Biology subjects

Uyeda, J. C.

Publications and source records attributed to Uyeda, J. C..

6 recordsLinked to original sources

bioRxiv2025

Universal genomic constraints in the evolvability of thermal physiology

Thermal physiological traits such as body temperature often show surprisingly slow evolutionary rates over macroevolutionary time, despite apparent lability at microevolutionary time scales. While long-term stabilizing selection may slow rates of thermal evolution, we propose an alternative hypothesis from a bottom-up, population genomic perspective: the nature of body temperature (Tb) as an organism-level trait that must accommodate diverse protein thermal performances leads to evolutionary constraints at the organismal level. We support this hypothesis using a simulation framework in which we modeled and compared the rates of evolution for Tb alongside one or more proteins. Protein performances and organismal Tb were modeled as evolving, QTL-encoded traits, and organismal fitness was determined based on Tb given the performance curves of each protein. As predicted, a greater number of proteins led to drastic decrease in the rate of Tb evolution. When a shift in environmental temperature was simulated, Tb evolved with an initial rapid pulse toward the new optimum, followed by a phase of gradual evolution as the cumulative fitness costs of mismatching Tb and protein optima constrained thermal adaptation. That is, lability and stasis are predictable features of body temperature evolution: rapid, yet bounded microevolutionary bursts followed by long phases of sluggish evolution are both expected outcomes of directional selection operating on hierarchically structured traits like Tb. We suggest that protein thermal coordination might contribute to intrinsic, universal macroevolutionary patterns of stasis in organismal physiology across endotherms and ectotherms.

evolutionary biology↗

bioRxiv2025

Loss of a morph is associated with asymmetric character release in a radiation of woodland salamanders

Color polymorphism, the occurrence of multiple discrete color morphs with co-adapted sets of traits within the same population, may provide the raw materials for rapid species formation. It has been hypothesized that fixation of a single morph can result in character release, whereby the monomorphic form evolves without the constraint of accommodating multiple adaptive peaks. However, the rates of evolution between populations fixed for different morphs likely depend on the specific adaptive zones occupied by each morph. We studied the evolution of dorsal color polymorphism (striped and unstriped morphs) in woodland salamanders (Plethodon), a North American radiation in which the polymorphism can be found in even the most distantly related species ([~]44 Ma divergence). We estimated a phylogenomic tree of Plethodon, representing all extant taxa with multiple samples for most species. Morphometric data suggest that between-species variation exists predominantly along an axis of relative body elongation, likely corresponding to a terrestrial-fossorial continuum. Polymorphic species occupy an intermediate phenotypic space between the evolutionary optima of striped and unstriped species, although polymorphic species did not have elevated speciation rates. Faster rates of body shape evolution were observed in unstriped species, suggesting that body elongation, which is co-adapted with the unstriped morph, is constrained by the polymorphism. Striped species had slower rates of evolution than polymorphic species, despite lacking the genetic constraints often associated with polymorphism. Our results demonstrate that rates of phenotypic evolution and speciation following character release can be asymmetric and idiosyncratic depending on the alternative adaptations of each morph.

evolutionary biology↗

bioRxiv2022

A Timeline of Bacterial and Archaeal Diversification in the Ocean

Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event (GOE), during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I, to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.

evolutionary biology↗

bioRxiv2022

Developmental rules of primate dental evolution align microevolution with macroevolution

Macroevolutionary biologists have classically rejected the notion that higher level patterns of divergence arise through microevolutionary processes acting within populations. For morphology, this consensus partly derives from the inability of quantitative genetics models to correctly predict the behavior of evolutionary processes at the scale of millions of years. Developmental studies (evo-devo) have been proposed to reconcile micro and macroevolution. However, there has been little progress in establishing a formal framework to apply evo-devo models of phenotypic diversification. Here, we reframe this issue by asking if using evo-devo models to quantify biological variation can improve the explanatory power of comparative models, thus helping us bridge the gap between micro- and macroevolution. We test this prediction by evaluating the evolution of primate lower molars in a comprehensive dataset densely sampled across living and extinct taxa. Our results suggest that biologically-informed morphospaces alongside quantitative genetics models allow a seamless transition between the micro and macro scales, while biologically uninformed spaces do not. We show that the adaptive landscape for primate teeth is corridor-like, with changes in morphology within the corridor being nearly neutral. Overall, our framework provides a basis for integrating evo-devo into the modern synthesis, allowing an operational way to evaluate the ultimate causes of macroevolution.

evolutionary biology↗

bioRxiv2022

Jointly Modeling Species Niche and Phylogenetic Model in a Bayesian Hierarchical Framework

When studying how species will respond to climatic change, a common goal is to predict how species distributions change through time. Environmental niche models (ENMs) are commonly used to estimate a species environmental niche from observed patterns of occurrence and environmental predictors. However, species distributions are often shaped by non-environmental factors-including biotic interactions and dispersal barriers--truncating niche estimates. Though a truncated niche estimate may accurately predict present-day species distribution within the sampled area, this accuracy decreases when predicting occurrence at different places and under different environmental conditions. Modeling niche in a phylogenetic framework leverages a clades shared evolutionary history to pull species estimates closer towards phylogenetic conserved values and farther away from species specific biases. We propose a new Bayesian model of phylogenetic niche estimation implemented in R called BePhyNE (Bayesian environmental Phylogenetic Niche Estimation). Under our model, species ENM parameters are transformed into biologically interpretable continuous parameters of environmental niche optimum, breadth, and tolerance evolving as a multivariate Brownian motion. Through simulation analyses, we demonstrate model accuracy and precision that improve as phylogeny size increases. We also demonstrate our model on eastern United States Plethodontid salamanders and recover accurate estimates of species niche, even when species occurrence data is lacking and entirely informed by the evolutionary model. Our model demonstrates a novel framework where niche changes can be studied forwards and backwards through time to understand ancestral ranges, patterns of environmental specialization, and estimate niches of data-deficient species.

evolutionary biology↗

bioRxiv2017

Rethinking phylogenetic comparative methods

As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have been framed as a solution to this problem. In this paper, we argue that this way of thinking about PCMs is deeply misleading. Not only has this sowed widespread confusion in the literature about what PCMs are doing but has led us to develop methods that are susceptible to the very thing we sought to build defenses against -- unreplicated evolutionary events. Through three Case Studies, we demonstrate that the susceptibility to singular events is indeed a recurring problem in comparative biology that links several seemingly unrelated controversies. In each Case Study we propose a potential solution to the problem. While the details of our proposed solutions differ, they share a common theme: unifying hypothesis testing with data-driven approaches (which we term \"phylogenetic natural history\") to disentangle the impact of singular evolutionary events from that of the factors we are investigating. More broadly, we argue that our field has, at times, been sloppy when weighing evidence in support of causal hypotheses. We suggest that one way to refine our inferences is to re-imagine phylogenies as probabilistic graphical models; adopting this way of thinking will help clarify precisely what we are testing and what evidence supports our claims.

evolutionary biology↗