Mus spretus A2 lineage

The root is a computed node where the domesticus A2 lineage joins the domesticus TF lineage. It is essentially a consensus of L1MdA2, L1- reeler, and L1FTE, with other sequences called upon to settle a few otherwise undetermined positions.

The individual sequences are all recovered from SPRET/Ei by PCR and cover the positions 6112..7111 or 6110..7152 (because there were two different libraries with different primers)

Coordinates are from Loeb et al (1985); the ORF2 ter is at 6998.

The copy numbers detected by probing this library with an oligo specific for each substitution in the upper stem are each ~2000, except for 6626, which is in parallel with a substitution of the other major spretus lineage.

• Bootstrap support for the Ancestral node to the radiation is 100.
• Bootstrap support for the earliest sequence out to the last is 90.
• This is weak support for SK + SAG representing an early stage of the radiation.
• Copy number of sequences with patterns like SK/SAG is not > 80.
• Order of SK/SAG is indeterminant.
• Other groupings in radiation are without statistical support except for the 6998 A subset.

Total nonsynonymous:synonymous ratio on branches leading to extant sequences is 42:18; on ancestral lineage it's 1:2.

Numbers of parallel substitutions does not exceed random expectation.

Numbers of reversions is 2 vs. an expectation of 0.5 by random chance.

Ave. branch length in radiation is 8.23. Variance is 3.7^2.

Sequence Source

• SHA, SFA, SEA from SPLW31
• SK, SAG, SG, SAC, SA, SAB, SJ, SAA, SAD, SAE from SPLW39