Biology subjects

Galvez-Morante, A.

Publications and source records attributed to Galvez-Morante, A..

5 recordsLinked to original sources

bioRxiv2025

Looks can be deceiving: discordances in phylogeny and morphology within loricate choanoflagellates

Choanoflagellates are heterotrophic holozoans that are classified into two groups based on their morphology: loricates, which possess a silica-based extracellular structure, and craspedids, which do not. Although the craspedid versus loricate morphological separation is currently supported by their phylogenetic relationship, recent evidence has suggested inconsistencies between morphology and phylogeny within each group. Loricate choanoflagellate taxonomy has historically been based on selected aspects of their lorica morphology, and on their mode of cell division, in which tectiform daughter cells emerge into a lorica synthesized by their mother cell following division, and nudiform daughter cells do not. Here, we characterize two new loricate strains that display unexpected morphological features when compared to their nearest genetic relatives. The strain BEAP0094 very closely matched the 18S ribosomal gene of the tectiform Pseudostephanoeca paucicostata, but its morphology clearly differed, due to the absence of the characteristic anterior ring found in all Stephanoeca species. Instead, its features resembled more closely those of the Acanthocorbis genus, raising the possibility of the existence of either multiple lorica morphologies within the same or very closely related species, or multiple morphological species sharing the same 18S ribosomal gene. The second strain we investigated, BEAP0360, presented a morphological match to Stephanoeca cauliculata, but its 18S ribosomal sequence did not, suggesting that different species could share the same lorica architecture. BEAP0360, here described as Cepoeca plumata (n. gen. n. sp.), possesses a key phylogenetic placement, potentially as the earliest branching member within nudiform loricates, which would be informative for investigating the evolution of the nudiform lifestyle. Our findings are inconsistent with a strict classification based on currently defined aspects of lorica morphology and support the usage of genetic data as primary criterion for genus-level taxonomic assignment.

evolutionary biology↗

bioRxiv2025

Protists Exhibit Stronger and More Recent Oceanic Genetic Structure than Archaeplastida and Metazoa

The global distribution of biodiversity is shaped by a complex interplay of evolutionary history and ecological processes. While biogeographic patterns are well defined for animals and plants, the global distributions of protists remain unclear. A key question is whether protists follow the same broad biogeographic principles as macroscopic life. To address this, we compiled 88 marine COI metabarcoding studies performing population-genetic analyses across ocean basins. Our results reveal that most protist phyla exhibit pronounced genetic structure among oceans, a pattern exceeding that reported for Archaeplastida and Metazoa. This likely reflects recent, and potentially human-mediated, introductions, influencing protist dispersal and contemporary community assembly. By demonstrating that protist distributions are not historically cosmopolitan, our study supports the existence of common eukaryotic biogeographic patterns that transcend organismal size.

microbiology↗

bioRxiv2025

Description of a new Telonemia genus and species with novel observations providing insights into its hidden diversity

Telonemia is a fascinating and understudied group of microbial eukaryotes known to have a vast diversity that is still uncharacterized. In fact, although they are thought to be the closest relatives of the eukaryotic supergroup SAR (Stramenopiles, Alveolata and Rhizaria), their diversity and biology are largely unexplored: to date, there are only seven described species in three genera, although there are estimated to be hundreds more unknown lineages. Here, we describe the isolation and characterization of two new strains, including a new genus (Hyaliora molinica gen. et sp. nov.) and a new species (Telonema blandense sp. nov.), and the re-isolation of a previously characterized telonemid, Telonema subtile, accompanied by new behavioral observations. We present morphological measurements highlighting differences among the isolates and a phylogenetic tree incorporating their 18S rRNA gene sequences. Furthermore, key aspects of their cell biology and structure are highlighted to provide insights into the evolution of TSAR. Since they are relevant not only phylogenetically, but also play a crucial role in food webs with some very abundant representatives in aquatic ecosystems, the findings of this study provide a further sampling and culturing of Telonemia to increase the knowledge of the hidden diversity and evolution of this mysterious group.

evolutionary biology↗

bioRxiv2025

The evolution of gene functional repertoire in Amorphea: Divergent strategies across Amoebozoa, Fungi, and Metazoa.

