DOI: 10.5061/dryad.qfttdz0s2
title: Phylogenomic resolution of lampreys reveals the recent evolution of an ancient vertebrate lineage

description: Jawless vertebrates once dominated Paleozoic waters, but just two lineages
 persisted to the present day: lampreys and hagfishes. Living lampreys are
 a relatively small clade, with just over fifty species described, but
 knowledge of their evolutionary relationships has always been based on
 either a few mitochondrial genes or a small number of taxa. Biogeographers
 have noted the disjunct antitropical distribution of living lamprey
 families. Here we present a comprehensive phylogenomic analysis of living
 and fossil lampreys, sampling 36 species with phylogenomic data and 46 in
 total with genetic data. We present new divergence time estimates based on
 comprehensive nuclear data and analysis of their diversification dynamics.
 Our analysis indicates a central role for extreme global warming during
 the Late Cretaceous Cenomanian-Turonian Boundary Event as a likely cause
 for the antitropical distribution of living lampreys, and a notable
 increase in lineage diversification in northern hemisphere lampreys during
 the Miocene corresponding with a period of global cooling.
description: # Phylogenomic resolution of lampreys reveals the recent evolution of an
 ancient vertebrate lineage Results of ASTRAL multispecies coalescent
 analysis in Newick format **ASTRAL.zip** * astral.nc.tre: input gene trees
 were fully resolved * astral.c30.tre: nodes with &lt; 30% bootstrap
 support were collapsed into polytomies in gene trees ## BEAST .xml files,
 consensus trees, and morphological matrix **BEAST.zip** * 148genes.xml:
 BEAST XML file containing genes and morphological data. * morphology.nex:
 annotated nexus alignment of morphological characters combined from two
 studies * cytb_combined.xml: BEAST XML file with sequences added for
 cytochrome *b* * cytb_combined.con.tre.nex: consensus of 10,000 posterior
 trees from two combined runs (shown in main Fig. 2) ## Concatenated
 sequence alignments in FASTA format and results of Maximum Likelihood
 analyses **Concatenation.zip** * Lampreys.NT.fasta: concatenated matrix of
 355 exons (nucleotides) * Lampreys.NT.tre: resulting ML tree in Newick
 format * Lampreys.NT.part.best_scheme.nex: favored partitioning scheme and
 models for NT alignment * Lampreys.AA.fasta: concatenated matrix of 355
 exons (amino acids) * Lampreys.AA.tre: resulting ML tree in Newick format
 * GHOST.NT.fasta: reduced concatenated matrix with 40 taxa for analysis
 under the GHOST model * GHOST.NT.tre.nex: resulting ML tree in nexus tree
 format ## Concordance factor analysis results from IQ-Tree
 **ConcordanceFactor.zip** * GCF: results from gene tree concordance factor
 analysis * SCF: results from site concordance factor analysis (based on
 updated likelihood model) ## Gene trees, alignments, and best models for
 355 genes **Gene Trees.zip** * Alignments ending .fasta * Models ending in
 .best_model.nex * Gene trees ending in .treefile ## Probe set for
 conserved lamprey exons **Probes.zip** * lamprey_exon_probes.fasta:
 Sequences for target-capture probes (baits) designed in this study ##
 Change log 20 Nov 2024 - Added code under related works