An evolution revolution provides further revelation

The extent of copy-number variation (CNV) in the human genome has been appreciated only recently. Nevertheless, for almost four decades, gene duplication has been a prevailing hypothesis for evolutionary change. Recently, gene CNV spanning 60 million years of human and primate evolution has been determined enabling lineage-specific gene CNV to be identified. Primate lineage-specific gene CNV studies reveal that almost one third of all human genes exhibit a copy-number change in one or more primate species. Intriguingly, human lineage-specific gene amplification can be correlated to the emergence of human-specific traits such as cognition and endurance running.     

The apolipoprotein L gene cluster has emerged recently in evolution and is expressed in human vascular tissue

We previously isolated APOL3 (CG12-1) cDNA and now describe the isolation of APOL1 and APOL2 cDNA from an activated endothelial cell cDNA library and show their endothelialspecific expression in human vascular tissue. APOL1-APOL4 are clustered on human chromosome 22q13.1, as a result of tandem gene duplication, and were detected only in primates (humans and African green monkeys) and not in dogs, pigs, or rodents, showing that this gene cluster has arisen recently in evolution. The specific tissue distribution and gene organization suggest that these genes have diverged rapidly after duplication. This has resulted in the emergence of an additional signal peptide encoding exon that ensures secretion of the plasma high-density lipoprotein-associated APOL1. Our results show that the APOL1-APOL4 cluster might contribute to the substantial differences in the lipid metabolism of humans and mice, as dictated by the variable expression of genes involved in this process.     

Multiplication of the class I alcohol dehydrogenase locus in mammalian evolution

Chromosomal DNA samples derived from various primates and other mammals (horse, sheep, rabbit, and mouse) were digested with restriction endonuclease and hybridized with a probe of the sixth exon of the human ADH gene, which is highly conserved in the class I alcohol dehydrogenase of these mammalian species. The copy number of the class I ADH gene in each species was estimated from the number of hybridized bands. Primate DNA samples showed three distinct bands in the blots of PstI digest and DraI digest. Moreover, most of the bands from primate DNA showed a similarity in size so as to allow us to assign the ADH1, ADH2, and ADH3 homologues in each species. In contrast, mouse has only one gene, and rabbit, sheep, and horse seem to have only two genes, for the class I ADH, which showed divergent hybridization bands. These results are consistent with the view that the human class I ADH gene cluster has been generated through gene multiplication events which occurred before the Catarrhini branch point in the course of primate evolution.     

The origin and evolution of peptide YY (PYY) and pancreatic polypeptide (PP)

It is generally accepted that the neuropeptide Y (NPY) family of homologous peptides arose as a result of a series of gene duplication events. Recent advances in comparative genomics allow to formulate a hypothesis that explains, at least in part, the complexity of the family. Chromosome mapping studies reveal that the gene encoding PYY may have arisen from a common ancestral gene (termed NYY) in an ancient chromosomal duplication event that also involved the hox gene clusters. A tandem duplication of the PYY gene concomitant with or just before the emergence of tetrapods generated the PPY gene encoding PP. In the primate and ungulate lineages, the PYY-PPY gene cluster has undergone a more recent gene duplication event to create a PYY2-PPY2 gene cluster on the same chromosome. In the human and baboon, this cluster probably does not encode functional NPY family peptides but expression of the bovine PYY2 gene generates seminalplasmin, a major biologically active component of bull semen. An independent duplication of the PYY gene in the lineage of teleost fish has generated peptides of the PY family that are synthesized in the pancreatic islets of Acanthomorpha. The structural organization of the biosynthetic precursors of PYY and PP (preproPYY and preproPP) has been quite well preserved during the evolution of vertebrates but conservative pressure on individual domains in the proteins has not been uniform. The duplication of the PYY gene that generated the PPY gene appears to have resulted in a relaxation of conservative pressure on the functional domain with the result that the amino acid sequences of tetrapod PYYs are more variable than the PYYs of jawed fish. Although the primary structure of PP has been quite strongly conserved in mammals, with the exception of the rodents, the extreme variability in the sequences of amphibian and reptilian PPs means that the peptide is a useful molecular marker to study the branching order in early tetrapod evolution     

