The 2R hypothesis or Ohno's hypothesis, first proposed by Susumu Ohno in 1970, [1] is a hypothesis that the genomes of the early vertebrate lineage underwent two complete genome duplications, and thus modern vertebrate genomes reflect paleopolyploidy. The name derives from the 2 rounds of duplication originally hypothesized by Ohno, but refined in a 1994 version, and the term 2R hypothesis was probably coined in 1999. Variations in the number and timings of genome duplications typically still are referred to as examples of the 2R hypothesis. [2]
The 2R hypothesis has been the subject of much research and controversy; however, with growing support from genome data, including the human genome, the balance of opinion has shifted strongly in favour of support for the hypothesis. According to Karsten Hokamp, Aoife McLysaght and Kenneth H. Wolfe, [2] the version of the genome duplication hypothesis from which 2R hypothesis takes its name appears in Holland et al. [3] and the term was coined by Austin L. Hughes. [4]
Ohno presented the first version of the 2R hypothesis as part of his larger argument for the general importance of gene duplication in evolution. Based on relative genome sizes and isozyme analysis, he suggested that ancestral fish or amphibians had undergone at least one and possibly more cases of "tetraploid evolution". He later added to this argument the evidence that most paralogous genes in vertebrates do not demonstrate genetic linkage. Ohno argued that linkage should be expected in the case of individual tandem duplications (in which a duplicate gene is added adjacent to the original gene on the same chromosome), but not in the case of chromosome duplications. [5]
In 1977, Schmidtke and colleagues showed that isozyme complexity is similar in lancelets and tunicates, contradicting a prediction of Ohno's hypothesis that genome duplication occurred in the common ancestor of lancelets and vertebrates. [6] However, this analysis did not examine vertebrates, so could say nothing about later duplication events. [7] (Furthermore, much later molecular phylogenetics has shown that vertebrates are more closely related to tunicates than to lancelets, thus negating the logic of this analysis. [8] ) The 2R hypothesis saw a resurgence of interest in the 1990s for two reasons. First, gene mapping data in humans and mice revealed extensive paralogy regions - sets of genes on one chromosome related to sets of genes on another chromosome in the same species, indicative of duplication events in evolution. [9] Paralogy regions were generally in sets of four. Second, cloning of Hox genes in lancelet revealed presence of a single Hox gene cluster, [10] in contrast to the four clusters in humans and mice. Data from additional gene families revealed a common one-to-many rule when lancelet and vertebrate genes were compared. [7] Taken together, these two lines of evidence suggest that two genome duplications occurred in the ancestry of vertebrates, after it had diverged from the cephalochordate evolutionary lineage.
Controversy about the 2R hypothesis hinged on the nature of paralogy regions. It is not disputed that human chromosomes bear sets of genes related to sets of genes on other chromosomes; the controversy centres on whether they were generated by large-scale duplications that doubled all the genes at the same time, or whether a series of individual gene duplications occurred followed by chromosomal rearrangement to shuffle sets of genes together. Hughes and colleagues found that phylogenetic trees built from different gene families within paralogy regions had different shapes, suggesting that the gene families had different evolutionary histories. [12] [13] This was suggested to be inconsistent with the 2R hypothesis. However, other researchers have argued that such 'topology tests' do not test 2R rigorously, because recombination could have occurred between the closely related chromosomes generated by polyploidy, [14] [15] because inappropriate genes had been compared [16] and because different predictions are made if genome duplication occurred through hybridisation between species. [17] In addition, several researchers were able to date duplications of gene families within paralogy regions consistently to the early evolution of vertebrates, after divergence from amphioxus, consistent with the 2R hypothesis. [18] [19] When complete genome sequences became available for vertebrates, Ciona intestinalis and lancelets, it was found that much of the human genome was arranged in paralogy regions that could be traced to large-scale duplications, [20] and that these duplications occurred after vertebrates had diverged from tunicates [11] and lancelets. [21] This would date the two genome duplications to between 550 and 450 million years ago.
