Biology subjects

Mendez Sandin, M.

Publications and source records attributed to Mendez Sandin, M..

4 recordsLinked to original sources

bioRxiv2025

Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid Proterozoic

1.Molecular clock and preservation of early microfossil assemblages suggest that eukaryotes were present and already diverse more than [~]1600 million years ago (Ma). Yet, the earliest identifiable eukaryotic crown group fossil only appeared around 1050 Ma, leaving a [~]600 million years gap in the Mesoproterozoic during which the evolution and diversification of early eukaryotes remain poorly understood. Here, we inferred a timeline of eukaryote evolution using molecular clock and birth-death diversification models, including the great diversity of environmental sequences to take into account the uncultured majority of microbial life. Our analyses, based on a unique dataset of 75,975 non-redundant Operational Taxonomic Units and 77 well-supported fossil calibrations, indicate a steady diversification of crown group eukaryotes during the Proterozoic after the Last Eukaryotic Common Ancestor (LECA). We show that Archaeplastida was one of the earliest diversifying supergroups and the most diverse throughout the Proterozoic, suggesting that the first successful plastid endosymbiosis gave Archaeplastida a measurable evolutionary advantage. Discoba, Amoebozoa and Rhizaria followed Archaeplastida in phylogenetic diversity throughout the Proterozoic, suggesting that crown eukaryotes were already thriving in this Era. These results contrast with the common view that the geologically stable Proterozoic Era experienced little eukaryotic evolutionary innovation, and indicate that it was already at the dawn of eukaryote evolution that all current supergroups were established.

evolutionary biology↗

bioRxiv2025

OligoN-design: A simple and versatile tool to design specific probes and primers from large heterogeneous datasets

High-throughput environmental DNA sequencing has ushered ecological and evolutionary studies into the big data era. With thousands to millions of DNA sequences, designing taxon-specific oligonucleotides is a current bottleneck of molecular studies that rely on primers for Polymerase Chain Reactions (PCRs) or probes for Fluorescence in situ Hybridization (FISH). No software currently exists to design specific oligonucleotides starting from a custom set of sequences. Existing tools rely on specific databases, alignments or phylogenetic trees, or cannot accommodate increasingly large molecular environmental datasets. Here we present oligoN-design, a versatile tool to design oligonucleotides specific to a set of target sequences while minimizing predicted binding to non-target sequences. OligoN-design is simple, reproducible, and adaptable to high-throughput sequencing data analyses. It requires only two fasta files as input, one containing target taxa and the other containing non-target taxa. Using standard bioinformatic formats, it integrates easily with other tools such as BLAST, VSEARCH or MAFFT. OligoN-design allows a range of strategies that we present in detail, from an unsupervised end-to-end usage all the way to a detailed and thorough expert usage. Starting with large, comprehensive ribosomal databases that are widely used by the community (i.e., PR2, SILVA) and the unsupervised function, we were able to replicate known taxa-specific oligonucleotides in under 30 minutes and up to 6 Gb of RAM on a personal laptop. OligoN-design v1, available at github.com/MiguelMSandin/oligoN-design under GNU General Public License version 3.0, is easily installed via bioconda bioconda.github.io/recipes/oligon-design/README.html.

bioinformatics↗

bioRxiv2024

Diversity and evolution of Radiolaria: Beyond the stars of the ocean

Since Ernst Haeckel and the Challenger expedition (1872-1876), Radiolaria have been known as ubiquitous and abundant star-shaped oceanic plankton. Their exquisite biomineralized skeletons have left an extensive fossil record which is extremely valuable for biostratigraphic and paleo-environmental research. In contemporary oceans, there is growing evidence that Radiolaria are significant contributors to marine food webs and global biogeochemical cycles. Here we provide a comprehensive morpho-molecular framework to assess the extant diversity, biogeography and evolutionary history of Radiolaria. Our analyses reveal that half of radiolarian diversity is morphologically undescribed, with a large part forming three hyper-diverse environmental clades, named Rad-A, Rad-B and Rad-C. We suggest that most of this undescribed diversity likely comprises skeleton-less life forms or endosymbionts, explaining their elusive nature. Phylogenetic analyses highlight the need for major revision of high-level Radiolaria taxonomy, including placement of the Collodaria within the order Nassellaria. Fossil calibration of a molecular clock revealed the first appearance of Radiolaria [~]760 million years ago (Ma), the development of the skeleton in the early Paleozoic ([~]500 Ma) and the onset of photosymbiotic relationships during the mid to late Mesozoic ([~]140 Ma), related to geological periods of oligotrophy and anoxia. The results presented here provide an extensive and robust framework for developing new perspectives on early eukaryotic diversification, paleo-environmental impacts on plankton evolution, and marine microbial ecology in rapidly evolving ecosystems.

evolutionary biology↗

bioRxiv2018

Time calibrated morpho-molecular classification of Nassellaria (Radiolaria)

Nassellaria are marine radiolarian protists belonging to the Rhizaria lineage. Their skeleton, made of opaline silica, exhibit an excellent fossil record, extremely valuable in micro-paleontological studies for paleo-environmental reconstruction. Yet, to date very little is known about the extant diversity and ecology of Nassellaria in contemporary oceans, and most of it is inferred from their fossil record. Here we present an integrative classification of Nassellaria based on taxonomical marker genes (18S and 28S ribosomal DNA) and morphological characteristics obtained by optical and scanning electron microscopy imaging. Our phylogenetic analyses distinguished 11 main morpho-molecular clades relying essentially on the overall morphology of the skeleton and not on internal structures as previously considered. Using fossil calibrated molecular clock we estimated the origin of Nassellaria among radiolarians primitive forms in the Devonian (ca. 420 Ma), that gave rise to living nassellarian groups in the Triassic (ca. 250 Ma), during the biggest diversification event over their evolutionary history. This morpho-molecular framework provides both a new morphological classification easier to identify under light microscopy and the basis for future molecular ecology surveys. Altogether, it brings a new standpoint to improve our scarce understanding of the ecology and worldwide distribution of extant nassellarians.

molecular biology↗