Biology subjects

Lozano-Fernandez, J.

Publications and source records attributed to Lozano-Fernandez, J..

6 recordsLinked to original sources

bioRxiv2025

Evaluating 18S Phylogenetic Placement Accuracy to Uncover Hidden Diversity in Early Branching Animals

Small subunit ribosomal RNA (SSU rRNA) - 18S in eukaryotes - is a gene universally present across the Tree of Life and it was central in resolving ancient relationships in early molecular phylogenies. Nowadays, despite multi-locus phylogenomic approaches dominate, SSU rRNA sequences still serv as a molecular identifier of biodiversity. Phylogenetic placement uses a reference phylogeny and a given evolutionary model to annotate taxonomically environmental DNA. As such, it enables more accurate identification of divergent sequences that may belong to unknown lineages across the Tree of Life. Here we first created the largest dataset of 18S sequences belonging to non-Bilateria metazoans, by curating the sequences found in PR2 database. We then used it as a case study to test the performance of different 18S-based barcodes (V4, V9, and full-length 18S) within a phylogenetic placement framework. Employing a series of sensitivity analyses, we found that the V9 region generally lacks sufficient phylogenetic signal for reliable placements in most of the cases. The V4 region is accurate when the environmental diversity is well represented in the reference tree but struggles with divergent lineages. Full-length 18S overcome short-read limitations and emerges as the most robust option to uncover unknown major clades. Finally, we apply phylogenetic placement to empirical environmental 18S data. We observe geographical variation in non-bilaterians communities and recover a putative clade of early-branching Ctenophora based on long-sequence barcodes.

evolutionary biology↗

bioRxiv2024

ERGA-BGE Reference Genome of Gluvia dorsalis: An Endemic Sun Spider from Iberian Arid Regions

The reference genome of Gluvia dorsalis is the first of its order Solifugae (sun spiders), offering insights into adaptations to arid environments and the evolutionary history of arachnids. The entirety of the genome sequence was assembled into 5 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 787 Mb, composed of 51 contigs and 10 scaffolds (including the mitogenome), with contig and scaffold N50 values of 38 Mb and 199 Mb, respectively.

genomics↗

bioRxiv2022

MATEdb, a data repository of high-quality metazoan transcriptome assemblies to accelerate phylogenomic studies

AO_SCPLOWBSTRACTC_SCPLOWWith the advent of high throughput sequencing, the amount of genomic data available for animals (Metazoa) species has bloomed over the last decade, especially from transcriptomes due to lower sequencing costs and easier assembling process compared to genomes. Transcriptomic data sets have proven useful for phylogenomic studies, such as inference of phylogenetic interrelationships (e.g., species tree reconstruction) and comparative genomics analyses (e.g., gene repertoire evolutionary dynamics). However, these data sets are often analyzed following different analytical pipelines, particularly including different software versions, leading to potential methodological biases when analyzed jointly in a comparative framework. Moreover, these analyses are computationally expensive and not affordable for a large part of the scientific community. More importantly, assembled transcriptomes are usually not deposited in public databases. Furthermore, the quality of these data sets is hardly ever taken into consideration, potentially impacting subsequent analyses such as orthology and phylogenetic or gene repertoire evolution inference. To alleviate these issues, we present Metazoan Assemblies from Transcriptomic Ensembles (MATEdb), a curated database of 335 high-quality transcriptome assemblies from different animal phyla analyzed following the same pipeline. The repository is composed, for each species, of (1) a de novo transcriptome assembly, (2) its candidate coding regions within transcripts (both at the level of nucleotide and amino acid sequences), (3) the coding regions filtered using their contamination profile (i.e., only metazoan content), (4) the longest isoform of the amino acid candidate coding regions, (5) the gene content completeness score as assessed against the BUSCO database, and (6) an orthology-based gene annotation. We complement the repository with gene annotations from high-quality genomes, which are often not straightforward to obtain from individual sequencing projects, totalling 423 high-quality genomic and transcriptomic data sets. We invite the community to provide suggestions for new data sets and new annotation features to be included in subsequent versions, that will be analyzed following the same pipeline and be permanently stored in public repositories. We believe that MATEdb will accelerate research on animal phylogenomics while saving thousands of hours of computational work in a plea for open and collaborative science.

