Department of Ecology and Evolutionary Biology

Fucus distichus, a rockweed common to the mid-intertidal shoreline within the San Francisco Estuary (previously known as F. gardneri), was injured during the Cosco Busan oil spill in November 2007 and subsequent clean-up actions. Restoration planning activities are underway to help recover F. distichus at sites within central San Francisco Bay where damage occurred. As a first step, we conducted shoreline surveys during the summers of 2012–2013 to map the occurrence of this rockweed. Of the 151.73 km of rocky shoreline within the central bay, F. distichus covered 32.16 km of shoreline. The alga generally occurred in narrow bands but formed expansive beds at locations with natural, flat bedrock benches. We also observed F. distichus on artificial substrata such as seawalls and riprap, but not on pilings. Samples of F. distichus from 11 sites throughout the central / east San Francisco Bay were genetically analyzed (microsatellite genotyping). The populations analyzed (1) had low genetic diversity, (2) the frequency of homozygotes was higher than expected (suggesting high inbreeding), and (3) also displayed geographic population structure, in part driven by very small differences in the midst of extremely low within-population genetic diversity. However, these genetic data do not raise concerns for restoration methods in terms of choosing donor populations and mixing F. distichus from different sites within the central bay. The choice of donor populations should be based on practical criteria for effective restoration; individuals will nonetheless be taken from locations as nearby to donor sites as possible. Various locations throughout the central San Francisco Bay are composed of cobble or small riprap that are populated with F. distichus, which could provide efficient means of translocating rockweed for future restoration activities.

Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user-friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for a diploid species of conservation concern.

PREMISE: Floral pigments such as anthocyanins are well known to influence pollinator attraction, yet they also confer tolerance to abiotic stressors such as harsh soils, extreme temperatures, low precipitation, and UV radiation. In such cases, environmental variation in abiotic stressors over space or time could lead to the maintenance of flower color variation within species. Under this scenario, flower color in natural populations should covary with environmental stressors. METHODS: Using a comparative approach, we tested whether abiotic variables predict flower color in Leptosiphon parviflorus, a species with pink and white flower color morphs. We conducted in-depth field studies to assess morph frequency, soil chemistry, and climate. We then employed community scientist-powered iNaturalist observations to examine patterns across even larger spatial scales. RESULTS: Across 21 field sites, L. parviflorus had a higher frequency of pink morphs in sites with serpentine soil, higher average annual temperatures, and higher average climatic water deficit (a proxy for drought stress). iNaturalist observations supported this finding-the probability of flowers being pink is greater in locations with serpentine-derived soil, especially when the local average UV radiation and climatic water deficit are higher. CONCLUSIONS: Spatial variation in abiotic stressors may contribute to the maintenance of flower color variation across the geographic range of L. parviflorus. Future studies will examine mechanisms by which flower color affects stress tolerance and will assess whether fitness trade-offs in contrasting habitats across the range are associated with flower color.

Abstract: Fisheries science agencies are responsible for informing fisheries management and ocean planning worldwide, often requiring scientific analysis and management actions across multiple spatial scales. For example, catch limits are typically defined annually over regional scales, fishery bycatch rules are defined at fine spatial scales on daily to annual time scales, and aquaculture and energy lease areas are defined over decades for subregional permitting at intermediate scales. Similarly, these activities require synthesizing monitoring data and mechanistic knowledge operating across different spatial resolutions and domains. These needs drive a growing role for models that predict animal presence or densities at fine spatial scales, including daily, seasonal, and interannual variation, often called species distribution/density models (SDMs). SDMs can inform many ocean management needs; however, their development and usage are often haphazard. In this paper we discuss various ways SDMs can and have been used in stock, habitat, protected species, and ecosystem management activities as well as marine spatial planning, survey optimization, and as an interface with ecosystem and climate models. We conclude with a discussion of future directions, focusing on information needs and current development, and highlight avenues for furthering the community of practice around SDM development and use.

The federally endangered sister species, Eucyclogobius newberryi (northern tidewater goby, NTG) and E. kristinae (southern tidewater goby) comprise the California endemic genus Eucyclogobius, which historically occurred in all coastal California counties. Isolated lagoons that only intermittently connect to the sea are their primary habitat. Reproduction occurs during lagoon closure, minimizing marine dispersal and generating the most genetically subdivided vertebrate genus on the California coast. We present a new genome assembly for E. newberryi using HiFi long reads and Hi-C chromatin-proximity sequencing. The 980 Mb E. newberryi reference genome has an N50 of 34 Mb with 22 well-described scaffolds comprising 88% of the genome and a complete BUSCO (Benchmarking Universal Single-Copy Orthologs) score of 96.7%. This genome will facilitate studies addressing selection, drift, and metapopulation genetics in subdivided populations, as well as the persistence of the critically endangered E. kristinae, where reintroduction will be an essential element of conservation actions for recovery. It also provides tools critical to the recovery of the genetically distinct management units in the NTG, as well as broader ecological and evolutionary studies of gobies, the most speciose family of fishes in the world.

