The answer may be both. Researchers from Sun Yat-Sen University, Beijing Institute of Genomics (BIG) and the University of Chicagostudied the kinship of rice by examining the 50,000 or so genes in the Asian wild rice O. rufipogon genome and comparing it to its domestic descendants. They found that, for most of the genes, indica and japonica are no closer to each other than each is to the wild rice but when the gene regions for traits influenced by artificial selection were examined, indica and japonica appear to share a surprisingly strong kinship.
Their conclusion: since loci in rice show patterns of variation inconsistent with the independent domestication hypothesis but phylogenetic studies have tended to support independent domestication, perhaps the domestication of rice occurred at least twice independently but with extensive "borrowing" between the two subspecies. The two theories may not need to be mutually exclusive.
Early northern and southern farmers may have cultivated rice independently but it seems more likely that they got desired traits extensively from rice farmed by others, resulting in the opposing kinships reported.
In other words, piracy - the literal or the intellectual kind- may have been with us since humans first began agricultural agricultural production.
(A) Independent domestication – In the simplest form of independent domestication, indica and japonica were separately domesticated from O. rufipogon at about the same time, resulting in a trifurcation phylogeny. The most recent common ancestor of three taxa was time T from present. The two dashed circles highlight the coalesced lineages (xI and xJ, respectively) at the time of domestication, Td. Branch widths reflect the relative population sizes (NI, NR and NJ) of the three taxa. (B) Sequential domestication – In this model, indica and japonica share a common history of domestication (Td'), and they are most closely related to each other.
Citation: He Z, Zhai W, Wen H, Tang T, Wang Y, et al. (2011) Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes. PLoS Genet 7(6): e1002100. doi:10.1371/journal.pgen.1002100
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