Evolutionary history of tissue kallikreins

The gene family of human kallikrein-related peptidases (KLKs) encodes proteins with diverse and pleiotropic functions in normal physiology as well as in disease states. Currently, the most widely known KLK is KLK3 or prostate-specific antigen (PSA) that has applications in clinical diagnosis and monitoring of prostate cancer. The KLK gene family encompasses the largest contiguous cluster of serine proteases in humans which is not interrupted by non-KLK genes. This exceptional and unique characteristic of KLKs makes them ideal for evolutionary studies aiming to infer the direction and timing of gene duplication events. Previous studies on the evolution of KLKs were restricted to mammals and the emergence of KLKs was suggested about 150 million years ago (mya). In order to elucidate the evolutionary history of KLKs, we performed comprehensive phylogenetic analyses of KLK homologous proteins in multiple genomes including those that have been completed recently. Interestingly, we were able to identify novel reptilian, avian and amphibian KLK members which allowed us to trace the emergence of KLKs 330 mya. We suggest that a series of duplication and mutation events gave rise to the KLK gene family. The prominent feature of the KLK family is that it consists of tandemly and uninterruptedly arrayed genes in all species under investigation. The chromosomal co-localization in a single cluster distinguishes KLKs from trypsin and other trypsin-like proteases which are spread in different genetic loci. All the defining features of the KLKs were further found to be conserved in the novel KLK protein sequences. The study of this unique family will further assist in selecting new model organisms for functional studies of proteolytic pathways involving KLKs.     

Evolutionary history of the cancer immunity antigen MAGE gene family

The evolutionary mode of a multi-gene family can change over time, depending on the functional differentiation and local genomic environment of family members. In this study, we demonstrate such a change in the melanoma antigen (MAGE) gene family on the mammalian X chromosome. The MAGE gene family is composed of ten subfamilies that can be categorized into two types. Type I genes are of relatively recent origin, and they encode epitopes for human leukocyte antigen (HLA) in cancer cells. Type II genes are relatively ancient and some of their products are known to be involved in apoptosis or cell proliferation. The evolutionary history of the MAGE gene family can be divided into four phases. In phase I, a single-copy state of an ancestral gene and the evolutionarily conserved mode had lasted until the emergence of eutherian mammals. In phase II, eight subfamily ancestors, with the exception for MAGE-C and MAGE-D subfamilies, were formed via retrotransposition independently. This would coincide with a transposition burst of LINE elements at the eutherian radiation. However, MAGE-C was generated by gene duplication of MAGE-A. Phase III is characterized by extensive gene duplication within each subfamily and in particular the formation of palindromes in the MAGE-A subfamily, which occurred in an ancestor of the Catarrhini. Phase IV is characterized by the decay of a palindrome in most Catarrhini, with the exception of humans. Although the palindrome is truncated by frequent deletions in apes and Old World monkeys, it is retained in humans. Here, we argue that this human-specific retention stems from negative selection acting on MAGE-A genes encoding epitopes of cancer cells, which preserves their ability to bind to highly divergent HLA molecules. These findings are interpreted with consideration of the biological factors shaping recent human MAGE-A genes.     

Chromosome 6 phylogeny in primates and centromere repositioning

A panel of 15 human BAC/PAC probes, covering the entire chromosome 6, was used in FISH experiments on great apes and on representatives of Old World monkeys, New World monkeys, and lemurs to delineate the chromosome 6 phylogeny in primates. The domestic cat was used as an outgroup. The analysis showed a high marker order conservation, with few rearrangements required to reconcile the hypothesized chromosome 6 organization in primate ancestor with marker arrangement in all the examined species. Contrary to this simple evolutionary scenario, however, the centromere was found to be located in three distinct regions, without any evidence of chromosomal rearrangement that would account for its movement. One of the two centromere repositioning events occurred in great apes ancestor. The centromere moved from 6p22.1 to the present day location after the inversion event that differentiated marker order of the primate ancestor from the ancestor of Catarrhini. A cluster of intrachromosomal segmental duplications was found at 6p22.1, scattered in a region of about 9 Mb, which we interpret as remains of duplicons that flanked the ancestral centromere. Our data, therefore, suggest that some duplicon clusters found in noncentromeric/nontelomeric locations may represent traces of evolutionary silenced centromeres that inactivated after the occurrence of a centromere repositioning. In addition, the neocentromere emergence we have documented in Old World monkeys at 6q24.3 appears to have arisen and progressed without affecting the displaced flanking sequences.     

