Coevolution with hosts underpins speciation in brood parasitic cuckoos

Coevolution is considered to be a likely driver of speciation, but evidence linking macroevolutionary patterns to microevolutionary processes is scarce. We report that coevolution with hosts drives divergence in bronze-cuckoos. Bronze-cuckoo hosts reject cuckoo nestlings, selecting for mimicry of host nestlings by cuckoos. This has generated a diversity of bronze-cuckoo nestling morphologies matching those of their respective hosts across their geographic range and promotes diversification in sympatry; little bronze-cuckoos that exploit multiple host species in sympatry show evidence of genetic differentiation and corresponding divergence in nestling morphology. This process is reflected in macroevolutionary patterns: rates of speciation are faster in virulent cuckoos than in more benign species and simulation models indicate greater support for a sympatric mode of speciation in bronze-cuckoos than in sister taxa., DNA was extracted from the liver tissue of adult Little Bronze Cuckoos, as well as the feathers and embryos of chicks and museum eggshells. Shotgun libraries were prepared from the DNA following Caroe et al. (2018) and Gansauge et al. (2017). Libraries were enriched for RAD loci following Suchan et al. (2016), after in-house RNA probe generation using double restriction enzyme digestion of high-quality DNA (also following Suchan et al. 2016). After high-throughput NGS sequencing, mitochondrial genomes were reconstructed, aligned, and partitioned (protein coding genes into 1st, 2nd, and 3rd codon positions; RNA coding genes into stems and loops, and; control region by domains). The best substitution model for phylogenetic analysis was determined using Model Test within IQTree, and a maximum likelihood phylogeny was inferred using IQTree. Bayesian phylogenetic inference was performed using MrBayes. , , # Coevolution with hosts underpins speciation in brood parasitic cuckoos

### (1) Coevolution\_Dryad\_JUN23

#### 11\_Alignments

```
│   ├── 55_taxa_with_less_than_10%_missing_data: alignments from the 55 taxa with less than 10% missing data.
│   │   ├── With_control_region: alignments that include the control region as a partition
│   │   │   ├── 30_taxa_with_host_data: alignments that only include the 30 taxa with host data
│   │   │   │   ├── *.phy: mitochondrial genomes from the 30 taxa with less than 10% missing data AND host data aligned, partitioned (including the control region) and concatenated. Alignment in phylip format.
│   │   │   │   └── part.nex: the partition file describing where in the alignment each partition begins and ends and the best models for phylogenetic inference determined by IQtree.
│   │   │   └── All_55_taxa: alignemnts from the 55 taxa with less than 10% missing data which include the control region
│   │   │   ├── 55_CR1.phy: alignment of control re...