Revisiting Past Biodiversity with the divDyn R Package

Post provided by ÁDÁM T. KOCSIS

The source of occurrence data: fossil collections (Early Jurassic ammonites in the collection of the University of Erlangen-Nuremberg, photo by Konstantin Frisch)

The source of occurrence data: fossil collections (photo by Konstantin Frisch).

To find out about changes in ancient ecosystems we need to analyse fossil databases that register the taxonomy and stratigraphic (temporal) positions of fossils. These data can be used to detect changes of taxonomic diversity and to draft time series of originations and extinctions.

The story would be so simple if it wasn’t the effects of heterogeneous and incomplete sampling: the white spots in our understanding of where and when species lived exactly. This phenomenon decreases the fidelity of face-value patterns extracted from the fossil record, making them less reliable. It must be considered if we want to get a glimpse into the biology or the distribution of life in space and time. Naturally, several metrics have been proposed to overcome this problem, each claiming to accurately depict the patterns of ancient life. Continue reading

Phylogenetic Tip Rates: How Well Can We Estimate Diversification?

Post provided by Pascal Title and Dan Rabosky

Analyzing diversification rate heterogeneity across phylogenies allows us to explore all manner of questions, including why Australia has such an incredible diversity of lizards and snakes.

Analyzing diversification rate heterogeneity across phylogenies allows us to explore all manner of questions, including why Australia has such an incredible diversity of lizards and snakes.

Within the tree of life there are differences in speciation and extinction rates over time and across lineages. Biologists have long been interested in how speciation rates change as a function of ecological opportunity or whether key innovations lead to increases in the rate of speciation. Exploring this rate variation and examining how clades differ in terms of their diversification dynamics can help us to understand why species diversity varies so dramatically in time and space. Learning more about the relationship between traits and diversification rates is especially important because it has the potential to reveal the causes of pervasive variation in species richness among clades and across geographic regions.

Several different classes of methods are available for studying the effects of species traits on lineage diversification rates. These include state-dependent diversification models (e.g., BiSSE, QuaSSE, HiSSE) and several non-model-based approaches. In our article – ‘Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates?’ – we assessed the accuracy of a number of model-free metrics (the DR statistic, node density metric, inverse of terminal branch lengths) and model-based approaches (Bayesian Analysis of Macroevolutionary Mixtures, BAMM) to determine how they perform under a variety of different types of rate heterogeneity. The “tip rates” using these approaches have become widely used for a few reasons, including ease of computation and how easy it is to pair them with other types of data. Continue reading