Molecular evolution of growth hormone gene family in old world monkeys and hominoids

Growth hormone is a classic molecule in the study of the molecular clock hypothesis as it exhibits a relatively constant rate of evolution in most mammalian orders except primates and artiodactyls, where dramatically enhanced rate of evolution (25–50-fold) has been reported. The rapid evolution of primate growth hormone occurred after the divergence of tarsiers and simians, but before the separation of old world monkeys (OWM) from new world monkeys (NWM). Interestingly, this event of rapid sequence evolution coincided with multiple duplications of the growth hormone gene, suggesting gene duplication as a possible cause of the accelerated sequence evolution. Here we determined 21 different GH-like sequences from four species of OWM and hominoids. Combining with published sequences from OWM and hominoids, our analysis demonstrates that multiple gene duplications and several gene conversion events both occurred in the evolutionary history of this gene family in OWM/hominoids. The episode of recent duplications of CSH-like genes in gibbon is accompanied with rapid sequence evolution likely resulting from relaxation of purifying selection. GHN genes in both hominoids and OWM are under strong purifying selection. In contrast, CSH genes in both lineages are probably not. GHV genes in OWM and hominoids evolved at different evolutionary rates and underwent different selective constraints. Our results disclosed the complex history of the primate growth hormone gene family and raised intriguing questions on the consequences of these evolutionary events.     

Emergence of young human genes after a burst of retroposition in primates

The origin of new genes through gene duplication is fundamental to the evolution of lineage- or species-specific phenotypic traits. In this report, we estimate the number of functional retrogenes on the lineage leading to humans generated by the high rate of retroposition (retroduplication) in primates. Extensive comparative sequencing and expression studies coupled with evolutionary analyses and simulations suggest that a significant proportion of recent retrocopies represent bona fide human genes. We estimate that at least one new retrogene per million years emerged on the human lineage during the past ∼63 million years of primate evolution. Detailed analysis of a subset of the data shows that the majority of retrogenes are specifically expressed in testis, whereas their parental genes show broad expression patterns. Consistently, most retrogenes evolved functional roles in spermatogenesis. Proteins encoded by X chromosome−derived retrogenes were strongly preserved by purifying selection following the duplication event, supporting the view that they may act as functional autosomal substitutes during X-inactivation of late spermatogenesis genes. Also, some retrogenes acquired a new or more adapted function driven by positive selection. We conclude that retroduplication significantly contributed to the formation of recent human genes and that most new retrogenes were progressively recruited during primate evolution by natural and/or sexual selection to enhance male germline function.     

Two rounds of whole genome duplication in the ancestral vertebrate

The hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, but remains unresolved. We reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, and then determined when each gene duplicated relative to the evolutionary tree of the organisms. We confirmed the results of earlier studies that there remains little signal of these events in numbers of duplicated genes, gene tree topology, or the number of genes per multigene family. However, when we plotted the genomic map positions of only the subset of paralogous genes that were duplicated prior to the fish–tetrapod split, their global physical organization provides unmistakable evidence of two distinct genome duplication events early in vertebrate evolution indicated by clear patterns of four-way paralogous regions covering a large part of the human genome. Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage.     

Hox, ParaHox, ProtoHox: facts and guesses

The Hox gene cluster has captivated the imagination of evolutionary and developmental biologists worldwide. In this review, the origin of the Hox and ParaHox gene clusters by duplication of a ProtoHox gene cluster, and the changes in their gene numbers in major Metazoan Transitions are reviewed critically. Re-evaluation of existing data and recent findings in Cnidarians, Acoels, and critical stages of vertebrate evolution suggest alternative scenarios for the origin, structure, and changes in Hox gene numbers in relevant events of Metazoan evolution. I discuss opposing views and propose that (i) the ProtoHox cluster had only two genes, and not four as commonly believed: a corollary is that the origin of Bilaterians was coincident with the invention of new Hox and ParaHox gene classes, which may have facilitated such a transition; (ii) the ProtoHox cluster duplication was a cis duplication event, rather than a trans duplication event, as previously suggested, and (iii) the ancestral vertebrate cluster possessed 14 Hox genes, and not the 13 generally assumed. These hypotheses could be verified or refuted in the near future, but they may help critical discussion of the evolution of the Hox/ParaHox family in the metazoan kingdom.     

