Albert Ch. Soewongsono

Today at WashU’s EEB seminar, I presented a new species diversification model that incorporates regional species diversity into rates of evolution through time (a joint work w/ @landismj.bsky.social).

Slides here: sites.google.com/view/albert-...

Preprint hopefully will be here this month #evobio

Thank you! It was great meeting with you again 😊

[11/11] You can actually see this from their phylogenetic tree. For example, it has long tip branches, indicating a decreasing rate of diversification. Moreover, clades are grouped to a specific geographical ranges, indicating no back-dispersal events.

Fig source: www.nature.com/articles/s41...

[10/11] Applying to an empirical system of previously-published tree of 38 extant cloud forest-dwelling Viburnum plants, our model supports the scenario in which local species richness played a major role in decreasing both within-region speciation rate and dispersal rate into occupied regions.

[9/11] As an inference model, we use phyddle (phyddle.org), which is a software for phylogenetic analysis using deep learning, for parameter estimation and model selection.

[8/11] Since we can analytically determine this point from a set of parameter values, we can then confirm the theory by simulating phylogenetic trees using the same parameter set.

Here is an example where we show it reaches a carrying capacity of 100 extant species.

[7/11] This leads back to the equilibrium theory of island biogeography by MacArthur and Wilson. Here, we are interested in the intersection point between sum of rates that correspond to species influx in a particular region and sum of rates that correspond to species outflux from the same region.

[6/11] For example, adding density-dependent component to the extinction event creates a distinct branching pattern on tree and distribution of species ranges through time.

Here, we can see that the number of locally co-existing species reaches an equilibrium phase (carrying capacity).

[5/11] Our model is flexible in a way that it can associate species richness across many cladogenetic and anagenetic events, such as within-region speciation, between-region speciation, species dispersal, and extinction.

It forms a general class of density-dependent biogeographic models.

[4/11] DDGeoSSE is a a fully generative and event-based model, meaning it can be used to simulate phylogenetic trees under a range of density-dependent scenarios.

[3/11] A recent review paper published in 2024 (www.annualreviews.org/content/jour...) showing the need of linking state-dependent SSE, diversity-dependent, and geographic model together.

[2/11] The biological question we want to answer: How does species diversity influence diversification in biogeographic context?

That means, we would want a biogeographic model that associates local species richness (diversity-dependence) and state-dependent rates.

[1/11] A quick rundown to our density-dependent biogeographic model of species diversification below:

P.S. Preprint coming up soon! #Evol2025

What a blast attending my first in-person Evolution meetings!
Had the opportunity to present our work on:

1. A new biogeographic model of species diversification that accounts for species richness.

2. Phylogeography model for infectious disease transmission with visitor dynamics.

#Evol2025

Honored to be elected as a member of the
@sigmaxi.bsky.social
- one of the oldest honor societies in science.

Thank you to the two anonymous committee members for the nomination!

About 11 years ago, I received financial support from Van-Deventer Maas Indonesia (VDMI) to fund my undergraduate studies.

Fast-forward to 2025, I will be sharing about living and working abroad from a perspective of an international scholar.

Thank you VDMI for organizing this event!

#outreach

Matrix-analytic Methods for the Evolution of Species Trees, Gene Trees, and Their Reconciliation - Methodology and Computing in Applied Probability We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree. In this paper we present a method, where for a given choice of parameters, we are abl...

Our article on "matrix-analytic methods for the evolution of species trees, gene trees, and their reconciliation" is recently published on Methodology and Computing in Applied Probability journal. #evobio

Link here: link.springer.com/article/10.1...

Earlier this year my advisor @landismj.bsky.social and I published this cool work at BMB; looking at applying diffusion in macroevolutionary context for state-dependent diversification models to learn about evolutionary patterns that these models produce. #evobio

www.smb.org/news/13402507

Just recently joined Bluesky to connect with phylo community here. So, here is my first trace on this platform :)

I am a postdoc in Landis lab at WashU and a mathematician by training with interests in models of species diversification and phylodynamics. #evobio

sites.google.com/view/albert-...