Biology subjects

Roger, A. J.

Publications and source records attributed to Roger, A. J..

24 records · Page 2Linked to original sources

bioRxiv2022

Are profile mixture models over-parameterized?

Biochemical constraints on the admissible amino acids at specific sites in proteins leads to heterogeneity of the amino acid substitution process over sites in alignments. It is well known that phylogenetic models of protein sequence evolution that do not account for site heterogeneity are prone to long-branch attraction (LBA) artifacts. Profile mixture models were developed to model heterogeneity of preferred amino acids at sites via a finite distribution of site classes each with a distinct set of equilibrium amino acid frequencies. However, it is unknown whether the large number of parameters in such models associated with the many amino acid frequency classes can adversely affect tree topology estimates because of over-parameterization. Here we demonstrate theoretically that for long sequences, over-parameterization does not create problems for estimation with profile mixture models. Under mild conditions, tree, amino acid frequencies and other model parameters converge to true values as sequence length increases, even when there are large numbers of components in the frequency profile distributions. Because large sample theory does not necessarily imply good behavior for shorter alignments we explore performance of these models with short alignments simulated with tree topologies that are prone to LBA artifacts. We find that over-parameterization is not a problem for complex profile mixture models even when there are many amino acid frequency classes. In fact, simple models with few site classes behave poorly. Interestingly, we also found that misspecification of the amino acid frequency classes does not lead to increased LBA artifacts as long as the estimated cumulative distribution function of the amino acid frequencies at sites adequately approximates the true one. In contrast, misspecification of the amino acid exchangeability rates can severely negatively affect parameter estimation. Finally, we explore the effects of including in the profile mixture model an additional F-class representing the overall frequencies of amino acids in the data set. Surprisingly, the F-class does not help parameter estimation significantly, and can decrease the probability of correct tree estimation, depending on the scenario, even though it tends to improve likelihood scores.

evolutionary biology↗

bioRxiv2021

Comparative transcriptomics reveals the molecular toolkit used by an algivorous protist for cell wall perforation

Microbial eukaryotes display a stunning diversity of feeding strategies, ranging from generalist predators to highly specialised parasites. The unicellular "protoplast feeders" represent a fascinating mechanistic intermediate, as they penetrate other eukaryotic cells (algae, fungi) like some parasites, but then devour their cell contents by phagocytosis. Besides prey recognition and attachment, this complex behaviour involves the local, pre-phagocytotic dissolution of the prey cell wall, which results in well-defined perforations of species-specific size and structure. Yet, the molecular processes that enable protoplast feeders to overcome cell walls of diverse biochemical composition remain unknown. We used the flagellate Orciraptor agilis (Viridiraptoridae, Rhizaria) as a model protoplast feeder, and applied differential gene expression analysis to examine its penetration of green algal cell walls. Besides distinct expression changes that reflect major cellular processes (e.g. locomotion, cell division), we found lytic carbohydrate-active enzymes that are highly expressed and upregulated during the attack on the alga. A putative endocellulase (family GH5_5) with a secretion signal is most prominent, and a potential key factor for cell wall dissolution. Other candidate enzymes (e.g. lytic polysaccharide monooxygenases) belong to families that are largely uncharacterised, emphasising the potential of non-fungal micro-eukaryotes for enzyme exploration. Unexpectedly, we discovered various chitin-related factors that point to an unknown chitin metabolism in Orciraptor, potentially also involved in the feeding process. Our findings provide first molecular insights into an important microbial feeding behaviour, and new directions for cell biology research on non-model eukaryotes.

microbiology↗

bioRxiv2021

A free-living protist that lacks canonical eukaryotic DNA replication and segregation systems

Cells must replicate and segregate their DNA with precision. In eukaryotes, these processes are part of a regulated cell-cycle that begins at S-phase with the replication of DNA and ends after M-phase. Previous studies showed that these processes were present in the last eukaryotic common ancestor and the core parts of their molecular systems are conserved across eukaryotic diversity. However, some unicellular parasites, such as the metamonad Giardia intestinalis, have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a high-quality draft genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. We found that parasitic and free-living metamonads harbor a conspicuously incomplete set of canonical proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and other replisome components, most structural kinetochore subunits including the Ndc80 complex, as well as several canonical cell-cycle checkpoint proteins. Carpediemonas is the first eukaryote known to have lost this large suite of conserved complexes, suggesting that it has a highly unusual cell cycle and that unlike any other known eukaryote, it must rely on novel or alternative set of mechanisms to carry out these fundamental processes.

evolutionary biology↗

bioRxiv2020

The ups and downs of amino acid co-evolution: evolutionary Stokes and anti-Stokes shifts

The most fundamental form of epistasis occurs between residues within a protein. Epistatic interactions can have significant consequences for evolutionary dynamics. For example, a substitution to a deleterious amino acid may be compensated for by replacements at other sites which increase its propensity (a function of its average fitness) over time - this is the evolutionary Stokes shift. We discovered that an opposite trend -the decrease in amino acid propensity with time-can also occur via the same epistatic dynamics. We define this novel and pervasive phenomenon as the evolutionary anti-Stokes shift. Our extensive simulations of three natural proteins show that evolutionary Stokes and anti-Stokes shifts occur with similar frequencies and magnitudes across the protein. This high-lights that decreasing amino acid propensities, on their own, are not conclusive evidence of adaptive responses to a changing environment. We find that stabilizing substitutions are often permissive (i.e., expand potential evolutionary paths) whereas destabilizing substitutions are restrictive. We show how these dynamics explain the variations in amino acid propensities associated with both evolutionary shifts in propensities.

evolutionary biology↗

bioRxiv2018

An updated phylogeny of the Alphaproteobacteria reveals that the Rickettsiales and Holosporales have independent origins

The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. Furthermore, we find that the Rhodospirillales might be paraphyletic and that the Geminicoccaceae could be sister to all ancestrally free-living alphaproteobacteria. Our robust phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.

evolutionary biology↗

bioRxiv2017

Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group

Recent phylogenetic analyses position certain orphan protist lineages deep in the tree of eukaryotic life, but their exact placements are poorly resolved. We conducted phylogenomic analyses that incorporate deeply sequenced transcriptomes from representatives of collodictyonids (diphylleids), rigifilids, Mantamonas and ancyromonads (planomonads). Analyses of 351 genes, using site-heterogeneous mixture models, strongly support a novel supergroup-level clade that includes collodictyonids, rigifilids and Mantamonas, which we name CRuMs. Further, they robustly place CRuMs as the closest branch to Amorphea (including animals and fungi). Ancyromonads are strongly inferred to be more distantly related to Amorphea than are CRuMs. They emerge either as sister to malawimonads, or as a separate deeper branch. CRuMs and ancyromonads represent two distinct major groups that branch deeply on the lineage that includes animals, near the most commonly inferred root of the eukaryote tree. This makes both groups crucial in examinations of the deepest-level history of extant eukaryotes.

evolutionary biology↗