Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis

Table 2 Nucleotide diversity for the plastid, mitochondrial, and nuclear genomes of Chlamydomonas reinhardtii.

	Protein-coding regions			Intronic/intergenic regions^e			Silent sites^f
	ptDNA	mtDNA	nucDNA	ptDNA	mtDNA	nucDNA	ptDNA	mtDNA	nucDNA
# of sites ^a	7272	8160	1623	9438	2457	4510	16710	5550	5051
S	45	44	26	276	58	355	321	104	377
# of Indels ^b (length nt)	1 (21)	1 (6)	1 (9)	85 (1672)	9 (23)	47 (216)	86 (1679)	11 (31)	48 (222)
π ^c × 10 ^-3 (SD × 10 ^-3 )	2.82 (0.34)	2.06 (0.43)	6.02 (0.99)	15.17 (1.70)	8.92 (1.88)	33.50 (3.15)	14.53 (1.18)	8.51 (1.03)	32.29 (3.01)
π ₊ ^d × 10 ^-3 (SD × 10 ^-3 )	---	---	---	19.54 (2.03)	10.29 (2.02)	38.63 (3.70)	18.36 (1.40)	9.23 (1.96)	36.00 (3.51)
π _syn × 10 ^-3	8.46	8.52	19.57	---	---	---	---	---	---
π _nsyn × 10 ^-3	1.14	0	1.42	---	---	---	---	---	---

Note: S, number of segregating (i.e., polymorphic) sites; Indels, insertion-deletion events; π, nucleotide diversity; π₊, nucleotide diversity including both polymorphic sites and insertion-deletion events; π_syn, nucleotide diversity at synonymous sites; π_nsyn, nucleotide diversity at nonsynonymous sites; SD, standard deviation. Mitochondrial- and nuclear-genome data come from [7].
^a Comprises all sites in the nucleotide alignment, including those with indels.
^b Indels involving more than 1 nucleotide are counted as a single event. Indel length includes the sum of all indels and includes consecutive indel events.
^c Only includes sites in the alignment without indels.
^d Considers all sites, including those with indels. Consecutive indels are counted as a single polymorphic event. Indel states were measured using a multiallelic approach.
^e For the ptDNA and mtDNA these values were generated from intergenic nucleotide sites, whereas for the nucDNA they came from intronic sites.
^f Includes noncoding and synonymous sites; π₊ values for the mtDNA and nucDNA differ slightly from those previously reported [7] due to a different interpretation of indel sites in nucleotide-diversity calculations.

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