The controversy raging in the late 1990s was summarized in a 2001 review of the subject by Wojciech Makałowski, who stated that "the hypothesis of whole genome duplications in the early stages of vertebrate evolution has as many adherents as opponents". [5]
In contrast, a more recent review in 2007 by Masanori Kasahara states that there is now "incontrovertible evidence supporting the 2R hypothesis" and that "a long-standing debate on the 2R hypothesis is approaching the end". [22] Michael Benton, in the 2014 edition of Vertebrate Palaeontology , states, "It turns out that, in places where amphioxus has a single gene, vertebrates often have two, three, or four equivalent genes as a result of two intervening whole-genome duplication events." [23]
Ohnologous genes are paralogous genes that have originated by a process of this 2R duplication. The name was first given in honour of Susumu Ohno by Ken Wolfe. [24] It is useful for evolutionary analysis because all ohnologues in a genome have been diverging for the same length of time (since their common origin in the whole genome duplication). [25] [26]
Well-studied ohnologous genes include genes in human chromosome 2, 7, 12 and 17 containing Hox gene clusters, collagen genes, keratin genes and other duplicated genes, [27] genes in human chromosomes 4, 5, 8 and 10 containing neuropeptide receptor genes, NK class homeobox genes and many more gene families, [28] [29] [30] and parts of human chromosomes 13, 4, 5 and X containing the ParaHox genes and their neighbors. [31] The Major histocompatibility complex (MHC) on human chromosome 6 has paralogy regions on chromosomes 1, 9 and 19. [32] Much of the human genome seems to be assignable to paralogy regions. [33]
A chordate is an animal belonging to the phylum Chordata. All chordates possess, at some point during their larval or adult stages, five distinctive physical characteristics (synapomorphies) that distinguish them from other taxa. These five synapomorphies are a notochord, a hollow dorsal nerve cord, an endostyle or thyroid, pharyngeal slits, and a post-anal tail. The name "chordate" comes from the first of these synapomorphies, the notochord, which plays a significant role in chordate structure and movement. Chordates are also bilaterally symmetric, have a coelom, possess a circulatory system, and exhibit metameric segmentation.
A craniate is a member of the Craniata, a proposed clade of chordate animals with a skull of hard bone or cartilage. Living representatives are the Myxini (hagfishes), Hyperoartia, and the much more numerous Gnathostomata. Formerly distinct from vertebrates by excluding hagfish, molecular and anatomical research in the 21st century has led to the reinclusion of hagfish as vertebrates, making living craniates synonymous with living vertebrates.
Gene duplication is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.
A cephalochordate is an animal in the chordate subphylum Cephalochordata. Cephalochordates are commonly called lancelets, and possess 5 synapomorphies, or primary characteristics, that all chordates have at some point during their larval or adulthood stages. These 5 synapomorphies are a notochord, dorsal hollow nerve cord, endostyle, pharyngeal slits, and a post-anal tail. The fine structure of the cephalochordate notochord is best known for the Bahamas lancelet, Asymmetron lucayanum. Cephalochordates are represented in modern oceans by the Amphioxiformes and are commonly found in warm temperate and tropical seas worldwide. With the presence of a notochord, adult amphioxus are able to swim and tolerate the tides of coastal environments, but they are most likely to be found within the sediment of these communities.
The lancelets, also known as amphioxi, consist of some 30 to 35 species of "fish-like" benthic filter feeding chordates in the order Amphioxiformes. They are modern representatives of the subphylum Cephalochordata. Lancelets closely resemble 530-million-year-old Pikaia, fossils of which are known from the Burgess Shale. However, according to phylogenetic analysis, the lancelet group itself probably evolved around the Cretaceous, 97.7 million years ago for Pacific species and 112 million years ago for Atlantic species. Palaeobranchiostoma from the Permian may be part of the fossil record of lancelets; however, due to poor preservation, some doubt about its nature remains. Zoologists are interested in them because they provide evolutionary insight into the origins of vertebrates. Lancelets contain many organs and organ systems that are closely related to those of modern fish, but in a more primitive form. Therefore, they provide a number of examples of possible evolutionary exaptation. For example, the gill-slits of lancelets are used for feeding only, and not for respiration. The circulatory system carries food throughout their body, but does not have red blood cells or hemoglobin for transporting oxygen. Lancelet genomes hold clues about the early evolution of vertebrates: by comparing genes from lancelets with the same genes in vertebrates, changes in gene expression, function and number as vertebrates evolved can be discovered. The genome of a few species in the genus Branchiostoma have been sequenced: B. floridae,B. belcheri, and B. lanceolatum.
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal gene transfer event (xenologs).
Pharyngeal slits are filter-feeding organs found among deuterostomes. Pharyngeal slits are repeated openings that appear along the pharynx caudal to the mouth. With this position, they allow for the movement of water in the mouth and out the pharyngeal slits. It is postulated that this is how pharyngeal slits first assisted in filter-feeding, and later, with the addition of gills along their walls, aided in respiration of aquatic chordates. These repeated segments are controlled by similar developmental mechanisms. Some hemichordate species can have as many as 200 gill slits. Pharyngeal clefts resembling gill slits are transiently present during the embryonic stages of tetrapod development. The presence of pharyngeal arches and clefts in the neck of the developing human embryo famously led Ernst Haeckel to postulate that "ontogeny recapitulates phylogeny"; this hypothesis, while false, contains elements of truth, as explored by Stephen Jay Gould in Ontogeny and Phylogeny. However, it is now accepted that it is the vertebrate pharyngeal pouches and not the neck slits that are homologous to the pharyngeal slits of invertebrate chordates. Pharyngeal arches, pouches, and clefts are, at some stage of life, found in all chordates. One theory of their origin is the fusion of nephridia which opened both on the outside and the gut, creating openings between the gut and the environment.
