Pseudo Dollo models for the evolution of binary characters along a tree

Bouckaert, R.; Robbeets, M.

doi:10.1101/207571

Home/Archive/bioRxiv

bioRxiv · 10.1101/207571

Pseudo Dollo models for the evolution of binary characters along a tree

Bouckaert, R.·Robbeets, M.

View original source ↗Export metadata ↓

Abstract

The stochastic Dollo model is a model for capturing evolution of features, for example cognate data in language evolution. However, it is rather sensitive to borrowing events, coding errors, semantic shift and other anomalies, so other models, in particular the covarion model, tends to have a better fit to the data. Here, we introduce the pseudo Dollo model, a model of character evolution along a tree that can be formulated as a three-state continuous time Markov chain (CTMC) model. The initial state represent absence of a feature, then a birth event allows the feature to be present. A death event can follow so that the feature becomes absent again. However, no new birth events are allowed after a death event has taken place.\n\nWe examine the model in a fully Bayesian setting, and demonstrate it can have a better fit than some of the popular alternative models on some real world datasets. Some variations on the pseudo Dollo model are introduced as well, including the multi-state pseudo Dollo model and pseudo Dollo covarion model.\n\nThe model is implemented in open source software Babel, a package to BEAST [2] licensed under LGPL. A user friendly way to set up an analysis is available through BEAUti, the graphical user interface of BEAST.

Explore related subjects

evolutionary biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Bouckaert, R., Robbeets, M.. 2017-10-23. Pseudo Dollo models for the evolution of binary characters along a tree. https://doi.org/10.1101/207571

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Efficient growth factor production stabilizes cooperation in a cellular public goods game

Eukaryotic cells secrete growth factors that facilitate the proliferation and survival of neighboring cells in a coordinated manner essential for tissue development, repair, and homeostasis. However, mutant cells that fail to produce these factors may exploit the benefits provided by neighboring producers, thereby gaining a proliferative advantage that could lead to the extinction of the producer clone. Evolutionary theory predicts that preventing this "tragedy of the commons" requires a fixed spatial structure or other mechanisms that enable cells to interact preferentially with copies of themselves. Contrary to this expectation, we found that, in competition experiments, cells producing the diffusible growth factor interleukin-3 (IL3) resist invasion by non-producing mutant cells even in well-mixed populations, and that non-producers are driven to extinction instead. Using evolutionary game theory, we show that this outcome arises when the cost-to-benefit ratio of growth factor production falls below a critical threshold. We derive this tipping point analytically across the full parameter space of benefit function shape and group size and confirm that IL3 production in our experimental system satisfies this condition with a production cost less than 0.1% of the benefit conferred. These results demonstrate that efficient public good production alone can resolve the tragedy of the commons in populations of cells, and potentially in other biological systems.

evolutionary biology↗

bioRxiv2026

Repeated Transitions in Migratory Behavior Across a Songbird Radiation Are Not Driven by Selection on Shared Variation in Candidate Genes

Understanding the mechanisms facilitating the repeated evolution of traits is a core question in evolutionary biology. While repeated evolution has been observed across many systems, behavioral phenotypes have been less well studied than morphological traits. Migration is a behavioral adaptation to seasonality that has evolved independently in many animals, and repeated gains and losses of migratory behavior have been especially prevalent throughout the diversification of birds. While migratory traits are heritable in many taxa and candidate genes underlying intraspecific variation in migratory behavior have been identified, whether similar genetic changes are responsible for the repeated evolution of migration remains poorly understood. We used a phylogenomic approach to investigate the relationship between variation in candidate genes and migratory propensity across nearly all species in the parulid warbler radiation (n = 101), a group of songbirds in which migratory behavior has been lost and gained multiple times. Comparisons of candidate gene tree topologies to the parulid warbler species tree revealed cases of discordance, though these were explained by differences in the number of phylogenetically informative sites among genes rather than by elevated genetic similarity among species sharing migratory strategies. Testing models of coding sequence evolution identified sites with elevated dN/dS in five candidate genes, suggestive of positive selection; however, variation at these sites showed no clear association with migratory strategy, nor did we detect recurrent selection across lineages where transitions in migratory behavior most likely occurred. Together, these results contradict the hypothesis that selection on shared variation (ancestral polymorphisms or introgressed alleles) facilitated the repeated evolution of migration in this clade.

evolutionary biology↗

bioRxiv2026

Polygenic evolution towards a morning chronotype in modern humans

Chronotype is a behavioural phenotype, and its phenotypic trend is considered to change at higher latitudes. In the current study, we performed a polygenic assessment of chronotype trend using associated single nucleotide polymorphisms identified by a genome wide-association study. We found that the phenotypic trend towards morningness increased drastically during the migration of anatomically modern humans above 20 degrees north. Furthermore, two types of latitudinal selection of morningness alleles contributed to establishing the trend towards the morning chronotype at higher latitudes. We propose that the trend towards morningness is stronger in present-day modern humans living above 20 degrees north than in Neanderthals.

evolutionary biology↗