Understanding habitat preferences for endangered species is a high priority for management strategies to ensure minimum conflict between human uses and wildlife conservation. The purpose of this study was to identify oceanographic variables that predict occurrences of humpback whales Megaptera novaeangliae within the Cordell Bank and Gulf of the Farallones National Marine Sanctuaries, California, USA, to assess potential conflict with vessel traffic. We used data collected by Applied California Current Ecosystem Studies (ACCESS) conducted from 2004 to 2011. Using zero-inflated negative binomial regression, we developed predictive models and identified locations highly used by whales to characterize humpback whale habitat. We analyzed whale encounter rates at 3-km bin intervals in relation to bathymetric, surface and midwater hydrographic predictor variables and temporal variables characterizing oceanographic conditions. Our models included variables that accounted for detectability of whales. Two models were compared and contrasted: (1) a surface-only model, using only surface oceanographic variables, and (2) a surface + mid-water model, using both surface and mid-water variables. The surface + mid-water model performed significantly better than the surface-only model, which underestimated the amount of suitable whale habitat in the northern half of our study area. We compared resulting predicted habitat areas with previous and current San Francisco Bay Area shipping lane poly gonal footprints to investigate whether newly accepted changes in routes reduced areal overlap with humpback whale habitat. Although our analyses show that the area occupied by shipping traffic has decreased in areas of high predicted humpback whale habitat use, changes in vessel lane footprints do not account for several important aspects of ship-strike risk, including vessel frequency, speed, size and density patterns within the shipping lanes and variability between lanes.

Understanding seabird habitat preferences is critical to future wildlife conservation and threat mitigation in California. The objective of this study was to investigate drivers of seabird habitat selection within the Gulf of the Farallones and Cordell Bank National Marine Sanctuaries to identify areas for targeted conservation planning. We used seabird abundance data collected by the Applied California Current Ecosystem Studies Program (ACCESS) from 2004–2011. We used zero-inflated negative binomial regression to model species abundance and distribution as a function of near surface ocean water properties, distances to geographic features and oceanographic climate indices to identify patterns in foraging habitat selection. We evaluated seasonal, inter-annual and species-specific variability of at-sea distributions for the five most abundant seabirds nesting on the Farallon Islands: western gull (Larus occidentalis), common murre (Uria aalge), Cassin’s auklet (Ptychorampus aleuticus), rhinoceros auklet (Cerorhinca monocerata) and Brandt’s cormorant (Phalacrocorax penicillatus). The waters in the vicinity of Cordell Bank and the continental shelf east of the Farallon Islands emerged as persistent and highly selected foraging areas across all species. Further, we conducted a spatial prioritization exercise to optimize seabird conservation areas with and without considering impacts of current human activities. We explored three conservation scenarios where 10, 30 and 50 percent of highly selected, species-specific foraging areas would be conserved. We compared and contrasted results in relation to existing marine protected areas (MPAs) and the future alternative energy footprint identified by the California Ocean Uses Atlas. Our results show that the majority of highly selected seabird habitat lies outside of state MPAs where threats from shipping, oil spills, and offshore energy development remain. This analysis accentuates the need for innovative marine spatial planning efforts and provides a foundation on which to build more comprehensive zoning and management in California’s National Marine Sanctuaries.

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As global ocean-bound commerce increases, managing human activities has become important in reducing conflict with threatened wildlife. This study investigates environmental factors determining abundance and distribution of blue whales ( Balaenoptera musculus ), humpback whales ( Megaptera novaeangliae ) and their prey ( Euphausia pacifica and Thysanoessa spinifera ) in central California. We provide insights into environmental drivers of the ecology and distribution of these species, model whale distributions and determine coincident hotspots of whales and their prey that will help decrease human threats to whales and protect critical feeding habitat. We developed separate predictive models of whale abundances (using negative binomial regression on count data) and krill abundance (using a two-part hurdlemodel combining logistic and negative binomial regressions) over a 14 year period (2004–2017). Variables included in situ surface and midwater oceanographic measures (temperature, salinity, and fluorescence), basin-scale climate indices, and bathymetric- and distance-related data. Predictions were applied to 1 km 2 cells spanning the study area for May, June, July, and September during each of the 14 years of surveys to identify persistent distribution patterns. Both whales and krill were found to consistently use the northeast region of Cordell Bank, the Farallon Escarpment, and the shelf-break waters. The main identified blue whale hotspots were also krill hotspots, while co-occurrence was more limited and varied seasonally for humpback whales and krill. These results are valuable in identifying patterns in important areas of ecological interaction to assist management of whales. Areas north of Cordell Bank are of particular management concern since they overlap with the end of the San Francisco Bay northern shipping lane. Our findings can help decrease threats to whales, particularly in important foraging areas, by supporting implementation of vessel management and informing potential conflicts with other human uses.

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