L. Chikhi

Questioning Neanderthal admixture: on models, robustness and consensus in human evolution

This paper challenges the consensus on Neanderthal admixture by showing that admixture methods can produce false positives under structured population models.

Life history traits influence the dynamics of genetic diversityin a refugium population undergoing expansion andcontraction

This study investigates how life history traits affect genetic diversity dynamics in refugium populations during range expansion and contraction.

African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

This study analyzes whole genomes of African bushpigs and Malagasy bushpigs, revealing recent divergence and gene flow, challenging species boundaries and linking their arrival in Madagascar to human migration.

The effect of habitat loss and fragmentation on isolation-by-distance and time

This study simulates the effects of habitat loss and fragmentation on isolation-by-distance, showing that genetic structure can persist long after habitat changes.

On the genetic consequences of habitat contraction: edge effects and habitat loss

The paper investigates how habitat loss and edge effects impact genetic diversity in fragmented habitats using simulations and a statistical framework.

The Genomic Diversity of the Eliurus genus in northern Madagascar with a Putative New Species

The paper identifies a new Eliurus species in northern Madagascar using genomic and morphological analyses and finds that Eliurus myoxinus is more common in humid forests than previously thought.

Inferring number of populations and changes in connectivity under the n-island model

The paper infers population structure and connectivity changes using the n-island model and IICR curves from PSMC data, finding ancient human population structure.

Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent

The paper investigates species boundaries in mouse lemurs using multispecies coalescent methods, finding that some previously recognized species are not distinct while an undescribed lineage is supported as a new species.

Selective packaging of mitochondrial proteins into extracellular vesicles prevents the release of mitochondrial DAMPs

The paper shows cells selectively package mitochondrial proteins into EVs while excluding damaged proteins, using distinct MDVs pathways and Parkin to prevent inflammation.

Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

The paper sequenced genomes of Iberian cattle breeds to study genomic diversity and differentiation, finding high diversity and significant admixture from African cattle.

The IICR and the Non-Stationary Structured Coalescent: demographic inference with arbitrary changes in population structure

The paper introduces the Non-Stationary Structured Coalescent framework to infer demographic history by accounting for changes in population structure and gene flow, applying it to human and Neanderthal genomic data.

Contribution of spatial heterogeneity in effective population sizes to the variance in pairwise measures of genetic differentiation

This paper introduces and tests metrics to quantify the impact of spatial heterogeneity in effective population sizes on genetic differentiation, finding SHNe explains significant variance in Fst values.