Effective Population Size and Population Subdivision in Demographically Structured Populations

Valérie Laporte; Brian Charlesworth

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Figure 1.
—The F_ST parameters (A-C) and the ratios (R) of total diversities between genes with different modes of inheritance (D-F) in a subdivided plant population (m_f = 0), as functions of the number of migrants per deme, N(m_m + m_z). (A and D) Equal pollen and seed migration. (B and E) Predominantly pollen migration (m_m = 100m_z). (C and F) Predominantly seed migration (m_z = 100m_m). We assume N_eA = N, N_e_X = ¾.N, N_e_Y = N_ec = ¼.N.
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Figure 2.
—The F_ST parameters (A-C) and the R values (D-F) in a subdivided animal population (m_z = 0), as functions of the number of migrants per deme, N(m_m + m_f). (A and D) Equal male and female migration. (B and E) Predominantly male migration (m_m = 6m_f). (C and F) Predominantly female migration (m_f = 6m_m). We assume N_eA = N, N_e_X = ¾.N, N_e_Y = N_ec = ¼.N.
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Figure 3.
—Same as Figure 2 but assuming an increased variance of male fertility compared to the Poisson expectation (ΔV_m = 10).
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Figure 4.
—Same as Figure 1 but assuming an increased variance of female fertility compared to the Poisson expectation (ΔV_f = 5).
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Figure 5.
—Same as Figure 1 but assuming N_e_Y = N_e_X/30. The figures also give the F_ST and R_XY estimates from Silene latifolia populations with the number of migrants expected under an island model (Triangle, Fˆ_ST,_Y; square, Fˆ_ST,A; circle, Fˆ_ST,_X; and cross, Rˆ_XY).

Tables

Figures

TABLE 1

Origins of genes sampled from a given deme

Sexes of sampled individuals	Sex of parent	Probability of parent of given sex
Female, female	Female
Male, male	Female
Male, female	Female
Female, female	Male
Male, male	Male
Male, female	Male

i indicates the identity of the deme. is the excess over the Poisson expectation (equal to the mean number of progeny per capita of sex s) of the variance of the number of progeny of sex s of parents of sex r.

TABLE 2

Transmission parameters for different modes of inheritance

		Mode of inheritance
Sexes of sampled individuals (r, s)	Sex of parent (u)	Autosomal			X-linkage			Y-linkage
Sexes of sampled individuals (r, s)	Sex of parent (u)	α_irα_is	β_irsu	γ_irsu	α_irα_is	β_irsu	γ_irsu	α_irα_is	β_irsu	γ_irsu
Female, female	Female							—	—	—
Male, male	Female					1		—	—	—
Male, female	Female							—	—	—
Female, female	Male						1	—	—	—
Male, male	Male				—	—	—	1	1	1
Male, female	Male				—	—	—	—	—	—

F_i is the inbreeding coefficient due to consanguineous matings within deme i. Maternally transmitted organelle genomes have similar properties to Y-linked genes, except that female and male parameters are interchanged.

TABLE 3

Review of F_ST estimates at a worldwide spatial scale in human populations

No. of groups or populations		Gene heredity
No. of groups or populations	F_ST statistics	Y	A	MtDNA	Reference
15	G_ST (1)	0.18^a; 0.54^b	0.10^a; 0.11^b; 0.15^c	0.25^d	Jorde et al. (2000)
	Ψ_ST (2)	0.17^a	0.12^a; 0.15^b; 0.19^c	0.30^d
19	Ψ_ST (2)	0.19^e	—	0.27^f	Poloni et al. (1997)
15	Ψ_ST (2)	0.16^a; 0.30^e	—	—	Hammer et al. (1997)
50	Ψ_ST (2)	0.36^g	—	—	Hammer et al. (2001)
10	F_ST (1)	0.41^h	—	—	Reviewed in Hammer et al. (2001), data from Underhill et al. (1997)
	Ψ_ST (2)	0.54^h
—	Ψ_ST (2)	0.65^h	—	—	Seielstad et al. (1998) from Underhill et al. (1997)
20	Ψ_ST (2)	0.23^a	—	—	Kayser et al. (2001)
21	Ψ_ST (2)	0.09^a; 0.40^c	—	—	Quintana-Murci et al. (1999)
5	K_ST (3)	0.14^d	—	—	Thomson et al. (2000)
10; 14	Ψ_ST (2)	—	0.16^e; 0.16^a	—	Barbujani et al. (1997)
5	F_ST (1)	—	0.14^e	—	Bowcock et al. (1991)
31	F_ST (1)	—	0.112^c	—	Watkins et al. (2001)
3	Equation 24a, 24b	—	0.034^d^,ⁱ	—	Yu et al. (2001)
4	Equation 24a, 24b	—	0.165^d^,ⁱ	—	Zhao et al. (2000)
13	F_ST (1)	—	0.147^j^,^k	—	Zietkiewicz et al. (1998)
10	Ψ_ST (2)	—	—	0.25^f	Excoffier et al. (1992)

(1) F_ST or G_ST, Cockerham and Weir (1993); Wright (1951); (2) Ψ_ST, Excoffier et al. (1992); (3) K_ST Hudson et al. (1992).
↵^a Microsatellites.
↵^b Restriction site polymorphism (RSP).
↵^c Alu.
↵^d Sequences.
↵^e RFLP.
↵^f mtDNA RFLP.
↵^g SSCP + DHPLC.
↵^h Denaturing high-performance liquid chromatography (DHPLC).
↵ⁱ Introns or noncoding regions.
↵^j SSCP + heteroduplex analysis + sequencing.
↵^k Neutral polymorphisms.

TABLE 4

Silent site diversity in Silene latifolia

Mode of inheritance	Gene (no. of silent sites)	S	(%)	(%)	F̂_ST
Y-linkage	SlY1 (1652)	4	0.048	0.088	0.45
	SlY4 (829)	5	0.073	0.189	0.62
	SlY1 + SlY4 (2481)	9	0.056	0.113	0.50
X-linkage	SlX1 (1262)	88	1.567	2.172	0.28
	SlX4 (362)	42	1.933	3.974	0.51
	SlX1 + SlX4 (1624)	78	1.649	2.574	0.36
Autosomal	CCLS37.1 (955)	22	0.610	0.743	0.18

Diversity was estimated from a sample of 13 individuals from five populations: one Danish (n = 3), one U.S. (Van, n = 3), one Portuguese (SC, n = 3), and two British (Dal, n = 2; Art, n = 2) except for the autosomal gene where the Danish population was not studied (Filatov et al. 2001; V. Laporte, unpublished data). F_ST was estimated following Equation 24a, 24b.