Biology subjects

Kopperud, B. T.

Publications and source records attributed to Kopperud, B. T..

6 recordsLinked to original sources

bioRxiv2025

Phylogenetic Estimation of branch-specific Shifts in the Tempo of Origination

AO_SCPLOWBSTRACTC_SCPLOWStudying rates of species diversification is one of the key themes in macroevolution. In particular, we are interested in if some clades in a phylogeny diversify more rapidly/slowly than others due to branch-specific diversification rates. A common approach in neontological studies is to use a phylogenetic birth-death process to model species diversification. Specifically, the birth-death-shift process is used to model branch-specific shifts in the tempo of diversification. Here, we present Pesto, a new method and software for estimating branch-specific diversification rates that does not rely on Markov chain Monte Carlo simulations for fitting the model and instead deterministically computes the posterior mean branch-specific diversification rates using only two traversals of the tree. This method is blazingly fast: the birth-death-shift model can be fitted to large phylogenies (> 20k taxa) in minutes on a personal computer while also providing branch-specific inference of diversification rate shift events. Thus, we can robustly infer branch-specific diversification rates and the number of diversification rate shift events for large-scale phylogenies as well as exploring the characteristic of the birth-death-shift model through complex and large-scale simulations. Here, we first describe the method and the software implementation Pesto and explore its behavior using trees simulated under the birth-death-shift model. Then, we explore the behavior of inferring significant branch-specific diversification rate shifts using both Bayes factors and effect sizes. We find few to none false positive inferences of diversification rate shift events but many false negatives (reduced power). The most difficult parameter to estimate is the rate at which diversification rate shifts occur (shift rate). Despite this, branch-specific diversification rate estimates are precise and nearly unbiased.

evolutionary biology↗

bioRxiv2023

Commonly used Bayesian diversification-rate models produce biologically meaningful differences on empirical phylogenies

Identifying along which lineages shifts in diversification rates occur is a central goal of comparative phylogenetics; these shifts may coincide with key evolutionary events such as the development of novel morphological characters, the acquisition of adaptive traits, polyploidization or other structural genomic changes, or dispersal to a new habitat and subsequent increase in environmental niche space. However, while multiple methods now exist to estimate diversification rates and identify shifts using phylogenetic topologies, the appropriate use and accuracy of these methods is hotly debated. Here we test whether five Bayesian methods--Bayesian Analysis of Macroevolutionary Mixtures (BAMM), two implementations of the Lineage-Specific Birth-Death-Shift model (LSBDS and PESTO), the approximate Multi-Type Birth-Death model (MTBD; implemented in BEAST2), and the cladogenetic diversification rate shift model (CLaDS2)--produce comparable results. We apply each of these methods to a set of 65 empirical time-calibrated phylogenies and compare inferences of speciation rate, extinction rate, and net diversification rate. We find that the five methods often infer different speciation, extinction, and net-diversification rates. Consequently, these different estimates may lead to different interpretations of the macroevolutionary dynamics. The different estimates can be attributed to fundamental differences among the compared models. Therefore, the inference of shifts in diver-sification rates is strongly method-dependent. We advise biologists to apply multiple methods to test the robustness of the conclusions or to carefully select the method based on the validity of the underlying model assumptions to their particular empirical system. Lay SummaryUnderstanding why some groups of organisms have more species than others is key to understanding the origin of biodiversity. Theory and empirical evidence suggest that multiple distinct historical events--such as the evolution of particular morphological features (e.g., the flower, the tetrapod limb) and competition amongst species--can produce this pattern of divergent species richness. Identifying when and where on the tree of life shifts in diversification rates occur is important for explaining the origin of modern-day biodiversity and understanding how disparity among species evolves. Several statistical methods have been developed to infer diversification rates and identify these shifts. While these methods each attempt to make inferences about changes in the tempo of diversification, they differ in their underlying statistical models and assumptions. Here we test if these methods draw similar conclusions using a dataset of 65 time-calibrated phylogenies from across multicellular life. We find that inferences of where rate shifts occur strongly depends on the chosen method. Therefore, biologists should choose the model whose assumptions they believe to be the most valid and justify their model choice a priori, or consider using several independent methods to test an evolutionary hypothesis.

