Biology subjects

Vasquez, Y.

Publications and source records attributed to Vasquez, Y..

4 recordsLinked to original sources

bioRxiv2025

Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem

Giant viruses represent key ecological players in aquatic ecosystems, yet their evolutionary dynamics in response to environmental change remain poorly understood, particularly in freshwater environments. We leveraged an unprecedented 20-year time series (2000-2019) of 471 co-assembled metagenomes from Lake Mendota (USA) to reconstruct 1,512 high-quality giant virus metagenome-assembled genomes (GVMAGs), providing a unique framework to track viral genome evolution across decades. Viruses in the order Imitervirales dominated the Lake Mendota virome, exhibiting consistent presence across all seasons and years. We identified gene duplication (23% of genes) and horizontal gene transfer (29% of genes) as drivers of genomic innovation in giant viruses. Co-occurrence network analysis between viral DNA polymerase B and eukaryotic 18S rRNA sequences revealed significantly increased virus-host associations following the 2009 invasion of a predatory zooplankton. Genome-wide single nucleotide polymorphism analysis demonstrated predominantly purifying selection across viral genes, but revealed a significant increase in positively selected genes post-invasion, including in functions related to host infection (such as protein translation). Comparative evolutionary analyses revealed that giant viruses exhibit genome-wide substitution rates similar to co-occurring bacteria but significantly slower than smaller dsDNA phages, positioning them as evolutionary intermediates with bacterial-like genomic stability but virus-like adaptive capacity. By analyzing a vicennial (20-year) time series, we show that freshwater giant viruses employ sophisticated evolutionary strategies. They broaden their host range without abandoning established partners and maintain stable genomic backbones while rapidly adapting infection-related genes. These dynamics highlight their critical yet previously underappreciated role in freshwater ecosystem dynamics and resilience to environmental change.

microbiology↗

bioRxiv2025

A genomic catalog of Earth's bacterial and archaeal symbionts

1Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth, yet remains underexplored due to culturing challenges. This study employed machine learning (ML) to predict symbiotic lifestyles in hundreds of thousands of microbial genomes from diverse environmental metagenome samples and reference genomes. Predictions were performed using symclatron, a novel ML framework developed here to identify genomic signatures of symbionts. Predictions were deposited in a novel Symbiont Genomes catalog (SymGs). The results indicated that 15-23% of uncultivated microbes likely engage in symbiotic relationships with other organisms and are present in half of all known bacterial and archaeal phyla. We also identified genomic signatures of symbiotic lifestyles, including the loss of certain metabolic functions and the differential presence of others that may enable host-dependent living. The symclatron software and the SymGs catalog represent valuable resources for studying symbioses, facilitating future mechanistic investigations of host-microbe associations.

genomics↗

bioRxiv2021

Genome of the parasitoid wasp Dinocampus coccinellae reveals extensive duplications, accelerated evolution, and independent origins of thelytokous parthenogeny and solitary behavior

Dinocampus coccinellae (Hymenoptera: Braconidae) is a generalist parasitoid wasp that parasitizes >50 species of predatory lady beetles (Coleoptera: Coccinellidae), with thelytokous parthenogeny as its primary mode of reproduction. Here we present the first high quality genome of D. coccinellae using a combination of short and long read sequencing technologies, followed by assembly and scaffolding of chromosomal segments using Chicago+ HiC technologies. We also present a first-pass ab initio genome annotation, and resolve timings of divergence and evolution of (1) solitary behavior vs eusociality, (2) arrhenotokous vs thelytokous parthenogenesis, and (3) rates of gene loss and gain among Hymenopteran lineages. Our study finds (1) at least two independent origins of eusociality and solitary behavior among Hymenoptera, (2) two independent origins of thelytokous parthenogenesis from ancestral arrhenotoky, and (3) accelerated rates of gene duplications, loss, and gain along the lineages leading to D. coccinellae. Our work both affirms the ancient divergence of Braconid wasps from ancestral Hymenopterans and accelerated rates of evolution in response to adaptations to novel hosts, including polyDNA viral co-evolution.

genomics↗

bioRxiv2018

Coccinellid host morphology dictates morphological diversity of the parasitoid wasp Dinocampus coccinellae

Pararsitoid-host interactions involving host species that are newly introduced into the range of a generalist parasitoid provide systems that can be examined for phenotypic plasticity and evolutionary changes in parasitoid-host dynamics. The solitary Braconid parasitoid wasp, Dinocampus coccinellae, has a cosmopolitan distribution and parasitizes approximately 50 species of predatory lady beetles (ladybirds) in the family Coccinellidae. In this study we quantified the effect of six (4 native North American and 2 non-native North American) host species on the morphometrics of D. coccinellae. Adult lady beetles were collected from 13 locations in the United States and reared in the laboratory until D.coccinellae exited from their adult beetle hosts. Eighty-nine individual D. coccinellae females and their associated host were weighed and morphometric measurements were taken. The smallest lady beetle host Hippodamia parenthesis produced the smallest adult wasps; the largest host species, Coccinella septempunctata, produced the largest female wasps. A directional cline in morphology of wasps and their coccinellid hosts was also observed in a dry-weight regression (R2 = 0.4066, p-value < 0.0001). Two underlying mechanisms may explain the results of our study: (1) morphometric variation in D. coccinellae is governed by phenotypic plasticity with the size of the emerging offspring contingent on the size of the coccinellid host, and/or (2) that morphometric variation in D. coccinellae is governed by genomic adaptation to coccinellid host populations.

evolutionary biology↗