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.

Mitogenomics supports an unexpected taxonomic relationship for the extinct diving duck Chendytes lawi and definitively places the extinct Labrador Duck.

Chendytes lawi, an extinct flightless diving anseriform from coastal California, was traditionally classified as a sea duck, tribe Mergini, based on similarities in osteological characters. We recover and analyze mitochondrial genomes of C. lawi and five additional Mergini species, including the extinct Labrador Duck, Camptorhynchus labradorius. Despite its diving morphology, C. lawi is reconstructed as an ancient relictual lineage basal to the dabbling ducks (tribe Anatini), revealing an additional example of convergent evolution of characters related to feeding behavior among ducks. The Labrador Duck is sister to Steller's Eider which may provide insights into the evolution and ecology of this poorly known extinct species. Our results demonstrate that inclusion of full length mitogenomes, from taxonomically distributed ancient and modern sources can improve phylogeny reconstruction of groups previously assessed with shorter single-gene mitochondrial sequences.

A biting commentary: Integrating tooth characters with molecular data doubles known species diversity in a lineage of sea slugs that consume "killer algae".

Predicting biotic resistance to highly invasive strains of "killer algae" (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates. Four delimitation methods applied to datasets comprising mtDNA and/or nuclear alleles yielded up to 16 species hypotheses for samples comprising five nominal taxa, including five highly divergent species in Lobiger and five in Oxynoe. Depending on the analysis, a further four to six species were recovered in the O. antillarum-viridis complex, a clade in which mitochondrial divergence was low and nuclear alleles were shared among lineages. Bayesian species delimitation using only morphological data supported most candidate species, however, and integrative analyses combining morphological and genetic data fully supported all complex members. Collectively, our findings double the recognized biodiversity in Oxynoidae, and illustrate the value of including data from traits that mediate fast-evolving ecological interactions during species delimitation. Preference for Caulerpa spp. and radular tooth characteristics covaried among newly delimited species, highlighting an unappreciated degree of host specialization and coevolution in these taxa that may help predict their role in containing outbreaks of invasive algae.

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.

Species Selection Favors Dispersive Life Histories in Sea Slugs, but Higher Per-Offspring Investment Drives Shifts to Short-Lived Larvae.

For 40 years, paleontological studies of marine gastropods have suggested that species selection favors lineages with short-lived (lecithotrophic) larvae, which are less dispersive than long-lived (planktotrophic) larvae. Although lecithotrophs appeared to speciate more often and accumulate over time in some groups, lecithotrophy also increased extinction rates, and tests for state-dependent diversification were never performed. Molecular phylogenies of diverse groups instead suggested lecithotrophs accumulate without diversifying due to frequent, unidirectional character change. Although lecithotrophy has repeatedly originated in most phyla, no adult trait has been correlated with shifts in larval type. Thus, both the evolutionary origins of lecithotrophy and its consequences for patterns of species richness remain poorly understood. Here, we test hypothesized links between development mode and evolutionary rates using likelihood-based methods and a phylogeny of 202 species of gastropod molluscs in Sacoglossa, a clade of herbivorous sea slugs. Evolutionary quantitative genetics modeling and stochastic character mapping supported 27 origins of lecithotrophy. Tests for correlated evolution revealed lecithotrophy evolved more often in lineages investing in extra-embryonic yolk, the first adult trait associated with shifts in development mode across a group. However, contrary to predictions from paleontological studies, species selection actually favored planktotrophy; most extant lecithotrophs originated through recent character change, and did not subsequently diversify. Increased offspring provisioning in planktotrophs thus favored shifts to short-lived larvae, which led to short-lived lineages over macroevolutionary time scales. These findings challenge long-standing assumptions about the effects of alternative life histories in the sea. Species selection can explain the long-term persistence of planktotrophy, the ancestral state in most clades, despite frequent transitions to lecithotrophy.

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.

Acute Toxicity of the Lampricide 4-Nitro-3-(trifluoromethyl)phenol to the Mussel (Obovaria subrotunda), Its Host (Percina maculata), and a Surrogate Mussel Species (Obovaria olivaria).

The risk of lampricide applications (such as 4-nitro-3-[trifluoromethyl]phenol [TFM]) to nontarget fauna continues to be a concern within the Great Lakes Fishery Commission Sea Lamprey Control Program, especially among imperiled aquatic species-such as native freshwater mussels. The Grand River (Ohio, USA) is routinely treated for larval sea lampreys (Petromyzon marinus), and this river contains populations of the federally threatened mussel Obovaria subrotunda. Given this spatial overlap, information on the sensitivity of O. subrotunda to TFM is needed. Our objectives were to assess the toxicity of TFM to (1) adult Obovaria olivaria (a surrogate for O. subrotunda), (2) glochidial larvae of O. olivaria and O. subrotunda, (3) juveniles of O. olivaria and O. subrotunda, and (4) adult Percina maculata (host for O. subrotunda glochidia). In acute toxicity tests, TFM was not toxic to glochidia and adult mussels at exposure concentrations that exceed typical treatment rates. Although significant dose-response relationships were observed in hosts and juveniles, survival was ≥95% (Percina maculata), ≥93% (O. olivaria), and ≥74% (O. subrotunda) at typical treatment rates. However, the steep slope of these dose-response relationships indicates that an approximately 20% difference in the treatment level can result in nearly an order of magnitude difference in survival. Collectively, these data indicate that routine sea lamprey control operations are unlikely to acutely affect these species or their host. However, given that many mussel species are long-lived (30-100 years), the risks posed by lampricide treatments in the Great Lakes would be further informed by research on the potential long-term effects of lampricides on imperiled species. Environ Toxicol Chem 2024;43:1423-1430. Published 2024. This article is a U.S. Government work and is in the public domain in the USA.

