Cultivated rice, Oryza sativa, is one of the most important human foods. The two main sub-species of cultivated rice are O. sativa indica and O. sativa japonica. O. rufipogon is a wild species from which they probably evolved. To investigate whether the sub-species of cultivated rice evolved independently from the wild species, scientists analysed their chromosomes to find areas with similar DNA base sequences. Wild species tend to have many different alleles of genes present on each chromosome, but during the development of a crop plant by artificial selection from a wild species, this diversity drops considerably, increasing the base sequence similarity. The number of different alleles of the genes on a chromosome can be represented by a diversity index. The following graph of part of chromosome 7 shows the diversity index of O. rufipogon and two varieties of cultivated rice, O. sativa indica and O. sativa japonica. The gene PROG1 allows the plant to stand upright, which is typical of cultivated rice. Its position is indicated by the vertical arrow on the graph. 
In another experiment, scientists retrieved genome sequences of the wild rice O. rufipogon taken from a wide range of geographical sites (I, II and III) and those of the two sub-species of O. sativa from gene banks. The pie charts, presented along with a cladogram, show the proportion of alleles for three genes which confer specific characteristics to O. sativa. Mutations can produce derived alleles that are different from the original ancestral alleles. The control group represents wild rice species other than O. rufipogon. 
State the reason that O. sativa and O. rufipogon are classified as different species.
[1]cannot interbreed to produce fertile offspring ✔ Accept converse or a good explanation.
Determine which type of rice has the lowest overall diversity index.
[1]«O. sativa» japonica ✔
Compare and contrast the trends for O. rufipogon and O. sativa indica.
[2]a SIM both show diversity OR similar pattern/peaks and troughs in the first part of the chromosome / up to «approximately» 1.5 megabases OR similar diversity between 2.4 to 2.7 mb OR both highest at 0.7 mb ✔ b DIFF there are «two» major drops in diversity for O. sativa indica whereas none for O. rufipogon/much wider fluctuations in O. s. indica OR O. s. indica much lower at PROG1 OR O. rufipogon does not drop < 2.5 whereas O. s. indica approaches 0 OR O. rufipogon generally higher than O. s. indica after 1.4-1.5 ✔ One answer from mpa and one from mpb required for 2 [max]. Accept a statement of where the drops occur.
State the proportion of the ancestral allele for the gene GS3 in the O. rufipogon-III population.
[1]Distinguish between the proportion of ancestral and derived alleles for all three genes in O. sativa indica and O. sativa japonica.
[2]State one reason for having a control group.
[1]Using all of the data, discuss whether there is evidence that the two sub-species of O. sativa might have evolved independently from O. rufipogon.
[4]a large difference in diversity index between O. s. indica and O. s. japonica «suggests independent evolution» ✔ b «some of the» peaks/troughs for O. s. indica and O. s. japonica in different positions «suggests independent evolution» ✔ c O. s. indica has a similar diversity index to O. rufipogon «which suggests closer relationship/recent divergence» ✔ Allow converse for japonica d O. s. japonica has very different proportions of ancestral and derived alleles compared to O. s. indica ✔ e O. s. indica has similar large number of ancestral alleles to O. rufipogon I/IJ Allow converse for derived f O. s. japonica has a large number of derived alleles similar to O. rufipogon III OR «but» the number of derived alleles is greater in O. s. japonica than in O. rufipogon III ✔ Allow converse for ancestral g O.s. indica and O. s. japonica are in different clades ✔ OR O. s. indica and O. rufipogon I are in the same clade ✔ h evidence from one chromosome/3 genes/2 studies is not sufficient to form a conclusion ✔ 4 max
