Recent ucsc_eeb_oapdeposits items

Widespread thiamine deficiency in California salmon linked to an anchovy-dominated marine prey base

Thu, 18 Jun 2026 00:00:00 +0000

Thiamine (vitamin B₁) deficiency in marine systems is a globally significant threat to marine life. In 2020, newly hatched Chinook salmon (Oncorhynchus tshawytscha) fry in California's Central Valley (CCV) hatcheries swam in corkscrew patterns and died at unusually high rates due to a lack of this essential vitamin. We subsequently investigated the impacts and causes of thiamine deficiency in California's anadromous salmonids. Our laboratory studies defined the relationship between thiamine concentrations in Chinook salmon eggs and early life-stage survival in offspring; we used these data to develop a model that estimated 26 to 48% thiamine-dependent fry mortality across consecutive years (2020-2021) for winter-run Chinook salmon. We established an egg surveillance effort that found widespread thiamine deficiency in CCV Chinook salmon in 2020 and 2021, and emerging thiamine deficiency in Klamath River and Trinity River coho salmon (Oncorhynchus kisutch)...

Mating system plasticity promotes persistence and adaptation of colonizing populations of hermaphroditic angiosperms

Thu, 18 Jun 2026 00:00:00 +0000

Persistence and adaptation in novel environments are limited by small population size, strong selection, and maladaptive gene flow. Mating system plasticity is common in angiosperms and may provide both demographic and genetic benefits that promote niche evolution, including reproductive assurance and isolation from maladaptive gene flow. Yet increased self-fertilization may also cause inbreeding depression, accumulation of deleterious mutations, and reduced adaptive potential. Here we use individual-based simulations to examine the consequences of mating system plasticity for persistence and adaptation in a novel environment that imposes selection on a quantitative trait. We examine the joint evolution of local adaptation, inbreeding depression, and genetic load. We find that a plastic shift to a mixed mating system generally promotes niche evolution by decreasing the risk of extinction, providing isolation from maladaptive gene flow, and temporarily increasing genetic variance...

Beyond the Grant–Stebbins model: floral adaptive landscapes and plant speciation

Thu, 18 Jun 2026 00:00:00 +0000

BACKGROUND: Floral diversity, a striking feature of angiosperm evolution, provides the impetus and rationale for linking pollinator-driven selection to speciation processes. Perhaps the most widely adopted model for pollinator-driven speciation is the Grant-Stebbins model, in which plant populations locally adapt to the most effective pollinator, leading to floral ecotype formation and, eventually, reproductive isolation and speciation. However, modelling and empirical studies suggest that populations need not adapt to the most effective pollinator, and major floral transitions remain poorly explained. SCOPE: We evaluate the Grant-Stebbins model, focusing especially on the most effective pollinator principle. We use floral adaptive landscapes to articulate a more complete and accurate framework for understanding floral adaptation, starting with the premise that plants evolve to maximize fitness. We highlight ways to improve the assessment of pollinator fitness functions, both...

Mating System Plasticity Promotes Persistence and Adaptation of Colonizing Populations of Hermaphroditic Angiosperms

Thu, 18 Jun 2026 00:00:00 +0000

Pollinator efficiency, rather than bee decline, explains a shift to hummingbird pollination in tropical montane forests.

Thu, 18 Jun 2026 00:00:00 +0000

A longstanding but untested hypothesis proposes that reduced bee visitation in tropical montane cloud forests has repeatedly driven the evolution of hummingbird pollination. Here, we test whether recently diverged bee and hummingbird pollination syndromes in two sister species are adapted to their pollination environments, and whether this reflects declining bee activity at higher elevations. Alternatively, we ask whether higher pollen transfer efficiency drives adaptation to hummingbirds regardless of bee availability. We measured visitation and per-visit efficiency to estimate pollinator effectiveness and conducted reciprocal translocations of Costus kuntzei, with ancestral bee pollination, and Costus wilsonii, with derived hummingbird pollination, across an elevational gradient in Costa Rica, including sites within and outside each species' range and at their elevational boundary. In their ranges, the species are specialized on bees or hummingbirds. However, pollinator effectiveness...

Corrigendum

Thu, 18 Jun 2026 00:00:00 +0000

Corrigendum

The scale of local adaptation in Mimulus guttatus: comparing life history races, ecotypes, and populations

Thu, 18 Jun 2026 00:00:00 +0000

Fitness trade-offs between environments are central to the evolution of biodiversity. Although transplant studies often document fitness trade-offs consistent with local adaptation (LA), many have also found an advantage of foreign genotypes (foreign advantage (FA)). Understanding the mechanisms driving the magnitude and distribution of fitness variation requires comparative approaches that test the ecological scales at which these different patterns emerge. We used a common garden transplant experiment to compare the relative fitnesses of native vs foreign genotypes at three nested ecological scales within Mimulus guttatus: annual vs perennial life history races, perennial ecotypes across an elevational range, and populations within perennial elevational ecotypes. We integrated fitness across the life-cycle and decomposed LA vs FA into contributions from different fitness components. We found LA, measured as home-site advantage, between annual and perennial races and a trend...

Linking Community‐Climate Disequilibrium to Ecosystem Function

Thu, 28 May 2026 00:00:00 +0000

Turnover in species composition often lags behind the pace of climate change, resulting in mismatches between climate and communities. However, the impact of these community-climate disequilibria on ecosystem functions is rarely considered, and current methods for measuring disequilibria assume that species ranges were, until recently, in equilibrium with climate. Here, we develop a simple theoretical model to address both of these problems by linking community-climate disequilibrium with ecosystem functioning. We show how disequilibrium can impair functioning in the near-term even when climate change is expected to enhance functioning in the long-term. Responses are most likely to change over time in communities where turnover is slow, the impact of disequilibrium counteracts the direct effects of climate on ecosystem function, and pre-existing disequilibrium is large. These findings emphasise the importance of precise and unbiased estimates of community-climate disequilibria...

Field immobilisation of adult Weddell seals using intramuscular butorphanol and midazolam.

Fri, 22 May 2026 00:00:00 +0000

Background

When working with free-ranging phocid seals, methods of chemical immobilisation require ongoing refinement to reduce complications, particularly apnoea, during research procedures.

Methods

Adult Weddell seals (n = 20) at Cape Crozier, Antarctica, were chemically immobilised with intramuscular injection of butorphanol and midazolam in 2024 and 2025.

Results

Butorphanol and midazolam were administered intramuscularly at 0.16 ± 0.03 and 0.19 ± 0.03 mg/kg, respectively. No apnoea lasting more than 2 minutes was observed, nor were any other adverse effects.

Limitations

The sample was limited to 20 adults, predominantly mid-lactation females (n = 14). Additional data on other demographic groups, varying the dose combination, more detailed records of seal vital signs, and additional physiological measurements (e.g., blood gases) would provide valuable insight into this drug combination for Weddell seals.

Conclusion

In this limited...

Environmental Heterogeneity Predicts Behavioural Diversity in a Widely Distributed Group of Marine Carnivores

Fri, 22 May 2026 00:00:00 +0000

ABSTRACT: Aim: Environmental heterogeneity shapes species diversity by creating ecological niches (habitat heterogeneity hypothesis). Yet its role in driving behavioural diversity within species remains only partially understood. Behavioural diversity enhances a population's ability to exploit ecological niches and adapt to environmental change, making it critical to understand how behaviour is shaped by environmental factors. Here we test whether spatial and temporal heterogeneity predict behavioural diversity at population and individual levels across species and environments. Location: Global. Methods: We synthesised biologging data from five species of sea lions (15 colonies, 370 individuals, ~927,000 dives) to test the relationship between population‐level...

A global decision framework for reducing bat fatalities at wind energy facilities

Mon, 13 Apr 2026 00:00:00 +0000

Abstract: Ensuring wind energy development does not cause biodiversity loss is a global priority. Wind turbines kill large numbers of bats, raising concern that global expansion of wind energy increases the threat of extinction of vulnerable bat species. Uncertainty about bat population size and status has hindered efforts to implement regulatory policies based on solutions known to reduce bat fatalities at wind energy facilities, in large part because the amount of fatality reduction necessary to protect bats has been difficult to define. Adoption of the full mitigation hierarchy for bats is urgently needed, including informed siting to avoid impacts to bats, minimization of bat fatalities using fatality thresholds to set operational conditions (e.g. curtailment) and compensation through offsets. We introduce a method...

Foraging behavior of a mesopelagic predator, the northern elephant seal, in northeastern Pacific eddies

Thu, 9 Apr 2026 00:00:00 +0000

The role of mesoscale features in structuring trophic transfer in the mesopelagic zone is poorly understood. Deploying sensors on marine animals, or “biologging,” is a powerful tool to infer the organism's behavior and simultaneously collect high-resolution oceanographic data to describe physical-biological interactions. We investigated whether mesoscale eddies are used by a mesopelagic predator, the northern elephant seal (Mirounga angustirostris), and if so, what mechanisms might create beneficial foraging conditions in association with eddies. We hypothesized seals would increase their foraging behavior in both cyclonic and anticyclonic eddies due to nutrient enhancement and physical aggregation of prey and that seals would dive deeper in anticyclonic eddies in response to a deeper prey field. We used tracking data and continuous in situ temperature measurements from 221 adult female northern elephant seals collected between 2004 and 2019. These predators primarily targeted...

