Table 1

Literature survey of empirical studies focusing on phylogeography, hybridization and speciation that used PHASE for haplotype reconstruction (see Additional file 4 for a complete list of references).

Birds

Herpetofauna

Mammals

Fish

Invertebrates

Total

(N = 15)

(N = 12)

(N = 10)

(N = 8)

(N = 15)

(N = 60)


PHASE threshold used

0.95

3

-

1

4

2

10

0.90

-

4

1

1

2

8

0.75-0.80

4

-

-

-

-

4

0.70

1

1

-

-

-

2

0.60

-

-

-

2

3

5

Best of replicate runsa

-

1

-

-

2

3

Not reported

7

6

8

1

6

28


Unresolved genotypes

Excluded or coded as missing

5

5

1

5

3

19

Resolved experimentally

2

-

-

-

2

4

Included despite uncertainty

3

-

-

-

-

3

None present

1

1

-

3

4

9

Not reported

4

6

9

-

6

25


Experimental validation

Cloning

1

2

-

1

4

8

Allele-specific PCR

3

-

-

-

-

3

None

11

10

10

7

11

49


Downstream analyses

Theta (Θ)b

14

6

9

4

7

40

Nucleotide diversity (Π)

9

7

9

4

7

36

Neutrality or population growth

7

6

4

6

5

28

Network or phylogenetic tree

10

9

9

6

10

44


aUses all inferred haplotypes from the run with the best average goodness-of-fit

bIncludes studies that implicitly calculated theta as part of coalescent analyses (e.g., MIGRATE, FLUCTUATE, IM)

Garrick et al. BMC Evolutionary Biology 2010 10:118   doi:10.1186/1471-2148-10-118

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