Biology subjects

Gubry-Rangin, C.

Publications and source records attributed to Gubry-Rangin, C..

3 recordsLinked to original sources

bioRxiv2022

The new archaeal order Lutiacidiplasmatales reveals convergent evolution in Thermoplasmatota

The archaeal Terrestrial Miscellaneous Euryarchaeota Group (TMEG) has been identified in various environments, and the single genome investigated thus far suggests that these organisms are anaerobic sulfite reducers. We assembled 35 new TMEG genomes that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) "Lutiacidiplasmatales" due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. A phylum-level analysis revealed that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutiacidiciplasmatales and indicates convergent evolution as an important evolutionary driving force in archaeal lineages with complex histories.

microbiology↗

bioRxiv2021

Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography

Defining appropriate null expectations for species distribution hypotheses is important because sampling bias and spatial autocorrelation can produce realistic, but ecologically meaningless, geographic patterns. Generating null species occurrences with similar spatial structure to observed data can help overcome these problems, but existing methods focus on single or pairs of species and do not incorporate between-species spatial structure that may occlude comparative biogeographic analyses. Here, we describe an algorithm for generating randomised species occurrence points that mimic the within- and between-species spatial structure of real datasets and implement it in a new R package - fauxcurrence. The algorithm can be implemented on any geographic domain for any number of species, limited only by computing power. To demonstrate its utility, we apply the algorithm to two common analysis-types: testing the fit of species distribution models (SDMs) and evaluating niche-overlap. The method works well on all tested datasets within reasonable timescales. We found that many SDMs, despite a good fit to the data, were not significantly better than null expectations and identified only two cases (out of a possible 32) of significantly higher niche divergence than expected by chance. The package is user-friendly, flexible and has many potential applications beyond those tested here, such as joint SDM evaluation and species co-occurrence analysis, spanning the areas of ecology, evolutionary biology and biogeography.

ecology↗

bioRxiv2020

Gene duplication drives genome expansion in Thaumarchaeota

Ammonia-oxidising archaea of the phylum Thaumarchaeota are keystone species in global nitrogen cycling. However, only three of the six known families of the terrestrially ubiquitous order Nitrososphaerales possess representative genomes. Here we provide genomes for the three remaining families and examine the impact of gene duplication, loss and transfer events across the entire phylum. Much of the genomic divergence in this phylum is driven by gene duplication and loss, but we also detected early lateral gene transfer that introduced considerable proteome novelty. In particular, we identified two large gene transfer events into Nitrososphaerales. The fate of gene families originating on these branches was highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles within soil and sediment environments. Overall, our results suggest that lateral gene transfer followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.

evolutionary biology↗