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Phylogeographic pattern and population structure of the Persian stone loach, Oxynoemacheilus persa (Heckel 1847) (family: Nemacheilidae) in southern Iran with implications for conservation

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Phylogeographic pattern, genetic diversity, and historical demography of the endemic loach, Oxynoemacheilus persa, sampled from the endorheic Kor River and exorheic Persis basins in southern Iran, were analyzed using D-loop sequences of mitochondrial DNA. The sequence analysis of 53 specimens detected six haplotypes; all were related closely, yet some were highly localized. Hap_2 with high frequency was restricted to the Persis basin. The ancestral haplotype, Hap_1, was broadly distributed geographically among the Kor River basin populations. The rest of the haplotypes were shared between two populations from the Kor River basin (Hap_4 and Hap_5) or restricted to one of its populations (Hap_3 and Hap_6). AMOVA showed that 42.28% of total variation was related to differences among the basins, while inter- and intra-population differences explained 16.8% and 40.91%, respectively. The Mantel test indicated that the levels of genetic resemblance between populations are moderately dependent on geographic distance (r = 0.669, p = 0.008). All these clues imply that the Kor River and Persis basin populations of O. persa may qualify as two distinct management units. The implication is that contemporary gene flow among these basins has been low enough to have permitted lineage sorting and random drift to promote genetic divergence among these basins that nonetheless were in historical contact recently. The close phylogenetic relationships among other fishes, their previously inferred recent ages of divergence, and the patterns of affinity among them in the Persis and Kor River basins all suggest that these now isolated river systems were interconnected during the Last Glacial Maximum by a Paleo-Kor River and remained so until the sea-level rise of the Early Holocene.

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We are grateful to M. Masoudi and S. Echreshavi for helping with fish collection and Dr. M. Ansari for helping with primer design. We also thank three anonymous reviewers for their helpful comments and technical advices, which greatly improved the manuscript. The research work was approved by Ethics Committee of Biology Department, Shiraz University (ECBD-SU-9233856).


We would like to thank the Fars Environment Department (grant number 97/500/7931) and Shiraz University for funding this research.

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Correspondence to Hamid Reza Esmaeili.

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Esmaeili, H.R., Sayyadzadeh, G., Zarei, F. et al. Phylogeographic pattern and population structure of the Persian stone loach, Oxynoemacheilus persa (Heckel 1847) (family: Nemacheilidae) in southern Iran with implications for conservation. Environ Biol Fish 103, 77–88 (2020).

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