PREMISE: Understanding how plants successfully diversified in novel environments is a central question in evolutionary biology. Linanthus occurs in arid areas of western North America and exhibits extensive floral trait variation, multiple color polymorphisms, differences in blooming time, and variation in life history strategies. We reconstructed the evolutionary history of this genus. METHODS: We generated restriction-site associated (ddRAD) sequences for 180 individuals and target capture (TC) sequences for 63 individuals, with complete species sampling. Using maximum likelihood and pseudo-coalescent approaches, we inferred phylogenies of Linanthus and used them to model the evolution of phenotypic traits and investigate the genuss geographic speciation history. RESULTS: Relationships are consistent and well supported with both ddRAD and TC data. Most species are monophyletic despite extensive local sympatry and range overlap, suggesting strong isolating barriers. The non-monophyly of the night-blooming and perennial species may be due to rapid speciation or cryptic diversity. Perenniality likely evolved from annuality, a rare shift in angiosperms. Night-blooming evolved three times independently. Flower color polymorphism is an evolutionarily labile trait that is likely ancestral. No single geographic mode of speciation characterizes this diversification, but most species overlap in range, which suggests that they evolved in parapatry. CONCLUSIONS: Our results illustrate the complexity of phylogenetic inference for recent radiations, even with multiple sources of genomic data and extensive sampling. This analysis provides a foundation for understanding aridity adaptations, such as evolution of flower color polymorphisms, night-blooming, and perenniality, as well as speciation mechanisms.

Understanding the habitat of highly migratory species is aided by using species distribution models to identify species-habitat relationships and to inform conservation and management plans. While Generalized Additive Models (GAMs) are commonly used in ecology, and particularly the habitat modeling of marine mammals, there remains a debate between modeling habitat (presence/absence) versus density (# individuals). Our study assesses the performance and predictive capabilities of GAMs compared to boosted regression trees (BRTs) for modeling both fin whale density and habitat suitability alongside Hurdle Models treating presence/absence and density as a two-stage process to address the challenge of zero-inflated data. Fin whale data were collected from 2008 to 2022 along fixed transects crossing the NW Mediterranean Sea during the summer period. Data were analyzed using traditional line transect methodology, obtaining the Effective Area monitored. Based on existing literature, we select various covariates, either static in nature, such as bathymetry and slope, or variable in time, for example, SST, MLD, Chl concentration, EKE, and FSLE. We compared both the explanatory power and predictive skill of the different modeling techniques. Our results show that all models performed well in distinguishing presences and absences but, while density and presence patterns for the fin whale were similar, their dependencies on environmental factors can vary depending on the chosen model. Bathymetry was the most important variable in all models, followed by SST and the chlorophyll recorded 2 months before the sighting. This study underscores the role SDMs can play in marine mammal conservation efforts and emphasizes the importance of selecting appropriate modeling techniques. It also quantifies the relationship between environmental variables and fin whale distribution in an understudied area, providing a solid foundation for informed decision making and spatial management.

Baleen whales migrate from productive high-latitude feeding grounds to usually oligotrophic tropical and subtropical reproductive winter grounds, translocating limiting nutrients across ecosystem boundaries in their bodies. Here, we estimate the latitudinal movement of nutrients through carcasses, placentas, and urea for four species of baleen whales that exhibit clear annual migration, relying on spatial data from publicly available databases, present and past populations, and measurements of protein catabolism and other sources of nitrogen from baleen whales and other marine mammals. Migrating gray, humpback, and North Atlantic and southern right whales convey an estimated 3784 tons N yr^-1 and 46,512 tons of biomass yr^-1 to winter grounds, a flux also known as the "great whale conveyor belt"; these numbers might have been three times higher before commercial whaling. We discuss how species recovery might help restore nutrient movement by whales in global oceans and increase the resilience and adaptative capacity of recipient ecosystems.

Turnover in species composition through time is a dominant form of biodiversity change, which has profound effects on the functioning of ecological communities^1-4. Turnover rates differ markedly among communities⁴, but the drivers of this variation across taxa and realms remain unknown. Here we analyse 42,225 time series of species composition from marine, terrestrial and freshwater assemblages, and show that temporal rates of turnover were consistently faster in locations that experienced faster temperature change, including both warming and cooling. In addition, assemblages with limited access to microclimate refugia or that faced stronger human impacts on land were especially responsive to temperature change, with up to 48% of species replaced per decade. These results reveal a widespread signal of vulnerability to continuing climate change and highlight which ecological communities are most sensitive, raising concerns about ecosystem integrity as climate change and other human impacts accelerate.