Genome complexity: de novo or orphan genes (Introduction)

by David Turell , Thursday, January 21, 2021, 23:07 (1402 days ago) @ David Turell

More from Richard Buggs: (David Turell, 2019-02-23, 19:57)

https://inference-review.com/article/the-origin-of-novel-genes

"The four studies find that organisms with different morphologies possess different sets of genes. Given that genes provide much of the information encoding the morphology of living organisms, this finding may not seem a surprise. That novel genes do not accumulate with Darwinian gradualism in the phylogeny is perhaps more surprising. The authors describe bursts of innovation: upon the origin of placental mammals, 357 novel genes; upon the origin of the metazoan, 1,189 novel genes; upon the origin of the land plants, 1,167 novel genes; and upon the origin of the flowering plants, 2,525 novel genes.

"Equally surprising is evidence that the patterns of presence and absence of many genes in these studies do not form a nested hierarchy congruent with the accepted phylogeny. Particular genes often appear in more than one clade (Figure 1). This leads the authors to infer massive gene losses and frequent horizontal gene transfer in the history of life.

"The unexpected nature of these findings was not lost on the authors of the studies, nor the editors of the journals that published their manuscripts. Three of the paper titles emphasize unexpected novelty and one emphasizes unexpected loss. But all four show similar patterns. More is revealed in each than a single title can convey.

***

"In the 1850s, Charles Darwin considered it obvious that the morphological variation of life was continuous: “all the parts and organs of many independent beings” are “linked together by graduated steps.”

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"It is far from clear how these homology groups might be linked in graduated steps. The evolution of novel genes is a subject with a substantial literature all its own, which has recently shifted from the view that all new genes begin as duplicates of pre-existing genes to a view that many genes evolve de novo from noncoding sequences. The mechanisms underlying this process are not well understood.

***

"Rather than emerging gradually, a few at a time, the evidence presented in these four papers suggests the occurrence of punctuated bursts. At every major phylogenetic node that was examined, the appearance of hundreds, and in some cases thousands, of novel homology groups was detected.

"Evolution by bursts is, of course, not expected if natural selection is the main driver. “[N]atural selection acts only by taking advantage of slight successive variations,” Darwin remarked; “she can never take a great and sudden leap, but must advance by the short and sure, though slow steps.”5 The findings presented in these papers suggest otherwise. It seems that the evolution of life is characterized by leaps involving large numbers of novel homology groups.

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"The fossil record depicts the appearance of the first angiosperms as a sudden event, with no clear progenitors. This was known, in part, to Darwin, who famously complained to the director of Kew Gardens in 1879 that the origin of the dicotyledonous angiosperms was an “abominable mystery.”7 The mystery has since deepened to include all other angiosperms.

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"These studies by the teams of Holland and Paps are not alone in finding bursts of novel genes in the history of life. In a paper published earlier this year, Zhang et al. conducted an analysis of plants similar to Bowles et al., with better sampling of charophytes and bryophytes.10 Despite using different gene clustering methods and a smaller set of species, they found gene gains at key nodes on similar orders of magnitude.

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"ALL FOUR STUDIES under review found massive gene losses for phylogenetic nodes at the base of the major groups of living organisms. This suggests that major evolutionary transitions do not occur solely by means of tinkering with existing genes. Instead, it seems that vast numbers of existing genes are jettisoned and replaced by entirely different ones. Such processes would represent a radical overhaul in the genetic composition of organisms. How this might be accomplished is another mystery.

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"Bowles et al. found that 323 homology groups were present in fungal and land plant genomes, but absent from all other taxa.12 Instead of being lost in the lineages between fungi and land plants, the genes could simply have jumped. This may turn out to be a more elegant solution to the problem.

"The incongruence between patterns in the absence or presence of homology groups and widely accepted phylogenies raises a broader issue. A single phylogeny is clearly an inadequate model for the history of life, but there is no obvious replacement. This question is wide open."

Comment: Gould's gaps and punctuation stares at you in your face. Behe laughs about the losses. This question is not 'wide open' as this discontinuity is perfect evidence of God the designer at work stepping in.