DOI: 10.5061/dryad.v6wwpzh24
title: Phylogenomics and pervasive genome-wide phylogenetic discordance among fin whales (Balaenoptera physalus)

description: Phylogenomics has the power to uncover complex phylogenetic scenarios
 across the genome. In most cases, no single topology is reflected across
 the entire genome as the phylogenetic signal differs among genomic regions
 due to processes, such as introgression and incomplete lineage sorting.
 Baleen whales are among the largest vertebrates on Earth with a high
 dispersal potential in a relatively unrestricted habitat, the oceans. The
 fin whale (Balaenoptera physalus) is one of the most enigmatic baleen
 whale species, currently divided into four subspecies. It has been a
 matter of debate whether phylogeographic patterns explain taxonomic
 variation in fin whales. Here we present a chromosome-level whole genome
 analysis of the phylogenetic relationships among fin whales from multiple
 ocean basins. First, we estimated concatenated and consensus phylogenies
 for both the mitochondrial and nuclear genomes. The consensus phylogenies
 based upon the autosomal genome uncovered monophyletic clades associated
 with each ocean basin, aligning with the current understanding of
 subspecies division. Nevertheless, discordances were detected in the
 phylogenies based on the Y chromosome, mitochondrial, autosomal genome and
 X chromosome. Furthermore, we detected signs of introgression and
 pervasive phylogenetic discordance across the autosomal genome. This
 complex phylogenetic scenario could be explained by a puzzle of
 introgressive events, not yet documented in fin whales. Similarly,
 incomplete lineage sorting and a low phylogenetic signal could equally be
 the mechanisms leading to such phylogenetic discordances. Our study
 reinforces the pitfalls of relying on concatenated or single locus
 phylogenies to determine taxonomic relationships below the species level
 by illustrating the underlying nuances which some phylogenetic approaches
 may fail to capture. We emphasize the significance of accurate taxonomic
 delineation in fin whales by exploring crucial information revealed
 through genome-wide assessments.
description: # Phylogenomics and pervasive genome-wide phylogenetic discordance among
 fin whales (Balaenoptera physalus)
 [https://doi.org/10.5061/dryad.v6wwpzh24](https://doi.org/10.5061/dryad.v6wwpzh24) ## Description of the data and file structure # DATA OVERVIEW 1. **Alignments** File: final_phylogeny_auto_filt_snps.min4.phy.gz Description: Whole autosomal genome alignment containing a total of monomorphic and SNP sites. Format: Phylip File: chromX_alignment.phy.gz Description: Chromosome X genome alignment containing a total of monomorphic and SNP sites. Format: Phylip File: chromY_alignment.phy.gz Description: Chromosome Y alignment containing a total of monomorphic and SNP sites. Format: Phylip File: all_mitochondrial_200.fa Description: Whole mitochondrial genome alignment including published sequences Format: fasta File: only_new_mitochondria_alignment.fa Description: Whole mitochondrial genome alignment including only newly generated 38 sequences with whole genomes.\ Format: fasta 2. **Output trees** Concatenated Data Trees File: all_mitochondrial_200.nwk Description: Tree topology with support values for the best-fitting phylogenetic estimation based on the whole mitochondrial data (including new + published sequences). Format: Newick File: only_new_mitochondria.nwk Description: Tree topology with support values for the best-fitting phylogenetic estimation based on the whole mitochondrial data including only new sequences (from whole genomes). Format: Newick File: whole_autosomal.concat.support.nwk Description: Tree topology with support values for the best-likelihood phylogeny estimation for the whole autosomal genome data. Format: Newick File: chromX.concat.support.nwk Description: Tree topology with support values for the best-fitting phylogenetic estimation based on the X chromosome concatenated data. Format: Newick File: chromY.concat.support.nwk Description: Tree topology with support values for the best-fitting phylogenetic estimation based on the Y chromosome concatenated data. Format: Newick 3. **Consensus Data Trees (ASTRAL)** Consensus Trees for every windows-based analysis Files: 100k_Y_chromosome_astral_consensus.nwk 100k_X_chromosome_astral_consensus.nwk 100k_autosomal_astral_consensus.nwk 50kb_autosomal_astral_consensus.nwk 50k_X_chromosome_astral_consensus.nwk 50k_autosomal_astral_consensus.nwk 1mb_X_chromosome_astral_consensus.nwk 1mb_autosomal_astral_consensus.nwk Format: nwk 4. **Data Tables**: File: 1mbp_windows_autosomal results_final.txt Description: 1mbp genomic window results including the following information: ML trees with support values, window start and end position in the chromosome, D-statistics, Z-values, p-values, ABBA, BABA, BBAA for Dsuite analysis, monophyly test results (TRUE or FALSE) based on ocean basin origin, Adjusted_P_Value. Format: Tab-delimited File: 100kbp_windows_results_info.txt Description: 100kbp genomic window results including the following information: ML trees with support values, window start and end position in the chromosome, D-statistics, Z-values, p-values, ABBA, BABA, BBAA for Dsuite analysis, monophyly test results (TRUE or FALSE) based on ocean basin origin, Adjusted_P_Value. Format: Tab-delimited File: 50kbp_windows_results_info.txt Description: ML trees with support values, window start and end position in the chromosome, D-statistics, Z-values, p-values, ABBA, BABA, BBAA for Dsuite analysis,  Adjusted_P_Value. Format: Tab-delimited 5. **Abbreviations**: SOU: Southern Ocean NAT: North Atlantic NOP: North Pacific ANT: Antarctica NAT: North Atlantic ENP: Eastern North Pacific MNG: Megaptera novaeangliae ## ACCESS INFORMATION Published genomes used in this study are available on: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA74029](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA74029 [https://datadryad.org/stash/dataset/doi:10.5061/dryad.qt528n0](https://datadryad.org/stash/dataset/doi:10.5061/dryad.qt528n0 [https://www.ncbi.nlm.nih.gov/sra/SRX323050](https://www.ncbi.nlm.nih.gov/sra/SRX323050 ## SCRIPTS AND CODE Scripts are available on : [https://github.com/fabriciofurni/phylo_fin/tree/main}](https://github.com/fabriciofurni/phylo_fin/tree/main})