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.

Temporal activity patterns of animals can indicate how individuals respond to changing conditions. Gregarious roosting bats provide an opportunity to compare activity patterns among individuals living in the same location to investigate how reproductive status or sex may influence activity budgets. We examined how the activity patterns of the nectarivorous bat Leptonycteris yerbabuenae vary depending on reproductive conditions, sex, and environmental conditions. We analyzed 5 years of individual mark-resighting data using daily detections of L. yerbabuenae marked with passive integrated transponder tags (PIT-tags) at 3 subterranean roosts on the Baja California Peninsula, Mexico. We derived 4 metrics using PIT-tag detections at roost entrances to calculate periods inside the roost and time spent outside the roost (time of emergence, returns to the roost, hours inside the roost, and hours of activity). We found differences among pregnant, lactating, and nonreproductive females for roost returns, hours inside the roost, and hours of activity outside the roost. Lactating females spent the longest time outside the roost, suggesting that the energetic demands of lactation require longer foraging bouts. Contrary to our expectations, lactating females had the fewest returns to the roost during the night, suggesting that lactating females did not shorten foraging bouts to return to nurse pups. Activity patterns differed between females and males and among seasons associated with different food availability. Females had fewer returns during the night and spent more time outside the roost than males. The time of emergence for males was earlier than for females except during the nectar season when most females are reproductively active. Differences in activity patterns among reproductive status, sex, and environmental conditions show how individuals modify behaviors to meet their energetic demands. We demonstrate how mark-resighting data from PIT-tag systems at roost entrances can be used to compare activity patterns of gregarious roosting bats.

The worlds rich diversity of bats supports healthy ecosystems and important ecosystem services. Maintaining healthy biological systems requires prompt identification of threats to biodiversity and immediate action to protect species, which for wide-ranging bat species that span geopolitical boundaries warrants international coordination. Anthropogenic forces drive the threats to bats throughout North America and the world. We conducted an international expert elicitation to assess the status of 153 bat species in Canada, the United States, and Mexico. We used expert assessment to determine the conservation status, highest impact threats, and recent population trends for these species. We found that 53% of North American bat species have moderate to very high risk of extinction in the next 15 years. The highest impact threats varied with species and country, and four IUCN threat categories had the greatest overall impacts: Climate Change, Problematic Species (including disease), Agriculture, and Energy Production. Experts estimated that 90% of species assessed had decreasing population trends over the past 15 years, demonstrating the need for conservation action. Although the state of North American bats is concerning, we identify threats that can be addressed through internationally collaborative, proactive, and protective actions to support the recovery and resilience of North American bat species.

Wildlife researchers must balance the need to safely capture and handle their study animals to sample tissues, collect morphological measurements, and attach dataloggers while ensuring their results are not confounded by stress artifacts caused by handling. To determine the physiological effects of research activities including chemical immobilization, transport, instrumentation with biologgers, and overnight holding on a model marine mammal species, we collected hormone, blood chemistry, hematology, and heart rate data from 19 juvenile northern elephant seals (Mirounga angustirostris) throughout a translocation experiment. Across our six sampling timepoints, cortisol and aldosterone data revealed a moderate hormonal stress response to handling accompanied by minor changes in hematocrit and blood glucose, but not ketone bodies or erythrocyte sedimentation rate. We also examined heart rate as a stress indicator and found that interval heart rate, standard deviation of heart rate, and apnea-eupnea cycles were influenced by handling. However, when seals were recaptured after several days at sea, all hormonal and hematological parameters had returned to baseline levels. Furthermore, 100 % of study animals were resighted in the wild post-translocation, with some individuals observed over four years later. Together, these findings suggest that while northern elephant seals exhibit measurable physiological stress in response to handling, they recover rapidly and show no observable long-term deleterious effects, making them a robust species for ecological and physiological research.

Air-breathing vertebrates must balance their response to diel shifts in prey accessibility with physiological thresholds and the need to surface after each dive. Weddell seal (Leptonychotes weddellii) dive behaviors were tracked across the year under rapidly-changing light regimes in the Ross Sea, Antarctica ( ~ 75-77°S). This provides a natural experiment with free-living seals experiencing 24-hrs of light (Polar Day), light/dark cycling, and continuous darkness (Polar Night). The Weddell seals temporal niche switches from nocturnal diving in the summer to diurnality for the remainder of the year. Rhythmicity in dive efforts (depth, duration, post-dive surface recuperation, bottom time, and exceeding physiologic thresholds) is stronger and more closely circadian during times of the year with light/dark cycling compared with Polar Day or Night. With light/dark cycling, animals also make the most extreme dives (those that far exceed the calculated aerobic dive limit, cADL) significantly earlier than solar noon. Offsetting the longest dives that require longer surface recuperation times from mid-day allows animals to maximize total dive time under high-light conditions conducive for visual hunting. We identify an optimal foraging strategy to exploit a diel preyscape in a highly-seasonal environment, while balancing tradeoffs imposed by physiological thresholds in a diving mammal.

