Population genetic structure of Indian oil sardine, Sardinella longiceps along Indian coast

Abstract

Genetic stock structure and historical demography of Indian oil sardine, a commercially and ecologically important small pelagic fish, was studied using mitochondrial control region and Cytochrome C Oxidase I (COI) sequences. A 758 bp portion of the control region in 287 individuals and a 576 bp portion of the COI gene in 291individuals from 10 locations along the distribution range were amplified resulting in 236 and 84 haplotypes, respectively. The high haplotype and low nucleotide diversity values (0.99 and 0.19 for control region and 0.85 and 0.004 for COI, respectively) are characteristic of populations having undergone a demographic expansion. Genetic differentiation, Φ ST , was low and insignificant between populations using both control region and COI gene markers. Mismatch analysis showed a recent demographic and spatial expansion coinciding with the late Pleistocene epoch. Mantel tests revealed the lack of isolation by distance which is attributable either to high levels of migration overriding the effect of genetic drift or to insufficient time for accomplishing a balance between migration and drift after a recent range expansion.

Restriction Site-Associated DNA Sequencing Reveals Local Adaptation Despite High Levels of Gene Flow in Sardinella lemuru (Bleeker, 1853) Along the Northern Coast of Mindanao, Philippines

“…Spatial genetic homogeneity of S. lemuru corroborates previous reports based on the mtDNA CR (Pedrosa-Gerasmio et al, 2015;Labrador et al, 2021). Most marine pelagic fishes, including this species, have large effective population sizes, are highly migratory, and have high dispersal capabilities at both larval and adult stages (Waples, 1998;Tinti et al, 2002;Lecomte et al, 2004;Ravago-Gotanco and Juinio-Meñez, 2004;Atarhouch et al, 2007;Nielsen et al, 2009b;Ruggeri et al, 2013;Pedrosa-Gerasmio et al, 2015;Sukumaran et al, 2016); all these biological properties increase the homogenizing effects of gene flow while minimizing the structuring effects of genetic drift. Moreover, agents that facilitate gene flow are not limited to biological characteristics, since oceanographic features such as the dynamic movement of water interconnecting the different geopolitical boundaries, ocean circulation shifts due to monsoon cycle, and tidal shifts are known to mediate larval dispersal and influence adult migration (Campos et al, 2015;Pedrosa-Gerasmio et al, 2015;Pata et al, 2021).…”

“…However, the absence of regional genetic differentiation could be attributed to the low resolving power of mtDNA. In general, mtDNA markers may perform poorly at detecting recent genetic divergence, especially in species with large effective population sizes and high dispersal potential (Corander et al, 2013;Pedrosa-Gerasmio et al, 2015;Sukumaran et al, 2016). Furthermore, mtDNA markers are often associated with historical processes and are thus unable to detect adaptive variation occurring at a more contemporary ecological timescale (Conover et al, 2006;Rocha et al, 2007).…”

“…Furthermore, mtDNA markers are often associated with historical processes and are thus unable to detect adaptive variation occurring at a more contemporary ecological timescale (Conover et al, 2006;Rocha et al, 2007). Genome-wide single nucleotide polymorphisms (SNPs) offer a better alternative in providing the resolving power needed to detect low levels of genetic divergence expected for organisms with high dispersal potential and large effective population sizes (Corander et al, 2013;Sukumaran et al, 2016). Moreover, since local adaptation can still occur despite high levels of genetic connectivity (Hemmer-Hansen et al, 2007a;Nielsen et al, 2009b), concurrent examination of both neutral and non-neutral genetic variation is needed to understand the relative contribution of gene flow, genetic drift, and selection in shaping the population (Funk et al, 2012;Yadav et al, 2019).…”

The sequence and de novo assembly of the genome of the Indian oil sardine, Sardinella longiceps

“…The fishery of this species peaks around the Malabar upwelling zone of the western Indian Ocean upwelling system 6 , 7 and the fishery exhibited high variability on a decadal scale, with periods of abundance and crashes during this century 8 , 9 . A comprehensive investigation of its population genetic structure, selection and adaptive variation has been carried out by the present authors 10 – 13 , revealing the presence of genetic structuring and local adaptation. The adaptation patterns have also been linked to the environmental and oceanographic characteristics of the Indian Ocean 13 .…”

Economic impact of fluctuations in oilsardine landings in India

“…Balan and Sathianandan (2007) estimated the maximum sustainable yield (MSY) of oilsardine in Kerala. The population and stock structure of oilsardine were studied by Rohit and Baht (2006), Sebastian et al (2017), Sukumaran et al (2016) and Rohit et al (2018).…”