Biology subjects

Polly, P. D.

Publications and source records attributed to Polly, P. D..

4 recordsLinked to original sources

bioRxiv2025

Genome Report: De novo genome assembly of the greater Bermuda land snail, Poecilozonites bermudensis (Mollusca:Gastropoda), confirms ancestral genome duplication

Poecilozonites bermudensis, the greater Bermuda land snail, is a critically endangered species and one of only two extant members in its genus. These snails are one of Bermudas few endemic animal clades and their rich fossil record was the basis for the punctuated equilibria model of speciation. Once thought extinct, recent conservation efforts have focused on the recovery of the species, yet no genomic information or other molecular sequences have been available to inform these initiatives. We present a high-quality, annotated genome for P. bermudensis generated using PacBio long read and Omni-C short read sequencing. The resulting assembly is approximately 1.36 Gb with a scaffold N50 of 44.t Mb and 31 chromosome-length scaffolds. Nearly 43 percent of the genome was identified as repeat content. This assembly will serve as a resource for the conservation and study of P. bermudensis, and its only close extant and also critically endangered relative, P. circumfirmatus. Additionally, this genome adds to the growing body of data needed for a more complete understanding of gastropod evolution and for evolutionary processes in general. Article summaryThis paper is aimed primarily at researchers studying genomic evolution and phylogenetics of mollusks, and secondarily researchers studying evolution and conservation of Bermuda land snails. It reports not only the first genome sequence for the Bermuda land snails, but the first sequence of any kind from the group and the first genome from the larger clade to which they belong. The paper presents a complete de novo genome annotation and first order analyses. The results support previous hypotheses that a genome duplication occurred at the base of land snails, and they facilitate future molecular work on Bermudian and other snails.

genomics↗

bioRxiv2024

The extended 'common cause': causal links between punctuated evolution and sedimentary processes

The common-cause hypothesis says that factors regulating the sedimentary record also exert macroevolutionary controls on speciation, extinction, and biodiversity. I show through computational modeling that common cause factors can, in principle, also control microevolutionary processes of trait evolution. Using Bermuda and its endemic land snail Poecilozonites, I show that the glacial-interglacial sea level cycles that toggle local sedimentation between slow pedogenesis and rapid eolian accumulation could also toggle evolution rates between long slow phases associated with large geographic ranges and short rapid phases associated with small, fragmented ranges and "genetic surfing" events. Patterns produced by this spatially driven process are similar to the punctuated equilibria patterns that Gould inferred from the fossil record of Bermuda, but without speciation or true stasis. Rather, the dynamics of this modeled system mimic a two-rate Brownian motion process (even though the rate parameter is technically constant) in which the contrast in rate and duration of the phases makes the slower one appear static. The link between sedimentation and microevolution in this model is based on a sediment-starved island system, but the principles may apply to any system where physical processes jointly control the areal extents of sedimentary regimes and species distributions. Non-Technical SummaryThe history of life is known from the fossils preserved in the geological record. The common-cause hypothesis suggests that processes like mountain building and sea-level change can affect both the structure of the geological record and species diversity. Using the snails of Bermuda as an example, this paper develops a computational model to show that sea level cycles could affect morphological evolution within species, not just species diversity. As sea level rose on Bermuda, the available snail habitat would have become smaller and more fragmented, which would be expected to drive rapid bursts of genetic drift (the random component of evolutionary change). When sea level fell, the snails habitat would have expanded and coalesced, resulting in slower rates of evolution because the total population size would increase. This process would produce an uneven cycle of rapid and slow evolution similar to what paleontologist Steven Gould observed in the fossil snails of Bermuda and led him to propose the theory of punctuated equilibria. While these simulations are focused specifically on an island system, the principles are applicable to other situations suggesting that geological and evolutionary processes may be linked in more ways than previously understood.

evolutionary biology↗

bioRxiv2022

A cautionary note on quantitative measures of phenotypic convergence

Tests of phenotypic convergence can provide evidence of adaptive evolution, and the popularity of such studies has grown in recent years due to the development of novel, quantitative methods for identifying and measuring convergence. These methods include the commonly applied C1-C4 measures of Stayton (2015), which measure morphological distances between lineages, and Ornstein-Uhlenbeck (OU) evolutionary model-fitting analyses, which test whether lineages convergently evolved toward adaptive peaks. We test the performance of C-measures and other convergence measures under various evolutionary scenarios and reveal a critical issue with C-measures: they often misidentify divergent lineages as convergent. We address this issue by developing novel convergence measures--Ct1-Ct4-measures--that measure distances between lineages at specific points in time, minimizing the possibility of misidentifying divergent taxa as convergent. Ct-measures are most appropriate when focal lineages are of the same or similar geologic ages (e.g., extant taxa), meaning that the lineages evolutionary histories include considerable overlap in time. Beyond C-measures, we find that all convergence measures are influenced by the position of focal taxa in phenotypic space, with morphological outliers often statistically more likely to be measured as strongly convergent by chance. Further, we mimic scenarios in which researchers assess convergence using OU models with a priori regime assignments (e.g., classifying taxa by ecological traits), and we find that multiple-regime OU models with phenotypically divergent lineages assigned to a shared selective regime often outperform simpler models. This highlights that model support for these multiple-regime OU models should not be assumed to always reflect convergence among focal lineages of a shared regime. Our new Ct1-Ct4-measures provide researchers with an improved comparative tool, but we emphasize that all available convergence measures are imperfect, and researchers should recognize the limitations of these methods and use multiple lines of evidence when inferring and measuring convergence.

evolutionary biology↗

bioRxiv2020

Morphological Integration and Modularity in the Hyperkinetic Feeding System of Aquatic-foraging Snakes

The kinetic skull is a key innovation that allowed snakes to capture, manipulate, and swallow prey exclusively using their heads using the coordinated movement of 8 bones. Despite these unique feeding behaviors, patterns of evolutionary integration and modularity within the feeding bones of snakes in a phylogenetic framework have yet to be addressed. Here, we use a dataset of 60 {micro}CT scanned skulls and high-density geometric morphometric methods to address the origin and patterns of variation and integration in the feeding bones of aquatic-foraging snakes. By comparing alternate superimposition protocols allowing us to analyze the entire kinetic feeding system simultaneously, we find that the feeding bones are highly integrated, driven predominantly by functional selective pressures. The most supported pattern of modularity contains four modules each associated with distinct functional roles: the mandible, the palatopterygoid arch, the maxilla, and the suspensorium. Further, the morphological disparity of each bone is not linked to its magnitude of integration, indicating that integration within the feeding system does not constrain morphological evolution and that adequate biomechanical solutions to a wide range of feeding ecologies and behaviors is readily evolvable within the constraint due to integration in the snake feeding system.

evolutionary biology↗