| Literature DB >> 32341417 |
Lotanna M Nneji1,2, Adeniyi C Adeola3,4, Moshood K Mustapha5, Segun O Oladipo6, Chabi A M S Djagoun7, Ifeanyi C Nneji8, Babatunde E Adedeji9, Omotoso Olatunde9, Adeola O Ayoola10, Agboola O Okeyoyin11, Odion O Ikhimiukor12, Galadima F Useni13, Oluyinka A Iyiola5, Emmanuel O Faturoti14, Moise M Matouke15, Wanze K Ndifor16, Yun-Yu Wang10, Jing Chen17, Wen-Zhi Wang10,17, Jolly B Kachi18, Obih A Ugwumba9, Adiaha A A Ugwumba9, Christopher D Nwani19.
Abstract
The silver butter catfish (Schilbe intermedius) is widely distributed across African river systems. To date, information on its mitochondrial genetic diversity, population structure, and historical demography are not well-established. Herein, we combined newly generated mitochondrial cytochrome c oxidase (COI) subunit I gene sequences with previously published COI sequences in the global databases to reconstruct its phylogeography, population genetic structure, and historical demography. Results from the mtDNA phylogeography and species delimitation tests (Cluster algorithm - Species Identifier, Automatic Barcode Gap Discovery and Poison Tree Process model) revealed that S. intermedius comprises at least seven geographically defined matrilines. Although the overall haplotype diversity of S. intermedius was high (h = 0.90), results showed that East (Kenya) and West (Nigeria) African populations had low levels of haplotype diversity (h = ~0.40). In addition, population genetic polymorphism and historical demographics showed that S. intermedius populations in both East and West Africa underwent severe contractions as a result of biogeographic influences. The patterns of genetic diversity and population structure were consistent with adaptive responses to historical biogeographic factors and contemporary environmental variations across African river systems. This is suggestive of the influence of historical biogeographic factors and climatic conditions on population divergence of S. intermedius across African river systems. Given our discovery of previously underappreciated diversity within S. intermedius, we recommend that this species be considered for increased conservation and management.Entities:
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Year: 2020 PMID: 32341417 PMCID: PMC7184614 DOI: 10.1038/s41598-020-63837-4
Source DB: PubMed Journal: Sci Rep ISSN: 2045-2322 Impact factor: 4.379
Figure 1Map of collection sites for the newly sampled Schilbe intermedius in Nigeria.
Figure 2(a) Map showing the geographic distribution of matrilines of Schilbe intermedius in sub-Saharan Africa; (b) Phylogenetic tree inferred from ML analysis of S. intermedius based on mtDNA COI data set. Support values at each node are Bayesian posterior probability (left) and bootstrap values from ML (right). Asterisk (*) indicates full support (Bayesian posterior probability for BI ≥ 0.95, bootstrap proportions for ML ≥ 70%) in both analyses and hyphen (−) indicates moderate to weak support (Bayesian posterior probability for BI ≤ 0.95, bootstrap proportions for ML ≤ 70%). Letters A–G above the branches indicate matriline, while Roman numeral (i – ii) indicate sub-matriline; (c) Median-joining network of cytochrome c oxidase subunit I haplotypes of S. intermedius from the African river systems. Node sizes are proportional to total haplotype frequencies. The numbers on the internodes indicate mutation steps.
Population genetic polymorphism of Schilbe intermedius based on mtDNA COI dataset.
| Nucleotide Polymorphism | Matriline | |||||
|---|---|---|---|---|---|---|
| A | B | C | D | E | G | |
| Sample size | 82 | 48 | 9 | 5 | 58 | 17 |
| Number of polymorphic sites | 16 | 22 | 3 | 1 | 11 | 16 |
| Number of haplotype | 13 | 8 | 3 | 2 | 7 | 9 |
| Haplotype (gene) diversity | 0.571 | 0.62 | 0.417 | 0.400 | 0.410 | 0.846 |
| Nucleotide diversity (%) | 0.333 | 1.03 | 0.103 | 0.062 | 0.35 | 0.579 |
| Average number of pairwise nucleotide differences | 1.816 | 6.577 | 0.66 | 0.400 | 1.91 | 2.61 |
Note: Matriline F was excluded as it was represented by single unique haplotype.
Figure 3Population demographics for matrilines of Schilbe intermedius based on mtDNA COI dataset. Matriline F was excluded as it was represented by one unique haplotype.
Population demography statistics of Schilbe intermedius based on mtDNA COI dataset.
| Matrilines | A | B | C | D | E | G |
|---|---|---|---|---|---|---|
| Fu & Li’s D | −2.640 | 1.039 | −1.682 | −0.817 | −0.346 | −2.719 |
| <0.05 | >0.10 | >0.10 | >0.10 | >0.10 | <0.05 | |
| Fu & Li’s F | −2.592 | 1.241 | −1.820 | −0.772 | −0.491 | −2.819 |
| <0.05 | >0.10 | >0.10 | >0.10 | >0.10 | <0.05 | |
| Fu’s Fs | −3.94 | 5.288 | −1.513 | 0.090 | 0.382 | −2.817 |
| 0.33 | >0.10 | >0.10 | >0.10 | >0.10 | 0.10 | |
| Tajima’s D | −1.358 | 1.06 | −0.380 | −0.817 | −0.553 | −1.732 |
| >0.10 | >0.10 | >0.10 | >0.10 | >0.10 | 0.10 > P > 0.05 | |
| SSD | 0.073 | 0.135 | 0.250 | NA | 0.109 | 0.05 |
| P | 0.22 | 0.09 | 0.00 | NA | 0.100 | 0.22 |
| Raggedness Index | 0.237 | 0.397 | 0.180 | NA | 0.447 | 0.179 |
| P | 0.190 | 0.450 | 1.00 | NA | 0.370 | 0.21 |
Note: - NA; matrilines for which the variance of the mismatch distribution was too small and, SSD and Raggedness Index were not estimated. Population demographics were not estimated for Matriline F as it was represented by one unique haplotype.