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Researchers: “Phylogenetic comparative methods (PCMs) “deeply misleading,” “have sowed confusion”

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Abstract: As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have been framed as a solution to this problem. In this paper, we argue that this way of thinking about PCMs is deeply misleading. Not only has this sowed widespread confusion in the literature about what PCMs are doing but has led us to develop methods that are susceptible to the very thing we sought to build defenses against — unreplicated evolutionary events. Through three Case Studies, we demonstrate that the susceptibility to singular events is indeed a recurring problem in comparative biology that links several seemingly unrelated controversies. In each Case Study we propose a potential solution to the problem. While the details of our proposed solutions differ, they share a common theme: unifying hypothesis testing with data-driven approaches (which we term “phylogenetic natural history”) to disentangle the impact of singular evolutionary events from that of the factors we are investigating. More broadly, we argue that our field has, at times, been sloppy when weighing evidence in support of causal hypotheses. We suggest that one way to refine our inferences is to re-imagine phylogenies as probabilistic graphical models; adopting this way of thinking will help clarify precisely what we are testing and what evidence supports our claims. (paywall) – Rethinking phylogenetic comparative methods Josef C Uyeda Rosana Zenil-Ferguson Matthew W Pennell, Systematic Biology, syy031, https://doi.org/10.1093/sysbio/syy031, 25 April 2018

Hat tip: Pos-Darwinista

6 Replies to “Researchers: “Phylogenetic comparative methods (PCMs) “deeply misleading,” “have sowed confusion”

  1. 1
    PaV says:

    Here’s the pdf

    From the Abstract:

    We suggest that one way to refine our inferences is to re-imagine phylogenies as probabilistic graphical models;

    I can imagine lots of things–like flying pigs.

  2. 2
    vmahuna says:

    “the impact of singular evolutionary events”

    Isn’t that some kind of back-construction? That is, a biologist trips over root and discovers that 2 species of oak tree are both, well, OAK TREES. The biologist then invents a series of “evolutionary events”, which were never properly recorded on the 10 million BC edition of Wikipedia. So clearly a now extinct prehistoric sabre-toothed cave tree “adapted” to the Evolutionary Event #1 by evolving down Path 1A. And then later adapted to Evolutionary Event #2 by growing a shorter beak and longer canines…

  3. 3
    bornagain77 says:

    From Leisola’s new book “Heretic”

    In 1965 one of the most important scentist of the last century, Linus Pauling, and biologist Emil Zuckerkandl, considered by some as the father of molecular biology, suggested a way that macroevolution could be tested and proved; If th comparison of anatomical and DNA sequences led to the same family tree of organisms, this would be strong eidence for macroevolution. According to them, only evolution would explain the convergence of these two independent chains of evidence. By implication, the opposite finding would count against macroevolution.
    So what were the results? Over the past 28 years, experimental evidence has revealed that family trees based on anatomical features contradict family trees based on molecular similarities, and at many points. They do not converge. Just as troubling for the idea of macroevolution. family trees based on different molecules yeild conflicting and contradictory family trees. As a 2012 paper published in Biological Reviews of the Cambridge philosophical Society reported, “Incongruence between phylogenies derived from morphological versus molecular analysis, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species”.
    Another paper published the following year in the journal Nature, highlighted the extent of the problem. The authers compared 1,070 genes in twenty different yeasts and got 1,070 different trees. An article in Quanta magazine, reporting on the paper in Nature, highlighted he challenge these findings pose for the Darwinian tree of life:

    “According to a new study partly focused on yeast, the conflicting picture from individual genes is even broader than scientists suspected. “They report that every single one of the 1,070 genes conflicts somewhat,” said Michael Donoghue, an evolutionary biologist at Yale who was not involved in the study. “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 [types of] yeast,” he said.”
    A New Approach to Building the Tree of Life – June 2013

    These results aren’t what we should expect from a process of blind, gradual macroevolution.,,,,

    Evolutionary biologist Seirian Sumner describes the emerging problem,

    “These data are telling us to put to bed the idea that all life is underlain by a common toolkit of conserved genes. Instead, we need to turn our attention to the role of genomic novelty in the evolution of phenotypic diversity and innovation.,,,
    We can now sequence de novo the genomes and transcriptomes (the genes expressed at any one time/place) of any organism. We have sequence data for algae, pythons, green sea turtles, puffer fish, pied flycatchers, platypus, koala, bonobos, giant pandas, bottle-nosed dolphins, leafcutter ants, monarch butterfly, pacific oysters, leeches…the list is growing exponentially. And each new genome brings with it a suit of unique genes. Twenty percent of genes in nematodes are unique. Each lineage of ants contains about 4000 novel genes, but only 64 of these are conserved across all seven ant genomes sequenced so far.
    Many of these unique (‘novel’) genes are proving important in the evolution of biological innovations. Morphological differences between closely related fresh water polyps, Hydra, can be attributed to a small group of novel genes. Novel genes are emerging as important in the worker castes of bees, wasps and ants. Newt-specific genes may play a role in their amazing tissue regenerative powers.”
    – WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? – Life Evolves Via A Shared Genetic Toolkit
    Seirian Sumner
    – Matti Leisola, Heretic (2018), pages 83-84 and 118-119

  4. 4
    Erasmus Wiffball says:

    Isn’t it amazing that this debunking of evolutionary theory got by the notorious

    Associate Editor: Nicholas Matzke,

    formerly of the National Center for Science Education? Surely the LORD has had a hand in this.

  5. 5
    Bob O'H says:

    Erasmus Wiffball – how does this paper debunk evolutionary theory?

  6. 6
    Mung says:

    Bob O’H. That’s sarcasm. Don’t be giving our good friend Erasmus a hard time. 🙂

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