Body Composition of Common Bottlenose Dolphins in Sarasota Bay, Florida

Thu, 9 Apr 2026 00:00:00 +0000

Marine mammal body composition has been an important tool that is used as a proxy for the health and condition of individuals within a population. Common bottlenose dolphin (Tursiops truncatus) body composition is influenced by variations in blubber thickness resulting from changes in temperature, prey availability, health, and life-history traits. We examined how environmental, ontogenetic, and reproductive variables influenced the body composition of common bottlenose dolphins in Sarasota Bay using data collected from a long-term monitoring project by the Sarasota Dolphin Research Program (SDRP). We found that both sea surface temperature (SST) and catch per unit effort (CPUE), used as a proxy for prey availability, influenced body composition. There was a high degree of seasonality in body composition, with higher values occurring in winter when SST and CPUE were both low. Ontogeny also greatly influenced body composition, as younger dolphins typically had thicker blubber than...

First observations of Weddell seals foraging in sponges in Erebus Bay, Antarctica

Thu, 9 Apr 2026 00:00:00 +0000

Attaching cameras to marine mammals allows for first-hand observation of underwater behaviours that may otherwise go unseen. While studying the foraging behaviour of 26 lactating Weddell seals (Leptonychotes weddellii) in Erebus Bay during the austral spring of 2018 and 2019, we witnessed three adults and one pup investigating the cavities of Rossellidae glass sponges, with one seal visibly chewing when she removed her head from the sponge. To our knowledge, this is the first report of such behaviour. While the prey item was not identifiable, some Trematomus fish (a known Weddell seal prey) use glass sponges for shelter and in which to lay their eggs. Three of the four sponge foraging observations occurred around 13:00 (NZDT). Two of the three sponge foraging adults had higher-than-average reproductive rates, and the greatest number of previous pups of any seal in our study population, each having ten pups in 12 years. This is far higher than the study population average...

Spatiotemporal Variation in Marine Mammal Antipredator Behaviors Resulting From a Predation Pinch Point

Thu, 9 Apr 2026 00:00:00 +0000

Using 17 years of biologging data from 353 adult female northern elephant seals, we explored how seals modified their use of time and space when moving through nearshore areas where predation risk is high. We found that seals tended to depart at night, arrive during the day, and perform benthic dives along the continental shelf. These behaviors likely reduced the likelihood of seals being detected by predators, and help us understand how animals respond to varying levels of risk in their environment.

Genetic Diversity Impacts Climate-Induced Species Range Shifts.

Wed, 8 Apr 2026 00:00:00 +0000

Climate change threatens biodiversity when species cannot tolerate, adapt to, or track shifting environmental conditions to stay within their climatic niches. A major unresolved question is whether and how species genetic diversity modulates these dynamics, buffering against range contractions or facilitating range expansions. To test this, we integrated the largest global databases of species range shifts and genetic diversity, encompassing 4673 range shift estimates for 1888 species with available genetic data, including insects, arachnids, birds, fish, and plants. We found that range shifting rates were significantly shaped by the interaction of genetic diversity and climate change velocity. Under rapid warming, species with higher genetic diversity exhibited reduced trailing edge contractions, likely reflecting enhanced evolutionary potential or reduced vulnerability to drift. Under moderate warming, species with higher genetic diversity shifted more rapidly at leading edges...

Conservation energetics of beluga whales: using resting and swimming metabolism to understand threats to an endangered population

Mon, 30 Mar 2026 00:00:00 +0000

The balance between energetic costs and acquisition in free-ranging species is essential for survival, and provides important insights regarding the physiological impact of anthropogenic disturbances on wild animals. For marine mammals such as beluga whales (Delphinapterus leucas), the first step in modeling this bioenergetic balance requires an examination of resting and active metabolic demands. Here, we used open-flow respirometry to measure oxygen consumption during surface rest and submerged swimming by trained beluga whales, and compared these measurements with those of a commonly studied odontocete, the Atlantic bottlenose dolphin (Tursiops truncatus). Both resting metabolic rate (3012±126.0 kJ h-1) and total cost of transport (1.4±0.1 J kg-1 m-1) of beluga whales were consistent with predicted values for moderately sized marine mammals in temperate to cold-water environments, including dolphins measured in the present study. By coupling the rate of oxygen consumption...

Amphibians' Expansion to Record Elevations Influences Chytrid (Batrachochytrium dendrobatidis) Infection Dynamics

Mon, 30 Mar 2026 00:00:00 +0000

The climate‐driven range expansion of host species could impact emerging infectious disease events through several mechanisms, with repercussions for conservation and public health. For instance, infection outcomes may be affected by the different responses of hosts and pathogens to new environments. Additionally, range expansions may create novel transmission opportunities as host movement patterns change. Here, we use an integrative approach to explore how the infection dynamics of Marbled four‐eyed frogs (Pleurodema marmoratum) with the pathogen Batrachochytrium dendrobatidis (Bd) have been impacted by their elevational range expansion in the Cordillera Vilcanota, Peru. With field surveys, we establish that range expansion created new opportunities for Bd transmission: P. marmoratum are now continuously distributed along a recently deglaciated mountain pass between populations separated by heavily glaciated mountains. With sequence data, we identify Bd from the Vilcanota as...

Effects of carbon dioxide accumulation on post-dive physiological recovery in odontocetes.

Fri, 20 Mar 2026 00:00:00 +0000

Diving performance by marine mammals is associated with marked changes in tissue oxygen (O2) and carbon dioxide (CO2) levels. Yet, the primary metric for diving recovery in most studies has focused exclusively on restoring tissue O2, despite the importance of CO2 offloading as a major determinant for diving homeostasis. To assess the combined role of respiratory and blood gases, we compared post-exercise O2 and CO2 recovery rates in bottlenose dolphins (Tursiops truncatus, n=2) and beluga whales (Delphinapterus leucas, n=4). System-wide recovery mechanisms were also examined, including blood pH, breathing patterns, and peripheral vasodilation. Following maximal swim repetitions, respiratory O2 and CO2 levels returned to resting levels within 8.5 min for belugas (VO2: 8.4±0.8 min; VCO2: 8.5±0.9 min; mean±s.d.) and 3.5 min for dolphins (VO2: 3.4±0.8 min; VCO2: 3.4±0.7 min). Blood O2 and CO2 recovery durations also varied by species. Belugas required 12-15 min to reach resting levels,...

Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio

Wed, 11 Mar 2026 00:00:00 +0000

The strawberry poison frog, Oophaga pumilio, is a striking example of natural color variation, making it a valuable system for studying the genetic and evolutionary mechanisms underlying phenotypic diversity. While most populations of this poisonous frog are bright red, frogs from Bocas del Toro Province, Panama, exhibit remarkable variation in color, both within and among island populations. This diversity in warning coloration challenges conventional models of aposematism and has fueled extensive debate about its evolutionary and genetic origins. A major obstacle to understanding this phenomenon has been the species' large genome (∼6.7 Gb). To address this, we sequenced exomes from 347 individuals across ten populations and identified genetic factors associated with color variation. Our analyses identified kit as a major candidate gene linked to blue-red polymorphism, where an increase in the proportion and organization of melanosomes with respect to other pigments contributes...

The genetics, evolution, and maintenance of a biological rock-paper-scissors game

Fri, 6 Feb 2026 00:00:00 +0000

Side-blotched lizards (Uta stansburiana) play a biological rock-paper-scissors game in which three differently colored male morphs utilize alternative mating strategies. We identified the genetic basis of this polymorphism, which was previously posited to arise from three alleles at one locus. Orange usurper and blue mate-guarder morphs are associated with two divergent haplotypes in the regulatory region of the sepiapterin reductase gene, but yellow sneaker morphs appear to arise through phenotypic plasticity from the same genetic background as blue morphs. Our simulations show that rock-paper-scissors dynamics can better maintain a polymorphism with a genetic system of two alleles plus plasticity than with a three-allele system. This form of balancing selection that combines genetic determination with phenotypic plasticity expands the possibilities for how stable polymorphisms arise in nature.

Preservation of Genetic Diversity and Selection over a Century in a Coral Reef Fish ( Taeniamia zosterophora ) in the Philippines

Tue, 20 Jan 2026 00:00:00 +0000

Preservation of Genetic Diversity and Selection over a Century in a Coral Reef Fish ( Taeniamia zosterophora ) in the Philippines

Anthropocene genetic diversity loss in the marine tropics.

