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Open Access Publications from the University of California

Open Access Policy Deposits

This series is automatically populated with publications deposited by UC Santa Cruz Department of Ecology and Evolutionary Biology researchers in accordance with the University of California’s open access policies. For more information see Open Access Policy Deposits and the UC Publication Management System.

Cover page of Distribution and Genetic Structure of <em>Fucus distichus</em> Linnaeus 1953 (formerly <em>F. gardneri</em>) within Central San Francisco Bay

Distribution and Genetic Structure of Fucus distichus Linnaeus 1953 (formerly F. gardneri) within Central San Francisco Bay

(2017)

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.

Cover page of Geographically widespread and novel hemotropic mycoplasmas and bartonellae in Mexican free-tailed bats and sympatric North American bat species.

Geographically widespread and novel hemotropic mycoplasmas and bartonellae in Mexican free-tailed bats and sympatric North American bat species.

(2025)

UNLABELLED: Bacterial pathogens remain poorly characterized in bats, especially in North America. We describe novel (and in some cases panmictic) hemoplasmas (10.1% positivity) and bartonellae (25.6% positivity) across three colonies of Mexican free-tailed bats (Tadarida brasiliensis), a partially migratory species that can seasonally travel hundreds of kilometers. Molecular analyses identified three novel Candidatus hemoplasma species most similar to another novel Candidatus species in Neotropical molossid bats. We also detected novel hemoplasmas in sympatric cave myotis (Myotis velifer) and pallid bats (Antrozous pallidus), with sequences in the latter 96.5% related to Candidatus Mycoplasma haematohominis. We identified nine Bartonella genogroups, including those in cave myotis with 96.1% similarity to Candidatus Bartonella mayotimonensis. We also detected Bartonella rochalimae in migratory Mexican free-tailed bats, representing the first report of this human pathogen in the Chiroptera. Monthly sampling of migratory Mexican free-tailed bats during their North American occupancy period also revealed significant seasonality in infection for both bacterial pathogens, with prevalence increasing following spring migration, peaking in the maternity season, and declining into fall migration. The substantial diversity and seasonality of hemoplasmas and bartonellae observed here suggest that additional longitudinal, genomic, and immunological studies in bats are warranted to inform One Health approaches. IMPORTANCE: Bats have been intensively sampled for viruses but remain mostly understudied for bacterial pathogens. However, bacterial pathogens can have significant impacts on both human health and bat morbidity and even mortality. Hemoplasmas and bartonellae are facultative intracellular bacteria of special interest in bats, given their high prevalence and substantial genetic diversity. Surveys have also supported plausible zoonotic transmission of these bacteria from bats to humans, including Candidatus Mycoplasma haematohominis and Candidatus Bartonella mayotimonensis. Greater characterization of these bacteria across global bat diversity (over 1,480 species) is therefore warranted to inform infection risks for both bats and humans, although little surveillance has thus far been conducted in North American bats. We here describe novel (and in some cases panmictic) hemoplasmas and bartonellae across three colonies of Mexican free-tailed bats and sympatric bat species. We find high genetic diversity and seasonality of these pathogens, including lineages closely related to human pathogens, such as Bartonella rochalimae.

Cover page of Direct Measurement of the Mutation Rate and Its Evolutionary Consequences in a Critically Endangered Mollusk.

Direct Measurement of the Mutation Rate and Its Evolutionary Consequences in a Critically Endangered Mollusk.

(2025)

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.

Cover page of Unfriendly neighbors: When facilitation does not contribute to restoration success in tidal marsh.

Unfriendly neighbors: When facilitation does not contribute to restoration success in tidal marsh.

(2025)

Large-scale restoration projects are an exciting and often untapped opportunity to use an experimental approach to inform ecosystem management and test ecological theory. In our $10M tidal marsh restoration project, we installed over 17,000 high marsh plants to increase cover and diversity, using these plantings in a large-scale experiment to test the benefits of clustering and soil amendments across a stress gradient. Clustered plantings have the potential to outperform widely spaced ones if plants alter conditions in ways that decrease stress for close neighbors. Here, we test whether intraspecific facilitation improves restoration outcomes using a suite of seven high marsh species native to central California salt marshes. We also applied a biochar treatment to test whether soil amendment boosts restoration success. We compared the performance of clustered and uniform plantings across the high marsh elevation gradient for 3 years. There was a strong effect of elevation on plant performance and clear signs of plant stress related to soil conditions. Clustering slightly improved the survival of one species out of seven, although clustering did not benefit that species in a follow-up experiment under more stressful conditions. By contrast, clustering had strong negative effects on the growth and/or cover of all species tested. The stressors in this system-likely related to compaction and soil salinity-were not mitigated by neighbors or biochar. The prevailing negative effect on seven species from distinct evolutionary lineages lends strong generality to our findings. We therefore conclude that for this and similar high marsh systems, intraspecific facilitation confers no benefits and practitioners should space plants widely to minimize competition. To take full advantage of the learning opportunities provided by large-scale restoration projects, we recommend including experimental treatments and monitoring the response of multiple species across years to refine best practices and inform adaptive management.

Cover page of Co‐Benefits From Species‐Level Conservation Contribute to Multilateral Environmental Agreement Targets

Co‐Benefits From Species‐Level Conservation Contribute to Multilateral Environmental Agreement Targets

(2025)

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.

Cover page of Contrasting demographic processes underlie uphill shifts in a desert ecosystem.

Contrasting demographic processes underlie uphill shifts in a desert ecosystem.

(2025)

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.

Cover page of The Metapopulation Bridge to Macroevolutionary Speciation Rates: A Conceptual Framework and Empirical Test.

The Metapopulation Bridge to Macroevolutionary Speciation Rates: A Conceptual Framework and Empirical Test.

(2025)

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.

Cover page of Two decades of three-dimensional movement data from adult female northern elephant seals.

Two decades of three-dimensional movement data from adult female northern elephant seals.

(2024)

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.

Cover page of Long‐term studies should provide structure for inclusive education and professional development

Long‐term studies should provide structure for inclusive education and professional development

(2024)

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.