Table 2 Summary of nucleotide polymorphisms for African C. elegans and C. briggsae isolates

From: Hakuna Nematoda: genetic and phenotypic diversity in African isolates of Caenorhabditis elegans and C. briggsae

Locus (chromosome)

African population samples

South Africa

Kenya

 

Silent sites

S

h

H d

Indels

πsi

θsi

πsi

θsi

πsi

θsi

C. elegans

 Y25C1A.5 (II)

658.8

7

4

0.596

4

0.0036

0.0031

0.0033

0.0031

0.0013

0.0022

 ZK430.1 (II)

542.8

1

2

0.529

1

0.0010

0.0005

0

0

0.0004

0.0007

 E01G4.6 (II)

521.4

16

3

0.324

2

0.0066

0.0091

0.0092

0.0125

0

0

 D1005.1 (X)

480.0

0

1

0

0

0

0

0

0

0

0

 R160.7 (X)

605.2

0

1

0

0

0

0

0

0

0

0

 T24D11.1 (X)

651.0

1

2

0.309

0

0.0005

0.0005

0.0007

0.0006

0

0

Concatenated

3459.2

25

6

0.743

7

0.0019

0.0021

0.0021

0.0026

0.0003

0.0005

Average

576.5

4.2

2.2

0.293

1.2

0.0019

0.0022

0.0022

0.0027

0.0003

0.0005

C. briggsae

 p09

484.7

      

0

0

0

0

 p10

581.3

      

0.0004

0.0006

0.0004

0.0007

 p11

571.3

      

0

0

0

0

 p12

623.7

      

0.0007

0.0012

0

0

 p13

593.5

      

0

0

0

0

 p14

599.5

      

0

0

0

0

Concatenated

3452.0

      

0.0002

0.0003

0.0001

0.0001

Average

575.7

      

0.0002

0.0003

0.0001

0.0001

  1. Abbreviations: S, segregating sites; h, haplotypes; Hd, haplotype diversity; πsi, silent-site diversity from pairwise differences; θsi, silent-site diversity from the number of segregating sites.
  2. Diversity estimates were calculated for each country in both species, and for all African samples for C. elegans but not for C. briggsae due to the distinct geographical structuring between countries in this species. For C. elegans, there were a total of 17 strains—7 from South Africa, 9 from Kenya and 1 from Madagascar (LKC34). For C. briggsae, there were a total of 17 strains—9 from South Africa (including DF5100) and 8 from Kenya.
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