Thu, 15 Jan 2026 00:00:00 +0000

Genetic diversity is a crucial component of biodiversity, and as such, its maintenance and preservation is of high conservation concern. Tropical environments are undergoing intense rates of environmental change, and these changes may be driving large declines in genetic diversity. However, data on genetic diversity are highly skewed towards temperate regions. The degree to which diversity loss has occurred in tropical species, particularly marine species, remains an open and important question. Here, we directly compare genomic data from modern and museum collections of two commercially harvested nearshore marine fishes (Equulites laterofenestra and Gazza minuta) gathered from a single location in the Philippines, spanning a century of intense environmental change. These data reveal a marked loss in genetic diversity and evidence for multiple orders of magnitude reductions in effective population size (N_e) in both species, indicating substantial...

Matching the Dispersal of Baby Clownfish to Oceanographic Currents

Thu, 15 Jan 2026 00:00:00 +0000

Matching the Dispersal of Baby Clownfish to Oceanographic Currents

Key components of sustainable climate-smart ocean planning

Thu, 15 Jan 2026 00:00:00 +0000

Planning of marine areas has spread widely over the past two decades to support sustainable ocean management and governance. However, to succeed in a changing ocean, marine spatial planning (MSP) must be ‘climate-smart’— integrating climate-related knowledge, being flexible to changing conditions, and supporting climate actions. While the need for climate-smart MSP has been globally recognized, at a practical level, marine managers and planners require further guidance on how to put it into action. Here, we suggest ten key components that, if well-integrated, would promote the development and implementation of sustainable, equitable, climate-smart MSP initiatives around the globe.

Low‐Coverage Whole‐Genome Analysis of Population Structure, Bottlenecks, and Selection in Indiana Bats Before and After White‐Nose Syndrome

Wed, 14 Jan 2026 00:00:00 +0000

Conservation successes for the endangered Indiana bat (Myotis sodalis) in the early 2000s were largely reversed by white-nose syndrome (WNS), a novel fungal disease that emerged in North America in 2006. Impacts have been variable among Indiana bat colonies leading to uncertainty regarding the full impact of WNS on this species. However, many colonies maintain negative population growth, threatening long-term viability. Adaptive evolution could allow populations to persist despite disease, as has happened for other species; however, the evolutionary potential of Indiana bats remains unclear. Here, we perform low-coverage whole-genome sequencing to identify population structure, test for potential population bottlenecks, and scan for signatures of selection by comparing bat tissue samples from four states before and after WNS emergence. We found evidence of high connectivity across the Indiana bat range, but reduced gene flow to the colony from Northern New York. There was little...

The Need for Shifting Baselines to Guide Fisheries and Ocean Activities From Days to Decades

Wed, 14 Jan 2026 00:00:00 +0000

ABSTRACT With novel ocean conditions rapidly appearing as the result of climate change, basing decisions about fisheries and other ocean activities on historical conditions is no longer tenable. There is instead a widespread need for shifting ecological baselines to more effectively guide decisions into the future. What has not been as widely recognised is that the relevant timescales differ substantially across ocean‐related decisions, from lead times of hours to decades depending on the decision being made, and that this range necessitates a matching range of ecological forecast products across similar timescales. At the moment, a predictability gap exists at intermediate timescales, from multi‐annual to multi‐decadal forecasts. Because most fisheries and many other ocean activities rely on biological conditions like fish abundance or distribution, the ecological inertia of organismal growth, generational turnover, movement, and food web dynamics can help push ecological forecasts...

MoveTraits-A Database for Integrating Animal Behaviour Into Trait-Based Ecology.

Mon, 12 Jan 2026 00:00:00 +0000

Trait-based approaches are key to understanding eco-evolutionary processes but rarely account for animal behaviour despite its central role in ecosystem dynamics. We propose integrating behaviour into trait-based ecology through movement traits-standardised and comparable measures of animal movement derived from biologging data, such as daily displacements or range sizes. Accounting for animal behaviour will advance trait-based research on species interactions, community structure and ecosystem functioning. Importantly, movement traits allow for quantification of behavioural reaction norms, offering insights into species acclimation and adaptive capacity to environmental change. We outline a vision for a living global movement trait database that enhances trait data curation by (1) continuously growing alongside shared biologging data, (2) calculating traits directly from individual-level data using standardised, consistent methodology and (3) providing information on multi-level...

Repeating Historical Studies to Understand Functional Responses to Environmental Change

Thu, 18 Dec 2025 00:00:00 +0000

Repeating Historical Studies to Understand Functional Responses to Environmental Change

The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana

Wed, 17 Dec 2025 00:00:00 +0000

Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with a broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelp's accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of N. luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1,562 scaffolds with 449.82 Mb, 80× of coverage, and 22,952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Kb and 131 Mb, respectively. The orthology...

Recent Adaptation in a Threatened Salmonid Revealed by Museum Genomics

Tue, 14 Oct 2025 00:00:00 +0000

Steelhead/rainbow trout (Oncorhynchus mykiss) is an imperilled salmonid with two main life history strategies: migrate to the ocean or remain in freshwater. Domesticated hatchery forms of this species have been stocked into almost all California waterways, possibly resulting in introgression into natural populations and altered population structure. We compared whole-genome sequence data from contemporary populations against a set of museum population samples of steelhead from the same locations that were collected prior to most hatchery stocking. We observed minimal introgression and few steelhead-hatchery trout hybrids despite a century of extensive stocking. Our historical data show signals of introgression with a sister species and indications of an early hatchery facility. Finally, we found that migration-associated haplotypes have become less frequent over time, a likely adaptation to decreased opportunities for migration. Since contemporary migration-associated haplotype...

A centurial signature of anthropogenic nitrogen and carbon in California serpentine ecosystems

Thu, 9 Oct 2025 00:00:00 +0000

Abstract: Increasing anthropogenic emissions of nitrogen (N) and carbon (C) are major threats to ecosystems globally. Although atmospheric N deposition is likely affecting N cycling and community composition in California's serpentine ecosystems, a historical record of N inputs to vegetation has yet to be reconstructed for these nutrient‐limited biodiversity hotspots. For leather oak (Quercus durata var. durata), a foundational, serpentine‐endemic species, we investigated leaf N and C isotopic composition (δ15N and δ13C) and leaf %N of herbarium and modern leaf samples collected from 1899 to 2009 from serpentine ecosystems in two study areas in California: Santa Clara County, and Lake and Napa Counties combined. We also evaluated tree ring growth over a similar time period in long‐lived leather oak individuals. Leaf δ15N and δ13C values decreased over time in both study areas, likely reflecting changes in the regional and local atmospheric N and C pools caused by human perturbation....

Extreme events drive rapid and dynamic range fluctuations

Wed, 8 Oct 2025 00:00:00 +0000

Climate change is altering species' distributions globally. Increasing frequency of extreme weather and climate events (EWCEs) is one of the hallmarks of climate change. Despite species redistribution being widely studied in response to long-term climatic trends, the contribution of EWCEs to range shifts is not well understood. We outline how EWCEs can trigger rapid and unexpected range boundary fluctuations by impacting dispersal, establishment, and survival. Whether these mechanisms cause temporary or persistent range shifts depends on the spatiotemporal context and exposure to EWCEs. Using the increasing availability of data and statistical tools to examine EWCE impacts at fine spatiotemporal resolutions on species redistribution will be critical for informing conservation management of ecologically, economically, and culturally important species.

A cautious approach to subsidies for environmental sustainability

Wed, 8 Oct 2025 00:00:00 +0000

Transformational change is possible, but design and implementation must seek to avoid lock-in.

Ecological acclimation: A framework to integrate fast and slow responses to climate change

Thu, 2 Oct 2025 00:00:00 +0000

Ecological responses to climate change occur across vastly different time-scales, from minutes for physiological plasticity to decades or centuries for community turnover and evolutionary adaptation. Accurately predicting the range of ecosystem trajectories will require models that incorporate both fast processes that may keep pace with climate change and slower ones likely to lag behind and generate disequilibrium dynamics. However, the knowledge necessary for this integration is currently fragmented across disciplines. We develop ‘ecological acclimation’ as a unifying framework to emphasize the similarity of dynamics driven by processes operating on dramatically different time-scales and levels of biological organization. The framework focuses on ecoclimate sensitivities, measured as the change in an ecological response variable per unit of climate change. Acclimation processes acting at different time-scales cause these sensitivities to shift in magnitude and even direction...

Marine communities do not follow the paradigm of increasing similarity through time

Thu, 2 Oct 2025 00:00:00 +0000

Humans have transformed ecosystems through habitat modification, harvesting, species introduction, and climate change. Changes in species distribution and composition are often thought to induce biotic homogenization, defined as an increase in the spatial similarity of species compositions through time. However, it is unclear whether homogenization is common in ocean ecosystems and if changes in similarity exhibit linear or more complex dynamics. Here, we assessed patterns of homogenization or its converse (differentiation) across more than 175,000 samples of 2,006 demersal fish species from 34 regions spanning six decades and 20% of the planet’s continental shelf area. While ten regions (29%) recorded significant homogenization, eleven (32%) recorded significant differentiation. Non-monotonic temporal fluctuations in species composition occurred in 15 regions, highlighting complex dynamics missed by before-and-after snapshots that can drive spurious conclusions about trends in...

