Paleopolyploidy

Ancient genome duplications are widespread throughout eukaryotic lineages, particularly in plants. In more ancient monocot lineages one or likely multiple rounds of additional whole genome duplications had occurred, which were however not shared with the ancestral eudicots. Further independent more recent whole genome duplications have occurred in the lineages leading to maize, sugar cane and wheat, but not the most common cultivar of rice, sorghum A polyploidy event is theorized to have created the ancestral line that led to all modern flowering plants. That paleopolyploidy event was studied by sequencing the genome of an ancient flowering plant, Amborella trichopoda. The core eudicots also shared a common whole genome triplication (paleo-hexaploidy), which was estimated to have occurred after monocot-eudicot divergence but before the divergence of rosids and asterids. Many eudicot species have experienced additional whole genome duplications or triplications. For example, the model plant Arabidopsis thaliana, the first plant to have its entire genome sequenced, has experienced at least two additional rounds of whole genome duplication since the duplication shared by the core eudicots. The most recent event took place before the divergence of the Arabidopsis and Brassica lineages, about to . Other examples include the sequenced eudicot genomes of apple, soybean, tomato, cotton, etc. Compared with plants, paleopolyploidy is much rarer in the animal kingdom. Through genome streamlining, yeast has lost 90% of the duplicated genome over evolutionary time and is now recognized as a diploid organism. == Detection method ==

Duplicated genes can be identified through sequence homology on the DNA or protein level. Paleopolyploidy can be identified as massive gene duplication at one time using a molecular clock. To distinguish between whole-genome duplication and a collection of (more common) single gene duplication events, the following rules are often applied: • Duplicated genes are located in large duplicated blocks. Single gene duplication is a random process and tends to make duplicated genes scattered throughout the genome. • Duplicated blocks are non-overlapping because they were created simultaneously. Segmental duplication within the genome can fulfill the first rule; but multiple independent segmental duplications could overlap each other. In theory, the two duplicated genes should have the same "age"; that is, the divergence of the sequence should be equal between the two genes duplicated by paleopolyploidy (homeologs). Synonymous substitution rate, Ks, is often used as a molecular clock to determine the time of gene duplication. Thus, paleopolyploidy is identified as a "peak" on the duplicate number vs. Ks graph (shown on the right). However, using Ks plots to identify and document ancient polyploid events can be problematic, as the method fails to identify genome duplications that were followed by massive gene elimination and genome refinement. Other mixed model approaches that combined Ks plots with other methods are being developed to better understand paleopolyploidy. Duplication events that occurred a long time ago in the history of various evolutionary lineages can be difficult to detect because of subsequent diploidization (such that a polyploid starts to behave cytogenetically as a diploid over time) as mutations and gene translations gradually make one copy of each chromosome unlike its counterpart. This usually results in a low confidence for identifying ancient paleopolyploidy. == Evolutionary importance ==

Paleopolyploidization events lead to massive cellular changes, including doubling of the genetic material, changes in gene expression and increased cell size. Gene loss during diploidization is not completely random, but heavily selected. Genes from large gene families are duplicated. On the other hand, individual genes are not duplicated. Overall, paleopolyploidy can have both short-term and long-term evolutionary effects on an organism's fitness in the natural environment. Enhanced phenotypic evolution Whole genome duplication may increase the rates and efficiency by which organisms acquire new biological traits. However, one test of this hypothesis, which compared evolutionary rates in innovation in early teleost fishes (with duplicate genomes) to early holostean fishes (without duplicated genomes) found little difference between the two. Hybrid vigor Polyploids often have larger cells and even larger organs. Many important crops, including wheat, maize and cotton, are paleopolyploids which were selected for domestication by ancient peoples. Speciation It has been suggested that many polyploidization events created new species, via a gain of adaptive traits, or by sexual incompatibility with their diploid counterparts. An example would be the recent speciation of allopolyploid Spartina — S. anglica; the polyploid plant is so successful that it is listed as an invasive species in many regions. ==Allopolyploidy and autopolyploidy==

