Biology subjects

Nicolas, V.

Publications and source records attributed to Nicolas, V..

4 recordsLinked to original sources

bioRxiv2026

Incipient speciation, rapid expansion and repeated introgressive hybridization in an African Giant Shrew (Crocidura olivieri)

The African giant shrew (Crocidura olivieri) is one of the most widespread native small mammals in sub-Saharan Africa, occupying habitats ranging from humid tropical forests to arid Savanna. Its broad distribution, ecological diversity, and unresolved evolutionary relationships suggest a history of rapid diversification, yet the roles of hybridization and demographic expansion remain poorly understood. We combined genome-wide ddRAD and mitochondrial data from populations sampled across sub-Saharan Africa to reconstruct the evolutionary history of African giant shrews. We reveal extensive mitonuclear discordance across the clade and show that it reflects a complex history of repeated introgressive hybridization rather than a single evolutionary event. Genomic analyses resolve three major evolutionary lineages and identify four introgression events, including extensive bidirectional genome-wide introgression between the ancestors of the C. olivieri and arid adapted species followed by later unidirectional introgression associated with range expansion. Within the C. olivieri group, we identify five geographically structured lineages connected by ongoing gene flow, representing different stages of incipient speciation. Demographic analyses further reveal repeated population expansion during the Late Pleistocene and Early Holocene, with lineage-specific timing consistent with climatic fluctuations and a possible contribution of increasing human association. Our results identify repeated range expansion and hybridization as major drivers of diversification in African giant shrews and establish this system as a powerful model for studying the genomic processes underlying early speciation.

evolutionary biology↗

bioRxiv2026

Evolutionary history of alpha satellite DNA in Cercopithecini: comparative cytogenomics highlights the diversification pattern of primate centromere repeats

BackgroundAlpha satellites, a superfamily of AT-rich tandem repeats, are the primary DNA component of centromeres in Platyrrhini and Catarrhini. Analyses of the human genome suggest that centromeres behave like biological ridges, with new alpha satellite families expanding at the centromere core, splitting and displacing older ones towards the pericentromeres. The Cercopithecini tribe, which displays an unusual chromosomal evolution involving multiple chromosomal fissions and centromere formations, represents a promising model to enhance our understanding of alpha satellite DNA evolutionary history. We previously applied targeted sequencing to centromere DNA from two distant species drawn from the Cercopithecini terrestrial and arboreal lineages, and characterized six alpha satellite families exhibiting varying mean sequence identities. MethodsCombining classical and molecular cytogenetics, we mapped the chromosomal distribution of these alpha satellite families across 13 Cercopithecini, one Papionini, and one Colobinae species. A nuclear marker-based phylogeny provided an evolutionary framework for interpretation. ResultsOur phylogeny identifies the terrestrial and arboreal lineages, and a newly designated swamp clade. We observed significant interspecies variations in alpha satellite patterns, including differences in presence/absence and distinct chromosomal distribution patterns (centromeric, pericentromeric, or subtelomeric). Families previously described as heterogeneous (83-87% mean sequence identity) exhibit a centromeric position in the swamp lineage, which is characterized by conserved karyotypes. In contrast, these families show a pericentromeric distribution in the terrestrial and arboreal lineages, replaced at the centromere core by more homogeneous families (95-98% mean sequence identity). In the arboreal clade, which is characterized by highly fissioned karyotypes, putative evolutionary new centromeres show a unique co-occurrence of highly homogeneous and heterogeneous families. Conclusion & ImplicationsWe propose a comprehensive evolutionary scenario for alpha satellite DNA in Cercopithecini, where younger families arise at the centromere core, shift toward the pericentromeres as they age, and eventually face extinction. Our study suggests that alpha satellite DNA and chromosomes evolve in an interdependent manner, with satellite diversification and displacement occurring in parallel with chromosome fissions and centromere repositioning. This comparative cytogenomic approach provides both support for the human-based evolutionary model for alpha satellite DNA and novel temporal insights into its diversification dynamics. Beyond evolutionary genomics, our findings highlight the potential of alpha satellite DNA to complement systematic studies in deciphering complex primate evolutionary histories.

evolutionary biology↗

bioRxiv2021

tdLanYFP, a yellow, bright, photostable and pH insensitive fluorescent protein for live cell imaging and FRET-based sensing strategies

Yellow fluorescent proteins (YFP) are widely used as optical reporters in Forster Resonance Energy Transfer (FRET) based biosensors. Although great improvements have been done, the sensitivity of the biosensors is still limited by the low photostability and the poor fluorescence performances of YFPs at acidic pHs. Here, we characterize the yellow fluorescent protein, tdLanYFP, derived from the tetrameric protein from the cephalochordate B. lanceolatum, LanYFP. With a quantum yield of 0.92 and an extinction coefficient of 133 000 mol-1.L.cm-1, it is, to our knowledge, the brightest dimeric fluorescent protein available. Contrasting with EYFP and its derivatives, tdLanYFP has a very high photostability in vitro and in live cells. As a consequence, tdLanYFP allows imaging of cellular structures with sub-diffraction resolution using STED nanoscopy and is compatible with the use of spectro-microscopies in single molecule regimes. Its very low pK1/2 of 3.9 makes tdLanYFP an excellent tag even at acidic pHs. Finally, we show that tdLanYFP is valuable FRET partner either as donor or acceptor in different biosensing modalities. Altogether, these assets make tdLanYFP a very attractive yellow fluorescent protein for long-term or single-molecule live cell imaging including FRET experiments at acidic pH.

biophysics↗

bioRxiv2017

Population networks from DNA sequences: methodological developments

Several classes of methods have been proposed for inferring the history of populations from genetic polymorphism data. As connectivity is a key factor to explain the structure of populations, several graph-based methods have been developed to this aim, using population genetics data. Here we propose an original method based on graphical models that uses DNA sequences to provide relationships between populations. We tested our method on various simulated data sets, describing typical demographic scenarios, for different parameters values. We found that our method behaved noticeably well for realistic demographic evolutionary processes and recovered suitably the migration processes. Our method provides thus a complementary tool for investigating population history based on genetic material.

bioinformatics↗