{"id":2399,"date":"2012-07-21T05:20:45","date_gmt":"2012-07-21T05:20:45","guid":{"rendered":"http:\/\/thetravellerslastjourney.com\/shai\/2018\/12\/08\/2034-revision-v1\/"},"modified":"2019-07-22T03:24:58","modified_gmt":"2019-07-22T03:24:58","slug":"phylotypic-stage","status":"publish","type":"post","link":"https:\/\/thetravellerslastjourney.com\/shai\/2012\/07\/21\/phylotypic-stage\/","title":{"rendered":"Phylotypic stage"},"content":{"rendered":"

I have two small\u00a0embryos preserved in alcohol<\/a>, that I forgot to\u00a0label<\/a>. At present I am unable to determine the genus to which they belong. They may be lizards, small birds, or even mammals.<\/p>\n

Karl von Baer<\/a>\u00a0(1828)<\/p>\n<\/blockquote>\n

The changes undergone by a developing\u00a0embryo<\/a>\u00a0forms an hourglass: early on embryos from different species vary significantly, later on, they converge to be similar, and finally, they diverge again, to develop into very different animals. This middle stage – the\u00a0phylotypic stage<\/strong>\u00a0– is when different animals from different threads of life, whether they be\u00a0zebrafish<\/a>\u00a0or\u00a0mice<\/a>\u00a0or\u00a0chicken<\/a>\u00a0all resemble each other.<\/p>\n

Why?<\/p>\n

Von Baer was a Christian believer, and saw the handiwork of God implicit in the similarities. The elegance of having different species appear similar before sprouting variations suggested a proto-plan to which each animal abided before going its own way. The nineteenth-century scientist was right to see a single plan maintained across the various species, but his explanation was too simple.<\/p>\n

In late 2010 the science journal\u00a0Nature<\/a><\/i>\u00a0published two studies that addressed this problem, here’s what they found:<\/p>\n

1.\u00a0Gene expression divergence recapitulates the developmental hourglass model.<\/h5>\n

The\u00a0central dogma of biology<\/a>\u00a0says that\u00a0DNA<\/a>\u00a0is the instruction manual. DNA is used by being made into\u00a0RNA<\/a>\u00a0and then into\u00a0protein<\/a>s.\u00a0All<\/a>\u00a0cells have the same DNA, but they use it differently. The DNA that is being read by a cell is being\u00a0expressed<\/a><\/strong>.<\/p>\n

Samples were taken from embryos at different time points and measured using\u00a0microarray<\/a>\u00a0technology: the expressed genes from the sample were\u00a0copied<\/a>,\u00a0labelled<\/a>, and washed over a microarray containing a pattern of DNA fragments. The microarray was scanned for the label, and\u00a0computed<\/a>, providing an output of which genes were expressed.<\/p>\n

Once they had measured gene expression over time for a single\u00a0species<\/a>, it was easy to repeat the\u00a0procedure<\/a>\u00a0for the other\u00a0species<\/a>.<\/p>\n

With this data, the group could\u00a0ask<\/a>: how doe the\u00a0difference<\/i>\u00a0in gene expression between species change as the animals’ develop? And the answer: Gene expression is very different at the beginning and end of\u00a0embryo development<\/a>, but is most similar in\u00a0the middle<\/a>. The group also\u00a0showed<\/a>\u00a0that the genes that best conformed to this hourglass model were genes known to be involved in embryo development. Thus they could conclude the phylotypic stage of development could be defined, not just on the basis of morphology, but also on the basis of developmental genes’ expression.<\/p>\n

2.\u00a0A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns.<\/h5>\n

Whereas the above study compared gene expression across species, this study looked at gene expression in a single\u00a0animal<\/a>.<\/p>\n

This group had previously developed a technique called phylostratigraphy<\/a>\u00a0(phylum<\/a>\u00a0+\u00a0stratigraphy<\/a>). This is a bioinfomatic<\/a>\u00a0technique that analyzes the contents of a DNA, and attributes ages to the genes. It achieves this by determining when a particular gene arose on the basis of which forms of life have it, and which don’t. If, for example, a gene is present in a mouse and a human, it means that the gene was likely present in the common ancestor of mice and humans. If the gene only appears in one of mice or humans, then it likely arose\u00a0after<\/em>\u00a0the two lineages diverged.<\/p>\n

Here too, the group took samples at different stages of embryonic development, then submitted the samples to analysis using microarrays. This output told them which genes were activated at different stages of development. They then submitted this data to their phylostraitographic algorithm.<\/p>\n

The output of\u00a0this<\/em>\u00a0was to tell them the evolutionary age of the genes expressed, and how this changes as the animal develops. Here too they found an hourglass pattern: The genes at early and late stages are the most recent, whereas those in the\u00a0middle<\/a>\u00a0are the oldest. In other words, during the phylotypic stage of development, organisms tend toward using their older genes.<\/p>\n

3. What does it all mean?<\/h5>\n

To restate, the two papers showed that, as compared to other stages, the genes expressed during the phylotypic stage:<\/p>\n