Transcriptomic evidence of cytokine storm and sepsis in little brown bats exposed to white-nose syndrome

Thu, 2 Oct 2025 00:00:00 +0000

Much progress has been made in understanding the pathophysiology of white-nose syndrome (WNS), a devastating disease that has impacted North American hibernating bats for nearly two decades. Growth of the causative fungal pathogen, Pseudogymnoascus destructans, on exposed epidermal tissue of bats creates an immune reaction that disrupts natural hibernation physiology and leads to premature expenditure of energy reserves and often death. Past work has highlighted the similarities between WNS and immune reconstitution inflammatory syndrome, but other conditions that have not been considered yet may also be relevant. We performed a transcriptomic analysis of wing tissue from naïve and exposed bats to further investigate the implications of observed differential gene expression patterns. For this analysis, we collected wing biopsy samples from 41 individuals prior to WNS emergence and 58 individuals 2-5 years after WNS emergence. We generated poly-A enriched tag-Seq libraries...

Sparse genetic data limit biodiversity assessments in protected areas globally

Thu, 2 Oct 2025 00:00:00 +0000

Global conservation targets include protecting genetic diversity within species. Yet few studies have assessed whether protected areas (PAs) include genetically diverse populations across species globally. A first step is understanding the availability of population genetic data that could be used in these assessments. We surveyed georeferenced population‐level nuclear (as opposed to mitochondrial or plastid‐based) genetic data across continents and marine biomes (36,354 populations, 2809 species) and found substantial geographic and taxonomic gaps. Most data were concentrated in Europe and North America, with major gaps in Africa and Asia. For most taxonomic groups, data were available for <1% of described species. Globally, 52.08% of the total areal extent of PAs lacked genetically sampled populations. These gaps in data availability highlight the need for targeted genetic data collection, harmonization, and sharing to improve genetic diversity monitoring and conservation...

Direct Effects of Polyploidization on Floral Scent

Mon, 15 Sep 2025 00:00:00 +0000

Polyploidy is an important driver of the evolution and diversification of flowering plants. Several studies have shown that established polyploids differ from diploids in floral morphological traits and that polyploidization directly affects these traits. However, for floral scent, which is key to many plant-pollinator interactions, only a few studies have quantified differences between established cytotypes, and the direct effects of polyploidization on floral scent are not yet known. We compared the floral scent of established polyploids and diploids from a natural mixed-ploidy population of the plant Lithophragma bolanderi (Saxifragaceae), a species pollinated by two highly specialized moth pollinators of the genus Greya (Prodoxidae). We also compared the floral scent of neopolyploids synthetically generated from diploids with the floral scent of the diploid progenitors to quantify the direct effects of polyploidization on floral scent. Established tetraploids had a higher...

Factorial field manipulation reveals CO2 and temperature effects on a critical habitat-forming shellfish.

Wed, 27 Aug 2025 00:00:00 +0000

Ocean acidification and warming could have substantial negative impacts on marine organisms, particularly shell-building species. These environmental drivers may operate independently or interactively, amplifying or mitigating their impacts. Previous results have primarily come from lab studies, yet these climate drivers co-occur within naturally dynamic systems with high abiotic and biotic variability. Within intertidal habitats, the impacts of these drivers in situ remain poorly understood. We conducted a 6-month field manipulation to determine the effects of ocean acidification and warming on a habitat-forming shellfish, the Pacific blue mussel (Mytilus trossulus), in a dynamic intertidal system. Fourteen tide pools containing mussels were manipulated, including ambient (unmanipulated control), CO2 added, warmed, and combined CO2 added and warmed treatments. We measured mussel shell thickness, strength and corrosion at 0, 3 and 6 months of exposure to treatment conditions....

Reimagining species on the move across space and time

Thu, 14 Aug 2025 00:00:00 +0000

Climate change is already leaving a broad footprint of impacts on biodiversity, from an individual caterpillar emerging earlier in spring to dominant plant communities migrating poleward. Despite the various modes of how species are on the move, we primarily document shifting species along only one gradient (e.g., latitude or phenology) and along one dimension (space or time). In this opinion article we present a unifying framework for integrating the study of species on the move over space and time and from micro to macro scales. Future conservation planning and natural resource management will depend on our ability to use this framework to improve understanding, attribution, and prediction of species on the move.

Biomechanical consequences of epiphytism in intertidal macroalgae

Thu, 14 Aug 2025 00:00:00 +0000

Epiphytic algae grow on other algae rather than hard substrata, perhaps circumventing competition for space in marine ecosystems. Aquatic epiphytes are widely thought to negatively affect host fitness; it is also possible that epiphytes benefit from associating with hosts. This study explored the biomechanical costs and benefits of the epiphytic association between the intertidal brown algal epiphyte Soranthera ulvoidea and its red algal host Odonthalia floccosa. Drag on epiphytized and unepiphytized hosts was measured in a recirculating water flume. A typical epiphyte load increased drag on hosts by ~50%, increasing dislodgment risk of epiphytized hosts compared with hosts that did not have epiphytes. However, epiphytes were more likely to dislodge from hosts than hosts were to dislodge from the substratum, suggesting that drag added by epiphytes may not be mechanically harmful to hosts if epiphytes break first. Concomitantly, epiphytes experienced reduced flow when attached...

The genomic history of Iberian horses since the last Ice Age.

Sat, 9 Aug 2025 00:00:00 +0000

Horses have inhabited Iberia (present-day Spain and Portugal) since the Middle Pleistocene, shaping a complex history in the region. Iberia has been proposed as a potential domestication centre and is renowned for producing world-class bloodlines. Here, we generate genome-wide sequence data from 87 ancient horse specimens (median coverage = 0.97X) from Iberia and the broader Mediterranean to reconstruct their genetic history over the last ~26,000 years. Here, we report that wild horses of the divergent IBE lineage inhabited Iberia from the Late Pleistocene, while domesticated DOM2 horses, native from the Pontic-Caspian steppes, already arrived ~1850 BCE. Admixture dating suggests breeding practices involving continued wild restocking until at least ~350 BCE, with IBE disappearing shortly after. Patterns of genetic affinity highlight the far-reaching influence of Iberian bloodlines across Europe and north Africa during the Iron Age and Antiquity, with continued impact extending...

Fine resolution satellite sea surface temperatures capture the conditions experienced by corals at monthly but not daily timescales

Tue, 1 Jul 2025 00:00:00 +0000

Abstract: Water temperature is a strong driver of growth, survival, and local adaptation in corals, but our knowledge of the temperatures experienced by corals on reefs worldwide remains limited. While in situ temperature loggers can provide high quality data, they are relatively expensive to place and retrieve. Alternatively, remotely sensed sea surface temperature data are globally available but may be a biased representation of the temperatures experienced by corals. Here, we compared data from 314 temperature loggers on coral reefs to the ~ 1 km2 resolution remotely sensed Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR) product from NASA. We found good agreement (Pearson’s r = 0.95) between maximum monthly mean temperatures calculated from remote and in situ data, with 84% of temperatures within 0.5 °C of each other. However, remotely sensed temperature did not effectively capture sub-diel temperature fluctuations and the highest peak...

TinyCO2: High‐performance, low‐cost CO2 enrichment for field‐grown plants

Tue, 24 Jun 2025 00:00:00 +0000

Rising atmospheric CO2 levels place terrestrial ecosystems under novel environmental conditions, and research in field settings is key to understanding how real plant communities will respond. Despite decades of progress in elevated CO2 (eCO2) experiments, major gaps persist in our knowledge of plant responses to interacting influences of climate change, especially in areas outside North America and Western Europe. With a goal to expand access to field-based eCO2 research, we designed, built, and tested TinyCO2, a low-cost field experiment for climate change research on plants. TinyCO2 features sixteen 0.62-m² plot areas, half with ambient and half with elevated (+200 ppm) CO2 concentrations, and is suitable for short-stature plants (≤0.5 m in height). Using a proportional-integral control algorithm and constant sampling of air within the plots, TinyCO2 achieves consistent elevation of [CO2] averaging +196.9 ppm. During testing, 95.1% of measured CO2 concentrations...

Quantifying local fishing mortality rates to inform monitoring design for marine reserves

Fri, 6 Jun 2025 00:00:00 +0000

In the spatial management of marine resources, there are a variety of contexts in which it is valuable to estimate local, site-specific demographic rates, particularly harvest rates. For example, in the case of no-take marine reserves, estimating the fishing mortality rate (F) prior to reserve implementation can inform quantitative expectations for increases in the abundance of protected populations in the reserve. Additionally, estimating F after implementation could be used to detect poaching. Often the data available for these estimates are length-abundance survey data, such as from visual diver or camera surveys. One can estimate F by fitting models to population size-structure data; understanding how the accuracy of such estimates depends on sampling effort and fish life history can inform monitoring approaches. Here, we quantified the capacity of a state-space integral projection model (SS-IPM) to estimate local F, and how that depends on life history, the true value of...

