Biology subjects

Gallo, G. R.

Publications and source records attributed to Gallo, G. R..

3 recordsLinked to original sources

bioRxiv2025

The end of the American dream: a hard to Swallow reality - How the Barn Swallow (Hirundo rustica) returned from America, a complete mtDNA phylogeny

The barn swallow (Hirundo rustica, H.r.) is one of the most iconic and fascinating migratory birds since ancient times, their philopatry and pair bonding have been the symbol of travellers and lovers throughout history. The barn swallow subspecies complex has been the main focus of many latest papers, focusing mainly on the Eurasian and Levant subspecies (H.r. rustica and H.r. transitiva). The remaining subspecies have either not been studied or few complete mitogenome sequences have been obtained. We present a comprehensive phylogeographic analysis of 580 complete mitochondrial genomes of barn swallows representing all recognized subspecies. We identified 553 unique haplotypes, 166 of which are novel, with high haplotype diversity and notable nucleotide diversity among subspecies. Phylogenetic analysis by maximum parsimony supports a single maternal ancestor and reveals five main haplogroups, confirming and refining prior classifications. A novel, distinct haplogroup (E) was identified for H.r. tytleri, previously classified as a sub-branch of H.r. erythrogaster. The inclusion of 66 hybrid individuals confirmed extensive maternal introgression and revealed multiple cases of mitogenome-subspecies mismatches, notably in savignii, transitiva, and tytleri populations. We further integrated 13 mitogenomes from 12 other Hirundo species, three of which are newly sequenced, to contextualize H. rustica evolution within the genus. Our findings support a southern African origin with subsequent diversification and a northward expansion. This study significantly enhances resolution of barn swallow mitogenomic diversity, revises phylogenetic relationships, identifies new haplogroups, hints at inter-subspecies gene flow and refines coalescent-based divergence times, offering key insights into the evolutionary history and hybridisation patterns of this iconic migratory species.

evolutionary biology↗

bioRxiv2023

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last [~]500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).

bioinformatics↗

bioRxiv2022

Pangenomics provides insights into the role of synanthropy in barn swallow evolution

Insights into the evolution of non-model organisms are often limited by the lack of reference genomes. As part of the Vertebrate Genomes Project, we present a new reference genome and a pangenome produced with High-Fidelity long reads for the barn swallow Hirundo rustica. We then generated a reference-free multialignment with other bird genomes to identify genes under selection. Conservation analyses pointed at genes enriched for transcriptional regulation and neurodevelopment. The most conserved gene is CAMK2N2, with a potential role in fear memory formation. In addition, using all publicly available data, we generated a comprehensive catalogue of genetic markers. Genome-wide linkage disequilibrium scans identified potential selection signatures at multiple loci. The top candidate region comprises several genes and includes BDNF, a gene involved in stress response, fear memory formation, and tameness. We propose that the strict association with humans in this species is linked with the evolution of pathways typically under selection in domesticated taxa.

genomics↗