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

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.

Sea-level driven glacial-age refugia and post-glacial mixing on subtropical coasts, a palaeohabitat and genetic study.

Using a novel combination of palaeohabitat modelling and genetic mixture analyses, we identify and assess a sea-level-driven recolonization process following the Last Glacial Maximum (LGM). Our palaeohabitat modelling reveals dramatic changes in estuarine habitat distribution along the coast of California (USA) and Baja California (Mexico). At the LGM (approx. 20 kya), when sea level was approximately 130 m lower, the palaeo-shoreline was too steep for tidal estuarine habitat formation, eliminating this habitat type from regions where it is currently most abundant, and limiting such estuaries to a northern and a southern refugium separated by 1000 km. We assess the recolonization of estuaries formed during post-LGM sea-level rise through examination of refugium-associated alleles and approximate Bayesian computation in three species of estuarine fishes. Results reveal sourcing of modern populations from both refugia, which admix in the newly formed habitat between the refuges. We infer a dramatic peak in habitat area between 15 and 10 kya with subsequent decline. Overall, this approach revealed a previously undocumented dynamic and integrated relationship between sea-level change, coastal processes and population genetics. These results extend glacial refugial dynamics to unglaciated subtropical coasts and have significant implications for biotic response to predicted sea-level rise.

Chriolepis prolata, a new species of Atlantic goby (Teleostei: Gobiidae) from the North American continental shelf.

A new species of seven-spined goby of the genus Chriolepis is described from five specimens collected from the continental shelf of the northeastern Gulf of Mexico and Atlantic Ocean off South Carolina in depths of ca 54 to 110 m. The "Platform Goby", Chriolepis prolata, is distinguishable from all other western Atlantic species currently assigned to the genus Chriolepis and the morphologically similar genus Varicus in having pelvic-fin rays one through four branched, the fifth (innermost) pelvic-fin ray unbranched and relatively long (longer than the second ray to longer than all other pelvic-fin rays); most lateral body scales ctenoid, extending anteriorly in a wedge to a level anterior to the first dorsal-fin insertion or nearly to the pectoral-fin axil, with two or more rows of small cycloid scales extending anteriorly to near the pectoral-fin axil, cycloid scales along the bases of the dorsal and anal fins, and no scales on the belly; and the first two anal-fin pterygiophores inserted anterior to the first haemal spine. It closely resembles C. bilix but differs from that species which has a scaled belly, a shorter fifth pelvic-fin ray, prolonged dorsal-fin spines and smaller teeth in the lower jaw. An earlier report of C. bilix from Florida waters apparently refers to C. prolata. 

Convergent evolution of ecomorphological adaptations in geographically isolated Bay gobies (Teleostei: Gobionellidae) of the temperate North Pacific.

North Pacific Bay gobies (Teleostei: Gobioidei: Gobionellidae) inhabit bays, beaches, coastal lagoons, and estuaries of temperate Asia and North America, but are absent from the boreal northernmost Pacific. Previously, morphological characters conventionally subdivided the clade into two groups - an elongate-bodied, infaunal-inhabiting "Astrabe" group, and a deeper-bodied, non-infaunal "Chasmichthys" group - each with a disjunct East-West (amphi-) Pacific distribution. Here we use mitochondrial and multi-locus nuclear DNA sequence data to show that several morphological characters previously used to delimit these two groups have in fact arisen independently on both sides of the Pacific, revealing convergence of ecologically adaptive characters within a geographically divided clade. Basal divergence of the resultant tree coincides with a dramatic global cooling event at the Eocene/Oligocene transition, without evidence of subsequent trans-Pacific migration. A novel approach to partitioning sequence data by relative rate, as opposed to traditional gene/codon position partitioning, was used to help distinguish phylogenetic signal from noise on a per-site basis. Resulting improvements in topology and nodal support, along with decreased computational effort, suggest that this partitioning strategy may be useful for future studies in phylogenetics and phylogenomics.

Chriolepis bilix, a new species of goby (Teleostei: Gobiidae) from deep waters of the western Atlantic.

A new species of seven-spined goby of the genus Chriolepis is described from four specimens from four widely separate western Atlantic localities (Little Bahama Bank; off southwestern Florida; Tobago Island; and northeastern Colombia) from depths ranging from 62 to 138 m. The species is distinct from all other western Atlantic species currently assigned to the genus Chriolepis in having a fully scaled body, the first two dorsal-fin spines greatly elongated in both sexes, especially so in females, and two anal-fin pterygiophores inserted anterior to the first haemal spine. It differs from members of the similar genus Varicus in having branched pelvic-fins rays, a longer fifth pelvic-fin ray and more numerous meristic elements. It closely resembles Chriolepis atrimelum, known from a similar depth at Isla del Coco in the eastern Pacific Ocean.