Climate change impacts to foraging seascapes for a highly migratory top predator

Thu, 22 May 2025 00:00:00 +0000

BackgroundClimate change is impacting the distribution and movement of mobile marine organisms globally. Statistical species distribution models are commonly used to explain past patterns and anticipate future shifts. However, purely correlative models can fail under novel environmental conditions, or omit key mechanistic processes driving species habitat use.MethodsHere, we used a unique combination of laboratory measurements, field observations, and environmental predictors to investigate spatial variability in energetic seascapes for juvenile North Pacific albacore tuna (Thunnus alalunga). This species undertakes some of the longest migrations of any finfish, but their susceptibility to climate-driven habitat changes is poorly understood. We first built a framework based on Generalized Additive Models to understand mechanisms of energy gain and loss in albacore, and how these are linked to ocean conditions. We then applied the framework to projections from an ensemble of earth...

Interspecific combat between Nymphargus aff. Grandisonae and Espadarana prosoblepon (Anura, Centrolenidae)

Thu, 8 May 2025 00:00:00 +0000

Interspecific combat between Nymphargus aff. Grandisonae and Espadarana prosoblepon (Anura, Centrolenidae)

Of Islands on Islands: Natural Habitat Fragmentation Drives Microallopatric Differentiation in the Context of Distinct Biological Assemblages

Thu, 8 May 2025 00:00:00 +0000

An important evolutionary hypothesis posits that much of the biodiversity we see today arose during episodes of natural habitat fragmentation through the interplay of colonization, extinction, adaptation, and speciation. To interrogate the generality of this hypothesis, we leverage the natural experiment provided by arthropod communities in kīpuka—patches of Hawaiian wet forest isolated by lava flows. With DNA metabarcoding, we provide the first simultaneous exploration of ecological and evolutionary characteristics in the kīpuka system. At both species-equivalent (3% radius OTUs) and haplotype-equivalent (zOTUs) scales, we find that richness increases with kīpuka area, and that kīpuka exhibit faster distance decay of similarity compared to continuous forest. Kīpuka also differ in OTU and zOTU composition from continuous forest, notably hosting higher proportions of non-native OTUs for an arthropod order in which we can comprehensively classify native/non-native OTUs (Araneae)....

Elevational range extension of the marsupial frog, Gastrotheca marsupiata (Duméril & Bibron, 1841) (Anura, Hemiphractidae), from southern Peru

Thu, 8 May 2025 00:00:00 +0000

We extend by 300 m the known upper elevational range of the Marsupial frog, Gastrotheca marsupiata (Dumeril & Bi-bron, 1841), to 4,660 m a.s.l. This record makes G. marsupiata the highest occurring frog in its genus, which is already characterized by high-elevation distributions. We suggest that this record may represent a case of climate-induced range shifting and discuss this record in the context of our still limited understanding of how amphibian distributions are being affected by climate change.

Temperature Drives Seagrass Recovery Across the Western North Atlantic

Sat, 26 Apr 2025 00:00:00 +0000

Climate-driven shifts in herbivores, temperature, and nutrient runoff threaten coastal ecosystem resilience. However, ecological resilience, particularly for foundation species, remains poorly understood due to the scarcity of field experiments conducted across appropriate spatial and temporal scales that investigate multiple stressors. This study evaluates the resilience of a widespread tropical marine plant (turtlegrass) to disturbances across its geographic range and examines how environmental gradients in (a)biotic factors influence recovery. We assessed turtlegrass resilience by following recovery rates for a year after a simulated pulse disturbance (complete above- and belowground biomass removal). Contrary to studies in temperate areas, higher temperature generally enhanced seagrass recovery. While nutrients had minimal individual effects, they reduced aboveground recovery when combined with high levels of herbivore grazing (meso and megaherbivore). Belowground recovery...

Multi‐Species Telemetry Quantifies Current and Future Efficacy of a Remote Marine Protected Area

Sat, 26 Apr 2025 00:00:00 +0000

Large-scale marine protected areas (LSMPAs; > 1000 km²) provide important refuge for large mobile species, but most do not encompass species' ranges. To better understand current and future LSMPA value, we concurrently tracked nine species (seabirds, cetaceans, pelagic fishes, manta rays, reef sharks) at Palmyra Atoll and Kingman Reef (PKMPA) in the U.S. Pacific Islands Heritage Marine National Monument. PKMPA and the U.S. Exclusive Economic Zone encompassed 39% and 54% of species movements (n = 83; tracking duration range: 0.5-350 days), respectively. Species distribution models indicated 73% of PKMPA contained highly suitable habitat. Under two projected future scenarios (SSP 1-2.6, "Sustainability"; SSP 3-7.0, "Rocky Road"), strong sea surface temperature gradients initially could cause abrupt oceanic change resulting in predicted habitat loss in 2040-2050, followed by an equilibrium response and regained habitat by 2090-2100. Current and future suitable habitats...

Distributed urban forest patch sampling detects edge effects and woodland condition for monitoring and management

Thu, 24 Apr 2025 00:00:00 +0000

Abstract: Urban forest patches, including woodland interiors and bounding edge habitat, result from secondary succession and fragmentation of more extensive forested landscapes in the eastern United States. Management regimes, surrounding land use, and successional processes lead to distinct environments and contribute to local and regional heterogeneity. However, many woodlands are degraded due to frequent disturbance, aggressive exotic species, and heavy browsing, which stress canopies, reduce regeneration, and may reduce ecosystem services. Effective management requires rapid, repeatable assessment of forest composition, structure, and condition at the scale of local decision‐making. We present and apply a protocol for characterizing urban woodlands that generates new insight into the status of urban woodlands and baseline data for change detection over time. Samples of overstory composition, ground cover, surface soil measurements, and the Schumacher Vine Encroachment Index...

Evaluating the robustness of generalized additive models as a tool for threshold detection in variable environments

Thu, 24 Apr 2025 00:00:00 +0000

As global climate change and anthropogenic activities amplify widespread environmental variability, there is a strong need for management strategies that incorporate relationships between ecosystem components. This need is especially apparent when changes in environmental drivers cause threshold responses (abrupt, nonlinear changes) in ecosystems. Such ecological thresholds can provide useful reference points for management decisions. However, methods for detecting thresholds in empirical datasets may fail to find an existing threshold, find one that does not exist, or be biased in their estimates of threshold locations. These types of threshold misspecifications can result in high conservation and socioeconomic costs. Simulation studies can mitigate these risks by providing information about method performance across different scenarios. Here, we constructed a series of simulations to evaluate the robustness of threshold detection with generalized additive models (GAMs) when...

A novel method for estimating pathogen presence, prevalence, load, and dynamics at multiple scales

Mon, 21 Apr 2025 00:00:00 +0000

The use of quantitative real-time PCR (qPCR) to monitor pathogens is common; however, quantitative frameworks that consider the observation process, dynamics in pathogen presence, and pathogen load are lacking. This can be problematic in the early stages of disease progression, where low level detections may be treated as ‘inconclusive’ and excluded from analyses. Alternatively, a framework that accounts for imperfect detection would provide more robust inferences. To better estimate pathogen dynamics, we developed a hierarchical multi-scale dynamic occupancy hurdle model (MS-DOHM). The model used data gathered during sampling for Pseudogymnoascus destructans (Pd), the causative agent of white-nose syndrome, a fungal disease that has cause severe declines in several species of hibernating bats in North America. The model allowed us to estimate initial occupancy, colonization, persistence and prevalence of Pd at bat hibernacula. Additionally, utilizing the relationship between...

Land use and life history constrain adaptive genetic variation and reduce the capacity for climate change adaptation in turtles

Fri, 11 Apr 2025 00:00:00 +0000

BackgroundRapid anthropogenic climate change will require species to adapt to shifting environmental conditions, with successful adaptation dependent upon current patterns of genetic variation. While landscape genomic approaches allow for exploration of local adaptation in non-model systems, most landscape genomics studies of adaptive capacity are limited to exploratory identification of potentially important functional genes, often without a priori expectations as to the gene functions that may be most important for climate change responses. In this study, we integrated targeted sequencing of genes of known function and genotyping of single-nucleotide polymorphisms to examine spatial, environmental, and species-specific patterns of potential local adaptation in two co-occuring turtle species: the Blanding’s turtle (Emydoidea blandingii) and the snapping turtle (Chelydra serpentina).ResultsWe documented divergent patterns of spatial clustering between neutral and putatively adaptive...

Does gene flow aggravate or alleviate maladaptation to environmental stress in small populations?

