Biology subjects

Goldberg, E. E.

Publications and source records attributed to Goldberg, E. E..

8 recordsLinked to original sources

bioRxiv2026

Are theoretical advances in distance-based tree learning practical for phylogenetic inference?

The phylogenetic tree of relatedness for species, viral samples, or other biological taxa is essential information for all fields of evolutionary biology. Many different statistical and computational tools for phylogeny inference are used by practicing biologists, but none take advantage of a body of theoretical work on fast-converging algorithms that guarantee correctness with high probability under particular conditions. Here, we assess the utility of one of the most advanced of these algorithms when applied in reasonable biological situations. Our simulation study shows that realistic datasets will often not meet the assumptions of the algorithm, but also that the results are relatively robust to this problem. We additionally provide guidance on how the algorithm can be deployed when the true tree is not known, which is essential for any real-world application. Overall, our intention is to bring a class of methods to the attention of the phylogenetics community, and to make the algorithmic community aware of the needs of practicing biologists.

evolutionary biology↗

bioRxiv2023

Modeling the evolution of segment trees reveals deficiencies in current inferential methods for genomic reassortment

Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Because large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded. In this paper, we argue that, in general, the number and pattern of reassortment events are not identifiable from segment trees alone, even with theoretically ideal data. We call this fact the fundamental problem of reassortment, which we illustrate using the concept of the first-infection tree, a typically but not always counterfactual genealogy that would have been observed in the segment trees had no reassortment occurred. Further, we illustrate four additional problems that can arise logically in the inference of reassortment events and show, using simulated data, that these problems are not rare and can potentially distort our perception of reassortment even in small data sets. Finally, we discuss how existing methods can be augmented or adapted to account for not only the fundamental problem of reassortment but also the four additional situations that can complicate the inference of reassortment.

evolutionary biology↗

bioRxiv2023

Inferring viral transmission time from phylogenies for known transmission pairs

When the time of an HIV transmission event is unknown, methods to identify it from virus genetic data can reveal the circumstances that enable transmission. We developed a single-parameter Markov model to infer transmission time from an HIV phylogeny constructed of multiple virus sequences from people in a transmission pair. Our method finds the statistical support for transmission occurring in different possible time slices. We compared our time-slice model results to previously-described methods: a tree-based logical transmission interval, a simple parsimony-like rules-based method, and a more complex coalescent model. Across simulations with multiple transmitted lineages, different transmission times relative to the sources infection, and different sampling times relative to transmission, we found that overall our time-slice model provided accurate and narrower estimates of the time of transmission. We also identified situations when transmission time or direction was difficult to estimate by any method, particularly when transmission occurred long after the source was infected and when sampling occurred long after transmission. Applying our model to real HIV transmission pairs showed some agreement with facts known from the case investigations. We also found, however, that uncertainty on the inferred transmission time was driven more by uncertainty from time-calibration of the phylogeny than from the model inference itself. Encouragingly, comparable performance of the Markov time-slice model and the coalescent model--which make use of different information within a tree--suggests that a new method remains to be described that will make full use of the topology and node times for improved transmission time inference.

evolutionary biology↗

bioRxiv2023

adequaSSE: Model Adequacy Testing for Trait-Dependent Diversification Models

The presence of large variation in speciation and extinctin rates across the tree of life has long been hypothesized to be driven by the evolution of traits that affect diversification. To test such hypotheses, phylogenetic biologists have developed a wide class of state-dependent birth-death processes that jointly model trait evolution and the diversification process. However, it has since been shown that these models are sensitive to falsely linking traits to diversification. Here we present a Bayesian approach to test the adequacy of statedependent birth-death models by statistically checking whether they describe the variation observed in the data. Our method generates posterior predictive distributions for a suite of informative test statistics, providing a general framework for testing diversification processes and models of trait evolution. We simulate data sets under different violations of model assumptions and find that our approach successfully detects the inadequacy of the model for them. We further show that the manner in which a model fails to fit the data can reveal insights into the processes of trait evolution and diversification.