The ParaHox gene cluster is an array of homeobox genes from the Gsx, Xlox (Pdx) and Cdx gene families.
Paleopolyploidy is the result of genome duplications which occurred at least several million years ago (MYA). Such an event could either double the genome of a single species (autopolyploidy) or combine those of two species (allopolyploidy). Because of functional redundancy, genes are rapidly silenced or lost from the duplicated genomes. Most paleopolyploids, through evolutionary time, have lost their polyploid status through a process called diploidization, and are currently considered diploids, e.g., baker's yeast, Arabidopsis thaliana, and perhaps humans.
Hox genes, a subset of homeobox genes, are a group of related genes that specify regions of the body plan of an embryo along the head-tail axis of animals. Hox proteins encode and specify the characteristics of 'position', ensuring that the correct structures form in the correct places of the body. For example, Hox genes in insects specify which appendages form on a segment, and Hox genes in vertebrates specify the types and shape of vertebrae that will form. In segmented animals, Hox proteins thus confer segmental or positional identity, but do not form the actual segments themselves.
Ciona intestinalis is an ascidian, a tunicate with very soft tunic. Its Latin name literally means "pillar of intestines", referring to the fact that its body is a soft, translucent column-like structure, resembling a mass of intestines sprouting from a rock. It is a globally distributed cosmopolitan species. Since Linnaeus described the species, Ciona intestinalis has been used as a model invertebrate chordate in developmental biology and genomics. Studies conducted between 2005 and 2010 have shown that there are at least two, possibly four, sister species. More recently it has been shown that one of these species has already been described as Ciona robusta. By anthropogenic means, the species has invaded various parts of the world and is known as an invasive species.
Susumu Ohno was a Japanese-American geneticist and evolutionary biologist, and seminal researcher in the field of molecular evolution.
A gene family is a set of homologous genes within one organism. A gene cluster is a group of two or more genes found within an organism's DNA that encode similar polypeptides, or proteins, which collectively share a generalized function and are often located within a few thousand base pairs of each other. The size of gene clusters can vary significantly, from a few genes to several hundred genes. Portions of the DNA sequence of each gene within a gene cluster are found to be identical; however, the resulting protein of each gene is distinctive from the resulting protein of another gene within the cluster. Genes found in a gene cluster may be observed near one another on the same chromosome or on different, but homologous chromosomes. An example of a gene cluster is the Hox gene, which is made up of eight genes and is part of the Homeobox gene family.
In genetics, an isochore is a large region of genomic DNA with a high degree of uniformity in GC content; that is, guanine (G) and cytosine (C) bases. The distribution of bases within a genome is non-random: different regions of the genome have different amounts of G-C base pairs, such that regions can be classified and identified by the proportion of G-C base pairs they contain.
Chordate genomics is the study of the evolution of the chordate clade based on a comparison of the genomes of several species within the clade. The field depends on whole genome data of organisms. It uses comparisons of synteny blocks, chromosome translocation, and other genomic rearrangements to determine the evolutionary history of the clade, and to reconstruct the genome of the founding species.
Ohno's law was proposed by a Japanese-American biologist Susumu Ohno, saying that the gene content of the mammalian species has been conserved over species not only in the DNA content but also in the genes themselves. That is, nearly all mammalian species have conserved the X chromosome from their primordial X chromosome of a common ancestor.
In evolutionary developmental biology, inversion refers to the hypothesis that during the course of animal evolution, the structures along the dorsoventral (DV) axis have taken on an orientation opposite that of the ancestral form.
Branchiostoma floridae, the Florida lancelet, is a lancelet of the genus Branchiostoma. The genome of this species has been sequenced, revealing that among the chordates, the morphologically simpler tunicates are actually more closely related to vertebrates than lancelets. An embryo of a Florida amphioxus has a larval pharynx with gill slits that is asymmetrical. The gill slits in the larval pharynx form in the center of the embryo when it is in its earliest stage of development (primordial) meaning the thick layer of endoderm is overlapped by a thin layer; which aids into making the B. floridae asymmetrical from left to right. The lancelet Branchiostoma floridae maintains a high level of Fox transcription factor gene diversity, with 32 distinct Fox genes in its genome, and 21,229 clusters of cDNA clones, making it very useful to the research community.
Aoife McLysaght is an Irish geneticist and a professor in the Molecular Evolution Laboratory of the Smurfit Institute of Genetics, Trinity College Dublin in Ireland.
Linda Zimmerman Holland is a research biologist at Scripps Institution of Oceanography known for her work examining the evolution of vertebrates.