From Newsgroup: sci.bio.paleontology

This isn't really paleontology, since fossils are nowhere to be found,
but the basic question addressed is whether sponges or ctenphores are
the sister group to all other metazoa. This controversy has been
ongoing for many years, and traditional phylogentic (of the respective genomes) hasn't resolved the question to general satisfaction. This is,
after all, the longest branch in the animal kingdom, and all the
difficulties is resolution that implies. This paper, that I missed this
last year

https://www.nature.com/articles/s41586-023-05936-6

addresses the problem using the concept of synteny.

Wiki: In current biology, synteny more commonly refers to colinearity,
i.e. conservation of blocks of order within two sets of chromosomes that
are being compared with each other. These blocks are referred to as
syntenic blocks.

Abstract

A central question in evolutionary biology is whether sponges or
ctenophores (comb jellies) are the sister group to all other animals.
These alternative phylogenetic hypotheses imply different scenarios for
the evolution of complex neural systems and other animal-specific traits1,2,3,4,5,6. Conventional phylogenetic approaches based on
morphological characters and increasingly extensive gene sequence
collections have not been able to definitively answer this question7,8,9,10,11. Here we develop chromosome-scale gene linkage, also
known as synteny, as a phylogenetic character for resolving this
question12. We report new chromosome-scale genomes for a ctenophore and
two marine sponges, and for three unicellular relatives of animals (a choanoflagellate, a filasterean amoeba and an ichthyosporean) that serve
as outgroups for phylogenetic analysis. We find ancient syntenies that
are conserved between animals and their close unicellular relatives. Ctenophores and unicellular eukaryotes share ancestral metazoan
patterns, whereas sponges, bilaterians, and cnidarians share derived chromosomal rearrangements. Conserved syntenic characters unite sponges
with bilaterians, cnidarians, and placozoans in a monophyletic clade to
the exclusion of ctenophores, placing ctenophores as the sister group to
all other animals. The patterns of synteny shared by sponges,
bilaterians, and cnidarians are the result of rare and irreversible
chromosome fusion-and-mixing events that provide robust and unambiguous phylogenetic support for the ctenophore-sister hypothesis. These
findings provide a new framework for resolving deep, recalcitrant
phylogenetic problems and have implications for our understanding of
animal evolution.

The paper concludes with the cautionary note:

"Sponge-sister and ctenophore-sister hypotheses are sometimes
erroneously interpreted as suggesting that the most recent common
ancestor of animals was sponge-like or ctenophore-like. We must be
mindful, however, that the living representatives of sponges,
ctenophores, bilaterians and placozoans may be poor surrogates for the earliest members of each stem-lineage, as the crown group of each clade
arose hundreds of millions of years after their divergence from each
other, let alone from the common metazoan ancestor"
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