Transgenic Arabidopsis expressing osmolyte glycine betaine synthesizing enzymes from halophilic methanogen promote tolerance to drought and salt stress

Gene duplication events exert key functions on gene innovations during the evolution of the eukaryotic genomes. A large portion of the total gene content in plants arose from tandem duplications events, which often result in paralog genes with high sequence identity. Ubiquitin ligases or E3 enzymes are components of the ubiquitin proteasome system that function during the transfer of the ubiquitin molecule to the substrate. In plants, several E3s have expanded in their genomes as multigene families. To gain insight into the consequences of gene duplications on the expansion and diversification of E3s, we examined the evolutionary basis of a cluster of six genes, duplC-ATLs, which arose from segmental and tandem duplication events in Brassicaceae. The assessment of the expression suggested two patterns that are supported by lineage. While retention of expression domains was observed, an apparent absence or reduction of expression was also inferred. We found that two duplC-ATL genes underwent pseudogenization and that, in one case, gene expression is probably regained. Our findings provide insights into the evolution of gene families in plants, defining key events on the expansion of the Arabidopsis Tóxicos en Levadura family of E3 ligases.     

Hox gene duplication in fish

The study of Hox gene clusters continues to serve as a paradigm for those interested in vertebrate genome evolution. Recent exciting discoveries about Hox gene composition in fishes challenges conventional views about vertebrate Hox gene evolution, and has initiated lively debates concerning the evolutionary events making the divergence of the major vertebrate lineages. Comparative analyses indicate that Hox cluster duplications occurred in early vertebrate evolution, and again within the order Cypriniformes of teleost fish. Loss of Hox genes was more widespread than duplication during fish evolution.     

On the origins of Mendelian disease genes in man: the impact of gene duplication

Over 3,000 human diseases are known to be linked to heritable genetic variation, mapping to over 1,700 unique genes. Dating of the evolutionary age of these disease-associated genes has suggested that they have a tendency to be ancient, specifically coming into existence with early metazoa. The approach taken by past studies, however, assumes that the age of a disease is the same as the age of its common ancestor, ignoring the fundamental contribution of duplication events in the evolution of new genes and function. Here, we date both the common ancestor and the duplication history of known human disease-associated genes. We find that the majority of disease genes (80%) are genes that have been duplicated in their evolutionary history. Periods for which there are more disease-associated genes, for example, at the origins of bony vertebrates, are explained by the emergence of more genes at that time, and the majority of these are duplicates inferred to have arisen by whole-genome duplication. These relationships are similar for different disease types and the disease-associated gene's cellular function. This indicates that the emergence of duplication-associated diseases has been ongoing and approximately constant (relative to the retention of duplicate genes) throughout the evolution of life. This continued until approximately 390 Ma from which time relatively fewer novel genes came into existence on the human lineage, let alone disease genes. For single-copy genes associated with disease, we find that the numbers of disease genes decreases with recency. For the majority of duplicates, the disease-associated mutation is associated with just one of the duplicate copies. A universal explanation for heritable disease is, thus, that it is merely a by-product of the evolutionary process; the evolution of new genes (de novo or by duplication) results in the potential for new diseases to emerge.     

Recent origins of sperm genes in Drosophila

Newly created genes often acquire testis-specific or enhanced expression but neither the mechanisms responsible for this specificity nor the functional consequences of these evolutionary processes are well understood. Genomic analyses of the Drosophila melanogaster sperm proteome has identified 2 recently evolved gene families on the melanogaster lineage and 4 genes created by retrotransposition during the evolution of the melanogaster group that encode novel sperm components. The expanded Mst35B (protamine) and tektin gene families are the result of tandem duplication events with all family members displaying testis-specific expression. The Mst35B family encodes rapidly evolving protamines that display a robust signature of positive selection within the DNA-binding high-mobility group box consistent with functional diversification in genome repackaging during sperm nuclear remodeling. The Mst35B paralogs also reside in a significant regional cluster of testis-overexpressed genes. Tektins, known components of the axoneme, are encoded by 3 nearly identical X-linked genes, a finding consistent with very recent gene family expansion. In addition to localized duplication events, the evolution of the sperm proteome has also been driven by recent retrotransposition events resulting in Cdlc2, CG13340, Vha36, and CG4706. Cdlc2, CG13340, and Vha36 all display high levels of overexpression in the testis, and Cdlc2 and CG13340 reside within testis-overexpressed gene clusters. Thus, gene creation is a dynamic force in the evolution of sperm composition and possibly function, which further suggests that acquisition of molecular functionality in sperm may be an influential pathway in the fixation of new genes.