Biology subjects

Saulsbury, J. G.

Publications and source records attributed to Saulsbury, J. G..

4 recordsLinked to original sources

bioRxiv2025

Measuring and modeling ecological rates with neutral theory

The pace of change in ecological communities is central to classic and emerging problems in paleobiology and ecology. Yet measuring rates of change in community composition is problematic: when measured as ecological distance divided by time, rates appear faster when measured over shorter time intervals, preventing straightforward interpretation of rates when timescales vary. Similar problems arise when richness or sample size varies. We develop an approach that mitigates these issues using Hubbells neutral theory, a model in which species abundances change through stochastic births and deaths in a community with a fixed number of individuals J. Change in community composition is faster for smaller J, so 1/J provides a process-based rate metric that can be estimated from empirical time-series. We derive the likelihood for changes in community composition under neutral theory. Our approach accurately estimates rates in simulated data even when timescale, richness, and sample size vary. We use Quaternary pollen assemblage timeseries to demonstrate the power of this method for comparing rates between sites and through time and testing for rate shifts. Our approach can be flexibly adapted to test hypotheses on the causes of ecological change, including tests of coordinated stasis, neutral theory, and the timing of anthropogenic change.

ecology↗

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↗

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↗

bioRxiv2020

Permutation tests for comparative data

The analysis of patterns in comparative data has come to be dominated by least-squares regression, mainly as implemented in phylogenetic generalized least-squares (PGLS). This approach has two main drawbacks: it makes relatively restrictive assumptions about distributions and can only address questions about the conditional mean of one variable as a function of other variables. Here I introduce two new non-parametric constructs for the analysis of a broader range of comparative questions: phylogenetic permutation tests, based on cyclic permutations and permutations conserving phylogenetic signal. The cyclic permutation test, an extension of the restricted permutation test that performs exchanges by rotating nodes on the phylogeny, performs well within and outside the bounds where PGLS is applicable but can only be used for balanced trees. The signal-based permutation test has identical statistical properties and works with all trees. The statistical performance of these tests compares favorably with independent contrasts and surpasses that of a previously developed permutation test that exchanges closely related pairs of observations more frequently. Three case studies illustrate the use of phylogenetic permutations for quantile regression with non-normal and heteroscedastic data, testing hypotheses about morphospace occupation, and comparative problems in which the data points are not tips in the phylogeny.

evolutionary biology↗