Bishop Et Al. Supplementary Files

Bishop et al. Supplementary Files

Mitogenomic analysis of the Australian lungfish (Neoceratodus forsteri) reveals structuring of indigenous riverine populations and late Pleistocene movement between drainage basins.

Supplementary File S1.

Haplotype table and GenBank accession codes. Haplotype codes correspond with the mitogenome haplotype network shown in Figure 1.

Haplotype code / Genbank Accession / Sample Code
01 / MF489911 / BNE004, BNE030, BNE033, BNE041, BNE044, BNE062, BNE070, MAR166
02 / MF489912 / BNE005, BNE019, BNE029, BNE194
03 / MF489913 / BNE026, BNE125
04 / MF489914 / MAR162
05 / MF489915 / BNE020
06 / MF489916 / BUR02, BUR03, BUR07
07 / MF489917 / BUR08
08 / MF489918 / BUR09
09 / MF489919 / BUR04
10 / MF489920 / BUR15
11 / MF489921 / BUR06
12 / MF489922 / BUR10
13 / MF489923 / TIN14, TIN20
14 / MF489924 / TIN21
15 / MF489925 / TIN15, TIN18, TIN23, TIN27
16 / MF489926 / TIN29
17 / MF489927 / TIN12
18 / MF489928 / TIN16
19 / MF489929 / BUR13
20 / MF489930 / MAR164
21 / MF489931 / MAR173
22 / MF489932 / MAR167
23 / MF489933 / MAR203
24 / MF489934 / BUR14
25 / MF489935 / BUR01
26 / MF489936 / BUR05, BUR12
27 / MF489937 / BUR194
28 / MF489938 / MAR163, MAR204, NPD05, NPD09, NPD10, NPD12
29 / MF489939 / MAR169, MAR205
30 / MF489940 / TIN19
31 / MF489941 / NPD04
32 / MF489942 / BNE075
33 / MF489943 / BNE092
34 / MF489944 / MAR161, NPD03, NPD07, NPD14
35 / MF489945 / NPD01 , NPD11, NPD13, PD15
36 / MF489946 / MAR170
37 / MF489947 / MAR165
38 / MF489948 / MAR172
39 / MF489949 / MAR202
40 / MF489950 / NPD08
41 / MF489951 / NPD06

Supplementary File S2.

A maximum likelihood tree was estimated for the full mitogenome alignment, including the NCBI Reference Sequence (NC_003127), using RAxML v8.2.9 via the CIPRES science gateway (Miller et al. 2010; Stamatakis 2006). The best tree was found under the GTR+G substitution model with separate partitions as used in the BEAST analysis (see Materials and Methods section). Figure S1 shows the best tree from the RAxML analysis, highlighting the position of NC_003127 (Brinkmann et al. 2004) on a long terminal branch.

Supplementary File S3.

Density plot showing distribution of polymorphic sites along the 16,573 bp mitogenome alignment for 71 Neoceratodus forsteri samples. Density plot produced using the function snpposi.plot in the R package adegenet v2.0.1 in R (Jombart 2008). Additionally the function snpposi.test was used to test whether SNPs were randomly distributed along the mitogenome. Based on 1000 randomisations, there was no evidence for significant clustering of SNPs (median distance between adjacent SNPs = 38; p-value = 0.308).

Supplementary File S4.

Coalescent simulation illustrating the appearance of “apparent” private polymorphic sites in a recently founded population when diversity of the source population is undersampled. Data was simulated using software fastsimcoal2 v .5.2.21 (Excoffier and Foll 2011) and summary statistics processed using software arlsumstat v.3.5.2 (Excoffier and Lischer 2010). The simulation scenario involved simulating a population exhibiting segregating sites similar to the observed Mary population (S = 88). A new population was founded six generations ago by randomly sampling five gene copies from the Mary source population (mimicking the proposed translocation history of lungfish in the Brisbane River). The number of private polymorphic sites in the translocated population relative to the source population were counted after randomly sampling 15 gene copies from the source population (=Mary) and 16 gene copies from the translocated population (=Brisbane). A total of 1000 simulations were performed under this scenario. Distribution of private polymorphic sites in the simulated translocated population shown below. The observed number of private polymorphic sites in the Brisbane sample was nine.

Parameter file used for simulating 1000 datasets in fastsimcoal2:

//Number of population samples (demes)

//Population effective sizes (number of genes)

1000 //MAR

1000 //BNE

//Sample sizes

15 //MAR

16 //BNE

//Growth rates: negative growth implies population expansion

//Number of migration matrices : 0 implies no migration between demes

//historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix

2 historical event

4 1 1 0 0.005 0 0 //4 gens ago pop1 bottlenecks to 5ind for 2 generations

6 1 0 1 1 0 0 //6 gens ago, pop1 sends all its genes to pop0

//Number of independent loci [chromosome]

1 0

//Per chromosome: Number of linkage blocks

//per Block: data type, num loci, rec. rate and mut rate + optional parameters

DNA 16570 0.00000 0.0000006 0.33

References

Brinkmann H, Denk A, Zitzler J, Joss JJ, Meyer A (2004) Complete mitochondrial genome sequences of the South American and the Australian lungfish: Testing of the phylogenetic performance of mitochondrial data sets for phylogenetic problems in tetrapod relationships Journal of Molecular Evolution 59:834-848 doi:10.1007/s00239-004-0122-8

Excoffier L, Foll M (2011) fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios Bioinformatics 27:1332-1334 doi:10.1093/bioinformatics/btr124

Excoffier L, Lischer H (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows Molecular ecology resources 10:564-567

Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers Bioinformatics 24:1403-1405 doi:10.1093/bioinformatics/btn129

Miller MA, Pfeiffer W, Schwartz T Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA, 2010. pp 1-8

Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Bioinformatics 22:2688-2690 doi:10.1093/bioinformatics/btl446