Table 2 Nucleotide diversity for Y, W, dot fourth chromosomes (compared with diversity for X or Z chromosomal or autosomal loci) and mtDNA and cpDNA (compared with nuclear loci) as a proportion of that expected from neutral theory (corrected for differences in copy number and mutation rates)

From: How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination

Species	Proportion of neutral expectation ^a	References
W chromosome
Barn swallow	0	1
Black grouse	0	1
Blue tit	0	1
Chiffchaff	0	2
Chicken	0.075	3
Collared flycatcher	0	1
Dusky warbler	0	2
Kestrel	0	1
Pied flycatcher	0	1
White-throated sparrow	0.056	3, 4
Willow warbler	0, 0	1, 2
Y chromosomes
Bonobo	1.08	5, 6
Cattle	0	7
Chimpanzee^b	0.02	5, 6
Field vole	0.43	7
Greater white-toothed shrew	0.49	8
Horse	0	9
Human	0.44, 0.62, 0.29, 0.47	5, 6, 10, 11, 12
Lynx	0	7
Mouse	0.53	6, 11
Reindeer	0	7
Sheep	0.11	13
Wolf	0.16	7
Drosophila melanogaster	0	14
Drosophila miranda	0.11	15, 16
Drosophila santomea	0.05	17
Drosophila. simulans	0.08	14, 16
Drosophila teissieri	0	17
Drosophila yakuba	0.09	17
Silene dioica	0.08	18
Silene latifolia	0.15	19
Chromosome-4 in Drosophila
Dot (very low recombination)
D. americana	0.06	20
D. mauritiana	0.05	21
D. melanogaster	0, 0.04, 0.41, 0.13	21, 22, 23, 24, 25
D. sechellia	0	21
D. simulans	0.03, 0.02, 0.08, 0.07	21, 22, 23, 25, 26, 27
D. yakuba	0.10	15,23,25
Fused to another autosome (∼normal recombination)
D. insularis	1.34	28
D. willistoni	0.92, 1.28	28
mtDNA
Greater white-toothed shrew	0.48	8
Mice (two sub-species)	0.91, 0.88	29
Beetle (Adalia bipunctata) (with three strains of Ricksettsia)	10.12	30
Butterfly (Acraea encedana) (with Wolbachia)	0	31
Drosophila innubila (with Wolbachia)	0.17	32
D. melanogaster	0.18	14, 33
D. recens (with Wolbachia)	0.03	34, 35
D. santomea	0.18	17, 35
D. simulans	0.04	17, 33
D. subquinaria (no Wolbachia)	0.63	34, 35
D. teissieri	0.05	17, 35
D. yakuba	0.09	17, 35
Arabidopsis lyrata	0.81	36
Caenorhabditis remani	1.19	35, 37
Chylamdomonas reinhardtii	0.53	38
cpDNA
Arabidopsis lyrata	0.80	36
Arabidopsis thaliana	0.75^c	36

^aWhere the referenced publication did not provide the corrected ratio, I have calculated it from the original data.
^bOnly Pan troglodytes verus data were used as there are diverged sub-species that may complicate matters and this sub-species had much higher sample sizes than the others.
^cCorrected for selfing.
References: 1, Montell et al. (2001); 2, Bensch et al. (2006); 3, Berlin and Ellegren (2004); 4, Huynh et al. (2010); 5, Stone et al. (2002); 6, Ellegren (2007); 7, Hellborg and Ellegren (2004); 8, Handley et al. (2006); 9, Lindgren et al. (2004); 10, Sachidanandam et al. (2001); 11, Nachman (1998); 12, Shen et al. (2000); 13, Meadows et al. (2004); 14, Zurovcova and Eanes (1999); 15, Bachtrog and Charlesworth (2000); 16, Bauer and Aquadro (1997); 17, Bachtrog et al. (2006); 18, Filatov et al. (2001); 19, Qiu et al. (2010); 20, Betancourt et al. (2009); 21, Hilton et al. (1994); 22, Jensen et al. (2002); 23, Moriyama and Powell (1996); 24, Wang et al. (2002); 25, Arguello et al. (2010); 26, Wang et al. (2004); 27, Begun et al. (2007); 28, Powell et al. (2011); 29, Baines and Harr (2007); 30, Jiggins and Tinsley (2005); 31, Jiggins (2003); 32, Dyer and Jaenike (2004); 33, Haag-Liautard et al. (2008); 34, Shoemaker et al. (2004); 35, Kondrashov and Kondrashov (2010); 36, Wright et al. (2008); 37, Graustein et al. (2002); 38, Smith and Lee (2008).
The neutral expectation is 1.

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Table 2 Nucleotide diversity for Y, W, dot fourth chromosomes (compared with diversity for X or Z chromosomal or autosomal loci) and mtDNA and cpDNA (compared with nuclear loci) as a proportion of that expected from neutral theory (corrected for differences in copy number and mutation rates)

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