José Cerca

Phylogenomics and biogeography of the parrot genus Pyrrhura with implications for systematics and conservation

This study uses whole-genome and mitogenome data from Pyrrhura parrots to reconstruct phylogenies, revealing mito-nuclear discordance, captive lineages, and historical colonization events.

Chromosome-level genome assembly of Norwegian wild alpine reindeer (Rangifer tarandus tarandus)

The paper presents a chromosome-level genome assembly for wild alpine reindeer and improves the assembly for Svalbard reindeer, providing gene annotations and comparisons with prior assemblies.

Reference genome bias in light of species-specific chromosomal reorganization and translocations

The paper evaluates reference genome bias in population sequencing datasets of Arctic and polar cod using species-specific chromosome-anchored genomes, showing its impact on genetic statistics and chromosomal inversion detection.

Chromosomal inversions mediated by tandem insertions of transposable elements

The paper identifies and quantifies transposable elements in chromosomal inversion breakpoints in Atlantic cod, showing their role in driving ectopic recombination and chromosomal reorganization.

Geographical variation in mitogenomes of the largetooth sawfish Pristis pristis: challenges and perspectives for conservation efforts

This study examines geographical variation in the mitogenomes of largetooth sawfish and develops a new species-specific probe set to improve detection for conservation.

Genomic stability in the Galapagos Scalesia adaptive radiation: Consistent transposable element accumulation despite hybridization and ecological niche shifts

The paper examines TE accumulation in Scalesia species and finds no significant variation despite hybridization and niche shifts, challenging the role of TEs in diversification.