This publication [pdf file attached] was requested by several GEITP-ers to be featured. This topic might seem a bit distant from “gene-environment interactions.” However, from the earliest Life on Earth, organisms have been evolving — due to their genomes interacting with their environment at that their specific evolutionary time. For example, evolutionarily ancient animals (e.g., jellyfish, corals) have only one opening to their digestive tract (protostomes), whereas later in evolution an entrance and an exit in the digestive tract appeared (deuterostomes). Evolution of plants went from simple algae to bryophytes (mosses) to pteridophytes (ferns) to angiosperms (flowering plants) — with obvious advantages to complex plants that arose later in evolution. From sea animals there arose land animals — due to the environmental pressure of increasingly abundant plants on land that were impossible for fish in the sea to reach.
Thus, from the earliest of Life, organisms began to diverge into distinctly different groups, which we human scientists have now divided and subdivided into increasingly smaller and distinct subgroups of subgroups, etc. In the U.S. from the 2nd grade, surely we all remember well the mnemonic, “King Philip Came Over For Good Soup”, right? (K-P-C-O-F-G-S). This helped us memorize the hierarchy of biological classification that we all know by heart to this day: Kingdom, Phylum, Class, Order, Family, Genus, species; each word in the mnemonic corresponds to a specific taxonomic rank, helping us to memorize this gradient as little kids… From a classification of three kingdoms when I was a little kid — today all living organisms are classified into one of six kingdoms: Archaebacteria, Eubacteria, Protista, Fungi, Plantae, and Animalia.
Within the kingdom Animalia, there are now 35 phyla in total — although only nine of them are the most well-known and understood (the other 26 being relatively obscure). These nine include: Porifera (sponges), Cnidaria (including jellyfish, sea anemones, corals, and some of the smallest marine parasites), Platyhelminthes (flatworms: soft-bodied, unsegmented, with bilateral symmetry), Nematoda (unsegmented roundworms), Annelida (segmented worms, earthworms, leeches), Arthropoda (insects, spiders, crustaceans), Mollusca (the largest marine phylum), Echinodermata (starfish, brittle stars, sea urchins, sand dollars and sea cucumbers — having a water vascular system and five-sided radial symmetry), and Chordata (almost always having a backbone; tunicates and lancelets are chordates having a notochord but lacking a backbone).
The Mollusca Phylum in the topic of this email blog [see attached article]. Mollusks are characterized by soft bodies, often protected by a hard, calcareous shell. All mollusks are protostomes — meaning they are a group of animals in which (embryologically) the mouth develops from the first embryonic opening (blastopore) and their body cavity (coelomic cavity) forms from a split in the mesoderm (mollusks, like arthropods and annelid worms, are classified as “protostomes,” based on their embryonic development). Moreover, mollusks are bilaterally symmetrical and triploblastic [meaning the body originates from three embryonic cell layers (ectoderm, mesoderm, and endoderm) — as happens in all multicellular animals except sponges and coelenterates]. Other key features of mollusks include a mantle that may secrete a shell, a muscular foot used for locomotion, and a visceral mass containing internal organs.
Extreme morphological disparity within the Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. The most familiar molluscan groups — gastropods, bivalves, and cephalopods — each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, authors reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 90 genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans (small, limpet-like animals, having a single, cap-like shell). Authors’ analyses confirmed a phylogeny proposed from morphology and showed (not surprising) widespread genomic variation. Authors conclude that the flexibility of the molluscan genome likely explains both historic challenges (to scientists) with the genomes and the evolutionary success of this diverse phylum.
This publication presents an ENORMOUS amount of data from 90 genomes of animals in this diverse phylum. Authors present a total group phylogeny for Mollusca based on genome-wide markers — comprising all metazoan BUSCO genes in a phylogenomic analysis — which included all major clades and multiple representatives from all eight living classes. Authors assembled two near-complete genomes of the (enigmatic) deep-sea class Monoplacophora, and they generated genomes for five additional taxonomic classes: Caudofoveata, Scaphopoda, Gastropoda, Bivalvia, and Polyplacophora.
This dataset, combined with previously published genome assemblies, underpins the authors’ new phylogenetic analysis — which supports the origin of the phylum in the Cambrian Period (~541 million to 485.4 million years ago) and a rapid split into the major clades Aculifera and Conchifera (Figure 1). Phylogenetic topology was computed by ASTRAL-Pro using a set of 954 BUSCO family trees from 77 species and three outgroups (Fig. 1C). Congruent with the extensive fossil record of Mollusca and phylogenetic hypotheses proposed from morphology (Figure 2), authors found that Monoplacophora is sister to the remaining Conchifera, and Cephalopoda is sister to the clade Gastropoda + Diasoma (Scaphopoda + Bivalvia).
My hat goes off to the print-setters of how this article appears in the journal. If one looks at the publication in the journal issue, the molluscan tree of life in Fig. 1 (p 1002) and Fig. 2 (p 1003) line up — so that the eight living classes (Fig. 1B) are ranked as a schematic polytomy (Fig. 2A), illustrating a subset of proposed molluscan ingroup relationships — colors illustrating other previous data that support this evolutionary tree of life.
Extensive economic and research interests have consistently held Mollusca at the forefront of diverse disciplines — including fisheries, neurobiology, ecotoxicology, and biomimetic design; however, their extraordinary diversity has fundamentally hindered a confident assessment of their evolutionary history. The question of why early genetic studies struggled to recover reliable evolutionary patterns is potentially answered by the extreme variability among genomes that are now available for all classes, and their major clades within the phylum. Large-scale genomic analyses across the tree of life had provided inconclusive evidence regarding the drivers of genetic diversity.
The previous analyses were presently limited by incomplete sampling; to establish general principles of the organismal phenome (the complete set of all observable characteristics, or phenotypes, of an organism — including both visible traits and those related to function. The phenome encompasses all phenotypic information — including biochemical, physiological, and morphological traits. Essentially, it’s the measurable result of the interaction between an organism’s genetic makeup and its environment) and the genome, the analyses [attached article] also included all eight classes of the phylum Mollusca, which represents the most extensive experiment in animal body plans.
A stable topology for the total group Mollusca is fundamental for understanding the evolution of body plans and the fossil record. Based on this new phylogeny, authors infer that the molluscan ancestor had a solid dorsal shell, a foot, multiple dorsal-ventral and oblique foot-retractor muscles, a radula, and no eyes.
Throughout the long evolutionary history of Mollusca and continuing today, aspects of a flexible genome led to a flexible phenome: Endless forms of mollusks showcase the power of animal evolution.
DwN
Science 28 Feb 2025; 387: 1001-1007