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.

The rate at which mutations arise is a fundamental parameter of biology. Despite progress in measuring germline mutation rates across diverse taxa, such estimates are missing for much of Earths biodiversity. Here, we present the first estimate of a germline mutation rate from the phylum Mollusca. We sequenced three pedigreed families of the white abalone Haliotis sorenseni, a long-lived, large-bodied, and critically endangered mollusk, and estimated a de novo mutation rate of 8.60 × 10-9 single nucleotide mutations per site per generation. This mutation rate is similar to rates measured in vertebrates with comparable generation times and longevity to abalone, and higher than mutation rates measured in faster-reproducing invertebrates. The spectrum of de novo mutations is also similar to that seen in vertebrate species, although an excess of rare C > A polymorphisms in wild individuals suggests that a modifier allele or environmental exposure may have once increased C > A mutation rates. We use our rate to infer baseline effective population sizes (Ne) across multiple Pacific abalone and find that abalone persisted over most of their evolutionary history as large and stable populations, in contrast to extreme fluctuations over recent history and small census sizes in the present day. We then use our mutation rate to infer the timing and pattern of evolution of the abalone genus Haliotis, which was previously unknown due to few fossil calibrations. Our findings are an important step toward understanding mutation rate evolution and they establish a key parameter for conservation and evolutionary genomics research in mollusks.

ABSTRACT: Conservation investments do not operate within a zero‐sum paradigm, but instead provide opportunities for co‐benefits across sustainable development and conservation goals. Recognizing the interconnectedness of conservation efforts within socioenvironmental systems can amplify support for conservation actions, ultimately creating additional co‐benefits across the social, ecological, and economic sectors. As an ecologically diverse taxonomic group with broad conservation needs, we explore how conserving bats contributes to both biodiversity and society's economic and social needs. We align bat conservation goals with Global Biodiversity Framework targets and explore their contribution to the United Nations Sustainable Development Goals. The benefits of targeted bat conservation actions extend beyond species‐level conservation goals and the preservation of bat‐derived ecosystem services, encompassing broader contributions to global sustainability goals. Our findings underscore the potential for conservation investments to generate positive outcomes across multiple sectors, fostering sustainability and resilience within socioenvironmental systems.

Climate change is projected to cause extensive plant range shifts, and, in many cases such shifts already are underway. Most long-term studies of range shifts measure emergent changes in species distributions but not the underlying demographic patterns that shape them. To better understand species elevational range shifts and their underlying demographic processes, we use the powerful approach of rephotography, comparing historical (1978-1982) and modern (2015-2016) photographs taken along a 1000-m elevational gradient in the Colorado Desert of Southern California. This approach allowed us to track demographic outcomes for 4263 individual plants of 11 long-lived, perennial species over the past ~36 years. All species showed an upward shift in mean elevation (average = 45 m), consistent with observed increasing temperature and severe drought in the region. We found that varying demographic processes underlaid these elevational shifts, with some species showing higher recruitment and some showing higher survival with increasing elevation. Species with faster life-history rates (higher background recruitment and mortality rates) underwent larger elevational shifts. Our findings emphasize the importance of demography and life history in shaping range shift responses and future community composition, as well as the sensitivity of desert systems to climate change despite the typical slow motion population dynamics of perennial desert plants.

Whether large-scale variation in lineage diversification rates can be predicted by species properties at the population level is a key unresolved question at the interface between micro- and macroevolution. All else being equal, species with biological attributes that confer metapopulation stability should persist more often at timescales relevant to speciation and so give rise to new (incipient) forms that share these biological traits. Here, we develop a framework for testing the relationship between metapopulation properties related to persistence and phylogenetic speciation rates. We illustrate this conceptual approach by applying it to a long-term dataset on demersal fish communities from the North American continental shelf region. We find that one index of metapopulation persistence has phylogenetic signal, suggesting that traits are connected with range-wide demographic patterns. However, there is no relationship between demographic properties and speciation rate. These findings suggest a decoupling between ecological dynamics at decadal timescales and million-year clade dynamics, raising questions about the extent to which population-level processes observable over ecological timescales can be extrapolated to infer biodiversity dynamics more generally.

Northern elephant seals (Mirounga angustirostris) have been integral to the development and progress of biologging technology and movement data analysis, which continue to improve our understanding of this and other species. Adult female elephant seals at Año Nuevo Reserve and other colonies along the west coast of North America were tracked annually from 2004 to 2020, resulting in a total of 653 instrument deployments. This paper outlines the compilation and curation process of these high-resolution diving and location data, now accessible in two Dryad repositories. The code used for data processing alongside the corresponding workflow is available through GitHub and Zenodo. This data set represents 3,844,927 dives and 596,815 locations collected from 475 individual seals with 178 repeat samplings over 17 years. We anticipate that these data will stimulate further analysis and investigation into elephant seal biology and aid in developing new analytical approaches for large marine predators.

Long-term studies are critical for ecological understanding, but they are underutilized as inclusive opportunities for training ecologists. We use our perspective from the Año Nuevo elephant seal programme along with surveys from community members to propose that long-term studies could be better leveraged to promote inclusive education and professional development in ecology. Drawing on our experiences as mentors and mentees, we demonstrate how long-term studies can use their resources, including rich data, robust logistics and extensive professional networks, to improve recruitment and retention of diverse groups of trainees. However, practices such as unpaid labour and unclear expectations limit the utility of these resources for diversifying ecology. We discuss how we have structured our long-term study to create more inclusive and equitable training opportunities. Acknowledging these transformations required substantial resources, we highlight funding sources and organizational partnerships that can promote investment in long-term studies for broadening participation.

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.

Maternal age can influence reproductive success and offspring fitness, but the timing, magnitude and direction of those impacts are not well understood. Evolutionary theory predicts that selection on fertility senescence is stronger than maternal effect senescence, and therefore, the rate of maternal effect senescence will be faster than fertility senescence. We used a 36-year study of northern elephant seals (Mirounga angustirostris) to investigate reproductive senescence. Our dataset included 103,746 sightings of 1203 known-age female northern elephant seals. We hypothesized that fertility (maternal reproductive success), offspring survival and recruitment into the breeding population, and male offspring production would decline with advanced maternal age. Furthermore, we hypothesized that older females would shorten their moulting haul out to allow for more time spent foraging. We found evidence for both fertility and maternal effect senescence, but no evidence for senescence impacting offspring recruitment or sex ratio. Breeding probability declined from 96.4% (95% CI: 94.8%-97.5%) at 11 years old to 89.7% (81.9%-94.3%) at 19 years old, and the probability of offspring survival declined from 30.3% (23.6%-38.0%) at 11 years old to 9.1% (3.2%-22.9%) at 19 years old. The rates of decline for fertility and maternal effect senescence were not different from each other. However, maternal effect senescence had a substantially greater impact on the number of offspring surviving to age 1 compared to fertility senescence. Compared to a hypothetical non-senescent population, maternal effect senescence resulted in 5.3% fewer surviving pups, whereas fertility senescence resulted in only 0.3% fewer pups produced per year. These results are consistent with evolutionary theory predicting weaker selection on maternal effect than fertility senescence. Maternal effect senescence may therefore be more influential on population dynamics than fertility senescence in some systems.