Biology subjects

Lombard, J.

Publications and source records attributed to Lombard, J..

4 recordsLinked to original sources

bioRxiv2026

Evolution at experimental epidemic fronts speeds up parasite spread

Spreading epidemics can foster the rapid emergence of novel parasite variants. Similar to range expansions, parasites at the front of an epidemic wave may evolve traits facilitating their spatial spread. Typically, higher transmissibility and virulence are expected to evolve at the epidemic front, but predictions change if virulence reduces dispersal of infected hosts. We investigated the feedbacks between epidemiology and evolution in interconnected microcosms of the ciliate Paramecium caudatum and its bacterial parasite Holospora undulata. First, two long-term treatments mimicked the moving front of epidemic waves, with and without the natural dispersal of infected hosts. Phenotypic trait assays revealed an eco-to-evo feedback: front parasites (i.e., travelling with infected hosts) were less virulent and interfered less with host dispersal, but also showed higher infectivity, compared to parasites from the control treatment. Whole-genome resequencing and analyses of functional genomic diversity corroborated such phenotypic divergence. Second, measurement of the spread of evolved parasites in linear landscapes demonstrated an evo-to-eco feedback: front parasites produced stronger infection outbreaks and faster spreading epidemic waves than did control parasites. A simulation model assessed the relative importance of the different parasite traits in determining infectious spread over a broad parameter range. It suggests that, if dispersal is generally low, higher infectivity alone can produce the observed differences in epidemic spread speed. Our study illustrates how the need to travel with the host shapes eco-evolutionary feedbacks at parasite invasion fronts, and it highlights the importance of considering concomitant evolutionary change when predicting epidemic speed. Significance StatementWhen predicting disease spread across spatial scales it is fundamental to consider host dispersal, but also the concomitant evolution of parasite traits such as infectivity and virulence. We tested how dispersal constraints affect parasite evolution and epidemic spread in an aquatic model system, by combining experimental evolution, genetic analysis and mathematical modelling. Our results suggest that epidemics can be accelerated by the evolution of highly infectious, but not necessarily more virulent parasites, in contrast to conventional views. This illustrates the important role of eco-evolutionary feedback loops can play in shaping the spread of emerging or geographically expanding parasites.

evolutionary biology↗

bioRxiv2025

Surveillance on California dairy farms reveals multiple sources of H5N1 transmission

Transmission routes of highly pathogenic H5N1 between cows or to humans remain unclear due to limited data from affected dairy farms. We performed air, farm wastewater, and milk sampling on 14 H5N1 positive dairy farms across two different California regions. Infectious virus was detected in the air in milking parlors and in wastewater streams, while viral RNA was found in exhaled breath of cows. Sequence analysis of infectious H5N1 virus from air and wastewater samples on one farm revealed viral variants relevant for potential human susceptibility. Longitudinal analysis of milk from the individual quarters of cows revealed a high prevalence of subclinical H5N1 positive cows. Additionally, a heterogeneous distribution of infected quarters that maintained a consistent pattern over time was observed, inconsistent with shared milking equipment serving as the sole transmission mode. The presence of subclinically infected cows was further supported by detection of antibodies in the milk of animals that exhibited no clinical signs during the H5N1 outbreak on one farm. Our data highlight additional sources and potential modes of H5N1 transmission on dairy farms.

microbiology↗

bioRxiv2023

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

In the ongoing debates about eukaryogenesis, the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors, members of the Asgard archaea play a key role as the closest archaeal relatives of eukaryotes. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved. Here, we analyze distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea, as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree/species tree reconciliation approaches, we show that, in analogy to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared to other archaea. Finally, we infer that the last common ancestor of Asgard archaea likely was a thermophilic chemolithotroph, and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and the platform for the emergence of cellular complexity in eukaryotic cells.

evolutionary biology↗

bioRxiv2019

New Asgard archaea capable of anaerobic hydrocarbon cycling

Large reservoirs of natural gas in the oceanic subsurface sustain a complex biosphere of anaerobic microbes, including recently characterized archaeal lineages that extend the potential to mediate hydrocarbon oxidation (methane and butane) beyond the Methanomicrobia. Here we describe a new archaeal phylum, Helarchaeota, belonging to the Asgard superphylum with the potential for hydrocarbon oxidation. We reconstructed Helarchaeota genomes from hydrothermal deep-sea sediment metagenomes in hydrocarbon-rich Guaymas Basin, and show that these encode novel methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea. Based on these results as well as the presence of several alkyl-CoA oxidation and Wood-Ljungdahl pathway genes in the Helarchaeota genomes, we suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize short-chain hydrocarbons. These findings link a new phylum of Asgard archaea to the microbial utilization of hydrothermally generated hydrocarbons, and extend this genomic blueprint further through the archaeal domain.

microbiology↗