amongst the strangest examples are balanced lethal systems, such as that found in newts of the genus Triturus. These systems halve reproductive output, and the evolution of such a deleterious trait is difficult to explain. For Triturus an intriguing model proposes that the balanced lethal system evolved from an ancestral Y-chromosome. To test this hypothesis, we identify the Y-chromosome of Triturus and verify whether it, or the balanced lethal system, is homologous to the Y-chromosome of its sister genus Lissotriton, which does not possess the balanced lethal system. We identify a set of candidate Y-linked markers in T. ivanbureschi and place them on a high-density linkage map that we construct with 7,233 RADseq markers. We validate male specificity of the markers across the genus, and then place both the Triturus and Lissotriton Y-linked regions within previously constructed target capture linkage maps that include genes linked to the balanced lethal system. We observe that neither the Triturus balanced lethal system, nor the Triturus Y-chromosome are homologous to the Lissotriton Y-chromosome. This is the first molecular evidence of a transition between Y-chromosome systems within salamanders. However, unless additional sex chromosome turnover events are involved, our data does not support a sex chromosome origin of the balanced lethal system.

evolutionary biology↗

bioRxiv2024

Genomic evidence suggests the balanced lethal system in Triturus newts originated in an instantaneous speciation event.

Triturus newts are afflicted by a balanced lethal system causing the spontaneous death of half of their offspring. How could such a maladaptive trait evolve? We construct genetic maps for Triturus and its sister genus Lissotriton, identifying genes involved in the balanced lethal system. Triturus chromosome 1 has diverged into two versions, which each carry a single massive deletion that is compensated for by duplication of the same region in the alternate version - indicating that the balanced lethal system arose instantaneously, in a single macromutation. Simulations show that, counterintuitively, the deleterious nature of the rearranged chromosomes protects them against competition with the ancestral arrangement via reproductive isolation. We conclude that the origin of the Triturus balanced lethal system also led to instantaneous speciation.

evolutionary biology↗

bioRxiv2020

Mitigating ecosystem impacts of bottom trawl fisheries for North Sea sole Solea solea by replacing mechanical by electrical stimulation

Ecosystem effects of bottom trawl fisheries are a major concern. We analysed whether the replacement of mechanical stimulation by electrical stimulation may reduce the adverse impacts on the benthic ecosystem in the beam trawl fishery for sole. Although the use of electricity is not allowed to catch fish in European Union waters, a number of beam trawlers got derogation and switched to pulse trawling to explore the potential to reduce impacts. We extended a recently developed assessment framework and showed that the switch to pulse trawling substantially reduced benthic impacts when exploiting the Total Allowable Catch of sole in the North Sea. We applied the framework to Dutch beam trawl logbook data from 2009 to 2017 and estimated that the trawling footprint decreased by 23%; the precautionary impact indicator of the benthic community decreased by 39%; the impact on median longevity decreased by 20%; the impact on benthic biomass decreased by 61%; the amount of sediment mobilised decreased by 39%. The decrease is due to the replacement of tickler chains by electrode arrays, a lower towing speed and higher catch efficiency for sole. The effort and benthic impact of the beam trawl fishery targeting plaice Pleuronectes platessa in the central North Sea increased with the recovery of the plaice stock. This study illustrates the usefulness of a standardized methodological framework to assess the differences in time trends and trawling impact between gears.

ecology↗