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1. Extensive loss of Wnt genes in Tardigrada

   https://doi.org/10.1186/s12862-021-01954-y  

   Chavarria, Raul A.; Game, Mandy; Arbelaez, Briana; Ramnarine, Chloe; Snow, Zachary K.; Smith, Frank W. (December 2021, BMC Ecology and Evolution)

   Abstract Background Wnt genes code for ligands that activate signaling pathways during development in Metazoa. Through the canonical Wnt (cWnt) signaling pathway, these genes regulate important processes in bilaterian development, such as establishing the anteroposterior axis and posterior growth. In Arthropoda, Wnt ligands also regulate segment polarity, and outgrowth and patterning of developing appendages. Arthropods are part of a lineage called Panarthropoda that includes Onychophora and Tardigrada. Previous studies revealed potential roles of Wnt genes in regulating posterior growth, segment polarity, and growth and patterning of legs in Onychophora. Unlike most other panarthropods, tardigrades lack posterior growth, but retain segmentation and appendages. Here, we investigated Wnt genes in tardigrades to gain insight into potential roles that these genes play during development of the highly compact and miniaturized tardigrade body plan. Results We analyzed published genomes for two representatives of Tardigrada, Hypsibius exemplaris and Ramazzottius varieornatus . We identified single orthologs of Wnt4 , Wnt5 , Wnt9 , Wnt11 , and WntA , as well as two Wnt16 paralogs in both tardigrade genomes. We only found a Wnt2 ortholog in H. exemplaris . We could not identify orthologs of Wnt1 , Wnt6 , Wnt7 , Wnt8 , or Wnt10 . We identified most other components of cWnt signaling in both tardigrade genomes. However, we were unable to identify an ortholog of arrow / Lrp5/6 , a gene that codes for a Frizzled co-receptor of Wnt ligands. Additionally, we found that some other animals that have lost several Wnt genes and are secondarily miniaturized, like tardigrades, are also missing an ortholog of arrow / Lrp5/6 . We analyzed the embryonic expression patterns of Wnt genes in H. exemplaris during developmental stages that span the establishment of the AP axis through segmentation and leg development. We detected expression of all Wnt genes in H. exemplaris besides one of the Wnt16 paralogs. During embryo elongation, expression of several Wnt genes was restricted to the posterior pole or a region between the anterior and posterior poles. Wnt genes were expressed in distinct patterns during segmentation and development of legs in H. exemplaris , rather than in broadly overlapping patterns. Conclusions Our results indicate that Wnt signaling has been highly modified in Tardigrada. While most components of cWnt signaling are conserved in tardigrades, we conclude that tardigrades have lost Wnt1 , Wnt6 , Wnt7 , Wnt8 , and Wnt10 , along with arrow / Lrp5/6 . Our expression data may indicate a conserved role of Wnt genes in specifying posterior identities during establishment of the AP axis. However, the loss of several Wnt genes and the distinct expression patterns of Wnt genes during segmentation and leg development may indicate that combinatorial interactions among Wnt genes are less important during tardigrade development compared to many other animals. Based on our results, and comparisons to previous studies, we speculate that the loss of several Wnt genes in Tardigrada may be related to a reduced number of cells and simplified development that accompanied miniaturization and anatomical simplification in this lineage. 

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2. Cambrian lobopodians shed light on the origin of the tardigrade body plan

   https://doi.org/10.1073/pnas.2211251120  

   Kihm, Ji-Hoon; Smith, Frank W; Kim, Sanghee; Rho, Hyun Soo; Zhang, Xingliang; Liu, Jianni; Park, Tae-Yoon S (July 2023, Proceedings of the National Academy of Sciences)

   Phylum Tardigrada (water bears), well known for their cryptobiosis, includes small invertebrates with four paired limbs and is divided into two classes: Eutardigrada and Heterotardigrada. The evolutionary origin of Tardigrada is known to lie within the lobopodians, which are extinct soft-bodied worms with lobopodous limbs mostly discovered at sites of exceptionally well-preserved fossils. Contrary to their closest relatives, onychophorans and euarthropods, the origin of morphological characters of tardigrades remains unclear, and detailed comparison with the lobopodians has not been well explored. Here, we present detailed morphological comparison between tardigrades and Cambrian lobopodians, with a phylogenetic analysis encompassing most of the lobopodians and three panarthropod phyla. The results indicate that the ancestral tardigrades likely had a Cambrian lobopodian–like morphology and shared most recent ancestry with the luolishaniids. Internal relationships within Tardigrada indicate that the ancestral tardigrade had a vermiform body shape without segmental plates, but possessed cuticular structures surrounding the mouth opening, and lobopodous legs terminating with claws, but without digits. This finding is in contrast to the long-standing stygarctid-like ancestor hypothesis. The highly compact and miniaturized body plan of tardigrades evolved after the tardigrade lineage diverged from an ancient shared ancestor with the luolishaniids. 