There are two major divisions of polyploidy, allopolyploidy and autopolyploidy. Allopolyploids arise as a result of the hybridization of two related species, while autopolyploids arise from the duplication of a species' genome as a result of hybridization of two conspecific parents, or somatic doubling in reproductive tissue of a parent. Allopolyploid species are believed to be much more prevalent in nature, which can be either deleterious, or advantageous. Autopolyploidy, however, is generally considered to be a neutral process, Following polyploidy events, there are several possible fates for duplicated genes; both copies may be retained as functional genes, change in gene function may occur in one or both copies, gene silencing may mask one or both copies, or complete gene loss may occur. Polyploidy events will result in higher levels of heterozygosity, and, over time, can lead to an increase in the total number of functional genes in the genome. As time passes after a genome duplication event, many genes will change function as a result of either change in duplicate gene function for both allo- and autopolyploid species, or there will be changes in gene expression caused by genomic rearrangements induced by genome duplication in allopolyploids. When both copies of a gene are retained, and thus the number of copies doubled, there is a chance that there will be a proportional increase in expression of that gene, resulting in twice as much mRNA transcript being produced. There is also the possibility that transcription of a duplicated gene will be down-regulated, resulting in less than two-fold increase in transcription of that gene, or that the duplication event will yield more than a two-fold increase in transcription. In one species, Glycine dolichocarpa (a close relative of the soybean, Glycine max), it has been observed that following a genome duplication roughly 500,000 years ago, there has been a 1.4 fold increase in transcription, indicating that there has been a proportional decrease in transcription relative to gene copy number following the duplication event. ==Vertebrates as paleopolyploid==

The hypothesis of vertebrate paleopolyploidy originated as early as the 1970s, proposed by the biologist Susumu Ohno. He reasoned that the vertebrate genome could not achieve its complexity without large scale whole-genome duplications. The "two rounds of genome duplication" hypothesis (2R hypothesis) came about, and gained in popularity, especially among developmental biologists. Some researchers have questioned the 2R hypothesis because it predicts that vertebrate genomes should have a 4:1 gene ratio compared with invertebrate genomes, and this is not supported by findings from the 48 vertebrate genome projects available in mid-2011. For example, the human genome consists of ~20,500 protein coding genes according to counts from the Ensembl genome browser while an average invertebrate genome size is about 15,000 genes. Additional arguments against 2R were based on the lack of the (AB)(CD) tree topology amongst four members of a gene family in vertebrates. However, if the two genome duplications occurred close together, we would not expect to find this topology. The amphioxus genome sequence provided support for the hypothesis of two rounds of whole genome duplication, followed by loss of duplicate copies of most genes. Additional amphioxus genomes further strengthen this hypothesis, with many chromosomal segments showing the expected (AB)(CD) tree topology. A 2015 study generated the sea lamprey genetic map, which yielded strong support for the hypothesis that a single whole-genome duplication occurred in the basal vertebrate lineage, preceded and followed by several evolutionarily independent segmental duplications that occurred over chordate evolution. A 2021 study sequenced the genome of the Japanese lamprey. It upended the results of the 2015 study and supports the existence of a universal 1R duplication before the Cyclostomata (the extant jawless fish, which includes hagfish and lemprey) and Gnathostomata (jawed fish, which includes the tetrapods, e.g. humans) split. The two lineages then each carried out their own 2R: a duplication/tetraploidization in the jawed fish, a triplication/hexaploidization in the Cyclostomata. A 2024 study sequenced the genome of the brown hagfish and compared it to other vertebrate genomes, both jawed and jawless. The "shared 1R, then separate 2R" framework of the 2021 study is strongly supported by gene tree and synteny. It is also shown that although the 1R event has underwent rediploidization (i.e. homeologous chromosomes stopped recombining, making the genome once again act as diploid) at the Cyclostomata-Gnathostomata split, the Cyclostomata 2R event has not underwent full rediploidization at the time of the hagfish-lamprey split. This helps recontextualize the messy picture found by the 2015 study. == See also ==