Secondary contact and asymmetrical gene flow in a cosmopolitan marine fish across the Benguela upwelling zone

Abstract

The combination of oceanographic barriers and habitat heterogeneity are known to reduce connectivity and leave specific genetic signatures in the demographic history of marine species. However, barriers to gene flow in the marine environment are almost never impermeable which inevitably allows secondary contact to occur. In this study, eight sampling sites (five along the South African coastline, one each in Angola, Senegal and Portugal) were chosen to examine the population genetic structure and phylogeographic history of the cosmopolitan bluefish (Pomatomus saltatrix), distributed across a large South-east Atlantic upwelling zone. Molecular analyses were applied to mtDNA cytochrome b, intron AM2B1 and 15 microsatellite loci. We detected uncharacteristically high genetic differentiation (F 0.15-0.20; P<0.001) between the fish sampled from South Africa and the other sites, strongly influenced by five outlier microsatellite loci located in conserved intergenic regions. In addition, differentiation among the remaining East Atlantic sites was detected, although mtDNA indicated past isolation with subsequent secondary contact between these East Atlantic populations. We further identified secondary contact, with unidirectional gene flow from South Africa to Angola. The directional contact is likely explained by a combination of the northward flowing offshore current and endogenous incompatibilities restricting integration of certain regions of the genome and limiting gene flow to the south. The results confirm that the dynamic system associated with the Benguela current upwelling zone influences species distributions and population processes in the South-east Atlantic.

Genetic analysis provides insights into species distribution and population structure in East Atlantic horse mackerel (Trachurus trachurus and T. capensis)

“…There was no significant mtDNA differentiation between the T. capensis samples from Angola and South Africa. This is a striking result in light of the high level of mtDNA divergence, including examples of reciprocal monophyly, between Angolan and South African sites for a number of marine taxa due to the BUS biogeographic boundary (Gwilliam et al ., ; Henriques et al ., , ; Reid et al ., ). This could be due to a combination of the previously mentioned slow mtDNA mutation rates for Trachurus as well as effective gene flow across the BUS as might be expected based on the species' life history.…”

Historical Processes and Contemporary Anthropogenic Activities Influence Genetic Population Dynamics of Nassau Grouper (Epinephelus striatus) within The Bahamas

“…Two putative genetic clusters were revealed by STRUCTURE analysis, but these do not appear related to geography. Possible explanations for this finding include panmixia, temporal differences in spawning between two sympatric stocks, and secondary contact from previously isolated Nassau grouper populations (e.g., Reid et al, 2016). However, our study was not designed to investigate these hypotheses, and to address it would require expanding spatial and temporal sampling of Nassau grouper throughout The Bahamas and the Caribbean.…”

Population panmixia and demographic expansion of a highly piscivorous marine fish Scomberomorus niphonius

“…estimated for S. niphonius in the East China and Yellow Seas using mtDNA-CR sequences assuming the mutation rates of 0·05-0·08 (Shui et al, 2009). The molecular clock rate is a crucial parameter in the inference of the population history (Ho et al, 2005;Liu et al, 2011;Grant et al, 2012;Reid et al, 2016;Hoareau, 2016). A mutation rate of 2·8% per site per million years was used for the S. concolor (Domínguez-López et al, 2015) and much slower alternative of 0·28%.…”