Biology subjects

Godsoe, W.

Publications and source records attributed to Godsoe, W..

6 recordsLinked to original sources

bioRxiv2024

Structural variants underlie parallel adaptation following global invasion

Rapid adaptation during invasion has historically been considered limited and unpredictable. We leverage whole-genome sequencing of >2600 plants across six continents to investigate the relative roles of colonization history and adaptation during the worldwide invasion of Trifolium repens. Introduced populations contain high levels of genetic variation with independent colonization histories evident on different continents. Five large structural variants on three chromosomes exist as standing genetic variation within the native range, and exhibit strong signatures of parallel climate-associated adaptation across continents. Common gardens in the native and introduced ranges demonstrate that three structural variants exhibit patterns of selection consistent with local adaptation across each range. Our results provide strong evidence that rapid and parallel adaptation during invasion is caused by large-effect structural variants introduced throughout the world. Significance StatementBiological invasions occur over short timescales and introductions are often hypothesized to include limited genetic diversity, making the role of adaptation in invasion success controversial. We demonstrate that the invasion of a human-commensal species, Trifolium repens, likely stems from multiple, diverse introductions with significant evidence of climate-associated adaptation following introduction. The genetic basis of adaptation is most strongly linked to five chromosomal rearrangements that each span hundreds of genes - matching theoretical predictions that large-effect variants are key to the initial stages of adaptation to novel environments. Chromosomal rearrangements have remarkably parallel signatures of adaptation across different introductions despite initial colonization from different areas of Europe. Our study highlights the impact of globalization and rapid adaptation for the invasion success of human commensal species.

evolutionary biology↗

bioRxiv2022

Jaccard dissimilarity in stochastic community models based on the species-independence assumption

A fundamental problem in ecology is understanding the causes of change in species composition among sites (i.e. beta diversity). At present it is unclear how spatial heterogeneity in species occupancy across sites shapes these patterns. To address this question, we develop probabilistic models that consider two spatial or temporal sites, where presence probabilities vary both among species and between the sites. We derive analytical and approximate formulae for the expectation of pairwise beta-diversity. Using a novel graphical tool, Stochastic Incidence Plots (SIPs), which depict the presence probabilities in two sites across species labels, we develop a means to conceptualize the heterogeneity in presence probabilities: the steepness or unevenness of SIPs reflects species-level heterogeneity, while the degree of overlap between SIPs indicates site-level heterogeneity. Utilizing SIPs and a combinatorial approach in a two-species scenario, we demonstrate that beta-diversity is lower when SIPs are parallel compared to when they are anti-parallel. We also find that this prediction is testable with the well-known checkerboard pattern in incidence matrices. Finally, we applied the method to the species distribution models for five woodpecker species in Switzerland, showing that their spatial distributions will change significantly in the future. Overall, this work improves our understanding of how pairwise beta-diversity responds to occupancy heterogeneity.

ecology↗

bioRxiv2022

Species interactions and diversity: a unified framework using Hill numbers

Biodiversity describes the variety of organisms on planet earth. Ecologists have long hoped for a synthesis between analyses of biodiversity and analyses of biotic interactions among species, such as predation, competition, and mutualism. However, it is often unclear how to connect details of these interactions with complex modern analyses of biodiversity. To resolve this gap, we propose a unification of models of biotic interactions and measurements of diversity. We show that analyses of biodiversity obscure details about biotic interactions. For example, identical changes in biodiversity can arise from predation, competition or mutualism. Our approach indicates that traditional models of community assembly miss key facets of diversity change. Instead, we suggest that analyses of diversity change should focus on partitions, which measure mechanisms that directly shape changes in diversity, notably species level selection and immigration, rather than traditional analyses of biotic interactions. SpeculationsOur paper proposes that observations of biodiversity cannot be used to distinguish different types of biotic interactions. For generations ecologists have been fascinated with the links between biodiversity and biotic interactions (i.e. competition, mutualism and predation). Many of us expect that observations of biodiversity provide vital clues about how biotic interactions operate in nature, but it is hard to tell when these clues are reliable. Our work integrates models of biotic interactions and measurements of biodiversity diversity change. This highlights how an observed change in diversity can be compatible with any type of biotic interaction (i.e. competition, mutualism, predation etc.). So for example, the same increase in Shannon diversity could indicate the superior ability of a competitor the success of mutualists or a predators tendency to harvest dominant prey species. This is so because diversity measures are designed to be concerned with changes in relative abundances but not account for absolute abundance changes. Observations of biodiversity change are unlikely to yield insights about biotic interactions per se because biodiversity itself obscures species absolute abundances. Therefore, models of diversity change should focus on mechanisms that are less influenced by changes in absolute abundances such as species-level selection.

ecology↗

bioRxiv2021

Disentangling niche theory and beta diversity change

Beta diversity describes the differences in species composition among communities. Changes in beta diversity over time are thought to be due to selection based on species niche characteristics. For example, theory predicts that selection that favours habitat specialists will increase beta diversity. In practice, ecologists struggle to predict how beta diversity changes. To remedy this problem, we propose a novel solution that formally measures selections effects on beta diversity. Using the Price equation, we show how change in beta diversity over time can be partitioned into fundamental mechanisms including selection among species, variable selection among communities, drift, and immigration. A key finding of our approach is that a species short-term impact on beta diversity cannot be predicted using information on its long-term environmental requirements (i.e. its niche). We illustrate how our approach can be used to partition causes of diversity change in a montane tropical forest before and after an intense hurricane. Previous work in this system highlighted the resistance of habitat specialists and the recruitment of light-demanding species but was unable to quantify the importance of these effects on beta diversity. Using our approach, we show that changes in beta diversity were consistent with ecological drift. We use these results to highlight the opportunities presented by a synthesis of beta diversity and formal models of selection.

ecology↗

bioRxiv2020

The generalized Price equation: forces that change population statistics

The Price equation partitions the change in the expected value of a population measure. The first component describes the partial change caused by altered frequencies. The second component describes the partial change caused by altered measurements. In biology, frequency changes often associate with the direct effect of natural selection. Measure changes reflect processes during transmission that alter trait values. More broadly, the two components describe the direct forces that change population composition and the altered frame of reference that changes measured values. The classic Price equation is limited to population statistics that can expressed as the expected value of a measure. Many statistics cannot be expressed as expected values, such as the harmonic mean and the family of rescaled diversity measures. We generalize the Price equation to any population statistic that can be expressed as a function of frequencies and measurements. We obtain the generalized partition between the direct forces that cause frequency change and the altered frame of reference that changes measurements.

evolutionary biology↗

bioRxiv2019

Transmission bias's fundamental role in biodiversity change

There is a great need to understand how and why biodiversity, which we define as the variety of organisms found in a given place, changes over time. Current estimates suggest strikingly slow change in traditional measures of biodiversity. These estimates seem to contradict rapid shifts in the abundance of individual species and have led to a rethinking of the mechanisms shaping biodiversity. Conceptual models emphasize the role of competition among species or, more recently, selection on species identity (i.e. selection that favors some species at the expense of others). However, it is difficult to quantify how these mechanisms contribute to biodiversity change. To illustrate this point we present cases where strong competition or selection on species identity leads to no biodiversity change. In view of this disconnect we develop a new approach to studying biodiversity change using the Price equation. We show that biodiversity change responds to selection on species rarity, rather than to either competition or selection on species identity. We then show how this insight can be used to quantify the effects of the mechanisms previously thought to influence biodiversity: 1) selection, 2) (ecological) drift, 3) immigration and 4) speciation. Our results suggest the connection between species fates and their rarity is fundamental to understanding biodiversity change.

ecology↗