Metazoa and Fungi have been extensively studied to reconstruct the trajectory of Opisthokont evolution. Their sister group, Amoebozoa, provides additional potential to generate valuable insights into the origins of Opisthokont lineages. Amoebozoa represent a diverse group of amoeboid organisms, which have adapted to a wide range of environments and ecological niches. Studying Amoebozoa not only helps to illuminate Opisthokont evolution but also reveals the mechanisms that have driven their ecological success. Here we report the discovery of Apostamoeba explorator strain BEAP0066, representing a novel lineage within Amoebozoa with intriguing behaviors like the "double-amoeba", a behavior characterized by the bipolarization of a cell into two poles that coexist and act as two semi-independent cells; and the "colonizing rings", the generation of a front of amoebae advancing together and grazing on bacterial mats. By analyzing the gene content of A. explorator and diverse amoebozoans with ancestral gene content reconstructions, correspondence analyses of Clusters of Orthologous Groups (COG) category composition and Pfam clan clustering, we revealed distinct evolutionary trajectories for Amoebozoa, Metazoa, and Fungi. Amoebozoa retained an ancestral Amorphea-like state, characterized by an enrichment of genes related to motility, phagocytosis, and environmental adaptability; while Metazoa specialized in multicellularity-related genes and Fungi in metabolism and transport. These findings suggest that retention of gene function composition, rather than gene loss, played a key role in shaping Amoebozoa evolution. SIGNIFICANCE STATEMENTAmoebae are cells with no defined shape that move by extending temporary cell membrane projections, usually composed of actin, called pseudopodia. Amoeboid cells are present in all major eukaryotic lineages, from the well-known Amoeba proteus in Amoebozoa to human macrophages in Metazoa, Salpingoeca rosetta in Choanoflagellatea, Vampyrella lateritia in Rhizaria, and other examples such as Naegleria fowleri in Heterolobosea. The prevalence of this lifestyle highlights the evolutionary success of the amoeboid form and its ability to adapt to diverse environmental conditions and ecological roles. The study of amoebae and amoeboid cell types is crucial for advancing research in medicine, ecology, and evolution. Understanding the phylogeny of Amoebozoa remains a key focus in phylogenomics, as deep divergences within the group complicate the taxonomic placement of certain taxa and have implications for character evolution. Thus, the discovery, identification, and characterization of new Amoebozoa species can help resolve current uncertainties. Recent studies have identified divergent trajectories in gene content composition within one lineage of Amorphea, the Opisthokonts. Fungi evolved through an expansion of metabolic genes, whereas Metazoa accumulated genes associated with multicellularity. Inspired by these findings, we analyzed the proteomes of Amoebozoa, Metazoa, and Fungi. Using correspondence analysis of the relative composition of Clusters of Orthologous Groups (COG), ancestral reconstruction and the analysis of Pfam domain clan presence in supergroup-specific gene clusters, we aimed to determine whether the three supergroups within Amorphea exhibit distinct clustering patterns. Our results provide evidence of divergent functional evolution in Amoebozoa, Fungi, and Metazoa. Amoebozoa retained an ancestral Amorphea-like state, characterized by an enrichment of genes related to motility, phagocytosis, and environmental adaptability; while Metazoa specialized in multicellularity-related genes and Fungi in metabolism and transport. These findings suggest that retention of gene function composition, rather than gene loss, played a key role in shaping Amoebozoa evolution.

evolutionary biology↗

bioRxiv2024

A Novel Taxonomic Database for eukaryotic Mitochondrial Cytochrome Oxidase subunit I Gene (eKOI): Enhancing taxonomic resolution at community-level in metabarcoding analyses

Metabarcoding has emerged as a robust method for understanding biodiversity patterns by retrieving environmental DNA (eDNA) directly from ecosystems. Its low cost and accessibility have extended its use across biological topics, from symbiosis to biogeography, and ecology. A successful metabarcoding application depends on accurate and comprehensive reference databases for proper taxonomic assignment. The 18S rRNA gene is the primary genetic marker used for general/broad eukaryotic metabarcoding due to its combination of conserved and hypervariable regions, and the availability of extensive taxonomically-informed reference databases like PR2 and SILVA. Despite its advantages, 18S rRNA has certain limitations at lower taxonomic levels, depending on the lineage. Alternative fast-evolving molecular markers, such as the mitochondrial cytochrome oxidase subunit I (COI) gene, have been adopted as widely used "barcoding genes" for eukaryotes due to their resolution to the species level. However, the COI gene lacks a curated taxonomically-informed database covering all eukaryotes, including protists, comparable to those available for 18S rRNA. To address this gap, we introduce eKOI, a curated COI gene database aimed at enhancing the taxonomic annotation and primer design for COI-based metabarcoding at the community level. This database integrates COI gene data from GenBank and mitochondrial genomes that are publicly available, followed by rigorous manual curation to eliminate redundancies and contaminants and to correct taxonomic annotations. We validate using the eKOI database for taxonomic annotation of protists by re-annotating several COI-based metabarcoding studies, revealing previously unidentified biodiversity. Phylogenetic analyses confirmed the accuracy of the taxonomic annotations, highlighting the potential of eKOI to uncover new biodiversity in various eukaryotic lineages.

ecology↗