Fri, 11 Apr 2025 00:00:00 +0000

Environmental change can expose populations to unfamiliar stressors, and maladaptive responses to those stressors may result in population declines or extirpation. Although gene flow is classically viewed as a cause of maladaptation, small and isolated populations experiencing high levels of drift and little gene flow may be constrained in their evolutionary response to environmental change. We provide a case study using the model Trinidadian guppy system that illustrates the importance of considering gene flow and genetic drift when predicting (mal)adaptive response to acute stress. We compared population genomic patterns and acute stress responses of inbred guppy populations from headwater streams either with or without a recent history of gene flow from a more diverse mainstem population. Compared to "no-gene flow" analogues, we found that populations with recent gene flow showed higher genomic variation and increased stress tolerance-but only when exposed to a stress familiar...

Genome‐wide diversity and habitat underlie fine‐scale phenotypic differentiation in the rainbow darter (Etheostoma caeruleum)

Fri, 11 Apr 2025 00:00:00 +0000

Adaptation to environmental change requires that populations harbor the necessary genetic variation to respond to selection. However, dispersal-limited species with fragmented populations and reduced genetic diversity may lack this variation and are at an increased risk of local extinction. In freshwater fish species, environmental change in the form of increased stream temperatures places many cold-water species at-risk. We present a study of rainbow darters (Etheostoma caeruleum) in which we evaluated the importance of genetic variation on adaptive potential and determined responses to extreme thermal stress. We compared fine-scale patterns of morphological and thermal tolerance differentiation across eight sites, including a unique lake habitat. We also inferred contemporary population structure using genomic data and characterized the relationship between individual genetic diversity and stress tolerance. We found site-specific variation in thermal tolerance that generally...

Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species

Fri, 11 Apr 2025 00:00:00 +0000

In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and generated additional data from nine populations for the mitochondrial control region (n = 302) and for eleven nuclear microsatellite loci (n = 247). We created a present-day ecological niche model (ENM) for C. picta and hindcast this model to three reconstructions of historical climate to define three potential scenarios with one, two, or three refugia. Finally, we employed spatially-explicit coalescent simulations and an...

Resource partitioning among pelagic predators remains stable despite annual variability in diet composition

Thu, 10 Apr 2025 00:00:00 +0000

Diet data are critical for describing predator resource use and partitioning among competitors. However, time series needed to properly assess variability in resource use and partitioning are limited, especially in pelagic (open ocean) ecosystems where predators and prey make broad use of horizontal and vertical habitats. We examined a diet time series spanning two decades (1998-2018) consisting of 2749 stomachs from 10 pelagic predators in the southern California Current Ecosystem (SCCE): albacore tuna (Thunnus alalunga), Pacific bluefin tuna (Thunnus orientalis), swordfish (Xiphias gladius), blue shark (Prionace glauca), shortfin mako (Isurus oxyrinchus), common thresher shark (Alopias vulpinus), bigeye thresher shark (Alopias superciliosus), short-beaked common dolphin (Delphinus delphis), long-beaked common dolphin (Delphinus capensis) and northern right whale dolphin (Lissodelphis borealis). We quantified feeding habits with respect to prey taxonomy, length, vertical habitat...

Risk and Reward in Foraging Migrations of North Pacific Albacore Determined From Estimates of Energy Intake and Movement Costs

Thu, 10 Apr 2025 00:00:00 +0000

North Pacific albacore (Thunnus alalunga) is a commercially important tuna species known to undertake extensive migratory movements between nearshore waters of the California Current and offshore environments in the central Pacific. However, these migration behaviors are highly variable, with some individuals traveling thousands of kilometers within a season, and others largely resident in the southern California Current throughout the year. In this study, we use data from 33 archival-tagged albacore (released between 2003 and 2011) to examine the movements, physiology and ecology of tuna following different migratory pathways. We used direct measurements of body temperature and ambient water temperature from internal archival tags to estimate energy intake via the Heat Increment of Feeding (HIF), the increased internal heat production associated with digestion of a meal. Our results indicate that HIF was variable in space and time, but it was highest for individuals foraging...

Balancing Inbreeding and Outbreeding Risks to Inform Translocations Throughout the Range of an Imperiled Darter

Thu, 10 Apr 2025 00:00:00 +0000

Restoring connectivity via assisted migration is a useful but currently underused approach for maintaining genetic diversity and preventing extirpations of threatened species. The use of assisted migration as a conservation strategy may be limited by the difficulty of balancing the benefits of reconnecting populations (including reduced inbreeding depression and increased adaptive capacity) with the perceived risk of outbreeding depression, which requires comprehensive knowledge of the landscape of adaptive, neutral, deleterious, and structural variation across a species' range. Using a combination of reduced-representation and whole-genome sequencing, we characterized genomic diversity and differentiation for the Arkansas Darter (Etheostoma cragini) across its range in the Midwestern US. We found strong population structure and large differences in genetic diversity and effective population sizes across drainages. The strength of genetic isolation by river distance differed...

Search for an eV-Scale Sterile Neutrino Using Improved High-Energy νμ Event Reconstruction in IceCube

Mon, 7 Apr 2025 00:00:00 +0000

This Letter presents the result of a 3+1 sterile neutrino search using 10.7 yr of IceCube data. We analyze atmospheric muon neutrinos that traverse the Earth with energies ranging from 0.5 to 100 TeV, incorporating significant improvements in modeling neutrino flux and detector response compared to earlier studies. Notably, for the first time, we categorize data into starting and throughgoing events, distinguishing neutrino interactions with vertices inside or outside the instrumented volume, to improve energy resolution. The best-fit point for a 3+1 model is found to be at sin^{2}(2θ_{24})=0.16 and Δm_{41}^{2}=3.5 eV^{2}, which agrees with previous iterations of this Letter. The result is consistent with the null hypothesis of no sterile neutrinos with a p value of 3.1%.

When the sand blossoms: Phylogeny, trait evolution, and geography of speciation in Linanthus

Sat, 5 Apr 2025 00:00:00 +0000

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 genus's 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...

Evaluating Three Modelling Frameworks for Assessing Changes in Fin Whale Distribution in the Mediterranean Sea

Thu, 3 Apr 2025 00:00:00 +0000

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...

Environmental Health and Societal Wealth Predict Movement Patterns of an Urban Carnivore

Wed, 2 Apr 2025 00:00:00 +0000

How societal, ecological and infrastructural attributes interact to influence wildlife movement is uncertain. We explored whether neighbourhood socioeconomic status and environmental quality were associated with coyote (Canis latrans) movement patterns in Los Angeles, California and assessed the performance of integrated social-ecological movement models. We found that coyotes living in more anthropogenically burdened regions (i.e. higher pollution, denser development, etc.) had larger home ranges and showed greater daily displacement and mean step length than coyotes in less burdened regions. Coyotes experiencing differing levels of anthropogenic burdens demonstrated divergent selection for vegetation, pollution, road densities and other habitat conditions. Further, movement models that included societal covariates performed better than models that only assessed ecological features and linear infrastructure. This study provides a unique social-ecological lens examining the anthropogenic...

Environmental genomics of Late Pleistocene black bears and giant short-faced bears

Tue, 1 Apr 2025 00:00:00 +0000

Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,^1-3 by allowing for parallel sequencing of DNA from all trophic levels.^4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,⁹ the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.⁵^,⁶^,¹⁰^,¹¹ This is in contrast to data from fossils¹²^,¹³ where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.^14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced...

A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non‐Model Species

Tue, 1 Apr 2025 00:00:00 +0000

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...

Reference genome for the endangered, genetically subdivided, northern tidewater goby, Eucyclogobius newberryi

Tue, 1 Apr 2025 00:00:00 +0000

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...

Phylogenetic Signal in Primate Tooth Enamel Proteins and its Relevance for Paleoproteomics

Tue, 1 Apr 2025 00:00:00 +0000

Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil taxa. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentation in vivo and post mortem. This raises the question as to whether the enamelome alone provides enough information for reliable phylogenetic inference. We address these considerations on a selection of enamel-associated proteins that has been computationally predicted from genomic data from 232 primate species. We created multiple sequence alignments for each protein and estimated the evolutionary rate for each site. We examined which sites overlap with the parts of the protein sequences that are typically isolated from fossils. Based on this, we simulated ancient data with different degrees of sequence fragmentation,...

Comparative Genomics Supports Ecologically Induced Selection as a Putative Driver of Banded Penguin Diversification

Tue, 1 Apr 2025 00:00:00 +0000

The relative importance of genetic drift and local adaptation in facilitating speciation remains unclear. This is particularly true for seabirds, which can disperse over large geographic distances, providing opportunities for intermittent gene flow among distant colonies that span the temperature and salinity gradients of the oceans. Here, we delve into the genomic basis of adaptation and speciation of banded penguins, Galápagos (Spheniscus mendiculus), Humboldt (Spheniscus humboldti), Magellanic (Spheniscus magellanicus), and African penguins (Spheniscus demersus), by analyzing 114 genomes from the main 16 breeding colonies. We aim to identify the molecular mechanism and genomic adaptive traits that have facilitated their diversifications. Through positive selection and gene family expansion analyses, we identified candidate genes that may be related to reproductive isolation processes mediated by ecological thermal niche divergence. We recover signals of positive selection on...

