How sea level change mediates genetic divergence in coastal species across regions with varying tectonic and sediment processes

Abstract

Plate tectonics and sediment processes control regional continental shelf topography. We examine the genetic consequences of how glacial-associated sea level change interacted with variable nearshore topography since the last glaciation. We reconstructed the size and distribution of areas suitable for tidal estuary formation from the last glacial maximum, ~20 thousand years ago, to present from San Francisco, California, USA (~38°N) to Reforma, Sinaloa, Mexico (~25°N). We assessed range-wide genetic structure and diversity of three codistributed tidal estuarine fishes (California Killifish, Shadow Goby, Longjaw Mudsucker) along ~4,600 km using mitochondrial control region and cytB sequence, and 16-20 microsatellite loci from a total of 524 individuals. Results show that glacial-associated sea level change limited estuarine habitat to few, widely separated refugia at glacial lowstand, and present-day genetic clades were sourced from specific refugia. Habitat increased during postglacial sea level rise and refugial populations admixed in newly formed habitats. Continental shelves with active tectonics and/or low sediment supply were steep and hosted fewer, smaller refugia with more genetically differentiated populations than on broader shelves. Approximate Bayesian computation favoured the refuge-recolonization scenarios from habitat models over isolation by distance and seaway alternatives, indicating isolation at lowstand is a major diversification mechanism among these estuarine (and perhaps other) coastal species. Because sea level change is a global phenomenon, we suggest this top-down physical control of extirpation-isolation-recolonization may be an important driver of genetic diversification in coastal taxa inhabiting other topographically complex coasts globally during the Mid- to Late Pleistocene and deeper timescales.

Common barriers, but temporal dissonance: Genomic tests suggest ecological and paleo‐landscape sieves structure a coastal riverine fish community

“…Note that any isolation associated among the basins contained within the inferred regional genetic groups (see Figure and Figure ) is necessarily more ephemeral (i.e., it is not as old) as the shared regional geographic divisions (Figure ). It is possible that different degrees of connectivity, or conversely isolation, might relate to bathymetric differences (e.g., continental shelf width and its slope) and/or differences in habitat suitability (distribution of habitat over time), as is often invoked when studying connectivity in terrestrial communities on islands (Ali & Aitchison, ; Papadopoulou & Knowles, , ; Shaw & Gillespie, ), estuarine fishes (Dolby et al, ), and the geographic ranges of freshwater fishes (Carvajal‐Quintero et al, ). Given the regional structure (Figure ), we can rule out the possibility that the fish did not have sufficient time to colonize these basins (i.e., each of the species at some point would have been distributed within these regions).…”

Living on the edge: Exploring the role of coastal refugia in the Alexander Archipelago of Alaska

“…Assessments of genetic structure across an array of species in complex landscapes, such as this coastal archipelago which experienced dynamic sea level fluctuations (e.g., Dolby et al, 2018), provide an initial framework for scientifically defensible management decisions (Gutrich et al, 2005;Pritchard, Jones, & Cowley, 2007). Future SDMs for these species forecast serious impacts, especially on the outer islands of the AA (Figure 2).…”

“…But even in tropical island systems, understanding of island composition and genetic relationships is more complex than originally assumed (Filardi & Moyle, ). Recently, the various impacts of dynamic geologic events of the Quaternary (2.6 Ma – present), such as changes in sea level, are receiving closer scrutiny in lower latitude archipelagos (e.g., Esselstyn, Timm, & Brown, ; Heaney, Walsh, & Peterson, ) and along coastal ecosystems (Dolby, Ellingson, Findley, & Jacobs, ). Relatively few comparative studies (e.g., Pedreschi, Kelly‐Quinn, Caffrey, O'Grady, & Mariani, ; Sota & Nagata, ), however, have explicitly investigated the role of climatic history in evolutionary diversification in high‐latitude coastal archipelagos, where dynamic glacial advances potentially restructured entire communities repeatedly.…”

A legacy of geo‐climatic complexity and genetic divergence along the lower Colorado River: Insights from the geological record and 33 desert‐adapted animals

“…Rivers are important physiographical features that act as barriers to migration and gene flow among terrestrial species (Hayes & Sewlal, 2004;Vences, Wollenberg, Vieites, & Lees, 2009), provide dispersal corridors and niche space for freshwater aquatic species (Burridge, Craw, & Waters, 2006;Echelle, 2008;Snorrason & Skúlason, 2009;Spencer, Smith, & Dowling, 2008), and create ecologically important estuarine and deltaic habitats where they meet the sea (Dolby, Ellingson, Findley, & Jacobs, 2018;Lau & Jacobs, 2017;Loneragan & Bunn, 1999;Swift, Findley, Ellingson, Flessa, & Jacobs, 2011). Rivers therefore influence biological evolution by structuring or isolating populations, limiting species ranges, and driving ecological adaptations.…”