Biology subjects

Fernandez, R.

Publications and source records attributed to Fernandez, R..

60 records · Page 4Linked to original sources

bioRxiv2019

Local adaptation fuels cryptic speciation in terrestrial annelids

Uncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between seventeen populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. Genomic analyses revealed the existence of three cryptic species, with half of the previously-identified potential cryptic lineages clustering within them. Local adaptation was detected in more than 800 genes putatively involved in a plethora of biological functions (most notably reproduction, metabolism, immunological response and morphogenesis). Several genes with selection signatures showed shared mutations for each of the cryptic species, and genes under selection were enriched in functions related to regulation of transcription, including SNPs located in UTR regions. Finally, geometric morphometrics approaches partially confirmed the phylogenetic signal of relevant morphological characters such as genital chaetae. Our study therefore unveils that local adaptation and regulatory divergence are key evolutionary forces orchestrating genome evolution in soil fauna.

evolutionary biology↗

bioRxiv2019

Genome-informed integrative taxonomic description of three cryptic species in the earthworm genus Carpetania (Oligochaeta, Hormogastridae)

Research on cryptic species complexes has reached a consensus on the necessity of integrating multiple sources of evidence. Low-coverage genomic scan techniques like Genotyping-by-Sequencing (GBS) have proven useful to study these groups. Both integrative taxonomy and genome-wide single nucleotide polymorphism (SNP) data remain to be widely applied to earthworms, an animal group with widespread presence of cryptic diversity. The genus Carpetania (formerly the Hormogaster elisae species complex) was found to contain six deeply divergent genetic lineages and some inconspicuous morphological differentiation based in a handful of Sanger-sequenced markers. Marchan et al. (submitted) delimited three well supported species-level clades on the basis of a genomewide SNP dataset and geometric morphometric analyses, highlighting the necessity of a formal taxonomic description of these taxa. In this work, further analyses are applied to the SNP data and a thorough morphological study is performed in order to provide an integrative description of two new species and to redescribe Carpetania elisae. Species-specific SNPs are identified and used as diagnostic characters, and genome-wide and cytochrome oxidase C subunit 1 (COI) genetic distances are compared finding a strong correlation between them. The taxonomic description of these three cryptic species provides a useful tool to include them effectively in ecological studies and biodiversity conservation actions.

zoology↗

bioRxiv2019

Selection following gene duplication shapes recent genome evolution in the pea aphid Acyrthosiphon pisum

Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem-sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there is a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed to tackle the history of duplicated genes to pave the road towards understanding the role of gene duplication in ecological adaptation.

genomics↗

bioRxiv2019

Hairless as a novel component of the Notch signaling pathway

Suppressor of Hairless [Su(H)], the transcription factor at the end of the Notch pathway in Drosophila, utilizes the Hairless protein to recruit two co-repressors, Groucho (Gro) and C-terminal Binding Protein (CtBP), indirectly. Hairless is present only in the Pancrustacea, raising the question of how Su(H) in other protostomes gains repressive function. We show that Su(H) from a wide array of arthropods, molluscs, and annelids includes motifs that directly bind Gro and CtBP; thus, direct co-repressor recruitment is ancestral in the protostomes. How did Hairless come to replace this ancestral paradigm? Our discovery of a protein (S-CAP) in Myriapods and Chelicerates that contains a motif similar to the Su(H)-binding domain in Hairless has revealed a likely evolutionary connection between Hairless and Metastasis-associated (MTA) protein, a component of the NuRD complex. Sequence comparison and widely conserved microsynteny suggest that S-CAP and Hairless arose from a tandem duplication of an ancestral MTA gene.

evolutionary biology↗

bioRxiv2018

Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis

Pulmonary fibrosis is a devastating disorder that results in the progressive replacement of normal lung tissue with fibrotic scar. Available therapies slow disease progression, but most patients go on to die or require lung transplantation. Single-cell RNA-seq is a powerful tool that can reveal cellular identity via analysis of the transcriptome, but its ability to provide biologically or clinically meaningful insights in a disease context is largely unexplored. Accordingly, we performed single-cell RNA-seq on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and one bronchoscopic cryobiospy sample. Integrated single-cell transcriptomic analysis of donors and patients with pulmonary fibrosis identified the emergence of distinct populations of epithelial cells and macrophages that were common to all patients with lung fibrosis. Analysis of transcripts in the Wnt pathway suggested that within the same cell type, Wnt secretion and response are restricted to distinct non-overlapping cells, which was confirmed using in situ RNA hybridization. Single-cell RNA-seq revealed heterogeneity within alveolar macrophages from individual patients, which was confirmed by immunohistochemistry. These results support the feasibility of discovery-based approaches applying next generation sequencing technologies to clinically obtained samples with a goal of developing personalized therapies.\n\nOne Sentence SummarySingle-cell RNA-seq applied to tissue from diseased and donor lungs and a living patient with pulmonary fibrosis identifies cell type-specific disease-associated molecular pathways.

systems biology↗

bioRxiv2017

Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies

The interrelationships of the four classes of Myriapoda have been an unresolved question in arthropod phylogenetics and an example of conflict between morphology and molecules. Morphology and development provide compelling support for Diplopoda (millipedes) and Pauropoda being closest relatives, and moderate support for Symphyla being more closely related to the diplopod-pauropod group than any of them are to Chilopoda (centipedes). In contrast, several molecular datasets have contradicted the Diplopoda-Pauropoda grouping (named Dignatha). Here we present the first transcriptomic data including a pauropod and both families of symphylans, allowing myriapod interrelationships to be inferred from phylogenomic data from representatives of all main lineages. Phylogenomic analyses consistently recovered Dignatha with strong support. Taxon removal experiments identified outgroup choice as a critical factor affecting myriapod interrelationships. Diversification of millipedes in the Ordovician and centipedes in the Silurian closely approximates fossil evidence whereas the deeper nodes of the myriapod tree date to various depths in the Cambrian-Early Ordovician, roughly coinciding with recent estimates of terrestrialisation in other arthropod lineages, including hexapods and arachnids. We provide a summary state-of-the-art Myriapoda Tree of Life at the ordinal level, the resolution of which has been improved by phylogenomics.

evolutionary biology↗