Overview of Paleopolyploidy Process. Many higher eukaryotes were paleopolyploids at some point during their evolutionary history.

Paleopolyploidy refers to ancient genome duplications which occurred at least several million years ago (mya). The genome doubling event could either be an autopolyploidy or an allopolyploidy. Due to functional redundancy, genes are rapidly silenced and/or lost from the duplicated genomes. Most paleopolyploids, through evolutionary time, have lost their polyploid status through a process called diploidization, and are referred to as "diploids" nowadays (eg. baker's yeast, Arabidopsis and perhaps humans).

Paleopolyploidy is extensively studied in plant lineages. It has been found that almost all flowering plants have undergone at least one round of genome duplication at some point during their evolutionary history. Ancient genome duplications are also found in the early ancestor of vertebrates (which includes the human lineage) and another near the origin of the bony fishes. Interestingly, evidence suggests that baker's yeast (Saccharomyces cerevisiae), which has a compact genome, experienced polyploidzation during its evolutionary history.

[edit] Eukaryotes

A diagram that summarizes all well-known paleoploidization events.

Ancient genome duplications are widespread throughout eukaryotic lineages, particularly in plants. Almost all important cereal crops are paleopolyploids. Studies suggest that the common ancestor of Poaceae, the grass family, had a genome duplication 50–70 mya. Subsequent genome doublings occurred in maize, and twice in wheat. A duplication which is shared by all eudicots occurred 50-70 mya, and perhaps an earlier duplication affected the ancestor of all the world's flowering plants over 200 mya.

Furthermore, Arabidopsis thaliana, which has a small genome for a plant, experienced at least two rounds of paleopolyploidy. The most recent event took place before the divergence of the Arabidopsis and Brassica lineages, 25–40 mya.

Compared with plants, paleopolyploidy is much rarer in the animal kingdom. It is identified mainly in the amphibians and bony fishes. Although some studies suggested one (some say two) common genome duplications are shared by all vertebrates (including humans), the evidence is not as strong as in the other cases, and it is still under debate. However, many researchers are interested in the reasons why animal lineages had fewer paleopolyploidization events than did plants.

Lastly, a well-supported paleopolyploidy has been found in baker's yeast (Saccharomyces cerevisiae), despite its small, compact genome (~13Mbp) after the divergence from K. waltii. Through genome streamlining, yeast has lost 90% of the duplicated genome over evolutionary time and is recognized as a diploid organism nowadays.

[edit] 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 single gene duplication (which is a common phenomenon in the genome) events, the following rules are often applied:

Detection of Paleopolyploidy using Ks.

1. 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.
2. Duplicated blocks are non-overlapping because they were created simultaneously. Segmental duplication within the genome can fulfill Rule #1; 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).

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 a very ancient paleopolyploidy.

[edit] Evolutionary importance

Paleopolyploidization events lead to massive cellular changes, including doubling of the genetic material, changes in gene expression and increased cell size. Genes lost 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.

• Genome Diversity

genome doubling provided the organism with redundant alleles that can evolve freely with little selection pressure. The duplicated genes can undergo neofunctionalization or subfunctionalization which could help the organism adapt to the new environment or survive different stress conditions.

• Heterosis

polyploids often have larger cell sizes 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 invasive species in many regions.

[edit] Human as paleopolyploid

The hypothesis of human paleopolyploidy originated as early as the 1970's, 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.

However, the 2R hypothesis has been questioned by many researchers. Based on the theory, the human genome should have a 4:1 gene ratio compared with invertebrate genomes. This did not appear to be supported by findings from various genome projects – the human genome consists of ~35,000 genes while an average invertebrate genome size is about 15,000 genes. However, the recent completion of the amphioxus genome sequence has revealed the presence of a 4:1 ratio of genes, as predicted by the hypothesis.^[1] 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.^[2]

These recent findings have largely supported the 2R hypothesis.

[edit] See also

• Gene duplication
• Genomics
• Karyotype
• Ploidy
• Polyploidy
• Speciation

[edit] References

1. Adams KL, Wendel JF (April 2005). "Polyploidy and genome evolution in plants". Curr. Opin. Plant Biol. 8 (2): 135–41. doi:10.1016/j.pbi.2005.01.001. PMID 15752992. http://linkinghub.elsevier.com/retrieve/pii/S1369-5266(05)00005-1. 
2. Cui L, Wall PK, Leebens-Mack JH, et al. (June 2006). "Widespread genome duplications throughout the history of flowering plants". Genome Res. 16 (6): 738–49. doi:10.1101/gr.4825606. PMID 16702410. PMC 1479859. http://www.genome.org/cgi/pmidlookup?view=long&pmid=16702410. 
3. Wolfe KH (May 2001). "Yesterday's polyploids and the mystery of diploidization". Nat. Rev. Genet. 2 (5): 333–41. doi:10.1038/3507200910.1038/35072009. PMID 11331899. 
4. Blanc G, Wolfe KH (July 2004). "Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes". Plant Cell 16 (7): 1667–78. doi:10.1105/tpc.021345. PMID 15208399. PMC 514152. http://www.plantcell.org/cgi/pmidlookup?view=long&pmid=15208399. 
5. Blanc G, Wolfe KH (July 2004). "Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution". Plant Cell 16 (7): 1679–91. doi:10.1105/tpc.021410. PMID 15208398. PMC 514153. http://www.plantcell.org/cgi/pmidlookup?view=long&pmid=15208398. 
6. Comai L (November 2005). "The advantages and disadvantages of being polyploid". Nat. Rev. Genet. 6 (11): 836–46. doi:10.1038/nrg171110.1038/nrg1711. PMID 16304599. 
7. Otto SP, Whitton J (2000). "Polyploid incidence and evolution". Annu. Rev. Genet. 34: 401–437. doi:10.1146/annurev.genet.34.1.401. PMID 11092833. http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.34.1.401?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov. 
8. Makalowski W (May 2001). "Are we polyploids? A brief history of one hypothesis". Genome Res. 11 (5): 667–70. doi:10.1101/gr.188801. PMID 11337465. http://www.genome.org/cgi/pmidlookup?view=long&pmid=11337465. 
9. Kellis M, Birren BW, Lander ES (April 2004). "Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae". Nature 428 (6983): 617–24. doi:10.1038/nature0242410.1038/nature02424. PMID 15004568.