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Table 2 Comparison of percentage of admixed ancestry results

From: Galaxy tools to study genome diversity

A.

 

2-ancestor model

3-ancestor model

Putatively admixed group

Coyote

Wolf

Coyote

Wolf

Dog

Red wolf (n = 12)

76.1 (144)

23.9 (184)

--

--

--

Algonquin wolf (n = 2)

41.9 (100)

58.1 (100)

--

--

--

Great Lakes wolf (n = 12)

14.9 (298)

85.1 (230)

--

--

--

Northeastern coyote (n = 13)

--

--

82.2 (96)

8.7 (51)

9.1 (16)

Midwestern coyote (n = 19)

--

--

90.1 (75)

2.4 (140)

7.5 (15)

B.

Switch value

Red wolf (n = 12)

Algonquin wolf (n = 2)

Great Lakes wolf (n = 12)

Northeastern coyote (n = 13)

Midwestern coyote (n = 19)

 

2-ancestor model

3-ancestor model

0.5

     

Coyote

66.9

52.8

41.9

71.2

76.4

Wolf

33.1

47.2

58.1

17.4

13.4

Dog

----

----

----

11.5

10.2

1.0

     

Coyote

66.8

51.2

38.9

70.8

77.0

Wolf

33.2

48.8

61.1

17.4

12.9

Dog

----

----

----

11.7

10.2

3.0

     

Coyote

71.0

47.3

30.1

73.2

82.3

Wolf

29.0

52.7

69.9

16.3

8.7

Dog

----

----

----

10.6

9.0

7.0

     

Coyote

76.1

44.7

21.6

76.7

87.7

Wolf

23.9

55.3

78.4

14.0

4.4

Dog

----

----

----

9.3

7.9

10

     

Coyote

78.8

40.5

18.1

78.1

89.2

Wolf

21.2

59.5

81.9

12.9

3.4

Dog

----

----

----

9.0

7.4

C.

   

Coyote Ancestry Proportion:

F ST

SNV Spacing

n SNV

Switch = 2

Switch = 5

Switch = 10

Any

Any

48,036

67.8%

70.0%

71.3%

Any

≥ 0.5 Mb

3,838

67.7%

70.1%

71.9%

≥ 0.4

Any

7,875

69.4%

72.6%

75.4%

≥ 0.4

≥ 0.5 Mb

2,562

70.9%

76.2%

81.2%

  1. A) Results from SABER [13], using the 2- or 3-ancestor model (initial admixture times, in generation units, are provided in parentheses from reference [33]) B) Results from Galaxy’s Admixture tool with various switch values; C) the variability of estimated average coyote percentage contributing towards the Red wolf genomes, depending on possible lower bounds imposed on F ST and/or spacing between SNVs, as well as switch penalty (nSNV, number of SNVs).