Biology subjects

Parins-Fukuchi, C. T.

Publications and source records attributed to Parins-Fukuchi, C. T..

4 recordsLinked to original sources

bioRxiv2023

Age-dependent extinction and the neutral theory of biodiversity

Red Queen (RQ) theory states that adaptation does not protect species from extinction because their competitors are continually adapting alongside them. RQ was founded on the apparent independence of extinction risk and fossil taxon age, but analytical developments have since demonstrated that age-dependent extinction is widespread, usually most intense among young species. Here we develop ecological neutral theory as a general framework for modeling fossil species survivorship under incomplete sampling. We show that it provides excellent fit to a high-resolution dataset of species durations for Paleozoic zooplankton, and more broadly can account for age-dependent extinction seen throughout the fossil record. Unlike widely used alternative models, the neutral model has parameters with biological meaning, thereby generating testable hypotheses on changes in ancient ecosystems. The success of this approach suggests novel interpretations of mass extinctions and of scaling in eco-evolutionary systems. Intense extinction among young species does not necessarily refute RQ or require a special explanation, but can instead be parsimoniously explained by neutral dynamics operating across species regardless of age. Significance StatementRed Queen theory predicts that competition among species should cause extinction risk to be independent of species age, but recent analyses have refuted this central prediction. To fill the resulting theoretical vacuum, we used ecological neutral theory to build a model of the lifespans of incompletely sampled species evolving under zero-sum competition. This model predicts survivorship among fossil zooplankton with surprising accuracy and accounts for empirical deviations from the predictions of Red Queen more generally. A neutral model of background extinction allows for interpreting survivorship curves in terms of biological process, suggests a novel understanding of mass extinctions, and supports a role for competition in extinction.

paleontology↗

bioRxiv2023

Sorting of persistent morphological polymorphisms links paleobiological pattern to population process

Biological variation fuels evolutionary change. Across longer timescales, however, polymorphisms at both the genomic and phenotypic levels often persists longer than would be expected under standard population genetic models such as positive selection or genetic drift. Explaining the maintenance of this variation within populations across long timespans via balancing selection has been a major triumph of theoretical population genetics and ecology. Although persistent polymorphisms can often be traced in fossil lineages over long periods through the rock record, paleobiology has had little to say about either the long-term maintenance of phenotypic variation or its macroevolutionary consequences. I explore the dynamics that occur when persistent polymorphisms maintained over long lineage durations are filtered into descendant lineages during periods of demographic upheaval that occur at speciation. I evaluate these patterns in two lineages: Ectocion, a genus of Eocene mammals, and botryocrinids, a Mississippian cladid crinoid family. Following origination, descendants are less variable than their ancestors. The patterns by which ancestral variation is sorted cannot be distinguished from drift. Maintained and accumulated polymorphisms in highly variable ancestral lineages such as Barycrinus rhombiferus (Owen and Shumard 1852) may fuel radiations as character states are sorted into multiple descendant lineages. Interrogating the conditions under which trans-specific polymorphism is either maintained or lost during periods of demographic and ecological upheaval can explain how population-level processes contribute to the emergent macroevolutionary dynamics that shape the history of life as preserved in the fossil record. Non-technical abstractUnderstanding how morphological variation changes within populations over relatively short timescales in response to environmental changes and ecology (i.e., thousands of years) is a major focus of paleontology and evolutionary biology. A distinct focus is in understanding the broad-scale patterns by which lineages have diversified into distinct environments over geologic time (i.e., millions of years). One major challenge has been reconciling how and whether processes acting over shorter timescales shape the patterns observed over long timescales. One way of examining morphological variation at the population level is by examining the distribution of polymorphic character states--discrete anatomical features that vary within a population. Fossil species often maintain such polymorphisms for long periods of time, with such variation even sometimes inherited by new species from their ancestors. In this article, I suggest that examining how these polymorphisms are distributed among incipient descendant lineages might help link the ecological and evolutionary processes that act at the population level (e.g., natural selection, genetic drift, competition, predation) to the paleobiological patterns that are often reconstructed across many species and over long timescales. I explore these dynamics in two lineages: Ectocion, a genus of Eocene mammals, and botryocrinids, a Mississippian cladid crinoid family. I found that new lineages typically have fewer polymorphisms than their ancestors, suggesting that ancestral variation is "sorted" into incipient lineages during speciation. This variation appears to be sorted randomly, which means that it is not possible to detect the influence of natural selection in guiding the inheritance of ancestral morphologies. I suggest that the patterns by which ancestral variation is sorted into new species may explain patterns of lineage diversification over long timescales, highlighting how population processes can extend their influence over longer timescales to shape large-scale evolutionary dynamics.

paleontology↗

bioRxiv2022

Molecular early burst associated with the diversification of birds at the K-Pg boundary

Complex patterns of genome and life-history evolution associated with the end-Cretaceous (K- Pg) mass extinction event limit our understanding of the early evolutionary history of crown group birds [1-9]. Here, we assess molecular heterogeneity across living birds using a technique enabling inferred sequence substitution models to transition across the history of a clade [10]. Our approach identifies distinct and contrasting regimes of molecular evolution across exons, introns, untranslated regions, and mitochondrial genomes. Up to fifteen shifts in the mode of avian molecular evolution map to rapidly diversifying clades near the Cretaceous-Palaeogene boundary, demonstrating a burst of genomic disparity early in the evolutionary history of crown birds [11-13]. Using simulation and machine learning techniques, we show that shifts in developmental mode [14] or adult body mass [4] best explain transitions in the mode of nucleotide substitution. These patterns are related, in turn, to macroevolutionary shifts in the allometric scaling relationship between basal metabolic rate and body mass [15, 16]. In agreement with theoretical predictions, this scaling relationship appears to have weakened across the end-Cretaceous transition. Overall, our study provides evidence that the Chicxulub bolide impact [17] triggered integrated patterns of evolution across avian genomes, physiology, and life history that structured the evolutionary potential of modern birds.

evolutionary biology↗

bioRxiv2022

Functional morphological innovation corresponds to shifting lines of genetic least resistance

Phenotypic traits are often constrained in their evolution by the genetic and developmental map underlying them. However, the extent to which these constraints themselves evolve has not been well-characterized. Traits that are integrated are generally thought to be constrained in their ability to evolve because their shared developmental and genetic architecture causes any change in one to be mirrored in the other. Nevertheless, it is not yet clear whether correlations can constrain major episodes of phenotypic diversification over longer timescales. We reconstruct patterns in integration within nine primate lineages and model the evolution of the resulting modules in a phylogenetic context. We find that patterns in integration are generally evolvable across lineages, with apes displaying particular lability in the composition of morphological modules. This increased turnover in module composition corresponds to both divergent evolution of skeletal shape and the formation of novel complexes of locomotor behaviors and postures. While integration may play a role in constraining evolutionary innovation, its effects are dynamic, shifting as the structure of integration itself evolves during episodes of exceptional ecomorphological diversification.

evolutionary biology↗