Finding coarse and fine scale population structure in a coastal species: population demographics meets genomics

Abstract

Often population genetic studies focus on patterns at a regional scale and use spatially aggregated samples to draw inferences about population structure and drivers, potentially masking ecologically relevant population sub-structure and dynamics. In this study we use a multidisciplinary approach combining genomic, demographic, and habitat data with an oceanographic particles drift model, to unravel the patterns of genetic structure on different scales in the black goby (Gobius niger) along the Norwegian coast. Using a high-density sampling protocol, we observed restricted gene flow both at a surprisingly fine (kilometres) and large (100km) scale. Our results showed a pattern of isolation by distance related to the level of ocean exposure along the Skagerrak coast, where sheltered sampling stations had an overall level of genetic divergence about three times higher (FST =0.0046) than that among exposed samples (FST =0.0015). These results were also supported by demographic analyses which showed that synchrony decreases with increasing distance at much smaller scales for sheltered samples (20 km) that for exposed ones (80 km), suggesting higher levels of gene flow among the latter. We also found a pronounced genetic discontinuity between populations along the Norwegian west and east coasts with sharp increasing in genetic divergence around the southern tip of Norway, likely driven by both lack of habitat and oceanography.

Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species

“…The corkwing wrasse and the black goby displayed weaker genetic structure within Skagerrak as compared to the broadnosed pipefish, although still statistically significant (Blanco et al, 2016; Catarino et al, 2022; Knutsen et al, 2013) and either no or very weak IBD (cf. Figure 5), and indicating restriction in gene flow also in these two species.…”

“…Spatial population structure in the broadnosed pipefish was contrasted with published genetic data from the corkwing wrasse and the black goby (Blanco et al, 2016; Catarino et al, 2022) and archived abundance data from the long‐term beach seine survey, described above. For this, genetic structure along the coast was analysed by regressing pairwise F ST between the easternmost sample (at Hvaler or the closely situated Oslofjord) with the other samples.…”

“…For comparative purposes, we reiterate some findings of those studies herein and supply some new analyses (spatial decorrelation scale: below), while referring to the original publications for details. The corkwing wrasse ( Symphodus melops : Knutsen et al, 2013; Blanco et al, 2016; Faust et al, 2021) and black goby ( Gobius niger ; Catarino et al, 2022) are common in coastal waters of southern Norway. Like the broadnosed pipefish, both prefer eelgrass but may also be found in habitats with macroalgae in sandy or muddy sheltered areas.…”

“…Here, we estimate and compare spatial genetic structure and demographic decorrelation scales (geographical distance at which correlation in annual fluctuations in abundance falls below a certain threshold value) in three coastal fish species. We provide new genetic and demographic data for broadnosed pipefish ( Syngnathus typhle ) and contrast it with two unrelated fish species, the corkwing wrasse ( Symphodus melops ) (Blanco et al, 2016) and the black goby ( Gobius niger ) (Catarino et al, 2022). All three species were sampled over ~900 km of coastline, typically from the exact same locations or nearly so, providing a unique opportunity for assessing drivers of population stratification in a consistent sampling design.…”