Biology subjects

Gonzalez-Miguens, R.

Publications and source records attributed to Gonzalez-Miguens, R..

5 recordsLinked to original sources

bioRxiv2026

Widespread decoupling between abundance and genetic diversity, and strong local genetic structuring in marine unicellular eukaryotes

How abundance, connectivity, and genetic diversity covary across space remains a central question in evolutionary biology. Using a global environmental DNA metabarcoding dataset targeting mitochondrial cytochrome c oxidase subunit I (COI), we examined relationships among metabarcoding-derived abundance, nucleotide diversity, and spatial genetic connectivity across marine eukaryotes. We found a widespread but incomplete decoupling between abundance and genetic diversity, particularly in unicellular lineages. By contrast, distance-decay patterns in abundance, diversity, and connectivity were broadly similar across eukaryotes and more strongly associated with cellularity. Focusing on the Iberian Peninsula, we reconstructed locality-centred haplotype networks to quantify the spatial organization of intraspecific genetic variation. Unicellular lineages showed stronger local genetic structuring, whereas multicellular organisms exhibited clearer large-scale biogeographic partitioning. Overall, our results reveal shared biogeographic organization across eukaryotes while demonstrating that abundance-based biodiversity metrics alone cannot fully capture evolutionary and demographic processes, especially in microbial organisms.

ecology↗

bioRxiv2025

Quaternary ice ages shaped protists phylogeography: the case of Arcellinida in the Iberian Peninsula

The Quaternary glaciations profoundly shaped the biogeography of plants and animals, yet their impact on microbial eukaryotes remains largely unexplored. We tested the "genetic legacy of the Quaternary" (GLQ) paradigm in terrestrial protists using Arcellinida testate amoebae diversity distribution across the Iberian Peninsula, a well-established glacial refugium. To do so, we compiled the most extensive Arcellinida metabarcoding dataset to date (ArKOI), including 615 samples from multiple continents and ecosystems. Our results showed that hotspots of intra-OTU genetic diversity align with known Iberian refugia, supporting the concept of "refugia within refugia", and displaying clear ecoregion-specific climatic niches. Patterns of spatial clustering, niche breadth, and historical demographic reconstruction revealed repeated range contractions and expansions during the Pleistocene, mirroring those observed in macro-organisms. These findings extend the GLQ paradigm to protists, highlighting shared historical and ecological processes across the eukaryotic tree of life and contributing to a unified theory of biogeographic responses to climatic change.

ecology↗

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↗

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↗

bioRxiv2022

A needle in a haystack: a new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)

Environmental DNA-based diversity studies have increased in popularity with the development of high throughput sequencing technologies. This permits the potential simultaneous retrieval of vast amounts of molecular data from many different organisms and species, thus contributing to a wide range of biological disciplines. Environmental DNA protocols designed for protists often focused on the highly conserved small subunit of the ribosome gene, that does not permit species-level assignments. On the other hand, eDNA protocols aiming at species-level assignments allow a fine level ecological resolution and reproducible results. These protocols are currently applied to organisms living in marine and shallow lotic freshwater ecosystems, often in a bioindication purpose. Therefore, in this study, we present a species-level eDNA protocol, designed to explore diversity of Arcellinida (Amoebozoa: Tubulinea) testate amoebae taxa, that is based on mitochondrial cytochrome oxidase subunit I (COI). These organisms are widespread in lentic water bodies and soil ecosystems. We applied this protocol to 42 samples from peatlands, estuaries and soil environments, recovering all the infraorders in Glutinoconcha (with COI data), except for Hyalospheniformes. Our results revealed an unsuspected diversity in morphologically homogeneous groups such as Cylindrothecina, Excentrostoma or Sphaerothecina. With this protocol we expect to revolutionize the design of modern distributional Arcellinida surveys. Our approach involve a rapid and cost effective analysis of testate amoeba diversity living in contrasted ecosystems. Therefore, Arcellinida clade have the potential to be established as a model group for an array of theoretical and applied studies.

microbiology↗