Biology subjects

Martin, S. L. F.

Publications and source records attributed to Martin, S. L. F..

4 recordsLinked to original sources

bioRxiv2026

Historical genomes reveal scale-dependent predictability of climate adaptation

Predicting evolution remains a central challenge in biology. Contemporary spatial patterns are increasingly used as space-for-time proxies to forecast evolutionary responses to environmental change, yet the reliability of such predictions--and whether it varies among biological scales--remains unclear. Using historical and contemporary genomes of the invasive weed Ambrosia artemisiifolia--spanning the species' native range, invasions on two continents and nearly two centuries--we show that genomically predicted flowering-time clines remained stable in the native range while introduced populations re-evolved them. Haploblocks--likely structural variants--were likewise temporally stable in the native range, and two showed striking parallel evolution across all three ranges. Climate-associated SNPs with the strongest contemporary clines showed the greatest temporal change, with limited and variable parallelism among introduced ranges. Together, these results suggest adaptive evolution is partly predictable even when individual genomic trajectories remain flexible and contingent, with predictability emerging most clearly at the level of polygenic traits and large structural variants.

evolutionary biology↗

bioRxiv2025

Pleistocene reindeer dental calculus as a source for ancient oral and digestive flora

Dental calculus offers an extraordinary window into the past, preserving a rich archive of genetic material that can unlock new insights into ancient ecosystems. By capturing traces of oral microbiomes, dietary components, and even gut microbes regurgitated by ruminants, dental calculus provides an extraordinary window into the past to reconstruct ecological interactions and past environmental conditions. Here, we harness the power of ancient metagenomics to explore the oral microbiome, digestive microbiomes and diet of Pleistocene reindeer (Rangifer tarandus) from archaeological sites in France, a region that once served as a glacial refugium before reindeer disappeared from the area. We used shotgun metagenomic sequencing to assemble microbial genomes (MAGs) and classify microbial and dietary reads from dental calculus of 19 ancient reindeer (ca. 12,000 - 23,000 years BP) and 27 modern and historical (1861 - 1958 CE) Scandinavian reindeer. Notably, six bacterial taxa associated with the rumen microbiome were consistently detected across both ancient and modern samples, offering a rare glimpse into the continuity of digestive adaptations over thousands of years. Our recovery of oral microbial and putative dietary plant DNA suggest adaptive capability. Our results suggest a spatio-temporal turnover in oral microbiome and putative dietary plant DNA, which might be explained by ecological differences between Pleistocene France and contemporary Scandinavia. As soft tissue preservation is rare in ancient remains, dental calculus emerges as an exciting and powerful tool for reconstructing the environmental and ecological histories of both past and extinct populations.

evolutionary biology↗

bioRxiv2025

Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids

Arctic and alpine insects face extreme environmental stressors, yet the genomic basis of their adaptation remains poorly understood. Here, we present the first haplotype-resolved, chromosome-level genomes for four species of Diamesa (Diptera: Chironomidae), a genus of cold-adapted midges inhabiting glacial and high-altitude freshwater ecosystems. Using PacBio HiFi sequencing and Hi-C scaffolding, we assembled high-quality genomes with chromosome-level resolution and high k-mer completeness. Phylogenomic analyses support Diamesinae as sister to other Chironomidae except Podonominae, and genomic comparisons provide evidence for introgression between the evolutionary distinct D. hyperborea and D. tonsa. Comparative genomic analyses across 20 Diptera species revealed significant gene family contractions in Diamesa associated with oxygen transport and metabolism, suggesting adaptations to high-altitude, low-oxygen environments. Conversely, expansions were detected in histone-related and Toll-like receptor gene families, likely enhancing chromatin remodeling and immune regulation under cold stress. A single gene family encoding glucose dehydrogenase was significantly expanded across all cold-adapted species studied, implicating its role in cryoprotectant synthesis and oxidative stress mitigation. Notably, Diamesa species exhibit the largest gene family contraction at any node, with minimal overlap in expansions with other cold-adapted Diptera, indicating lineage-specific adaptation. Our findings support the hypothesis that genome size condensation and selective gene family changes underpin survival in cold environments. These genome assemblies represent a valuable resource for investigating adaptation, speciation, and conservation in cold-specialist insects. Future work integrating gene expression and population genomics will further illuminate the evolutionary resilience of Diamesa in a warming world.

genomics↗

bioRxiv2023

Loss of alkyladenine DNA glycosylase alters gene expression in the developing mouse brain and leads to reduced anxiety and improved memory

Neurodevelopment is a tightly coordinated process, during which the genome is exposed to spectra of endogenous agents at different stages of differentiation. Emerging evidence indicates that DNA damage is an important feature of developing brain, tightly linked to gene expression and neuronal activity. Some of the most frequent DNA damage includes changes to DNA bases, which are recognized by DNA glycosylases and repaired through base excision repair (BER) pathway. The only mammalian DNA glycosylase able to remove frequent alkylated DNA based is alkyladenine DNA glycosylase (Aag, aka Mpg). We recently demonstrated that, besides its role in DNA repair, AAG affects expression of neurodevelopmental genes in human cells. Aag was further proposed to act as reader of epigenetic marks, including 5-hydroxymethylcytosine (5hmC), in the mouse brain. Despite the potential Aag involvement in the key brain processes, the impact of Aag loss on developing brain remains unknown. Here, by using Aag knockout (Aag-/-) mice, we show that Aag absence leads to reduced DNA break levels, evident in lowered number of {gamma}H2AX foci in postnatal day 5 (P5) hippocampi. This is accompanied by changes in 5hmC signal intensity in different hippocampal regions. Transcriptome analysis of hippocampi and prefrontal cortex, at different developmental stages, indicates that lack of Aag alters gene expression, primarily of genes involved in regulation of response to stress. Across all developmental stages tested aldehyde dehydrogenase 2 (Aldh2) emerged as one of the most prominent genes deregulated in Aag-dependent manner. In line with the changes in hippocampal DNA damage levels and the gene expression, adult Aag-/- mice exhibit altered behavior, evident in decreased anxiety levels determined in the Elevated Zero Maze and increased alternations in the Elevated T Maze tests. Taken together these results suggests that Aag has functions in modulation of genome dynamics during brain development, important for animal behavior. HighlightsO_LIAag loss results in reduced DNA damage signal in developing hippocampus; C_LIO_LI5hmC signal intensity is perturbed in hippocampal regions of Aag-/- mice; C_LIO_LIGene expression is altered in Aag-/- hippocampus and prefrontal cortex; C_LIO_LIAag represses Aldh2 expression; C_LIO_LIAag-/- mice have reduced anxiety and improved memory. C_LI

molecular biology↗