evolutionary biology↗

bioRxiv2022

Rapidly changing speciation and extinction rates can be inferred in spite of non-identifiability

The birth-death model is commonly used to infer speciation and extinction rates by fitting the model to extant phylogenetic trees. Recently, it was demonstrated that speciation and extinction rates are not identifiable if the rates are allowed to vary freely over time. The group of birth-death models that are not identifiable from each other is called a congruence class. Every model in a congruence class is equally likely, and there is no statistical evidence that can be used to favor one over the other. This issue has led researchers to question if and what patterns can reliably be inferred, and whether time-variable birth-death models should be fitted at all. We explore the congruence class in the context of several empirical phylogenies as well as hypothetical scenarios and summarize shared patterns in the congruence class. We show that strong directional trends in speciation and extinction rates are ubiquitous among most models within the congruence class, and conclude that inference of strong directional trends is therefore robust. Conversely, estimates of constant rates or gentle slopes are not robust and must be treated with caution. Additionally, most conflict in trends within the congruence class is observed near the present, implying that very recent rate changes should be treated carefully. Interestingly, the space of valid speciation rates is limited in contrast to extinction rates, which are less constrained. These results provide further evidence and insights that speciation rates can be estimated more reliably than extinction rates.

evolutionary biology↗

bioRxiv2022

ACDC: Analysis of Congruent Diversification Classes

1. Diversification rates inferred from phylogenies are not identifiable. There are infinitely many combinations of speciation and extinction rate functions that have the exact same likelihood score for a given phylogeny, building a congruence class. The specific shape and characteristics of such congruence classes have not yet been studied. Whether speciation and extinction rate functions within a congruence class share common features is also not known. 2. Instead of striving to make the diversification rates identifiable, we can embrace their inherent non-identifiable nature. We use two different approaches to explore a congruence class: (i) testing of specific alternative hypotheses, and (ii) randomly sampling alternative rate function within the congruence class. 3. Our methods are implemented in the open-source R package ACDC (https://github.com/afmagee/ACDC). ACDC provides a flexible approach to explore the congruence class and provides summaries of rate functions within a congruence class. The summaries can highlight common trends, i.e. increasing, flat or decreasing rates. Although there are infinitely many equally likely diversification rate functions, these can share common features. ACDC can be used to assess if diversification rate patterns are robust despite non-identifiability. In our example, we clearly identify three phases of diversification rate changes that are common among all models in the congruence class. Thus, congruence classes are not necessarily a problem for studying historical patterns of biodiversity from phylogenies.

evolutionary biology↗

bioRxiv2021

RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes

O_LIStatistical phylogenetic methods are the foundation for a wide range of evolutionary and epidemiological studies. However, as these methods grow increasingly complex, users often encounter significant challenges with summarizing, visualizing, and communicating their key results. C_LIO_LIWe present RevGadgets, an R package for creating publication-quality figures from the results of a large variety of phylogenetic analyses performed in RevBayes (and other phylogenetic software packages). C_LIO_LIWe demonstrate how to use RevGadgets through a set of vignettes that cover the most common use cases that researchers will encounter. C_LIO_LIRevGadgets is an open-source, extensible package that will continue to evolve in parallel with RevBayes, helping researchers to make sense of and communicate the results of a diverse array of analyses. C_LI [Bayesian phylogenetics, data visualization, R, RevBayes]

evolutionary biology↗

bioRxiv2020

Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps

We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences [TMO]) in an automated procedure. We compare these results with data from the Ocean Biogeographic Information System (OBIS). Using OBIS and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined OBIS and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for cheilostomes for the first time, with peaks in the temperate zones. 79% of the georeferenced species we retrieved from TMO (N = 1780) and OBIS (N = 2453) are non-overlapping and underestimate known species richness, even in combination. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that latitudinal species richness patterns deviate from the canonical LDG. Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.

ecology↗