Biology subjects

Vazquez, G.

Publications and source records attributed to Vazquez, G..

3 recordsLinked to original sources

bioRxiv2022

Complex hybridization between deeply diverged fish species in a disturbed ecosystem

Over the past two decades researchers have documented the extent of natural hybridization between closely related species using genomic tools. Many species across the tree of life show evidence of past hybridization with their evolutionary relatives. In some cases, this hybridization is complex - involving gene flow between more than two species. While hybridization is common over evolutionary timescales, some researchers have proposed that it may be even more common in contemporary populations where anthropogenic disturbance has modified myriad aspects of the environments in which organisms live and reproduce. Here, we develop a flexible tool for local ancestry inference in hybrids derived from three source populations and describe a complex, recent hybridization event between distantly related swordtail fish lineages (Xiphophorus) and its potential links to anthropogenic disturbance. Impact SummaryAs sequencing tools have advanced, we have found that barriers between animal species are more porous than once thought. Researchers have found evidence for hybridization between species throughout many branches of the tree of life. In some cases, these hybridization events can involve more than two species. Here, we develop a flexible and user-friendly tool that can be used to identify three-way hybrids and report the discovery of hybrids with ancestry from three swordtail (Xiphophorus) species from an anthropogenically impacted site on the Rio Calnali in Hidalgo, Mexico. Researchers have studied hybrids between two Xiphophorus species along this river for decades, but this is the first documented case of hybridization involving three species. We explore hypotheses for what drove this hybridization event, including anthropogenic pollutants and reduced water quality.

evolutionary biology↗

bioRxiv2021

Robust Single-cell Matching and Multi-modalAnalysis Using Shared and Distinct FeaturesReveals Orchestrated Immune Responses

The ability to align individual cellular information from multiple experimental sources, techniques and systems is fundamental for a true systems-level understanding of biological processes. While single-cell transcriptomic studies have transformed our appreciation for the complexities and contributions of diverse cell types to disease, they can be limited in their ability to assess protein-level phenotypic information and beyond. Therefore, matching and integrating single-cell datasets which utilize robust protein measurements across multiple modalities is critical for a deeper understanding of cell states, and signaling pathways particularly within their native tissue context. Current available tools are mainly designed for single-cell transcriptomics matching and integration, and generally rely upon a large number of shared features across datasets for mutual Nearest Neighbor (mNN) matching. This approach is unsuitable when applied to single-cell proteomic datasets, due to the limited number of parameters simultaneously accessed, and lack of shared markers across these experiments. Here, we introduce a novel cell matching algorithm, Matching with pARtIal Overlap (MARIO), that takes into account both shared and distinct features, while consisting of vital filtering steps to avoid sub-optimal matching. MARIO accurately matches and integrates data from different single-cell proteomic and multi-modal methods, including spatial techniques, and has cross-species capabilities. MARIO robustly matched tissue macrophages identified from COVID-19 lung autopsies via CODEX imaging to macrophages recovered from COVID-19 bronchoalveolar lavage fluid via CITE-seq. This cross-platform integrative analysis enabled the identification of unique orchestrated immune responses within the lung of complement-expressing macrophages and their impact on the local tissue microenvironment. MARIO thus provides an analytical framework for unified analysis of single-cell data for a comprehensive understanding of the underlying biological system.

bioinformatics↗

bioRxiv2020

Genomic analysis of early SARS-CoV-2 strains introduced in Mexico

The COVID-19 pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to implement effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, the SARS-CoV-2 lineage A/G, containing mostly sequences from North America, and the lineage B/S containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized fourteen independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represent local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described in the country. Within this Mexican cluster, we also identified an H49Y amino acid change in the spike protein. This mutation is a homoplasy occurring independently through time and space, and may function as a molecular marker to follow on any further spread of these viral variants throughout the country. Our results depict the general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts. This work is the result of the collaboration of five institutions into one research consortium: three public health institutes and two universities. From the beginning of this work, it was agreed that the experimental leader of each institution would share the first authorship. Those were the criteria followed to assign first co-first authorship in this manuscript. The order of the other authors was randomly assigned. IMPORTANCEUnderstanding the introduction, spread and establishment of SARS-CoV-2 within distinct human populations is crucial to implement effective control strategies as well as the evolution of the pandemics. In this work, we describe that the initial virus strains introduced in Mexico came from Europe and the United States and the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains having the mutation H49Y in the Spike protein, that could be further used as a molecular marker to follow viral spread within the country and the region.

genomics↗