Evolution of poecilogony from planktotrophy: cryptic speciation, phylogeography, and larval development in the gastropod genus Alderia.

Poecilogony, a rare phenomenon in marine invertebrates, occurs when alternative larval morphs differing in dispersal potential or trophic mode are produced from a single genome. Because both poecilogony and cryptic species are prevalent among sea slugs in the suborder Sacoglossa (Gastropoda: Opisthobranchia), molecular data are needed to confirm cases of variable development and to place them in a phylogenetic context. The nominal species Alderia modesta produces long-lived, feeding larvae throughout the North Atlantic and Pacific, but in California can also produce short-lived larvae that metamorphose without feeding. We collected morphological, developmental, and molecular data for Alderia from 17 sites spanning the eastern and western Pacific and North Atlantic. Estuaries south of Bodega Harbor, California, contained a cryptic species (hereafter Alderia sp.) with variable development, sister to the strictly planktotrophic A. modesta. The smaller Alderia sp. seasonally toggled between planktotrophy and lecithotrophy, with some individuals differing in development but sharing mitochondrial DNA haplotypes. The sibling species overlapped in Tomales Bay, California, but showed no evidence of hybridization; laboratory mating trials suggest postzygotic isolation has arisen. Intra- and interspecific divergence times were estimated using a molecular clock calibrated with geminate sacoglossans. Speciation occurred about 4.1 million years ago during a major marine radiation in the eastern Pacific, when large inland embayments in California may have isolated ancestral populations. Atlantic and Pacific A. modesta diverged about 1.7 million years ago, suggesting trans-Arctic gene flow was interrupted by Pleistocene glaciation. Both Alderia species showed evidence of late Pleistocene population expansion, but the southern Alderia sp. likely experienced a more pronounced bottleneck. Reduced body size may have incurred selection against obligate planktotrophy in Alderia sp. by limiting fecundity in the face of high larval mortality rates in warm months. Alternatively, poecilogony may be an adaptive response to seasonal opening of estuaries, facilitating dispersal by long-lived larvae. An improved understanding of the forces controlling seasonal shifts in development in Alderia sp. may yield insight into the evolutionary forces promoting transitions to nonfeeding larvae.

Reduced genetic diversity and increased reproductive isolation follow population-level loss of larval dispersal in a marine gastropod.

Population-level consequences of dispersal ability remain poorly understood, especially for marine animals in which dispersal is typically considered a species-level trait governed by oceanographic transport of microscopic larvae. Transitions from dispersive (planktotrophic) to nondispersive, aplanktonic larvae are predicted to reduce connectivity, genetic diversity within populations, and the spatial scale at which reproductive isolation evolves. However, larval dimorphism within a species is rare, precluding population-level tests. We show the sea slug Costasiella ocellifera expresses both larval morphs in Florida and the Caribbean, regions with divergent mitochondrial lineages. Planktotrophy predominated at 11 sites, 10 of which formed a highly connected and genetically diverse Caribbean metapopulation. Four populations expressed mainly aplanktonic development and had markedly reduced connectivity, and lower genetic diversity at one mitochondrial and six nuclear loci. Aplanktonic dams showed partial postzygotic isolation in most interpopulation crosses, regardless of genetic or geographic distance to the sire's source, suggesting that outbreeding depression affects fragmented populations. Dams from genetically isolated and neighboring populations also exhibited premating isolation, consistent with reinforcement contingent on historical interaction. By increasing self-recruitment and genetic drift, the loss of dispersal may thus initiate a feedback loop resulting in the evolution of reproductive isolation over small spatial scales in the sea.

A New Species of the Bay Goby Genus Eucyclogobius, Endemic to Southern California: Evolution, Conservation, and Decline.

A geographically isolated set of southern localities of the formerly monotypic goby genus Eucyclogobius is known to be reciprocally monophyletic and substantially divergent in mitochondrial sequence and nuclear microsatellite-based phylogenies relative to populations to the north along the California coast. To clarify taxonomic and conservation status, we conducted a suite of analyses on a comprehensive set of morphological counts and measures from across the range of Eucyclogobius and describe the southern populations as a new species, the Southern Tidewater Goby, Eucyclogobius kristinae, now separate from the Northern Tidewater Goby Eucyclogobius newberryi (Girard 1856). In addition to molecular distinction, adults of E. kristinae are diagnosed by: 1) loss of the anterior supratemporal lateral-line canals resulting in higher neuromast counts, 2) lower pectoral and branched caudal ray counts, and 3) sets of measurements identified via discriminant analysis. These differences suggest ecological distinction of the two species. Previous studies estimated lineage separation at 2-4 million years ago, and mitochondrial sequence divergence exceeds that of other recognized fish species. Fish from Santa Monica Artesian Springs (Los Angeles County) northward belong to E. newberryi; those from Aliso Creek (Orange County) southward constitute E. kristinae. The lagoonal habitat of Eucyclogobius has been diminished or degraded, leading to special conservation status at state and federal levels beginning in 1980. Habitat of the newly described species has been impacted by a range of anthropogenic activities, including the conversion of closing lagoons to open tidal systems in the name of restoration. In the last 30 years, E. kristinae has only been observed in nine intermittently occupied lagoonal systems in northern San Diego County; it currently persists in only three sites. Thus, the new species is in imminent danger of extinction and will require ongoing active management.