Biology subjects

Tamre, E.

Publications and source records attributed to Tamre, E..

3 recordsLinked to original sources

bioRxiv2026

Variability and scale-dependence in molecular evolution rate impacts interpretation of eukaryotic evolutionary histories

Molecular evolution is often modeled as proceeding at consistent rates over time, with some deviations accommodated by relaxed molecular clock models. Here, we quantify the full extent of variability in branch-specific substitution rates across relatively well-calibrated eukaryotic phylogenies, confirming that punctuated change at the molecular level underlies evolution at the morphological level where punctuated dynamics are more commonly recognized. We also show how inferred substitution rates decrease systematically when measured across increasing time intervals. This scale-dependence persists across alternative clock models, calibration strategies, and prior assumptions, but disappears in simulated data evolved under a constant rate - suggesting that the phenomenon arises from time-varying substitution rates and reflects genuine properties of evolutionary histories rather than model artifacts. The observed pattern is analogous to the Sadler effect in sedimentary geology, where time-averaged rates decline with increasing measurement interval because sedimentation is episodic, with longer hiatuses occurring less frequently. The recognized scale-dependent bias in molecular evolution is not captured in current molecular clock models and significantly impacts inferences of evolutionary history, such as estimating the age of Metazoa and understanding the timing and nature of the Cambrian Explosion. Significance StatementRates of molecular evolution are central to reconstructing the history of life, yet they are often assumed to be approximately constant over sufficiently long timescales. By analyzing relatively well-dated evolutionary trees of eukaryotes, we show how inferred rates of genome change systematically decrease as the timescale of measurement increases. This pattern is analogous to a well-known phenomenon in sedimentary geology where apparent sedimentation rates decline over longer intervals due to episodic processes. Our results demonstrate how long-term variability in evolutionary rates similarly produces a significant scale-dependent bias which is overlooked in current evolutionary models. Recognizing and quantifying this effect is important for dating key evolutionary events, such as the origin of animals, and for understanding the cadence of evolutionary processes.

evolutionary biology↗

bioRxiv2024

Recent origin of modern clades of iron oxidizers and low clade fidelity of iron metabolisms

Reduced iron was abundant in Earths surface environments before their oxygenation, so iron oxidation could have been a common metabolism on the early Earth. Consequently, modern microbial iron oxidation is sometimes seen as a holdover from an earlier biosphere, but the continuity of involved lineages or the metabolic process itself has not been verified. Modern neutrophilic iron oxidizers use cytochrome-porin Cyc2 as the initial electron acceptor in iron oxidation. With the protein as a proxy for the metabolism, we performed a phylogenetic analysis of Cyc2 to understand the evolutionary history of this microbial iron oxidation pathway. In addition to known iron oxidizers, we identified Cyc2 orthologs in gammaproteobacterial endosymbionts of lucinid bivalves. These bivalves have a robust fossil record and rely on sea-grass meadows that only appear in the Cretaceous, providing a valuable time calibration in the evolutionary history of Cyc2. Our molecular clock analysis shows that extant sampled Cyc2 diversity has surprisingly recent common ancestry, and iron oxidation metabolisms in Gallionellaceae, Zetaproteobacteria, and photoferrotrophic Chlorobi likely originated in the Neoproterozoic or the Phanerozoic via multiple transfer events. The groups responsible for microbial iron oxidation have thus changed over Earth history, possibly reflecting the instability of niches with sufficient reduced iron. We note that frequent transfer and changing taxonomic distribution may be a general pattern for traits which are selected for sporadically across space and time. Based on iron metabolism and other processes, we explore this concept of a traits "clade fidelity" (or lack thereof) and establish its evolutionary importance. ImportanceBacteria can oxidize iron to produce energy. As there was plenty of reduced iron available on the early Earth and there is only a little today, it was sometimes thought that bacteria who oxidize iron today are a small remnant of a larger group that used to do it. We studied the evolutionary history of the iron oxidation pathway that modern bacteria use, and we found that they developed that pathway relatively recently: whoever did it in the past is no longer around today. It would probably be hard for any group of organisms to keep doing iron oxidation over billions of years, since iron availability is so variable: they are likely to go extinct or lose this ability at some point. We suggest this as general trend in evolution that traits which are only sporadically useful are commonly lost - and then re-invented or re-distributed, or the trait will go extinct.

evolutionary biology↗

bioRxiv2023

Selection by differential survival among marine animals in the Phanerozoic

The Gaia hypothesis posits that Earths biosphere functions as a single self-stabilizing system, but a key challenge is explaining how this could have arisen through Darwinian evolution. One theory is that of "selection by differential survival", in which a clades extinction probability decreases with age as it accumulates adaptations resisting environmental disturbances. While this is hard to assess during early Earth history, we can assess whether this process operated among marine animal genera throughout the Phanerozoic. To that end, we analyzed time ranges of 36,117 extinct animal genera using fossil occurrence data from the Paleobiology Database in order to calculate marine metazoan extinction age selectivity, extinction rates, and speciation rates over the Phanerozoic. We identify four signatures of selection by differential survival: lower extinction rates among older lineages, heritability and taxonomically nested propagation of extinction resistance, reduced age selectivity during rare environmental perturbations, and differential extinction rather than speciation as the primary driver of the phenomenon. Evidence for this process at lower taxonomic levels also implies its possibility for life as a whole - indeed, the possibility of Gaia.

evolutionary biology↗