Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity
Data files
May 24, 2024 version files 25.36 MB
Abstract
Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred. Our results, presented as ancestral-state reconstructions, show that multicellularity arose independently twice in this clade. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae.
README: Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity
This README is for:
"Fossil-calibrated molecular clock enables reconstruction of steps leading to differentiated multicellularity in the Volvocine algae" by CR Lindsey, AH Knoll, MD Herron, and F Rosenzweig.
DOI = https://doi.org/10.1186/s12915-024-01878-1
The contents of this file include the following:
- phytools_r_scripts.zip: R scripts used to run simmap analyses in Phytools Specifically, these are the R scripts used to generate simmap analyses for Kirk's 12 developmental traits, certain sexual traits, and misc. traits in the Volvocine algae.
- MBASR_run_script_template: MBASR template script used to run all the ancestral state reconstructions in MBASR
- gene_alns_263.zip): All 263 alignment files used in our maximum likelihood and Mr. Bayes phylogenetic analyses .
phylobayes_<8/16>gene_
input_files.zip: 8-gene and 16-gene alignment files used in our Phylobayes molecular clock analyses. Fossil calibration include the specific node calibrations for our molecular clock analyses.Each zip file contains the following:
archaeplastida_fossil_calibrations_mins_and_ranges
.txt : fossil calibration files
ds<1/5>gshop_trimalv7v3_042723<8/16>genes_: a gene alignment file
nwk_trimalv7v3_042723.tre : newick tree formatted file
outgroup.txt: outgroup taxa fileIQtree_files.zip: Concatenated 263-gene alignment files used in our IQtree and Mr. Bayes phylogenetic analyses. Contains the concatenated gene alignment IQtree_aln_file.fa and character partition files IQtree_charpartition.nex. MrBayes input is mrbayes_file_263genes.nex
astral_263genetrees_file.tre: ASTRAL 263-gene tree file . This is file has all of our single-gene phylogenies concatenated into one file. All single-gene trees (263 total) have been individually uploaded in the following ZIP file: single_gene_trees_trimalv7v3_042723.zip.
Usage Notes
A) .tre files may be viewed but not limited to the following software: Figtree or TreeGraph2.
B) alns = alignments
C) FASTA (.fa) and NEXUS (.nex) files may be viewed using any text editor such as Sublime Text.
D) MBASR template script is a text file used with the program MBASR (https://www.biorxiv.org/content/10.1101/2021.01.10.426107v1.full.pdf)
E) "CB" and "ML" acronyms are used in filenames to specify which phylogenetic analysis the tree branching order belongs. "CB" and "ML" correspond to coalescent-based and maximum-likelihood, respectively.
Additional files uploaded to Zenodo:
7. phylobayes_fossil_calibrations_and_chronograms.zip: Phylobayes outputs of the following items for each clock model from 16-gene analyses: chronograms, dates, and labels
8. command_line_arguments.pdf: Command line PDF with software repo links.