Coevolution with hosts underpins speciation in brood parasitic cuckoos
Data files
Nov 27, 2023 version files 14.76 GB
Apr 22, 2024 version files 14.76 GB
Abstract
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.
(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.
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.