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Vertebrate Gene Expression and Other Properties Don't Support a "Phylotypic" Stage

In the past, we've discussed evidence from the physical features of embryological development (in both space and time) that contradict the supposed "pharyngula" or "phylotypic" stage of vertebrate development, often cited as evidence for common ancestry. The idea is that vertebrates go through a similar stage midway through development, and the similarities of this mid-stage are said to reflect the common ancestry of vertebrates. Indeed the pharyngula, or phylotpyic stage is such an icon of Darwinian argumentation that the popular atheist blogger PZ Myers named his blog after it.

However, a new article in PLoS Genetics, "The Hourglass and the Early Conservation Models -- Co-Existing Patterns of Developmental Constraints in Vertebrates," shows that even an analysis of the genome based on Darwinian assumptions fails to confirm many predictions of the "phylotypic" stage. The implication is that, as other papers have more explicitly suggested, the phylotypic stage may not clearly exist. As the paper explains:

During development, vertebrate embryos pass through a "phylotypic" stage, during which their morphology is most similar between different species. This gave rise to the hourglass model, which predicts the highest developmental constraints during mid-embryogenesis. In the last decade, a large effort has been made to uncover the relation between developmental constraints and the evolution of the genome. Several studies reported gene characteristics that change according to the hourglass model, e.g. sequence conservation, age, or expression. Here, we first show that some of the previous conclusions do not hold out under detailed analysis of the data.

(Barbara Piasecka, PaweĊ‚ Lichocki, Sebastien Moretti, Sven Bergmann, Marc Robinson-Rechavi, "The Hourglass and the Early Conservation Models -- Co-Existing Patterns of Developmental Constraints in Vertebrates Barbara Piasecka," PLoS Genetics, Vol. 9(4) (April, 2013).)

The researchers looked at zebrafish genes that are highly expressed at particular stages of development, and based upon those findings assigned them to one of seven developmental stages, from the beginning to the end of embryological development. Two of those seven stages represented the phylotypic stage.

As you can see in the passage I cited above, the "hourglass model" of development predicts that the highest degree of "conservation" (i.e., the least amount of evolution) between genes in a stage should exist for those genes highly expressed during the phylotypic stage. The paper of course assumed common descent and a Darwinian evolutionary history of the genome, and then used these assumptions to attempt to assess the degree of evolution that had taken place in the genes that were overexpressed at each developmental stage. To do this, the study looked at various properties of the genes from each stage: (a) whether the genes had experienced selective pressure (i.e., conservation of gene sequence), (b) the approximate age of the genes, (c) gene family size, (d) constraints on gene expression, and (e) conservation of regulatory regions.

As the authors explained, their "goal was to study developmental constraints acting on various gene properties in vertebrates," since the "hourglass model" predicts maximum constraints on the phylotypic stage. But this is not what they found. Keeping the numbering of the properties they looked at the same as above, they found:

  • (a) Gene sequence: "There is notably no evidence for change in selective pressure acting on sequences of protein-coding genes (i.e., dN/dS) over development."

  • (b) Gene age: "We do not find any support for the hypothesis that the phylotypic stage would be characterized by the oldest transcriptome."

  • (c) Gene family size: This property did not support the phylotypic stage, but instead supported the "early conservation" model where they found "early stages are less prone to tolerate both gene duplication ... and gene introduction."

  • (d) Gene expression: "Unfortunately, the available data does not allow a strong conclusion concerning the conservation of expression ... despite the probable importance of this feature in the evolution of development."

  • (e) Conservation of regulatory regions: For this one property, they did find support for conservation in the phylotypic stage, as Hox genes (long known to be highly expressed during the phylotypic stage) are highly conserved. They thus found: "The sequence of regulatory regions is most conserved for genes expressed in mid-development, consistent with the hourglass model."
Their results not only failed to support strong constraints on the phylotypic stage, but instead found that there was often no clear pattern of constraints: "Several features do not show any significant pattern over embryonic development, often in contradiction to previous reports." It seems not only do many physical characteristics of embryological development fail to support a "phylotypic stage," but many properties of genes fail to do so as well.