Phylogenetics Evolutionary Relationships Between Maize & Other Grass SpeciesMaize is a member of the grass family Poaceae (Gramineae), a classification it shares with many other important agricultural crops, including wheat (Triticum aevestium), rice (Orzya sativa), oats (Avena), sorghum (Sorghum), barley (Hordeum) and sugarcane (Saccharum). Based on fossil evidence, it is estimated that these major grass lineages arose from a common ancestor within the last 55-70 million years, near the end of the reign of dinosaurs. Maize is further organized in genus Zea, a group of annual and perennial grasses native to Mexico and Central America. Genus Zea includes the wild taxa, known collectively as “teosinte” (Zea ssp.), as well as domesticated corn, or “maize” (Zea mays ssp. mays). Grass Relationships: Over the last 20 years, technological advances have made it possible to sequence the DNA of many grass species. By comparing the similarities and differences of this sequence data, we now have a better understanding of the evolutionary relationships between various grass species. The figure below illustrates some of these relationships based on sequencing ribosomal DNA (Buckler & Holtsford 1996). There are three ancient lineages: (1) Rice (Orzya) and the bamboos, (2) Wheat (Triticum), oats (Avena), and barley (Hordeum), and (3) Maize (Zea), sorghum (Sorghum), and sugarcane (Saccharum). 
The above phylogeny also indicates that genus Zea (including maize) is closely related to the genus Tripsacum. Members of the genus Tripsacum are found throughout North and South America. Tripsacum species (N=18 or 36) have almost twice as many chromosome as does Zea (N=10). One interesting species of note, Tripsacum dactyloides, is used as a forage crop for cattle in the US. 
Five species of Zea are currently recognized: - Zea diploperennis: a perennial, diploid teosinte found in very limited regions of the highlands of Western Mexico
- Zea perennis: a perennial, tetraploid teosinte, also with a very narrow distribution in the highlands of Western Mexico
- Zea luxurians: an annual teosinte found in the more equatorial regions of southeastern Guatemala and Honduras
- Z. nicaraguensis (Iltis and Benz, 2000): closely related to Zea luxurians and found in very mesic environments in Nicaragua
- Zea mays: a highly polymorphic, diploid annual species, including both wild teosinte and cultivated maize
This last species, Zea mays, is further divided into four subspecies. Some of these subspecies could also be considered species: - Z. mays ssp. huehuetenangensis, an annual teosinte found in a few highlands of northwestern Guatemala
- Z. mays ssp. mexicana, an annual teosinte from the highlands of central and northern Mexico
- Z. mays ssp. parviglumis, an annual teosinte, common in the middle and low elevations of southwestern Mexico
- Z. mays ssp. mays, maize or “Indian corn,” most likely domesticated in the Balsas river valley of southern Mexico
Several molecular studies have helped clarify how the various species and subspecies are related to one another. These relationships are shown in the following figure: 
Although maize has been studied intensively, ambiguities still exist in this phylogenetic tree: Known with High Confidence | Still Uncertain | | Maize is most closely related to Z. mays ssp. parviglumis. | Exact position of Zea luxurians. | | Z. mays ssp. parviglumis, mexicana, and maize are all closely related. | Exact relationship between Z. mays ssp. mexicana and parviglumis. | | Zea diploperennis and Z. perennis are closely related. | | | Tripsacum is a sister genus that diverged several million years ago. | |
These ambiguities stem from the very large effective population size and very high diversity found in Zea. This large effective population size results in alleles segregating for a very long time. For example, the effective population size of Z. mays ssp. parviglumis might be 1,000,000 individuals or even higher, whereas the historical effective population size of humans may have been only 50,000 individuals. As a result, Zea boasts a level of nucleotide diversity roughly 30 fold higher than humans! The bottom line: While no single gene can provide a perfect picture of the evolutionary relationships in this genus, technological improvements of the last decade have permitted the survey of numerous genes, and these surveys consistently support the phylogenetic tree presented above. BUCKLER, E. S., IV, and T. P. HOLTSFORD, 1996 Zea systematics: ribosomal ITS evidence. Molecular Biology & Evolution 13: 612-622. DOEBLEY, J., W. RENFROE and A. BLANTON, 1987 Restriction site variation in the Zea chloroplast genome. Genetics 117: 139-147. DOEBLEY, J. F., M. M. GOODMAN and C. W. STUBER, 1984 Isoenzymatic variation in Zea (Gramineae). Systematic Botany 9: 203-218.
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