Admixture results obtained from using 174 ’private SNPs’ based on the ADMIXTURE software.

(TIF)</p

Distribution of minor allele frequency (MAF) for different <i>Macrobrachium</i> species: <i>M</i>. <i>dux</i>, <i>M</i>. <i>macrobrachion</i>, <i>M</i>. <i>sollaudii</i>, <i>M</i>. <i>vollenhovenii</i>, <i>M</i>. <i>chevalieri; M</i>. <i>felicinum</i>, and <i>M</i>. <i>sp</i>.

Distribution of minor allele frequency (MAF) for different Macrobrachium species: M. dux, M. macrobrachion, M. sollaudii, M. vollenhovenii, M. chevalieri; M. felicinum, and M. sp.</p

Admixture results obtained from using 72 ’private SNPs’ based on the ADMIXTURE software.

(TIF)</p

PCA (left plot) and DAPC (right plot) obtained from using the reduced set of ‘private SNPs’ (N = 72 SNPs, called ‘private SNPs80’ panel; see Methods).

PCA–principal component analysis; DAPC–discriminant analysis of the principal components. M_ch–M. chevalieri; M_dx–M. dux; M_fe–M. felicinum; M_ma–M. macrobrachion; M_so–M. sollaudii; M_sp–M. sp; M_vo–M. vollenhovenii.</p

PCA (left plot) and DAPC (right plot) obtained from using a full set of SNPs (N = 1,814).

PCA–principal component analysis; DAPC–discriminant analysis of principal components. M_ch–M. chevalieri;M_dx–M. dux;M_fe–M. felicinum; M_ma–M. macrobrachion; M_so–M. sollaudii; M_sp–M. sp; M_vo–M. vollenhovenii.</p

Cluster membership classification of <i>Macrobrachium</i> species and the Bayesian information criterion (BIC) plot obtained from the full set SNPs (N = 1,814) using the Adegenet package assuming four (K = 4) and five (K = 5) populations.

Each bar in the admixture plot (left) represents an individual: M.ch–M. chevalieri; M.dx–M. dux; M.so–M. sollaudii; M.fe–M. felicinum; M.sp–M. sp; M.ma–M. macrobrachion; M.vo–M. vollenhovenii.</p

S1 Fig -

PCA plot obtained from a full set of 1,814 SNPs (A), 174 private SNPs (B) and 72 ‘private SNPs 80’ (C). M_ch–M. chevalieri;M_dx–M. dux;M_fe–M. felicinum; M_ma–M. macrobrachion; M_so–M. sollaudii; M_sp–M. sp; M_vo–M. vollenhovenii. (TIF)</p

Pictures of seven <i>Macrobrachium</i> species in the coastal area of Cameroon identified based on morphological analysis using [10, 31] keys.

Pictures of seven Macrobrachium species in the coastal area of Cameroon identified based on morphological analysis using [10, 31] keys.</p

Summary statistics of the ’private SNPs’ (‘private SNPs80’; N = 72) identified in the study.

Summary statistics of the ’private SNPs’ (‘private SNPs80’; N = 72) identified in the study.</p

An overview of the identification and validation of ’private SNPs’ or informative SNPs.

Step 1: a total of 52,834 SNPs were generated from genotyping by sequencing of Macrobrachium species. Step 2: the SNPs from ‘Step 1’ were screened for quality parameters leaving a total of 1,814 SNPs for further analysis. Step 3: the SNPs from ‘Step 2’ were used to prioritise 178 informative SNPs based on allele frequency estimates. Step 4: a total of 72 high-quality SNPs (‘private SNPs’) were selected from the 178 SNPs in ‘Step 3’ based on repeat resampling approach. Step 5: the SNPs from ‘Step 4’ were “validated” using three methods: a) PCA–principal component analysis; b) Admixture, and c) DAPC–discriminant analysis of principal components. MAF–minor allele frequency.</p