High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test). We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence. Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.
Matrices and control files
Here we provide all the necessary files to run the analyses described in the paper. Files are organized by folders.
dating_analysis -> control files necessary to run the dating analysis.
ddrad_data -> Intermediate files from pyrad's steps 3 and 5, and matrices derived from the ddRAD method used for the phylogenetic and introgression analyses.
genome_skimming_matrices -> matrices derived from genome skimming method used in the phylogenetic analyses.
JML_analysis -> all the files used to run and visualize the JML analysis.
matrices_and_control_files.zip
read_subsets_1
Files with the subsets of reads used in the study
Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).
cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
read_subsets_2
Files with the subsets of reads used in the study
Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).
cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
read_subsets_3
Files with the subsets of reads used in the study
Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).
cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
read_subsets_4
Files with the subsets of reads used in the study
Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).
cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
read_subsets_5
Files with the subsets of reads used in the study
Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).
cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
read_subsets_6
Files with the subsets of reads used in the study
Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).
cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