evolutionary biology↗

bioRxiv2019

INTERACTION BETWEEN PLOIDY, BREEDING SYSTEM, AND LINEAGE DIVERSIFICATION

If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be understood as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rate differences is complicated by the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) have been repeatedly suggested as possible drivers of differential diversification. We investigate the connections of these traits, including their interaction, to speciation and extinction rates in Solanaceae. We show that the effect of ploidy on diversification can be largely explained by its correlation with breeding system and that additional unknown factors, alongside breeding system, influence diversification rates. These results are largely robust to allowing for diploidization. Finally, we find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization.

evolutionary biology↗

bioRxiv2019

Diversification or collapse of self-incompatibility haplotypes as outcomes of evolutionary rescue

Self-incompatibility systems in angiosperms are exemplars of extreme allelic polymorphism maintained by long-term balancing selection. Pollen that shares an allele with the pollen recipient at the self-incompatibility locus is rejected, and this rejection favors rare alleles as well as preventing self-fertilization. Advances in molecular genetics reveal that an ancient, deeply conserved, and well-studied incompatibility system functions through multiple tightly linked genes encoding separate pollen-expressed F-box proteins and pistil-expressed ribonucleases. We show that certain recombinant haplotypes at the incompatibility locus can drive collapse in the number of incompatibility types. We use a modified evolutionary rescue model to calculate the relative probabilities of increase and collapse in number of incompatibility types given the initial collection of incompatibility haplotypes and the population rate of gene conversion. We find that expansion in haplotype number is possible when population size or the rate of gene conversion is large, but large contractions are likely otherwise. By iterating a Markov chain model derived from these expansion and collapse probabilities, we find that a stable haplotype number distribution in the realistic range of 10-40 is possible under plausible parameters. However, small or moderate-sized populations should be susceptible to substantial additional loss of haplotypes beyond those lost by chance during bottlenecks. The same processes that can generate many incompatibility haplotypes in large populations may therefore be crushing haplotype diversity in smaller populations.

evolutionary biology↗

bioRxiv2018

Memory in trait macroevolution

The history of a trait within a lineage may influence its future evolutionary trajectory, but macroevolutionary theory of this process is not well developed. For example, consider the simple binary trait of living in cave versus surface habitat. The longer a species has been cave-dwelling, the more may accumulated loss of vision, pigmentation, and defense restrict future adaptation if the species encounters the surface environment. However, the Markov model of discrete trait evolution that is widely adopted in phylogenetics does not allow the rate of cave-to-surface transition to decrease with longer duration as a cave-dweller. Here, we describe three models of evolution that remove this memory-less constraint, using a renewal process to generalize beyond the typical Poisson process of discrete trait macroevolution. We then show how the two-state renewal process can be used for inference, and we investigate the potential of phylogenetic comparative data to reveal different influences of trait duration, or memory in trait evolution. We hope that such approaches may open new avenues for modeling trait evolution and for broad comparative tests of hypotheses that some traits become entrenched.

evolutionary biology↗

bioRxiv2018

Heterosis from local drift load is likely insufficient to favor reversions to outcrossing

The evolutionary trajectory from cross-to self-fertilization is widely documented in nature, but results from several taxa also suggest that outcrossing may evolve in a formerly selfing population. Population genetic theory explains that selfing can evolve when its advantages overcome its immediate cost of inbreeding depression, but that this process will not run in reverse because a self-fertilizing population purges itself of inbreeding depression. That is, the primary short-term advantage of cross-fertilization over self-fertilization depends on the existence of deleterious alleles exposed upon inbreeding. Here, we explore whether outcrossing can evolve in selfing populations if allelic variation exists as divergence among populations. We consider two monomorphic populations of entirely self-fertilizing individuals, introduce a modifier allele that increases the rate of cross-fertilization, and investigate whether the heterosis among populations is sufficient for the modifier to invade and fix. We find that, despite an initial increase in the frequency of the outcrossing modifier, its fixation is possible only when populations harbor extremely large unique fixed genetic loads. These rare reversions to outcrossing become more likely as the load becomes more polygenic, or when the modifier appears on a rare background, such as by dispersal of an outcrossing genotype into a selfing population.

evolutionary biology↗