Stochastic Morphometry and
Center for Computational Evolutionary Morphometrics

Stefan Sommer, Rasmus Nielsen, Christy Hipsley, Mads Nielsen

UCPH Data+

Phylogenetics

Darwin 1859

Phylogenetics - Estimating Trees

Until ca. 1980: morphological characters


After ca. 1980: DNA

Corbett-Deitig et al. MBE 37: 160-1614

Estimating trees using DNA

  • Modeling evolution using Markov chain with state space = {A, C, T, G}.
  • Transition probabilities of the process is calculated by exponentiating infinitesimal rate matrix.
  • Likelihood calculated using Felsenstein’s pruning algorithm and then numerically optimized or used in Bayesian inference.
  • Genomic sequencing provides millions of observations for accurate estimation of trees.

A return to morphology

Questions:

Rules of morphological change

Drivers of morphological change (ecology, historical contingency)

Mechanisms of morphological change (genetic basis)

Unsolved problem: shape

Current state-of-the-art:

Use of landmarks.

Procrustes alignment.

PCA analyses.

Assume top PCs evolve according to a Brownian motion process.

Then use of methods similar to DNA analyses for computation.

Challenges:

Loss of information in the use of landmarks

Loss of information in linearization of nonlinear shape space

Loss of information in only using the top PCs
Lack of biological interpretability and justification.

Lack of modeling flexibility.

State-of-the-art: full shape is reduced to selected landmarks

Unsolved problem: shape

State-of-the-art: We have high-res digital morphology images but we cannot use the full shape information

  • How to model evolution of shape?
  • What is the state-space?
  • What probability distribution governs the rules of change?

How we do it: Shape analysis

\( \phi \) warp of domain \(\Omega\) (2D or 3D space)

landmarks: \(s=(x_1,\ldots,x_n)\)      curves: \(s: \mathbb S^1\to\mathbb R^2\)

surfaces: \(s: \mathbb S^2\to\mathbb R^3\)

\( \phi \)

On growth and form, 1917
D'Arcy Thompson

Stochastically evolving shapes

shape \(s_0\)

shape \(s_1\)

stoch. evolution \(s_0\rightarrow s_1\)

dx_t= -\frac12g(x_t)^{kl}\Gamma(x_t)_{kl}dt + \sqrt{g(x_t)^*}dW_t

Riemannian Brownian motion:

Shapes in phylogenetics

  1. probabilistic model
  2. tree pruning for shapes
  3. stochastic shape matching
  4. MCMC / variational inference:
    1. likelihoods
    2. parameter estimation
    3. gene/character covariance
    4. interpolation
    5. hypothesis testing
    6. tree inference

inferring the laws of morphological change

Inference: Felsenstein's pruning in modern terms

Brown. motion

Brown. motion

Brown. motion

Brown. motion

branch (independent children)

incorporate leaf observations \(x_{V_T}\) into probabilistic model:
\(p(X_t|x_{V_T})\)

Doob’s h-transform

\(h_s(x)=\prod_{t\in\mathrm{ch(s)}}h_{s\to t}(x)\)

conditioned process \(X^*_t\)

approximations \(\tilde{h}\)

guided process \(X^\circ_t\)

 

Impact across biology:

Fluctuating asymmetry in butterflies

4 cases: Phylogenetics and morphology is foundation for much of bioscience

Impact across biology:

Test hypotheses on bird beak evolution genotype/phenotype associations

Impact across biology:
Canid evolution and dog domestication

Impact across biology:
Refine palaeohominid tree

Synergy between phylogenetics, shape analysis, morphology and image analysis

Rasmus Nielsen
GLOBE UCPH, Berkeley
Phylogenetics

Stefan Sommer
DIKU UCPH
Shape analysis

Christy Hipsley
BIO UCPH
Morphology

Mads Nielsen
DIKU UCPH
Image analysis

Collaborators:

Anders Jordan

Natural History Museum of Denmark

Tom Gilbert

GLOBE

Frido Welker

GLOBE

Guojie Zhang

UCPH BIO

Elizabeth Baker, Sofia Stroustrup, Marcus Teller, Lili Bao, Gefan Yang, Liwei Hu, Michael Severinsen, Chao Zhang,

Christine Sarah Andersen + more to come

Josefin Stiller

UCPH BIO

Stochastic Morphometry and CCEM

By Stefan Sommer

Stochastic Morphometry and CCEM

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