Stochastic simulation and evolution of morphology-towards a nomothetic paleontology
Blog Author: Altangerel Tsogtsaikhan
David M. Raup
- Professor of Paleontology at the University of Chicago
- Taught at Caltech, John Hopkins, and the University of Rochester
- Visiting professor Tübingen, Germany, and faculty of the College of the Virgin Island.
- MA, and Ph.D. from the Harvard University (geology, paleontology, and biology)
- Curator and dean of science at the Field Museum of Natural History in Chicago
He was born on April 24th, 1933 in Boston. Fossil records attracted him as a young kid. Through his career, he was involved with many joint programs in biology promoting paleontologists in marine environments. His research questions were mainly focused on biodiversity and extinction patterns of organisms. He died on July 9th, 2015.
Stephen Jay Gould
- Gould was born in Queens, New York on September 10th, 1941. He was raised in Bayside, Queens. He was taken to the Dinosaurs Hall in the American Museum of Natural History where he first saw the T. rex and ever since he wanted to become a paleontologist.
- Professor of geology at Harvard, and curator of invertebrate paleontology the Institutions Museum of Comparative Zoology, and American Museum of Natural History, New York.
- In 1963, graduated with a double major in geology and philosophy at Antioch College
- Also, he studied at the University of Leeds in the UK.
- He earned his Ph.D. at Columbia University in 1967.
His field of interests involved Paleontology, evolutionary biology, history of science. He made significant contributions to evolutionary developmental biology, especially through his work Ontogeny and Phylogeny. He was a champion of biological constraints, and against sociobiology criticizing his colleague E. O Wison by sending an open letter on "deterministic view of human society and human action". He also favored the arguments that evolution has no inherent drive towards long-term "progress" (not favoring ladder thinking". However, he never embraced cladistics as a method of investigating evolutionary lineages and process. Goud was considerably respected historian of science.
Raup, D. M., and S. J. Gould. 1974. Stochastic simulation and evolution of morphology-towards a nomothetic paleontology. Systematic Zoology 23: 305-322.
Background
The common methods of exploring relationships of species in biology are phylogenetic studies that use comparative analysis using species traits and characters to place their taxonomic order and status. It is common in paleontology. However, the assumption of uni-directional causes of the morphological order of evolutionary trees has been under debates for a long time. The main purpose of this research is to show artificial simulations can display similiar unidirectional selection patterns of morphological orders of evolutionary trees which are the results of evolution. Every occasion, the pattern was assumed for several decades brings a doubt of this patterns. Consideration of this uncertainty, the study aim to reveal some patterns by studying the order that can arise in a random system of change ran by the conventional assumptions of morphology, continuity, and equilibrium.
Methods: In this study, a stochastic simulation of randomly rotating or replacing morphological characters of the phylogenetic framework. A computer program simulated a hypothetical phylogeny by a computer program showing phyletic relationships of lineages using random numbers that generated predetermined probability values. Under the assumption of each morphology was independent, the presence or absence of morphological change has no influence to the topology of the tree. Ten hypothetical characters were used.
Results/Discussion: After running the computer program several times randomly with the same probability, the simulation produced well-ordered arrays of morphology having random change with no unidirectional selection. This concludes that the basic order of morphology on an evolutionary tree does not reflect any special biological process. Changing morphology behaves differently from the randomly-generated cladistic patterns. Clade quickly reached equilibrium. Steady changing characters are not common in the fossil record than computer simulations suggesting that in a long run, undirected selection may be the rule rather the exception of nature.
My question from this research is that how often we see this pattern with modern technological advances like phylogenetic programs. Also, how much of this findings is used in modern cladistic simulators. I find this paper is interesting but hard to read and engage with details to the main purpose of this research. An interesting topology of a phylogenetic tree shown in figure 1. The general pattern of this approach seems pretty similar to the jackknife simulation in statistics.
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ReplyDeleteI thought this study was elegant and the patterns they found were really interesting. Some parts were a bit difficult to follow, but on the whole, the authors did a good job of describing what they found and why they found it. When I first started reading, I didn't see how a random process could lead to such orderly variation between clades, but after finishing the paper, it makes sense to me.
ReplyDeleteI wonder how people reacted to this paper. I'm guessing a lot of evolutionary biologists were upset.
This paper is really hard to read. There are a lot of terms and references that I don't understand. Hopefully listening to the discussion in class would clear up some of these things for me.
ReplyDeleteI liked this paper, it shows the importance of null models in understanding biological processes. Like Maria, I didn´t expect the appearance of patterns such as the almost complete differentiation in morphological space of the clades from a completely random character evolution.
ReplyDeleteI think the patterns in character correlation are a very good example of why we need to account for phylogeny in comparative analyses.
I appreciated that this paper did not disregard unidirectional selection but recognized that random selection can produce similar results, suggesting both play a large role.
ReplyDeleteI agree with Lam about this being a more difficult paper to read. For example, I feel like they touched on unidirectional selection... but not enough so I just assumed that meant selection for one thing... Is that correct?
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DeleteThis paper can be really hard to understand specific components if you haven't taken classes for this. Life 121 first touch this but you have to take a specific class to fully understand this. I took two semesters on this and I still have hard time some of the interpretation parts like character mapping and hybridization.
ReplyDeleteVery interesting paper. I agree with Sebastian, this proves to be another example in which null models are useful. I am still confused about some parts of the arguments, but hopefully they will be cleared later in class.
ReplyDeleteFigure 1 is the first time I've seen phylogenies presented with this sort of structure, pretty interesting. Ditto on the vernacular, I'm interested to hear a distillation of the paper.
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