The origin of new genes

In the early 1990s, the first young gene to be described was jingwei in a group of African Drosophila species³². It provided enough details for the molecular mechanism underlying its origination to be deduced. A portion of jingwei was found to be a homologue of the Adh gene that encodes alcohol dehydrogenase⁹⁸ and was later characterized as a retrosequence of Adh⁹⁹. Further population genetic, molecular biological and comparative phylogenetic analyses showed it to be a new processed functional gene that originated around 2 million years ago in the common ancestor of two African Drosophila species, Drosophila yakuba and Drosophila teissieri.
In the ancestral species, there were two single copy genes, yellow-emperor (ymp) and Adh. yellow-emperor was duplicated into two copies: one also called yellow-emperor and the other called yande (ynd)^100,101.Whereas yellow-emperor maintained its original functions, yande was further involved in the origin of jingwei. In the short time before the speciation event, Adh mRNA retroposed into the third intron of yande as a fused exon and recombined with the first three yande exons. This formed jingwei, which is a gene that is translated into a chimeric protein.

The mechanism by which protein functional diversity expands is an important evolutionary issue. Studies of recently evolved chimeric genes permit direct investigation of the origin of new protein functions before they become obscured by subsequent evolution. Found in several African Drosophila species, jingwei (jgw), a recently evolved gene with a domain derived from the still extant short-chain alcohol dehydrogenase (ADH) through retroposition, provides an opportunity to examine this previously undescribed process directly. We expressed JGW proteins in a microbial expression system and, after purification, investigated their enzymatic properties. We found that, unexpectedly, positive Darwinian selection for amino acid replacements outside the active site of JGW produced a novel dehydrogenase with altered substrate specificity compared with the ancestral ADH. Instead of detoxifying and assimilating ethanol like its Adh parental gene, we observe that JGW efficiently utilizes long-chain primary alcohols found in hormone and pheromone metabolism. These data suggest that protein functional diversity can expand rapidly under the joint forces of exon shuffling, gene duplication, and natural selection.

faith writes: Considering how many alleles already exist in most populations of sexually reproducing animalia how on earth would you know if the occasional mutation contributed anything whatever to the processes that lead to variation, as opposed to the usual shuffling of gene frequencies among those already in existence?

I would really like to know how you think you KNOW that a mutation was involved.

Trichromacy in all Old World primates is dependent on separate X-linked MW and LW opsin genes that are organized into a head-to-tail tandem array flanked on the upstream side by a locus control region (LCR). The 5' regions of these two genes show homology for only the first 236 bp, although within this region, the differences are conserved in humans, chimpanzees, and two species of cercopithecoid monkeys. In contrast, most New World primates have only a single polymorphic X-linked opsin gene; all males are dichromats and trichromacy is achieved only in those females that possess a different form of this gene on each X chromosome. By sequencing the upstream region of this gene in a New World monkey, the marmoset, we have been able to demonstrate the presence of an LCR in an equivalent position to that in Old World primates. Moreover, the marmoset sequence shows extensive homology from the coding region to the LCR with the upstream sequence of the human LW gene, a distance of >3 kb, whereas homology with the human MW gene is again limited to the first 236 bp, indicating that the divergent MW sequence identifies the site of insertion of the duplicated gene. This is further supported by the presence of an incomplete Alu element on the upstream side of this insertion point in the MW gene of both humans and a cercopithecoid monkey, with additional Alu elements present further upstream. Therefore, these Alu elements may have been involved in the initial gene duplication and may also be responsible for the high frequency of gene loss and gene duplication within the opsin gene array. Full trichromacy is present in one species of New World monkey, the howler monkey, in which separate MW and LW genes are again present. In contrast to the separate genes in humans, however, the upstream sequences of the two howler genes show homology with the marmoset for at least 600 bp, which is well beyond the point of divergence of the human MW and LW genes, and each sequence is associated with a different LCR, indicating that the duplication in the howler monkey involved the entire upstream region

don't know why it is so hard to get this across, but I DO NOT DENY THAT NEW ALLELES ARE FORMED BY MUTATION. I don't know about genes. Genes are specific loci as I understand it, which are occupied by whatever number of alleles are available for that locus in a given population. I'm not aware that actual new genes are said to be created by mutation, merely alleles for that function

But the problem is that the evidence for a particular allele's being really the product of a mutation and yet also beneficial, truly novel and truly functional as well, is pretty scant. But of course I still can't read links so I may have missed THE evidence. Most of the new links I try cause my computer to freeze up.

How do you know it's a mutation as opposed to a normally occurring alternative allele?

If it's a mutation, how sure are you that it is not contributing something the organism would be better off without?

Although the complete genome sequences of over 50 representative species have revealed the many duplicated genes in all three domains of life1, 2, 3, 4, the roles of gene duplication in organismal adaptation and biodiversity are poorly understood. In addition, the evolutionary forces behind the functional divergence of duplicated genes are often unknown, leading to disagreement on the relative importance of positive Darwinian selection versus relaxation of functional constraints in this process5, 6, 7, 8, 9, 10. The methodology of earlier studies relied largely on DNA sequence analysis but lacked functional assays of duplicated genes, frequently generating contentious results11, 12. Here we use both computational and experimental approaches to address these questions in a study of the pancreatic ribonuclease gene (RNASE1) and its duplicate gene (RNASE1B) in a leaf-eating colobine monkey, douc langur. We show that RNASE1B has evolved rapidly under positive selection for enhanced ribonucleolytic activity in an altered microenvironment, a response to increased demands for the enzyme for digesting bacterial RNA. At the same time, the ability to degrade double-stranded RNA, a non-digestive activity characteristic of primate RNASE1, has been lost in RNASE1B, indicating functional specialization and relaxation of purifying selection. Our findings demonstrate the contribution of gene duplication to organismal adaptation and show the power of combining sequence analysis and functional assays in delineating the molecular basis of adaptive evolution.

So please address the evidence presented in the article that RNASE1B is the result of a duplication of RNASE1A and that RNASE1B evolved quickly to produce a enzyme necessary for digesting bacterial RNA.