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3. Lineage domains and cytoskeletal cables organize a cellular square grid in a crustacean

   https://doi.org/10.1101/2025.08.31.673345  

   Steinert, Beatrice L; Blondel, Leo; Kuyyamudi, Chandrashekar; Stamataki, Evangelia; Pavlopoulos, Anastasios; Extavour, Cassandra G (September 2025, bioRxiv)

   Abstract To build tissues, and ultimately functional bodies, cells in early embryos must arrange into specific patterns. In most animals, epithelial tissues exhibit a predominantly hexagonal space-packing geometry. However, in many species of the largest group of crustaceans, the Malacostraca, the embryonic epithelium takes on the striking form of a grid made up of predominantly square cells, sequential rows of which establish the adult segmented body plan. After square cells emerge, their organization appears to be maintained by specific cell division patterns. However, the mechanisms that initially generate square cells from hexagonal precursors are unknown. Here we address this problem by combining long-term multiview lightsheet microscopy, immunohistochemistry, laser ablation, and pharmacological perturbation. We show that in the emerging model crustaceanParhyale hawaiensisthis highly unusual grid geometry is first initiated from two perpendicular axes that are established sequentially according to different cellular mechanisms. The first axis arises dorso-ventrally at a tensile lineage compartment boundary, while the second emerges at the anterior-posterior axis along the ventral midline through lineage-independent cell intercalation driven by tensile actomyosin cables. We show that these midline cables are necessary for organizing square-cell packing as well as for proper expression of the segmentation geneengrailed. Our findings show that both cell lineage-specific behaviors, as well as lineage-independent supracellular structures, are required to establish square grid epithelial organization and a segmented body plan. 

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4. Somatic genome architecture and molecular evolution are decoupled in “young” linage-specific gene families in ciliates

   https://doi.org/10.1371/journal.pone.0291688  

   Maurer-Alcalá, Xyrus X; Cote-L’Heureux, Auden; Kosakovsky_Pond, Sergei L; Katz, Laura A (January 2024, PLOS ONE)

   Schmidt, Edward E (Ed.)

   The evolution of lineage-specific gene families remains poorly studied across the eukaryotic tree of life, with most analyses focusing on the recent evolution ofde novogenes in model species. Here we explore the origins of lineage-specific genes in ciliates, a ~1 billion year old clade of microeukaryotes that are defined by their division of somatic and germline functions into distinct nuclei. Previous analyses on conserved gene families have shown the effect of ciliates’ unusual genome architecture on gene family evolution: extensive genome processing–the generation of thousands of gene-sized somatic chromosomes from canonical germline chromosomes–is associated with larger and more diverse gene families. To further study the relationship between ciliate genome architecture and gene family evolution, we analyzed lineage specific gene families from a set of 46 transcriptomes and 12 genomes representing x species from eight ciliate classes. We assess how the evolution lineage-specific gene families occurs among four groups of ciliates: extensive fragmenters with gene-size somatic chromosomes, non-extensive fragmenters with “large’’ multi-gene somatic chromosomes, Heterotrichea with highly polyploid somatic genomes and Karyorelictea with ‘paradiploid’ somatic genomes. Our analyses demonstrate that: 1) most lineage-specific gene families are found at shallow taxonomic scales; 2) extensive genome processing (i.e., gene unscrambling) during development likely influences the size and number of young lineage-specific gene families; and 3) the influence of somatic genome architecture on molecular evolution is increasingly apparent in older gene families. Altogether, these data highlight the influences of genome architecture on the evolution of lineage-specific gene families in eukaryotes. 

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5. Whole-Body Regeneration in the Lobate Ctenophore Mnemiopsis leidyi

   https://doi.org/10.3390/genes12060867  

   Edgar, Allison; Mitchell, Dorothy G.; Martindale, Mark Q. (June 2021, Genes)

   Ctenophores (a.k.a. comb jellies) are one of the earliest branching extant metazoan phyla. Adult regenerative ability varies greatly within the group, with platyctenes undergoing both sexual and asexual reproduction by fission while others in the genus Beroe having completely lost the ability to replace missing body parts. We focus on the unique regenerative aspects of the lobate ctenophore, Mnemiopsis leidyi, which has become a popular model for its rapid wound healing and tissue replacement, optical clarity, and sequenced genome. M. leidyi’s highly mosaic, stereotyped development has been leveraged to reveal the polar coordinate system that directs whole-body regeneration as well as lineage restriction of replacement cells in various regenerating organs. Several cell signaling pathways known to function in regeneration in other animals are absent from the ctenophore’s genome. Further research will either reveal ancient principles of the regenerative process common to all animals or reveal novel solutions to the stability of cell fates and whole-body regeneration. 

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