Rapid adaptive radiation of Darwin’s finches depends on ancestral genetic modules

Abstract

Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is the relative importance of new mutations, ancestral variants, and introgressive hybridization for phenotypic evolution and speciation. Here, we address this issue using Darwin’s finches and investigate the genomic architecture underlying their phenotypic diversity. Admixture mapping for beak and body size in the small, medium, and large ground finches revealed 28 loci showing strong genetic differentiation. These loci represent ancestral haplotype blocks with origins predating speciation events during the Darwin’s finch radiation. Genes expressed in the developing beak are overrepresented in these genomic regions. Ancestral haplotypes constitute genetic modules for selection and act as key determinants of the unusual phenotypic diversity of Darwin’s finches. Such ancestral haplotype blocks can be critical for how species adapt to environmental variability and change.

Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches

“…The medium ground finch (G. fortis) was intermediate in frequency for these ERV loci. This segregation reflects the observed patterns in ground finches described by Rubin et al 9 , which indicates that low-frequency ERV variants were part of the selected haplotype.…”

“…The potential role of selection in shaping ERV variation is currently under investigation. Allele frequencies at the 13 ERV loci described in Table 1 covary with body and beak sizes among the ground finches 9 . While a possible causal role of an ERV locus in beak and/or body size phenotypes remains to be explored, we conclude that at least part of the identified ERV variation described herein has been shaped by selection or more likely through hitchhiking on linked variants.…”

“…1 | Galápagos islands and sample locations. A total of 293 Darwin's finch samples representing 18 species, 4 hybrids and 2 outgroup species (Loxigilla noctis and Tiaris bicolor) from 16 islands 6,[9][10][11] were included in the study. Island names are indicated above finch species, hybrids and their respective sampling sizes.…”

“…Though we assume a neutral mode of evolution for the majority of identified ERVs, potential effects on host genome function cannot be established from the currently available data. However, we investigated ERV frequencies in 28 genomic regions showing strong genetic differentiation between small, medium, and large ground finches, previously identified by Rubin et al 9 We identified 379 ERV loci within these regions, 13 of which segregated at high frequencies in the large ground finch (G. magnirostris), and low frequencies in the small ground finch (G. fuliginosa), or vice versa (Table 1). The medium ground finch (G. fortis) was intermediate in frequency for these ERV loci.…”

“…This genomic record provides an opportunity to investigate the utility of ERVs as a record of past retroviral infections to infer infection histories, and use ERVs as unique, age-directed sequence variants to trace gene flow between host populations post-speciation. Here, we take advantage of a recently released high-quality genome assembly of a Darwin's finch 9 to investigate the ERV abundance of 293 wholegenome sequenced individuals from across the Darwin's finch radiation and outgroup species, and reveal contrasting historical patterns of retrovirus-host dynamics.…”