Heredity

Table 1 Statistical measures used to detect bottlenecks

From: Inferring population size changes with sequence and SNP data: lessons from human bottlenecks

Data	Species	Statistics	Simulations	Bottleneck	Ref.
SNPs	Homo sapiens	LD decay	Coal.-1 pop	Non-African bott.	Reich et al. (2001)
SNPs	Homo sapiens	SFS-LD-Fst	Coal.-IM model	Out-of-Africa	Schaffner et al. (2005)
SNPs	Homo sapiens	SFS	Coal. 1 pop	Out-of-Africa	Adams and Hudson (2004), Marth et al. (2004) and Keinan et al. (2007)
50 10-kb sequences	Homo sapiens	Class I-LD decay	Coal. 1 pop	Out-of-Africa	Voight et al. (2005)
50 500-bp sequences	Homo sapiens	Class I-Fst	Coal.-IM model	Out-of-Africa +Toward America	Fagundes et al. (2007)
24 1-kb sequences	Homo sapiens	Class I-Fst-Stats based on Multipop-SFS	Coal.-IM model	Pygmies	Patin et al. (2009)
SNPs	Homo sapiens	Class II	Coal. 1 pop	European bott.	Lohmueller et al. (2009)
SNPs	Homo sapiens	Joint-SFS	Diffusion IM model	Out-of-Africa	Gutenkunst et al. (2009); Gravel et al. (2011)
SNPs	Homo sapiens	r² measure of LD	No simulations	Out-of-Africa	McEvoy et al. (2011)
SNPs	Homo sapiens	IBD segments	Coal. 1 pop	Ashkenazy Jewish	Atzmon et al. (2010) and Gusev et al. (2012)
SNPs	Homo sapiens	ROH	Coal. 1 pop	Hadza	Henn et al. (2011)
Whole genome	Homo sapiens	Local density of heterozygotes	Coal. 1 pop	Bott. in all continents	Li and Durbin (2011)
61 20-kb sequences	Homo sapiens	Class I	Coal. 1 pop	No speciation bott. during ice age	Sjödin et al. (2012)
X-linked and autosomal sequences	Drosophila melanogaster	Class I and II-LD	Coal. 1 pop	Non-African bott.	Haddrill et al. (2005) and Thornton and Andolfatto (2006)
X-linked and autosomal sequences	Drosophila melanogaster	SFS	Coal.-2pop IM model	European bott.	Hutter et al. (2007)
∼300 500-kb sequences	Drosophila melanogaster	Class I and II	Coal.-IM model	Southeast Asia	Laurent et al. (2011)

Abbreviations: bott., bottleneck; Coal., coalescent; IBD, identical by descent; IM model, Isolation and Migration model; LD, linkage disequilibrium; ROHs, runs of homozygosity; SFS, site-frequency spectrum.

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