evolutionary biology↗

bioRxiv2022

Resolving tricky nodes in the tree of life through amino acid recoding

Genomic data allowed for a detailed resolution of the tree of life. Yet, tricky nodes such as the root of the animal, plants, eukaryotes, bacterial and archaeal trees remain unresolved. Genomic datasets are heterogeneous as genes and species evolve under different selective pressures, impending the efficacy of evolutionary analyses. Amino acid recodings were developed to reduce heterogeneity, but clear evidence to justify their use is missing. We use simulated genomic-scale datasets and show that recodings can substantially improve phylogenetic accuracy when tackling tricky nodes. We apply our findings to address the root of the animal tree where the debate centers on whether sponges (Porifera) or comb jellies (Ctenophora) branched out first. We show that results from real data follow predictions from simulated data and indicate that a placement of the ctenophores as the first branching animal lineage is most likely artifactual.

evolutionary biology↗

bioRxiv2021

Compositional phylogenomic modelling resolves the 'Zoraptera problem': Zoraptera are sister to all other polyneopteran insects

The evolution of wings propelled insects to their present mega-diversity. However, interordinal relationships of early-diverging winged insects and the timescale of their evolution are difficult to resolve, in part due to uncertainties in the placement of the enigmatic and species-poor order Zoraptera. The Zoraptera problem has remained a contentious issue in insect evolution since its discovery more than a century ago. This is a key issue because different placements of Zoraptera imply dramatically different scenarios of diversification and character evolution among polyneopteran. Here, we investigate the systematic placement of Zoraptera using the largest protein-coding gene dataset available to date, deploying methods to mitigate common sources of error in phylogenomic inference, and testing historically proposed hypotheses of zorapteran evolution. We recover Zoraptera as the earliest-diverging polyneopteran order, while earwigs (Dermaptera) and stoneflies (Plecoptera) form a monophyletic clade (Dermoplectopterida) sister to the remainder of Polyneoptera. The morphology and palaeobiology of stem-zorapterans are informed by Mesozoic fossils. The gut content and mouthparts of a male specimen of Zorotypus nascimbenei from Kachin amber (Cretaceous) reveal a fungivorous diet of Mesozoic zorapterans, akin to extant species. Based on a set of 42 justified fossil and stratigraphic calibrations, we recover a Devonian origin of winged insects and Polyneoptera, suggesting that these groups coincided with the rise of arborescence during the diversification of early terrestrial plants, fungi, and animals. Our results provide a robust framework for understanding the pattern and timescale of early winged insect diversification.

zoology↗

bioRxiv2021

De novo transcriptome sequencing of the northern fowl mite, Ornithonyssus sylviarum, shed light into parasitiform poultry mites evolution and its chemoreceptor repertoires

The poultry red mite (PRM), Dermanyssus gallinae (De Geer), and the northern fowl mite (NFM), Ornithonyssus sylviarum (Canestrini and Fanzago), are the most serious pests of poultry, both of which have an expanding global prevalence. Research on NFM has been constrained by a lack of genomic and transcriptomic data. Here, we report and analyze the first transcriptome data for this species. A total of 28,999 unigenes were assembled, of which 19,750 (68.10%) were annotated using seven functional databases. The biological function of these unigenes was predicted using the GO, KOG, and KEGG databases. To gain insight into the chemosensory receptor-based system of parasitiform mites, we furthermore assessed the gene repertoire of gustatory receptors (GRs) and ionotropic receptors (IRs), both of which encode putative ligand-gated ion channel proteins. While these receptors are well characterized in insect model species, our understanding of chemosensory detection in mites and ticks is in its infancy. To address this paucity of data, we identified 9 IR/iGluRs and 2 GRs genes by analyzing transcriptome data in the NFM, while 9 GRs and 41 IR/iGluRs genes were annotated in the PRM genome. Taken together, the transcriptomic and genomic annotation of these two species provide a valuable reference for studies of parasitiform mites, and also helps to understand how chemosensory gene family expansion/contraction events may have been reshaped by an obligate parasitic lifestyle compared with their free-living closest relatives. Future studies should include additional species to validate this observation, and functional characterization of the identified proteins as a step forward in identifying tools for controlling these poultry pests.

molecular biology↗