Guido Roberto Gallo

We investigated mitochondrial diversity and phylogeographic structure across all subspecies of the barn swallow (Hirundo rustica) to clarify evolutionary relationships, identify novel haplogroups, and assess the extent of hybridisation and maternal introgression. We analysed 580 complete H. rustica mitochondrial genomes together with twelve additional Hirundo species, three of which were newly obtained. We identified 553 unique haplotypes, including 166 previously undescribed ones, revealing high nucleotide diversity among subspecies. Phylogenetic analyses found five major haplogroups. Of these, a novel haplogroup (E) was discovered and ascribed to H.r. tytleri, previously considered part of H.r. erythrogaster. Comparative analyses with other Hirundo species support a southern African origin of H. rustica at the end of the Pliocene, followed by diversification and northward expansion. Our comprehensive dataset substantially refines the phylogeographic resolution of the species. We identify a novel haplogroup, clarify subspecies-level relationships, and reveal pervasive hybridisation and maternal introgression. These findings revise the evolutionary history of H. rustica and underscore the complexity of its population structure and gene flow. Beyond reconstructing lineage history, our study provides an evolutionary framework crucial for predicting environmental change responses and guiding migratory species conservation strategies.

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.

Nebria (Oreonebria) tresignore (Szallies & Huber, 2014) stat. nov. a ground beetle living in high-altitude habitats of a restricted area of the Italian Alps (i.e., Orobic Alps), previously considered a subspecies of N. (Oreonebria) soror K. Daniel, 1903, was phylogenetically analyzed based on the combination of nuclear (Tpl and WG) and mitochondrial (COIa, COIb and 16S) markers. Given the morphological (male genitalia), biogeographical and ecological differences with closely related species and the newly performed phylogenetic reconstruction, its elevation to species level is proposed. This cold-adapted species is at high risk of extinction due the ongoing climate warming and glaciers retreat on the Italian Alps.

Complete datasets of genetic variants are key to biodiversity genomic studies. Long-read sequencing technologies allow the routine assembly of highly contiguous, haplotype-resolved reference genomes. However, even when complete, reference genomes from a single individual may bias downstream analyses and fail to adequately represent genetic diversity within a population or species. Pangenome graphs assembled from aligned collections of high-quality genomes can overcome representation bias by integrating sequence information from multiple genomes from the same population, species or genus into a single reference. Here, we review the available tools and data structures to build, visualize and manipulate pangenome graphs while providing practical examples and discussing their applications in biodiversity and conservation genomics across the tree of life.

[highlight=transparent]This introductory workshop shows how to effectively use genomic approaches in ecological and evolutionary studies, offering participants both theoretical foundations and practical skills in DNA sequencing and bioinformatics. Led by experts Prof. Giulio Formenti and Dr. Guido Gallo, attendees will gain hands-on experience using command line tools to analyze sequencing data and apply bioinformatics tools to address key research questions in ecology and evolution.[/highlight]

A new species of Campanula (Campanulaceae), C. bergomensis sp. nov., is described from the Bergamo Prealps (Orobic Prealps, Lombardy, Northern Italy), based on both morphological and molecular evidence. The new species was considered in the past as an isolated population of C. cespitosa, which presents an eastern Alpine distribution. C. bergomensis is morphologically well distinguishable from C. cespitosa on the number of flowers in the racemose inflorescence, the corolla shape, and the whitish-yellow pollen surface with many spinulae. Genetically, the presence of an insertion of 81-bp in the trnL-F sequences is very characteristic. Further studies are needed to better define the phylogenetic relationship among the three closely related species, C. bergomensis, C. cespitosa and C. cochleariifolia. C. bergomensis inhabits dolomitic debris cones at low elevations. The species is range-restricted and is severely threatened by human activities. Therefore, it is urgent to adopt protection and conservation measures for the new species.

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).

In the smallholder, low-input farming systems widespread in sub-Saharan Africa, farmers select and propagate crop varieties based on their traditional knowledge and experience. A data-driven integration of their knowledge into breeding pipelines may support the sustainable intensification of local farming. Here, we combine genomics with participatory research to tap into traditional knowledge in smallholder farming systems, using durum wheat (Triticum durumDesf.) in Ethiopia as a case study. We developed and genotyped a large multiparental population, called the Ethiopian NAM (EtNAM), that recombines an elite international breeding line with Ethiopian traditional varieties maintained by local farmers. A total of 1,200 EtNAM lines were evaluated for agronomic performance and farmers’ appreciation in three locations in Ethiopia, finding that women and men farmers could skillfully identify the worth of wheat genotypes and their potential for local adaptation. We then trained a genomic selection (GS) model using farmer appreciation scores and found that its prediction accuracy over grain yield (GY) was higher than that of a benchmark GS model trained on GY. Finally, we used forward genetics approaches to identify marker–trait associations for agronomic traits and farmer appreciation scores. We produced genetic maps for individual EtNAM families and used them to support the characterization of genomic loci of breeding relevance with pleiotropic effects on phenology, yield, and farmer preference. Our data show that farmers’ traditional knowledge can be integrated in genomics-driven breeding to support the selection of best allelic combinations for local adaptation.