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforests dynamism on wild primates genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics.

Hybridization is increasingly recognized as an important evolutionary process across the tree of life. In many clades, phylogenomic approaches have permitted unparalleled insight into the extent and frequency of hybridization. However, we continue to lack a deep understanding of the factors that limit and shape patterns of hybridization, especially in evolutionary radiations. In this study, we characterized patterns of introgression across Costus (Costaceae), a young evolutionary radiation of tropical understory plants that maintain widespread interfertility despite exhibiting strong prezygotic reproductive isolation. We analyzed a phylogenomic dataset of 756 genes from 54 Costus species using multiple complementary approaches - D-statistics, gene-tree-based tests, and phylogenetic network analyses - to detect and characterize introgression events throughout the evolutionary history of the radiation. Our results identified a moderate number of introgression events, including a particularly ancient, well-supported event spanning one of the deepest divergences in the clade. Most introgression events occurred between taxa or ancestral lineages that shared the same pollination syndrome (bee-pollinated or hummingbird-pollinated). These findings suggest that prezygotic barriers, including pollinator specialization, have been key to the balance between introgression and reproductive isolation in Costus.

Disentangling the effects of cyclical variability in environmental forcing and long-term climate change on natural communities is a major challenge for ecologists, managers, and policy makers across ecosystems. Here we examined whether the vertical distribution of rocky intertidal taxa has shifted with sea-level variability occurring at multiple temporal scales and/or long-term anthropogenic sea-level rise (SLR). Because of the distinct zonation characteristic of intertidal communities, any shift in tidal dynamics or average sea level is expected to have large impacts on community structure and function. We found that across the Northeast Pacific Coast (NPC), sea level exhibits cyclical seasonal variability, tidal amplitude exhibits ecologically significant variability coherent with the 18.6-year periodicity of lunar declination, and long-term sea-level rise is occurring. Intertidal taxa largely do not exhibit significant vertical distribution shifts coherent with short-term (monthly to annual) sea-level variability but do exhibit taxa-specific vertical distribution shifts coherent with cyclical changes in lunar declination and long-term SLR at decadal timescales. Finally, our results show that responses to cyclical celestial mechanics and SLR vary among taxa, primarily according to their vertical distribution. Long-term SLR is occurring on ecologically relevant scales, but the confounding effects of cyclical celestial mechanics make interpreting shifts in zonation or community structure challenging. Such cyclical dynamics alternatingly amplify and dampen long-term SLR impacts and may modify the impacts of other global change related stressors, such as extreme heat waves and swell events, on intertidal organisms living at the edge of their physiological tolerances. As a result, intertidal communities will likely experience cyclical periods of environmental stress and concomitant nonlinear shifts in structure and function as long-term climate change continues. Our results demonstrate that consistent, large-scale monitoring of marine ecosystems is critical for understanding natural variability in communities and documenting long-term change.

Many variables in biological research-from body size to life-history timing to environmental characteristics-are measured continuously (e.g. body mass in kilograms) but analysed as categories (e.g. large versus small), which can lower statistical power and change interpretation. We conducted a mini-review of 72 recent publications in six popular ecology, evolution and behaviour journals to quantify the prevalence of categorization. We then summarized commonly categorized metrics and simulated a dataset to demonstrate the drawbacks of categorization using common variables and realistic examples. We show that categorizing continuous variables is common (31% of publications reviewed). We also underscore that predictor variables can and should be collected and analysed continuously. Finally, we provide recommendations on how to keep variables continuous throughout the entire scientific process. Together, these pieces comprise an actionable guide to increasing statistical power and facilitating large synthesis studies by simply leaving continuous variables alone. Overcoming the pitfalls of categorizing continuous variables will allow ecologists, ethologists and evolutionary biologists to continue making trustworthy conclusions about natural processes, along with predictions about their responses to climate change and other environmental contexts.