DOI: 10.5061/dryad.x95x69ppf
title: Coevolution with hosts underpins speciation in brood parasitic cuckoos

description: 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.
description: 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. 
description: # 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 region
 partition 1 │   │   │   ├── 55_CR2.phy: alignment of control region
 partition 2 │   │   │   ├── JUL21_concatenated_55tax_w_CR_minus_10%.phy:
 alignments from the 55 taxa with less than 10% missing data which include
 the control region, partitioned and concatenated │   │   │   └── 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. │   │   └── Without_control_region: alignments that do not include
 the control region as a partition │   │   ├──
 JUL21_concatenated_72tax_minus10%.fasta: mitochondrial genomes from the 55
 taxa with less than 10% missing data aligned, partitioned (see below) and
 concatenated. Alignment in fasta format. │   │   ├──
 JUL21_concatenated_72tax_minus10%phy: mitochondrial genomes from the 55
 taxa with less than 10% missing data aligned, partitioned (see below) and
 concatenated. Alignment in phylip format. │   │   └── Partitioned │   │  
 ├── *.phy: mitochondrial genomes from the 55 taxa with less than 10%
 missing data aligned, and protein-coding regions partitioned into codon
 positions (m1, m2, m3), and RNA-coding regions partitioned into stems and
 loops. Alignments in phylip format. │   │   └── *.nex: mitochondrial
 genomes from the 55 taxa with less than 10% missing data aligned, and
 protein-coding regions partitioned into codon positions (m1, m2, m3), and
 RNA-coding regions partitioned into stems and loops. Alignments in nexus
 format. │   └── All_72_taxa │   ├── JUL21_concatenated_72tax.phy: all
 mitochondrial genomes aligned, partitioned, and the partitions
 concatenated together │   └── Partitioned │   └── *.phy: all mitochondrial
 genomes aligned, and protein-coding regions partitioned into codon
 positions (m1, m2, m3), and RNA-coding regions partitioned into stems and
 loops ``` --- #### 12\_Phylogenetic\_Inference: Outputs of phylogenetic
 inference ``` │   ├── Bayesian_MrBayes: Outputs of Bayesian phylogenetic
 inference │   │   └── 55_taxa_with_less_than_10%_missing_data: Bayesian
 phylogenetic inference using the alignment of 55 taxa with less than 10%
 missing data. │   │   ├── With_control_region | | | ├──
 Chami_55tax_75mt_wCR_minus10_Feb23: the output of the Bayesian analysis on
 the 55 taxa with and without host data and less than 10% missing data
 (with control region). The consensus tree is ChamiMT.con.tre. The input
 nexus alignment is infile.nex, and parameters set are under paramfile.txt.
 stdout.txt is the analysis log file. Other files are generated as part of
 the output. │   │   │   ├── Chami_30tax_75mt_wCR_minus10_Dec22: the output
 of the Bayesian analysis on the 30 taxa with host data and less than 10%
 missing data (with control region). The consensus tree is ChamiMT.con.tre.
 The input nexus alignment is infile.nex, and parameters set are under
 paramfile.txt. stdout.txt is the analysis log file. Other files are
 generated as part of the output. │   │   │   │   ├──
 Chami_30tax_75mt_wCR_minus10_Dec22.nex: the input nexus alignment for the
 Bayesian analysis above │   │   └── Without_control_region │   │   └──
 Chami_55tax_75mt_minus10_Jul21: the output of the Bayesian analysis on the
 55 taxa with less than 10% missing data (without control region). The
 consensus tree is ChamiMT.con.tre. The input nexus alignment is
 infile.nex, and parameters set are under paramfile.txt. stdout.txt is the
 analysis log file. Other files are generated as part of the output. │  
 └── Maximum_Likelihood_IQTree: Outputs of maximum likelihood phylogenetic
 inference │   └── 55_taxa_with_less_than_10%_missing_data: Bayesian
 phylogenetic inference using the alignment of 55 taxa with less than 10%
 missing data. │   ├── With_control_region │   │   ├──
 30_taxa_with_host_data: the output of the ML analysis on the 30 taxa with
 host data and less than 10% missing data (with control region). The
 consensus tree is *contree. The input nexus alignment is *.phy, and the
 partition file containing the best models is part.nex. *.iqtree is the
 analysis log file. Other files are generated as part of the output. │  
 │   └── All_55_taxa: the output of the ML analysis on the 55 taxa with
 less than 10% missing data (with control region). The consensus tree is
 *contree. The input nexus alignment is *.phy, and the partition file
 containing the best models is part.nex. *.iqtree is the analysis log file.
 Other files are generated as part of the output. │   └──
 Without_control_region: the output of the Bayesian analysis on the 55 taxa
 with less than 10% missing data (without control region). The consensus
 tree is *contree. *.iqtree is the analysis log file. Other files are
 generated as part of the output. ``` --- #### 13\_Map\_Damage
 results_*_mapped: MapDamage 2.0 outputs for each sample; of specific
 interest is the Fragmisincorporation_plot.pdf, the remaining files are
 other outputs of MapDamage 2.0. Naming convention of sub-folders:
 "DS*" refers to the double-stranded library ID for the sample;
 "SS*" refers to the single-stranded library ID for the sample;
 "RAD_MD*" refers to the RAD library for the extract ID; the
 suffix "_T_QF_R1_R2" indicates that MapDamage was run on data
 that had been trimmed and quality filtered with both read 1 (R1) and read
 2 (R2) reads mapped to a reference. --- ####
 14\_Eggshell\_specimens\_digitised * 28_08_2019 *
 20190828_*_ANWC_E*_gre511*.jpg: photographs of eggshell specimens
 (Accession ANWC_E*) from the apex (pointy end), blunt end, and sides
 (rotating 90 degrees). Note that there may be more than one specimen under
 the same accession because multiple eggs within a clutch have the same
 accession; therefore they are distinguished by subjective descriptors such
 as "long, left" or "small, right" to indicate their
 general shape (long/small) relative to others in the clutch, or their
 position in the specimen box (leftmost, centre most, or rightmost). ---
 #### **Diversification rates dataset** (added Apr 2024) Name:
 Copy_of_dataset_diversification_cuckoos.xlsx These are the the raw values
 of the diversification rates for the three different measures (Clads, DR,
 and ND, for the MCC, and for the average across multiple trees). The first
 sheet contains the raw values and the second sheet is the metadata
 explaining each column.