Trait‐based analyses reveal global patterns in diverse diets of albacore tuna (Thunnus alalunga)

Fri, 28 Mar 2025 00:00:00 +0000

Simplifying complex species interactions can facilitate tracking and predicting functional responses to ecological stressors. This is important for highly migratory pelagic predators, exploiting diverse prey fields as they respond to dynamic environments. We reconstructed the historical resource use of albacore tuna (Thunnus alalunga) globally from the 1900s to 2015 and confirmed highly biodiverse diets with 308 prey species, and an additional 238 taxa at coarser taxonomic resolution. We synthesised prey diversity into seven functional trait guilds using hierarchical divisive clustering algorithms as a function of four traits that describe habitat use and influence predator–prey encounter rates – prey habitat association vertically in the water column, horizontally along the coastal to pelagic gradient, seasonal and diel vertical migratory behaviour. We explored variability in historical composition of albacore diets across geographies based on species identity, individual trait...

Temperature and upwelling dynamics drive market squid (Doryteuthis opalescens) distribution and abundance in the California Current

Fri, 28 Mar 2025 00:00:00 +0000

Market squid (Doryteuthis opalescens) constitute one of California's largest fisheries by landings and are an essential prey item for numerous top predators in the California Current ecosystem. However, extreme fluctuations in market squid abundance inhibit our ability to forecast local recruitment. We generate a species distribution model for market squid with data from an annual survey to examine the mechanisms behind the variability in their regional abundance and occurrence. Our results indicate juvenile market squid abundance was controlled by local recruitment in connection with sea surface temperature and upwelling dynamics, with finer spatial variability connected to the extent of upwelling dominated regions. Recent changes in these environmental factors also appear to contribute to the recent northward range expansion of market squid. Our spatiotemporally explicit model estimates of juvenile market squid abundance predicted the occurrence and abundance of older market...

Projecting species distributions using fishery‐dependent data

Fri, 28 Mar 2025 00:00:00 +0000

Many marine species are shifting their distributions in response to changing ocean conditions, posing significant challenges and risks for fisheries management. Species distribution models (SDMs) are used to project future species distributions in the face of a changing climate. Information to fit SDMs generally comes from two main sources: fishery-independent (scientific surveys) and fishery-dependent (commercial catch) data. A concern with fishery-dependent data is that fishing locations are not independent of the underlying species abundance, potentially biasing predictions of species distributions. However, resources for fishery-independent surveys are increasingly limited; therefore, it is critical we understand the strengths and limitations of SDMs developed from fishery-dependent data. We used a simulation approach to evaluate the potential for fishery-dependent data to inform SDMs and abundance estimates and quantify the bias resulting from different fishery-dependent...

Population projections of Pacific sardine driven by ocean warming and changing food availability in the California Current

Fri, 28 Mar 2025 00:00:00 +0000

Small pelagic fish are important marine ecosystem components and highly variable fisheries resources. In the California Current upwelling system, Pacific sardine (Sardinops sagax) has supported important fisheries in the past, but contrary to expectations, remains at low biomass despite recent warm ocean conditions. We developed a data-driven, process-based population model that reproduces fluctuations of the US Pacific sardine population based on ocean temperature, early life stage and adult food, and upwelling strength. The lack of sardine recovery after 2014 can be explained by reduced food availability. Ensemble projections for the 21st century driven by downscaled ocean-biogeochemical simulations under three Earth system models (ESMs) show a likely recovery to early 2000s sardine abundance and catch by mid-century, due to increased recruitment. Ecological process uncertainty (ensemble configuration range) is of the same magnitude as uncertainty among ESM projections, and...

Soil and climate contribute to maintenance of a flower color polymorphism

Thu, 27 Mar 2025 00:00:00 +0000

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...

The Convergent Evolution of Hummingbird Pollination Results in Repeated Floral Scent Loss Through Gene Downregulation

Thu, 27 Mar 2025 00:00:00 +0000

The repeated evolution of the same trait in different lineages provides powerful natural experiments to study the phenotypic and genotypic predictability of trait gain and loss. A fascinating example is the repeated evolution of hummingbird pollination in plant lineages in the Americas, a widespread and often unidirectional phenomenon. The spiral gingers in the genus Costus are ancestrally bee pollinated, and hummingbird pollination has evolved multiple times independently in the tropical Americas. These pollinator transitions are accompanied by predictable morphological and color changes, but the changes in floral scent have not been described. In this study, we describe the floral scent composition of 30 species of Costus sampled across the phylogeny to understand how floral scent has evolved across the genus with respect to pollinator transitions. We then combine transcriptomics and genomics to identify gene expression differences and gene family evolution associated with pollinator...

Migrating baleen whales transport high-latitude nutrients to tropical and subtropical ecosystems

Thu, 27 Mar 2025 00:00:00 +0000

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 genetic basis of floral mechanical isolation between two hummingbird‐pollinated Neotropical understorey herbs

Thu, 27 Mar 2025 00:00:00 +0000

Floral divergence can contribute to reproductive isolation among plant lineages, and thus provides an opportunity to study the genetics of speciation, including the number, effect size, mode of action and interactions of quantitative trait loci (QTL). Moreover, flowers represent suites of functionally interrelated traits, but it is unclear to what extent the phenotypic integration of the flower is underlain by a shared genetic architecture, which could facilitate or constrain correlated evolution of floral traits. Here, we examine the genetic architecture of floral morphological traits involved in an evolutionary switch from bill to forehead pollen placement between two species of hummingbird-pollinated Neotropical understorey herbs that are reproductively isolated by these floral differences. For the majority of traits, we find multiple QTL of relatively small effect spread throughout the genome. We also find substantial colocalization and alignment of effects of QTL underlying...

Author Correction: Warming and cooling catalyse widespread temporal turnover in biodiversity

Tue, 25 Mar 2025 00:00:00 +0000

Author Correction: Warming and cooling catalyse widespread temporal turnover in biodiversity

Warming and cooling catalyse widespread temporal turnover in biodiversity

Tue, 25 Mar 2025 00:00:00 +0000

Turnover in species composition through time is a dominant form of biodiversity change, which has profound effects on the functioning of ecological communities1, 2, 3–4. Turnover rates differ markedly among communities4, but the drivers of this variation across taxa and realms remain unknown. Here we analyse 42,255 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...

Characterization and distribution of a 14-Mb chromosomal inversion in native populations of rainbow trout (Oncorhynchus mykiss).

Fri, 21 Mar 2025 00:00:00 +0000

Multiple studies in a range of taxa have found links between structural variants and the development of ecologically important traits. Such variants are becoming easier to find due, in large part, to the increase in the amount of genome-wide sequence data in nonmodel organisms. The salmonids (salmon, trout, and charr) are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture, fisheries, and variation in multiple ecologically important life-history traits. Previous research on rainbow trout (Oncorhynchus mykiss) has documented a large pericentric (∼55 Mb) chromosomal inversion (CI) on chromosome 5 (Omy05) and a second smaller (∼14 Mb) chromosome inversion on Omy20. While the Omy05 inversion appears to be associated with multiple adaptive traits, the inversion on Omy20 has received far less attention. In this study, we re-analyze RAD-seq and amplicon data from several populations of rainbow trout (O. mykiss) to better document the structure...

Evolutionary restoration potential evaluated through the use of a trait‐linked genetic marker

Thu, 20 Mar 2025 00:00:00 +0000

Human-driven evolution can impact the ecological role and conservation value of impacted populations. Most evolutionary restoration approaches focus on manipulating gene flow, but an alternative approach is to manipulate the selection regime to restore historical or desired trait values. Here we examined the potential utility of this approach to restore anadromous migratory behavior in coastal California steelhead trout (Oncorhynchus mykiss) populations. We evaluated the effects of natural and anthropogenic environmental variables on the observed frequency of alleles at a genomic marker tightly associated with migratory behavior across 39 steelhead populations from across California, USA. We then modeled the potential for evolutionary restoration at sites that have been impacted by anthropogenic barriers. We found that complete barriers such as dams are associated with major reductions in the frequency of anadromy-associated alleles. The removal of dams is therefore expected...

Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape

Thu, 20 Mar 2025 00:00:00 +0000

The streams draining of into San Francisco Bay, California, have been impacted by habitat alteration for over 150 years, and roads, dams, water diversions, and other impediments now block the paths of many aquatic migratory species. These changes can affect the genetic structure of fish populations, as well as driving adaptive evolution to novel environmental conditions. Here, we determine the evolutionary relationships of San Francisco Bay Area steelhead/rainbow trout (Oncorhynchus mykiss) populations and show that (i) they are more closely related to native coastal steelhead than to the California Central Valley lineage, with no evidence of introgression by domesticated hatchery rainbow trout, (ii) populations above and below barriers within watersheds are each other's closest relatives, and (iii) adaptive genomic variation associated with migratory life-history traits in O. mykiss shows substantial evolutionary differences between fish above and below dams....

