T. Marques-Bonet

Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

The paper evaluates the reliability of phylogenetic inference using primate enamel proteins by simulating sequence fragmentation and comparing results to a reference species tree.

Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates

This study identifies SLC22A10 as a nonfunctional pseudogene in humans due to a missense mutation, while great ape orthologs retain functional uptake of estradiol-17β-glucuronide.

Whole genomes of the amazonian Cacajao reveal complex connectivity and fast differentiation driven by high environmental dynamism

The paper presents whole genome data from 48 uakari monkeys, revealing genetic differentiation between bald and black uakaris due to environmental factors.

Enamel proteins reveal biological sex and genetic variability within southern African Paranthropus

This study uses enamel proteomics to determine biological sex and assess intraspecific variation in Paranthropus robustus from South Africa, supporting the idea that morphological variation may reflect taxonomic diversity.

Large-scale phylogenomics uncovers a complex evolutionary history and extensive ancestral gene flow in an African primate radiation

This study uses whole-genome sequencing of 22 guenon species to show widespread ancient hybridization and gene flow across deeply divergent lineages, with immune-related genes overrepresented in introgressed regions.

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Genomic data from 225 baboons reveal novel inter-species gene flow sites and local admixture effects across different lineages.

Ghost admixture in eastern gorillas

The paper identifies archaic admixture in eastern gorillas using whole genome sequences and ABC with neural networks, finding introgression from a ghost lineage into their common ancestor.

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

The paper uses long-read sequencing to identify novel transcripts and isoform changes in primate transcriptomes, highlighting immune-related regulatory divergence.

The molecular evolution of spermatogenesis across mammals

This study analyzes single-nucleus transcriptomes from testes across eleven mammalian species to uncover molecular evolution patterns in spermatogenesis.

Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species

The paper sequenced genomes of extinct and historical Xerces Blue butterflies and their relatives to study population decline and identify genetic markers for threatened species.

HuConTest: Testing human contamination in great ape samples

HuConTest detects human contamination in short read sequencing data from great apes using blood and tissue samples, showing its utility in complex samples with low endogenous DNA.

Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)

The paper analyzes genomic changes in white rhinoceros subspecies before and after population declines, finding reduced genetic diversity and increased inbreeding in both.

Epigenomic profiling of primate LCLs reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures

The paper profiles epigenomic features in primate LCLs to reveal evolutionary patterns of epigenetic activity in gene regulation.

Mutation distribution density in tumors reconstructs human’s lost diversity

The paper compares mutation density patterns between human and non-human Great Ape germlines and tumors, finding that non-human germlines better correlate with tumors than human germlines.

Evidence that viruses, particularly SIV, drove genetic adaptation in natural populations of eastern chimpanzees

The paper identifies genetic adaptations in eastern chimpanzees linked to SIV infection, showing distinct immune-related gene differentiation compared to central chimpanzees.