bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2020.11.30.404061

Chromosome-level genome assembly of the common chaffinch (Aves: Fringilla coelebs): a valuable resource for evolutionary biology

Recuerda Carrasco, M.·Vizueta, J.·Cuevas-Caballe, C.·Blanco Hervas, G.·Rozas, J.·Mila, B.
View original source ↗Export metadata ↓

Abstract

The common chaffinch, Fringilla coelebs, is one of the most common, widespread and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87 Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian dataset. Around 7.8 % of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian and vertebrate evolution.

Source connections

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Recuerda Carrasco, M., Vizueta, J., Cuevas-Caballe, C., Blanco Hervas, G., Rozas, J., Mila, B.. 2020-12-01. Chromosome-level genome assembly of the common chaffinch (Aves: Fringilla coelebs): a valuable resource for evolutionary biology. https://doi.org/10.1101/2020.11.30.404061

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Global homeostatic forces shape the composition of a hyperdiverse tropical insect fauna

Despite comprising the bulk of terrestrial biodiversity, we know surprisingly little about insect faunas, particularly in the tropics. Here, we characterize the insect fauna of Madagascar, a global biodiversity hotspot, based on extensive DNA metabarcoding of Malaise trap and leaf litter samples. We estimate that the fauna comprises at least 250,000 species, only 5% of which are currently recorded. The ecological and taxonomic composition is surprisingly similar to that of temperate forests. We show that this is likely caused by global homeostatic forces shaping net diversification rates after colonization of Madagascar rather than by the composition of colonizing lineages. Features differing from temperate forests include the dearth of parasitoids and richness of beetles. Understanding the forces shaping these patterns is key in sustainable management of tropical insect faunas.

evolutionary biology↗
bioRxiv2026

Do divergent mitochondrial backgrounds alter the fate of nuclear alleles during hybridization and admixture?

Hybridization brings together genetic variation from different populations or species into admixed genomes. As selection sorts this variation, the fate of each allele is determined by its fitness effect in the new hybrid genomic background. Because mitochondrial genes coevolve with the nuclear genome, they may be especially sensitive to foreign nuclear backgrounds, making them potential "hot-spots" for hybrid incompatibilities. Here, we test whether selection against mitonuclear incompatibilities drives repeatable hybridization outcomes. Specifically, we experimentally evolved three sets of five populations of hybrid Drosophila melanogaster, each carrying the same nuclear chromosomes but paired with one of three increasingly divergent mitochondrial DNA backgrounds. We hypothesized that accumulated incompatibilities would result in different patterns of nuclear admixture among mitochondrial backgrounds. To test this, we tracked nuclear allele frequencies in all 15 populations by whole-genome sequencing at intermediate time points. After 25 generations, we observed that rapid genomic evolution produced a strikingly parallel mosaic of both nuclear ancestries, independent of mitochondrial background. Contrary to our hypothesis, we found no evidence that mitochondrial background1 shaped nuclear admixture, even for interspecific combinations. These results suggest that in species with large effective population sizes, efficient purifying selection limits the accumulation of mitonuclear incompatibilities, allowing selection on nuclear alleles to promote repeatable ancestry sorting immediately following hybridization.

evolutionary biology↗
bioRxiv2026

Body size cascades from Neodiprion sawfly hosts to Perilampid parasitoids: An investigation of sequential divergence

Ecological speciation drives diversity in plant-eating insect systems, but it may also generate parallel specialization in parasitoid associates in a cascading effect of "sequential divergence." However, sequential divergence has never been successfully identified in parasitoids of externally feeding insects. To address this gap, we consider the Pinus-Neodiprion-Perilampus neodiprioni system, where plant-associated, externally feeding Neodiprion demonstrate ecological divergence, as supported by body size as a magic trait in sympatric species. It seems possible that this body size differentiation may cascade to Neodiprion's parasitoids via sequential divergence. Therefore, we asked, "Does P. neodiprioni exhibit host-specific divergence in body size that parallels patterns in Neodiprion hosts?" Further, "Does P. neodiprioni exhibit host-related variation in the abdominal region or sexually dimorphic features, supporting reproductive barriers?" Using by-catch samples, we measured body size of P. neodiprioni, reared from Neodiprion lecontei and Neodiprion pinetum hosts. We analyzed body size variation as predicted by host species, parasitoid sex, host sex, host cocoon size, latitude, and their interactions. In addition, we used mixed models to analyze the effects of parasitoid sex and Neodiprion host on three size-based facial features. We found that P. neodiprioni demonstrates host-associated body size variation that mirrors size differences in their Neodiprion hosts. In addition, host-associated size variation occurs in the abdominal region and two sexually dimorphic characters of P. neodiprioni, supporting possible reproductive isolation. Together, these patterns suggest that host magic traits may drive not only within-species ecological divergence, but they can facilitate parasitoids' subsequent morphological differentiation and possible sequential divergence.

evolutionary biology↗