Applications of species distribution modeling and future needs to support marine resource management

Thu, 13 Mar 2025 00:00:00 +0000

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...

Draft genome assemblies for two species of Escallonia (Escalloniales)

Thu, 13 Mar 2025 00:00:00 +0000

ObjectivesEscallonia (Escalloniaceae) belongs to the Escalloniales, a diverse clade of flowering plants with unclear placement in the tree of life. Escallonia species show impressive morphological and ecological diversity and are widely distributed across three hotspots of biodiversity in the Neotropics. To shed light on the genomic substrate of this radiation and the phylogenetic placement of Escalloniales as well as to generate useful data for comparative evolutionary genomics across flowering plants, we produced and annotated draft genomes for two species of Escallonia.Data descriptionGenomic DNA from E. rubra and E. herrerae was sequenced with Oxford Nanopore sequencing chemistry, generating 3.4 and 12 million sequence reads with an average read length of 9.4 and 9.1 Kb (approximately 31 and 111 Gb of sequence data), respectively. In addition, we generated Illumina 100-bp paired-end short read data for E. rubra (approximately 75 Gb of sequence data). The Escallonia rubra...

Drivers of spatiotemporal variability in a marine foundation species

Fri, 28 Feb 2025 00:00:00 +0000

Marine foundation species are critical for the structure and functioning of ecosystems and constitute the pillar of trophic chains while also providing a variety of ecosystem services. In recent decades, many foundation species have declined in abundance, sometimes threatening their current geographical distribution. Kelps (Laminariales) are the primary foundation species in temperate coastal systems worldwide. Kelp ecosystems are notoriously variable, challenging the identification of key factors controlling their dynamics. Identification of these drivers is key to predicting the fate of kelp ecosystems under climatic change and to informing management and conservation decisions such as restoration. Here, we used in situ data from long-term monitoring programs across 1350 km of coast spanning multiple biogeographic regions in the state of California (USA) to identify the major regional drivers of density of two dominant canopy-forming kelp species and to elucidate the spatial...

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

Mon, 17 Feb 2025 00:00:00 +0000

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...

Ocean Planning and Conservation in the Age of Climate Change: A Roundtable Discussion

Mon, 17 Feb 2025 00:00:00 +0000

Over recent years, recognition of the need to develop climate-smart marine spatial planning (MSP) has gained momentum globally. In this roundtable discussion, we use a question-and-answer format to leverage diverse perspectives and voices involved in the study of sustainable MSP and marine conservation under global environmental and social change. We intend this dialogue to serve as a stepping stone toward developing ocean planning initiatives that are sustainable, equitable, and climate-resilient around the globe.

Sex‐specific diet differences in harbor seals (Phoca vitulina) via spatial assortment

Wed, 5 Feb 2025 00:00:00 +0000

The lack of recovery of Chinook salmon (Oncorhynchus tshawytscha) in the Pacific Northwest has been blamed in part on predation by pinnipeds, particularly the harbor seal (Phoca vitulina). Previous work at a limited number of locations has shown that male seal diet contains more salmon than that of female seals and that sex ratios at haul-out sites differ spatiotemporally. This intrapopulation variation in predation may result in greater effects on salmon than suggested by models assuming equal spatial distribution and diet proportion. To address the generality of these patterns, we examined the sex ratios and diet of male and female harbor seals from 13 haul-out sites in the inland waters of Washington State and the province of British Columbia during 2012-2018. DNA metabarcoding was conducted to determine prey species proportions of individual scat samples. The sex of harbor seals was then determined from each scat matrix sample with the use of quantitative polymerase...

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

Fri, 31 Jan 2025 00:00:00 +0000

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...

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

Thu, 30 Jan 2025 00:00:00 +0000

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...

Oceanography’s Diversity Deficit: Identifying and Addressing Challenges for Marginalized Groups

Thu, 30 Jan 2025 00:00:00 +0000

Centuries of exclusion have resulted in a tangible human diversity deficit, where the diversity of oceanographers does not represent the global diversity of people impacted by ocean processes. We present six challenges faced by oceanographers who have one or more marginalized identities: (1) historical practices of conquest, discrimination, and exclusion underpin oceanography’s modern diversity deficit; (2) undervalued and uncompensated labor by oceanographers from underrepresented groups can perpetuate a lack of representation by leading to burnout and attrition; (3) marginalized individuals are often forced to hide parts of their identities (languages, appearances, partners, behaviors) that deviate from outdated expectations of professionalism; (4) oceanography requires trainees to navigate extensive logistical and financial hurdles; (5) individuals from non-Western cultural and religious traditions often conceal their spiritual obligations in attempts to assimilate or avoid...

Contrasting demographic processes underlie uphill shifts in a desert ecosystem

Mon, 20 Jan 2025 00:00:00 +0000

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...

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

Sat, 18 Jan 2025 00:00:00 +0000

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 Earth's 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 >...

Effect of kelp gull harassment on southern right whale calf survival: a long-term capture–recapture analysis

Fri, 17 Jan 2025 00:00:00 +0000

Kelp gulls (Larus dominicanus) commonly feed on the skin and blubber of surfacing southern right whales (SRW, Eubalaena australis) in the near shore waters of Península Valdés (PV), Argentina. Mothers and especially calves respond to gull attacks by changing their swimming speeds, resting postures and overall behaviour. Gull-inflicted wounds per calf have increased markedly since the mid-1990s. Unusually high mortality of young calves occurred locally after 2003, and increasing evidence points to gull harassment as a factor contributing to the excess deaths. After leaving PV, calves undertake a long migration with their mothers to summer feeding areas; their health during this strenuous exertion is likely to affect their probabilities of first-year survival. To explore the effects of gull-inflicted wounds on calf survival, we analysed 44 capture-recapture observations between 1974 and 2017, for 597 whales photo-identified in their years of birth between 1974 and...

Pitfalls and windfalls of detecting demographic declines using population genetics in long‐lived species

Fri, 17 Jan 2025 00:00:00 +0000

Detecting recent demographic changes is a crucial component of species conservation and management, as many natural populations face declines due to anthropogenic habitat alteration and climate change. Genetic methods allow researchers to detect changes in effective population size (N_e) from sampling at a single timepoint. However, in species with long lifespans, there is a lag between the start of a decline in a population and the resulting decrease in genetic diversity. This lag slows the rate at which diversity is lost, and therefore makes it difficult to detect recent declines using genetic data. However, the genomes of old individuals can provide a window into the past, and can be compared to those of younger individuals, a contrast that may help reveal recent demographic declines. To test whether comparing the genomes of young and old individuals can help infer recent demographic bottlenecks, we use forward-time, individual-based simulations with varying mean...

Genetic isolation by distance underlies colour pattern divergence in red‐eyed treefrogs (Agalychnis callidryas)

Fri, 17 Jan 2025 00:00:00 +0000

Investigating the spatial distribution of genetic and phenotypic variation can provide insights into the evolutionary processes that shape diversity in natural systems. We characterized patterns of genetic and phenotypic diversity to learn about drivers of colour-pattern diversification in red-eyed treefrogs (Agalychnis callidryas) in Costa Rica. Along the Pacific coast, red-eyed treefrogs have conspicuous leg colour patterning that transitions from orange in the north to purple in the south. We measured phenotypic variation of frogs, with increased sampling at sites where the orange-to-purple transition occurs. At the transition zone, we discovered the co-occurrence of multiple colour-pattern morphs. To explore possible causes of this variation, we generated a single nucleotide polymorphism data set to analyse population genetic structure, measure genetic diversity and infer the processes that mediate genotype-phenotype dynamics. We investigated how patterns of genetic relatedness...

Coalition-building for labor actions in life sciences departments: lessons from the largest academic strike in history

Thu, 16 Jan 2025 00:00:00 +0000

Abstract: In life sciences graduate programs in the United States, efforts are underway to address barriers to academic success—namely, using interventions targeted at addressing inclusivity and diversity concerns. However, graduate students are typically simultaneously workers for their institutions, where they face workplace challenges such as low wages, inadequate benefits, and vulnerability to harassment and abuse. These challenges may disproportionately affect workers with excluded identities and are thereby barriers to diversity and equity. In recent years, graduate student unionization has expanded. The outcomes of these movements may improve pay, benefits, and working conditions for graduate workers; however, labor organizing presents numerous challenges in academic environments. We reflect on our experiences in a life sciences department at the University of California, Santa Cruz, in 2022 during the largest graduate labor strike to date. We summarize...

Reproductive success and offspring survival decline for female elephant seals past prime age

Thu, 16 Jan 2025 00:00:00 +0000

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...